Symbiotic specificity, association patterns, and function determine community responses to global changes: defining critical research areas for coral-Symbiodiniumsymbioses

2013 ◽  
pp. n/a-n/a ◽  
Author(s):  
Nicholas S. Fabina ◽  
Hollie M. Putnam ◽  
Erik C. Franklin ◽  
Michael Stat ◽  
Ruth D. Gates
Keyword(s):  
Global Changes ◽  
Community Responses ◽  
Critical Research ◽  
Association Patterns ◽  
Research Areas ◽  
Symbiotic Specificity ◽  
And Function

scholarly journals Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19)

2019 ◽  
Vol 3 (Supplement_1) ◽  
Author(s):  
Debra Poutsiaka ◽  
Lori Stern ◽  
Virginia Riquelme ◽  
Emily Hollister ◽  
Julia Cope ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Lactobacillus Rhamnosus ◽  
Detailed Examination ◽  
Global Changes ◽  
Shotgun Metagenomics ◽  
Gene Abundance ◽  
Funding Sources ◽  
And Function ◽  
Relative Gene

Abstract Objectives This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI. Methods Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group). Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes. Results Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25. Conclusions We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI. Funding Sources Pfizer Inc.

Structure and function of ryanodine receptors

1994 ◽  
Vol 266 (6) ◽  
pp. C1485-C1504 ◽  
Author(s):  
R. Coronado ◽  
J. Morrissette ◽  
M. Sukhareva ◽  
D. M. Vaughan
Keyword(s):  
Ryanodine Receptor ◽  
Single Channel ◽  
Radioligand Binding ◽  
Ryanodine Receptors ◽  
Global Changes ◽  
Binding Assays ◽  
Pharmacological Agents ◽  
Planar Bilayers ◽  
Receptor Isoforms ◽  
And Function

Membrane depolarization, neurotransmitters, and hormones evoke a release of Ca2+ from intracellular Ca(2+)-storing organelles like the endoplasmic reticulum and, in muscle, the sarcoplasmic reticulum (SR). In turn, the released Ca2+ serves to trigger a variety of cellular responses. The presence of Ca2+ pumps to replenish intracellular stores was described more than 20 years ago. The presence of Ca2+ channels, like the ryanodine receptor, which suddenly release the organelle-stored Ca2+, is a more recent finding. This review describes the progress made in the last five years on the structure, function, and regulation of the ryanodine receptor. Numerous reports have described the response of ryanodine receptors to cellular ions and metabolites, kinases and other proteins, and pharmacological agents. In many cases, comparative measurements have been made using Ca2+ fluxes in SR vesicles, single-channel recordings in planar bilayers, and radioligand binding assays using [3H]ryanodine. These techniques have helped to relate the activity of single ryanodine receptors to global changes in the SR Ca2+ permeability. Molecular information on functional domains within the primary structure of the ryanodine receptor is also available. There are at least three ryanodine receptor isoforms in various tissues. Some cells, such as amphibian muscle cells, express more than a single isoform. The diversity of ligands known to modulate gating and the diversity of tissues known to express the protein suggest that the ryanodine receptor has the potential to participate in many types of cell stimulus-Ca(2+)-release coupling mechanisms.

scholarly journals Exact Maximum Clique Algorithm for Different Graph Types Using Machine Learning

Mathematics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 97
Author(s):  
Kristjan Reba ◽  
Matej Guid ◽  
Kati Rozman ◽  
Dušanka Janežič ◽  
Janez Konc
Keyword(s):  
Machine Learning ◽  
Maximum Clique ◽  
Dynamic Algorithm ◽  
Graph Theoretic ◽  
Research Areas ◽  
Novel Approach ◽  
Search Speed ◽  
Speed Up ◽  
Clique Algorithm ◽  
And Function

Finding a maximum clique is important in research areas such as computational chemistry, social network analysis, and bioinformatics. It is possible to compare the maximum clique size between protein graphs to determine their similarity and function. In this paper, improvements based on machine learning (ML) are added to a dynamic algorithm for finding the maximum clique in a protein graph, Maximum Clique Dynamic (MaxCliqueDyn; short: MCQD). This algorithm was published in 2007 and has been widely used in bioinformatics since then. It uses an empirically determined parameter, Tlimit, that determines the algorithm’s flow. We have extended the MCQD algorithm with an initial phase of a machine learning-based prediction of the Tlimit parameter that is best suited for each input graph. Such adaptability to graph types based on state-of-the-art machine learning is a novel approach that has not been used in most graph-theoretic algorithms. We show empirically that the resulting new algorithm MCQD-ML improves search speed on certain types of graphs, in particular molecular docking graphs used in drug design where they determine energetically favorable conformations of small molecules in a protein binding site. In such cases, the speed-up is twofold.

scholarly journals Acute condensin depletion causes genome decompaction without altering the level of global gene expression in Saccharomyces cerevisiae

2017 ◽  
Author(s):  
Matthew Robert Paul ◽  
Tovah Elise Markowitz ◽  
Andreas Hochwagen ◽  
Sevinç Ercan
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Genome Organization ◽  
Large Scale ◽  
Global Gene Expression ◽  
Higher Order ◽  
Gene Clustering ◽  
Global Changes ◽  
Chromatin Compaction ◽  
And Function

AbstractCondensins are broadly conserved chromosome organizers that function in chromatin compaction and transcriptional regulation, but to what extent these two functions are linked has remained unclear. Here, we analyzed the effect of condensin inactivation on genome compaction and global gene expression in the yeast Saccharomyces cerevisiae. Spike-in-controlled 3C-seq analysis revealed that acute condensin inactivation leads to a global decrease in close-range chromosomal interactions as well as more specific losses of homotypic tRNA gene clustering. In addition, a condensin-rich topologically associated domain between the ribosomal DNA and the centromere on chromosome XII is lost upon condensin inactivation. Unexpectedly, these large-scale changes in chromosome architecture are not associated with global changes in transcript levels as determined by spike-in-controlled mRNA-seq analysis. Our data suggest that the global transcriptional program of S. cerevisiae is resistant to condensin inactivation and the associated profound changes in genome organization.Significance StatementGene expression occurs in the context of higher-order chromatin organization, which helps compact the genome within the spatial constraints of the nucleus. To what extent higher-order chromatin compaction affects gene expression remains unknown. Here, we show that gene expression and genome compaction can be uncoupled in the single-celled model eukaryote Saccharomyces cerevisiae. Inactivation of the conserved condensin complex, which also organizes the human genome, leads to broad genome decompaction in this organism. Unexpectedly, this reorganization has no immediate effect on the transcriptome. These findings indicate that the global gene expression program is robust to large-scale changes in genome architecture in yeast, shedding important new light on the evolution and function of genome organization in gene regulation.

scholarly journals The Design of an Urban Roadside Automatic Sprinkling System: Mitigation of PM2.5–10 in Ambient Air in Megacities

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Shiyong Liu ◽  
Konstantinos Triantis ◽  
Lan Zhang
Keyword(s):  
System Architecture ◽  
Winter Season ◽  
Ambient Air ◽  
Street Dust ◽  
Conceptual System ◽  
The Road ◽  
Research Areas ◽  
Winter Road ◽  
And Function ◽  
Constituent Elements

The objective of this research paper is to describe the system architecture for an urban roadside automatic mist-generating system. Its primary purpose is to mitigate particulate matter especially PM2.5–10. In this paper, four graphs are provided to exhibit the constituent elements of this system. This paper also discusses the functional extensions of this system for alternative uses in civil engineering which include winter road deicing and desnowing with added salt; clean-up of street dust; lowering of temperature of a “hot island” during the summer; the addition of humidity in an arid area; and the suppression of flu virus in the winter season. The structure and function of this system are comprehensively discussed in this paper. This system is compared to existing and other proposed systems in terms of control options, efficiency, and primary functional issues. The unique design of the road automatic sprinkling system renders itself a prominent option. Although there are no data available for this conceptual system, some expected qualitative and quantitative outcomes are provided and justified. The paper concludes with some potential research areas and challenges associated with this system architecture.

scholarly journals Plant physiological ecology and the global changes

2012 ◽  
Vol 36 (3) ◽  
pp. 253-269 ◽  
Author(s):  
João Paulo Rodrigues Alves Delfino Barbosa ◽  
Serge Rambal ◽  
Angela Maria Soares ◽  
Florent Mouillot ◽  
Joana Messias Pereira Nogueira ◽  
...  
Keyword(s):  
Physiological Ecology ◽  
System Change ◽  
Global Changes ◽  
Earth System ◽  
Real Effects ◽  
Physiological Processes ◽  
The Earth ◽  
Plant Physiological Ecology ◽  
Biophysical Processes ◽  
And Function

The global changes are marked by alteration on the normal patterns of important biochemical and biophysical processes of the Earth. However, the real effects as well as the feedbacks of the global changes over vegetation are still unclear. Part of this uncertainty can be attributed to the inattention of stakeholders and scientists towards vegetation and its complex interrelations with the environment, which drive plant physiological processes in different space-time scales. Notwithstanding, some key subjects of the global changes could be better elucidated with a more plant physiological ecology approach. We discuss some issues related to this topic, going through some limitations of approaching vegetation as a static component of the biosphere as the other sub-systems of the Earth-system change. With this perspective, this review is an initial reflection towards the assessment of the role and place of vegetation structure and function in the global changes context. We reviewed the Earth-system and global changes terminology; attempted to illustrate key plant physiological ecology researches themes in the global changes context; consider approaching plants as complex systems in order to adequately quantify systems characteristics as sensibility, homeostasis, and vulnerability. Moreover, we propose insights that would allow vegetation studies and scaling procedures in the context of the Earth-system. We hope this review will assist researchers on their strategy to identify, understand and anticipate the potential effects of global changes over the most vulnerable vegetation processes from the leaf to the global levels.

scholarly journals Trends in Local Ecosystem Governance

2021 ◽  
Vol 3 ◽  
Author(s):  
Karrigan Bork ◽  
Keith Hirokawa
Keyword(s):  
Local Governance ◽  
Ecosystem Structure ◽  
Biological Factors ◽  
Critical Research ◽  
Viable Option ◽  
Legal Literature ◽  
Local Ecosystem ◽  
And Function ◽  
Ecosystem Structure And Function ◽  
Ecosystem Benefits

The physical and biological factors that together determine ecosystem structure and function will be subject to enormous pressures under future climate regimes. These pressures will impact ecosystem processes and services, ranging from impacts on biodiversity to loss of essential ecosystem benefits. Ecosystem management to maintain desired ecosystem conditions will become increasingly important. Existing governance structures are insufficient to provide the necessary guidance for these management efforts. The legal literature is increasingly focused on local ecosystem governance as a viable option to fill this governance gap. For example, increasing recognition of the value of ecosystem services to local communities has driven increased efforts to protect those services through local ecosystem initiatives. The local ecosystem governance scholarship is diffuse, making the literature difficult to access. Based on a review of the legal literature on local ecosystem governance over the last 20 years, this article marshals the theoretical arguments for and against local governance and identifies ongoing efforts to implement local ecosystem governance. The article also identifies both emerging challenges to local ecosystem governance and potential ways to address those challenges. From this review emerges actionable recommendations and critical research needs to improve local ecosystem governance.

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