scholarly journals Systematic Analysis of Metabolic Pathway Distributions of Bacterial Energy Reserves

2019 ◽  
Author(s):  
Liang Wang ◽  
Jianye Yang ◽  
Yue Huang ◽  
Qinghua Liu ◽  
Yaping Xu ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Distribution Patterns ◽  
Point Of View ◽  
Metabolic Adaptation ◽  
Effective Capacity ◽  
Wax Ester ◽  
Energy Reserves ◽  
Systematic Analysis

AbstractMetabolism of energy reserves are essential for bacterial functions such as pathogenicity, metabolic adaptation, and environmental persistence, etc. Previous bioinformatics studies have linked gain or loss of energy reserves such as glycogen and polyphosphate (polyP) with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the distribution patterns of energy reserves metabolism across bacterial species provides a shortcut route to look into bacterial lifestyle and physiology theoretically. So far, five major energy reserves have been identified in bacteria due to their effective capacity to support bacterial persistence under nutrient deprivation conditions, which include wax ester (WE), triacylglycerol (TAG), polyhydroxyalkanoates (PHA), polyphosphate, and glycogen. Although unknown pathways directly involved in energy reserves keep being discovered with the continuous endeavour of molecular microbiologists and it is currently rather clear about the enzymes related with the metabolism of energy reserves, there is a lack of systematic study of the pathway or key enzyme distributions of the five energy reserves in bacteria from an evolutionary point of view. With the fast development of sequencing technology, abundant bacterial proteomes are available in public database now. In this study, we sourced 8214 manually reviewed bacterial reference proteomes from UniProt database and used statistical models to search homologous sequences of key enzymes related with energy reserves. The distribution patterns of the pathways for energy reserves metabolism are visualized in taxonomy-based phylogenetic trees. According to the study, it was revealed that specific pathways and enzymes are associated with certain types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirmed that loss of energy reserves is correlated with bacterial genome reduction. Through this analysis, a much clearer picture about energy reserves metabolism in bacteria is present, which could serve a guide for further theoretical and experimental analyses of energy reserves metabolism in bacteria.

Public Investment Criteria: Benefit-Cost Analysis for Planned Economic Growth by Stephen A. Marglin. London: George Allen & Unwin Ltd., 1967. pp.103. 22s. 6d.********** Investments for Capacity Expansion: Size, Location and Time-Phasing edited by Alan S. Manne. London: George Allen & Unwin Ltd., 1967. pp.239. 45s.Investments for Capacity Expansion: Size, Location and Time-Phasing edited by Alan S. Manne. London: George Allen & Unwin Ltd., 1967. pp.239. 45s.

1967 ◽  
Vol 7 (3) ◽  
pp. 416-420
Author(s):  
Arthur MacEwan
Keyword(s):  
Cost Benefit Analysis ◽  
Public Investment ◽  
Cost Benefit ◽  
Capacity Expansion ◽  
Point Of View ◽  
Systematic Analysis ◽  
Benefit Cost Analysis ◽  
The Government ◽  
The Many ◽  
Benefit Cost

These books are numbers 4 and 5, respectively, in the series "Studies in the Economic Development of India". The two books are interesting complements to one another, both being concerned with the analysis of projects within national plan formulation. However, they treat different sorts of problems and do so on very different levels. Marglin's Public Investment Criteria is a short treatise on the problems of cost-benefit analysis in an Indian type economy, i.e., a mixed economy in which the government accepts a large planning responsibility. The book, which is wholely theoretical, explains the many criteria needed for evaluation of projects. The work is aimed at beginning students and government officials with some training in economics. It is a clear and interesting "introduction to the special branch of economics that concerns itself with systematic analysis of investment alternatives from the point of view of a government".

scholarly journals SCAPP: an algorithm for improved plasmid assembly in metagenomes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
David Pellow ◽  
Alvah Zorea ◽  
Maraike Probst ◽  
Ori Furman ◽  
Arik Segal ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Biological Knowledge ◽  
Assessment Procedure ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Human Gut ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Python Package

Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP.

scholarly journals Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Matthew R. Olm ◽  
Alexander Crits-Christoph ◽  
Spencer Diamond ◽  
Adi Lavy ◽  
Paula B. Matheus Carnevali ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Proteins ◽  
Large Scale ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Species Discrimination ◽  
Bacterial Genomes ◽  
Discrimination Power

ABSTRACT Longstanding questions relate to the existence of naturally distinct bacterial species and genetic approaches to distinguish them. Bacterial genomes in public databases form distinct groups, but these databases are subject to isolation and deposition biases. To avoid these biases, we compared 5,203 bacterial genomes from 1,457 environmental metagenomic samples to test for distinct clouds of diversity and evaluated metrics that could be used to define the species boundary. Bacterial genomes from the human gut, soil, and the ocean all exhibited gaps in whole-genome average nucleotide identities (ANI) near the previously suggested species threshold of 95% ANI. While genome-wide ratios of nonsynonymous and synonymous nucleotide differences (dN/dS) decrease until ANI values approach ∼98%, two methods for estimating homologous recombination approached zero at ∼95% ANI, supporting breakdown of recombination due to sequence divergence as a species-forming force. We evaluated 107 genome-based metrics for their ability to distinguish species when full genomes are not recovered. Full-length 16S rRNA genes were least useful, in part because they were underrecovered from metagenomes. However, many ribosomal proteins displayed both high metagenomic recoverability and species discrimination power. Taken together, our results verify the existence of sequence-discrete microbial species in metagenome-derived genomes and highlight the usefulness of ribosomal genes for gene-level species discrimination. IMPORTANCE There is controversy about whether bacterial diversity is clustered into distinct species groups or exists as a continuum. To address this issue, we analyzed bacterial genome databases and reports from several previous large-scale environment studies and identified clear discrete groups of species-level bacterial diversity in all cases. Genetic analysis further revealed that quasi-sexual reproduction via horizontal gene transfer is likely a key evolutionary force that maintains bacterial species integrity. We next benchmarked over 100 metrics to distinguish these bacterial species from each other and identified several genes encoding ribosomal proteins with high species discrimination power. Overall, the results from this study provide best practices for bacterial species delineation based on genome content and insight into the nature of bacterial species population genetics.

Amalgamated territorial hromadas as new local communities in Ukraine: mechanisms of social cohesion formation

2021 ◽  
pp. 14-21
Author(s):  
O. Deineko
Keyword(s):  
Social Cohesion ◽  
Social Order ◽  
Point Of View ◽  
Sociological Research ◽  
Systematic Analysis ◽  
Social Actors ◽  
Social Communities ◽  
Attitudes And Practices ◽  
Conflict Situations ◽  
Legislative Procedure

The article is dedicated to the systematic analysis of the peculiarities of the formation and functioning of amalgamated territorial communities in Ukraine as new local social communities. Analyzing the legislative procedure of amalgamation, the author distinguishes the essential features of amalgamated territorial communities that are different from other settlement communities. Within the framework of this investigation, the newly amalgamated hromadas appear as a “second-order” phenomenon, which is a socio-legal construct that is formed in a consensual manner and on a voluntary reciprocal basis. Basing on the analysis of qualitative sociological research data the author demonstrates the importance of the functioning of reciprocity mechanisms at the level of orientations and practices of all social actors involved in the procedure of territorial communities amalgamation. It is illustrated that the "failure" of reciprocity mechanisms contributes to the change of merger scenarios, causes the postponement of this process and the emergence of conflict situations. The paper substantiates that the legislative procedure of territorial communities amalgamation intensifies the formation of social capital and the establishment of a new civic social order. The special, different social status of amalgamated territorial communities in comparison with other settlement communities is explained by the emergence of the phenomenon of social cohesion, the mechanisms of activation of which are contained in the legislative order of territorial communities amalgamation. It is concluded that an important theoretical basis for the sociological conceptualization of ATC is the concept of reciprocity, which explains the mechanism of successful amalgamation, which is facilitated by the attitudes and practices of reciprocity of all involved social actors. According to the author’s point of view, the sociological synthesis of spatial and activity approaches to the analysis of social communities within the framework of sociological conceptualization of united territorial communities is considered heuristic. The synthesis of these approaches emphasizes both the importance of the spatial context of interactions emergence and reproduction, and their essential functionality in the formation and reproduction of hromada social order.

scholarly journals Educational audiovisual text design: empirical evidence and new research perspectives

2021 ◽  
Vol 13 (2) ◽  
pp. 28-35
Author(s):  
Giovanni Ganino
Keyword(s):  
Point Of View ◽  
Educational Technologies ◽  
Systematic Analysis ◽  
Design Elements ◽  
Research Perspectives ◽  
Close Relationship ◽  
Massive Online Open Courses ◽  
Depth Study ◽  
New Research ◽  
Instructional Design Principles

Abstract The article presents a systematic analysis of international literature concerning the design of educational audiovisual texts at university level. The theme appears very important in light of the extensive use of these cognitive artefacts in flipped, blended,Massive Online Open Courses (MOOCs) teaching processes. This is even more important in the era of health emergency that has led to the use of audiovisual text as the main teaching medium at school and university. The aim of the work is to provide a contribution to research on educational technologies for the purpose of identifying new instructional design principles that support multimedia learning. The analysis highlighted new research directions, such as the significant role of the camera point of view in learning complex manual procedures, new design elements on the ways of representing the teacher and his/her communicative attitude, and the increasingly close relationship between educational sciences and neuroscience. The result may be useful, on the one hand, as a stimulus for an in-depth study of the new lines of research identified, by researchers on educational technologies, and on the other, for a more informed evidence-based use of audiovisual texts in teaching practices.

scholarly journals Bactopia: a flexible pipeline for complete analysis of bacterial genomes

2020 ◽  
Author(s):  
Robert A. Petit ◽  
Timothy D. Read
Keyword(s):  
Standard Procedure ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Complete Analysis ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Analysis Pipeline ◽  
Genomic Analyses ◽  
Conserved Genes ◽  
Downstream Analysis

AbstractSequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a dataset setup step (Bactopia Datasets; BaDs) where a series of customizable datasets are created for the species of interest; the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly and several other functions based on the available datasets and outputs the processed data to a structured directory format; and a series of Bactopia Tools (BaTs) that perform specific post-processing on some or all of the processed data. BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes and taxonomic classification using highly conserved genes. It is expected that the number of BaTs will increase to fill specific applications in the future. As a demonstration, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on L. crispatus, a species that is a common part of the human vaginal microbiome. Bactopia is an open source system that can scale from projects as small as one bacterial genome to thousands that allows for great flexibility in choosing comparison datasets and options for downstream analysis. Bactopia code can be accessed at https://www.github.com/bactopia/bactopia.

Genome Analysis of the Enterococcus faecium Entfac.YE Prophage

2022 ◽  
Author(s):  
Yara Elahi ◽  
Ramin Mazaheri Nezhad Fard ◽  
Arash Seifi ◽  
Saeideh Mahfouzi ◽  
Ali Akbar Saboor Yaraghi
Keyword(s):  
Genome Analysis ◽  
Enterococcus Faecium ◽  
Clinical Sample ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Rapid Evolution ◽  
Housekeeping Genes ◽  
Water Sources ◽  
Clinical Samples ◽  
Transfer Resistance

Background: Bacteriophages are viruses that infect bacteria. Bacteriophages are widely distributed in various environments. The prevalence of bacteriophages in water sources, especially wastewaters, is naturally high. These viruses affect evolution of most bacterial species. Bacteriophages are able to integrate their genomes into the chromosomes of their hosts as prophages and hence transfer resistance genes to the bacterial genomes. Enterococci are commensal bacteria that show high resistance to common antibiotics. For example, prevalence of vancomycin-resistant enterococci has increased within the last decades. Methods: Enterococcal isolates were isolated from clinical samples and morphological, phenotypical, biochemical, and molecular methods were used to identify and confirm their identity. Bacteriophages extracted from water sources were then applied to isolated Enterococcus faecium (E. faecium). In the next step, the bacterial genome was completely sequenced and the existing prophage genome in the bacterial genome was analyzed. Results: In this study, E. faecium EntfacYE was isolated from a clinical sample. The EntfacYE genome was analyzed and 88 prophage genes were identified. The prophage content included four housekeeping genes, 29 genes in the group of genes related to replication and regulation, 25 genes in the group of genes related to structure and packaging, and four genes belonging to the group of genes associated with lysis. Moreover, 26 genes were identified with unknown functions. Conclusion: In conclusion, genome analysis of prophages can lead to a better understanding of their roles in the rapid evolution of bacteria.

scholarly journals A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

mSphere ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Michelle Spoto ◽  
Changhui Guan ◽  
Elizabeth Fleming ◽  
Julia Oh
Keyword(s):  
Gene Function ◽  
Large Scale ◽  
Essential Gene ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Model Organisms ◽  
Design Parameters ◽  
Bacterial Genomes ◽  
Wide Range ◽  
User Friendly

ABSTRACT The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species. IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

scholarly journals Molecular insights into the genome dynamics and interactions between core and acquired genomes ofVibrio cholerae

2020 ◽  
Vol 117 (38) ◽  
pp. 23762-23773
Author(s):  
Archana Pant ◽  
Satyabrata Bag ◽  
Bipasa Saha ◽  
Jyoti Verma ◽  
Pawan Kumar ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Genome ◽  
Genomic Islands ◽  
Host Bacterium ◽  
Metabolic Functions ◽  
Bipartite Genome ◽  
Ctx Prophage ◽  
Integrative Conjugative Elements

Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome ofVibrio choleraeharbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome ofV. choleraeand examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in theV. choleraechromosome. We have deleted more than 250 acquired genes from 6 different loci in theV. choleraechromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, includingEscherichia coli. In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypassV. choleraeimmunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome ofV. choleraeto remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.

From Long-term Contract to Market: An RBC Perspective on International Negotiations of Iron Ore Prices in the Asia-Pacific Region, 2009–2010

2020 ◽  
Vol 25 (2) ◽  
pp. 345-371
Author(s):  
Yue Wang ◽  
Akira Tanaka ◽  
Xiaochun Huang
Keyword(s):  
Iron Ore ◽  
Negotiation Process ◽  
Point Of View ◽  
International Negotiations ◽  
Asia Pacific ◽  
Pacific Region ◽  
Asia Pacific Region ◽  
Systematic Analysis ◽  
Term Contract

Abstract The collapse of a long-term contract-based (LTC) benchmark system and the rise of a market-based index system in international negotiations of iron ore prices in the Asia-Pacific region has attracted much media attention. However, a systematic analysis of why and how such a change occurred from a negotiation point of view is absent. Drawing upon a relationship-behavior-conditions (RBC) perspective from the international business (IB) negotiation literature, this article investigates how negotiations between parties unfolded during the 2009–2010 period. Specifically, the article contributes to a deeper understanding of the subject by evaluating the relationships between various negotiating parties, investigating some intriguing behaviors by negotiating parties, and identifying important conditions surrounding the negotiation process. The case of iron ore price negotiation also offers a vehicle to advance the RBC perspective in untangling complex IB negotiation problems and generate some broad implications for IB negotiation research and practices.

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