860 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
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
Horner Syndrome from a Pediatric Otolaryngology Perspective.
No full text© The Author(s) 2019. Introduction: Horner syndrome is described as the clinical triad of miosis, ptosis, and anhidrosis. In pediatric patients the condition may be congenital or acquired from neoplastic, infectious or traumatic conditions, including birth trauma. Most cases of pediatric Horner syndrome present first to a pediatric ophthalmologist however since the neural pathways involve the cervical sympathetic chain otolaryngologists should understand the pathophysiology to avoid delay in management of potentially malignant cases. Objectives: To aid otolaryngologists in recognizing and managing pediatric Horner syndrome by describing 3 unique cases from malignant, traumatic and/or congenital causes. Methods: Case report of 3 pediatric patients with Horner syndrome presenting to our pediatric otolaryngology department. Results: Case #1 is 5-month-old female with ptosis and a left level II 1.5 cm neck mass. Magnetic resonance imaging showed the mass displacing the common carotid artery and excisional biopsy revealed a poorly differentiated neuroblastoma. Case #2 is a 9-year-old female with anisocoria appearing after suffering a severe playground injury. Case #3 is a 3-year-old-male who developed ptosis and anisocoria following re-excision of a recurrent cervical lymphatic malformation. Conclusion: Pediatric Horner syndrome may be a benign finding that is easily overlooked but may reflect a serious underlying condition. Otolaryngologists should be aware of the pathophysiology and differential diagnosis, including malignant causes, to appropriately manage patients
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
CorGAT : a tool for the functional annotation of SARS-CoV-2 genomes
No full textWhile over 150 thousand genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
No full textAccurate and timely monitoring of the evolution of SARS-CoV-2 is crucial for identifying and tracking potentially more transmissible/virulent viral variants, and implement mitigation strategies to limit their spread. Here we introduce HaploCoV, a novel software framework that enables the exploration of SARS-CoV-2 genomic diversity through space and time, to identify novel emerging viral variants and prioritize variants of potential epidemiological interest in a rapid and unsupervised manner. HaploCoV can integrate with any classification/nomenclature and incorporates an effective scoring system for the prioritization of SARS-CoV-2 variants. By performing retrospective analyses of more than 11.5 M genome sequences we show that HaploCoV demonstrates high levels of accuracy and reproducibility and identifies the large majority of epidemiologically relevant viral variants - as flagged by international health authorities - automatically and with rapid turn-around times.Our results highlight the importance of the application of strategies based on the systematic analysis and integration of regional data for rapid identification of novel, emerging variants of SARS-CoV-2. We believe that the approach outlined in this study will contribute to relevant advances to current and future genomic surveillance methods
Horner's Syndrome as a rare complication of tube thoracostomy: Case reports and review of literature
No full textHorner's Syndrome (HS), caused by the interruption of the oculosympathetic pathway, is a rare yet morbid complication of tube thoracostomy. However, literature regarding HS secondary to tube thoracostomy is limited to case reports, with little comprehensive information available. We report two cases and review all cases from the published literature to assess the outcome of this complication. HS secondary to tube thoracostomy leaves sequelae in 45.8% of patients. Immediate removal or repositioning of the tube does not affect prognosis. Therefore, precautions must be taken to avoid this complication. (c) 2013 Elsevier Inc. All rights reserved
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