Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Molecular Sequence Data: 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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.Chromosome Deletion: Actual loss of portion of a chromosome.Mutation: 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.Amino Acid Sequence: 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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Clonal Deletion: Removal, via CELL DEATH, of immature lymphocytes that interact with antigens during maturation. For T-lymphocytes this occurs in the thymus and ensures that mature T-lymphocytes are self tolerant. B-lymphocytes may also undergo clonal deletion.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Mice, Knockout: Strains of mice in which certain GENES of their GENOMES have been disrupted, or "knocked-out". To produce knockouts, using RECOMBINANT DNA technology, the normal DNA sequence of the gene being studied is altered to prevent synthesis of a normal gene product. Cloned cells in which this DNA alteration is successful are then injected into mouse EMBRYOS to produce chimeric mice. The chimeric mice are then bred to yield a strain in which all the cells of the mouse contain the disrupted gene. Knockout mice are used as EXPERIMENTAL ANIMAL MODELS for diseases (DISEASE MODELS, ANIMAL) and to clarify the functions of the genes.Triticum: A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.Hordeum: A plant genus of the family POACEAE. The EDIBLE GRAIN, barley, is widely used as food.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Genes, Plant: The functional hereditary units of PLANTS.Interdisciplinary Communication: Communication, in the sense of cross-fertilization of ideas, involving two or more academic disciplines (such as the disciplines that comprise the cross-disciplinary field of bioethics, including the health and biological sciences, the humanities, and the social sciences and law). Also includes problems in communication stemming from differences in patterns of language usage in different academic or medical disciplines.Library Materials: Print and non-print materials collected, processed, and stored by libraries. They comprise books, periodicals, pamphlets, reports, microforms, maps, manuscripts, motion pictures, and all other forms of audiovisual records. (Harrod, The Librarians' Glossary, 4th ed, p497)Biotechnology: Body of knowledge related to the use of organisms, cells or cell-derived constituents for the purpose of developing products which are technically, scientifically and clinically useful. Alteration of biologic function at the molecular level (i.e., GENETIC ENGINEERING) is a central focus; laboratory methods used include TRANSFECTION and CLONING technologies, sequence and structure analysis algorithms, computer databases, and gene and protein structure function analysis and prediction.Periodicals as Topic: A publication issued at stated, more or less regular, intervals.Journalism: The collection, preparation, and distribution of news and related commentary and feature materials through such media as pamphlets, newsletters, newspapers, magazines, radio, motion pictures, television, and books. While originally applied to the reportage of current events in printed form, specifically newspapers, with the advent of radio and television the use of the term has broadened to include all printed and electronic communication dealing with current affairs.Publishing: "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.Point Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Glucosylceramidase: A glycosidase that hydrolyzes a glucosylceramide to yield free ceramide plus glucose. Deficiency of this enzyme leads to abnormally high concentrations of glucosylceramide in the brain in GAUCHER DISEASE. EC Duplication: Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.Genetic Predisposition to Disease: A latent susceptibility to disease at the genetic level, which may be activated under certain conditions.Cdh1 Proteins: Cdh1 is an activator of the anaphase-promoting complex-cyclosome, and is involved in substrate recognition. It associates with the complex in late MITOSIS from anaphase through G1 to regulate activity of CYCLIN-DEPENDENT KINASES and to prevent premature DNA replication.Spain: Parliamentary democracy located between France on the northeast and Portugual on the west and bordered by the Atlantic Ocean and the Mediterranean Sea.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Sex Chromosomes: The homologous chromosomes that are dissimilar in the heterogametic sex. There are the X CHROMOSOME, the Y CHROMOSOME, and the W, Z chromosomes (in animals in which the female is the heterogametic sex (the silkworm moth Bombyx mori, for example)). In such cases the W chromosome is the female-determining and the male is ZZ. (From King & Stansfield, A Dictionary of Genetics, 4th ed)PrimatesArchivesBiological Science Disciplines: 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.PubMed: 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.Directories as Topic: 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)High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Pelizaeus-Merzbacher Disease: A rare, slowly progressive disorder of myelin formation. Subtypes are referred to as classic, congenital, transitional, and adult forms of this disease. The classic form is X-chromosome linked, has its onset in infancy and is associated with a mutation of the proteolipid protein gene. Clinical manifestations include TREMOR, spasmus nutans, roving eye movements, ATAXIA, spasticity, and NYSTAGMUS, CONGENITAL. Death occurs by the third decade of life. The congenital form has similar characteristics but presents early in infancy and features rapid disease progression. Transitional and adult subtypes have a later onset and less severe symptomatology. Pathologic features include patchy areas of demyelination with preservation of perivascular islands (trigoid appearance). (From Menkes, Textbook of Child Neurology, 5th ed, p190)Diffuse Cerebral Sclerosis of Schilder: A rare central nervous system demyelinating condition affecting children and young adults. Pathologic findings include a large, sharply defined, asymmetric focus of myelin destruction that may involve an entire lobe or cerebral hemisphere. The clinical course tends to be progressive and includes dementia, cortical blindness, cortical deafness, spastic hemiplegia, and pseudobulbar palsy. Concentric sclerosis of Balo is differentiated from diffuse cerebral sclerosis of Schilder by the pathologic finding of alternating bands of destruction and preservation of myelin in concentric rings. Alpers' Syndrome refers to a heterogeneous group of diseases that feature progressive cerebral deterioration and liver disease. (From Adams et al., Principles of Neurology, 6th ed, p914; Dev Neurosci 1991;13(4-5):267-73)Myelin Proteolipid Protein: A myelin protein that is the major component of the organic solvent extractable lipoprotein complexes of whole brain. It has been the subject of much study because of its unusual physical properties. It remains soluble in chloroform even after essentially all of its bound lipids have been removed. (From Siegel et al., Basic Neurochemistry, 4th ed, p122)Mice, Jimpy: Myelin-deficient mutants which are from the inbred Tabby-Jimpy strain.X Chromosome: The female sex chromosome, being the differential sex chromosome carried by half the male gametes and all female gametes in human and other male-heterogametic species.Wiskott-Aldrich Syndrome: A rare, X-linked immunodeficiency syndrome characterized by ECZEMA; LYMPHOPENIA; and, recurrent pyogenic infection. It is seen exclusively in young boys. Typically, IMMUNOGLOBULIN M levels are low and IMMUNOGLOBULIN A and IMMUNOGLOBULIN E levels are elevated. Lymphoreticular malignancies are common.

Transformation mediated by RhoA requires activity of ROCK kinases. (1/14225)

BACKGROUND: The Ras-related GTPase RhoA controls signalling processes required for cytoskeletal reorganisation, transcriptional regulation, and transformation. The ability of RhoA mutants to transform cells correlates not with transcription but with their ability to bind ROCK-I, an effector kinase involved in cytoskeletal reorganisation. We used a recently developed specific ROCK inhibitor, Y-27632, and ROCK truncation mutants to investigate the role of ROCK kinases in transcriptional activation and transformation. RESULTS: In NIH3T3 cells, Y-27632 did not prevent the activation of serum response factor, transcription of c-fos or cell cycle re-entry following serum stimulation. Repeated treatment of NIH3T3 cells with Y-27632, however, substantially disrupted their actin fibre network but did not affect their growth rate. Y-27632 blocked focus formation by RhoA and its guanine-nucleotide exchange factors Dbl and mNET1. It did not affect the growth rate of cells transformed by Dbl and mNET1, but restored normal growth control at confluence and prevented their growth in soft agar. Y-27632 also significantly inhibited focus formation by Ras, but had no effect on the establishment or maintenance of transformation by Src. Furthermore, it significantly inhibited anchorage-independent growth of two out of four colorectal tumour cell lines. Consistent with these data, a truncated ROCK derivative exhibited weak ability to cooperate with activated Raf in focus formation assays. CONCLUSIONS: ROCK signalling is required for both the establishment and maintenance of transformation by constitutive activation of RhoA, and contributes to the Ras-transformed phenotype. These observations provide a potential explanation for the requirement for Rho in Ras-mediated transformation. Moreover, the inhibition of ROCK kinases may be of therapeutic use.  (+info)

Deletion analysis of the Drosophila Inscuteable protein reveals domains for cortical localization and asymmetric localization. (2/14225)

The Drosophila Inscuteable protein acts as a key regulator of asymmetric cell division during the development of the nervous system [1] [2]. In neuroblasts, Inscuteable localizes into an apical cortical crescent during late interphase and most of mitosis. During mitosis, Inscuteable is required for the correct apical-basal orientation of the mitotic spindle and for the asymmetric segregation of the proteins Numb [3] [4] [5], Prospero [5] [6] [7] and Miranda [8] [9] into the basal daughter cell. When Inscuteable is ectopically expressed in epidermal cells, which normally orient their mitotic spindle parallel to the embryo surface, these cells reorient their mitotic spindle and divide perpendicularly to the surface [1]. Like the Inscuteable protein, the inscuteable RNA is asymmetrically localized [10]. We show here that inscuteable RNA localization is not required for Inscuteable protein localization. We found that a central 364 amino acid domain - the Inscuteable asymmetry domain - was necessary and sufficient for Inscuteable localization and function. Within this domain, a separate 100 amino acid region was required for asymmetric localization along the cortex, whereas a 158 amino acid region directed localization to the cell cortex. The same 158 amino acid fragment could localize asymmetrically when coexpressed with the full-length protein, however, and could bind to Inscuteable in vitro, suggesting that this domain may be involved in the self-association of Inscuteable in vivo.  (+info)

Superimposed histologic and genetic mapping of chromosome 9 in progression of human urinary bladder neoplasia: implications for a genetic model of multistep urothelial carcinogenesis and early detection of urinary bladder cancer. (3/14225)

The evolution of alterations on chromosome 9, including the putative tumor suppressor genes mapped to the 9p21-22 region (the MTS genes), was studied in relation to the progression of human urinary bladder neoplasia by using whole organ superimposed histologic and genetic mapping in cystectomy specimens and was verified in urinary bladder tumors of various pathogenetic subsets with longterm follow-up. The applicability of chromosome 9 allelic losses as non-invasive markers of urothelial neoplasia was tested on voided urine and/or bladder washings of patients with urinary bladder cancer. Although sequential multiple hits in the MTS locus were documented in the development of intraurothelial precursor lesions, the MTS genes do not seem to represent a major target for p21-23 deletions in bladder cancer. Two additional tumor suppressor genes involved in bladder neoplasia located distally and proximally to the MTS locus within p22-23 and p11-13 regions respectively were identified. Several distinct putative tumor suppressor gene loci within the q12-13, q21-22, and q34 regions were identified on the q arm. In particular, the pericentromeric q12-13 area may contain the critical tumor suppressor gene or genes for the development of early urothelial neoplasia. Allelic losses of chromosome 9 were associated with expansion of the abnormal urothelial clone which frequently involved large areas of urinary bladder mucosa. These losses could be found in a high proportion of urothelial tumors and in voided urine or bladder washing samples of nearly all patients with urinary bladder carcinoma.  (+info)

Level of retinoblastoma protein expression correlates with p16 (MTS-1/INK4A/CDKN2) status in bladder cancer. (4/14225)

Recent studies have shown that patients whose bladder cancer exhibit overexpression of RB protein as measured by immunohistochemical analysis do equally poorly as those with loss of RB function. We hypothesized that loss of p16 protein function could be related to RB overexpression, since p16 can induce transcriptional downregulation of RB and its loss may lead to aberrant RB regulation. Conversely, loss of RB function has been associated with high p16 protein expression in several other tumor types. In the present study RB negative bladder tumors also exhibited strong nuclear p16 staining while each tumor with strong, homogeneous RB nuclear staining were p16 negative, supporting our hypothesis. To expand on these immunohistochemical studies additional cases were selected in which the status of the p16 encoding gene had been determined at the molecular level. Absent p16 and high RB protein expression was found in the tumors having loss of heterozygosity within 9p21 and a structural change (mutation or deletion) of the remaining p16 encoding gene allele, confirming the staining results. These results strongly support the hypothesis that the RB nuclear overexpression recently associated with poor prognosis in bladder cancer is also associated with loss of p16 function and implies that loss of p16 function could be equally deleterious as RB loss in bladder and likely other cancers.  (+info)

Expression of the naturally occurring truncated trkB neurotrophin receptor induces outgrowth of filopodia and processes in neuroblastoma cells. (5/14225)

We have investigated the effects of the truncated trkB receptor isoform T1 (trkB.T1) by transient transfection into mouse N2a neuroblastoma cells. We observed that expression of trkB.T1 leads to a striking change in cell morphology characterized by outgrowth of filopodia and processes. A similar morphological response was also observed in SH-SY5Y human neuroblastoma cells and NIH3T3 fibroblasts transfected with trkB.T1. N2a cells lack endogenous expression of trkB isoforms, but express barely detectable amounts of its ligands, brain-derived neurotrophic factor (BDNF) and neurotrophin-4 (NT-4). The morphological change was ligand-independent, since addition of exogenous BDNF or NT-4 or blockade of endogenous trkB ligands did not influence this response. Filopodia and process outgrowth was significantly suppressed when full-length trkB.TK+ was cotransfected together with trkB.T1 and this inhibitory effect was blocked by tyrosine kinase inhibitor K252a. Transfection of trkB.T1 deletion mutants showed that the morphological response is dependent on the extracellular, but not the intracellular domain of the receptor. Our results suggest a novel ligand-independent role for truncated trkB in the regulation of cellular morphology.  (+info)

Over-representation of a germline RET sequence variant in patients with sporadic medullary thyroid carcinoma and somatic RET codon 918 mutation. (6/14225)

The aetiology of sporadic medullary thyroid carcinoma is unknown. About 50% harbour a somatic mutation at codon 918 of RET (M918T). To investigate whether other RET sequence variants may be associated with or predispose to the development of sporadic medullary thyroid carcinoma, we analysed genomic DNA from the germline and corresponding tumour from 50 patients to identify RET sequence variants. In one patient, tumour DNA showed a novel somatic 12 bp in-frame deletion in exon 15. More interestingly, we found that the rare polymorphism at codon 836 (c.2439C > T; S836S) occurred at a significantly higher frequency than that in control individuals without sporadic medullary thyroid carcinoma (Fisher's exact test, P = 0.03). Further, among the nine evaluable cases with germline c.2439C/T, eight also had the somatic M918T mutation in MTC DNA which was more frequent than in patients with the more common c.2439C/C (89% vs 40%, respectively; Fisher's exact test, P = 0.01). These findings suggest that the rare sequence variant at codon 836 may somehow play a role in the genesis of sporadic medullary thyroid carcinoma.  (+info)

Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants. (7/14225)

The rice homeobox gene OSH15 (Oryza sativa homeobox) is a member of the knotted1-type homeobox gene family. We report here on the identification and characterization of a loss-of-function mutation in OSH15 from a library of retrotransposon-tagged lines of rice. Based on the phenotype and map position, we have identified three independent deletion alleles of the locus among conventional morphological mutants. All of these recessive mutations, which are considered to be null alleles, exhibit defects in internode elongation. Introduction of a 14 kbp genomic DNA fragment that includes all exons, introns and 5'- and 3'- flanking sequences of OSH15 complemented the defects in internode elongation, confirming that they were caused by the loss-of-function of OSH15. Internodes of the mutants had abnormal-shaped epidermal and hypodermal cells and showed an unusual arrangement of small vascular bundles. These mutations demonstrate a role for OSH15 in the development of rice internodes. This is the first evidence that the knotted1-type homeobox genes have roles other than shoot apical meristem formation and/or maintenance in plant development.  (+info)

Tight binding of the 5' exon to domain I of a group II self-splicing intron requires completion of the intron active site. (8/14225)

Group II self-splicing requires the 5' exon to form base pairs with two stretches of intronic sequence (EBS1 and EBS2) which also bind the DNA target during retrotransposition of the intron. We have used dimethyl sulfate modification of bases to obtain footprints of the 5' exon on intron Pl.LSU/2 from the mitochondrion of the alga Pylaiella littoralis, as well as on truncated intron derivatives. Aside from the EBS sites, which are part of the same subdomain (ID) of ribozyme secondary structure, three distant adenines become either less or more sensitive to modification in the presence of the exon. Unexpectedly, one of these adenines in subdomain IC1 is footprinted only in the presence of the distal helix of domain V, which is involved in catalysis. While the loss of that footprint is accompanied by a 100-fold decrease in the affinity for the exon, both protection from modification and efficient binding can be restored by a separate domain V transcript, whose binding results in its own, concise footprint on domains I and III. Possible biological implications of the need for the group II active site to be complete in order to observe high-affinity binding of the 5' exon to domain I are discussed.  (+info)

  • MLPA (Multiplex Ligation-dependent Probe Amplification) analysis confirmed a deletion in exon 6 of PLP1 inherited from asymptomatic carrier mother. (
  • To detect ABCC6 deletions/insertions, which can be missed by direct sequencing, multiplex ligation-dependent probe amplification (MLPA) was applied in PXE patients with an incomplete genotype. (
  • In this study, we aimed to screen for the presence of such deletions and/or insertions using the multiplex ligation-dependent probe amplification (MLPA) technique. (
  • The allele frequency of the mosaic deletions estimated by multiplex ligation‐dependent probe amplification and array comparative genomic hybridization was 25-40%, which was comparable to the mosaic ratio in lymphocytes and buccal mucosa cells observed by fluorescence in situ hybridization analysis. (
  • Deletions, an important type of SVs, have been suggested in association with genetic diseases. (
  • It has been previously shown that whole genome sequencing (WGS) can identify small variants contributing to the genetic illness of such patients in less than 50 hours. (
  • Deletion structural variants (SVs) 50 nucleotides are implicated in many genetic diseases and with WGS data can now be identified with a performance and timeframe sufficient for diagnosis in neonatal intensive care units. (
  • Moreover, proviruses that lack these genetic elements, yet contain strong donor splice sequences, increase relatively to other defective proviruses, especially among clones. (
  • Interestingly, defective proviruses that lack these genetic elements, but encode a strong donor splice sequence, are under relative positive selective pressure. (
  • Insertions or deletions (indels) of amino acids residues have been recognized as an important source of genetic and structural divergence between paralogous Bcl-2 family members. (
  • To avoid confusion, this condition is usually called 22q11.2 deletion syndrome, a description based on its underlying genetic cause. (
  • In this study, we examined prostate cancer specimens and cell lines/xenograft for genetic deletions at 13q21, using the methods of tissue microdissection and duplex PCR. (
  • Deletion of portions of chromosome 13 has been detected by various genetic approaches in human prostate cancer. (
  • To fine map the region of deletion and to evaluate the clinical significance of 13q21 deletion in prostate cancer, we analyzed a number of STS markers at 13q21 for genetic deletions in prostate cancer, using the approaches of tissue microdissection and duplex PCR. (
  • Whole-genome sequencing (WGS) has transformed the understanding of the genetic drivers of cancer and is increasingly being used in cancer medicine to identify personalized therapies. (
  • We show how genetic testing with functional assays, clinical transcriptome sequencing (RNA-seq) in particular, helped facilitate both the diagnosis and a better understanding of the genotype-phenotype relationship. (
  • We report the emergence and genetic characterization of a novel PEDV variant with a large genomic deletion, which was serendipitously recognized in fecal and intestinal samples of suckling pigs with diarrhea in South Korea as a result of a systematic surveillance program to monitor activity for porcine diarrhea-associated viruses. (
  • 16p11.2 distal deletion syndrome is a rare genetic disorder (copy number variation) caused by a deletion on chromosome 16 in the range 28.74-28.95-Mb. (
  • Deletions can be caused by errors in chromosomal crossover during meiosis, which causes several serious genetic diseases. (
  • Deletions that do not occur in multiples of three bases can cause a frameshift by changing the 3-nucleotide protein reading frame of the genetic sequence. (
  • Deletions are responsible for an array of genetic disorders, including some cases of male infertility and two thirds of cases of Duchenne muscular dystrophy. (
  • Deletions in the SMN-encoding gene cause spinal muscular atrophy, the most common genetic cause of infant death. (
  • Indel Chromosome abnormalities Null allele List of genetic disorders Medical genetics Microdeletion syndrome Chromosomal deletion syndrome Lewis, R. (2004). (
  • Genetic testing will start with standard sequencing of the MTM1 gene, isolated from the saliva specimen, followed by CGH Array if sequencing of the MTM1 gene isolated from the saliva sample or further from a blood sample if a variant consistent with the symptoms could not be detected using the saliva sample. (
  • This paradox is explained by a single recombinational event between the 2 deleted regions of one of the carrier's dystrophin genes, giving rise to a son with a partially "repaired" gene retaining only the 5' deletion. (
  • Numerous screens have been conducted with the budding yeast deletion libraries to uncover new genes involved in various biological pathways [ 3 ]. (
  • They carry a de novo heterozygous 126 Kbp deletion at chromosome 11q12.3 involving 5 genes, four of which, namely HRASLS5 , RARRES3 , HRASLS2 , and PLA2G16 , encode proteins that regulate cellular growth, differentiation, and apoptosis, mainly through Ras-mediated signaling pathways. (
  • As genes controlling cell growth and differentiation may be related to morphological defects originating during development, we postulate that the observed chromosome deletion could be causative of the phenotype observed in the twin girls and the deleted genes could play a role in PS development. (
  • Regulatory sequences controlling all aspects of mRNA processing, especially including message stability, are found in the 3'UTR sequence of most genes. (
  • Analysis of the incidence of mononucleotide repeat sequences in the 3'UTRs, 5'UTRs, and coding sequences of those genes most differentially expressed in RER+ versus RER- cell lines has shown that much of this differential expression can be explained by the occurrence of a massive enrichment of genes with 3'UTR T repeats longer than 11 base pairs in the most differentially expressed genes. (
  • Sequence analysis of the 3'UTRs of a selection of the most differentially expressed genes shows that they all contain deletions in these repeats in all RER+ cell lines studied. (
  • Deep sequencing of the renal transcriptome revealed significant changes in the expression of genes related to metabolic pathways and organic anion transport in cKO mice compared with control littermates. (
  • By visual inspection of candidate genes located on the X-chromosome, we identified a large deletion in the NSDHL gene, encoding NAD(P) dependent steroid dehydrogenase-like, a 3β-hydroxysteroid dehydrogenase involved in cholesterol biosynthesis. (
  • Researchers are working to identify all of the genes that contribute to the features of 22q11.2 deletion syndrome. (
  • The loss of additional genes in the deleted region likely contributes to the varied features of 22q11.2 deletion syndrome. (
  • All the exons have been sequenced, together with their immediate flanking regions, and these sequences compared to those of the mouse and human HPRT genes. (
  • The dmbo deletion region contains a highly conserved domain of ∼500 bp, which is a candidate distal enhancer and which exhibits a similar relationship to Hmx genes in all vertebrate species for which data are available. (
  • 1,25(OH) 2 D functions as a ligand for the nuclear vitamin D receptor (VDR) which, when paired with its heterodimeric retinoid X receptor partner, binds to sequence-specific recognition elements on DNA and stimulates or represses transcription of contiguous genes. (
  • In the first half of the course, we will compare two short biological sequences, such as genes (i.e., short sequences of DNA) or proteins. (
  • Microdeletion - a relatively small amount of deletion (up to 5Mb that could include a dozen genes). (
  • However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. (
  • Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions ('DNA bulge') or deletions ('RNA bulge') compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. (
  • The 20-nt guide sequence (orange line) in the sgRNA is shown with genomic target sequence (protospacer) containing single-base DNA bulge (red asterisk) or single-base sgRNA bulge (red Δ). (
  • This arrangement, by packing together highly similar sequence units in a 3.5 Mb contiguous genomic stretch, favours the occurrence of NAHR between amplicon copies belonging to the same sequence family. (
  • I have performed NGS and have identified a list of genomic deletions indicated by genomic position. (
  • This study wanted to assess the importance of deletions and insertions in the ABCC6 genomic region, which is known to have a high recombinational potential. (
  • Our results further illustrate the instability of the ABCC6 genomic region and stress the importance of screening for deletions in the molecular diagnosis of PXE. (
  • We hypothesized that because of the documented instability of the ABCC6 genomic region, the unidentified mutant alleles remaining after direct sequencing and screening for the recurrent exon 23-29 deletion, may consist of deletions and/or insertions. (
  • Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci. (
  • Here we describe a couple of MZ twin girls with PS, in whom a deletion at chromosome 11q12.3 was identified by array-comparative genomic hybridization (array-CGH). (
  • High-throughput resequencing of 1 Mb of rat chromosome 14 from dmbo/dmbo rats, encompassing the Hmx1 locus, reveals numerous divergences from the rat genomic reference sequence, but no coding changes in Hmx1 . (
  • We identified a novel 7.08 kb pathogenic deletion upstream of GNE using array comparative genomic hybridization (aCGH) and a common Val727Met variant. (
  • We conducted a large-scale investigation of the incidence of PEDV in pigs with diarrhea in South Korea and consequently identified and characterized a novel PEDV variant with a large genomic deletion. (
  • The complete S gene sequence of the PEDV variant with a large genomic deletion (strain MF3809/2008/South Korea) described here has been deposited in GenBank under accession no. (
  • however, most others can recombine with the genome due to sequence homology shared between the genomic and plasmid-borne copies of the markers. (
  • Pooled mutants grown in rich medium (YES) and minimal medium (EMM) for five generations were used for barcode sequencing analysis. (
  • (a) The growth inhibition scores (GI) of the deletion mutants grown in rich medium (YES) versus minimal medium (EMM). (
  • This resource allows all predicted open reading frames in the budding yeast genome to be studied by analyzing the phenotypes of their deletion mutants. (
  • Compared to one-by-one screen of individual deletion mutants, barcode-based analyses of pooled mutants significantly improve the throughput of screens, reduce the amount of reagents used, and avoid the problems associated with strain cross-contamination. (
  • The mutants constructed here have deletions in the lysA gene, encoding meso -diaminopimelate decarboxylase, an enzyme catalyzing the last step in lysine biosynthesis. (
  • Constructing knockout mutants by in-frame deletions would negate the concerns with using a targeted disruption method. (
  • In transformation experiments with chromosomal DNA from these mutants, erythromycin-resistance and lack of MN4A8B2 reactivity were always linked, showing that the insertion/deletion was in a locus involved in LPS biosynthesis. (
  • This simple procedure was used to identify total and partial gene deletions among Chinese hamster HPRT-deficient mutants. (
  • In addition, some patients express deletion mutants of BCR-ABL, apparently due to missplicing. (
  • Most commonly these deletion mutants lack a significant portion of the kinase domain that includes the P-loop. (
  • We hypothesized that coexpressing BCR-ABL deletion mutants has a dominant-negative effect on the native form through heterocomplex formation. (
  • Thus, it will be important to investigate the prognostic impact of coexpression of deletion mutants in CML patients during imatinib treatment. (
  • Deletion of ampG (encoding permease AmpG) and mrcA (encoding penicillin binding protein 1a, PBP1a) from both double LT mutants further increased the resistance to β-lactams. (
  • This rearrangement represented a deletion of exons 8-10 of one THRA1 allele that was also coamplified with ERBB2 . (
  • Sequences immediately flanking all exons but the first show considerable homology between the different species but the region around exon 1 is less conserved, apart from the preserved location of putative functional elements. (
  • Oligonucleotide primers derived from sequences flanking the HPRT gene exons were used to amplify simultaneously seven exon-containing fragments in a multiplex PCR. (
  • The present invention discloses nucleic acid sequences which encode infectious hepatitis C viruses and the use of these sequences, and polypeptides encoded by all or part of these sequences, in the development of vaccines and diagnostics for HCV and in the development of screening assays for the identification. (
  • 1. A purified and isolated nucleic acid molecule which encodes human hepatitis C virus, wherein expression of said molecule in transfected cells results in production of virus when transfected into cells, wherein said molecule encodes the amino acid sequence of SEQ ID NO:3 shown in FIGS. 14G-14H. (
  • 2. The nucleic acid molecule of claim 1, wherein said molecule comprises the nucleic acid sequence of SEQ ID NO:4 shown in FIGS. 14A-14F. (
  • 3. A cassette vector for cloning viral genomes, comprising, inserted therein, the nucleic acid sequence according to claim 1, said vector reading in the correct phase for the expression of said inserted molecule and having an active promoter molecule upstream thereof. (
  • 7. A purified and isolated nucleic acid molecule acid molecule which encodes human hepatitis C virus, wherein expression of said molecule in transfected cells results in production of virus, wherein said molecule encodes the amino acid sequence of SEQ ID NO: 1 shown in FIGS. 4G-4H. (
  • 10. The nucleic acid molecule of claim 9, wherein said molecule encodes the amino acid sequence of SEQ ID NO:5 shown in FIGS. 16G-16H. (
  • 11. The nucleic acid molecule of claim 10, wherein said molecule comprises the nucleic acid sequence of SEQ ID NO:6 shown in FIGS. 16A-16F. (
  • Cleavage activity for the corresponding sgRNA variants measured by T7E1 assay in HEK293T cells at ( C ) the HBB site or ( D ) CCR5 site for the sgRNA variants in (A) and (B). Sequence of the original sgRNA is in the top row of the grid. (
  • Results: We present a novel method called Sprites (SPlit Read re-alIgnment To dEtect Structural variants) which finds deletions from sequencing data. (
  • A small group of hemoglobin (Hb) variants result from 'in-frame' deletion/insertion (del/ins). (
  • Comparison of variants of this group, found in the HbVar database, shows that structural modifications resulting from insertions are frequently less damaging than that caused by deletions. (
  • This test uses Sanger sequencing to evaluate for the presence of PRKAR1A gene variants associated with Carney complex (CNC), acrodysostosis-1 with hormone resistance, or other PRKAR1A -associated conditions. (
  • It is assumed that structural variants can have a profound functional impact when they overlap with coding sequences. (
  • Whole genome sequencing of the affected daughter, and subsequent automated variant filtering with respect to 188 nonaffected control dogs of different breeds, revealed 332 hetero-zygous variants on the X-chromosome private to the affected dog. (
  • Comparative sequence analysis of Bordetella bronchiseptica pertactin gene (prn) repeat region variants in swine vaccines and field isolates. (
  • In addition, 436 chromosome deletion lines are available for the 21 wheat chromosomes that can be used for intrachromosomal mapping ( E ndo and G ill 1996 ). (
  • Ocular examination, Sanger sequencing of ZEB1 coding regions in all probands and whole genome sequencing in one proband was performed. (
  • Out of 8,708 barcodes (4,354 strains) covering 88.5% of all 4,919 open reading frames, 7,734 barcodes (88.8%) were validated as high-fidelity to be inserted at the correct positions by Sanger sequencing. (
  • Peculiarly, the frequency of substitutions (67.6%) was unexpectedly higher than in budding yeast (~28%) and well above the predicted error of Sanger sequencing (~2%), which might have arisen during the solid-phase oligonucleotide synthesis and PCR amplification of the barcodes during strain construction. (
  • To localize wheat ( Triticum aestivum L.) ESTs on chromosomes, 882 homoeologous group 6-specific ESTs were identified by physically mapping 7965 singletons from 37 cDNA libraries on 146 chromosome, arm, and sub-arm aneuploid and deletion stocks. (
  • For example, a large, complete deletion of a protein coding gene will obviously lead to the elimination of the expression of that protein. (
  • I describe an approach, termed deletion-specific targeting (DST), that employs HDs (not their effects on RNA/protein circuits, but deletions themselves) as the targets of cancer therapy. (
  • We have analyzed FliG, using 10-amino-acid deletions throughout the protein and testing the deletion clones for their motility and dominance properties and for interaction of the deletion proteins with the MS ring protein FliF. (
  • The second FliF-FliG fusion protein (called the deletion-fusion protein) was missing 56 amino acids from the C terminus of FliF and 94 amino acids from the N terminus of FliG. (
  • The strain carrying this deletion-fusion protein was also able to form flagella and swim, although much more poorly than the wild-type strain or the mutant carrying the full-length fusion protein. (
  • Here we have applied the scanning deletion approach to FliG, with special emphasis on its interaction with the MS ring protein FliF. (
  • The Needleman-Wunsch algorithm is an algorithm used in bioinformatics to align protein or nucleotide sequences. (
  • MLPA was performed in 35 PXE patients with at least one unidentified mutant allele after exonic sequencing and exclusion of the recurrent exon 23-29 deletion. (
  • This deletion region overlaps the BRCA1 locus, which predisposes to familial breast and ovarian cancer. (
  • We have analyzed patients with isolated lissencephaly sequence (ILS) by FISH with probes at D17S379, an anonymous locus distal to LIS1, and with LIS1 specific probes. (
  • The methodology is based on the preselection of target DNA by excluding redundant sequence within the NF2 locus using bioinformatics. (
  • Identification of a locus involved in meningococcal lipopolysaccharide biosynthesis by deletion mutagenesis. (
  • As phosphatase and tensin homolog deleted on chromosome 10 (PTEN) is a phosphatase that is critical for controlling cell growth, proliferation, and death, we investigated the role of PTEN in the ENS by generating mice with an embryonic, ENC-selective deletion within the Pten locus. (
  • The common deletion of the glutathione S-transferase Mu 1 ( GSTM1 ) gene in humans has been shown to be involved in xenobiotic metabolism and associated with bladder cancer. (
  • We further showed experimentally that the GSTM1 was polymorphically deleted in both humans and also in chimpanzees, through independent deletion events. (
  • To generalize our results, we searched for genic deletions that are polymorphic in both humans and chimpanzees. (
  • The examples are given below of types and effects of deletions are representative of eukaryotic organisms, particularly humans, but are not relevant to prokaryotic organisms such as bacteria. (
  • Such deletions in humans are referred to as hCONDELs may be responsible for the anatomical and behavioral differences between humans, chimpanzees and other mammals. (
  • 22q11.2 deletion syndrome has many possible signs and symptoms that can affect almost any part of the body. (
  • People with 22q11.2 deletion syndrome commonly have heart abnormalities that are often present from birth, recurrent infections caused by problems with the immune system, and distinctive facial features. (
  • Many children with 22q11.2 deletion syndrome have developmental delays, including delayed growth and speech development, and some have mild intellectual disability or learning disabilities. (
  • Additionally, affected children are more likely than children without 22q11.2 deletion syndrome to have attention-deficit/hyperactivity disorder (ADHD) and developmental conditions such as autism spectrum disorder that affect communication and social interaction. (
  • Because the signs and symptoms of 22q11.2 deletion syndrome are so varied, different groupings of features were once described as separate conditions. (
  • In addition, some children with the 22q11.2 deletion were diagnosed with the autosomal dominant form of Opitz G/BBB syndrome and Cayler cardiofacial syndrome. (
  • 22q11.2 deletion syndrome affects an estimated 1 in 4,000 people. (
  • A genome-wide deletion library is a powerful tool for probing gene functions and one has recently become available for the fission yeast Schizosaccharomyces pombe. (
  • Phylogenetic comparison of telomerase RNA sequences from several budding yeasts revealed a core structure common to Saccharomyces and Kluyveromyces yeast species. (
  • This toolbox for producing designer deletions, together with the newly developed strains and plasmids, will benefit the whole yeast community. (
  • Recently, in , a new computing model named Matrix insertion-deletion system has been introduced to model various bio-molecular structures such as hairpin, stem and loop, pseudoknot, attenuator, cloverleaf, dumbbell that occur at intramolecular level. (
  • Molecular evolutionary analysis of avian and primate sex chromosome sequence. (
  • In this paper, we model some of the intermolecular structures such as double strand languages, nick languages, hybrid molecules (with R-loops), holliday structure, replication fork and linear hybridization (ligated) languages using Matrix insertion-deletion system. (
  • We studied the relationship between p16/p19 ARF deletions, using fluorescence in situ hybridization, and in vitro drug resistance and prognosis in childhood T-ALL at diagnosis. (
  • We employed limiting dilution polymerase chain reaction (PCR) followed by DNA sequencing to obtain full-length sequences of integrated HIV proviruses in four subjects on suppressive ART over time. (
  • Further sequence analysis of this region reveals a 5777-bp deletion located ∼80 kb downstream in dmbo/dmbo rats that is not apparent in 137 other rat strains. (
  • Sequences were analyzed by ClustalX version 1.83 program ( ) and MegAlign software (DNAStar Inc., Madison, WI, USA), and compared with those of reference strains in GenBank. (
  • Here, we describe a CRISPR-Cas9 toolbox that can be used to quickly introduce "designer" auxotrophic marker deletions into host strains, including leu1 -Δ 0 , his3 -Δ 0 , and lys9 -Δ 0 . (
  • Analysis of the mutant transcripts revealed fusion of the THRA1 exon 7 by splicing to a novel sequence designated BTR for "BT474 transcribed rearrangement. (
  • The amounts of barcode PCR products serve as a quantitative measure of the cell number of each deletion strain in the mutant pool. (
  • Recent cryoelectron microscopic studies show that the basal body of the deletion-fusion mutant has a smaller-diameter C ring than the wild-type or full-length fusion structure ( 22 ). (
  • In this study, several deletion constructs of CLV3 were made and used to determine which domains are essential for CLV3 function by complementing the clv3 mutant. (
  • However, upon coexpression of native and deletion mutant BCR-ABL in Ba/F3 cells, growth factor independence is maintained and signaling is activated normally. (
  • Using multiple fluorescent exon dosage and fluorescent multiplex CA repeat linkage analyses, we show that the mother of each propositus carries both deletions on the same grandmaternal X chromosome. (
  • Conditional deletion of the EP2 receptor in myeloid lineage cells in Cd11bCre;EP2 lox/lox mice attenuated plasma inflammatory responses and transmission of systemic inflammation to the brain was inhibited, with decreased hippocampal inflammatory gene expression and cerebral cortical levels of IL-6. (
  • Conditional deletion of EP2 significantly blunted microglial and astrocytic inflammatory responses to the neurotoxin MPTP and reduced striatal dopamine turnover. (
  • In this study, we examined the p53 consensus sequences upstream of the IGFBP-3 promoter for the p53 induced expression of IGFBP-3. (
  • From these observations, we conclude that four out of eleven p53 consensus sequences upstream of the IGFBP-3 promoter are essential for the p53 induced expression of IGFBP-3, and hypermethylation of these sequences selectively suppresses p53 induced IGFBP-3 expression in HepG2 cells. (
  • Promoter analysis of IGFBP-3 indicated that the NaB-RE sequence is essential for the sodium butyrate (NaB) induced IGFBP-3 expression [ 15 ], but the importance of the eleven upstream p53 binding sites reported by Bourdon et al . (
  • These AZFc gene families exhibit slight sequence variations between copies which are considered to have functional relevance. (
  • Extending our study of the relationship between NCF-1 and psiNCF-1 to 53 unaffected control individuals, we found that although in most (n = 44), the ratio of pseudogene (DeltaGT) to functional gene (GTGT) sequence in amplicons spanning exon 2 was 2:1, as previously observed, surprisingly, in 7 persons the ratio was 1:1, and in 2 persons the ratio was 1:2. (
  • It is possible that this pseudogene has not undergone deletion of GT, but more likely, based on analysis of additional NCF-1/psiNCF-1 markers, it represents the previously unidentified product of the reciprocal crossover of DNA fragments between the functional gene and one of its pseudogenes. (
  • Thus, we propose that the CLE motif is the functional region of CLV3 and that this region acts independently of its adjacent sequences. (
  • As the hot spot locates at the putative upstream p53 consensus sequences, these p53 consensus sequences are really functional is a question to be answered. (