共查询到20条相似文献,搜索用时 31 毫秒
1.
Complete genome sequence of the motile actinomycete Actinoplanes missouriensis 431T (= NBRC 102363T)
Hideki Yamamura Yasuo Ohnishi Jun Ishikawa Natsuko Ichikawa Haruo Ikeda Mitsuo Sekine Takeshi Harada Sueharu Horinouchi Misa Otoguro Tomohiko Tamura Ken-ichiro Suzuki Yasutaka Hoshino Akira Arisawa Youji Nakagawa Nobuyuki Fujita Masayuki Hayakawa 《Standards in genomic sciences》2012,7(2):294-303
Actinoplanes missouriensis Couch 1963 is a well-characterized member of the genus Actinoplanes, which is of morphological interest because its members typically produce sporangia containing motile spores. The sporangiospores are motile by means of flagella and exhibit chemotactic properties. It is of further interest that members of Actinoplanes are prolific sources of novel antibiotics, enzymes, and other bioactive compounds. Here, we describe the features of A. missouriensis 431T, together with the complete genome sequence and annotation. The 8,773,466 bp genome contains 8,125 protein-coding and 79 RNA genes. 相似文献
2.
Hengshan Zhang Ane F. B. Zeidler Wei Song Christopher M. Puccia Ewa Malc Patricia W. Greenwell Piotr A. Mieczkowski Thomas D. Petes Juan Lucas Argueso 《Genetics》2013,193(3):785-801
The kinetochore is the macromolecular protein complex that mediates chromosome segregation. The Dsn1 component is crucial for kinetochore assembly and is phosphorylated by the Aurora B kinase. We found that Aurora B phosphorylation of Dsn1 promotes the interaction between outer and inner kinetochore proteins in budding yeast. 相似文献
3.
Dhamodharan Ramasamy Sahare Kokcha Jean-Christophe Lagier Thi-Thien Nguyen Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,7(2):246-257
Aeromicrobium massiliense strain JC14Tsp. nov. is the type strain of Aeromicrobium massiliense sp. nov., a new species within the genus Aeromicrobium. This strain, whose genome is described here, was isolated from the fecal microbiota of an asymptomatic patient. Aeromicrobium massiliense is an aerobic rod-shaped gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,322,119 bp long genome contains 3,296 protein-coding and 51 RNA genes. 相似文献
4.
Edward G. Hawkins Ian Martin Lindsay M. Kondo Meredith E. Judy Victoria E. Brings Chung-Lung Chan GinaMari G. Blackwell Jill C. Bettinger Andrew G. Davies 《Genetics》2015,199(1):135-149
The Prp43 DExD/H-box protein is required for progression of the biochemically distinct pre-messenger RNA and ribosomal RNA (rRNA) maturation pathways. In Saccharomyces cerevisiae, the Spp382/Ntr1, Sqs1/Pfa1, and Pxr1/Gno1 proteins are implicated as cofactors necessary for Prp43 helicase activation during spliceosome dissociation (Spp382) and rRNA processing (Sqs1 and Pxr1). While otherwise dissimilar in primary sequence, these Prp43-binding proteins each contain a short glycine-rich G-patch motif required for function and thought to act in protein or nucleic acid recognition. Here yeast two-hybrid, domain-swap, and site-directed mutagenesis approaches are used to investigate G-patch domain activity and portability. Our results reveal that the Spp382, Sqs1, and Pxr1 G-patches differ in Prp43 two-hybrid response and in the ability to reconstitute the Spp382 and Pxr1 RNA processing factors. G-patch protein reconstitution did not correlate with the apparent strength of the Prp43 two-hybrid response, suggesting that this domain has function beyond that of a Prp43 tether. Indeed, while critical for Pxr1 activity, the Pxr1 G-patch appears to contribute little to the yeast two-hybrid interaction. Conversely, deletion of the primary Prp43 binding site within Pxr1 (amino acids 102–149) does not impede rRNA processing but affects small nucleolar RNA (snoRNA) biogenesis, resulting in the accumulation of slightly extended forms of select snoRNAs, a phenotype unexpectedly shared by the prp43 loss-of-function mutant. These and related observations reveal differences in how the Spp382, Sqs1, and Pxr1 proteins interact with Prp43 and provide evidence linking G-patch identity with pathway-specific DExD/H-box helicase activity. 相似文献
5.
Stefan Spring Michael Visser Megan Lu Alex Copeland Alla Lapidus Susan Lucas Jan-Fang Cheng Cliff Han Roxanne Tapia Lynne A. Goodwin Sam Pitluck Natalia Ivanova Miriam Land Loren Hauser Frank Larimer Manfred Rohde Markus G?ker John C. Detter Nikos C. Kyrpides Tanja Woyke Peter J. Schaap Caroline M. Plugge Gerard Muyzer Jan Kuever Inês A. C. Pereira Sofiya N. Parshina Rizlan Bernier-Latmani Alfons J.M. Stams Hans-Peter Klenk 《Standards in genomic sciences》2012,7(2):304-319
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.Keywords : anaerobic, motile, sporulating, mesophilic, sulfate-reducer, hydrogen sulfide, incomplete oxidizer, mixotrophic, CSP 2009, Peptococcaceae, Clostridiales 相似文献
6.
Amos W 《Genome biology》2011,12(4):110
McLaughlin and Chadwick describe an X-linked tandem repeat that is transcribed, conserved and defies X inactivation. Is it selfish, functional or just an oddity?See research article: http://genomebiology.com/2011/12/4/R37 相似文献
7.
Background
The need for efficient algorithms to uncover biologically relevant phosphorylation motifs has become very important with rapid expansion of the proteomic sequence database along with a plethora of new information on phosphorylation sites. Here we present a novel unsupervised method, called Motif Finder (in short, F-Motif) for identification of phosphorylation motifs. F-Motif uses clustering of sequence information represented by numerical features that exploit the statistical information hidden in some foreground data. Furthermore, these identified motifs are then filtered to find “actual” motifs with statistically significant motif scores.Results and Discussion
We have applied F-Motif to several new and existing data sets and compared its performance with two well known state-of-the-art methods. In almost all cases F-Motif could identify all statistically significant motifs extracted by the state-of-the-art methods. More importantly, in addition to this, F-Motif uncovers several novel motifs. We have demonstrated using clues from the literature that most of these new motifs discovered by F-Motif are indeed novel. We have also found some interesting phenomena. For example, for CK2 kinase, the conserved sites appear only on the right side of S. However, for CDK kinase, the adjacent site on the right of S is conserved with residue P. In addition, three different encoding methods, including a novel position contrast matrix (PCM) and the simplest binary coding, are used and the ability of F-motif to discover motifs remains quite robust with respect to encoding schemes.Conclusions
An iterative algorithm proposed here uses exploratory data analysis to discover motifs from phosphorylated data. The effectiveness of F-Motif has been demonstrated using several real data sets as well as using a synthetic data set. The method is quite general in nature and can be used to find other types of motifs also. We have also provided a server for F-Motif at http://f-motif.classcloud.org/, http://bio.classcloud.org/f-motif/ or http://ymu.classcloud.org/f-motif/. 相似文献8.
9.
Wei Chun Au Anthony R. Dawson David W. Rawson Sara B. Taylor Richard E. Baker Munira A. Basrai 《Genetics》2013,194(2):513-518
Understanding the molecular basis of common traits is a primary challenge of modern genetics. One model holds that rare mutations in many genetic backgrounds may often phenocopy one another, together explaining the prevalence of the resulting trait in the population. For the vast majority of phenotypes, the role of rare variants and the evolutionary forces that underlie them are unknown. In this work, we use a population of Saccharomyces paradoxus yeast as a model system for the study of common trait variation. We observed an unusual, flocculation and invasive-growth phenotype in one-third of S. paradoxus strains, which were otherwise unrelated. In crosses with each strain in turn, these morphologies segregated as a recessive Mendelian phenotype, mapping either to IRA1 or to IRA2, yeast homologs of the hypermutable human neurofibromatosis gene NF1. The causal IRA1 and IRA2 haplotypes were of distinct evolutionary origin and, in addition to their morphological effects, associated with hundreds of stress-resistance and growth traits, both beneficial and disadvantageous, across S. paradoxus. Single-gene molecular genetic analyses confirmed variant IRA1 and IRA2 haplotypes as causal for these growth characteristics, many of which were independent of morphology. Our data make clear that common growth and morphology traits in yeast result from a suite of variants in master regulators, which function as a mutation-driven switch between phenotypic states. 相似文献
10.
Perrine Hugon Ajay Kumar Mishra Catherine Robert Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,6(3):356-365
We report the properties of a draft genome sequence of the bacterium Anaerococcus vaginalis strain PH9, a species within the Anaerococcus genus. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. A. vaginalis is an obligate anaerobic coccus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,048,125-bp long (one chromosome but no plasmid) and contains 2,095 protein-coding and 38 RNA genes, including three rRNA genes.Key words: Anaerococcus vaginalis, genome 相似文献
11.
Hon-Song Kim Yuko Kitano Masataka Mori Tomomi Takano Thomas Edward Harbaugh Kae Mizutani Haruka Yanagimoto Sayaka Miwa Shinji Ihara Yukihiko Kubota Yukimasa Shibata Kohji Ikenishi Gian Garriga Kiyoji Nishiwaki 《Genetics》2014,196(2):471-479
A fundamental question in hematopoietic development is how multipotent progenitors achieve precise identities, while the progenitors themselves maintain quiescence. In Drosophila melanogaster larvae, multipotent hematopoietic progenitors support the production of three lineages, exhibit quiescence in response to cues from a niche, and from their differentiated progeny. Infection by parasitic wasps alters the course of hematopoiesis. Here we address the role of Notch (N) signaling in lamellocyte differentiation in response to wasp infection. We show that Notch activity is moderately high and ubiquitous in all cells of the lymph gland lobes, with crystal cells exhibiting the highest levels. Wasp infection reduces Notch activity, which results in fewer crystal cells and more lamellocytes. Robust lamellocyte differentiation is induced even in N mutants. Using RNA interference knockdown of N, Serrate, and neuralized (neur), and twin clone analysis of a N null allele, we show that all three genes inhibit lamellocyte differentiation. However, unlike its cell-autonomous function in crystal cell development, Notch’s inhibitory influence on lamellocyte differentiation is not cell autonomous. High levels of reactive oxygen species in the lymph gland lobes, but not in the niche, accompany NRNAi-induced lamellocyte differentiation and lobe dispersal. Our results define a novel dual role for Notch signaling in maintaining competence for basal hematopoiesis: while crystal cell development is encouraged, lamellocytic fate remains repressed. Repression of Notch signaling in fly hematopoiesis is important for host defense against natural parasitic wasp infections. These findings can serve as a model to understand how reactive oxygen species and Notch signals are integrated and interpreted in vivo. 相似文献
12.
Understanding sensory systems that perceive environmental inputs and neural circuits that select appropriate motor outputs is essential for studying how organisms modulate behavior and make decisions necessary for survival. Drosophila melanogaster oviposition is one such important behavior, in which females evaluate their environment and choose to lay eggs on substrates they may find aversive in other contexts. We employed neurogenetic techniques to characterize neurons that influence the choice between repulsive positional and attractive egg-laying responses toward the bitter-tasting compound lobeline. Surprisingly, we found that neurons expressing Gr66a, a gustatory receptor normally involved in avoidance behaviors, receive input for both attractive and aversive preferences. We hypothesized that these opposing responses may result from activation of distinct Gr66a-expressing neurons. Using tissue-specific rescue experiments, we found that Gr66a-expressing neurons on the legs mediate positional aversion. In contrast, pharyngeal taste cells mediate the egg-laying attraction to lobeline, as determined by analysis of mosaic flies in which subsets of Gr66a neurons were silenced. Finally, inactivating mushroom body neurons disrupted both aversive and attractive responses, suggesting that this brain structure is a candidate integration center for decision-making during Drosophila oviposition. We thus define sensory and central neurons critical to the process by which flies decide where to lay an egg. Furthermore, our findings provide insights into the complex nature of gustatory perception in Drosophila. We show that tissue-specific activation of bitter-sensing Gr66a neurons provides one mechanism by which the gustatory system differentially encodes aversive and attractive responses, allowing the female fly to modulate her behavior in a context-dependent manner. 相似文献
13.
14.
Yoko Katano Shun Fujinami Akatsuki Kawakoshi Hidekazu Nakazawa Syoko Oji Takao Iino Akio Oguchi Akiho Ankai Shigehiro Fukui Yasuyuki Terui Sachi Kamata Takeshi Harada Satoshi Tanikawa Ken-ichiro Suzuki Nobuyuki Fujita 《Standards in genomic sciences》2012,6(3):406-414
Oscillibacter valericigenes is a mesophilic, strictly anaerobic bacterium belonging to the clostridial cluster IV. Strain Sjm18-20T (=NBRC 101213T =DSM 18026T) is the type strain of the species and represents the genus Oscillibacter Iino et al. 2007. It was isolated from the alimentary canal of a Japanese corbicula clam (Corbicula japonica) collected on a seacoast in Shimane Prefecture in Japan. Phylogenetically, strain Sjm18-20T is closest to uncultured bacteria in digestive tracts, including the enriched cells thought to represent Oscillospira guilliermondii Chatton and Perard 1913. The isolated phylogenetic position and some distinct characteristics prompted us to determine the complete genome sequence. The 4,410,036 bp chromosome and the 60,586 bp plasmid were predicted to encode a total of 4,723 protein-coding genes. 相似文献
15.
Ajay Kumar Mishra Gregory Gimenez Jean-Christophe Lagier Catherine Robert Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,6(3):1-16
Alistipes senegalensis strain JC50T is the type strain of A. senegalensis sp. nov., a new species within the Alistipes genus. This strain, whose genome is described here, was isolated from the fecal flora of an asymptomatic patient. A. senegalensis is an anaerobic Gram-negative rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,017,609 bp long genome (1 chromosome, but no plasmid) contains 3,113 protein-coding and 50 RNA genes, including 5 rRNA genes. 相似文献
16.
Avat Arman Taherpour Mohammad Rizehbandi Fatemeh Jahanian Ehsan Naghibi Nosrat-Allah Mahdizadeh 《Journal of chemical biology》2016,9(1):19-29
Neurotransmitters are the compounds which allow the transmission of signals from one neuron to the next across synapses. They are the brain chemicals that communicate information throughout brain and body. Fullerenes are a family of carbonallotropes, molecules composed entirely of carbon, that take the forms of spheres, ellipsoids, and cylinders. Various empty carbon fullerenes (Cn) with different carbon atoms have been obtained and investigated. Topological indices have been successfully used to construct effective and useful mathematical methods to establish clear relationships between structural data and the physical properties of these materials. In this study, the number of carbon atoms in the fullerenes was used as an index to establish a relationship between the structures of neurotransmitters (NTs) acetylcholine (AC) 1, dopamine (DP) 2, serotonin (SE) 3, and epinephrine (EP) 4 as the well-known redox systems and fullerenes Cn (n = 60, 70, 76, 82, and 86) which create [NT].Cn; A-1 to A-5 up to D-1 to D-5. The relationship between the number of carbon atoms and the free energy of electron transfer (ΔGet(n); n = 1–4) is assessed using the Rehm-Weller equation for A-1 to A-5 up to D-1 to D-5 supramolecular [NT].Cn complexes. The calculations are presented for the four reduction potentials (Red.E1 to Red.E4) of fullerenes Cn. The results were used to calculate the four free energy values of electron transfer (ΔGet(1) to ΔGet(4)) of the supramolecular complexes A-1 to A-8 up to D-1 to D-8 for fullerenes C60 to C120. The first to fourth free activation energy values of electron transfer and the maximum wavelength of the electron transfers, ΔG#et(n) and λet (n = 1–4), respectively, were also calculated in this study for A-1 to A-8 up to D-1 to D-8 in accordance with the Marcus theory. 相似文献
17.
While a huge amount of information about biological literature can be obtained by searching the PubMed database, reading
through all the titles and abstracts resulting from such a search for useful information is inefficient. Text mining makes it possible
to increase this efficiency. Some websites use text mining to gather information from the PubMed database; however, they are
database-oriented, using pre-defined search keywords while lacking a query interface for user-defined search inputs. We present
the PubMed Abstract Reading Helper (PubstractHelper) website which combines text mining and reading assistance for an
efficient PubMed search. PubstractHelper can accept a maximum of ten groups of keywords, within each group containing up to
ten keywords. The principle behind the text-mining function of PubstractHelper is that keywords contained in the same sentence
are likely to be related. PubstractHelper highlights sentences with co-occurring keywords in different colors. The user can
download the PMID and the abstracts with color markings to be reviewed later. The PubstractHelper website can help users to
identify relevant publications based on the presence of related keywords, which should be a handy tool for their research.
Availability
http://bio.yungyun.com.tw/ATM/PubstractHelper.aspx and http://holab.med.ncku.edu.tw/ATM/PubstractHelper.aspx 相似文献18.
19.
20.
Sahare Kokcha Dhamodharan Ramasamy Jean-Christophe Lagier Catherine Robert Didier Raoult Pierre-Edouard Fournier 《Standards in genomic sciences》2012,7(2):233-245
Brevibacterium senegalense strain JC43T sp. nov. is the type strain of Brevibacterium senegalense sp. nov., a new species within the Brevibacterium genus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy Senegalese patient. B. senegalense is an aerobic rod-shaped Gram-positive bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,425,960 bp long genome (1 chromosome but no plasmid) contains 3,064 protein-coding and 49 RNA genes. 相似文献