With an increasing amount of whole genome sequence data becoming available on a daily basis we have an opportunity to study the interactions and dynamics of different organisms on a whole genome level. In the past, reports of horizontal gene transfer have focused mainly on the identification of single genes that show distorted phylogenetic profiles to that of the organism it was isolated from. This study firstly did whole genome comparisons between the rice nuclear and plastid genomes to determine the level and dynamics gene transfer and insertion of the chloroplast ad mitochondrial genomes into that of the nuclear genome of rice. Secondly, it looked to identify sequence similarities between the rice genome and microbial genomes by performing whole genome comparisons between the rice genome and that of several microbial genomes. These sequences were analyzed further to identify possible instances of horizontal transfer of DNA from microbes to the rice genome. Using this approach, this study ...

Large-scale genome projects have paved the way to microbial pan-genome analyses. Pan-genomes describe the union of all genes shared by all members of the species or taxon under investigation. They offer a framework to assess the genomic diversity of a given collection of individual genomes and moreover they help to consolidate gene predictions and annotations. The computation of pan-genomes is often a challenge, and many techniques that use a global alignment-independent approach run the risk of not separating paralogs from orthologs. Also alignment-based approaches which take the gene neighbourhood into account often need additional manual curation of the results. This is quite time consuming and so far there is no visualisation tool available that offers an interactive GUI for the pan-genome to support curating pan-genomic computations or annotations of orthologous genes. We introduce Pan-Tetris, a Java based interactive software tool that provides a clearly structured and suitable way for the visual

Take-Home Message comic #5 celebrates an amazing milestone. During my PhD, I kept a little list pinned to the filing cabinet next to my desk, a list which contained details of every sequenced genome. This was something that was much easier when the number of published genomes was still in the single digits!. This is my favorite Take-Home Message comic to date. I feel that we are slowly settling in on a style that works well for this medium, and Abbys drawings just seem to get better and better. ...

TY - JOUR. T1 - Draft genome sequences of Escherichia coli strains isolated from septic patients. AU - Dunitz, Madison I.. AU - Coil, David A.. AU - Jospin, Guillaume. AU - Eisen, Jonathan A. AU - Adams, Jason Yeates. PY - 2014. Y1 - 2014. N2 - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. AB - We present the draft genome sequences of six strains of Escherichia coli isolated from blood cultures collected from patients with sepsis. The strains were collected from two patient sets, those with a high severity of illness, and those with a low severity of illness. Each genome was sequenced by both Illumina and PacBio for comparison.. UR - ...

It has been suggested that environmental constraints strongly shape nucleotide composition [26, 49-51]. If this were the case, two effects should be apparent in genome signatures of AMD populations. First, shared pressures deriving from the extreme AMD environment would drive genome signatures together, potentially obscuring differences between populations. Second, since each genome encodes proteins destined for diverse environments (that is, intracellular and extracellular), there should be prominent intra-genome variation of genome signature and scattering of fragments from the same genome into disparate regions of the SOM. Neither of these expectations is met in the AMD dataset. There are vast differences in nucleotide composition between populations, with genomic %GC ranging from 35% (ARMAN-4 and ARMAN-5) to 69% (low-abundance Actinobacteria) and genome signatures forming discrete clusters. Amino acid compositional constraints required for stability of proteins exposed to acidic solutions do ...

One realization that has come from comparing multiple bacterial genome sequences, including multiple isolates from the same species, is that gene transfer is an important force in bacterial genome evolution. In the laboratory gene transfer is essential for the study of bacteria and for learning more about all living organisms. Three processes in bacteria can broadly define the transfer of DNA: transformation, transduction, and conjugation. This chapter focuses on the many genetic tools available to manipulate the genetic content of Escherichia coli. A DNA molecule that does not have its own origin of replication must integrate into either the host chromosome or another autonomously replicating element such as an endogenous plasmid. In E. coli a modified derivative of the bacteriophage T4 offers some advantages for transduction in that it packages twice as much DNA as P1 and also is less sensitive to capsules found on many pathogenic strains of E. coli. Transformation of bacteria by use of either

The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of ...

Functional annotation of genomes is a critical aspect of the genomics enterprise. Without reliable assignment of gene function at the appropriate level of specificity, new genome sequences are plainly useless. The primary methodology used for genome annotation is the sequence database search, the results of which allow transfer of functional information from experimentally characterized genes (proteins) to their uncharacterized homologs in newly sequenced genomes [1,2,3]. However, general-purpose, archival sequence databases are not particularly suited for the purpose of genome annotation. The quality of the annotation of a new genome produced using a particular database critically depends on the reliability and completeness of the annotations in the database itself. As far as annotation is concerned, the purpose of primary sequence databases is to faithfully preserve the description attached to each sequence by its submitter. In their capacity as sequence archives, such databases include no ...

BacMap is a freely available web-accessible database containing fully annotated, fully zoomable and fully searchable chromosome maps from more than 2500 prokaryotic (archaebacterial and eubacterial) species.[1] BacMap was originally developed in 2005 to address the challenges of viewing and navigating through the growing numbers of bacterial genomes that were being generated through large-scale sequencing efforts. Since it was first introduced, the number of bacterial genomes in BacMap has grown by more than 15X. Essentially BacMap functions as an on-line visual atlas of microbial genomes. All of the genome annotations in BacMap were generated through the BASys genome annotation system.[3] BASys is a widely used microbial annotation infrastructure that performs comprehensive bionformatic analyses on raw (or labeled) bacterial genome sequence data. All of the genome (chromosome) maps in BacMap were constructed using the program known as CGView.[4] CGView is a popular visualization program for ...

The genus Bacillus comprises spore-forming rod-shaped Gram-positive bacteria, which usually grow aerobically or anaerobically. Members of this genus are common environmental microorganisms. Also, they can be monitored in the food production chain. Genome sequence of Bacillus sp. strain EE-W1 will provide helpful information to understand its ecology and genetics. Draft genome data may be useful in the field of using Bacillus species in industrial biotechnology. Also, these data can be a useful resource for the study of comparative genomics. Here, we present the draft genome sequence of Bacillus sp. strain EE-W1 isolated from a biogas reactor, Kazan, Russia. The assembled genome size was 5,769,164 bp, with a GC content 35.1%. This draft genome data can be accessed at DDBJ/ENA/GenBank under the accession WIPE00000000.

Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count. ...

Studies on the experimental evolution of microorganisms, on their in vivo evolution (mainly in the case of bacteria producing chronic infections), as well as the availability of multiple full genomic sequences, are placing bacteria in the playground of evolutionary studies. In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as gene modification, gene acquisition and gene loss may have when bacteria colonize different habitats that present characteristic ecological features. In particular, we review how the different processes contribute to evolution in microbial communities, in free-living bacteria or in bacteria living in isolation. In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from the perspective of processes of short-sighted evolution and punctual acquisition of evolutionary novelties followed by long stasis periods.

In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome (Bacteriophage MS2). The next year, Fred Sanger completed the first DNA-genome sequence: Phage Φ-X174, of 5386 base pairs.[7] The first complete genome sequences among all three domains of life were released within a short period during the mid-1990s: The first bacterial genome to be sequenced was that of Haemophilus influenzae, completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research.. The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of ...

sec id=bid.36, ,title,Microbial Genomes,/title, ,p,... A CON entry, containing instructions on how to put the pieces back together, is also made. The CON entry contains descriptor information, such as source organism and references, as well as a join statement providing explicit instructions on how to generate the complete genome from the pieces. The Accession number assigned to the CON record is also added as a secondary Accession number on each of the pieces that make up the complete genome (see ,xref ref-type=fig rid=bid.37,Figure 2,/xref,). ,fig id=bid.37, ,label,2,/label, ,caption,,title,A GenBank CON entry for a complete bacterial genome.,/title, ,p,The information toward the ,italic,bottom,/italic, of the record describes how to generate the complete genome from the pieces.,/p, ,/caption, ,graphic xmlns:xlink=http://www.w3.org/1999/xlink xlink:href=ch1f2 mime-subtype=gif/, ,/fig, ,/p, ... ,/sec ...

In 1995, the release of the first fully sequenced bacterial genome heralded a new era of bacterial genomic research (21). Over the past 20 years, the number of sequenced bacterial genomes has risen exponentially, and new research strategies, techniques, and applications have emerged to exploit the opportunities that these resources provide. While raw genomic sequence data are valuable, the availability of fully annotated genome sequences, outlining the positions of known genes and genomic features, dramatically increases their utility. Global expression analysis techniques such as microarrays and RNA-seq depend heavily on annotated genome sequences as a reference source for genes in the bacterial cell. These techniques have proved extremely useful; however, recently, certain limitations to their application are becoming apparent. A major concern in this regard is that they do not provide expression data for genes that are not included in genome annotation files. Bacterial sRNAs represent a class ...

Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the

TY - JOUR. T1 - Human contamination in bacterial genomes has created thousands of spurious proteins. AU - Breitwieser, Florian P.. AU - Pertea, Mihaela. AU - Zimin, Aleksey V.. AU - Salzberg, Steven L.. PY - 2019. Y1 - 2019. N2 - Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have ...

Escherichia coli exists in commensal and pathogenic forms. By measuring the variation of individual genes across more than a hundred sequenced genomes, gene variation can be studied in detail, including the number of mutations found for any given gene. This knowledge will be useful for creating better phylogenies, for determination of molecular clocks and for improved typing techniques. We find 3,051 gene clusters/families present in at least 95% of the genomes and 1,702 gene clusters present in 100% of the genomes. The former soft core of about 3,000 gene families is perhaps more biologically relevant, especially considering that many of these genome sequences are draft quality. The E. coli pan-genome for this set of isolates contains 16,373 gene clusters. A core-gene tree, based on alignment and a pan-genome tree based on gene presence/absence, maps the relatedness of the 186 sequenced E. coli genomes. The core-gene tree displays high confidence and divides the E. coli strains into the observed MLST

Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of paramount importance. However, increasing evidence indicates that currently annotated bacterial genomes have missed many genes encoding small proteins ≤60 aa (Wood et al. 2012; Warren et al. 2010). A small gene, or a small open reading frame (sORF), has previously been defined as one encoding proteins of ≤60 aa (Hemm et al. 2010); or alternatively, it accommodates those up to 100 aa (Andrews and Rothnagel 2014). While small proteins have been increasingly reported for their important cellular roles in bacteria (Alix and Blanc-Potard 2008; Martin et al. 2015; Hobbs et al. 2012), studies on small proteins are limited, partly because many small genes are unannotated in sequenced bacterial genomes (Alix and Blanc-Potard 2009; Storz et al. 2014). Despite much effort made to improve gene annotation, the accurate identification of small genes has been a persistent challenge ...

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Elucidating the adaptive strategies and plasticity of bacterial genomes in situ is crucial for understanding the epidemiology and evolution of pathogens threatening human health. While much is known about the evolution of E. coli in controlled laboratory environments, less effort has been made to elucidate the genome dynamics of E. coli in its native settings. Here, we follow the genome dynamics of co-existing E. coli lineages in situ of the infant gut during the first year of life. One E. coli lineage causes a urinary tract infection (UTI) and experiences several alterations of its genomic content during subsequent antibiotic treatment. Interestingly, all isolates of this uropathogenic E. coli strain carried a highly stable plasmid implicated in virulence of diverse pathogenic strains from all over the world. While virulence elements are certainly beneficial during infection scenarios, their role in gut colonization and pathogen persistence is poorly understood. We performed in vivo competitive

Given the size of modern sequence databases, finding the complete genome sequence for a bacterium among the many other partial sequences can be a challenge. In addition, if you want to download sequences for many bacterial species, an automated solution might be preferable. In this post well discuss how to download bacterial genomes programmatically for…

WASHINGTON, DC - January 28, 2013 - The American Society for Microbiology has published the first issue of its new online-only, open access journal, Genome AnnouncementsTM, focusing exclusively on reports of microbial genome sequences.. Genome Announcements features short manuscripts announcing the availability of recently sequenced genomes of prokaryotic and eukaryotic microbes and viruses in public databases. These announcements inform readers of the availability of new genome sequences and provide the rationale for sequencing a particular organism, as well as details of the methodologies and protocols used in assembly of the genome sequence.. Although genome sequence data typically are deposited in GenBank or other shared databases, the rationale for sequencing a particular organism and the detailed methodologies and protocols used often are not readily available. In the past, several ASM journals published Genome Announcement article types, brief reports stating that the genome of a ...

Draft genome sequences of Candidatus Chloroploca asiatica and Candidatus Viridilinea mediisalina, candidate representatives of the Chloroflexales order: phy

A potential user (customer) of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to write this post. The suggestions below are not absolute, just my thoughts on how one these days could go about sequencing a bacterial genome using one or more of the sequencing…

The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and Gram(+) bacteria. This kit combines the advantages of a silica-based system with a microspin format, eliminating the need for expensive resins and hazardous organic compounds.

The sensitivity of this procedure to resolve variation within a bacterial species is demonstrated: genome sizes and repeat structure of five environmental strains of E. coli from short Illumina reads were estimated by this method, and total genome sizes corresponded well with those obtained for the same strains by pulsed-field gel electrophoresis. In addition, this approach was applied to read-sets for completed genomes and shown to be accurate over a wide range of microbial genome sizes. ...

Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using real benchmark datasets we demonstrate that OrthoFinder is more accurate than other orthogroup inference methods by between 8 % and 33 %. Furthermore, we demonstrate the utility of OrthoFinder by providing a complete classification of transcription factor gene families in plants revealing 6.9 million previously unobserved relationships.

Identifying homology relationships between sequences is fundamental to biological research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. Using …

Species identification by sequencing the bacterial genome at seven key loci, uncovering achieved similar combinations of sequences with certain bacterial

Harvard scientists have unraveled the inner architecture of bacterial genomes in a breakthrough discovery that may shed light on how chromosomes organize within a cell.. The findings came after researchers applied a new visualization technique that generated the first fluorescence super-resolution images of chromosomes within a single bacterial cell.. The work demonstrates the massive potential provided by the combination of emerging super-resolution microscopy and clever biochemistry, wrote Stefan W. Hell, director at the Max Planck Institute for Biophysical Chemistry, in an emailed statement. He added that the findings open a new chapter in the study of bacteria molecular organization.. The findings provide the first detailed picture of a class of DNA-interacting proteins called nucleoid-associated proteins (NAPs). This close-up look helped scientists determine their role in organizing chromosomes in bacteria, according to Xiaoliang Sunney Xie, a Harvard professor of chemistry and chemical ...

The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe

Scientists at Harvard have used a modified CRISPR gene editing tool to insert coded sequences into bacterial genomes matching a video clip.

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of

Pan-Genomic Approaches for Comprehensive Screening of Novel or Emerging Infectious Agents in Blood Emerging infectious agents, the latest of which is Zika virus...

The workshop will focus on the design and analysis of pan-genomic microarrays. Due to the massive availability of sequences of genomes of microbes and other organisms, the degree of sequence variation is becomming measurable both across bacterial species, but also within different isolates of the same species. Indeed, the pan-genome, defined as the total number of unique genes observed in any isolates of a given species, can be much larger than the individual genome of any single isolate. For the microarray analyst, genetic variation between isolates of the same species presents new challenges since a traditional microarray designed to target one specific genome is likely to perform very poorly if used with another, different isolate. As the number of fully sequenced genomes of indepentent isolates for each bacterial species increases, it becommes possible to design pan-genomic microarrays capable of targeting any and all unique genes ever observed in that species. The advantages of this ...

The first step of bacterial cloning is to get the gene of interest into the bacterial genome. Bacteria are one-celled, prokaryotic organisms and have simpler cellular structures than humans, who are complex and multi-cellular eukaryotes. The genomes of each are stored slightly differently: both rely on large, long structures of DNA called chromosomes, but while you can think of a bacterial genome as one large, single circle of DNA twisted up like a convoluted rubber band and free-floating in the bacterial cell, the human chromosome structure (26 chromosomes in total) is a long linear string of DNA twisted up and tucked away neatly into a sub-packet of the cell called the nucleus-think what happens to your headphones when you put them in your pocket. In addition to their larger, circular chromosome, bacteria have other small, circular, free-floating pieces of DNA called plasmids. These plasmids are maintained and copied separately from the larger circular chromosome. Because bacteria can pick up ...

Here, we present the genome sequence and annotation of the novel bacterial strain HV4-5-C5C, which may represent a new genus within the family Oscillospiraceae (order Eubacteriales). This strain is a potential keystone species in the hydrolysis of complex polymers during anaerobic digestion of biomass. ...

All the genome sequences of organisms known throughout the world are stored in a database belonging to the National Center for Biotechnology Information in the United States. As of today, the database has an additional entry: Caulobacter ethensis-2.0. It is the worlds first fully computer-generated genome of a living organism, developed by scientists at ETH Zurich. However, it must be emphasised that although the genome for C. ethensis-2.0 was physically produced in the form of a very large DNA molecule, a corresponding organism does not yet exist.

Eric Smalley writes The worlds largest genome sequencing center once needed four days to analyze data describing a human genome. Now it needs just six hours. The trick is servers built with graphics chips — the sort of processors that were originally designed to draw images on your personal ...

Multiplex automated genome engineering (MAGE) is a powerful technology for in vivo genome editing that uses synthetic single-stranded DNA (ssDNA) to introduce targeted modifications directly into the Escherichia coli chromosome. MAGE is a cyclical process that involves transformation of ssDNA (by el …

MAGE, the older of the two techniques, made its debut two years ago. It stands for multiplex automated genome engineering, a fancy way of saying that it can easily change a genome many times over. It was originally used to create millions of small variants of bacterial genomes, producing a multitude of strains that can be tested for new abilities. As Jo Marchant puts it in her excellent feature, its an evolution machine. In its debut, within a matter of days, it had evolved a strain of E.coli that would produce large amounts of lycopene, a pigment that makes tomatoes red.. MAGE is a versatile editor. Not only can it create many diverse changes in a group of cells, it can also create many specific changes in a single cell. Thats what Isaacs, Carr and Wang have now done. TAG appears in 314 places throughout the E.coli genome as a stop codon. For each one, the team created a small stretch of DNA that had TAA instead of TAG, surrounded by exactly the same letters. They fed these edited ...

Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome ...

Bacteria generate small molecules to fend off their fellow microbes. They also produce molecules that affect the response of host organisms-including humans-to their presence. Such molecules have been a major source of antibiotics, immunosuppressants, anti-cancer agents, and other drugs. But their discovery has not been systematic and the products of bacteria living in our bodies have only recently drawn scientific notice.. However, thanks to genome sequencing, there are now databases containing the blueprints (sequences) of 160 million genes from nearly a quarter-million organisms, including the genes of bacteria species that live in and interact with us-the human microbiome. These bacterial genes encode molecules that could yield narrow-spectrum antibiotics, immune system regulators, and neuroactive drugs. But first scientists must find the potentially therapeutic needles in this genomic haystack.. Research in the laboratory of Michael Fischbach, PhD, a faculty member of the UCSF School of ...

We can think of the bacterial genome as having two parts, says Professor Young. The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world ...

The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format. By default, clicking on the export buttons will result in a download of the allowed maximum amount of items. To select a subset of the search results, click Selective Export button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export. After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format. ...

Use bioinformatics to explore DNA sequences and protein functions, to find the determinants of virulence in microbes with this free online course.

Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL., Nature 430(6995), 2004 ...

Back to the clever bit, the authors realized that putting these plasmids into E.coli represents HGT. These vectors are in fact derived from natural E.coli strains and are transferred naturally between strains. So, through the process of obtaining genome sequence for a variety of bacterial species, Sorek et al realized that the scientific community had inadvertantly set up an experiment to determine the limits of HGT. They simply (and by simply I mean anyone with a computer and knowledge of these systems could have done it, it is not meant to diminish the work or insights of the authors) took available genome sequence information from 79 distinct species and looked to see what was not sequenced using the process described above. Again, the idea being if a region was not sequenced, it must not have been propagated in E.coli (the gaps in a genome sequence are obtained using other more labor intensive methods). Indeed, the authors found regions from these species that were not able to be ...

TY - JOUR. T1 - Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. AU - Qu, Hongzhu. AU - Wu, Hao. AU - Zhang, Tongwu. AU - Zhang, Zhang. AU - Hu, Songnian. AU - Yu, Jun. N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: The study was supported by grants awarded to JY (2006CB910404) from the National Basic Research Program (973 Program) and from the National Science and Technology Key Project (2008ZX1004-013), the Ministry of Science and Technology of the Peoples Republic of China.. PY - 2010/12. Y1 - 2010/12. N2 - Nucleotide compositional asymmetry (NCA) between leading and lagging strands (LeS and LaS) is dynamic and diverse among eubacterial genomes due to different mutation and selection forces. A thorough investigation is needed in order to study the relationship between nucleotide composition dynamics and gene distribution biases. Based on a collection of 364 eubacterial genomes that were grouped according to a DnaE-based ...