*  How to sequence a bacterial genome at the end of 2012 | In between lines of code
The suggestions below are not absolute, just my thoughts on how one these days could go about sequencing a bacterial genome ... of our sequencing platform asked how to generate reference genomes for his 4 bacterial strains. His question inspired me to ... De novo bacterial genome assembly: a solved problem? * How to sequence and assemble a large eukaryote genome with long reads in ... 13 thoughts on "How to sequence a bacterial genome at the end of 2012" * BenK. says: ...
  https://flxlexblog.wordpress.com/2012/11/29/how-to-sequence-a-bacterial-genome-at-the-end-of-2012/
*  Community-wide analysis of microbial genome sequence signatures | Genome Biology | Full Text
Bacterial, archaeal, and viral populations in the AMD biofilm community have genome-wide signatures of nucleotide composition ... there should be prominent intra-genome variation of genome signature and scattering of fragments from the same genome into ... Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol. 1997, 44: 383-397. 10.1007/ ... Differences in genome signature of coding and non-coding sequences from the same genome are to be expected based on differing ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-8-r85
*  Using CRISPR Proteins To Record A Video Clip Into Bacterial Genomes
Scientists at Harvard have used a modified CRISPR gene editing tool to insert coded sequences into bacterial genomes matching a ... The research also showed that a significant amount of information can be added into the spacer part of the bacterial genome, ... It only acts upon the genome itself and any invading viral genetic material. How could it be used to view other parts of a cell ... meaning subsequent pixels from later frames can also be added in sequence and read off of the genome in order to reconstruct ...
  http://bioscriptionblog.com/2017/07/16/crispr-video-bacterial-genomes/
*  DNA & RNA Purification Bacterial Genomic Miniprep Kit | China-Mainland | Sigma-Aldrich
The GenElute Bacterial Genomic Kit provides a simple and convenient technique to isolate high quality DNA from both Gram(-) and ... Figure 3. Purified genomic DNA was isolated from various bacterial species using the GenElute Bacterial Genomic DNA kit. A 1 µg ... Typical DNA Yields with the GenElute Bacterial Genomic DNA Kit.. Source. Type of Media. Amount of Overnight Culture. OD600 per ... The GenElute Bacterial Genomic DNA Kit contains all of the reagents needed to purify genomic DNA from Gram negative bacteria ( ...
  https://www.sigmaaldrich.com/china-mainland/zh/life-science/molecular-biology/dna-and-rna-purification/bacterial-genomic-miniprep-kit.html
*  Angry by Choice: December 2007
So, through the process of obtaining genome sequence for a variety of bacterial species, Sorek et al realized that the ... 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 ... Despite this 10x coverage there are always regions of the genome that are not recovered.. Back to the clever bit, the authors ... To understand this you need to understand how genomes are sequenced.. In short, you purify genomic DNA from the organism you ...
  http://angrybychoice.fieldofscience.com/2007_12_01_archive.html
*  Genes | Free Full-Text | Ecological and Temporal Constraints in the Evolution of Bacterial Genomes | HTML
In addition, we discuss the temporal constraints in the evolution of bacterial genomes, considering bacterial evolution from ... In the present article we review the differential contribution to the evolution of bacterial genomes that processes such as ... bacterial core genomes are rather stable (see above), and it can be stated that the evolution of bacterial genome is an example ... each of which measures a different feature of bacterial genomes [45]. PFGE analyses the overall structure of bacterial genomes ...
  http://www.mdpi.com/2073-4425/2/4/804/htm
*  The Y.O.R.F.: Investigating the Smallest Bacterial Genome
... in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This ... I think this question is only really important when considering a minimal bacterial genome and if C. ruddii does turn out to be ... I remember at least one study claiming that the human genome contains bacterial genes. This was based on the fact that some ... One of the results of this coevolution was major changes to the original bacterial genome, which contained many genes that are ...
  http://theyorf.blogspot.com/2009/08/investigating-smallest-bacterial-genome.html
*  Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of...
Conversely, unexpected occurrences of the analyzed genomes in COGs, for example the first archaeal member of a purely bacterial ... Classification of genomes by co-occurrence in COGs. The table of co-occurrence of genomes in COGs is available on the COG ... The distance between genomes was calculated as Dij = 1 - (Cij/Ni + Nj - Cij), where Cij is the number of COGs in which genomes ... Koonin EV, Mushegian AR, Galperin MY, Walker DR: Comparison of archaeal and bacterial genomes: computer analysis of protein ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2000-1-5-research0009
*  Identification of Unannotated Small Genes in Salmonella | G3: Genes | Genomes | Genetics
Bacterial genomes serve as a blueprint in all aspects of biological research, and therefore accurate genome annotation is of ... 2012 Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biol. Direct 7: 37. ... The results of our study represent the prevailing inaccuracy in the current bacterial genome annotations of small genes, and ... Our findings add to the increasing recognition that current annotations of bacterial genomes have missed many small genes (Wood ...
  http://www.g3journal.org/content/7/3/983
*  9780521129619 - The Dynamic Bacterial Genome | eCampus.com
9780521129619 Our cheapest price for The Dynamic Bacterial Genome is $93.12. Free shipping on all orders over $35.00. ... Genome rearrangements are a result of the actions of discrete genetic elements such as conjugative transposons, plasmids, phage ... This book provides an in-depth analysis of the mechanisms and biological consequences of genome rearrangements in bacteria. ... The biological effects of these rearrangements are far-reaching and impact on bacterial virulence, antibiotic resistance and ...
  http://www.ecampus.com/dynamic-bacterial-genome-1st-edited-peter/bk/9780521129619
*  Bacterial Genome May Hold Answers To Mercury Mystery - Redorbit
A newly sequenced bacterial genome from a team led by the Department of Energy's Oak Ridge National Laboratory (ORNL) could ... The new genome, sequenced at the California-based DOE Joint Genome Institute (JGI) and published in the Journal of Bacteriology ... Few bacterial species are capable of this conversion, and exactly how the transformation takes place has been a matter of ... "This is the first Desulfovibrio genome that will methylate mercury that's been published," Brown said. "Now that we have this ...
  http://www.redorbit.com/news/science/2027236/bacterial_genome_may_hold_answers_to_mercury_mystery/
*  Discovering Complete Quasispecies in Bacterial Genomes | Genetics
We extracted REPIN populations from 10 bacterial genomes in the following manner: For each of the genomes we determined the ... REPETITIVE sequences are common in most bacterial genomes, but rare compared to their prevalence in most eukaryotic genomes ( ... REP sequences are ∼25-bp-long, highly abundant sequences in bacterial genomes (Higgins et al. 1982; Aranda-Olmedo et al. 2002; ... 2012 Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences. Nucleic Acids Res. 40: 3596-3609. ...
  http://www.genetics.org/content/206/4/2149
*  Inferring Bacterial Genome Flux While Considering Truncated Genes | Genetics
Daubin, V., and H. Ochman, 2004 Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. Genome Res. 14: 1036- ... Daubin, V., E. Lerat and G. Perriere, 2003a The source of laterally transferred genes in bacterial genomes. Genome Biol. 4: R57 ... Garcia-Vallvé, S., A. Romeu and J. Palau, 2000 Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. ... and most of them are transient in bacterial genomes (Lerat and Ochman 2005). Zhaxybayeva et al. (2007) reported that genomes ...
  http://www.genetics.org/content/186/1/411
*  JCVI: Impact of Donor-recipient Phylogenetic Distance on Bacterial Genome Transplantation.
Genome transplantation (GT) allows the installation of purified chromosomes into recipient cells, causing the resulting ... capricolum (Mcap), and the main factors driving the compatibility between a donor genome and a recipient cell are poorly ... Using Mcap as the recipient cell, we successfully transplanted the genome of six bacteria belonging to the Spiroplasma ... This key process remains a bottleneck in synthetic biology, especially for genome engineering strategies of intractable and ...
  http://www.jcvi.org/cms/publications/listing/abstract/article/impact-of-donor-recipient-phylogenetic-distance-on-bacterial-genome-transplantation/
*  Burkholderia contaminans Biofilm Regulating Operon and Its Distribution in Bacterial Genomes
... Olga L. Voronina,1 Marina S. ... For example, the Mumia flava genome was unexpectedly big: 16.4 Mb, in contrast to the few other Nocardioidaceae genomes that ... Preparation of genomic DNA for the whole genome sequencing was performed as described [9]. Whole genome sequencing of B. ... "The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes," Nucleic Acids Research, vol ...
  https://www.hindawi.com/journals/bmri/2016/6560534/
*  Whole genome sequencing of bacterial genomes - tools and applications | Coursera
This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant ... Whole genome sequencing of bacterial genomes - tools and applications from Technical University of Denmark (DTU). ... This course will cover the topic of Whole genome sequencing (WGS) of bacterial genomes which is becoming more and more relevant ... This course is for you if you are interested in getting to know more about Whole genome sequencing applied to bacterial ...
  https://www.coursera.org/learn/wgs-bacteria?lipi=urn%3Ali%3Apage%3Ad_flagship3_feed%3BzkGxet%2B6RIS0NW9VqVNfEQ%3D%3D
*  Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone | GenomeWeb
Researchers in Canada and the UK have used data from the Oxford Nanopore MinIon alone to assemble a bacterial genome into a ... Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone. Feb 23, 2015 ... Home » Team Demonstrates De Novo Assembly of Bacterial Genome from Nanopore Data Alone ... and the University of Birmingham in the UK have used data from the Oxford Nanopore MinIon to assemble a bacterial genome into a ...
  https://www.genomeweb.com/sequencing-technology/team-demonstrates-de-novo-assembly-bacterial-genome-nanopore-data-alone
*  New laptop program can identify drug resistance from bacterial genomes | University of Oxford
Scientists have developed an easy-to-use computer program that can quickly analyse bacterial DNA from a patient's infection and ... New laptop program can identify drug resistance from bacterial genomes. HealthResearchGeneticsInnovation ... Genome sequencing has the potential to transform the way we diagnose and treat bacterial infections in NHS hospitals, but one ... One of the barriers to making whole genome sequencing a routine part of NHS care is the need for powerful computers and ...
  http://www.ox.ac.uk/node/116208
*  Three bacterial genomes found lurking inside recently sequenced fruit fly genomes
... 28.02.2005 ... simulans and Wolbachia wMoj in the genome of D. mojavensis. The team compared the new Wolbachia genomes with the known genome ... We thought this was interesting as much for the novelty of the way the bacterial genomes were sequenced than what we learned ... The existence of these bacterial species inside the fruit fly genome database is an artifact of the way the fly was sequenced, ...
  http://www.innovations-report.com/html/reports/life-sciences/report-41001.html
*  Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism | Medgadget
... transplanted a bacterial chromosome from one type of bacteria into anothe ... Scientists Achieve First Bacterial Genome Transplantation; Promise to Develop First Synthetic Organism. June 29th, 2007 Editors ... Press release: JCVI Scientists Publish First Bacterial Genome Transplantation Changing One Species to Another …. ... and have completely replaced an entire bacterial genome and its expression. The work of Carole Lartigue, Ph.D. and colleagues ...
  https://www.medgadget.com/2007/06/scientists_achieve_first_bacterial_genome_transplantation_promise_to_develop_first_synthetic_organis.html
*  Bacterial genome - Wikipedia
Bacterial genomes are generally smaller and less variant in size among species when compared with genomes of animals and single ... One of the smallest bacterial genomes ever to be sequenced is that of the endosymbiont Carsonella rudii. At 160 kbp, the genome ... A study that included, but was not limited to, 478 bacterial genomes, concluded that as genome size increases, the number of ... The relationship between life-styles of bacteria and genome size raises questions as to the mechanisms of bacterial genome ...
  https://en.wikipedia.org/wiki/Bacterial_genome
*  BacMap: Bacterial Genome Atlas
Genome. RSA 493:. Chromosome: 1,995,275 bp. Plasmid pSAP1: 94,287 bp. Background. Coxiella burnetti is a gram-negative, non- ... From http://www.ebi.ac.uk/2can/genomes/bacteria.html). Sequenced By. RSA 493:. The Institute for Genomic Research, 9712 Medical ...
  http://wishart.biology.ualberta.ca/BacMap/cgi/getSpeciesCard.cgi?accession=NC_002971&ref=index_2.html
*  BacMap: Bacterial Genome Atlas
Genome. wMel:. Chromosome: 1,267,782 bp. Background. Wolbachia, which are found in a variety of invertebrate species, are of ... Wolbachia, a bacterial endosymbiont of diverse arthropods, affects its host's reproduction and so is consequential for its ... For example, the genome is unique among sequenced obligate intracellular species in both being highly streamlined and ... Analysis of the genome, in particular phylogenomic comparisons with other intracellular bacteria, has revealed many insights ...
  http://wishart.biology.ualberta.ca/BacMap/cgi/getSpeciesCard.cgi?accession=NC_002978&ref=index_2.html
*  ASMscience | Bacterial Genomes-All Sh
Overall, bacterial genomes range in size from about 0.6 to 9.4 Mb. In a recent review, it was suggested that there may be a ... The genome size of Bacillus cereus strains varies from 5.5 to 6.3 Mb, and great diversity is seen in the number and ... This chapter summarizes the recent findings of bacterial genomics and comments on the themes and trends which are emerging. A ... relationship between the genome sizes and the lifestyles of bacteria. ...
  http://www.asmscience.org/content/book/10.1128/9781555818180.chap3
*  Overview of the Technology
The two current methods used to engineer a transgenic crop are by the means of a gene gun or through bacterial vectors (mainly ... T-DNA regions are then transferred from the Ti plasmid and randomly inserted into the host plants genome. In the process, the ... new DNA that contains genes that encode for the desired trait is also spread throughout the plant's genome. ...
  https://www.macalester.edu/~montgomery/GMOs.htm