scholarly journals Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11447
Author(s):  
Akbar Adjie Pratama ◽  
Benjamin Bolduc ◽  
Ahmed A. Zayed ◽  
Zhi-Ping Zhong ◽  
Jiarong Guo ◽  
...  
Keyword(s):  
In Silico ◽  
Viral Metagenomics ◽  
Extensive Literature ◽  
Virus Identification ◽  
Viral Genomes ◽  
Network Analytics ◽  
Taxonomic Assignments ◽  
The Cost ◽  
Dsdna Viruses ◽  
Auxiliary Metabolic Genes

Background Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs). Results The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes. Conclusion Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses ‘hidden’ in diverse sequence datasets.

A generalized fuzzy cost efficiency model

2020 ◽  
Vol 54 (6) ◽  
pp. 1775-1791
Author(s):  
Nazila Aghayi ◽  
Samira Salehpour
Keyword(s):  
Cost Efficiency ◽  
Minimum Cost ◽  
Extensive Literature ◽  
Data Envelopment ◽  
Fuzzy Environment ◽  
Decision Making Unit ◽  
Production Possibility Set ◽  
Fuzzy Cost ◽  
The Cost ◽  
Generalized Cost

The concept of cost efficiency has become tremendously popular in data envelopment analysis (DEA) as it serves to assess a decision-making unit (DMU) in terms of producing minimum-cost outputs. A large variety of precise and imprecise models have been put forward to measure cost efficiency for the DMUs which have a role in constructing the production possibility set; yet, there’s not an extensive literature on the cost efficiency (CE) measurement for sample DMUs (SDMUs). In an effort to remedy the shortcomings of current models, herein is introduced a generalized cost efficiency model that is capable of operating in a fuzzy environment-involving different types of fuzzy numbers-while preserving the Farrell’s decomposition of cost efficiency. Moreover, to the best of our knowledge, the present paper is the first to measure cost efficiency by using vectors. Ultimately, a useful example is provided to confirm the applicability of the proposed methods.

A standardized terminology of spines in the order Siluriformes (Actinopterygii: Ostariophysi)

2021 ◽  
Author(s):  
Gustavo A Ballen ◽  
Mario C C De Pinna
Keyword(s):  
Comparative Anatomy ◽  
Appendicular Skeleton ◽  
Extensive Literature ◽  
Direct Examination ◽  
Dorsal Fin ◽  
Anatomical Nomenclature ◽  
Standardized Terminology ◽  
The Cost ◽  
First Time ◽  
Terminology System

Abstract A standardized terminology for the anatomy of pectoral- and dorsal-fin spines in the order Siluriformes is proposed based on an extensive literature review and direct examination of representatives of the order. The adult anatomy of the spines is described in detail. Terminology of various spine parts are reviewed and standardized, each term provided with a synonymic list organizing previous usage. Most of the structures treated have been recorded and named in the literature, but some are herein named for the first time. A quantitative approach is proposed for orienting decisions on name usage, aiming at minimizing differences between the terminology proposed and the vast amount of pre-existing literature, herein called the cost function. It is expected that this system will aid efforts in organizing the chaotic anatomical nomenclature of the appendicular skeleton in Siluriformes, and provide a solid basis for advances in comparative anatomy and nomenclature. The proposed terminology system has potential application on a number of fields that utilize information from catfish spines, ranging from taxonomy to phylogenetic systematics to paleontology and archaeology.

A Microcosting Study of Establishing a Baby Café® in Texas

2017 ◽  
Vol 34 (1) ◽  
pp. 77-83 ◽  
Author(s):  
Rigoberto I. Delgado ◽  
Sara L. Gill
Keyword(s):  
United States ◽  
San Antonio ◽  
The United States ◽  
Extensive Literature ◽  
Policy Makers ◽  
Discounted Cost ◽  
Informal Interview ◽  
Resource Requirements ◽  
The Cost ◽  
Discounted Costs

Background: This article focuses on the costs of opening and running a Baby Café. A Baby Café is an intervention that focuses on providing peer-to-peer support for breastfeeding mothers. Research aim: This study aimed to estimate the costs of establishing and running a Baby Café. Methods: The authors used a microcosting approach to identifying costs using the case of a Baby Café located in San Antonio, Texas, and modeled after other existing cafés in the United States. They also used extensive literature review and conducted an informal interview with a manager of an existing Baby Café in the United States to validate our cost data. The cost analysis was done from the provider perspective. Results: Costs of starting a Baby Café were $36,000, whereas annual operating costs totaled $47,000. Total discounted costs for a 5-year period amounted to $250,000, resulting in a cost per Baby Café session of $521 and cost per mother of $104. Varying the number of sessions per week and number of mothers attending each session, the discounted cost per Baby Café session ranged between $460 and $740 and the cost per mother varied between $65 and $246. Conclusion: These findings can be used by policy makers and organizations to evaluate local resource requirements for starting a Baby Café. Further research is needed to evaluate the effectiveness of this intervention against other breastfeeding promoting initiatives.

scholarly journals Design of Multiple Mailboxes

2020 ◽  
Vol 318 ◽  
pp. 01041
Author(s):  
Athena Baronos ◽  
Odysseas Manoliadis ◽  
Aristeidis Pavlidis
Keyword(s):  
3D Visualization ◽  
Building Blocks ◽  
Design Stage ◽  
Extensive Literature ◽  
3D Design ◽  
3D Cad ◽  
Domestic Use ◽  
The Right ◽  
The Cost ◽  
Apartment Complexes

In today’s world the design of multiple mailboxes comes to cover the evolution of logistics in delivering mail where the postman is not required to visit every user. In this research the 3D visualization is used for the design of multiple mailboxes for domestic use. It concerns the design of mailboxes in ergonomic building blocks and apartment complexes in 3D design so that they can be easily manufactured. Between the advantages of this design will be rapid production of ready-made products production of prototypes that enables testing at the design stage and reduces the time and the cost of production. The design when done with 3D CAD can be manufactured with modern machine tooling methods. In this paper after an extensive Literature Review the postal multiple mailboxes is used as a case study in the use of 3D CAD for 3D printing. A methodology is proposed that enables the examination of prototypes at the design stage according to specifications and allows the manufacturing department of a company to prepare the right tools and begin installing production lines. Conclusively this method gives the advantage of designing the product and supporting the production of scaffolds that can be functionally and ergonomically tested before finalizing the production.

In Silico Analysis of Evolution in Swine Flu Viral Genomes Through Re-assortment by Promulgation and Mutation

2009 ◽  
Vol 8 (4) ◽  
pp. 434-441 ◽  
Author(s):  
S. Sur ◽  
G. Sen ◽  
S. Thakur ◽  
A.K. Bothra ◽  
A. Sen
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Swine Flu ◽  
Viral Genomes ◽  
Silico Analysis

scholarly journals The global and local distribution of RNA structure throughout the SARS-CoV-2 genome

2020 ◽  
Author(s):  
Rafael de Cesaris Araujo Tavares ◽  
Gandhar Mahadeshwar ◽  
Han Wan ◽  
Nicholas C. Huston ◽  
Anna Marie Pyle
Keyword(s):  
In Silico ◽  
Rna Structure ◽  
Drug Targets ◽  
Rna Folding ◽  
Rna Viruses ◽  
Viral Agent ◽  
Rna Structures ◽  
Viral Rnas ◽  
Viral Genomes ◽  
Rna Genome

SARS-CoV-2 is the causative viral agent of COVID-19, the disease at the center of the current global pandemic. While knowledge of highly structured regions is integral for mechanistic insights into the viral infection cycle, very little is known about the location and folding stability of functional elements within the massive, ∼30kb SARS-CoV-2 RNA genome. In this study, we analyze the folding stability of this RNA genome relative to the structural landscape of other well-known viral RNAs. We present an in-silico pipeline to predict regions of high base pair content across long genomes and to pinpoint hotspots of well-defined RNA structures, a method that allows for direct comparisons of RNA structural complexity within the several domains in SARS-CoV-2 genome. We report that the SARS-CoV-2 genomic propensity for stable RNA folding is exceptional among RNA viruses, superseding even that of HCV, one of the most structured viral RNAs in nature. Furthermore, our analysis suggests varying levels of RNA structure across genomic functional regions, with accessory and structural ORFs containing the highest structural density in the viral genome. Finally, we take a step further to examine how individual RNA structures formed by these ORFs are affected by the differences in genomic and subgenomic contexts, which given the technical difficulty of experimentally separating cellular mixtures of sgRNA from gRNA, is a unique advantage of our in-silico pipeline. The resulting findings provide a useful roadmap for planning focused empirical studies of SARS-CoV-2 RNA biology, and a preliminary guide for exploring potential SARS-CoV-2 RNA drug targets. Importance The RNA genome of SARS-CoV-2 is among the largest and most complex viral genomes, and yet its RNA structural features remain relatively unexplored. Since RNA elements guide function in most RNA viruses, and they represent potential drug targets, it is essential to chart the architectural features of SARS-CoV-2 and pinpoint regions that merit focused study. Here we show that RNA folding stability of SARS-CoV-2 genome is exceptional among viral genomes and we develop a method to directly compare levels of predicted secondary structure across SARS-CoV-2 domains. Remarkably, we find that coding regions display the highest structural propensity in the genome, forming motifs that differ between the genomic and subgenomic contexts. Our approach provides an attractive strategy to rapidly screen for candidate structured regions based on base pairing potential and provides a readily interpretable roadmap to guide functional studies of RNA viruses and other pharmacologically relevant RNA transcripts.

scholarly journals Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

2020 ◽  
Author(s):  
M. Consuelo Gazitúa ◽  
Dean R. Vik ◽  
Simon Roux ◽  
Ann C. Gregory ◽  
Benjamin Bolduc ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Nitrogen Loss ◽  
Central Carbon Metabolism ◽  
N Cycling ◽  
Oxygen Minimum Zones ◽  
Viral Genomes ◽  
Anoxic Waters ◽  
Archaeal Viruses ◽  
Geochemical Models ◽  
Auxiliary Metabolic Genes

AbstractViruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

scholarly journals MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0160334 ◽  
Author(s):  
Martin Norling ◽  
Oskar E. Karlsson-Lindsjö ◽  
Hadrien Gourlé ◽  
Erik Bongcam-Rudloff ◽  
Juliette Hayer
Keyword(s):  
Experimental Design ◽  
In Silico ◽  
Viral Metagenomics ◽  
Analysis Tool

scholarly journals Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee Feces

2009 ◽  
Vol 84 (4) ◽  
pp. 1674-1682 ◽  
Author(s):  
Linlin Li ◽  
Amit Kapoor ◽  
Beth Slikas ◽  
Oderinde Soji Bamidele ◽  
Chunlin Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Sequences ◽  
The United States ◽  
Viral Metagenomics ◽  
Farm Animals ◽  
Tissue Samples ◽  
Viral Genomes ◽  
Wide Range ◽  
Stool Samples ◽  
Meat Samples

ABSTRACT Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named “Cyclovirus” whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.

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