scholarly journals Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pengshuo Yang ◽  
Chongyang Tan ◽  
Maozhen Han ◽  
Lin Cheng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Network Connectivity ◽  
Small Range ◽  
Environmental Disturbance ◽  
Target Species ◽  
Important Species ◽  
Metagenome Analysis ◽  
Occurrence Patterns ◽  
Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

scholarly journals Induced sterility in fish and its potential and challenges for aquaculture and germ cell transplantation technology: a review

Biologia ◽  
2016 ◽  
Vol 71 (8) ◽  
Author(s):  
Amin Golpour ◽  
Mohammad Abdul Momin Siddique ◽  
Diógenes Henrique Siqueira-Silva ◽  
Martin Pšenička
Keyword(s):  
Germ Cell ◽  
Cell Transplantation ◽  
Large Scale ◽  
Hormonal Treatment ◽  
Important Species ◽  
Genetic Ablation ◽  
Germ Cell Transplantation ◽  
Commercially Important ◽  
Alternative Approaches ◽  
Hormone Signalling

AbstractInterest in reproductively sterile fish in aquaculture has prompted research into their production. Several methods are available for inducing sterility and optimizing its application in the global fishery industry. Sterilization can potentially be accomplished through irradiation, surgery, or chemical and hormonal treatment. Alternative approaches include triploidization, hybridization, and generation of new lines via advanced biotechnological techniques. Triploids of many commercially important species have been studied extensively and have been produced on a large scale for many years. Novel approaches, including disruption of gonadotropin releasing hormone signalling and genetic ablation of germ cells, have been developed that are effective in producing infertile fish but have the disadvantage of not being 100% reliable or are impractical for large-scale aquaculture. We review currently used technologies and recent advances in induction of sterility in fish, especially those intended for use in germ cell transplantation. Knowledge of the implications of these approaches remains incomplete, imposing considerable limitations.

scholarly journals A network-based approach to deciphering a dynamic microbiome’s response to a subtle perturbation

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Grace Tzun-Wen Shaw ◽  
An-Chi Liu ◽  
Chieh-Yin Weng ◽  
Yi-Chun Chen ◽  
Cheng-Yu Chen ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Ecosystem Functioning ◽  
Environmental Changes ◽  
Ecosystem Dynamics ◽  
Environmental Research ◽  
Human Society ◽  
The Past ◽  
Environmental Perturbations ◽  
Before And After ◽  
Occurrence Patterns

Abstract Over the past decades, one main issue that has emerged in ecological and environmental research is how losses in biodiversity influence ecosystem dynamics and functioning, and consequently human society. Although biodiversity is a common indicator of ecosystem functioning, it is difficult to measure biodiversity in microbial communities exposed to subtle or chronic environmental perturbations. Consequently, there is a need for alternative bioindicators to detect, measure, and monitor gradual changes in microbial communities against these slight, chronic, and continuous perturbations. In this study, microbial networks before and after subtle perturbations by adding S. acidaminiphila showed diverse topological niches and 4-node motifs in which microbes with co-occurrence patterns played the central roles in regulating and adjusting the intertwined relationships among microorganisms in response to the subtle environmental changes. This study demonstrates that microbial networks are a good bioindicator for chronic perturbation and should be applied in a variety of ecological investigations.

scholarly journals Next Generation Middleware Technology for Mobile Computing

2011 ◽  
pp. 74-80
Author(s):  
B. Darsana ◽  
Karabi Konar
Keyword(s):  
Mobile Computing ◽  
Large Scale ◽  
Network Connectivity ◽  
Distributed Applications ◽  
Mobile Systems ◽  
Portable Devices ◽  
Next Generation ◽  
Mobile Middleware ◽  
Mobile Computing Environment ◽  
Middleware Technology

Current advances in portable devices, wireless technologies, and distributed systems have created a mobile computing environment that is characterized by a large scale of dynamism. Diversities in network connectivity, platform capability, and resource availability can significantly affect the application performance. Traditional middleware systems are not prepared to offer proper support for addressing the dynamic aspects of mobile systems. Modern distributed applications need a middleware that is capable of adapting to environment changes and that supports the required level of quality of service. This paper represents the experience of several research projects related to next generation middleware systems. We first indicate the major challenges in mobile computing systems and try to identify the main requirements for mobile middleware systems. The different categories of mobile middleware technologies are reviewed and their strength and weakness are analyzed.

Characterization of microbial communities in exhaust air treatment systems of large-scale pig housing facilities

2010 ◽  
Vol 62 (7) ◽  
pp. 1551-1559 ◽  
Author(s):  
J. Haneke ◽  
N. M. Lee ◽  
T. W. Gaul ◽  
H. F. A. Van den Weghe
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Dust Particles ◽  
Nitrifying Bacteria ◽  
Ammonium Concentration ◽  
Nitrogen Compounds ◽  
Air Treatment ◽  
Fattening Period ◽  
Washing Water ◽  
Housing Facilities

Exhaust air treatment has gained importance as an essential factor in intensive livestock areas due to the rising emissions in the environment. Wet filter walls of multi-stage exhaust air treatment systems precipitate gaseous ammonia and dust particles from exhaust air in washing water. Microbial communities in the biomass developed in the washing water of five large-scale exhaust air treatment units of pig housing facilities, were investigated by fluorescence in situ hybridization (FISH) and 16S rDNA sequence analyses. No “standard” nitrifying bacteria were found in the washing water. Instead mainly α-Proteobacteria, aggregating β- and χ-Proteobacteria, a large number of Actinobacteria, as well as individual Planctomycetales and Crenarchaeota were detected after more than twelve months' operation. The main Proteobacteria species present were affiliated to the families Alcaligenaceae, Comamonadaceae and Xanthomonadaceae. Furthermore, we investigated the consumption of inorganic nitrogen compounds in the washing water of one exhaust air treatment unit during a fattening period with and without pH control. Maintaining the pH at 6.0 resulted in a ca. fivefold higher ammonium concentration and a ca. fourfold lower concentration of oxidized nitrogen compounds after the fattening period was finished.

scholarly journals Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

2020 ◽  
Author(s):  
Youwen Qin ◽  
Aki S Havulinna ◽  
Yang Liu ◽  
Pekka Jousilahti ◽  
Scott C Ritchie ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Dietary Habits ◽  
Population Based ◽  
Genome Wide ◽  
Scale Population ◽  
Important Health ◽  
Disease Analysis

Co-evolution between humans and the microbial communities colonizing them has resulted in an intimate assembly of thousands of microbial species mutualistically living on and in their body and impacting multiple aspects of host physiology and health. Several studies examining whether human genetic variation can affect gut microbiota suggest a complex combination of environmental and host factors. Here, we leverage a single large-scale population-based cohort of 5,959 genotyped individuals with matched gut microbial shotgun metagenomes, dietary information and health records up to 16 years post-sampling, to characterize human genetic variations associated with microbial abundances, and predict possible causal links with various diseases using Mendelian randomization (MR). Genome-wide association study (GWAS) identified 583 independent SNP-taxon associations at genome-wide significance (p<5.0×10-8), which included notable strong associations with LCT (p=5.02×10-35), ABO (p=1.1×10-12), and MED13L (p=1.84×10-12). A combination of genetics and dietary habits was shown to strongly shape the abundances of certain key bacterial members of the gut microbiota, and explain their genetic association. Genetic effects from the LCT locus on Bifidobacterium and three other associated taxa significantly differed according to dairy intake. Variation in mucin-degrading Faecalicatena lactaris abundances were associated with ABO, highlighting a preferential utilization of secreted A/B/AB-antigens as energy source in the gut, irrespectively of fibre intake. Enterococcus faecalis levels showed a robust association with a variant in MED13L, with putative links to colorectal cancer. Finally, we identified putative causal relationships between gut microbes and complex diseases using MR, with a predicted effect of Morganella on major depressive disorder that was consistent with observational incident disease analysis. Overall, we present striking examples of the intricate relationship between humans and their gut microbial communities, and highlight important health implications.

scholarly journals Deforestation impacts network co-occurrence patterns of microbial communities in Amazon soils

2018 ◽  
Vol 95 (2) ◽  
Author(s):  
M A Wadud Khan ◽  
Brendan J M Bohannan ◽  
Klaus Nüsslein ◽  
James M Tiedje ◽  
Susannah G Tringe ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Occurrence Patterns

scholarly journals Regional Analysis of the Brain Transcriptome in Mice Bred for High and Low Methamphetamine Consumption

2019 ◽  
Vol 9 (7) ◽  
pp. 155 ◽  
Author(s):  
Hitzemann ◽  
Iancu ◽  
Reed ◽  
Baba ◽  
Lockwood ◽  
...  
Keyword(s):  
Large Scale ◽  
Drug Exposure ◽  
Regional Analysis ◽  
Drug Effects ◽  
Network Connectivity ◽  
Transcriptome Profiling ◽  
Rna Seq ◽  
Reward Circuitry ◽  
Brain Transcriptome ◽  
Differential Gene

Transcriptome profiling can broadly characterize drug effects and risk for addiction in the absence of drug exposure. Modern large-scale molecular methods, including RNA-sequencing (RNA-Seq), have been extensively applied to alcohol-related disease traits, but rarely to risk for methamphetamine (MA) addiction. We used RNA-Seq data from selectively bred mice with high or low risk for voluntary MA intake to construct coexpression and cosplicing networks for differential risk. Three brain reward circuitry regions were explored, the nucleus accumbens (NAc), prefrontal cortex (PFC), and ventral midbrain (VMB). With respect to differential gene expression and wiring, the VMB was more strongly affected than either the PFC or NAc. Coexpression network connectivity was higher in the low MA drinking line than in the high MA drinking line in the VMB, oppositely affected in the NAc, and little impacted in the PFC. Gene modules protected from the effects of selection may help to eliminate certain mechanisms from significant involvement in risk for MA intake. One such module was enriched in genes with dopamine-associated annotations. Overall, the data suggest that mitochondrial function and glutamate-mediated synaptic plasticity have key roles in the outcomes of selective breeding for high versus low levels of MA intake.

scholarly journals New Frontiers inSchistosomaGenomics and Transcriptomics

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Laila A. Nahum ◽  
Marina M. Mourão ◽  
Guilherme Oliveira
Keyword(s):  
Large Scale ◽  
Biological Research ◽  
Mitochondrial Genomes ◽  
Future Directions ◽  
Important Species ◽  
Blood Flukes ◽  
Causative Agents ◽  
Mitochondrial Sequences ◽  
Modern Technologies

Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium,S. japonicum, andS. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of sixSchistosomaspecies have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization ofSchistosomagenomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.

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