scholarly journals Comparative analysis of annotation pipelines using the first Japanese white-eye (Zosterops japonicus) genome

2021 ◽  
Author(s):  
Madhvi Venkatraman ◽  
Robert C Fleischer ◽  
Mirian T N Tsuchiya
Keyword(s):  
Comparative Analysis ◽  
Genome Annotation ◽  
Invasion Success ◽  
Rna Seq ◽  
Model Species ◽  
Invasive Range ◽  
Future Studies ◽  
Zosterops Japonicus ◽  
Land Bird ◽  
Annotation Quality

Abstract Introduced into Hawaii in the early 1900s, the Japanese white-eye or warbling white-eye (Zosterops japonicus) is now the most abundant land bird in the archipelago. Here, we present the first Z. japonicus genome, sequenced from an individual in its invasive range. This genome provides an important resource for future studies in invasion genomics. We annotated the genome using two workflows – standalone AUGUSTUS and BRAKER2. We found that AUGUSTUS was more conservative with gene predictions when compared to BRAKER2. The final number of annotated gene models was similar between the two workflows, but standalone AUGUSTUS had over 70% of gene predictions with Blast2GO annotations versus under 30% using BRAKER2. Additionally, we tested whether using RNA-seq data from 47 samples had a significant impact on annotation quality when compared to data from a single sample, as generating RNA-seq data for genome annotation can be expensive and requires well preserved tissue. We found that more data did not significantly change the number of annotated genes using AUGUSTUS but using BRAKER2 the number increased substantially. The results presented here will aid researchers in annotating draft genomes of non-model species as well as those studying invasion success.

A Comparative Analysis of Blind and Sighted Children's Communication Skills

1984 ◽  
Vol 78 (1) ◽  
pp. 1-5 ◽  
Author(s):  
Maryon M. Matsuda
Keyword(s):  
Comparative Analysis ◽  
Communication Skills ◽  
Future Studies

This study compared the development of communication skills in blind and sighted children. The specific skills investigated were the abilities to detect the communication-relevant characteristics of listeners and to construct messages adapted to those characteristics. The participants were 33 blind and 33 sighted children who ranged in age from 5 to 12 ½ and were matched for age, sex, and IQ. No significant differences were found between the two groups on development of these communication skills. However, the author discusses two important factors that should be investigated in future studies.

scholarly journals Plasma IL-6 levels following corticosteroid therapy as an indicator of ICU length of stay in critically ill COVID-19 patients

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Samir Awasthi ◽  
Tyler Wagner ◽  
A. J. Venkatakrishnan ◽  
Arjun Puranik ◽  
Matthew Hurchik ◽  
...  
Keyword(s):  
Distress Syndrome ◽  
Cell Types ◽  
Specific Cell ◽  
Cytokine Release ◽  
Cytokine Release Syndrome ◽  
Rna Seq ◽  
Future Studies ◽  
Icu Length Of Stay ◽  
Potential Association ◽  
Clinical Trial Results

AbstractIntensive care unit (ICU) admissions and mortality in severe COVID-19 patients are driven by “cytokine storms” and acute respiratory distress syndrome (ARDS). Interim clinical trial results suggest that the corticosteroid dexamethasone displays better 28-day survival in severe COVID-19 patients requiring ventilation or oxygen. In this study, 10 out of 16 patients (62.5%) that had an average plasma IL-6 value over 10 pg/mL post administration of corticosteroids also had worse outcomes (i.e., ICU stay >15 days or death), compared to 8 out of 41 patients (19.5%) who did not receive corticosteroids (p-value = 0.0024). Given this potential association between post-corticosteroid IL-6 levels and COVID-19 severity, we hypothesized that the glucocorticoid receptor (GR or NR3C1) may be coupled to IL-6 expression in specific cell types that govern cytokine release syndrome (CRS). Examining single-cell RNA-seq data from BALF of severe COVID-19 patients and nearly 2 million cells from a pan-tissue scan shows that alveolar macrophages, smooth muscle cells, and endothelial cells co-express NR3C1 and IL-6, motivating future studies on the links between the regulation of NR3C1 function and IL-6 levels.

scholarly journals A web server for comparative analysis of single-cell RNA-seq data

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Amir Alavi ◽  
Matthew Ruffalo ◽  
Aiyappa Parvangada ◽  
Zhilin Huang ◽  
Ziv Bar-Joseph
Keyword(s):  
Comparative Analysis ◽  
Single Cell ◽  
Web Server ◽  
Rna Seq

scholarly journals Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

2020 ◽  
Author(s):  
Viacheslav Mylka ◽  
Jeroen Aerts ◽  
Irina Matetovici ◽  
Suresh Poovathingal ◽  
Niels Vandamme ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Comparative Analysis ◽  
Single Cell ◽  
Cell Lines ◽  
Clinical Studies ◽  
Clinical Samples ◽  
Rna Seq ◽  
Batch Effects ◽  
Single Cell Sequencing ◽  
Single Nucleus

ABSTRACTMultiplexing of samples in single-cell RNA-seq studies allows significant reduction of experimental costs, straightforward identification of doublets, increased cell throughput, and reduction of sample-specific batch effects. Recently published multiplexing techniques using oligo-conjugated antibodies or - lipids allow barcoding sample-specific cells, a process called ‘hashing’. Here, we compare the hashing performance of TotalSeq-A and -C antibodies, custom synthesized lipids and MULTI-seq lipid hashes in four cell lines, both for single-cell RNA-seq and single-nucleus RNA-seq. Hashing efficiency was evaluated using the intrinsic genetic variation of the cell lines. Benchmarking of different hashing strategies and computational pipelines indicates that correct demultiplexing can be achieved with both lipid- and antibody-hashed human cells and nuclei, with MULTISeqDemux as the preferred demultiplexing function and antibody-based hashing as the most efficient protocol on cells. Antibody hashing was further evaluated on clinical samples using PBMCs from healthy and SARS-CoV-2 infected patients, where we demonstrate a more affordable approach for large single-cell sequencing clinical studies, while simultaneously reducing batch effects.

scholarly journals Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis

2021 ◽  
Author(s):  
Dennis A Sun ◽  
Nipam H Patel
Keyword(s):  
Gene Expression ◽  
Genome Annotation ◽  
Time Course ◽  
Regulatory Elements ◽  
Rna Seq ◽  
Genome Wide ◽  
Long Read ◽  
Amphipod Crustacean ◽  
Accessible Chromatin

AbstractEmerging research organisms enable the study of biology that cannot be addressed using classical “model” organisms. The development of novel data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-Seq, an improved form of the Assay for Transposase-Accessible Chromatin coupled with next-generation sequencing (ATAC-Seq), to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis, and limb development. In addition, we use short- and long-read RNA-Seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We leverage a variety of bioinformatic tools to discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions, and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach, including distal regulatory elements. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.Primary Findings-Omni-ATAC-Seq identifies cis-regulatory elements genome-wide during crustacean embryogenesis-Combined short- and long-read RNA-Seq improves the Parhyale genome annotation-ImpulseDE2 analysis identifies dynamically regulated candidate regulatory elements-NucleoATAC and HINT-ATAC enable inference of nucleosome occupancy and transcription factor binding-Fuzzy clustering reveals peaks with distinct accessibility and chromatin dynamics-Integration of accessibility and gene expression reveals possible enhancers and repressors-Omni-ATAC can identify known and novel regulatory elements

A Comparative Analysis of the Similar Word-formation Processes in English and Arabic

2020 ◽  
Vol 23 (4) ◽  
pp. 56-75
Author(s):  
Tareq Abdo Abdullah Al-Hamidi ◽  
Milana Abbasova ◽  
Azad Mammadov
Keyword(s):  
Comparative Analysis ◽  
Reference Material ◽  
Word Formation ◽  
Formation Processes ◽  
Future Studies ◽  
Similar Word ◽  
Arabic Linguistics ◽  
Research Findings ◽  
Linguistic Structures ◽  
Meta Theory

This paper sets out on a comparative analysis of similar word-formation processes in English and Arabic. In doing so, it hopes to emerge and serve as subsequent and reliable, albeit partial, reference material for English and Arabic linguistics, especially in reference to linguistic structures. The framework herein for the study and analysis of word-formation processes in both languages may also be applied in future studies and other genres, corpora, and texts. This study enriches the research findings and meta-theory in the field of linguistics, contributing to the current linguistic intellectualism trends. The specific processes discussed are acronyms, antonomasia, backformation, blending, borrowing, compounding, and derivation.

scholarly journals Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns

Open Biology ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 200149 ◽  
Author(s):  
Valerie Wood ◽  
Seth Carbon ◽  
Midori A. Harris ◽  
Antonia Lock ◽  
Stacia R. Engel ◽  
...  
Keyword(s):  
Quality Control ◽  
Gene Ontology ◽  
Biological Processes ◽  
Gene Products ◽  
Model Species ◽  
Ontology Term ◽  
Protein Coding ◽  
Ontology Structure ◽  
Exclusive Processes ◽  
Annotation Quality

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

scholarly journals Comparative Analysis of Apicoplast-Targeted Protein Extension Lengths in Apicomplexan Parasites

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Alexandr V. Seliverstov ◽  
Oleg A. Zverkov ◽  
Svetlana N. Istomina ◽  
Sergey A. Pirogov ◽  
Philip S. Kitsis
Keyword(s):  
Plasmodium Falciparum ◽  
Comparative Analysis ◽  
Protein Translocation ◽  
Neospora Caninum ◽  
Signal Peptides ◽  
Model Species ◽  
Apicomplexan Parasites ◽  
Important Region ◽  
Focus On Results ◽  
Species Comparisons

In general, the mechanism of protein translocation through the apicoplast membrane requires a specific extension of a functionally important region of the apicoplast-targeted proteins. The corresponding signal peptides were detected in many apicomplexans but not in the majority of apicoplast-targeted proteins inToxoplasma gondii. InT. gondiisignal peptides are either much diverged or their extension region is processed, which in either case makes the situation different from other studied apicomplexans. We propose a statistic method to compare extensions of the functionally important regions of apicoplast-targeted proteins. More specifically, we provide a comparison of extension lengths of orthologous apicoplast-targeted proteins in apicomplexan parasites. We focus on results obtained for the model speciesT. gondii,Neospora caninum, andPlasmodium falciparum. With our method, cross species comparisons demonstrate that, in average, apicoplast-targeted protein extensions inT. gondiiare 1.5-fold longer than inN. caninumand 2-fold longer than inP. falciparum. Extensions inP. falciparumless than 87 residues in size are longer than the corresponding extensions inN. caninumand, reversely, are shorter if they exceed 88 residues.

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