A Gram-stain-negative, non-motile, fine rod or short filament shaped, jacinth pigmented bacterium, designated strain WDS2C27T, was isolated from a marine solar saltern in Wendeng, Weihai, PR China (37°31′5″ N, 122°1′47″ E). Growth of WDS2C27T occurred at 20-42 °C (optimum 37 °C) and pH 6.5-8.5 (optimal pH 7.0-8.0). Optimal growth occurred in modified marine broth containing 6 % (w/v) NaCl. The major polar lipids in WDS2C27T were phosphatidylethanolamine, two unidentified aminolipids and one unidentified lipid. The major respiratory quinone of WDS2C27T was MK-6. The dominant fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The DNA G+C content was 35.0 mol%. The nucleotide sequence of the 16S rRNA gene indicated that the most closely related strain was Psychroflexus planctonicus X15M-8T (92.0 % over 1452 bp). WDS2C27T showed 60.7 % average amino acid identity, 55.6 % percentage of conserved proteins, 75.0 % average nucleotide identity and 13.1 % digital DNA-DNA hybridization identity with

Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A)

Polyomaviruses (PyVs) have a wide range of hosts, from humans to fish, and their effects on hosts vary. The differences in the infection characteristics of PyV with respect to the host are assumed to be influenced by the biochemical function of the LT-Ag protein, which is related to the cytopathic effect and tumorigenesis mechanism via interaction with the host protein. We carried out a comparative analysis of codon usage patterns of large T-antigens (LT-Ags) of PyVs isolated from various host species and their functional domains and sequence motifs. Parity rule 2 (PR2) and neutrality analysis were applied to evaluate the effects of mutation and selection pressure on codon usage bias. To investigate evolutionary relationships among PyVs, we carried out a phylogenetic analysis, and a correspondence analysis of relative synonymous codon usage (RSCU) values was performed. Nucleotide composition analysis using LT-Ag gene sequences showed that the GC and GC3 values of avian PyVs were higher than those of

When there are no strand-specific biases in mutation and selection rates (that is, in the substitution rates) between the two strands of DNA, the average nucleotide composition is theoretically expected to be A = T and G = C within each strand. Deviations from these equalities are therefore evidence for an asymmetry in selection and/or mutation between the two strands. By focusing on weakly selected regions that could be oriented with respect to replication in 43 out of 51 completely sequenced bacterial chromosomes, we have been able to detect asymmetric directional mutation pressures. Most of the 43 chromosomes were found to be relatively enriched in G over C and T over A, and slightly depleted in G+C, in their weakly selected positions (intergenic regions and third codon positions) in the leading strand compared with the lagging strand. Deviations from A = T and G = C were highly correlated between third codon positions and intergenic regions, with a lower degree of deviation in intergenic regions,

BACKGROUND:The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments.RESULTS:Here we compare expression data from Pinus taeda cDNA microarrays using transcripts amplified either exponentially by PCR or linearly by T7 transcription. The amplified transcripts vary significantly in estimated length, GC content and expression depending on amplification technique. Amplification by T7 RNA polymerase gives transcripts with a greater range of lengths, greater estimated mean length, and greater variation of expression levels, but lower average GC content, than those from PCR amplification. For genes with significantly higher expression after T7 transcription than after PCR, the transcripts were 27% longer and had about 2 percentage units lower GC content. The correlation of expression intensities between ...

TY - JOUR. T1 - Protein elemental sparing and codon usage bias are correlated among bacteria. AU - Bragg, Jason G.. AU - Quigg, Antonietta. AU - Raven, John A.. AU - Wagner, Andreas. PY - 2012/5. Y1 - 2012/5. N2 - Highly expressed proteins can exhibit relatively small material costs, in terms of the quantities of carbon (C), nitrogen (N) or sulphur (S) atoms they contain. This elemental sparing probably reflects selection to reduce the quantities of potentially growth-limiting elements in abundant proteins, but the evolutionary mechanisms for adaptive elemental sparing are still poorly understood. Here, we predict that the extent of elemental sparing in highly expressed proteins will vary among organisms, according to the effectiveness of selection in determining the fate of mutations. We test this hypothesis in bacteria by asking whether elemental sparing is correlated with codon usage bias. Bacteria exhibit extraordinary variation in their life histories and demography and consequently in the ...

Results for QLV parameters A, B, and τ2, and typical stress relaxation curve fits for IM and EX. A was significantly decreased in injured groups relative to CTL. A was significantly increased in the IM group compared to the EX and CA groups. B was significantly decreased in injured groups relative to CTL. B was significantly increased in the IM group compared to the EX and CA groups. τ2 was significantly decreased in the CA and EX groups relative to CTL. τ2 was significantly increased in the IM group compared to the EX groups. The IM group had a higher peak stress, and maintained this stress for a longer period of time, than the EX group. (Mean +/− standard deviation, *: significant difference relative to CTL [p,0.05], # significant difference due to activity level [p,0.05 ...

General Information: Environment: Soil; Isolation: Coal-cleaning residues; Temp: Mesophile; Temp: 30C. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. It is believed that present day Mollicutes (Eubacteria) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Known opportunistic toxin-producing pathogens in animals and humans. Some species are capable of producing organic solvents (acetone, ethanol, etc,), molecular hydrogen and ...

General Information: Environment: Soil; Isolation: Coal-cleaning residues; Temp: Mesophile; Temp: 30C. This genus comprises about 150 metabolically diverse species of anaerobes that are ubiquitous in virtually all anoxic habitats where organic compounds are present, including soils, aquatic sediments and the intestinal tracts of animals and humans. This shape is attributed to the presence of endospores that develop under conditions unfavorable for vegetative growth and distend single cells terminally or sub-terminally. Spores germinate under conditions favorable for vegetative growth, such as anaerobiosis and presence of organic substrates. It is believed that present day Mollicutes (Eubacteria) have evolved regressively (i.e., by genome reduction) from gram-positive clostridia-like ancestors with a low GC content in DNA. Known opportunistic toxin-producing pathogens in animals and humans. Some species are capable of producing organic solvents (acetone, ethanol, etc,), molecular hydrogen and ...

Because of polymer complexity, property variability must be taken into consideration. In this section, we will discuss possible sources of polymer inconsistency and offer suggestions to recognize and reduce these errors. Chemical or compositional heterogeneity refers to the chemical or structural difference among chains of the same polymer. Thus a measured property of a chemically heterogeneous sample will be an averaged value dependent upon sample source. For chemically homogeneous samples, property variability will not be a concern. In a similar fashion, polymers that are polydisperse in molecular weight have averaged property values, while monodisperse samples will give accurate data. Obviously, samples that are both chemically homogeneous and monodisperse will give the most accurate and precise values. As compared to synthetic polymers, almost all nucleic acids and mammalian proteins are compositionally (chemically) homogeneous and monodisperse, if not there would be no life; biopolymers ...

Application of chemical engineering principles to the study of tumor formation and treatment is fertile new ground for research and is necessary for the advancement of cancer therapy. Over the last century, researchers have discovered many of the genetic causes of cancer and yet nearly 46,000 people will die this year from cancer in the United States alone. Standard cancer therapies often fail because of spatial heterogeneity of nutrients, wastes, and therapeutics. Transport barriers prevent therapeutic agents from reaching effective concentrations throughout tumors. Models based on mass balance, transport phenomena and reaction kinetics are powerful tools able clarify the connection between the genetic aberrations and the compositional heterogeneity of tumors. Therapeutic strategies designed using engineering principles will be able to overcome transport barriers and create more effective therapies.. Single treatments of radiation or chemotherapy often do not kill all cancer cells within a ...

The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...

The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...

The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...

Empirical studies have shown that human beings cannot normally perceive changes in numeric data (e.g. price movements) occurring more frequently than once every 200ms.. Consequently for applications that have a human as their primary user, a useful rule of thumb is that Stop-The-World (STW) pause of 200ms or under is usually of no concern. Some applications (e.g. streaming video) need lower GC jitter than this, but many GUI applications will not. ...

DNA - A double helix DNA stands for Deoxyribonucleic acid.It is a nucleic which is used for storing information for long term in all living beings and some viruses. Base composition in DNA varies from one species to other but in all the cases the amount of adenine is equal to thymine and the amount

The species page of Empusa sp. IRT-2002. Also know as (German: große Mantiden). Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.

The species page of Magnaporthe sp. MG12. . Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.

德者，內也；得者，外也。「上德不德」，言其神不淫於外也。 神不淫於外則身全，身全之謂德。德者，得身也。凡德者，以無為集，以無欲成； 以不思安，以不用固。為之欲之，則德無舍；德無舍則不全。用之思之則不固，不固則無功， 無功則生於德。德則無德，不德則（在）有德。故曰：「上德不德，是以有德。」 所以貴無為無思為虛者，謂其意無所制也。夫無術者，故以無為無思為虛也。 夫故以無為無思為虛者，其意常不忘虛，是制於為虛也。虛者，謂其意（所無）〔無所〕制也。 今制於為虛，是不虛也。虛者之無為也，不以無為為有常。不以無為為有常，則虛；虛，則德盛； 德盛之謂上德。故曰：「上德無為而無不為也。」 仁者，謂其中心欣然愛人也；其喜人之有福，而惡人之有禍也；生心之所不能已也， ...

A Gram-positive, motile, round to ellipsoidal, endospore-forming, rod-shaped bacterial strain, SF-57T, was isolated from a marine solar saltern in Korea. This organism grew between 4 and 39 °C, with optimum growth at 30 °C. Strain SF-57T grew in the presence of 0·5-15·0 % NaCl, with optimum growth at 2-3 % NaCl. The peptidoglycan type of strain SF-57T was A1α linked directly through l-Lys. In strain SF-57T, menaquinone-7 (MK-7) was the predominant isoprenoid quinone and anteiso-C15 : 0 was the major fatty acid. The DNA G+C content was 41·8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SF-57T formed a coherent cluster with Marinibacillus marinus, with a bootstrap resampling value of 100 %. The level of 16S rRNA gene sequence similarity between strain SF-57T and M. marinus DSM 1297T was 98·9 %. The mean DNA-DNA relatedness level between strain SF-57T and the type strain of M. marinus was 20·6 %. Based on phenotypic properties, phylogenetic analyses and genomic

Strain JC267T was isolated from pebbles collected from Pingleshwar beach, Gujarat, India. Cells are Gram-stain-positive, facultatively anaerobic, non-motile rods forming sub-terminal endospores in swollen ellipsoidal to oval sporangia. Strain JC267T contains anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, C16 : 0 and anteiso-C17 : 0 as major (|5 %) cellular fatty acids. Polar lipids include phosphatidylglycerol, phospholipids (PL1-3), glycolipids (GL1-2) and an unidentified lipid. Cell-wall amino acids are composed of diagnostic meso-diaminopimelic acid, dl-alanine and a small amount of d-glutamic acid. The genomic DNA G+C content of strain JC267T is 45.5 mol%. The 16S rRNA gene sequence of strain JC267T showed highest sequence similarities of | 98.41 % with all species of the genus Bacillus when subjected to EzTaxon-e blast analysis. The reassociation values based on DNA-DNA hybridization of strain JC267T with Bacillus halosaccharovorans IBRC-M 10095T and Bacillus niabensis JCM 16399T were 26

Most RNA viruses infecting mammals and other vertebrates show profound suppression of CpG and UpA dinucleotide frequencies. To investigate this functionally, mutants of the picornavirus, echovirus 7 (E7), were constructed with altered CpG and UpA compositions in two 1.1-1.3 Kbase regions. Those with increased frequencies of CpG and UpA showed impaired replication kinetics and higher RNA/infectivity ratios compared with wild-type virus. Remarkably, mutants with CpGs and UpAs removed showed enhanced replication, larger plaques and rapidly outcompeted wild-type virus on co-infections. Luciferase-expressing E7 sub-genomic replicons with CpGs and UpAs removed from the reporter gene showed 100-fold greater luminescence. E7 and mutants were equivalently sensitive to exogenously added interferon-β, showed no evidence for differential recognition by ADAR1 or pattern recognition receptors RIG-I, MDA5 or PKR. However, kinase inhibitors roscovitine and C16 partially or entirely reversed the attenuated phenotype of

The relationship between the overall G+C content of the genome (GC) and the GC content at the third codon positions (GC3) of genes, which we refer to as a GC3-plot, was examined using 15 currently available complete genome sequences. A remarkably linear relationship was found between these two quantities, confirming previous observations of a strong positive correlation in the GC3-plot.. In order to conduct a more detailed analysis of the GC3-plot, we examined the GC3 content by separating orthologous codons into three categories: synonymously different codons (namely identical amino acids, IA), different amino acids (DA), and identical codons (IC), for a pairwise comparison of two closely related species. When we took pairwise species comparisons between Mycoplasma genitalium (Mg) and Mycoplasma pneumoniae (Mp) and between Mycobacterium tuberculosis (Mt) and Mycobacterium leprae (Ml) as examples, we found that for Mp and Ml, the GC3 for IA deviated the most from the linear expectation in the ...

TY - JOUR. T1 - An AT mutational bias in the tiny GC-rich endosymbiont genome of Hodgkinia. AU - Van Leuven, James T.. AU - McCutcheon, John P.. PY - 2012/1/1. Y1 - 2012/1/1. N2 - The fractional guanine p cytosine (GC) contents of sequenced bacterial genomes range from 13% to 75%. Despite several decades of research aimed at understanding this wide variation, the forces controlling GC content are not well understood. Recent work has suggested that a universal adenine + thymine (AT) mutational bias exists in all bacteria and that the elevated GC contents found in some bacterial genomes is due to genome-wide selection for increased GC content. These results are generally consistent with the low GC contents observed in most strict endosymbiotic bacterial genomes, where the loss of DNA repair mechanisms combined with the population genetic effects of small effective population sizes and decreased recombination should lower the efficacy of selection and shift the equilibrium GC content in the ...

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TY - JOUR. T1 - Preliminary aqnalysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. AU - Chow, S.. AU - Ueno, Y.. AU - Toyokawa, M.. AU - Oohara, I.. AU - Takeyama, Haruko. PY - 2009/6. Y1 - 2009/6. N2 - Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 ...

Redundancy of the genetic code implies that there are more codons than amino acids. Consequently, many amino acids are encoded by more than one codon, which are known as synonymous codons. As a result, some substitutions between these codons are silent and do not change the coded amino acid. For example, in the case of the codons known as fourfold degenerated (4FD), the third codon positions can be freely changed to any nucleotide, without consequences for the coded amino acid, and subsequently for protein composition and function. However, synonymous codons are not used uniformly in real protein coding sequences (e.g., Comeron 2004; Grantham et al. 1980; Ikemura 1985; Plotkin and Kudla 2011; Sharp and Li 1986). Such preference of one synonymous codon over others is commonly known as codon usage bias (Sharp and Li 1986). Usage can differ for various genomes and genes within one genome, and even within a single gene.. As far as the evolution of codon bias is concerned, two explanations, which are ...

Argos, P., Rossmann, M.G., Grau, U.M., Zuber, A., Frank, G. and Tratschin, J.D. (1979). «Thermal stability and protein structure». Biochemistry 18: pp. 5698-5703. • Dobzhansky, T. (1951). Genetics and the Origin of Species, 2ª ed.. Columbia University Press, New-York • Galtier, N. and Lobry, J.R. (1997). «Relationships between genomic G+C content, RNA secondary structure, and optimal growth temperature in prokaryotes». Journal of Molecular Evolution 44: pp. 632-636. • Gu, X., Hewett-Emmett, D. and Li, W-H. (1998). «Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria». Genetica 102/103: pp. 383-391. [1] • Graur, D. y [Wen-Hsiung Li (2000). Fundamentals of Molecular Evolution (second edition). Sinauer Associates. ISBN 0-87893-266-6. • Muto, A. and Osawa, S. (1987). «The guanine and cytosine content of genomic DNA and bacterial evolution». Proceedings of the National Academy of Sciences 84: pp. 166-169. [2] • Nei, M. ...

Codon usage bias is an essential feature of all genomes. If you continue browsing the site, you agree to the use of cookies on this website. Slideshare uses cookies to improve functionality and performance, and to provide you with relevant advertising. Codon optimization, a process where less-frequent codons in the coding sequence are replaced by more frequent synonymous codons, has long been used to address this issue (Burgess-Brown et al., 2008; Welch et al., 2009; Maertens et al., 2010). Codon Usage (deut. Moreover, the usage of some codons appears nonlinear, as a function of GC bias. CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. Start codons, stop codons, reading frame. If you continue browsing the site, you agree to the use of cookies on this website. INTRODUCTION:- One of the main characteristics of the genetic code is that it is degenerate, i.e., multiple synonymous codons specify the same amino acid. Here, we ...

Synonymous codon usage is based and the bias seems to be different in different organisms. Factors with proposed roles in causing codon bias include degree and timing of gene expression, codon-anticodon interactions, transcription and translation rate and fidelity, codon context, and global and loca …

(2017) B. Miller et al. Biomedical Genetics and Genomics. It is well-documented that codon usage biases affect gene translational efficiency; however, it is less known if viruses share their hosts codon usage motifs. We determined that human-infecting viruses share similar codon usage biases as ...

GENEWIZ is widely known for reliability and completion of projects with a wide range of complexity levels including repetitive and sequences with high or low GC content. Our 99.9% delivery rate makes us the partner of choice for top research institutions across the world. Our many years of synthetic gene assembly experience provide endless opportunities to create any custom synthetic DNA sequence for your synthetic biology research ...

The four bases found in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T). In genetics, GC-content is the percentage of Guanine (G) and Cytosine (C) bases on a DNA molecule that are ...

What is DNA? A DNA sequence contains only the letters A, C, G and T. (Each letter represents a small molecule, and a DNA sequence is a ``macromolecular chain of them.) Each letter in a DNA sequence is called a base, basepair, or nucleotide. Normally, DNA occurs as a double strand where each A is paired with a T and vice versa, and each C is paired with a G and vice versa. The reverse complement of a DNA sequence is formed by reversing the letters, interchanging A and T and interchanging C and G. Thus the reverse complement of ACCTGAG is CTCAGGT. What is a genome? A genome is all of an organisms DNA sequence. Each nucleus in one of your cells contains its own copy of your genome, which is about 3 billion letters. (More accurately, each cell has two nearly identical copies of the genome, except that the X and Y chromosomes are even more complicated.) Replication is the process of duplicating the genome when a cell divides. DNA composition. The genome of a warm-blooded animal is divided into ...

A new high-alkaline protease (ALTP) was purified to homogeneity from a culture of the strictly anaerobic and extremely alkaliphilic Alkaliphilus transvaale

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In bacteria, one example of such a characteristic is called the G+C content. Recall that DNA is made up of nucleotides: A, T, G and C. The A and T pair together (A+T) in the DNA double helix, as do the G and C (G+C). After a bacterias genome is sequenced, the G+C content is calculated simply by adding up all the Gs and Cs and dividing that number by the total number of nucleotides. The percentage, which can range from 13% to 75%, tends to be characteristic of the bacterial species. Why one species is, say, 47% and another is 58% is thought to be due solely to chance. Luck of the draw ...

The National Aquarium is excited to announce the addition of Living Seashore, an interactive exhibit opening in spring 2015 where guests can explore the shore and touch the animals that live between the tides.

Zonder Javascript is het niet mogelijk bestellingen te plaatsen in deze webwinkel en zijn een aantal functionaliteiten niet beschikbaar ...

[KCTC]한국생명공학연구원 생물자원센터 홈페이지 입니다. 생물 자원 기탁 분양, 특허 기탁 분양, 생물자원 연구성과 기탁 분양

[KCTC]한국생명공학연구원 생물자원센터 홈페이지 입니다. 생물 자원 기탁 분양, 특허 기탁 분양, 생물자원 연구성과 기탁 분양

sistem pertahanan tubuh antibodi dan anti gen Antibodi monoklonal Sistem kekebalan tubuh imunitas Sistem pertahanan tubuh antibodi dan anti gen Lr begini mekanisme pembentukan sistem antibodi tubuh

V banskobystrickej Fakultnej nemocnici s poliklinikou (FNsP) F. D. Roosevelta otvorili v minulých dňoch nové hepatologicko-gastroenterologické oddelenie II. Internej kliniky Slovenskej zdravotníckej univerzity

Tiesību akti un to izmaiņas: visi jaunumi un arhīvs. Sistematizēti tiesību akti. Plašas meklēšanas un personalizētās iespējas. Vietni uztur „Latvijas Vēstnesis

Discuss any cooroy mums due in nov and QLD in the Huggies Communities Forum. Raise your question or find answers in existing discussions.

Parablechnum roraimense and P. paucipinna spp. nov. (Blechnaceae: Polypodiopsida), lectotypification of P. stuebelii , and citation corrections in the family

A Gram-staining-positive, cocci, halotolerant bacterial strain, designated as SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurs at temperatures in the range between 25-37 °C (optimum 30 °C), pH 7.0-11.0 (optimum 8.0) and at NaCl concentrations up to 25 .0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids are diphosphatidylglycerol (DPG), phosphatidylinositol (PI) and phosphatidylglycerol (PG). The major cellular fatty acids are iso-C15: 0, anteiso-C15: 0, iso-C17: 0 and anteiso C17: 0. The draft genome of strain SV-16T consisted of 2,591,284 bp with G+C content of 48.7 mol %. On the basis of the phenotypic characteristics and genotypic ...

An obligately aerobic, chemoheterotrophic, mesophilic prosthecate bacterium, designated strain CGM1-3ENT, was isolated from the enrichment cultures of forest soil from Cheonggyesan Mountain, Republic of Korea. Cells were Gram-reaction-negative, motile rods (1.3–2.4 µm long by 0.30–0.75 µm wide) with single flagella. The strain grew at 10–37 °C (optimum 25–30 °C) and at pH 4.5–9.5 (optimum 5.0–7.0). The major cellular fatty acids were C16 : 0, C18 : 1ω7c 11-methyl, C12 : 1 3-OH and summed feature 8 (comprising C18 : 1ω7c/C18 : 1ω6c). The genomic DNA G+C content of strain CGM1-3ENT was 63.7 mol%. The closest phylogenetic neighbour to strain CGM1-3ENT was identified as Asticcacaulis biprosthecium DSM 4723T (97.2 % 16S rRNA gene sequence similarity) and the DNA–DNA hybridization value between strain CGM1-3ENT and A. biprosthecium DSM 4723T was less than 24.5 %. Strain ...

A bacterial strain, B5-2(T), was isolated from an ice core drilled from Muztagh Glacier, China. Strain B5-2(T) was a Gram-stainnegative, short rod-shaped, motile by polar flagella, aerobic bacterium. The major fatty acids of strain B5-2(T) were summed feature 8 (C-18 : 1 omega 7c and/ or C-18 : 1 omega 6c) and iso-C-13 : 0. The G+C content of the DNA from strain B5-2(T) was 69.3 mol%. The predominant isoprenoid quinone of strain B5-2(T) was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified phospholipid and sulfoquinovosyldiacylglycerol. Comparative 16S rRNA gene sequence analysis revealed that the novel strain B5-2(T) shared highest similarity (96.7 %) with Aureimonas altamirensis S21B(T). On the basis of the results of this polyphasic study, strain B5-2(T) represents a novel species of the genus Aureimonas, for which the name Aureimonas glaciei sp. nov. is ...

The type species for the genus Skermanella is Skermanella parooens ACM 2042T, which was originally proposed as Conglomeromonas largomobilis subsp. parooensis by Skerman et al. in 1983 [1]. Later, it was transferred to the genus Skermanella (family Rhodospirillaceae) on the basis of phylogenetic evidence and phenotypic characteristics, especially the inability to fix nitrogen [2,3]. At present, this genus comprises four validly published species, Skermanella parooensis [3], Skermanella aerolata [4], Skermanella xinjiangensis [5] and Skermanella stibiiresistens [6], which were isolated from fresh water, air, sandy soil and a coal mine, respectively.. Skermanella was characterized as a Gram-negative, non-spore-forming bacterium with unicellular and multicellular phases of growth, an obligate chemo-organotroph and facultative anaerobe, unable to fix nitrogen, and with a high DNA G+C content. To the best of our knowledge, genome information for Skermanella members is still not available. In this ...

A bacterium previously isolated from a diseased colony of the scleractinian coral Dichocoenia stokesi (common name elliptical star coral) was subjected to a detailed polyphasic taxonomic characterization. The isolate, designated WP1T, was halophilic and strictly aerobic and formed golden-orange-pigmented colonies after prolonged incubation. Cells of WP1T were Gram-negative, rod-shaped and showed a characteristic branching rod morphology. Chemotaxonomically, WP1T was characterized by having Q-10 as the major respiratory lipoquinone and sym-homospermidine as the main component of the cellular polyamine content. The predominant constituent in the cellular fatty acid profile was C18 : 1 ω7c, along with C19 : 0 cyclo ω8c and C16 : 0. Other fatty acids present in smaller amounts were C17 : 0, C18 : 0, C16 : 1 ω7c, C20 : 1 ω7c and C18 : 1 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Minor amounts of diphosphatidylglycerol,

A novel Gram-positive, aerobic, actinobacterial strain, CF6/1T, was isolated in 2007 during environmental screening of arid desert soil in the Sahara near to Ourba, Chad. The isolate was found to grow best in a temperature range of 20-37 °C and at pH 6.0-8.5 and showed no NaCl tolerance, forming black-coloured and nearly circular colonies on GYM agar. Chemotaxonomic and molecular characteristics determined for the isolate match those previously described for members of the genus Geodermatophilus. The DNA G + C content of the novel strain was determined to be 74.9 mol %. The peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid. The main phospholipids were determined to be phosphatidylethanolamine, phosphatidylinositol, phosphatidylcholine, diphosphatidylglycerol and traces of phosphatidylglycerol; MK-9(H4) was identified as the dominant menaquinone and galactose as the diagnostic sugar. The major cellular fatty acids were found to be the branched-chain ...

A bacterial strain designated LYH-12T was isolated from a freshwater fish culture pond in Taiwan, ROC and characterized by taking a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LYH-12T belonged to the genus Hymenobacter and was most closely related to Hymenobacter xinjiangensis X2-1gT and Hymenobacter rigui WPCB131T with a sequence similarity of 96.6 % and less than 96.5 % with other members of the genus. Cells of strain LYH-12T were Gram-stain-negative, aerobic, non-motile rods that were covered by large capsules and formed light pink-coloured colonies. Growth occurred at 10-37 C (optimum, 20-30 C), at pH 6.5-7.5 (optimum, pH 7) and with 0-1 % NaCl (optimum, 0.5 %). Strain LYH-12T contained iso-C15 : 0, C16 : 1ω5c, C16 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and anteiso-C17 : 1ω9c as the predominant fatty acids. The only isoprenoid quinone detected was MK-7. The polar lipid profile consisted of ...

Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons). There are 64 different codons (61 codons encoding for amino acids plus 3 stop codons) but only 20 different translated amino acids. The overabundance in the number of codons allows many amino acids to be encoded by more than one codon. Because of such redundancy it is said that the genetic code is degenerate. The genetic codes of different organisms are often biased towards using one of the several codons that encode the same amino acid over the others-that is, a greater frequency of one will be found than expected by chance. How such biases arise is a much debated area of molecular evolution. Codon usage tables detailing genomic codon usage bias for most organisms in GenBank and RefSeq can be found in the HIVE-Codon Usage ...

The structure and energetics of the base pairing and proton transfer in the Watson-Crick type of guanine-cytosine base pair are studied by the HF/MINI-1 method within the full gradient optimization and self-consistent reaction field techniques. Two minima and the transition state on the connecting minimum energy path were located on the potential energy surface (PES) of this complex. The minima involved the canonical amino-keto base pair (GC) and the 4-iminocytosine-6-hydroxyguanine base pair (G*C*), which the latter being formed from GC by a simultaneous transfer of two protons in neighbouring hydrogen bonds. A polar environment was found to stabilize the canonical structure by 1·3 kcal mol-1 with respect to the rare tautomer G*C*. The GC pair represents the global minimum on the HF/MINI-1 PES in both gas phase and polar environment. The polar environment was also found to decrease the interaction enthalpy of the GC base pair and to influence significantly the geometry of the hydrogen bonds. The

CpG islands are genome regions with an elevated Guanine + Cytosine content (GC content) and a higher CpG dinucleotide frequency than observed in the bulk genome. More than half of the human gene promoters colocalize with CpG islands and their methylation status has been shown to correlate with the expression level of the associated genes. As a consequence, CpG islands are assumed to be hotspots of epigenetic regulation.. However, an exact definition of CpG islands is still not agreed upon. The CgiHunter software tool follows the original sequence-based CpG island definition proposed by Gardiner-Garden and Frommer. They defined three requirements a genome region has to fulfill to qualify as a CpG island: a minimal length, a minimal GC content and a minimal ratio of its observed over its expected CpG dinucleotide frequency. Unlike many other heuristic-based approaches, the CgiHunter algorithm has been proven to identify all genome regions that meet a specified criteria and results in robust and ...

An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model ...

Here is presented the whole-genome sequence of Streptococcus thermophiles APC151, isolated from a marine fish. This bacterium produces gamma-aminobutyric acid (GABA) in high yields and is biotechnologically suitable to produce naturally GABA-enriched biofunctional yogurt. Its complete genome comprises 2,097 genes and 1,839,134 nucleotides, with an average GC content of 39.1 ...

Interaction of histone H 1 and models simulating histone chains was followed by monitoring the melting curves of supernatants after the sedimentation of aggregated complexes. In a mixture of two DNAs the histones reacted selectively with (A+T)-rich and non-methylated DNA, respectively. H 1 and (Ala-Lys-Pro)n also interacted preferentially with DNA in a mixture with double stranded RNA whereas (Lys30,Ala70)n did not show any selectivity. (G+C)-rich DNA in complexes showed CD spectra the intensity of which decreased with increasing DNA methylation to values comparable with these of complexes of (A+T)-rich DNA. In complexed with double stranded RNA only the polymer (Lys30,Ala70) displayed CD pattern similar to spectra of complexes with DNA. It was concluded that formation and structure of complexes depend selectively on the DNA conformation and base composition. ...

16. A method of stabilizing a spine with a spinal stabilization device comprising a rod-shaped implant comprising a continuous one-piece rod-shaped member having a first end and a second end opposite the first end along a longitudinal axis, the rod-shaped member being made from a plastic material exhibiting flexibility, a longitudinal bore provided in the rod-shaped member, a reinforcing rod accommodated in the bore and made from a more rigid material than the material of the rod-shaped member, the reinforcing rod having a first end and a second end, wherein the reinforcing rod is slidable in the bore; and wherein the reinforcing rod comprises a stop contacting the rod-shaped member to limit movement of the reinforcing rod relative to the rod-shaped member, and at least two bone anchoring elements, each bone anchoring element having a receiving part for receiving the rod-shaped member, the method comprising:attaching the first bone anchoring element to a bone or vertebra;attaching the second ...

Expression breadth and synonymous substitution patterns are most probably due to gene length effects: The above results are suggestive of selection possibly playing a role in codon usage bias in humans. However, as stated earlier, genes of different length are likely to have different MCB values owing to the nature of the method. Indeed, if we randomize our sequences and measure the mean MCB for 1000 simulants for each of our genes, we find that the MCB, on average, is higher for shorter genes. This is to be expected of any statistic that employs a multinomial distribution and applies equally to the method of Karlin and Mrazek.. Importantly, it so happens that in our data set longer genes have a slightly higher rate of synonymous substitutions and are not expressed in as broad a range of tissues. Therefore, plotting mean MCB for the randomized genes against breadth of expression for the real gene, we still find a weak positive correlation of the order of magnitude reported for the real genes (P ...

1. A comparison is made of several procedures for the extraction of tocopherols and isoprenoid quinones from plant tissues. 2. Gradient-elution column chromatography on acid-washed alumina efficiently separates the isoprenoid quinones and tocopherols into groups that can then be assayed spectrophotometrically or, with the tocopherols, separated into their individual components and determined by gas-liquid chromatography. 3. This improved analytical procedure was used to study the distribution of the tocopherols and of ubiquinone in the ungerminated wheat grain.. ...

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4Dipartimento di Biochimica e Biologia Molecolare, Università di Bari, Italy. The AUG start codon context features have been investigated by analyzing eukaryotic mRNAs belonging to various taxonomic groups. The functional relevance of each specific position surrounding the AUG start codon has been established as a function of the measured shift between base composition observed at that particular position, and base composition averaged over all the 5 untranslated regions. A more detailed analysis carried out on human genes belonging to different isochores showed significant isochore-specific features that cannot be explained only by a mutational bias effect.. The most represented heptamers spanning from position -3 to +4 with respect to the initiator AUG have been determined for mRNAs belonging to different taxonomic groups and a web page utility has been set up (http://bigarea.area.ba.cnr.it:8000/BioWWW/ATG.html) to determine the relative abundance of a user submitted oligonucleotide context ...

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A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C ...

PUZZLE VERSION 2.4 NOW AVAILABLE!! ==================================== Some *very* useful new features have been added to the PUZZLE program, partially due to requests of users of earlier versions: * AUTOMATIC RECOGNITION OF THE DATA TYPE. Depending on the input file PUZZLE switches automatically to the nucleotide or amino acid mode. * AUTOMATIC SELECTION OF THE MODEL OF SEQUENCE EVOLUTION. If the data set contains amino acids PUZZLE recogizes whether the amino acids are encoded on mtDNA or on nuclear DNA and selects accordingly one of the corresponding models of sequence evolution (Dayhoff, JTT, mtREV). If the data set consists of nucleotides the transition/transversion parameter is estimated by a maximum likelihood prodedure from the data. Thus, the Ts/Tv parameter needs not to be specified! * CHI^2 TEST ON BASE COMPOSITION. PUZZLE checks with the help of a 5% level chi^2 test whether the base composition of each taxon is identical with the average that serves as a basis for the maximum ...