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51.
Pati A Labutti K Pukall R Nolan M Glavina Del Rio T Tice H Cheng JF Lucas S Chen F Copeland A Ivanova N Mavromatis K Mikhailova N Pitluck S Bruce D Goodwin L Land M Hauser L Chang YJ Jeffries CD Chen A Palaniappan K Chain P Brettin T Sikorski J Rohde M Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP Lapidus A 《Standards in genomic sciences》2010,2(1):49-56
Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022(T) is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
52.
Sikorski J Lapidus A Copeland A Glavina Del Rio T Nolan M Lucas S Chen F Tice H Cheng JF Saunders E Bruce D Goodwin L Pitluck S Ovchinnikova G Pati A Ivanova N Mavromatis K Chen A Palaniappan K Chain P Land M Hauser L Chang YJ Jeffries CD Brettin T Detter JC Han C Rohde M Lang E Spring S Göker M Bristow J Eisen JA Markowitz V Hugenholtz P Kyrpides NC Klenk HP 《Standards in genomic sciences》2010,2(2):149-157
Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. 相似文献
53.
Alpizar YA Chain B Collins MK Greenwood J Katz D Stauss HJ Mitchison NA 《Cancer immunology, immunotherapy : CII》2011,60(8):1127-1135
Although cancer immunology has made vigorous progress over the last decade, its future remains uncertain. Tumors have clearly
proved subject to immune surveillance, leading to antigenic editing, and means of activating both T and B arms of the immune
system have been devised. Therapeutic vaccination and monoclonal antibody therapy have so far proved disappointing, because
tumors prove adept at evasion from immune control. Dual targeting could well counteract evasion, provided that the two targets
are independent and are attacked simultaneously. This stage has nearly but not quite been reached in several forms of immunotherapy,
particularly of B-cell cancers, although such treatment also carries hazards. 相似文献
54.
Silvina del Carmen Alejandra de Moreno de LeBlanc Rebeca Martin Florian Chain Philippe Langella Luis G. Bermúdez-Humarán Jean Guy LeBlanc 《Applied and environmental microbiology》2014,80(3):869-877
The aims of this study were to develop strains of lactic acid bacteria (LAB) having both immunomodulatory and antioxidant properties and to evaluate their anti-inflammatory effects both in vitro, in different cellular models, and in vivo, in a mouse model of colitis. Different Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus strains were cocultured with primary cultures of mononuclear cells. Analysis of the pro- and anti-inflammatory cytokines secreted by these cells after coincubation with candidate bacteria revealed that L. delbrueckii subsp. bulgaricus CRL 864 and S. thermophilus CRL 807 display the highest anti-inflammatory profiles in vitro. Moreover, these results were confirmed in vivo by the determination of the cytokine profiles in large intestine samples of mice fed with these strains. S. thermophilus CRL 807 was then transformed with two different plasmids harboring the genes encoding catalase (CAT) or superoxide dismutase (SOD) antioxidant enzymes, and the anti-inflammatory effects of recombinant streptococci were evaluated in a mouse model of colitis induced by trinitrobenzenesulfonic acid (TNBS). Our results showed a decrease in weight loss, lower liver microbial translocation, lower macroscopic and microscopic damage scores, and modulation of the cytokine production in the large intestines of mice treated with either CAT- or SOD-producing streptococci compared to those in mice treated with the wild-type strain or control mice without any treatment. Furthermore, the greatest anti-inflammatory activity was observed in mice receiving a mixture of both CAT- and SOD-producing streptococci. The addition of L. delbrueckii subsp. bulgaricus CRL 864 to this mixture did not improve their beneficial effects. These findings show that genetically engineering a candidate bacterium (e.g., S. thermophilus CRL 807) with intrinsic immunomodulatory properties by introducing a gene expressing an antioxidant enzyme enhances its anti-inflammatory activities. 相似文献
55.
Frédéric J. J. Chain Philine G. D. Feulner Mahesh Panchal Christophe Eizaguirre Irene E. Samonte Martin Kalbe Tobias L. Lenz Monika Stoll Erich Bornberg-Bauer Manfred Milinski Thorsten B. H. Reusch 《PLoS genetics》2014,10(12)
Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation. 相似文献
56.
Chih‐Yu Chang Lijian Zuo Hin‐Lap Yip Chang‐Zhi Li Yongxi Li Chain‐Shu Hsu Yen‐Ju Cheng Hongzheng Chen Alex K‐Y. Jen 《Liver Transplantation》2014,4(7)
Highly efficient tandem and semitransparent (ST) polymer solar cells utilizing the same donor polymer blended with [6,6]‐phenyl‐C61‐butyric acid methyl ester (PC61BM) and [6,6]‐phenyl‐C71‐butyric acid methyl ester (PC71BM) as active layers are demonstrated. A high power conversion efficiency (PCE) of 8.5% and a record high open‐circuit voltage of 1.71 V are achieved for a tandem cell based on a medium bandgap polymer poly(indacenodithiophene‐co‐phananthrene‐quinoxaline) (PIDT‐phanQ). In addition, this approach can also be applied to a low bandgap polymer poly[2,6‐(4,4‐bis(2‐ethylhexyl)‐4H‐cyclopenta[2,1‐b;3,4‐b′]dithiophene)‐alt‐4,7‐(5‐fluoro‐2,1,3‐benzothia‐diazole)] (PCPDTFBT), and PCEs up to 7.9% are achieved. Due to the very thin total active layer thickness, a highly efficient ST tandem cell based on PIDT‐phanQ exhibits a high PCE of 7.4%, which is the highest value reported to date for a ST solar cell. The ST device also possesses a desirable average visible transmittance (≈40%) and an excellent color rendering index (≈100), permitting its use in power‐generating window applications. 相似文献
57.
Background
Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform’s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.Results
Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.Conclusion
FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0366-2) contains supplementary material, which is available to authorized users. 相似文献58.
The human body consists of innumerable multifaceted environments that predispose colonization by a number of distinct microbial communities, which play fundamental roles in human health and disease. In addition to community surveys and shotgun metagenomes that seek to explore the composition and diversity of these microbiomes, there are significant efforts to sequence reference microbial genomes from many body sites of healthy adults. To illustrate the utility of reference genomes when studying more complex metagenomes, we present a reference-based analysis of sequence reads generated from 55 shotgun metagenomes, selected from 5 major body sites, including 16 sub-sites. Interestingly, between 13% and 92% (62.3% average) of these shotgun reads were aligned to a then-complete list of 2780 reference genomes, including 1583 references for the human microbiome. However, no reference genome was universally found in all body sites. For any given metagenome, the body site-specific reference genomes, derived from the same body site as the sample, accounted for an average of 58.8% of the mapped reads. While different body sites did differ in abundant genera, proximal or symmetrical body sites were found to be most similar to one another. The extent of variation observed, both between individuals sampled within the same microenvironment, or at the same site within the same individual over time, calls into question comparative studies across individuals even if sampled at the same body site. This study illustrates the high utility of reference genomes and the need for further site-specific reference microbial genome sequencing, even within the already well-sampled human microbiome. 相似文献
59.
Michael Visser Sofiya N. Parshina Joana I. Alves Diana Z. Sousa Inês A. C. Pereira Gerard Muyzer Jan Kuever Alexander V. Lebedinsky Jasper J. Koehorst Petra Worm Caroline M. Plugge Peter J. Schaap Lynne A. Goodwin Alla Lapidus Nikos C. Kyrpides Janine C. Detter Tanja Woyke Patrick Chain Karen W. Davenport Stefan Spring Manfred Rohde Hans Peter Klenk Alfons J.M. Stams 《Standards in genomic sciences》2014,9(3):655-675
60.
Wayne Reeve Ross Ballard John Howieson Elizabeth Drew Rui Tian Lambert Br?u Christine Munk Karen Davenport Patrick Chain Lynne Goodwin Ioanna Pagani Marcel Huntemann Konstantinos Mavrommatis Amrita Pati Victor Markowitz Natalia Ivanova Tanja Woyke Nikos Kyrpides 《Standards in genomic sciences》2014,9(3):514-526
Ensifer medicae strain WSM1115 forms effective nitrogen fixing symbioses with a range of annual Medicago species and is used in commercial inoculants in Australia. WSM1115 is an aerobic, motile, Gram-negative, non-spore-forming rod. It was isolated from a nodule recovered from the root of burr medic (Medicago polymorpha) collected on the Greek Island of Samothraki. WSM1115 has a broad host range for nodulation and N2 fixation capacity within the genus Medicago, although this does not extend to all medic species. WSM1115 is considered saprophytically competent in moderately acid soils (pH(CaCl2) 5.0), but it has failed to persist at field sites where soil salinity exceeded 10 ECe (dS/m). Here we describe the features of E. medicae strain WSM1115, together with genome sequence information and its annotation. The 6,861,065 bp high-quality-draft genome is arranged into 7 scaffolds of 28 contigs, contains 6,789 protein-coding genes and 83 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. 相似文献