Transcription goes digital.
Ontology highlight
ABSTRACT:
SUBMITTER: Lionnet T
PROVIDER: S-EPMC3321162 | biostudies-other | 2012 Apr
REPOSITORIES: biostudies-other
Similar Datasets
Project description: Not available
| S-EPMC1602038 | biostudies-literature
Project description:BackgroundGlobal Biodiversity Information Facility (GBIF) has uneven data coverage across taxonomic, spatial and temporal dimensions. Temporal imbalances in the data coverage are particularly dramatic. Thus, 188.3M GBIF records were made in 2020, more than the whole lot of the currently available pre-1986 electronic data. This underscores the importance of reliable and precise biodiversity spatial data collected in early times. Biological collections certainly play a key role in our knowledge of biodiversity in the past. However, digitisation of historical literature is underway, being a modern trend in biodiversity data mining. The grid dataset for the flora of Vladimir Oblast, Russia, includes many historical records borrowed from the "Flora des Gouvernements Wladimir" by Alexander F. Fleroff (also known as Flerov or Flerow). Intensive study of Fleroff's collections and field surveys exactly in the same localities where he worked, showed that the quality of his data is superb. Species lists collected across hundreds of localities form a unique source of reliable information on the floristic diversity of Vladimir Oblast and adjacent areas for the period from 1894 to 1901. Since the grid dataset holds generalised data, we made precise georeferencing of Fleroff's literature records and published them in the form of a GBIF-mediated dataset.New informationA dataset, based on "Flora des Gouvernements Wladimir. I. Pflanzengeographische Beschreibung des Gouvernements Wladimir" by Fleroff (1902), includes 8,889 records of 654 taxa (mainly species) from 366 localities. The majority of records originate from Vladimir Oblast (4,611 records of 534 taxa from 195 localities) and Yaroslavl Oblast (2,013 records of 409 taxa from 66 localities), but also from Nizhny Novgorod Oblast (942 records), Ivanovo Oblast (667 records) and Moscow Oblast (656 records). The leading second-level administrative units by the number of records are Pereslavsky District (2,013 records), Aleksandrovsky District (1,318 records) and Sergievo-Posadsky District (599 records). Georeferencing was carried out, based on the expert knowledge of the area, analysis of modern satellite images and old topographic maps. For 2,460 records, the georeferencing accuracy is 1,000 m or less (28%), whereas for 6,070 records it is 2,000 m or less (68%). The mean accuracy of records of the entire dataset is 2,447 m. That accuracy is unattainable for most herbarium collections of the late 19th century. Some localities of rare plants discovered by Fleroff and included into the dataset were completely lost in the 20th century due to either peat mining or development of urban areas.
| S-EPMC8551138 | biostudies-literature
Project description:Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest.
| S-EPMC5315695 | biostudies-literature
Project description:Laboratory cultivation of viruses is critical for determining requirements for viral replication, developing detection methods, identifying drug targets, and developing antivirals. Several viruses have a history of recalcitrance towards robust replication in laboratory cell lines, including human noroviruses and hepatitis B and C viruses. These viruses have tropism for tissue components of the enterohepatic circulation system: the intestine and liver, respectively. The purpose of this review is to discuss how key enterohepatic signaling molecules, bile acids (BAs), and BA receptors are involved in the replication of these viruses and how manipulation of these factors was useful in the development and/or optimization of culture systems for these viruses. BAs have replication-promoting activities through several key mechanisms: (1) affecting cellular uptake, membrane lipid composition, and endocytic acidification; (2) directly interacting with viral capsids to influence binding to cells; and (3) modulating the innate immune response. Additionally, expression of the Na+-taurocholate cotransporting polypeptide BA receptor in continuous liver cell lines is critical for hepatitis B virus entry and robust replication in laboratory culture. Viruses are capable of hijacking normal cellular functions, and understanding the role of BAs and BA receptors, components of the enterohepatic system, is valuable for expanding our knowledge on the mechanisms of norovirus and hepatitis B and C virus replication.
| S-EPMC8227374 | biostudies-literature
Project description:Positive transcription elongation factor b (P-TEFb), which comprises cyclin-dependent kinase 9 (CDK9) kinase and cyclin T subunits, is an essential kinase complex in human cells. Phosphorylation of the negative elongation factors by P-TEFb is required for productive elongation of transcription of protein-coding genes by RNA polymerase II (pol II). In addition, P-TEFb-mediated phosphorylation of the carboxyl-terminal domain (CTD) of the largest subunit of pol II mediates the recruitment of transcription and RNA processing factors during the transcription cycle. CDK9 also phosphorylates p53, a tumor suppressor that plays a central role in cellular responses to a range of stress factors. Many viral factors affect transcription by recruiting or modulating the activity of CDK9. In this review, we will focus on how the function of CDK9 is regulated by viral gene products. The central role of CDK9 in viral life cycles suggests that drugs targeting the interaction between viral products and P-TEFb could be effective anti-viral agents.
| S-EPMC4863834 | biostudies-literature
Project description:MOTIVATION:The use of experimental information has been demonstrated to increase the success rate of computational macromolecular docking. Many methods use information to post-filter the simulation output while others drive the simulation based on experimental restraints, which can become problematic for more complex scenarios such as multiple binding interfaces. RESULTS:We present a novel method for including interface information into protein docking simulations within the LightDock framework. Prior to the simulation, irrelevant regions from the receptor are excluded for sampling (filter of initial swarms) and initial ligand poses are pre-oriented based on ligand input information. We demonstrate the applicability of this approach on the new 55 cases of the Protein-Protein Docking Benchmark 5, using different amounts of information. Even with incomplete or incorrect information, a significant improvement in performance is obtained compared to blind ab initio docking. AVAILABILITY AND IMPLEMENTATION:The software is supported and freely available from https://github.com/brianjimenez/lightdock and analysis data from https://github.com/brianjimenez/lightdock_bm5. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.
| S-EPMC7005597 | biostudies-literature
Project description:BackgroundInsertion sequences (ISs) are small, mobile DNA entities able to expand in prokaryotic genomes and trigger important rearrangements. To understand their role in evolution, accurate IS taxonomy is essential. The IS4 family is composed of approximately 70 elements and, like some other families, displays extremely elevated levels of internal divergence impeding its classification. The increasing availability of complete genome sequences provides a valuable source for the discovery of additional IS4 elements. In this study, this genomic database was used to update the structural and functional definition of the IS4 family.ResultsA total of 227 IS4-related sequences were collected among more than 500 sequenced bacterial and archaeal genomes, representing more than a three fold increase of the initial inventory. A clear division into seven coherent subgroups was discovered as well as three emerging families, which displayed distinct structural and functional properties. The IS4 family was sporadically present in 17 % of analyzed genomes, with most of them displaying single or a small number of IS4 elements. Significant expansions were detected only in some pathogens as well as among certain extremophiles, suggesting the probable involvement of some elements in bacterial and archaeal adaptation and/or evolution. Finally, it should be noted that some IS4 subgroups and two emerging families occurred preferentially in specific phyla or exclusively inside a specific genus.ConclusionThe present taxonomic update of IS4 and emerging families will facilitate the classification of future elements as they arise from ongoing genome sequencing. Their narrow genomic impact and the existence of both IS-poor and IS-rich thriving prokaryotes suggested that these families, and probably ISs in general, are occasionally used as a tool for genome flexibility and evolution, rather than just representing self sustaining DNA entities.
| S-EPMC2266710 | biostudies-literature
Project description:Noninvasive prenatal genetic testing is becoming available worldwide--particularly in low- and middle-income countries--but practical and ethical challenges must be overcome.
| S-EPMC4112725 | biostudies-literature
Project description:Genetic abnormalities are present in all tumor types, although the frequency and type can vary. Chromosome abnormalities include highly aberrant structures, particularly chromothriptic chromosomes. The generation of massive sequencing data has illuminated the scope of the mutational burden in cancer genomes, identifying patterns of mutations (mutation signatures), which have the potential to shed light on the relatedness and etiologies of cancers and impact therapy response. Some mutation patterns are clearly attributable to disruptions in pathways that maintain genomic integrity. Here we review recent advances in our understanding of genetic changes occurring in cancers and the roles of genome maintenance pathways.
| S-EPMC4966655 | biostudies-literature
Project description:Mechanosensitive ion channels initiate sensory signals by converting mechanical information into electrochemical signals. In this issue of Neuron (Zhao et al., 2016), a data-rich structure-function study on mammalian mechanosensitive Piezo channels reveals a modular protein architecture that includes a central pore module surrounded by a force-sensing module.
| S-EPMC6341990 | biostudies-literature