The microRNA Registry Griffiths-Jones, Sam
Nucleic acids research,
01/2004, Letnik:
32, Številka:
suppl-1
Journal Article
Recenzirano
Odprti dostop
The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web ...interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for download. Release 2.0 of the database contains 506 miRNA entries from six organisms.
miRBase is the primary online repository for all microRNA sequences and annotation. The current release (miRBase 16) contains over 15 000 microRNA gene loci in over 140 species, and over 17 000 ...distinct mature microRNA sequences. Deep-sequencing technologies have delivered a sharp rise in the rate of novel microRNA discovery. We have mapped reads from short RNA deep-sequencing experiments to microRNAs in miRBase and developed web interfaces to view these mappings. The user can view all read data associated with a given microRNA annotation, filter reads by experiment and count, and search for microRNAs by tissue- and stage-specific expression. These data can be used as a proxy for relative expression levels of microRNA sequences, provide detailed evidence for microRNA annotations and alternative isoforms of mature microRNAs, and allow us to revisit previous annotations. miRBase is available online at: http://www.mirbase.org/.
Perception relies on the integration of sensory information and prior expectations. Here we show that selective neurodegeneration of human frontal speech regions results in delayed reconciliation of ...predictions in temporal cortex. These temporal regions were not atrophic, displayed normal evoked magnetic and electrical power, and preserved neural sensitivity to manipulations of sensory detail. Frontal neurodegeneration does not prevent the perceptual effects of contextual information; instead, prior expectations are applied inflexibly. The precision of predictions correlates with beta power, in line with theoretical models of the neural instantiation of predictive coding. Fronto-temporal interactions are enhanced while participants reconcile prior predictions with degraded sensory signals. Excessively precise predictions can explain several challenging phenomena in frontal aphasias, including agrammatism and subjective difficulties with speech perception. This work demonstrates that higher-level frontal mechanisms for cognitive and behavioural flexibility make a causal functional contribution to the hierarchical generative models underlying speech perception.
Rfam is a comprehensive collection of non-coding RNA (ncRNA) families, represented by multiple sequence alignments and profile stochastic context-free grammars. Rfam aims to facilitate the ...identification and classification of new members of known sequence families, and distributes annotation of ncRNAs in over 200 complete genome sequences. The data provide the first glimpses of conservation of multiple ncRNA families across a wide taxonomic range. A small number of large families are essential in all three kingdoms of life, with large numbers of smaller families specific to certain taxa. Recent improvements in the database are discussed, together with challenges for the future. Rfam is available on the Web at http://www.sanger.ac.uk/Software/Rfam/ and http://rfam.wustl.edu/.
Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and ...in the US at http://rfam.wustl.edu/. These websites allow the user to search a query sequence against a library of covariance models, and view multiple sequence alignments and family annotation. The database can also be downloaded in flatfile form and searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.
Artificial tree hollows (e.g., nest‐boxes) are commonly deployed to mitigate the loss of mature trees within human‐disturbed landscapes. Their effectiveness as a habitat resource, and thus ...conservation management tool, is strongly influenced by the suitability of internal microclimate conditions. In south‐eastern Australia, spout hollows are a nesting resource used by a diverse community of vertebrate species. We tested the suitability of a novel nest box design (spout boxes) that mimicked the physical characteristics of spout hollows. We monitored the occupancy (n = 193) and internal microclimate (n = 131) of natural hollows and spout boxes within a woodland where natural tree hollows were once abundant. Both natural hollows and spout boxes were occupied and used for breeding by birds and mammals. Natural hollows had consistently higher humidity, and thermal maxima and minima were buffered, when compared with spout boxes. These differences were largely explained by wall thickness. Spout boxes displayed even more extreme temperature variation and lower humidity when not shaded. While more extreme microclimate conditions did not prevent usage, tolerable thresholds for hollow‐dependent species may soon be exceeded under current climate change projections. Managers need to carefully consider nest box design and positioning to ensure the suitability of these supplementary resources for conservation purposes.
The reference sequence for each human chromosome provides the framework for understanding genome function, variation and evolution. Here we report the finished sequence and biological annotation of ...human chromosome 1. Chromosome 1 is gene-dense, with 3,141 genes and 991 pseudogenes, and many coding sequences overlap. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. Fine-scale recombination occurs in hotspots of varying intensity along the sequence, and is enriched near genes. These and other studies of human biology and disease encoded within chromosome 1 are made possible with the highly accurate annotated sequence, as part of the completed set of chromosome sequences that comprise the reference human genome.
Three albino skate specimens (Rajidae) were captured from the North Sea and English Channel between 2008 and 2011. Using DNA barcoding (COI gene) and morphometric analyses, species were identified as ...a spotted ray Raja montagui, a blonde ray Raja brachyura and a thornback ray Raja clavata. This finding represents the first record of full albinism (a lack of skin and retinal pigmentation) in rajid species.
It is unknown whether kinematic alignment (KA) objectively improves knee balance in total knee arthroplasty (TKA), despite this being the biomechanical rationale for its use. This study aimed to ...determine whether restoring the constitutional alignment using a restrictive KA protocol resulted in better quantitative knee balance than mechanical alignment (MA).
We conducted a randomized superiority trial comparing patients undergoing TKA assigned to KA within a restrictive safe zone or MA. Optimal knee balance was defined as an intercompartmental pressure difference (ICPD) of 15 psi or less using a pressure sensor. The primary endpoint was the mean intraoperative ICPD at 10° of flexion prior to knee balancing. Secondary outcomes included balance at 45° and 90°, requirements for balancing procedures, and presence of tibiofemoral lift-off.
A total of 63 patients (70 knees) were randomized to KA and 62 patients (68 knees) to MA. Mean ICPD at 10° flexion in the KA group was 11.7 psi (SD 13.1) compared with 32.0 psi in the MA group (SD 28.9), with a mean difference in ICPD between KA and MA of 20.3 psi (p < 0.001). Mean ICPD in the KA group was significantly lower than in the MA group at 45° and 90°, respectively (25.2 psi MA vs 14.8 psi KA, p = 0.004; 19.1 psi MA vs 11.7 psi KA, p < 0.002, respectively). Overall, participants in the KA group were more likely to achieve optimal knee balance (80% vs 35%; p < 0.001). Bone recuts to achieve knee balance were more likely to be required in the MA group (49% vs 9%; p < 0.001). More participants in the MA group had tibiofemoral lift-off (43% vs 13%; p < 0.001).
This study provides persuasive evidence that restoring the constitutional alignment with KA in TKA results in a statistically significant improvement in quantitative knee balance, and further supports this technique as a viable alternative to MA. Cite this article:
2020;102-B(1):117-124.
PDF
