14,617 research outputs found
Organelles, Genomes and Eukaryote Phylogeny: An Evolutionary Synthesis in the Age of Genomics
No full textSingle cell transcriptomics reveals specific RNA editing signatures in the human brain
No full textWhile RNA editing by A-to-I deamination is a requisite for neuronal function in humans, it is under investigated in single cells. Here we fill this gap by analysing RNA editing profiles of single cells from the brain cortex of living human subjects. We show that RNA editing levels per cell are bimodally distributed and distinguish between major brain cell types thus providing new insights into neuronal dynamics
Comparative genomics suggests limited variability and similar evolutionary patterns between major clades of SARS-Cov-2
No full textPhylogenomic analysis of SARS-CoV-2 as available from publicly available repositories suggests the presence of 3 prevalent groups of viral episomes (super-clades), which are mostly associated with outbreaks in distinct geographic locations (China, USA and Europe). While levels of genomic variability between SARS-CoV-2 isolates are limited, to our knowledge, it is not clear whether the observed patterns of variability in viral super-clades reflect ongoing adaptation of SARS-CoV-2, or merely genetic drift and founder effects. Here, we analyze more than 1100 complete, high quality SARS-CoV-2 genome sequences, and provide evidence for the absence of distinct evolutionary patterns/signatures in the genomes of the currently known major clades of SARS-CoV-2. Our analyses suggest that the presence of distinct viral episomes at different geographic locations are consistent with founder effects, coupled with the rapid spread of this novel virus. We observe that while cross species adaptation of the virus is associated with hypervariability of specific protein coding regions (including the RDB domain of the spike protein), the more variable genomic regions between extant SARS-CoV-2 episomes correspond with the 3’ and 5’ UTRs, suggesting that at present viral protein coding genes should not be subjected to different adaptive evolutionary pressures in different viral strains. Although this study can not be conclusive, we believe that the evidence presented here is strongly consistent with the notion that the biased geographic distribution of SARS-CoV-2 isolates should not be associated with adaptive evolution of this novel pathogen
Comparative genomics reveals early emergence and biased spatio-temporal distribution of SARS-CoV-2
No full textEffective systems for the analysis of molecular data are fundamental for monitoring the spread of infectious diseases and studying pathogen evolution. The rapid identification of emerging viral strains, and/or genetic variants potentially associated with novel phenotypic features is one of the most important objectives of genomic surveillance of human pathogens and represents one of the first lines of defense for the control of their spread. During the COVID 19 pandemic, several taxonomic frameworks have been proposed for the classification of SARS-Cov-2 isolates. These systems, which are typically based on phylogenetic approaches, represent essential tools for epidemiological studies as well as contributing to the study of the origin of the outbreak. Here, we propose an alternative, reproducible, and transparent phenetic method to study changes in SARS-CoV-2 genomic diversity over time. We suggest that our approach can complement other systems and facilitate the identification of biologically relevant variants in the viral genome. To demonstrate the validity of our approach, we present comparative genomic analyses of more than 175,000 genomes. Our method delineates 22 distinct SARS-CoV-2 haplogroups, which, based on the distribution of high-frequency genetic variants, fall into four major macrohaplogroups. We highlight biased spatiotemporal distributions of SARS-CoV-2 genetic profiles and show that seven of the 22 haplogroups (and of all of the four haplogroup clusters) showed a broad geographic distribution within China by the time the outbreak was widely recognized—suggesting early emergence and widespread cryptic circulation of the virus well before its isolation in January 2020. General patterns of genomic variability are remarkably similar within all major SARS-CoV-2 haplogroups, with UTRs consistently exhibiting the greatest variability, with s2m, a conserved secondary structure element of unknown function in the 30 -UTR of the viral genome showing evidence of a functional shift. Although several polymorphic sites that are specific to one or more haplogroups were predicted to be under positive or negative selection, overall our analyses suggest that the emergence of novel types is unlikely to be driven by convergent evolution and independent fixation of advantageous substitutions, or by selection of recombined strains. In the absence of extensive clinical metadata for most available genome sequences, and in the context of extensive geographic and temporal biases in the sampling, many questions regarding the evolution and clinical characteristics of SARS-CoV-2 isolates remain open. However, our data indicate that the approach outlined here can be usefully employed in the identification of candidate SARS-CoV-2 genetic variants of clinical and epidemiological importance
Newton's Laws
No full textAuthored and curated by David P. Stern, this series of web pages, part of "From Stargazers to Starships," describes Newton's three laws of motion and the two concepts on which they are based, force and inertia. The author breaks down the page in this fashion: the concept of force, motion against outside resistance, and motion with significant resistance. The author also provides additional links for further study on the life of Issac Newton. A lesson plan for instructors is also provided
FIGURE 6 in " Same-same, but different ": an unusual new species of the Limnonectes kuhlii Complex from West Sumatra (Anura: Dicroglossidae)
No full textFIGURE 6. Distribution of samples of Limnonectes siskdagu used in this study. Holotype indicated with star. Open square represents specimens collected from Batu Layang and identified as "Lineage 2" in McLeod (2010).Published as part of Mcleod, David S., Horner, Stephani J., Husted, Colin, Barley, Anthony & Iskandar, Djoko, 2011, " Same-same, but different ": an unusual new species of the Limnonectes kuhlii Complex from West Sumatra (Anura: Dicroglossidae), pp. 52-64 in Zootaxa 2883 on page 61, DOI: 10.5281/zenodo.20160
C.C. Slaughter's Lazy S Ranch in Cochran and Hockley counties, 1898-1921.
No full textLikely added to or created for the author's thesis: "A Cattle Kingdom on Texas' Last Frontier: C. C. Slaughter's Lazy S Ranch" (Texas Tech University, 1970).Scale approximately 1:337,920 (W 102°59'24"--W 102°18'53"/N 33°50'54"--N 33°24'07")The map illustrates the 250,000-acre holdings of C.C. Slaughter, known as the "Cattle King of Texas," before the ranch's liquidation and subdivision beginning in 1921 (following his death in 1919)
Dr. David Salisbury – Faculty Author Interview
No full textDavid Salisbury, Assistant Professor of Geography and the Environment, discusses his recent article, “Fronteras Vivas or Dead Ends? The Impact of Military Settlement Projects in the Amazon Borderlands”, in the Journal of Latin American Geography. This article describes a case study in the Peruvian Amazon which explores the natural resource management, household economics, and political geography of a borderland military base and associated settlement
Remembering BC\u27s 1983 Solidarity Uprising — with David Spaner
No full textBio: David Spaner has worked as a feature writer, movie critic, reporter, and editor for numerous newspapers and magazines. David\u27s also been a cultural/political organizer (Yippie, manager of the punk band The Subhumans). He is the author of Dreaming in the Rain and Shoot It! Hollywood, Inc. and the Rising of Independent Film.In 2021, Spaner published a behind-the-scenes book about the Solidarity resistance movement, Solidarity: Canada\u27s Unknown Revolution of 1983 (Ronsdale 2021) documenting the event using intimate storytelling and melding cultural and rebel politics to provide insight into the conflicts that are still with us. It was the largest political protest in the province\u27s history and threatened to end in an all-out general strike. Resources: Solidarity: Canada\u27s Unknown Revolution of 1983 (Ronsdale 2021): https://ronsdalepress.com/all-books/solidarity/SHOOT IT! Hollywood Inc. and the Rising of Independent Film (Arsenal Pulp Press 2012): https://arsenalpulp.com/Books/S/Shoot-ItDreaming in the Rain: How Vancouver Became Hollywood North by Northwest (Arsenal Pulp Press 2002): https://arsenalpulp.com/Books/D/Dreaming-in-the-Rai
De novo assembly of the transcriptome of the non-model plant Streptocarpus rexii employing a novel heuristic to recover locus-specific transcript clusters.
No full textDe novo transcriptome characterization from Next Generation Sequencing data has become an important approach in the study of non-model plants. Despite notable advances in the assembly of short reads, the clustering of transcripts into unigene-like (locus-specific) clusters remains a somewhat neglected subject. Indeed, closely related paralogous transcripts are often merged into single clusters by current approaches. Here, a novel heuristic method for locus-specific clustering is compared to that implemented in the de novo assembler Oases, using the same initial transcript collections, derived from Arabidopsis thaliana and the developmental model Streptocarpus rexii. We show that the proposed approach improves cluster specificity in the A. thaliana dataset for which the reference genome is available. Furthermore, for the S. rexii data our filtered transcript collection matches a larger number of distinct annotated loci in reference genomes than the Oases set, while containing a reduced overall number of loci. A detailed discussion of advantages and limitations of our approach in processing de novo transcriptome reconstructions is presented. The proposed method should be widely applicable to other organisms, irrespective of the transcript assembly method employed. The S. rexii transcriptome is available as a sophisticated and augmented publicly available online database
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