A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
A publication issued at stated, more or less regular, intervals.
A genus of small, two-winged flies containing approximately 900 described species. These organisms are the most extensively studied of all genera from the standpoint of genetics and cytology.
"The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.
The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).
Publications in any medium issued in successive parts bearing numerical or chronological designations and intended to be continued indefinitely. (ALA Glossary of Library and Information Science, 1983, p203)
Members of the phylum Arthropoda, composed of organisms having a hard, jointed exoskeleton and paired jointed legs. It includes the class INSECTS and the subclass ARACHNIDA, many species of which are important medically as parasites or as vectors of organisms capable of causing disease in man.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Reproduction without fusion of two types of cells, mostly found in ALGAE; FUNGI; and PLANTS. Asexual reproduction occurs in several ways, such as budding, fission, or splitting from "parent" cells. Only few groups of ANIMALS reproduce asexually or unisexually (PARTHENOGENESIS).
A large subphylum of mostly marine ARTHROPODS containing over 42,000 species. They include familiar arthropods such as lobsters (NEPHROPIDAE), crabs (BRACHYURA), shrimp (PENAEIDAE), and barnacles (THORACICA).
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The relationships of groups of organisms as reflected by their genetic makeup.
A subphylum of chordates intermediate between the invertebrates and the true vertebrates. It includes the Ascidians.
The only species of a cosmopolitan ascidian.
Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
Short, predominantly basic amino acid sequences identified as nuclear import signals for some proteins. These sequences are believed to interact with specific receptors at the NUCLEAR PORE.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Components of a cell produced by various separation techniques which, though they disrupt the delicate anatomy of a cell, preserve the structure and physiology of its functioning constituents for biochemical and ultrastructural analysis. (From Alberts et al., Molecular Biology of the Cell, 2d ed, p163)
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
A partitioning within cells due to the selectively permeable membranes which enclose each of the separate parts, e.g., mitochondria, lysosomes, etc.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
All of the divisions of the natural sciences dealing with the various aspects of the phenomena of life and vital processes. The concept includes anatomy and physiology, biochemistry and biophysics, and the biology of animals, plants, and microorganisms. It should be differentiated from BIOLOGY, one of its subdivisions, concerned specifically with the origin and life processes of living organisms.
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Lists of persons or organizations, systematically arranged, usually in alphabetic or classed order, giving address, affiliations, etc., for individuals, and giving address, officers, functions, and similar data for organizations. (ALA Glossary of Library and Information Science, 1983)
Sequential operating programs and data which instruct the functioning of a digital computer.
A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
An enzyme found mostly in plant tissue. It hydrolyzes glycerophosphatidates with the formation of a phosphatidic acid and a nitrogenous base such as choline. This enzyme also catalyzes transphosphatidylation reactions. EC 3.1.4.4.
Secondary headache attributed to TRAUMA of the HEAD and/or the NECK.
An enzyme that catalyzes the hydrolysis of CHOLESTEROL ESTERS and some other sterol esters, to liberate cholesterol plus a fatty acid anion.
A discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
The phenomenon of youthfulness, vitality, and freshness being restored. This can apply to appearance, TISSUES, organ functions, or other areas.
The act of knowing or the recognition of a distance by recollective thought, or by means of a sensory process which is under the influence of set and of prior experience.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
An enzyme that activates aspartic acid with its specific transfer RNA. EC 6.1.1.12.
Any of various diseases affecting the white matter of the central nervous system.
The process by which a DNA molecule is duplicated.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The performance of dissections with the aid of a microscope.
A moderately firm, benign, encapsulated tumor resulting from proliferation of SCHWANN CELLS and FIBROBLASTS that includes portions of nerve fibers. The tumors usually develop along peripheral or cranial nerves and are a central feature of NEUROFIBROMATOSIS 1, where they may occur intracranially or involve spinal roots. Pathologic features include fusiform enlargement of the involved nerve. Microscopic examination reveals a disorganized and loose cellular pattern with elongated nuclei intermixed with fibrous strands. (From Adams et al., Principles of Neurology, 6th ed, p1016)
The use of needles usually larger than 14-gauge to remove tissue samples large enough to retain cellular architecture for pathology examination.
A malignant form of astrocytoma histologically characterized by pleomorphism of cells, nuclear atypia, microhemorrhage, and necrosis. They may arise in any region of the central nervous system, with a predilection for the cerebral hemispheres, basal ganglia, and commissural pathways. Clinical presentation most frequently occurs in the fifth or sixth decade of life with focal neurologic signs or seizures.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
The study of the structure of various TISSUES of organisms on a microscopic level.
A salt produced by the reaction of zinc oxide with acetic acid and used as an astringent, styptic, and emetic.

The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (1/15406)

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription.  (+info)

A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (2/15406)

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

Telomerase reverse transcriptase gene is a direct target of c-Myc but is not functionally equivalent in cellular transformation. (3/15406)

The telomerase reverse transcriptase component (TERT) is not expressed in most primary somatic human cells and tissues, but is upregulated in the majority of immortalized cell lines and tumors. Here, we identify the c-Myc transcription factor as a direct mediator of telomerase activation in primary human fibroblasts through its ability to specifically induce TERT gene expression. Through the use of a hormone inducible form of c-Myc (c-Myc-ER), we demonstrate that Myc-induced activation of the hTERT promoter requires an evolutionarily conserved E-box and that c-Myc-ER-induced accumulation of hTERT mRNA takes place in the absence of de novo protein synthesis. These findings demonstrate that the TERT gene is a direct transcriptional target of c-Myc. Since telomerase activation frequently correlates with immortalization and telomerase functions to stabilize telomers in cycling cells, we tested whether Myc-induced activation of TERT gene expression represents an important mechanism through which c-Myc acts to immortalize cells. Employing the rat embryo fibroblast cooperation assay, we show that TERT is unable to substitute for c-Myc in the transformation of primary rodent fibroblasts, suggesting that the transforming activities of Myc extend beyond its ability to activate TERT gene expression and hence telomerase activity.  (+info)

Molecular phylogeny of the ETS gene family. (4/15406)

We have constructed a molecular phylogeny of the ETS gene family. By distance and parsimony analysis of the ETS conserved domains we show that the family containing so far 29 different genes in vertebrates can be divided into 13 groups of genes namely ETS, ER71, GABP, PEA3, ERG, ERF, ELK, DETS4, ELF, ESE, TEL, YAN, SPI. Since the three dimensional structure of the ETS domain has revealed a similarity with the winged-helix-turn-helix proteins, we used two of them (CAP and HSF) to root the tree. This allowed us to show that the family can be divided into five subfamilies: ETS, DETS4, ELF, TEL and SPI. The ETS subfamily comprises the ETS, ER71, GABP, PEA3, ERG, ERF and the ELK groups which appear more related to each other than to any other ETS family members. The fact that some members of these subfamilies were identified in early metazoans such as diploblasts and sponges suggests that the diversification of ETS family genes predates the diversification of metazoans. By the combined analysis of both the ETS and the PNT domains, which are conserved in some members of the family, we showed that the GABP group, and not the ERG group, is the one most closely related to the ETS group. We also observed that the speed of accumulation of mutations in the various genes of the family is highly variable. Noticeably, paralogous members of the ELK group exhibit strikingly different evolutionary speed suggesting that the evolutionary pressure they support is very different.  (+info)

A single membrane-embedded negative charge is critical for recognizing positively charged drugs by the Escherichia coli multidrug resistance protein MdfA. (5/15406)

The nature of the broad substrate specificity phenomenon, as manifested by multidrug resistance proteins, is not yet understood. In the Escherichia coli multidrug transporter, MdfA, the hydrophobicity profile and PhoA fusion analysis have so far identified only one membrane-embedded charged amino acid residue (E26). In order to determine whether this negatively charged residue may play a role in multidrug recognition, we evaluated the expression and function of MdfA constructs mutated at this position. Replacing E26 with the positively charged residue lysine abolished the multidrug resistance activity against positively charged drugs, but retained chloramphenicol efflux and resistance. In contrast, when the negative charge was preserved in a mutant with aspartate instead of E26, chloramphenicol recognition and transport were drastically inhibited; however, the mutant exhibited almost wild-type multidrug resistance activity against lipophilic cations. These results suggest that although the negative charge at position 26 is not essential for active transport, it dictates the multidrug resistance character of MdfA. We show that such a negative charge is also found in other drug resistance transporters, and its possible significance regarding multidrug resistance is discussed.  (+info)

A novel genetic screen for snRNP assembly factors in yeast identifies a conserved protein, Sad1p, also required for pre-mRNA splicing. (6/15406)

The assembly pathway of spliceosomal snRNPs in yeast is poorly understood. We devised a screen to identify mutations blocking the assembly of newly synthesized U4 snRNA into a functional snRNP. Fifteen mutant strains failing either to accumulate the newly synthesized U4 snRNA or to assemble a U4/U6 particle were identified and categorized into 13 complementation groups. Thirteen previously identified splicing-defective prp mutants were also assayed for U4 snRNP assembly defects. Mutations in the U4/U6 snRNP components Prp3p, Prp4p, and Prp24p led to disassembly of the U4/U6 snRNP particle and degradation of the U6 snRNA, while prp17-1 and prp19-1 strains accumulated free U4 and U6 snRNA. A detailed analysis of a newly identified mutant, the sad1-1 mutant, is presented. In addition to having the snRNP assembly defect, the sad1-1 mutant is severely impaired in splicing at the restrictive temperature: the RP29 pre-mRNA strongly accumulates and splicing-dependent production of beta-galactosidase from reporter constructs is abolished, while extracts prepared from sad1-1 strains fail to splice pre-mRNA substrates in vitro. The sad1-1 mutant is the only splicing-defective mutant analyzed whose mutation preferentially affects assembly of newly synthesized U4 snRNA into the U4/U6 particle. SAD1 encodes a novel protein of 52 kDa which is essential for cell viability. Sad1p localizes to the nucleus and is not stably associated with any of the U snRNAs. Sad1p contains a putative zinc finger and is phylogenetically highly conserved, with homologues identified in human, Caenorhabditis elegans, Arabidospis, and Drosophila.  (+info)

The highly conserved beta-hairpin of the paired DNA-binding domain is required for assembly of Pax-Ets ternary complexes. (7/15406)

Pax family transcription factors bind DNA through the paired domain. This domain, which is comprised of two helix-turn-helix motifs and a beta-hairpin structure, is a target of mutations in congenital disorders of mice and humans. Previously, we showed that Pax-5 (B-cell-specific activator protein) recruits proteins of the Ets proto-oncogene family to bind a composite DNA site that is essential for efficient transcription of the early-B-cell-specific mb-1 promoter. Here, evidence is provided for specific interactions between Ets-1 and the amino-terminal subdomains of Pax proteins. By tethering deletion fragments of Pax-5 to a heterologous DNA-binding domain, we show that 73 amino acids (amino acids 12 to 84) of its amino-terminal subdomain can recruit the ETS domain of Ets-1 to bind the composite site. Furthermore, an amino acid (Gln22) within the highly conserved beta-hairpin motif of Pax-5 is essential for efficient recruitment of Ets-1. The ability to recruit Ets proteins to bind DNA is a shared property of Pax proteins, as demonstrated by cooperative DNA binding of Ets-1 with sequences derived from the paired domains of Pax-2 and Pax-3. The strict conservation of sequences required for recruitment of Ets proteins suggests that Pax-Ets interactions are important for regulating transcription in diverse tissues during cellular differentiation.  (+info)

Analysis of a ubiquitous promoter element in a primitive eukaryote: early evolution of the initiator element. (8/15406)

Typical metazoan core promoter elements, such as TATA boxes and Inr motifs, have yet to be identified in early-evolving eukaryotes, underscoring the extensive divergence of these organisms. Towards the identification of core promoters in protists, we have studied transcription of protein-encoding genes in one of the earliest-diverging lineages of Eukaryota, that represented by the parasitic protist Trichomonas vaginalis. A highly conserved element, comprised of a motif similar to a metazoan initiator (Inr) element, surrounds the start site of transcription in all examined T. vaginalis genes. In contrast, a metazoan-like TATA element appears to be absent in trichomonad promoters. We demonstrate that the conserved motif found in T. vaginalis protein-encoding genes is an Inr promoter element. This trichomonad Inr is essential for transcription, responsible for accurate start site selection, and interchangeable between genes, demonstrating its role as a core promoter element. The sequence requirements of the trichomonad Inr are similar to metazoan Inrs and can be replaced by a mammalian Inr. These studies show that the Inr is a ubiquitous, core promoter element for protein-encoding genes in an early-evolving eukaryote. Functional and structural similarities between this protist Inr and the metazoan Inr strongly indicate that the Inr promoter element evolved early in eukaryotic evolution.  (+info)

Ultraconserved elements (UCEs), stretches of DNA that are identical between distantly related species, are enigmatic genomic features whose function is not well understood. First identified and characterized in mammals, UCEs have been proposed to play important roles in gene regulation, RNA processing, and maintaining genome integrity. However, because all of these functions can tolerate some sequence variation, their ultraconserved and ultraselected nature is not explained. We investigated whether there are highly conserved DNA elements without genic function in distantly related plant genomes. We compared the genomes of Arabidopsis thaliana and Vitis vinifera; species that diverged ∼115 million years ago (Mya). We identified 36 highly conserved elements with at least 85% similarity that are longer than 55 bp. Interestingly, these elements exhibit properties similar to mammalian UCEs, such that we named them UCE-like elements (ULEs). ULEs are located in intergenic or intronic regions and are ...
There are 481 segments longer than 200 base pairs (bp) that are absolutely conserved (100% identity with no insertions or deletions) between orthologous regions of the human, rat, and mouse genomes. Nearly all of these segments are also conserved in the chicken and dog genomes, with an average of 95 and 99% identity, respectively. Many are also significantly conserved in fish. These ultraconserved elements of the human genome are most often located either overlapping exons in genes involved in RNA processing or in introns or nearby genes involved in the regulation of transcription and development. Along with more than 5000 sequences of over 100 bp that are absolutely conserved among the three sequenced mammals, these represent a class of genetic elements whose functions and evolutionary origins are yet to be determined, but which are more highly conserved between these species than are proteins and appear to be essential for the ontogeny of mammals and other vertebrates.
Distribution of gene conservation across the Parcubacteria genomes. Shaded subsections represent degree of conservation across all genomes, with the lowest blac
Close The Infona portal uses cookies, i.e. strings of text saved by a browser on the users device. The portal can access those files and use them to remember the users data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser. ...
I am interested in determining if the secondary structure of several large (500bp+) sequences is conserved, with an ultimate goal of demonstrating greater divergence between the NTRs (the sequences here) versus ORFs between species. That is the coding regions have greater conservation than the non-coding. To do this I have been considering using the ViennaRNA services structure conservation analysis (SCA). However, after running the program I am finding the interpretation of the results not obvious to me.. The results can be found here: http://rna.tbi.univie.ac.at/cgi-bin/SCA.cgi?PAGE=3&ID=zwPrc7kAK8&r=36. For example the measure Basepair distance, pairwise provides a z-score of -7.045 with a p-value of zero. Obviously I can reject the null that my sequences are not different than the random sampling performed, but the sign of the value and how it related to conservation is where I am unsure. I pulled some of the papers they cite for the man pages of these programs and my thoughts are coming ...
Conservation has a cascading effect with numerous benefits, says a local biologist. Two entities in Stark County are furthering their missions of conservation in their own ways, but each wants to increase ties with the community and get people involved in conservation.
Care must be taken when choosing a suitable transformation, especially if conservation dollars are allocated to species in a ranked fashion. We advocate routine sensitivity analyses.
The Conservation Commission owns and maintains approximately 2,000 acres of protected land throughout Weston that is open to the public for passive recreation.
Alfaro, M.E., An inverse latitudinal gradient in speciation rate for marine fishes, Nature, 559 : 392-395 (2018) [link].. Gilbert, Princess S; Wu, Jing; Simon, Margaret W; Sinsheimer, Janet S; Alfaro, Michael E, Filtering nucleotide sites by phylogenetic signal to noise ratio increases confidence in the Neoaves phylogeny generated from ultraconserved elements, Mol. Phylogenet. Evol, 126 : 116-128 (2018) [link].. Prosanta Chakrabarty, Brant C Faircloth, Fernando Alda, William B Ludt, Caleb D Mcmahan, Thomas J Near, Alex Dornburg, James S Albert, Jairo Arroyave, Melanie LJ Stiassny, Laurie Sorenson, Michael E Alfaro, Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes, Systematic Biology, 66 : 881-895 (2017) [link].. Luz E Ochoa, Fabio F Roxo, Carlos DoNascimiento, Mark H Sabaj, Alessio Datovo, Michael Alfaro, Claudio Oliveira, Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: ...
All references with links attached are the resources I used myself, other resources in plain black are additional resources.. References. Andolfatto, P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.. Batten, D. 1998. Junk DNA (again). Creation Ex Nihilo Technical Journal 12: 5.. Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes. Proceedings of the Royal Society of London, Series B 266: 2053-2059.. Bejerano, G., M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, and D. Haussler. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.. Bennett, M.D. 1982. Nucleotypic basis of the spatial ordering of chromosomes in eukaryotes and the implications of the order for genome evolution and phenotypic variation. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 239-261. Academic Press, New York.. Bergman, J. 2001. The functions of ...
Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.
Read Evaluating conservation spending for species return: A retrospective analysis in California, Conservation Letters on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.
Prostate MR has come to play a key role in managing patients with prostate cancer. It has traditionally relied on T1 and T2 weighted imaging to image the prost...
Volunteer with Association for Rivers and Coastal-Ecosystems Conservation. Find Association for Rivers and Coastal-Ecosystems Conservation volunteering opportunities at VolunteerMatch!
Michael J. Conroy, John P. Carroll, Quantitative Conservation of Vertebrates 2009 | ISBN-10: 1405190981, 1405182288 | 352 pages | PDF | 5,4 MB This
It is suggested that parity conservation in the strong interactions may be a consequence of the bootstrap hypothesis. A model is presented to illustrate how this might come about. ...
This 14 days volunteering program, will take you to the heart of Uganda where you get involved in meaningful volunteer work. We ask volunteers interested in the Uganda environment conservation volunte
Learn about Middlesex County College conservation. Completion of an accredited engineering program can qualify you to enter the workforce as a paid intern immediately.
Learn more if you are interested in helping our dedicated and hardworking volunteers contribute to conservation and keep our zoo up and running!
TY - JOUR. T1 - Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia. AU - Bhatia, Shipra. AU - Bengani, Hemant. AU - Fish, Margaret. AU - Brown, Alison. AU - Divizia, Maria Teresa. AU - De Marco, Riccardo. AU - Damante, Guiseppe. AU - Grainger, Robert. AU - Van Heyningen, Veronica. AU - Kleinjan, Dirk A.. PY - 2013/12/5. Y1 - 2013/12/5. N2 - The strictly regulated expression of most pleiotropic developmental control genes is critically dependent on the activity of long-range cis-regulatory elements. This was revealed by the identification of individuals with a genetic condition lacking coding-region mutations in the gene commonly associated with the disease but having a variety of nearby chromosomal abnormalities, collectively described as cis-ruption disease cases. The congenital eye malformation aniridia is caused by haploinsufficiency of the developmental regulator PAX6. We discovered a de novo point mutation in an ultraconserved ...
G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. Co-clustered GPCRs from human and other genomes, organized as 32 clusters, were employed to study the amino acid conservation patterns and species-specific or cluster-specific motifs. Critical analysis on sequence composition and properties provide clues to connect functional relevance within and across genome for vast practical applications such as design of mutations and understanding of disease-causing genetic abnormalities. and GPCRs, leading to 32 clusters of eight major types as explained in our previous publication [9], we report the analysis of AAS and conserved motifs in all 32 492445-28-0 IC50 clusters of GPCRs. This 492445-28-0 IC50 study was further extended to a cross-genome analysis of and GPCRs. Methodology Physique 1 summarizes stepwise procedure for the identification of conserved AA (motifs) and residues exchanged at each position on MSA. ...
A gene is a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions.[1][2] The physical development and phenotype of organisms can be thought of as a product of genes interacting with each other and with the environment.[3] A concise definition of a gene, taking into account complex patterns of regulation and transcription, genic conservation and non-coding RNA genes, has been proposed by Gerstein et al.[4] A gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products. Colloquially, the term gene is often used to refer to an inheritable trait which is usually accompanied by a phenotype as in (tall genes or bad genes) -- the proper scientific term for this is allele. In cells, genes consist of a long strand of DNA that contains a promoter, which controls the activity of a gene, and coding and non-coding sequence. ...
Travelling on a Turtle conservation holiday with kids. Honest advice on going on a Turtle conservation holiday with kids including health & safety to the best things to do on family turtle conservation holidays.
The highly-conserved Notch signaling pathway is unique, as both the Notch receptor and most of its respective ligands (canonically the DSL or Delta/Serrate/...
The Conservation Leadership through Learning (CLTL) program is a masters degree which prepares leaders to address complex conservation issues.
Pathway expression conservation and divergence. (a) Top conserved and (b) diverged pathway responses as revealed by the soft clustering approach. Each pathway i
Kaiserstuhl Conservation Park is perfect for bushwalkers, who are rewarded with panoramic views, fascinating rock formations and a range of native plants and animals.
Find conservation news and resources for those seeking information about how The Nature Conservancy works to protect land & water for nature & people.
Help us maintain this website and keep it free and open for our community of scientists, students, and conservation managers, who depend on it to obtain the most up to date information. Help us save species and restore native ecosystems ...
Help us maintain this website and keep it free and open for our community of scientists, students, and conservation managers, who depend on it to obtain the most up to date information. Help us save species and restore native ecosystems ...
Find info concerning South Central College conservation. Engineering job offers command high salaries due to accelerating technical innovation in manufacturing and heavy industry.
Discover, support, and create campaigns about protection and conservation on Causes.com, the worlds largest community for doing good.
Founded in 1999, the Wolf Conservation Center in Salem, NY promotes wolf conservation by teaching about wolves, their relationship to the environment...
Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results
The zinc transporter SLC39A7 (ZIP7) harbours a highly-conserved histidinerich N-terminal region that potentially contributes to zinc homeostasis in the endoplasmic reticulum
Due date: March 15, 2021. Conservation Small Grants (up to $2,000): Grant proposals are solicited for conservation research or related projects, including conservation education. ASP members working in habitat countries are especially urged to apply or to help someone from a habitat country submit a meaningful project that can be a portion of a larger effort. Recipients of grants must agree to submit a brief report (maximum 1-2 pages, single spaced), in a form suitable for publication in the ASP Bulletin, to the chair of the ASP Conservation Committee within six months of completion of the project. Grant report templates can be found here. In lieu of a written report, recipients may submit a video documenting their conservation goals and project funded by the ASP. See examples of videos on the Conservation tab and contact the chair of the Conservation Committee for more information contact [email protected] To apply, please first visit the list of FAQ. Please download application ...
Discover entry requirements, content, fees and contact details for Biodiversity and Conservation at University of Southampton on prospects.ac.uk
AcylCoA binding protein (ACBP) is a highly-conserved protein found in the cells of all eukaryotes from yeast to humans. The protein binds activated fatt...
Download Thermodynamics, Conservation Of Energy notes PDF, DOC & PPT.This section provides the schedule of Thermodynamics, Conservation Of Energy lecture topics, lecture presentations
Share My Lesson is committed to bringing CC.3.5.9-10.B educators classroom resources aligned to CC.3.5.9-10.B state standards, the Common Core State Standards and Next Generation Science Standards.
Share My Lesson is committed to bringing HS-LS3-2 educators classroom resources aligned to HS-LS3-2 state standards, the Common Core State Standards and Next Generation Science Standards.
Vanhalst K، Kools P، Vanden Eynde E، van Roy F (2001). The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. FEBS Lett. 495 (1-2): 120-5. PMID 11322959. doi:10.1016/S0014-5793(01)02372-9. ...
Davis, F. W., C. Costello, and D. Stoms. 2006. Efficient conservation in a utility-maximization framework. Ecology and Society 11(1): 33. https://doi.org/10.5751/ES-01591-110133
Learn about nature conservation in California, including environmental issues and resources from The Nature Conservancy. Start Exploring California!
A lot can happen in a year. Browse some of the most important advances in bird conservation science that happened over 2019: part of the yearly update to our flagship publication, State of the Worlds Birds.
Programs are oriented toward the use, conservation, management, and appreciation of wildlife resources, and requests for such programs can be made through county Extension offices or directly with specialists ...
The Conservation Gateway is for the conservation practitioner, scientist and decision-maker. Here we share the best and most up-to-date information we use to inform our work at The Nature Conservancy.
Cephalochordates, the sister group of vertebrates + tunicates, are evolving particularly slowly. Therefore, genome comparisons between two congeners of Branchiostoma revealed so many conserved noncoding elements (CNEs), that it was not clear how many are functional regulatory elements. To more effectively identify CNEs with potential regulatory functions, we compared noncoding sequences of genomes of the most phylogenetically distant cephalochordate genera, Asymmetron and Branchiostoma, which diverged approximately 120-160 million years ago. We found 113,070 noncoding elements conserved between the two species, amounting to 3.3% of the genome. The genomic distribution, target gene ontology, and enriched motifs of these CNEs all suggest that many of them are probably cis-regulatory elements. More than 90% of previously verified amphioxus regulatory elements were re-captured in this study. A search of the cephalochordate CNEs around 50 developmental genes inseveral vertebrate genomes revealed ...
Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes. Low coverage shotgun sequencing has the potential to yield different data types throughout the genome. However, many studies using this method have often generated mitochondrial sequences, and few nuclear sequences, suggesting orthologous nuclear sequences are likely harder to recover. To determine the phylogenetic position of the galliform genus Tropicoperdix, whose phylogenetic position is currently
Transcription factors (TFs) regulate gene transcription and play pivotal roles in various biological processes such as development, cell cycle progression, cell differentiation and tumor suppression. Identifying cis-regulatory elements associated with TF-encoding genes is a crucial step in understanding gene regulatory networks. To this end, we have used a comparative genomics approach to identify putative cis-regulatory elements associated with TF-encoding genes in vertebrates. We have created a database named TFCONES (T ranscription F actor Genes & Associated CO nserved N oncoding E lementS) ( http://tfcones.fugu-sg.org ) which contains all human, mouse and fugu TF-encoding genes and conserved noncoding elements (CNEs) associated with them. The CNEs were identified by gene-by-gene alignments of orthologous TF-encoding gene loci using MLAGAN. We also predicted putative transcription factor binding sites within the CNEs. A significant proportion
TY - JOUR. T1 - Arabidopsis intragenomic conserved noncoding sequence. AU - Thomas, Brian C.. AU - Rapaka, Lakshmi. AU - Lyons, Eric. AU - Pedersen, Brent. AU - Freeling, Michael. N1 - Copyright: Copyright 2008 Elsevier B.V., All rights reserved.. PY - 2007/2/27. Y1 - 2007/2/27. N2 - After the most recent tetraploidy in the Arabidopsis lineage, most gene pairs lost one, but not both, of their duplicates. We manually inspected the 3,179 retained gene pairs and their surrounding gene space still present in the genome using a custom-made viewer application. The display of these pairs allowed us to define intragenic conserved noncoding sequences (CNSs), identify exon annotation errors, and discover potentially new genes. Using a strict algorithm to sort high-scoring pair sequences from the bl2seq data, we created a database of 14,944 intragenomic Arabidopsis CNSs. The mean CNS length is 31 bp, ranging from 15 to 285 bp. There are ≈1.7 CNSs associated with a typical gene, and Arabidopsis CNSs are ...
Strategic Habitat Conservation Final Report of the National Ecological Assessment Team Forest Breeding Bird DST July 2006 Strategic Habitat Conservation A Report from the National Ecological Assessment Team ~ June 29, 2006 ~ 1 2 TABLE OF CONTENTS Preface Executive Summary Chapter I. The Changing Nature of Conservation Introduction The Catalysts of Change The Science and Practice of Conservation Thriving Amidst Change Chapter II. The Strategic Habitat Conservation Framework Introduction Strategic Habitat Conservation - A Tool, Not a Rule Element 1 - Biological Planning Element 2 - Conservation Design Element 3 - Conservation Delivery Element 4 - Monitoring and Research Chapter III. Building Joint Capability for the FWS and USGS A Direction for Change Strengthening Institutional Relationships Strengthening Operational Relationships Chapter IV. Recommendations Introduction Recommended Actions Glossary Appendix A The National Ecological Assessment Team Charter Appendix B Draft MOU between the FWS ...
Strategic Habitat Conservation Final Report of the National Ecological Assessment Team Forest Breeding Bird DST July 2006 Strategic Habitat Conservation A Report from the National Ecological Assessment Team ~ June 29, 2006 ~ 1 2 TABLE OF CONTENTS Preface Executive Summary Chapter I. The Changing Nature of Conservation Introduction The Catalysts of Change The Science and Practice of Conservation Thriving Amidst Change Chapter II. The Strategic Habitat Conservation Framework Introduction Strategic Habitat Conservation - A Tool, Not a Rule Element 1 - Biological Planning Element 2 - Conservation Design Element 3 - Conservation Delivery Element 4 - Monitoring and Research Chapter III. Building Joint Capability for the FWS and USGS A Direction for Change Strengthening Institutional Relationships Strengthening Operational Relationships Chapter IV. Recommendations Introduction Recommended Actions Glossary Appendix A The National Ecological Assessment Team Charter Appendix B Draft MOU between the FWS ...
The Conservation Register holds detailed information on conservation-restoration practices from across the UK and Ireland. The operation of the Conservation Register is guided by an Advisory Board
Jalview 2.10.1 is now available from www.jalview.org. This is a minor release in the 2.10 series, and brings a range of bug fixes and minor new features including batch BioJS HTML page generation, interactive selection from structure highlights, and alignment conservation analysis. Jalview 2.10.1 is also significantly more memory efficient when working with very wide alignments.. With the release of Jalview 2.10.1, we also welcome Kira Mourão to the Jalview Authors. Kira joined Jalviews core development team in October 2016, and this is the first release to include her contributions.. As usual, please get in contact via our email lists or issue tracker if you have bugs, issues, new features or want to contribute to Jalviews development !. ...
Jalview 2.10.1 is now available from www.jalview.org. This is a minor release in the 2.10 series, and brings a range of bug fixes and minor new features including batch BioJS HTML page generation, interactive selection from structure highlights, and alignment conservation analysis. Jalview 2.10.1 is also significantly more memory efficient when working with very wide alignments.. With the release of Jalview 2.10.1, we also welcome Kira Mourão to the Jalview Authors. Kira joined Jalviews core development team in October 2016, and this is the first release to include her contributions.. As usual, please get in contact via our email lists or issue tracker if you have bugs, issues, new features or want to contribute to Jalviews development !. ...
Hello , I m confused by the plethora of information about Humane Genes online, Some say there is a difference between Non-Coding DNA and Junk DNA, some say there is NOT. I read it in rationalwiki Non-coding DNA refers to portions of the genome that dont code for proteins, the Rest are Junk. As it...
A group of conservation-minded farmers in the Sheboygan River watershed practice no-till, planting into green to boost soil health.
The Iowa Power Farming Show in Des Moines has about seven acres of floor space dedicated to the latest farm technology, but some of its devoted to a subject thats old as dirt. Healthy soils normally contain abundant organic matter, which aids in proper drainage and infiltration of water.
We may request cookies to be set on your device. We use cookies to let us know when you visit our websites, how you interact with us, to enrich your user experience, and to customize your relationship with our website. Click on the different category headings to find out more. You can also change some of your preferences. Note that blocking some types of cookies may impact your experience on our websites and the services we are able to offer.. ...
In PNAS this week: genetic susceptibility to lupus confers protection against malaria, ultraconserved RNA 338 and hepatocellular carcinoma pathobiology, H3K36 dimethylation and DNA repair, and more.
Alamo Resource Conservation & Development Area Inc - View photos and videos of Alamo Resource Conservation & Development Area Inc on GreatNonprofits.org by staff, volunteers, donors and clients.
View and download environmental conservation essays examples. Also discover topics, titles, outlines, thesis statements, and conclusions for your environmental conservation essay.
The local offices of the U.S. Department of Agriculture, the Natural Resources Conservation Service and the Eastern Connecticut Conservation District
One provision in the conservation title of the new Farm Bill re-couples federal crop insurance with conservation compliance, but only on highly erodible ground or wetlands.
Over the years, many (though not all) Darwinists have stated that non-coding DNA is not worth exploring because it is thought to be mere evolutionary junk.
S. 754. A bill to encourage partnerships among public agencies and other interested parties to promote fish conservation, and for other purposes. In GovTrack.us, a database of bills in the U.S. Congress.
The Council migrated to this website in May 2018. Please visit our help page so we can help find what you need, or click the Documents tab if youre looking for a specific PDF file.. ...
The Conservation Gateway is for the conservation practitioner, scientist and decision-maker. Here we share the best and most up-to-date information we use to inform our work at The Nature Conservancy.
Ndalohet hixhamja për këto persona: 1.Femrat ne ditet e para te menstruacioneve 2.Grate shtatzëna (sidomos ato në tre mujorin e parë) 3.Gratë lehona 4.
Conserved sequence Ott, Alban; Idali Anouar; Marchais Antonin; Gautheret Daniel (Jan 2012). "NAPP: the Nucleic Acid ... The Nucleic acid phylogenetic profiling (NAPP) is a database of coding and non-coding sequences according to their pattern of ...
A highly conserved sequence (. . .PRCGXPD. . .) is present in the propeptide. Removal of the propeptide by proteolysis results ... The hemopexin-like domain of MMPs is highly conserved and shows sequence similarity to the plasma protein, hemopexin. The ... Most members of the MMP family are organized into three basic, distinctive, and well-conserved domains based on structural ... the three histidine residues that coordinate with the catalytic zinc are conserved among all the MMPs. Little is known about ...
Class I has two highly conserved sequence motifs. It aminoacylates at the 2'-OH of a terminal adenosine nucleotide on tRNA, and ... Class II has three highly conserved sequence motifs. It aminoacylates at the 3'-OH of a terminal adenosine on tRNA, and is ... This new domain's functionality is conserved from that point on.[13] Application in biotechnology[edit]. In some of the ... For instance, one can start with the gene for a protein that binds a certain sequence of DNA, and, by directing an unnatural ...
The MADS box is a conserved sequence motif. The genes which contain this motif are called the MADS-box gene family.[1] The MADS ... The MADS domain binds to DNA sequences of high similarity to the motif CC[A/T]6GG termed the CArG-box.[2] MADS-domain proteins ... MEF2-like MADS-domain proteins in animals and fungi have the MEF2 domain as a second conserved domain.[14] In plants, the MEF2- ... There is evidence that the MADS domain evolved from a sequence stretch of a type II topoisomerase in a common ancestor of all ...
This sequence is conserved among species. Human CNGB1 features a C-terminal RVxP motif at amino acids 821-824 which if mutated ... Human FAM154A has a ciliary localization sequence. Tetrahymena GEF1 has a ciliary localization sequence and mutating it causes ... Mutating this sequence in mice knocked out for PKD1 causes PKD2 to accumulate at the foot of the cilia. Other proteins ... Human PDGFRA has a RVxP sequence and may localize to cilia thanks to it. Human PKD2 trafficking into cilia has been found in ...
It has a GC content of 47%. Each segment has conserved terminal sequences. The 3' end sequence (UCAUC-3') is the same as ... Although not entirely conserved, the active regions of (λ2) exhibit fidelity to MRV and ARV sequences, suggesting λ2 is the ... Comparison with PRV-1 showed a 72.9% similarity in nucleotide sequence and 80.0% amino acid sequence similarity. PVR-2 has only ... Comparison with PRV-1 showed a 73.4% and 80.3% similarity in nucleotide sequence and amino acid sequence, respectively. As a ...
... of amino acid sequence conserved) and STIM2 (31% identical; 46% of amino acid sequence conserved). Unicellular eukaryotes such ... Their N-terminal regions share 66% similarity over 577 aas (85% of the amino acid sequence of STIM1). Only the extreme of the C ... It shows a significant sequence divergence between both isoforms and in STIM1, the C-terminal region is essential for the ... Ercan E, Momburg F, Engel U, Temmerman K, Nickel W, Seedorf M (December 2009). "A conserved, lipid-mediated sorting mechanism ...
This sequence is conserved in eukaryotes. C1orf94 is a Protein tissue co-expression partner for RBBP8NL. the isoelectric point ... "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2020-05-01. "PEST sequence", Wikipedia, 2020-04-15, retrieved ... This sequence is associated with proteins that have a short intracellular half-life. C1orf94 goes through Palmitoylation, ... Proline is the most abundant amino acid in the protein sequence (11.7%) then followed closely by Leucine (10.4%). Seven PEST ...
The 5' terminal sequences are not conserved between RNA transmissions, but all of the 5' termini fold into conserved stem-loop ... The RdRp encoded has five conserved motifs (A-E). The SDD sequence which is a characteristic sequence for segmented negative ... The 3' terminal of all three RNAs are identical and conserved. The conserved nucleotide sequence is 'AAUAUC'. Ophiovirdae have ... B1MaV has nuclear localization signals within its protein sequences. These amino acid sequences tag the protein for import into ...
LepA has a highly conserved sequence. LepA orthologs have been found in bacteria and almost all eukaryotes. The conservation in ... The amino acid sequence of LepA indicates that it is a G protein, which consists of five known domains. The first four domains ... However, Domain IV of EF-G has been shown through several studies to occupy the decoding sequence of the A site after the tRNAs ... March PE, Inouye M (November 1985). "GTP-binding membrane protein of Escherichia coli with sequence homology to initiation ...
The conserved sequence motif 'AUACAAnACCC' was boxed. The phylogenetic tree of sRNA-Xcc1 homologs based on multiple alignments ...
Its sequence is highly conserved between strains. Interestingly, while viral attachment appears to involve both F and G ...
These domains are highly conserved monomeric sequences. The second group consists of only the Caenorhabditis elegans protein ... Thorough analysis of the TOG3 domain in zyg-9 provides a basic understanding of this domain that is conserved throughout all ... The XMAP215/Dis1 family is a highly conserved group of microtubule-associated proteins (MAPs) in eukaryotic organisms. These ... Cullen, C. Fiona; Peter Deák; David Glover; Hiroyuki Ohkura (September 1999). "A Gene Encoding a Conserved Microtubule- ...
Among these subtypes, genetic sequences are mostly conserved; however, wide-ranging genetic differences exist between species ... Of FIV's genome, Pol is the most conserved across FIV strains along with gag. On the contrary, env, vif, orfa, and rev are the ... Barr, Margaret C; Zou, Lily; Long, Fan; Hoose, Wendy A; Avery, Roger J (February 1997). "Proviral Organization and Sequence ... sequence divergence, and recombination of feline immunodeficiency virus from lions in the wild". BMC Genomics. 9 (1): 66. doi: ...
... a Robust Tool for Conserved Sequence Identification". Bioinformatics. 21 (24): 4420-4422. doi:10.1093/bioinformatics/bti719. ... Numerous short DNA capture sequences were designed, and used to both type and subtype influenza A viruses by taking advantage ... Dawson, Erica D.; Rowlen, Kathy L. (February 2010). FluChip: Robust Sequence Selection Method for a Diagnostic Influenza ... "Robust Sequence Selection Method Used To Develop the FluChip Diagnostic Microarray for Influenza Virus". Journal of Clinical ...
"Identification and characterization of multi-species conserved sequences". Genome Research. 13 (12): 2507-18. doi:10.1101/gr. ... His research focuses on developing new algorithms for the detection of functional regions in DNA sequences. Blanchette studied ... His research focuses on developing computational methods for detecting functional regions in DNA sequences. His postdoctoral ... 2003). "Comparative analyses of multi-species sequences from targeted genomic regions". Nature. 424 (6950): 788-93. Bibcode: ...
The sequence across these species are highly conserved. GRCh38: Ensembl release 89: ENSG00000197982 - Ensembl, May 2017 "Human ...
The sequence of GVPa is extremely well conserved. GvpJ and gvpM, two proteins encoded in the cluster of genes required for gas ...
Its sequences is highly conserved in different vertebrate species. SPP cleaves remnant signal peptides left behind in membrane ... It is an intramembrane aspartyl protease with the conserved active site motifs 'YD' and 'GxGD' in adjacent transmembrane ... as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a ...
The highly conserved chimpanzee sequences were searched against the human genome using BLAT to identify conserved regions not ... Chimpanzee sequences highly conserved in other species were then identified by pairwise alignment of chimpanzee with macaque, ... hCONDELs, on average, remove about 95 base pairs (bp) of highly conserved sequences from the human genome. The median size of ... The mechanisms and time of occurrence of hCONDELs are not entirely understood but given that conserved non-coding sequences ...
... 's amino acid sequence is highly evolutionarily conserved. Even distantly related species have extremely similar ... They are dually regulated by the cluster promoter sequences and their specific promoter sequences. Histone code Nucleosome ... All variants of histone H2B contain the same number of amino acids, and the variations in sequence are few in number. Only two ... histone H2B genes share a promoter region with sequences that code for histone H2A. While all genes in the histone cluster are ...
In humans, these SH3 domains have a common amino acid sequence Asp-Glu-Leu. This sequence motif is also conserved in other ... "Conserved Domain Analysis of SH3D21". NCBI Conserved Domain Search. Retrieved 2 May 2013. "BioGPS Expression Profile". ... Sequence identity was calculated using available sequence data and ALIGN software. GRCh38: Ensembl release 89: ENSG00000214193 ... SH3D21 is well-conserved in mammals. BLAST analysis found distant orthologs in Osteichthyes with a max identity of 28%. ...
Furthermore, it is conserved in most sequenced archeal genomes. The acetylation state of Alba, as an example, affects promoter ... The complete sequence the genome of S. solfataricus was completed in 2001. On a single chromosome, there are 2,992,245 base ... Bell SD, Botting CH, Wardleworth BN, Jackson SP, White MF (April 2002). "The interaction of Alba, a conserved archaeal ... The major motivation for sequencing these microorganisms is because of the thermostability of proteins that normally denature ...
The card sequence in the tricks must be conserved. Dealer collect all stacks together without shuffling and offers the ...
Zhang ML, Li ML, Ayoola AO, Murphy RW, Wu DD, Shao Y (November 2019). "Conserved sequences identify the closest living ... Major DNA sequence analyses of predominantly nuclear sequences (Murphy et al., 2001) support the Euarchonta hypothesis, while a ... Goodman M, Czelusniak J, Page S, Meireles CM (2001). "Where DNA Sequences Place Homo sapiens in a Phylogenetic Classification ... major study investigating mitochondrial sequences supports a different tree topology (Arnason et al., 2002). A study ...
Proteins have two conserved sequence motifs: PPTCYSR and DDC. GRCh38: Ensembl release 89: ENSG00000170891 - Ensembl, May 2017 " ...
8 and identification of conserved protein and DNA sequences." Applied Microbiology and Biotechnology 75.4 (2007): 843-851. LPSN ...
It is the only domain whose sequence is conserved. Models show oleosins having a hairpin-like hydrophobic shape that is ...
RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
... residue in the sequence Asn-X-Ser or Asn-X-Thr where X is any amino acid except proline. This sequence is called a ... "STT3, a highly conserved protein required for yeast oligosaccharyl transferase activity in vivo". EMBO J. 14 (20): 4949-60. ... The high sequence similarity between the prokaryotic and the eukaryotic STT3 suggests that their structures are similar. ...
... inside chloroplasts increases the rate of mutation so post-transcription repairs are needed to conserve functional sequences. ... Its existence was first proven in 1962,[4] and first sequenced in 1986-when two Japanese research teams sequenced the ... both very common in chloroplast transit sequences-making up 20-30% of the sequence)[45] are often the amino acids that accept ... The inverted repeat regions are highly conserved among land plants, and accumulate few mutations.[8][11] Similar inverted ...
The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage ... A variation in the last exon of this gene has previously served as the basis for an additional ZP3 locus; however, sequence and ... Jovine L, Qi H, Williams Z, Litscher E, Wassarman PM (2002). "The ZP domain is a conserved module for polymerization of ... "Conserved furin cleavage site not essential for secretion and integration of ZP3 into the extracellular egg coat of transgenic ...
Both the structures and editing sites are conserved in the coleoid genome and the mutation rates for the sites are severely ... The California two-spot octopus has had its genome sequenced, allowing exploration of its molecular adaptations.[151] Having ... Octopuses and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic acid sequence ... The arms can be described based on side and sequence position (such as L1, R1, L2, R2) and divided into four pairs.[23][22] The ...
In 2010, the Caulobacter NA1000 strain was sequenced and all differences with the CB15 "wild type" strain were identified.[6] ... The pattern is that the internal functionality of the network circuitry is conserved, but the coupling at the "edges" of the ... However, the positioning of the stalk is not necessarily conserved at the pole of the cell body in different closely related ... The proteins of the Caulobacter cell cycle control system and its internal organization are co-conserved across many ...
They also planted squash, whose broad leaves cut down on weeds and conserved moisture in the soil. The women devoted their ... According to historian Steven Harper, what followed was a "convoluted sequence of deception, fraud, and extortion orchestrated ...
... to Conserve or not to Conserve". canids.org. Archived from the original on 2013-08-14. Retrieved 14 August 2013.. ... "Large sequence divergence among mitochondrial DNA genotypes within populations of eastern African black-backed jackals" (PDF) ...
As of 2013, three turtle genomes have been sequenced.[33] The results place turtles as a sister clade to the archosaurs, the ... so landowners have an incentive to conserve their habitat. Crocodile leather is made into wallets, briefcases, purses, handbags ...
Breast-conserving surgery *Lumpectomy. *Mastectomy *Radical mastectomy. *Mammoplasty *Breast implant. *Breast reduction plasty ...
Wong AK, Pero R, Ormonde PA, Tavtigian SV, Bartel PL (Dec 1997). "RAD51 interacts with the evolutionarily conserved BRC motifs ... RAD51 catalyses strand transfer between a broken sequence and its undamaged homologue to allow re-synthesis of the damaged ... Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, ... They each share about 25% amino acid sequence identity with RAD51 and with each other.[28] ...
1992). "The antigen-specific induction of normal human lymphocytes in vitro is down-regulated by a conserved HIV p24 epitope ... Ruegg CL, Strand M (1991). "A synthetic peptide with sequence identity to the transmembrane protein GP41 of HIV-1 inhibits ... "Exon-intron organization and sequence comparison of human and murine T11 (CD2) genes.". Proc. Natl. Acad. Sci. U.S.A. 85 (5): ... "The SH3 domain of p56lck binds to proline-rich sequences in the cytoplasmic domain of CD2". J. Exp. Med. (UNITED STATES) 183 ...
In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that ... Comparative analysis of archaeal genomes has also identified several molecular signatures in the form of conserved signature ... He sequenced a variety of different species and happened upon a group of methanogens that had vastly different patterns than ... Archaea were first classified as a separate group of prokaryotes in 1977 by Carl Woese and George E. Fox based on the sequences ...
Measures taken to conserve the habitats of some high-profile charismatic species have also protected many of the less ... de Kloet, RS; de Kloet SR (2005). "The evolution of the spindlin gene in birds: Sequence analysis of an intron of the spindlin ... Conservation measures to conserve the habitats of some of the high-profile charismatic parrot species has also protected many ... inferred from mitochondrial and nuclear DNA sequences". Systematic Biology. 55 (3): 454-470. doi:10.1080/10635150600697390. ...
This sequence was originally called Box A, which is now known to be the sequence that interacts with the homologue of the ... 35 region that are both conserved.[10] ... Kozak consensus sequence. References[edit]. *^ a b c .mw-parser ... In the 1980s, while investigating nucleotide sequences in mouse genome loci, the Hogness box sequence was found and "boxed in" ... For example, one study used the adenovirus TATA promoter sequence (5'-CGCTATAAAAGGGC-3') as a model binding sequence and found ...
... they found Histone IV sequence to be highly conserved between peas and calf thymus.[22] However, their work on the biochemical ... 3. Complete amino acid sequence of pea seedling histone IV; comparison with the homologous calf thymus histone". The Journal of ... The 4 'core' histones (H2A, H2B, H3 and H4) are relatively similar in structure and are highly conserved through evolution, all ... In the early 1960s, before the types of histones were known and before histones were known to be highly conserved across ...
... a highly conserved protein complex that recognizes and binds to specific DNA sequences, marking starting points for replication ... deep sequencing; single-cell sequencing and analytics; chromatin dynamics; structural biology; advanced proteomics; mass ... Plant genome sequencing; epigenetics and stem cell fate; stem cell signaling; plant-environment interactions; using genetic ... In 2007, Hannon, Emily Hodges, Z. Xuan and W. Richard McCombie develop technology to sequence the exome, the small subset of ...
Bieniasz PD, Grdina TA, Bogerd HP, Cullen BR (1999). "Analysis of the effect of natural sequence variation in Tat and in cyclin ... The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic ... and mitochondrial DNA sequence elements from cultured mouse and human fibroblasts". DNA Cell Biol. 20 (9): 531-54. doi:10.1089/ ...
a b Wink, M., & Sauer-Gürth, H. (2004). Phylogenetic relationships in diurnal raptors based on nucleotide sequences of ... Tingay, R. E., & Katzner, T. E. (Eds.). (2010). The eagle watchers: Observing and conserving raptors around the world. Cornell ... Seibold, I., & Helbig, A. J. (1995). Evolutionary history of New and Old World vultures inferred from nucleotide sequences of ... These will increase in tempo and pitch, with about 15-30 calls in a sequence. Often pairs will duet during early spring, in ...
2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724-31. doi:10.1038/ ... Katoh Y, Katoh M (2007). "Conserved POU-binding site linked to SP1-binding site within FZD5 promoter: Transcriptional ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ... "Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs" ...
One is shallow, biogenically derived gas in mixed sand and shale sequences. Shallow biogenic gas is considered to be an ... and included provisions aimed at conserving the natural gas often produced along with the oil. For this reason, these plants ... volumes of gas molecules are trapped in shales which represent one of the commonest rock types in any sedimentary sequence. ...
2001). "The sequence of the human genome". Science. 291 (5507): 1304-51. doi:10.1126/science.1058040. PMID 11181995.. ... These subunits are conserved across many species, as the function of this complex is essential for the generation of ATP for ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Schmidt TM, Relman DA (1994). Phylogenetic identification of uncultured pathogens using ribosomal RNA sequences. Methods in ... "On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in ... James, Greg (15 May 2018). "Universal Bacterial Identification by PCR and DNA Sequencing of 16S rRNA Gene". PCR for Clinical ... Kolbert CP, Persing DH (June 1999). "Ribosomal DNA sequencing as a tool for identification of bacterial pathogens". Current ...
Li XZ, McNeilage LJ, Whittingham S (1989). «The nucleotide sequence of a human cDNA encoding the highly conserved nucleolar ... 1986). «Amino acid sequence of a specific antigenic peptide of protein B23.». J. Biol. Chem. 261 (30): 14335-41. PMID 2429957. ... Chan PK, Aldrich M, Cook RG, Busch H (1986). «Amino acid sequence of protein B23 phosphorylation site.». J. Biol. Chem. 261 (4 ... Hale TK, Mansfield BC (1990). «Nucleotide sequence of a cDNA clone representing a third allele of human protein B23.». Nucleic ...
Otsuki T., Ota T., Nishikawa T. et al. Signal sequence and keyword trap in silico for selection of full-length human cDNAs ... glycoprotein is conserved in humans (англ.) // Immunology : journal. - 2001. - Vol. 102, no. 2. - P. 173-179. - DOI:10.1046/j. ... Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences (англ.) // Proceedings of the ...
2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Lesche R, Rüther U (1998). "Close linkage of p130 and Ft1 is conserved among mammals". Mamm. Genome. 9 (3): 253-5. doi:10.1007/ ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
The simplified biosynthetic sequence is acyclic precursors → mono-pyrrole (porphobilinogen) → tetrapyrrole, also known as a ... Despite the wide range of organisms that synthesize protoporphyrin IX the process is largely conserved from bacteria to mammals ...
The sequence of steps in which the reorganization of chemical bonds may be taking place in the course of a chemical reaction is ... Law of conservation of mass continues to be conserved in isolated systems, even in modern physics. However, special relativity ...
2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-5. doi:10.1038/ ... Donaldson JC, Dise RS, Ritchie MD, Hanks SK (2002). "Nephrocystin-conserved domains involved in targeting to epithelial cell- ...
... inferred from nuclear and mitochondrial DNA sequence data"". Molecular Phylogenetics and Evolution. 40 (1): 315. doi:10.1016/j. ... "Conserving honey bees does not help wildlife" (PDF). Science. 359 (6374): 392-393. doi:10.1126/science.aar2269 ... inferred from nuclear and mitochondrial DNA sequence data". Molecular Phylogenetics and Evolution. 37 (1): 25-35. doi:10.1016/j ... has apparently increased the speed of its evolution and confounded the DNA sequence data to a point where little of substance ...
conserved noncoding sequence. TFBS. transcription factor binding site. CMM. Comparative Motif Mapping. FDR. false discovery ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ... Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis. Jan Van de Velde, Ken S. ...
... and vwb Promoters Reveals a Conserved Octanucleotide Sequence That Is Essential for Expression of These Genes Niamh Harraghy, ... Conserved Repeat Motifs and Glucan Binding by Glucansucrases of Oral Streptococci and Leuconostoc mesenteroides Deepan S. H. ... Conserved Region 2.1 of Escherichia coli Heat Shock Transcription Factor σ32 Is Required for Modulating both Metabolic ... Characterization of YvcJ, a Conserved P-Loop-Containing Protein, and Its Implication in Competence in Bacillus subtilis ...
A conserved sequence in the T-cell receptor beta-chain promoter region. S J Anderson, H S Chou, and D Y Loh ... Sequence analysis indicates that these promoters do not contain the conserved octamer that is located upstream of all ... However, a unique decanucleotide sequence, not present in immunoglobulin genes, is conserved in the promoter region of murine ... A conserved sequence in the T-cell receptor beta-chain promoter region ...
The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins.. Haynes SR1, Dollard C, Winston F, Beck S ...
This sequence predicts that sifB encodes a 10-aa protein. To determine the sequence of sifB, DNA sequences containing sifB were ... A conserved amino acid sequence directing intracellular type III secretion by Salmonella typhimurium. Edward A. Miao and Samuel ... SspH1 and SlrP both contain a conserved sequence, MFNIXNXQ, at the amino terminus, whereas the remainder of the family contains ... PCR and DNA sequence analyses were performed as described (16). sseI was sequenced from pEM55 (which was cloned from a size- ...
Rapid identification of flaviviruses based on conserved NS5 gene sequences.. Fulop L1, Barrett AD, Phillpotts R, Martin K, ... Two conserved regions in the sequence of the NS5 gene of Flaviviruses were identified. Primers were designed from the consensus ... The authenticity of the amplified fragment was confirmed by nucleotide sequencing. A band of the expected size was also ... sequence of these regions and were used in a reverse transcription/polymerase chain reaction (RT/PCR) to amplify a region of ...
Sequences may also recombine or be deleted due to chromosomal rearrangements. Conserved sequences are sequences which persist ... In coding sequences, the nucleic acid and amino acid sequence may be conserved to different extents, as the degeneracy of the ... Conserved sequences with a known function, such as protein domains, can also be used to predict the function of a sequence. ... Amino acid sequences can be conserved to maintain the structure or function of a protein or domain. Conserved proteins undergo ...
Untranslated regulatory sequences need to be conserved, for example. But regulatory sequences have more error tolerance than ... Conserved Non-Genic Sequences WhatsNEW. There are about 60,000 CNGs in the human genome, about twice the number of coding ... "conserved non-genic sequences" (CNGs) of unknown function that are better conserved than genes, and twice as abundant. It was ... Len A. Pennacchio et al., "In vivo enhancer analysis of human conserved non-coding sequences" [text], 10.1038/nature05295, p ...
Brandt, A., Bast, J., Scheu, S. et al. No signal of deleterious mutation accumulation in conserved gene sequences of extant ... No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods. *Alexander Brandt. ORCID ... We curated these multiple sequence alignments using Gblocks version 0.91b with sequence type set to codons (t = c) and minimum ... No signal of deleterious mutation accumulation in conserved gene sequences of extant asexual hexapods ...
Genomes and Genes about Experts and Doctors on conserved sequence in Kagoshima, Japan ... Experts and Doctors on conserved sequence in Kagoshima, Japan. Summary. Locale: Kagoshima, Japan ... You are here: Locale , Japan , Experts and Doctors on conserved sequence in Kagoshima, Japan ... These results and phylogenetic analysis suggested that the medaka neu3a is an evolutionally conserved sialidase with regard to ...
A conserved non-coding sequence (CNS) is a DNA sequence of noncoding DNA that is evolutionarily conserved. These sequences are ... Conserved non-coding sequences can be important sites of evolutionary divergence as mutations in these regions may alter the ... Jan 2005). "Plant conserved non-coding sequences and paralogue evolution". Trends in Genetics. 21 (1): 60-65. doi:10.1016/j.tig ... Intron sequences may be conserved, often because they contain expression regulating elements that put functional constraints on ...
Amino Acid Sequence, Cells, Computational Biology, Conserved Sequence, Databases, Protein, Protein Sorting Signals, Protein ... We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP ... The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs ... The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein ...
DNA Ultra-Conserved Sequences Found Between Humans, Mice Rats Comparisons between the DNA sequences of humans, mice, rats, and ... The first indication of the existence of ultra-conserved sequence regions was found in the initial comparison of the human and ... Researchers have found precisely the same sequences in the genomes of humans, rats, and mice; sequences that are 95 to 99 ... Comparison between the genomes of humans, mice, and rats showed many identical sequences. Most of those sequences do not code ...
Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs) Message Subject. (Your Name) has forwarded a page ... Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs). By Emmanouil T. Dermitzakis, Alexandre Reymond, ... Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences (CNGs). By Emmanouil T. Dermitzakis, Alexandre Reymond, ... Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). The significance and ...
... Saikat Chakrabarti, Christopher J. Lanczycki, Anna R. ... A block model represents conserved sequence/structure regions which are highly unlikely to contain gaps and are common to all ... Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile and at the same ... Realignment of each sequence can correct misalignments between a given sequence and the rest of the profile by shifting the ...
A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating −1 frameshifting in HIV-1. The GGG ... This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two ... glycine codon immediately following the slippery sequence (the intercodon) contributes structurally to the start of the stem- ...
Although cis- and trans-regulatory changes can contribute to sequence divergence without dramatically altering gene expression ... Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between ... Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same Trends Genet. ... Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between ...
Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved ... THE THREE-DIMENSIONAL STRUCTURE OF GLUTATHIONE S-TRANSFERASE OF SCHISTOSOMA JAPONICUM FUSED WITH A CONSERVED NEUTRALIZING ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1GNE Legend Entity #1 , Chains: A GLUTATHIONE S-TRANSFERASE protein, ...
In conclusion, the binding of PSI and dsx pre-mRNA are generally conserved in both B. mori and S. litura. These findings ... "P-element Somatic Inhibitor Protein Binding a Target Sequence in dsx Pre-mRNA Conserved in Bombyx mori and Spodoptera litura." ... P-element Somatic Inhibitor Protein Binding a Target Sequence in dsx Pre-mRNA Conserved in Bombyx mori and Spodoptera litura ... P-element Somatic Inhibitor Protein Binding a Target Sequence in dsx Pre-mRNA Conserved in Bombyx mori and Spodoptera litura. ...
STRUCTURE AND FUNCTION OF THE CATALYTIC SITE MUTANT ASP99ASN OF PHOSPHOLIPASE A2: ABSENCE OF CONSERVED STRUCTURAL WATER. ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1CEH Legend Entity #1 , Chains: A PHOSPHOLIPASE A2 protein, length: 123 ( ... Blast this sequence against all of PDB Archive.. Rank. In each cluster, the chains are sorted (i.e. ranked) according to the ...
The toxins were all highly conserved in amino acid sequence (Fig. 2), and only five different alpha-toxin sequence types (I to ... Highly Conserved Alpha-Toxin Sequences of Avian Isolates of Clostridium perfringens. Scott A. Sheedy, Aaron B. Ingham, Julian I ... Highly Conserved Alpha-Toxin Sequences of Avian Isolates of Clostridium perfringens. Scott A. Sheedy, Aaron B. Ingham, Julian I ... Highly Conserved Alpha-Toxin Sequences of Avian Isolates of Clostridium perfringens. Scott A. Sheedy, Aaron B. Ingham, Julian I ...
The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, ... The structural organization of oriC, datA, DARS1 and DARS2 were found conserved between 59 fully sequenced E. coli genomes, ... The relative distances from oriC to datA, DARS1 and DARS2, respectively, was also conserved despite of large variations in ... We suggest that this fitness cost contribute to conservation of both sequence and chromosomal location for datA, DARS1 and ...
Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice ... Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice ... Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice ... Sequence and expression pattern of pax-6 are highly conserved between zebrafish and mice ...
... were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), ... Isolation and sequence analysis of rpoH genes encoding sigma 32 homologs from gram negative bacteria: conserved mRNA and ... of the heat shock response known in E.coli are very well conserved among the gamma subgroup and partially conserved among the ... Both the sequence complementary to part of 16S rRNA (the downstream box) and a predicted mRNA secondary structure similar to ...
The box with the solid black border indicates the C-terminal sequence conserved among Tar, Tsr, and Tcp, and the box with the ... We here investigated the effects of mutations altering the C-terminal NWET/SF sequence which is conserved among the major ... Chemotactic Adaptation Is Altered by Changes in the Carboxy-Terminal Sequence Conserved among the Major Methyl-Accepting ... Chemotactic Adaptation Is Altered by Changes in the Carboxy-Terminal Sequence Conserved among the Major Methyl-Accepting ...
Subsequently, screening of the presence of Bet v 1 conserved genomic sequence was performed in 45 clinically relevant plant ... the bioinformatic algorithms were applied for known Bet v 1 homologous nucleic acids sequences to find homology and conserved ... Genomic sequences of PR proteins of two different fruit species, which allergens belong to PR proteins of the same type as Bet ... Application of Genomic Data for PCR Screening of Bet v 1 Conserved Sequence in Clinically Relevant Plant Species. By Jana ...
A short peptide sequence is conserved between three tick-borne Borrelia. LYN HAYES, LEONARD C. ARCHARD, DAVID J. M. WRIGHT ... A short peptide sequence is conserved between three tick-borne Borrelia Message Subject (Your Name) has forwarded a page to you ...
... Jan Van de Velde (UGent) , ... "Inference of Transcriptional Networks in Arabidopsis Through Conserved Noncoding Sequence Analysis." Plant Cell 26 (7): 2729- ... "Inference of Transcriptional Networks in Arabidopsis Through Conserved Noncoding Sequence Analysis." PLANT CELL 26.7 (2014): ... We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 ...
Highly Conserved RNA Sequences That Are Sensors of Environmental Stress. Albert Spicher, Oivin M. Guicherit, Laurent Duret, ... Highly Conserved RNA Sequences That Are Sensors of Environmental Stress. Albert Spicher, Oivin M. Guicherit, Laurent Duret, ... Highly Conserved RNA Sequences That Are Sensors of Environmental Stress. Albert Spicher, Oivin M. Guicherit, Laurent Duret, ... Highly Conserved RNA Sequences That Are Sensors of Environmental Stress Message Subject (Your Name) has forwarded a page to you ...
A highly conserved genomic region in baculoviruses: sequence analysis of an 11.3 kbp DNA fragment (46.5-55.1 m.u.) of the ...
  • Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. (plantcell.org)
  • Unlike proteins exported by the general secretory pathway, TTSS effector proteins are not proteolytically cleaved and have not previously been identified by conserved amino acid sequence motifs within their secretion/translocation signals ( 1 ). (pnas.org)
  • Regulatory motifs in UTRs often conserved in genes belonging to the same metabolic family could potentially be used to develop highly specific medicines that target RNA transcripts. (wikipedia.org)
  • Although nonconserved UTR sequences may also have a role, these results provide evidence that sequences that are highly conserved during evolution are good candidates for RNA motifs with posttranscriptional regulatory functions in gene expression. (asm.org)
  • Unique hot spots for sulfhydryl inactivation of Cys mutants of the metal-tetracycline/H+ antiporter (TetA) were found at the fourth positions of the dual conserved sequence motifs, GKXXDRXGRR and GRXXXKXGEK [Yamaguchi, A., Kimura, T., Someya, Y., & Sawai, T. (1993) J. Biol. (nih.gov)
  • This result confirmed that plant NCS contain evolutionary signal, which might be hypothesized to reside in the conserved motifs sought in phylogenetic footprinting. (biomedcentral.com)
  • Within these domains are highly conserved "motifs" necessary for the proper binding and orientation of both the NADH coenzyme and the FAD cofactor. (usf.edu)
  • To address the importance of these conserved motifs site-directed mutagenesis was utilized to generate a series of variants upon residues found within the motifs to allow for the full characterizations. (usf.edu)
  • Second, naturally occurring recessive congenital methemoglobinemia (RCM) mutants that are found within or in close proximity to these highly conserved motifs were analyzed utilizing site-directed mutagenesis. (usf.edu)
  • Consistent with a previous report, no conserved sequence element was found except the slippery site sequence 5′-WWW TAR-3′ (W=A or T, Fig. 4), suggesting that frameshifting does not depend on other sequence motifs. (nih.gov)
  • Conserved domains - are recurring units in polypeptide chains (sequence and structure motifs), determined and classified by comparative analysis. (academic.ru)
  • A workflow to improve the clusterization of protein families based on the array of linear conserved motifs is designed. (biomedcentral.com)
  • In this scenario, an efficient strategy to detect more divergent sequences within protein families is the use of sequence motifs. (biomedcentral.com)
  • The conserved sequences we are looking for are called regulatory motifs. (commonlounge.com)
  • Despite lacking enzymatic functions and having few protein domains, disordered regions are functionally important for protein regulation and contain short linear motifs (short peptide sequences involved in protein-protein interactions), but in most disordered regions, the functional amino acid residues remain unknown. (northwestern.edu)
  • Among the conserved sequences that we identified were previously known and newly identified short linear motifs, and we experimentally verified key examples, including a motif that may mediate interaction between protein kinase Cbk1 and its substrates.We also observed that hub proteins, which interact with many partners in a protein interaction network, are highly enriched in these conserved sequences. (northwestern.edu)
  • NestedMICA is a new, scalable, pattern-discovery system for finding transcription factor binding sites and similar motifs in biological sequences. (psu.edu)
  • It also performs robustly on synthetic sequences containing multiple significant motifs. (psu.edu)
  • When tested on a real set of regulatory sequences, NestedMICA produced motifs which were good predictors for all five abundant classes of annotated binding sites. (psu.edu)
  • Online Cover This week features a Research Resource that describes a method for identifying the functional, conserved motifs in the disordered regions of proteins. (sciencemag.org)
  • Conserved Domains (CD) contain conserved sequence patterns or motifs, which allow for their detection in polypeptide sequences (www.ncbi.nlm.nih.gov/ Structure/cdd). (symbiosisonlinepublishing.com)
  • The TIGR and olfactomedin sequences display conserved motifs including a residual leucine zipper region and maintain a similar secondary structure throughout the N-terminal region. (mcponline.org)
  • Additionally, we have identified a group of chitinase sequences containing several of the highly conserved motifs present in the C-terminal region of the olfactomedin domain-containing sequences. (mcponline.org)
  • Karavanich and Anholt ( 2 ) first compared the olfactomedin-related proteins from rat, mouse, human, and frog and identified several conserved motifs. (mcponline.org)
  • Sequence analysis indicates that these promoters do not contain the conserved octamer that is located upstream of all immunoglobulin genes. (pnas.org)
  • However, a unique decanucleotide sequence, not present in immunoglobulin genes, is conserved in the promoter region of murine and human V beta genes. (pnas.org)
  • A team of seven geneticists have found something amazing in the genomes of humans and at least twelve other mammals, "conserved non-genic sequences" (CNGs) of unknown function that are better conserved than genes, and twice as abundant. (panspermia.org)
  • It was already known that there are sequences outside of genes that are well-conserved between the human and mouse genomes. (panspermia.org)
  • But regulatory sequences have more error tolerance than genes, not less. (panspermia.org)
  • The most highly conserved ones have a nucleotide substitution rate, across the studied mammals, that is less than half that of protein-coding genes. (panspermia.org)
  • In general, for any genome that's sequenced, we only really know what about a third of the genes do. (panspermia.org)
  • Conserved non-coding sequences can be important sites of evolutionary divergence as mutations in these regions may alter the regulation of conserved genes, producing species-specific patterns of gene expression. (wikipedia.org)
  • Introns are stretches of sequence found mostly in eukaryotic organisms which interrupt the coding regions of genes, with basepair lengths varying across three orders of magnitude. (wikipedia.org)
  • Although 111 of these ultra-conserved elements overlapped with genes known to code for proteins, 256 showed no evidence that they overlap genes, and another 114 appeared inconclusively related to genes. (futurepundit.com)
  • We found that CNGs are significantly more conserved than protein-coding genes and noncoding RNAS (ncRNAs) within the mammalian class from primates to monotremes to marsupials. (sciencemag.org)
  • To identify ultraconserved CNS s, we included genomes of additional plant families and identified 715 binding sites for 501 genes conserved in dicots, monocots, mosses, and green algae. (plantphysiol.org)
  • Additionally, we found that genes that are part of conserved mini-regulons have a higher coherence in their expression profile than other divergent gene pairs. (plantphysiol.org)
  • All identified CNS s were integrated in the PLAZA 3.0 Dicots comparative genomics platform ( http://bioinformatics.psb.ugent.be/plaza/versions/plaza_v3_dicots/ ) together with new functionalities facilitating the exploration of conserved cis-regulatory elements and their associated genes. (plantphysiol.org)
  • The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. (epfl.ch)
  • Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. (epfl.ch)
  • In all instances the putative hup sequences were located on a plasmid that also contained nif genes. (asm.org)
  • These results suggest that the identified DNA region contains genes essential for hydrogenase activity in R. leguminosarum and that its organization is highly conserved within Hup + strains in this symbiotic species. (asm.org)
  • The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. (plantcell.org)
  • Genes coding for transcription factors and developmental regulators have a high likelihood to harbour cis-regulatory regions that are structurally conserved among orthologous genes in the vertebrate lineage. (semanticscholar.org)
  • One CTCF binding site, conserved in mouse and human c-myc genes, is found immediately downstream of the major P2 promoter at a sequence which maps precisely within the region of RNA polymerase II pausing and release. (asm.org)
  • This flexibility in Zn finger usage reveals CTCF to be a unique "multivalent" transcriptional factor and provides the first feasible explanation of how certain homologous genes (i.e., c-myc) of different vertebrate species are regulated by the same factor and maintain similar expression patterns despite significant promoter sequence divergence. (asm.org)
  • Annotation of the Arabidopsis genome sequence has made it possible to identify peptide-encoding genes. (semanticscholar.org)
  • The nuclear-encoded ribosomal RNA genes (rDNA) of fungi exist as a multiple-copy gene family comprised of highly similar DNA sequences (typically from 8-12 kb each) arranged in a head-to-toe manner. (duke.edu)
  • We explored the possibilities of evolutionary analysis of phylogenetic footprints in 5'-noncoding sequences (NCS) from 27 ribulose-1,5-bisphosphate carboxylase small subunit ( rbcS ) genes, from three dicot families (Brassicaceae, Fabaceae and Solanaceae). (biomedcentral.com)
  • With sufficient samples of +1 PRF genes, the conserved sequence elements which might facilitate frameshifting were checked. (nih.gov)
  • Using primers designed for conserved regions flanking these signatures, fragments of most of these genes were amplified from 23 actinobacterial species, covering many different families and orders, for which no sequence information was previously available. (microbiologyresearch.org)
  • conserved sequence - An identical or highly similar sequence of nucleotides or amino acids which occurs as part, or all of a number of different genes or proteins, in either the same or different species. (academic.ru)
  • A repetitive DNA sequence has been identified in the Drosophila melanogaster genome that appears to be localized specifically within genes of the bithorax and Antennapedia complexes that are required for correct segmental development. (harvard.edu)
  • Initially identified in cloned copies of the genes Antennapedia, Ultrabithorax and fushi tarazu, the sequence is also contained within two other DNA clones that have characteristics strongly suggesting that they derive from other homoeotic genes. (harvard.edu)
  • The display of these pairs allowed us to define intragenic conserved noncoding sequences (CNSs), identify exon annotation errors, and discover potentially new genes. (elsevier.com)
  • A conserved-region vaccine (CRV) delivering genes for these four regions as equal mixtures of three mosaics each (each region at a separate injection site) was compared to a whole-protein vaccine (WPV) delivering equimolar amounts of genes for whole Gag, Env, and Nef as clade B consensus sequences (separate injection sites). (elsevier.com)
  • Background: This work addresses the problem of detecting conserved transcription factor binding sites and in general regulatory regions through the analysis of sequences from homologous genes, an approach that is becoming more and more widely used given the ever increasing amount of genomic data available. (uniba.it)
  • Results: We present an algorithm that identifies conserved transcription factor binding sites in a given sequence by comparing it to one or more homologs, adapting a framework we previously introduced for the discovery of sites in sequences from co-regulated genes. (uniba.it)
  • Citation Query Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. (psu.edu)
  • It is a truth (almost) universally acknowledged that conserved non-coding genomic sequences function in the cis regulation of neighbouring genes. (biologists.org)
  • Sequenced crop plants are the good resources in identification of important genes for quality, insect pest and disease resistance, resistance to abiotic stresses like temperature, drought, salinity etc. which are possible to transfer to cultivable background by combining traditional and molecular breeding methods [28]. (symbiosisonlinepublishing.com)
  • In particular, developmental process-related TF genes showed significantly higher conservation of the upstream sequences than other TF genes. (edu.sa)
  • Such extreme upstream conservation of the developmental process-related TF genes suggests that the regulatory networks involved with developmental processes have been evolutionarily well conserved in both human and mouse lineages. (edu.sa)
  • Iwama, H & Gojobori, T 2004, ' Highly conserved upstream sequences for transcription factor genes and implications for the regulatory network ', Proceedings of the National Academy of Sciences of the United States of America , vol. 101, no. 49, pp. 17156-17161. (edu.sa)
  • A total of 14,958 and 2184 genes were predicted to be targeted by the 186 conserved and 41 novel miRNAs. (beds.ac.uk)
  • The bromodomain: a conserved sequence found in human, Drosophila and yeast proteins. (nih.gov)
  • Previously, no consensus signal sequence for translocation has been identified among TTSS effector proteins. (pnas.org)
  • In this work, seven proteins, termed Salmonella -translocated effectors (STE), are described that contain conserved amino acid sequences that direct translocation by TTSS in Salmonella typhimurium . (pnas.org)
  • Secretion signals have been mapped in several Yop proteins to sequences encoding the amino-terminal 15 amino acid residues ( 11 ). (pnas.org)
  • In evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). (wikipedia.org)
  • Conserved proteins undergo fewer amino acid replacements, or are more likely to substitute amino acids with similar biochemical properties. (wikipedia.org)
  • As with proteins, nucleic acids that are important for the structure and function of non-coding RNA (ncRNA) can also be conserved. (wikipedia.org)
  • Most of these ultra-conserved regions do not appear to code for proteins, but may instead play a regulatory role. (futurepundit.com)
  • The amount of conservation of sequence that was found suggested most of the genome that has functionality is not coding for proteins. (futurepundit.com)
  • Most of those sequences do not code for proteins. (futurepundit.com)
  • The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. (rostlab.org)
  • The alpha-toxin structural gene ( plc or cpa ) has been isolated from several strains of C. perfringens and characterized ( 4 ), and the encoded proteins were found to be highly conserved in all but one recently identified strain ( 8 ). (asm.org)
  • Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. (pubmedcentralcanada.ca)
  • Genomic sequences of PR proteins of two different fruit species, which allergens belong to PR proteins of the same type as Bet v 1, were selected to design degenerate primers. (intechopen.com)
  • Correct targeting of nuclear proteins is mediated by nuclear localization sequences (NLS) which permit specific binding to the nucleus and subsequent translocation across the nuclear envelope via the nuclear pore complex. (biologists.org)
  • We have generated anti-idiotype antibodies against the SV40 T-antigen nuclear localization sequence that allowed us to study NLS-binding proteins in a variety of different organisms. (biologists.org)
  • Our results suggest that a set of proteins common to various eukaryotes recognizes nuclear localization sequences. (biologists.org)
  • These data provide valuable information for future experiments aimed at identifying host and/or viral proteins which interact with this highly conserved RNA element. (asm.org)
  • Although there is 100% sequence identity in the DNA binding domains of the avian and human CTCF proteins, the regulatory sequences recognized by CTCF in chicken and human c-myc promoters are clearly diverged. (asm.org)
  • A multiple sequence alignment of homologous proteins demonstrates that some of the missense variants are located in highly conserved regions of the NTPase domain and possibly impair NTP-hydrolysis. (uni-kiel.de)
  • In this work, three conserved indels (i.e. inserts or deletions) are described in three widely distributed proteins that are distinctive characteristics of the Actinobacteria and are not found in any other groups of bacteria. (microbiologyresearch.org)
  • Conserved domain database - CDD Content Description Conserved Domain Database for the functional annotation of proteins. (academic.ru)
  • Clustering of proteins in families sharing functional characteristics and derived from a common ancestor is a key purpose of sequence comparative analyses. (biomedcentral.com)
  • These are highly conserved regions across a subset of proteins sharing the same function. (biomedcentral.com)
  • In InterPro the PNDR includes around 10,000 proteins divided in two main subfamilies: class I (IPR001100) with 6,701 sequences and class II (IPR000103) with 2,809 sequences. (biomedcentral.com)
  • Here we have identified and characterised the distribution of common variant sequences from individual repeat units of the C-repeat region (CRR) of M-proteins representing 77 different M-types. (edu.au)
  • A current trend in the design of universal flu vaccines is the construction of recombinant proteins based on combinations of various conserved epitopes of viral proteins (M1, M2, HA2, NP). (springer.com)
  • Recent studies show that conserved influenza viral proteins (such as HA2, M2, NP and M1) can provide protective immune response against a range of influenza virus subtypes. (springer.com)
  • These showed little similarity to other known sequences except for one pair of predicted proteins (Hqrw_6002 and its ortholog Hqrw_7002), which closely resembled proteins encoded by a wide variety of haloarchaea and that were located nearby halovirus-related gene clusters. (frontiersin.org)
  • In evolutionary biology and genetics, conserved sequences refer to identical or similar sequences of DNA or RNA or amino acids (proteins) that occur in different or same species over generations. (commonlounge.com)
  • In this image we are looking at the amino acid sequence of mammalian histone proteins and their conserved regions. (commonlounge.com)
  • The identification of a conserved domain footprint may be the only clue towards cellular or molecular function of a protein, as it indicates local or partial similarity to other proteins, some of which may have been characterized experimentally. (symbiosisonlinepublishing.com)
  • Although the N-terminal domain of olfactomedin is divergent ( 2 ), the C-terminal domain is highly conserved among the TIGR and olfactomedin proteins. (mcponline.org)
  • 5 ) extended their evaluations to a slightly more divergent set of proteins, including a rat latrophilin sequence and a human olfactomedin-related sequence. (mcponline.org)
  • In their study, the researchers concentrated their analysis on the olfactomedin domain of the sequences because of extreme differences in sequence lengths among the olfactomedin-related proteins. (mcponline.org)
  • This striking structural and sequence conservation in MSP2s from organisms with different animal host and cell tropisms suggests that these proteins share similar functions that are important for survival. (jimmunol.org)
  • Although no cDNAs have yet been isolated, genomic sequencing shows a short open reading frame with weak similarity to collagen proteins. (ox.ac.uk)
  • Advances in high-throughput DNA sequencing and protein mass spectrometry has substantially increased the availability of protein sequences and whole genomes for comparison since the early 2000s. (wikipedia.org)
  • The CNGs in mammalian genomes are much more extensive and more highly conserved than anything seen in yeast, even though the evolutionary time separating [the studied] mammals. (panspermia.org)
  • Comparisons between the DNA sequences of humans, mice, rats, and other species have turned up a surprising number of sections of the genomes that have no differences. (futurepundit.com)
  • sequences that are 95 to 99 percent identical to these can be found in the chicken and dog genomes, as well. (futurepundit.com)
  • The first indication of the existence of ultra-conserved sequence regions was found in the initial comparison of the human and mouse genomes. (futurepundit.com)
  • When we had compared the human and mouse genomes, we found that about five percent of each of these showed some kind of evolutionary selection that partially preserved the sequence, he said. (futurepundit.com)
  • Comparison between the genomes of humans, mice, and rats showed many identical sequences. (futurepundit.com)
  • And when they extended their comparisons to the even more ancient genomes of the sea squirt, fruit fly and roundworm, they found very little evidence of these conserved elements. (futurepundit.com)
  • Analysis of the human and mouse genomes identified an abundance of conserved non-genic sequences (CNGs). (sciencemag.org)
  • Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between genomes. (nih.gov)
  • The structural organization of oriC, datA, DARS1 , and DARS2 were found conserved among 59 fully sequenced E. coli genomes, with differences primarily in the non-functional spacer regions between key protein binding sites. (frontiersin.org)
  • The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes. (epfl.ch)
  • The presence of OAT15.1 (GATA) 3.75 and OAT15.2 (GACA) 3.75 sequences in different genomes were ascertained by independent dot-blot hybridization prior to using them for RAPD reactions. (ias.ac.in)
  • Conserved Domains database available at NCBI has extensive resources on conserved sequences in different organisms and genomes. (commonlounge.com)
  • Example of orthologous conserved sequences: A research on genomes of vertebrate, worm, insect and a yeast genome (PubMed Central PMCID:PMC1182216) found conserved elements across genome wide alignments of 5 species of vertebrates (human, rat, mouse, chicken and Fugu rubripes) , 2 species of Caenorhabditis and 7 species of Saccharomyces . (commonlounge.com)
  • The conserved element that was analyzed was found to be 3%-8% of the human genome and substantially higher fractions of the more compact Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharaomyces cerevisiae (47%-68%) genomes. (commonlounge.com)
  • Conserved sequences found in different genomes can be either coding sequences or non coding sequences. (commonlounge.com)
  • By comparing genomes which have a certain conserved sequence common to them we can easily identify anomalies, any exist. (commonlounge.com)
  • Here we assess these possibilities by comparing unannotated conserved islands in the human and mouse genomes to transcribed regions and to RFBSs, relying on a detailed case study of one human and one mouse cell type. (edu.au)
  • Extending these findings across multiple cell types and tissues, we propose that most conserved non-coding genomic DNA in vertebrate genomes corresponds to promoter-distal regulatory elements. (edu.au)
  • This study presented detailed sequences and structural variations of chloroplast genomes of Sect. (springer.com)
  • Our study [1] has discovered intriguing conserved regions in some 5′ UTRs in a large set of genomes. (phdposition.com)
  • The study of sequence conservation overlaps with the fields of genomics, proteomics, evolutionary biology, phylogenetics, bioinformatics and mathematics. (wikipedia.org)
  • Over many generations, nucleic acid sequences in the genome of an evolutionary lineage can gradually change over time due to random mutations and deletions. (wikipedia.org)
  • Patterns of conserved introns between species of different kingdoms have been used to make inferences about intron density at different points in evolutionary history. (wikipedia.org)
  • If these regions perform an important regulatory function, the increase in 3'-UTR length over evolutionary time suggests that conserved UTRs contribute to organism complexity. (wikipedia.org)
  • Evolutionary theory suggests these sequences may be so central to mammalian biology that even small changes in them would compromise the animal's fitness. (futurepundit.com)
  • The most exciting thing for me is that the ultra-conserved regions we have identified do represent evolutionary innovations that must have happened sometime during vertebrate development, because we see such large pieces that no longer match in fish, and almost nothing in sea squirt. (futurepundit.com)
  • In this study we have been identified the various conserved domains, super families having putative functions for fundamental, metabolic, developmental, evolutionary processes and physiogenic nature from the query sequences. (vixra.org)
  • For this objective, we needed to conduct sufficiently comprehensive phylogenetic footprinting for meaningful evolutionary analysis of conserved sequence blocks. (biomedcentral.com)
  • Our findings suggest that evolutionary gene duplication can give rise to disease families because variants affect conserved sequence in a similar fashion. (uni-kiel.de)
  • Sequence alignment - In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. (academic.ru)
  • Keeping all above points in view the computational identification study was carried out to identify the conserved domains having putative function like insect pest resistance, improved quality parameters or for resistance to abiotic stresses like temperature, drought, salinity or any other evolutionary functions from Green gram GSS and their possible use in Green gram and also its related crops improvement. (symbiosisonlinepublishing.com)
  • Presumably, sequence elements conserved across long evolutionary times are likely to be essential to the structural or functional success of a protein family ( 7 ). (mcponline.org)
  • Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. (rostlab.org)
  • We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. (rostlab.org)
  • Bet v 1 has been identified as existing in three subfamilies, based on the sequence similarity. (intechopen.com)
  • While all of the resources share a common interest in protein family classification using sequence similarity as a key factor to achieve their purposes, the focus of each database is different. (biomedcentral.com)
  • The predicted amino acid sequence has 50-65% identity with the human, rat and mouse CD2 sequences with greatest similarity shared with the human homologue. (ox.ac.uk)
  • Conserved sequences help us find homology (similarity) among different organisms and species. (commonlounge.com)
  • Furthermore, comparison of the amino acid sequence of A. marginale MSP2 with that of E. phagocytophila MSP2 in these conserved regions revealed 96% and 87% similarity in the respective N and C termini ( 7 ). (jimmunol.org)
  • Though the species of this group show a high degree of karyotypic similarity, D. soaresi was unique in presenting large blocks of het- ITSs (heterochromatic internal telomeric sequences) in the majority of the centromeres. (pensoft.net)
  • Homology search tools may take an individual nucleic acid or protein sequence as input, or use statistical models generated from multiple sequence alignments of known related sequences. (wikipedia.org)
  • This can be inferred from the increased alignment score and enhanced sensitivity for database searching using the sequence profiles derived from refined alignments compared with the original alignments. (pubmedcentralcanada.ca)
  • Several domain databases are now available which combine homologous protein domains into the distinct families and represent them in the form of domain multiple sequence alignments. (pubmedcentralcanada.ca)
  • The accuracy of domain identification, protein classification and reconstruction of phylogenetic history of domain families crucially depends on the quality of underlying sequence alignments. (pubmedcentralcanada.ca)
  • The CDD database contains alignments that are carefully curated to be consistent with structure-structure alignments to preserve the conserved core of a protein domain family. (pubmedcentralcanada.ca)
  • The large phylogenetic distance between the currently sequenced dicot plant species hampers the use of lift overs, in which detected transcription factor binding sites ( TFBS s) are transferred from one species to another through whole-genome alignments. (plantphysiol.org)
  • Various software tools also have been developed to identify regulatory regions without using sequence alignments but based on experimental features, such as coregulation, or using advanced computational methods ( MacIsaac and Fraenkel, 2006 ). (plantphysiol.org)
  • For a given species or group within the family, the polyprotein coding sequences (CDSs) were extracted, translated, aligned with CLUSTALW [ 5 ], and back-translated to nucleotide sequence alignments. (biomedcentral.com)
  • 1999. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. (bcgsc.ca)
  • However, a region of markedly suppressed synonymous codon variability was identified in alignments of HAV sequences near the 5' end of the 3D(pol)-coding sequence of HAV, consistent with noncoding constraints imposed by an underlying RNA secondary structure. (ox.ac.uk)
  • The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domain conserved in molecular evolution [24]. (symbiosisonlinepublishing.com)
  • Multiple sequence alignments and secondary structure analyses were used to identify conserved sequence elements. (mcponline.org)
  • The aim of this study was to identify conserved and novel miRNAs in grass carp in response to GCRV infection, as well as attempt to reveal the mechanism underlying GCRV pathogenesis and hemorrhagic symptoms. (biomedcentral.com)
  • It uses protein specific scoring matrices to identify conserved sequences. (commonlounge.com)
  • Among the chemoreceptors of these species, Tsr, Tar, and Tcp have a well-conserved carboxy-terminal motif (NWET/SF) that is absent in Trg and Tap. (asm.org)
  • In three species, the identified CNS s were evaluated using TF chromatin immunoprecipitation sequencing data, resulting in significant overlap for the majority of data sets. (plantphysiol.org)
  • DNA sequences that are not actively transcribed and that are conserved across a large number of related species are called conserved noncoding sequences ( CNS s). (plantphysiol.org)
  • Subsequently, screening of the presence of Bet v 1 conserved genomic sequence was performed in 45 clinically relevant plant species. (intechopen.com)
  • Results In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. (uncg.edu)
  • Domesticated dogs exhibit the greatest skeletal size diversity of any species and, given the regulatory role of FGFR3 on growth plate proliferation, we asked whether sequence differences in FGFR3 could account for some of the size differences. (biomedcentral.com)
  • Our findings demonstrate that OdAdV-1 is highly conserved between 10 isolates recovered from multiple related cervid species, but genotypic differences, largely localized to a variable region, define two strains. (microbiologyresearch.org)
  • We propose that the virus type name be changed to cervid adenovirus 1, with the species name Cervid atadenovirus A. Sequence data were used to develop molecular assays for improved detection and genotyping. (microbiologyresearch.org)
  • The RAPD amplicons generated by evolutionarily conserved primer(s) or sequences shared by many species may be useful for clad identification in controversial systematics, comparative genome analysis, and for establishing the phylogenetic status of an organism. (ias.ac.in)
  • Those indicated in grey are conserved in all the species while we see the gaps in white which tend to change over different species. (commonlounge.com)
  • A conserved sequence is called orthologous when identical sequences are found across species and it is called paralogous when identical sequences are found within the same genome over generations. (commonlounge.com)
  • Here, we review the emerging picture, examining the extent to which conserved non-coding sequences equivalently regulate gene expression in different species, or at different developmental stages, and how genomics approaches are revealing the relationship between sequence conservation and functional use of cis -regulatory elements. (biologists.org)
  • A non-coding region of the genome identified by conventional alignment of genomic sequences from two or more species. (biologists.org)
  • A technique to identify potential CRMs within conserved non-coding sequences through comparison with orthologous sequences from one or more other species. (biologists.org)
  • A recent collaborative study of the Tauber (Leicester) and Ott (Warwick) research teams, we compared the genome sequence of insect species and searched for highly conserved sequences as more important sequence elements are more likely to be conserved over time than less important sequence elements, leaving behind a 'footprint' of functionality. (phdposition.com)
  • A total of 235 putative miRNA families were predicted, including 192 conserved families and 43 species-specific families. (beds.ac.uk)
  • We identify this sequence as a potential regulatory element, based on its position, conservation, and sequence homology to sites known to bind transcription-activating factors. (pnas.org)
  • Conservation indicates that a sequence has been maintained by natural selection. (wikipedia.org)
  • Conservation can occur in coding and non-coding nucleic acid sequences. (wikipedia.org)
  • However, sequence conservation in ncRNAs is generally poor compared to protein-coding sequences, and base pairs that contribute to structure or function are often conserved instead. (wikipedia.org)
  • In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. (rostlab.org)
  • The challenge of understanding the concrete mechanisms underlying cis-regulatory evolution - including the conservation of function without the conservation of sequence - relates to the challenge of understanding the function of regulatory systems in general. (nih.gov)
  • We suggest that this fitness advantage has contributed to conservation of both sequence and chromosomal location for datA, DARS1 , and DARS2 . (frontiersin.org)
  • Thirteen Rhizobium leguminosarum strains previously reported as H 2 -uptake hydrogenase positive (Hup + ) or negative (Hup − ) were analyzed for the presence and conservation of DNA sequences homologous to cloned Bradyrhizobium japonicum hup -specific DNA from cosmid pHU1 (M. A. Cantrell, R. A. Haugland, and H. J. Evans, Proc. (asm.org)
  • WebLogo displaying conserved sequences associated with frameshift sites.Sizes of letters denote information content, or sequence conservation, at each position. (nih.gov)
  • Plotting the conservation at synonymous sites along the polyprotein coding sequence reveals strong conservation peaks at the very 5' end of the coding sequence, and also at the 5' end of the sequence encoding the NS2A protein. (biomedcentral.com)
  • Beginning with pairwise sequence comparisons, conservation at synonymous sites (only) was evaluated by comparing the observed number of base substitutions with the number expected under a neutral evolution model. (biomedcentral.com)
  • Conserved region - may refer to: Conservation (genetics) Highly conserved sequence This disambiguation page lists articles associated with the same title. (academic.ru)
  • We often see cases of extreme conservation of nucleic acid or amino acid sequences, these are called ultra conserved sequences . (commonlounge.com)
  • We searched for evolutionarily conserved sequences within disordered regions according to the hypothesis that conservation would indicate functional residues. (northwestern.edu)
  • The main novel idea we introduce is a relative measure of conservation, assuming that true functional elements should present a higher level of conservation with respect to the rest of the sequence surrounding them. (uniba.it)
  • 2] Davies N, Krusche P. Tauber E and Ott S. Analysis of 5' untranslated regions reveals extraordinary conservation of novel non-coding sequences across wide range of Arthropods. (phdposition.com)
  • In this study, with the aim of elucidating the architecture of the regulatory network, we systematically estimated the degree of conservation of the upstream sequences of 3,750 human-mouse orthologue pairs along 8-kb stretches. (edu.sa)
  • Sparse sequence conservation in non-coding sequences and the unreliable natu. (biomedcentral.com)
  • We have examined the functional effects of substitutions of a conserved aspartic acid residue in the second transmembrane domain (D71A) and of residues in the conserved NPXXY motif in the seventh transmembrane domain (N297A and Y301A). (biochemj.org)
  • Substituting either of the threonine residues in the TRAT sequence with negatively charged residues decreases the binding of lamin Dm 0 to chromatin, indicating that this binding could be regulated by phosphorylation. (biologists.org)
  • The role of the "124GRxxST127" was determined by the introduction of a positive charge, charge reversal, and conserved amino acid mutations through site-directed mutagenesis of the G124, K125, and M126 residues. (usf.edu)
  • Conserved sequence - Residues conserved among various G protein coupled receptors are highlighted in green. (academic.ru)
  • The key conserved features of the extracellular region included core residues necessary to preserve the structural integrity of the molecule, residues in the linker region likely to maintain the unique domain organization of CD2, an array of highly charged residues in the putative ligand-binding face of the molecule and glycosylation-signal distributions that render the putative ligand-binding GFCC'C" face of domain 1 relatively unhindered by glycosylation. (ox.ac.uk)
  • The correlation between conserved elements and disease-associated mutations and apparent polymorphisms in human TIGR was also examined to evaluate the apparent importance of conserved residues to the function/structure of TIGR. (mcponline.org)
  • Amino acid sequences can be conserved to maintain the structure or function of a protein or domain. (wikipedia.org)
  • We have isolated and analyzed human CTCF cDNA clones and show here that the ubiquitously expressed 11-zinc-finger factor CTCF is an exceptionally highly conserved protein displaying 93% identity between avian and human amino acid sequences. (asm.org)
  • Margaret Dayhoff's 1966 comparison of ferrodoxin sequences showed that natural selection would act to conserve and optimise protein sequences essential to life. (wikipedia.org)
  • As coding sequences, amino acids and nucleic acids are often conserved to retain the structure and function of a certain protein. (commonlounge.com)
  • Similarly, other mRNA related nucleic acid sequences are often conserved. (commonlounge.com)
  • Transcription factor binding sites ( TFBSs ) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. (plantcell.org)
  • Highly conserved DNA sequences are thought to have functional value, although the role for many highly conserved non-coding DNA sequences is poorly understood. (wikipedia.org)
  • Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains. (wikipedia.org)
  • Nucleic acid sequences that cause secondary structure in the mRNA of a coding gene may be selected against, as some structures may negatively affect translation, or conserved where the mRNA also acts as a functional non-coding RNA. (wikipedia.org)
  • Intron sequences may be conserved, often because they contain expression regulating elements that put functional constraints on their evolution. (wikipedia.org)
  • Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. (epfl.ch)
  • Dicot 5'-NCS contain conserved modular arrays of recurrent sequence blocks, which are coincident with functional elements. (biomedcentral.com)
  • We hypothesize, therefore, that the functional importance of the pseudoknot is to stimulate a portion of ribosomes to shift -1 nt into a short (45 codon), conserved, overlapping open reading frame, termed foo . (biomedcentral.com)
  • sequences that had lost their coding ability or partially duplicated Functional and physical units of heredity passed from parent to offspring. (godandscience.org)
  • These GSS and EST sequences used for the identification of "Functional Molecular Markers" (FMM) which are associated with trait of interest and may be transferable in closely related genera [3]. (symbiosisonlinepublishing.com)
  • In contrast to protein-coding regions that are relatively easy to identify (e.g. by looking for open-reading frames), other functional elements such as transcriptional and translational regulatory regions may be short and lacking a clear sequence motif that would allow them to be detected in a single genome. (phdposition.com)
  • These ancient conserved non-coding elements are associated with the two ribosomal stalk components and would have been functional in some of the earliest animals. (phdposition.com)
  • We would now like to carry experimental work that would uncover the functional role of these conserved non-coding sequences (CNS). (phdposition.com)
  • Untranslated regulatory sequences need to be conserved, for example. (panspermia.org)
  • It binds specifically to regulatory sequences in the promoter-proximal regions of chicken, mouse, and human c-myc oncogenes. (asm.org)
  • Because this approach does not rely on any previously described transcription factor consensus DNA-binding site information or any other predicted motif or the presence of overrepresented sequences, cis -Decoder analysis affords an unbiased 'evo-centric' view of shared single or multiple sequence homologies between different enhancers. (biomedcentral.com)
  • To search the potential conserved sequence elements, 30 bp upstream and downstream of the conserved slippery sequence motif from 4,545 predicted slippery sites were extracted and analysed using WebLogo36. (nih.gov)
  • The pseudoknot is preceded by a conserved slippery heptanucleotide (Y CCU UUU), thus forming a classical stimulatory motif for -1 ribosomal frameshifting. (biomedcentral.com)
  • Sequence motif - In genetics, a sequence motif is a nucleotide or amino acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance. (academic.ru)
  • We show that the new method is significantly more sensitive than MEME: in one case, it successfully extracted a target motif from background sequence four times longer than could be handled by the existing program. (psu.edu)
  • Mutations that disrupted secondary RNA structure or the AAACA/G motif, without altering the amino acid sequence of 3D(pol), ablated replication of a subgenomic HAV replicon in transfected human hepatoma cells. (ox.ac.uk)
  • 200 bp) islands of evolutionarily conserved sequences, the function of most of these unannotated conserved islands remains unknown. (edu.au)
  • Van de Velde J, Heyndrickx K, Vandepoele K. Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. (ugent.be)
  • Conserved non-coding sequences and transcriptional regulation. (semanticscholar.org)
  • An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. (asm.org)
  • The threonine-to-alanine substitution is within the putative signal peptide sequence ( 21 ) and would not be present in the mature protein and therefore cannot affect the properties of the mature toxin ( 4 ). (asm.org)
  • The putative function of highly conserved regions (HCRs) within 3′ untranslated regions (3′UTRs) as regulatory RNA sequences was efficiently and quantitatively assessed by using modular retroviral vectors. (asm.org)
  • With recent advances in the field of genome sequencing, analysis and availability of large genomic data in the public domain, we made an attempt to survey the presence of the conserved domains, super families and multi domains having putative functions identified from green gram [Vigna radiata (L.) R. Wilczek] Genomic Survey Sequences (GSS) using computational tools. (vixra.org)
  • Computer analysis of sequence data revealed a single open reading frame (ORF1, 146 amino acids, MW 16.525.5 Da) encoding a putative replication protein which is similar to the Rep protein of Ruminobacter, amylophilus plasmid pRAO1. (elsevier.com)
  • We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences ( CNSs ) across 12 dicot plants. (plantcell.org)
  • A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time. (wikipedia.org)
  • These results and phylogenetic analysis suggested that the medaka neu3a is an evolutionally conserved sialidase with regard to enzymatic properties, whereas neu3b is likely to have originally evolved in medaka. (labome.org)
  • Powerful comparative genomics methods, such as phylogenetic footprinting, can be used for the detection of conserved noncoding sequences ( CNS s), which are functionally constrained and can greatly help in reducing the number of false-positive elements. (plantphysiol.org)
  • There are also perceived challenges in the use of sequence alignment for phylogenetic analysis of NCS [ 9 ], as complex mutational processes (slipped-strand mispairing, stem-loop secondary structure excision/repair, minute inversions, intramolecular recombination) are prevalent. (biomedcentral.com)
  • 10 ] found chloroplast NCS to be of similar utility to coding sequences in phylogenetic tree construction for asterids. (biomedcentral.com)
  • Phylogenetic relationships and trees could be developed and effective ancestry could be found using the data on conserved sequences. (commonlounge.com)
  • A common example is the conserved sequence "16S RNA" which is used to reconstruct phylogenetic relationship among various bacterial phyla. (commonlounge.com)
  • 2004. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. (bcgsc.ca)
  • The method relies on a modified version of the phylogenetic hidden Markov model that analyzes "windows" of short sequences. (sciencemag.org)
  • Repeat sequences and hotspot regions can be scanned to detect the intraspecific and interspecific variability, and selected to infer the phylogenetic relationships of Sect. (springer.com)
  • Deep sequencing identifies novel and conserved microRNAs in peanuts (L. (uncg.edu)
  • Here, the bioinformatic algorithms were applied for known Bet v 1 homologous nucleic acids sequences to find homology and conserved regions. (intechopen.com)
  • Then, we'll see how we can reduce the problem of finding conserved sequences to the problem of finding most common K-mer in a given sequence and further revise the problem to handle mismatches, in-order to make our problem more biologically plausible. (commonlounge.com)
  • Secondary structure determination of the conserved 98-base sequence at the 3' terminus of hepatitis C virus genome RNA. (asm.org)
  • The RNA genome of hepatitis C virus (HCV) terminates with a highly conserved 98-base sequence. (asm.org)
  • A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged, and so has been conserved, throughout evolution. (academic.ru)
  • A potentially homologous RNA structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and HAV. (ox.ac.uk)
  • Search for conserved domains within query GS sequence (nucleotide sequence) was analyzed using conserved domain search service (CDD search) available online (http://www.ncbi. (symbiosisonlinepublishing.com)
  • We queried each subdatabase with each possible 7-nucleotide sequence. (elsevier.com)
  • Analysis of the alpha-toxin of 25 chicken-derived C. perfringens strains demonstrated high homology to mammal-derived strains rather than to the only avian-derived C. perfringens alpha-toxin sequence reported previously. (asm.org)
  • abstract = "Cellular immunity is pivotal in HIV-1 pathogenesis but is hampered by viral sequence diversity. (elsevier.com)
  • These signals are insensitive to frameshift mutations ( 12 ), suggesting that the recognized signal lies within the mRNA sequence. (pnas.org)
  • Zha, X.-F. P-element Somatic Inhibitor Protein Binding a Target Sequence in dsx Pre-mRNA Conserved in Bombyx mori and Spodoptera litura . (mdpi.com)
  • For the regulation of target gene, in some cases micro RNA binds fully with mRNA, whereas in other cases it binds only through a specific conserved region in it, called the seed. (alliedacademies.org)
  • Translational regulation of the protamine 1 mRNA is mediated by sequences in its 3' untranslated region. (jax.org)
  • Genome Survey Sequences (GSS) are nucleotide sequences similar to EST's that the only difference is that most of them are genomic in origin, rather than mRNA, While Expressed Sequence Tags sequences represent the expressed region of the genome [4]. (symbiosisonlinepublishing.com)
  • The literature is strewn with examples of conserved non-coding sequences being able to drive reporter expression, but the extent to which such sequences are actually used endogenously in vivo is only now being rigorously explored using unbiased genome-scale approaches. (biologists.org)
  • Scans of the genomic sequences of four EBV strains (EBV-1, EBV-2, GD1, and GD2) and of the closely related Macacine herpesvirus 4 using the RNAz program discovered 265 regions with high probability of forming conserved RNA structures. (biomedcentral.com)
  • Identifying evolutionarily conserved blocks in orthologous genomic sequences is an effective way to detect regulatory elements. (edu.sa)
  • According to Haussler, the researchers were launched on their analysis when initial studies hinted at major regions of conserved DNA sequences. (futurepundit.com)
  • Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. (epfl.ch)
  • A highly conserved genomic region in baculoviruses: sequence analysis of an 11.3 kbp DNA fragment (46.5-55.1 m.u.) of the Spodoptera exigua multicapsid nucleopolyhedrovirus. (wur.nl)
  • Analysis with several oligonucleotides and restriction enzymes, which identify the mutations most common in the Mediterranean area, allowed the identification of only one mutation, namely T----C at position 6 of the first intervening sequence (IVS-I). In order to characterize the other mutation the beta gene was amplified with polymerase chain reaction and sequenced. (biomedsearch.com)
  • A systematic approach is described for analysis of evolutionarily conserved cis -regulatory DNA using cis- Decoder, a tool for discovery of conserved sequence elements that are shared between similarly regulated enhancers. (biomedcentral.com)
  • Analysis of 2,086 conserved sequence blocks (CSBs), identified from 135 characterized enhancers, reveals most CSBs consist of shorter overlapping/adjacent elements that are either enhancer type-specific or common to enhancers with divergent regulatory behaviors. (biomedcentral.com)
  • Sequence analysis of the Arabidopsis thaliana genome has revealed numerous transmembrane receptors predicted to bind proteinacious ligands, emphasizing the importance of identifying peptides with signaling function. (semanticscholar.org)
  • Secondary structure models are proposed for these regions based on a combination of free energy minimization and comparative sequence analysis. (biomedcentral.com)
  • The analysis of RNA-Seq data uncovered the first observation of a stable intronic sequence RNA (sisRNA) in EBV. (biomedcentral.com)
  • qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts. (uncg.edu)
  • and cladistic analysis of conserved blocks. (biomedcentral.com)
  • The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. (microbiologyresearch.org)
  • Structure-based analysis of conserved sequence elements. (ox.ac.uk)
  • Comparative analysis of all PL6-like plasmids provided better resolution of conserved sequences and coding regions, confirmed the strong link to haloviruses, and showed that their sequences are highly conserved among examples from Haloquadratum isolates and metagenomic data that collectively cover geographically distant locations, indicating that these genetic elements are widespread. (frontiersin.org)
  • Regulatory sequence analysis tools. (bcgsc.ca)
  • The GS query sequences of more than 170 bp in length were used for the analysis. (symbiosisonlinepublishing.com)
  • Conserved sequences are typically identified by bioinformatics approaches based on sequence alignment. (wikipedia.org)
  • Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. (uncg.edu)
  • In this study, 254 high-confidence miRNAs (203 conserved miRNAs and 51 novel miRNAs) were identified by sRNA deep sequencing (sRNA-seq) combined with bioinformatics. (beds.ac.uk)
  • The codon usage bias in some organisms may restrict the types of synonymous mutations in a sequence. (wikipedia.org)
  • Such peaks are generally indicative of functionally important non-coding sequence elements. (biomedcentral.com)
  • Open' (nucleosome depleted) chromatin, which represents functionally active sequences, is more susceptible to DNase degradation. (biologists.org)
  • This article presents a new algorithm, REFINER, that refines a multiple sequence alignment by iterative realignment of its individual sequences with the predetermined conserved core (block) model of a protein family. (pubmedcentralcanada.ca)
  • Some domain resources, such as PFAM ( 1 ) and ProDom ( 2 ), rely on the automated methods of multiple sequence alignment while others, such as SMART ( 3 ) and CDD ( 4 ), employ careful manual intervention in constructing the domain models. (pubmedcentralcanada.ca)
  • Each curated CDD alignment records conserved features within the family members in terms of 'blocks', the regions where every sequence is aligned without the gaps. (pubmedcentralcanada.ca)
  • Different methods have been proposed to produce a multiple sequence alignment. (pubmedcentralcanada.ca)
  • Some of them align all sequences simultaneously ( 5 , 6 ), while others apply a progressive alignment strategy ( 7 - 10 ). (pubmedcentralcanada.ca)
  • Moreover, the final alignment strongly depends on the order of sequences being aligned. (pubmedcentralcanada.ca)
  • To overcome these flaws, iterative approaches have introduced the capacity to reconsider and realign previously aligned sequences at each iteration with the goal of improving the overall alignment score ( 7 , 12 - 19 ). (pubmedcentralcanada.ca)
  • Due to their different copy numbers, positions and/or orientations within the different enhancers, the conserved short sequence elements may otherwise go unnoticed by more conventional DNA alignment programs. (biomedcentral.com)
  • 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. (bcgsc.ca)
  • 1998. DIALIGN: Finding local similarities by multiple sequence alignment. (bcgsc.ca)
  • 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. (bcgsc.ca)
  • Differently from the most commonly used methods, the approach we present does not need or compute an alignment of the sequences investigated, nor resorts to descriptors of the binding specificity of known transcription factors. (uniba.it)
  • According to the latter, the sequences are aligned in a predetermined order dictated usually by the guide tree which groups similar sequences together with the subsequent addition of more dissimilar ones. (pubmedcentralcanada.ca)
  • The identification of similar sequences in this report is based on clustering as described here . (rcsb.org)
  • In the table for each entity, view a list of similar sequences by selecting the link associated with the percentage cutoff. (rcsb.org)
  • Examples of highly conserved sequences include the RNA components of ribosomes present in all domains of life, the homeobox sequences widespread amongst Eukaryotes, and the tmRNA in Bacteria. (wikipedia.org)
  • Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. (rostlab.org)
  • Over the years, our lab has compiled a useful list of conserved primer sequences useful for amplification and sequencing of nuclear rDNA from most major groups of fungi (primarily Eumycota), as well as other eukaryotes. (duke.edu)
  • For example, the promoter of a conserved gene or operon may also be conserved. (wikipedia.org)
  • When conserved regulatory transposable elements are active in a genome, they can introduce new promoter regions, disrupt existing regulatory sites, or, if inserted into transcribed regions, alter splicing patterns. (wikipedia.org)
  • To this end, we developed a modular retroviral vector that can allow for a direct comparison of the effects of different HCRs on gene expression independent of their gene-intrinsic 5′UTR, promoter, protein coding region, or poly(A) sequence. (asm.org)
  • Sequences of up to 400 bp encompassing proximal promoter and 5'-untranslated regions were analyzed. (biomedcentral.com)
  • All exons, the promoter region, and 60 bp of the 3' flanking region of the canine FGFR3 gene were sequenced for nine different dog breeds representing a spectrum of skeletal size. (biomedcentral.com)
  • There was no variation in sequence for any FGFR3 exons, promoter region, or 3' flanking sequence across all breeds evaluated. (biomedcentral.com)
  • alternatively, unannotated conserved islands could serve as promoter-distal regulatory factor binding sites (RFBSs) like enhancers. (edu.au)
  • WPV responses preferentially targeted proteome areas outside the selected conserved regions in direct proportion to sequence lengths, indicating similar immunogenicities for the conserved regions and the outside regions. (elsevier.com)
  • Overall, these findings demonstrate that the selected conserved regions are highly immunogenic and that anatomically isolated vaccinations with these regions focus immunodominance compared to the case for full-length protein vaccination. (elsevier.com)
  • lactilytica strain JW13 has been cloned in Escherichia coli vector pBluescriptSK(-) and completely sequenced. (elsevier.com)
  • Conserved noncoding sequences ( CNSs ) in DNA are reliable pointers to regulatory elements controlling gene expression. (plantcell.org)
  • Using a strict algorithm to sort high-scoring pair sequences from the bl2seq data, we created a database of 14,944 intragenomic Arabidopsis CNSs. (elsevier.com)
  • These CNSs provide a unique set of noncoding sequences enriched for function. (elsevier.com)
  • A tetraploidy left Arabidopsis thaliana with 6358 pairs of homoeologs that, when aligned, generated 14,944 intragenomic conserved noncoding sequences (CNSs). (elsevier.com)
  • We present tests where we applied the algorithm to the identification of conserved annotated sites in homologous promoters, as well as in distal regions like enhancers. (uniba.it)
  • Ramprasad E, Prasad Gajula MNV, Durga Rani V, Anuradha, Vanisri S (2017) Computational Identification of Conserved Domains from Genomic Survey Sequences in Green Gram [Vigna radiata (L.) R. Wilczek]. (symbiosisonlinepublishing.com)
  • Comparison of MSP2 variants reveals conserved N and C termini flanking the central, surface-exposed hypervariable region that represents the variant B lymphocyte epitopes. (jimmunol.org)
  • Primers were designed from the consensus sequence of these regions and were used in a reverse transcription/polymerase chain reaction (RT/PCR) to amplify a region of the central european tick-borne encephalitis virus Kumlinge NS5 gene. (nih.gov)
  • Key words: Hepatitis B virus (HBV) genome, HBV conserved region, polymerase chains reaction (PCR) primers, primer designing. (academicjournals.org)
  • Conserved sequences are sequences which persist in the genome despite such forces, and have slower rates of mutation than the background mutation rate. (wikipedia.org)
  • The extent to which a sequence is conserved can be affected by varying selection pressures, its robustness to mutation, population size and genetic drift. (wikipedia.org)
  • A new beta-thalassemia mutation produced by a single nucleotide substitution in the conserved dinucleotide sequence of the IVS-I consensus acceptor site (AG----AA). (biomedsearch.com)
  • In this study, DNA fragments encoding miR-BARTs and miR-BHRF1 were amplified by PCR from DNA samples extracted from EBV-positive lymphoma patients and were directly sequenced to determine the mutation, deletion, and/or insertion status of the regions encoding miRNAs. (biomedcentral.com)
  • Mutation of the conserved sequence causes premature translation of a transgene containing a fusion between the human growth hormone coding sequence and the protamine 1 3' untranslated region. (jax.org)
  • Five strains, including H 2 oxidation-ATP synthesis-coupled and -uncoupled strains, induced significant rates of H 2 -uptake hydrogenase activity and contained DNA sequences homologous to three probe DNA fragments (5.9-kilobase [kb] Hin dIII, 2.9-kb Eco RI, and 5.0-kb Eco RI) from pHU1. (asm.org)
  • No common DNA sequences homologous to B. japonicum hup DNA were found in genomic DNA from any of the eight remaining strains showing no significant hydrogenase activity in pea bacteroids. (asm.org)
  • Although transcription factor consensus DNA-binding sites are detected within CSBs, searches of 2,086 CSBs (27,996 total bp) curated from 35 mammalian and 99 Drosophila characterized enhancers reveal that well over half of the sequences do not correspond to known DNA-binding sites and, as yet, have no assigned function(s) (this paper). (biomedcentral.com)
  • Here we show that binding of lamin Dm 0 to chromatin requires both NLS and TRAT sequences. (biologists.org)
  • CSBs that are over 10 base-pairs (bp) long are likely to be made up of adjacent or overlapping sequence-specific transcription factor DNA-binding sites. (biomedcentral.com)
  • Conclusion: Results of the tests show how the algorithm can provide fast and reliable predictions of conserved transcription factor binding sites regulating the transcription of a gene, with better performances than other available methods for the same task. (uniba.it)
  • Sequence organization within CRMs, such as consistent spacing, number and orientation of transcription factor-binding sites, that allows their sequence-based (indirect) identification. (biologists.org)
  • However, the researchers found these regions to be significantly less conserved in the genome of the fish called fugu. (futurepundit.com)
  • 8 ) found that the SWCP alpha-toxin had only 80% amino acid sequence identity to the other C. perfringens alpha-toxins and questioned if this difference in sequence was typical of all avian isolates. (asm.org)
  • In this study, we examined the alpha-toxin sequences encoded by a range of isolates of C. perfringens derived from chickens to determine if the divergent SWCP alpha-toxin sequence is common in avian isolates. (asm.org)
  • The toxins were all highly conserved in amino acid sequence (Fig. 2 ), and only five different alpha-toxin sequence types (I to V) were identified among the 25 isolates sampled from several different outbreaks of necrotic enteritis in different locations (Table 1 ). (asm.org)
  • All the alpha-toxin sequence types from the chicken isolates closely resembled that of the toxin from the human isolate, strain 13 ( 20 ), with greater than 98% identity, but differed considerably from the swan isolate (SWCP), with only 82 to 84% identity. (asm.org)
  • The SWCP isolate has between 67 and 70 amino acid differences from the chicken isolates, and of all the changes in the SWCP sequence, only two amino acid changes are found in the field isolates reported here. (asm.org)
  • Schematic representation of the arrangement of sequences in the cpe-iap region of the five type E veterinary enteritis isolates and NCIB 10748. (asm.org)
  • The consensus cpe sequence present in type E isolates (upper line) was compared with the cpe ORF of the CPE-positive type A strain NCTC 8239 (lower line). (asm.org)
  • Ten field isolates recovered from naturally infected mule deer ( Odocoileus hemionus ), white-tailed deer ( Odocoileus virginiana ) and moose ( Alces alces ) from Wyoming, black-tailed deer ( Odocoileus hemionus columbianus ) from California, and Rocky Mountain elk ( Cervus elaphus nelsoni ) from Colorado and Washington state were sequenced. (microbiologyresearch.org)
  • Antibodies raised against SV1, containing five variant sequences, also kill heterologous S. pyogenes isolates in in vitro bactericidal assays. (edu.au)
  • Non-coding sequences important for gene regulation, such as the binding or recognition sites of ribosomes and transcription factors, may be conserved within a genome. (wikipedia.org)
  • DNA sequence comparisons of different co-regulating enhancers suggest that many may rely on different combinations of transcription factors to achieve coordinate gene regulation. (biomedcentral.com)