scholarly journals A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities

2018 ◽  
Vol 9 ◽  
Author(s):  
Qi Li ◽  
Feibi Lin ◽  
Chen Yang ◽  
Juanping Wang ◽  
Yan Lin ◽  
...  
Keyword(s):  
Large Scale ◽  
Functional Interactions ◽  
Metagenomic Study

scholarly journals Integrative Functional Network Interactions Underlie the Association between Physical Activity and Cognition in Neurodegenerative Diseases

2019 ◽  
Author(s):  
Chia-Hao Shih ◽  
Miriam Sklerov ◽  
Nina Browner ◽  
Eran Dayan
Keyword(s):  
Physical Activity ◽  
Neurodegenerative Diseases ◽  
Cognitive Decline ◽  
Cognitive Performance ◽  
Large Scale ◽  
Healthy Aging ◽  
Brain Networks ◽  
Neural Substrates ◽  
Functional Interactions ◽  
False Discovery

Physical activity (PA) has preventive and possibly restorative effects in aging-related cognitive decline, which relate to intrinsic functional interactions (functional connectivity, FC) in large-scale brain networks. Preventive and ameliorative effects of PA on cognitive decline have also been documented in neurodegenerative diseases, such as Parkinson's disease (PD). However, the neural substrates that mediate the association between PA and cognitive performance under such neurological conditions remain unknown. Here we set out to examine if the association between PA and cognitive performance in PD is mediated by FC in large-scale sensorimotor and association brain networks. Data from 51 PD patients were analyzed. Connectome-level analysis based on a whole-brain parcellation showed that self-reported levels of PA were associated with increased FC between, but not within the default mode (DMN) and salience networks (SAL) (p < .05, false discovery rate corrected). Additionally, multiple parallel mediation analysis further demonstrated that FC between left lateral parietal nodes in the DMN and rostral prefrontal nodes in the SAL mediated the association between PA and executive function performance. These findings are in line with previous studies linking FC in large-scale association networks with the effects of PA on cognition in healthy aging. Our results extend these previous results by demonstrating that the association between PA and cognitive performance in neurodegenerative diseases such as PD is mediated by integrative functional interactions in large-scale association networks.

scholarly journals Metabolic potential for reductive acetogenesis and a novel energy-converting [NiFe] hydrogenase in Bathyarchaeia from termite guts – a genome-centric analysis

2020 ◽  
Author(s):  
Hui Qi Loh ◽  
Vincent Hervé ◽  
Andreas Brune
Keyword(s):  
Large Scale ◽  
Binding Motif ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Cofactor Binding ◽  
A Genome ◽  
Key Enzyme ◽  
Metagenomic Study ◽  
Acetate Formation ◽  
Energy Converting

AbstractSymbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes (MAGs) of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from H2 and CO2 via an archaeal variant of the Wood–Ljungdahl pathway. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4g. We propose that this novel Fpo-like hydrogenase provides the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are not capable of lithotrophic acetogenesis because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, including methylated compounds, in other uncultured representatives of the phylum.

scholarly journals Intrinsic Connectivity of the Globus Pallidus: An Uncharted Marker of Functional Prognosis in People With First-Episode Schizophrenia

2019 ◽  
Vol 46 (1) ◽  
pp. 184-192 ◽  
Author(s):  
Goda Tarcijonas ◽  
William Foran ◽  
Gretchen L Haas ◽  
Beatriz Luna ◽  
Deepak K Sarpal
Keyword(s):  
Globus Pallidus ◽  
Large Scale ◽  
Resting State Fmri ◽  
Anterior Cingulate ◽  
First Episode ◽  
Functional Interactions ◽  
Early Functional Outcome ◽  
Intrinsic Connectivity ◽  
Dorsolateral Prefrontal ◽  
First Episode Schizophrenia

AbstractThere is growing evidence suggesting that abnormalities in cortical-basal ganglia circuitry may play a significant role in determining outcomes in schizophrenia. The globus pallidus (GP), a critical structure within this circuitry, unique in its role as a mediator of competing inputs through the striatum, has not been well characterized in schizophrenia. The following study examined functional interactions of the GP in individuals with first-episode schizophrenia (FES). To probe the large-scale intrinsic connectivity of the GP, resting-state fMRI scans were obtained from patients with FES and sex and age-matched healthy controls. Participants with FES were also evaluated after 6 months via the Strauss–Carpenter Outcomes Scale to assess overall functional trajectory. The GP was parcellated to generate seeds within its substructures, and connectivity maps were generated. Our FES cohort showed significantly lower functional connectivity between the left GP interna and a network of regions including the dorsolateral prefrontal cortex, caudate, and cerebellum at baseline. In addition, FES participants with lower overall scores of functioning at 6 months showed significantly decreased connectivity between the GP interna and the dorsal anterior cingulate and bilateral insula, all regions important for motivational salience. These results provide novel evidence for unique abnormalities in functional interactions of the GP with key prefrontal cortical regions in FES. Our findings also suggest that reduced prefrontal-pallidal connectivity may serve as a predictor of early functional outcome.

NetBrainWork: a toolbox for studying functional interactions in large-scale brain networks in fMRI.

NeuroImage ◽  
2009 ◽  
Vol 47 ◽  
pp. S80 ◽  
Author(s):  
V Perlbarg ◽  
G Marrelec ◽  
P Bellec ◽  
D Coynel ◽  
M Pélégrini-Issac ◽  
...  
Keyword(s):  
Large Scale ◽  
Brain Networks ◽  
Functional Interactions

scholarly journals Metabolic Potential for Reductive Acetogenesis and a Novel Energy-Converting [NiFe] Hydrogenase in Bathyarchaeia From Termite Guts – A Genome-Centric Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Hui Qi Loh ◽  
Vincent Hervé ◽  
Andreas Brune
Keyword(s):  
Large Scale ◽  
The Other ◽  
Binding Motif ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Cofactor Binding ◽  
A Genome ◽  
Key Enzyme ◽  
Metagenomic Study ◽  
Acetate Formation

Symbiotic digestion of lignocellulose in the hindgut of higher termites is mediated by a diverse assemblage of bacteria and archaea. During a large-scale metagenomic study, we reconstructed 15 metagenome-assembled genomes of Bathyarchaeia that represent two distinct lineages in subgroup 6 (formerly MCG-6) unique to termite guts. One lineage (TB2; Candidatus Termitimicrobium) encodes all enzymes required for reductive acetogenesis from CO2 via an archaeal variant of the Wood–Ljungdahl pathway, involving tetrahydromethanopterin as C1 carrier and an (ADP-forming) acetyl-CoA synthase. This includes a novel 11-subunit hydrogenase, which possesses the genomic architecture of the respiratory Fpo-complex of other archaea but whose catalytic subunit is phylogenetically related to and shares the conserved [NiFe] cofactor-binding motif with [NiFe] hydrogenases of subgroup 4 g. We propose that this novel Fpo-like hydrogenase provides part of the reduced ferredoxin required for CO2 reduction and is driven by the electrochemical membrane potential generated from the ATP conserved by substrate-level phosphorylation; the other part may require the oxidation of organic electron donors, which would make members of TB2 mixotrophic acetogens. Members of the other lineage (TB1; Candidatus Termiticorpusculum) are definitely organotrophic because they consistently lack hydrogenases and/or methylene-tetrahydromethanopterin reductase, a key enzyme of the archaeal Wood–Ljungdahl pathway. Both lineages have the genomic capacity to reduce ferredoxin by oxidizing amino acids and might conduct methylotrophic acetogenesis using unidentified methylated compound(s). Our results indicate that Bathyarchaeia of subgroup 6 contribute to acetate formation in the guts of higher termites and substantiate the genomic evidence for reductive acetogenesis from organic substrates, possibly including methylated compounds, in other uncultured representatives of the phylum.

scholarly journals RNA structure-wide discovery of functional interactions with multiplexed RNA motif library

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Kaoru R. Komatsu ◽  
Toshiki Taya ◽  
Sora Matsumoto ◽  
Emi Miyashita ◽  
Shunnichi Kashida ◽  
...  
Keyword(s):  
Rna Structure ◽  
Large Scale ◽  
Regulatory Elements ◽  
Rna Structures ◽  
Rna Sequences ◽  
Functional Interactions ◽  
Affinity Enrichment ◽  
Target Binding ◽  
Rna Motif ◽  
Computational Analyses

AbstractBiochemical assays and computational analyses have discovered RNA structures throughout various transcripts. However, the roles of these structures are mostly unknown. Here we develop folded RNA element profiling with structure library (FOREST), a multiplexed affinity assay system to identify functional interactions from transcriptome-wide RNA structure datasets. We generate an RNA structure library by extracting validated or predicted RNA motifs from gene-annotated RNA regions. The RNA structure library with an affinity enrichment assay allows for the comprehensive identification of target-binding RNA sequences and structures in a high-throughput manner. As a proof-of-concept, FOREST discovers multiple RNA-protein interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST reveals different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovers rG4 structures in the terminal loops of precursor microRNAs. Overall, FOREST serves as a versatile platform to investigate RNA structure-function relationships on a large scale.

A Large‐Scale Metagenomic Study for Enzyme Profiles Using the Focused Identification of the NGS‐Based Definitive Enzyme Research (FINDER) Strategy

2021 ◽  
Author(s):  
Jae‐Yoon Sung ◽  
Yong‐Jik Lee ◽  
Yong‐Joon Cho ◽  
Myeong‐Na Shin ◽  
Sang‐Jae Lee ◽  
...  
Keyword(s):  
Large Scale ◽  
Metagenomic Study

Cerebral Organization of Music Processing

2018 ◽  
pp. 87-121
Author(s):  
Thenille Braun Janzen ◽  
Michael H. Thaut
Keyword(s):  
Neural Networks ◽  
Large Scale ◽  
Current Knowledge ◽  
Brain Networks ◽  
Music Listening ◽  
Functional Basis ◽  
Functional Interactions ◽  
The Past ◽  
Neuroscience Research ◽  
New Generation

This chapter presents a broad panorama of the current knowledge concerning the anatomical and functional basis of music processing in the healthy brain. Neuroimaging studies developed over the past 20 years provide evidence that music processing takes place in widely distributed neural networks. Here, attention is focused on core brain networks implicated in music processing, emphasizing the anatomical and functional interactions between cortical and subcortical areas within auditory-frontal networks, auditory-motor networks, and auditory-limbic networks. Finally, the authors review recent studies investigating how brain networks organize themselves in a naturalistic music listening context. Collectively, this robust body of literature demonstrates that music processing requires timely coordination of large-scale cognitive, motor, and limbic brain networks, setting the stage for a new generation of music neuroscience research on the dynamic organization of brain networks underlying music processing.

scholarly journals Contribution of Exploratory Methods to the Investigation of Extended Large-Scale Brain Networks in Functional MRI: Methodologies, Results, and Challenges

2008 ◽  
Vol 2008 ◽  
pp. 1-14 ◽  
Author(s):  
V. Perlbarg ◽  
G. Marrelec
Keyword(s):  
Large Scale ◽  
Blood Oxygen Level Dependent ◽  
Brain Network ◽  
Data Driven ◽  
Blood Oxygen ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Blood Oxygen Level ◽  
Functional Interactions ◽  
Efficient Exploration

A large-scale brain network can be defined as a set of segregated and integrated regions, that is, distant regions that share strong anatomical connections and functional interactions. Data-driven investigation of such networks has recently received a great deal of attention in blood-oxygen-level-dependent (BOLD) functional magnetic resonance imaging (fMRI). We here review the rationale for such an investigation, the methods used, the results obtained, and also discuss some issues that have to be faced for an efficient exploration.

scholarly journals Global distribution of mcr gene variants in 214,095 metagenomic samples

2021 ◽  
Author(s):  
Hannah-Marie Martiny ◽  
Patrick Munk ◽  
Christian Brinch ◽  
Judit Szarvas ◽  
Frank Aarestrup ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Large Scale ◽  
Metagenomic Data ◽  
Gene Variants ◽  
Genomic Context ◽  
Antimicrobial Resistance Genes ◽  
History Of ◽  
Metagenomic Study ◽  
Initial Discovery ◽  
Plasmid Replicons

Abstract Since the initial discovery of a mobilized colistin resistance gene (mcr-1), several other variants have been reported, some of which might have circulated a while before being discovered. Metagenomic data provides an opportunity to re-analyze available older data to understand the evolutionary history of recently discovered antimicrobial resistance genes (ARGs). Here, we present a large-scale metagenomic study of 442 Tbp of sequencing reads from 214,095 samples to identify the host and geographical distribution and genomic context of nine mcr gene variants (mcr-1 to mcr-9). Our results show that the dissemination of each variant is not uniform. Instead, the source and location play a role in the spread. Despite the very diverse distribution, the genomic background of the mcr genes remains unchanged as the same mobile genetic elements and plasmid replicons occur. This work emphasizes the importance of sharing genomic data for surveillance of ARGs in our fight against antimicrobial resistance.

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