scholarly journals Co-occurring soil bacteria exhibit a robust competitive hierarchy and lack of non-transitive interactions

2017 ◽  
Author(s):  
Logan M. Higgins ◽  
Jonathan Friedman ◽  
Hao Shen ◽  
Jeff Gore
Keyword(s):  
Species Diversity ◽  
Community Assembly ◽  
Soil Bacteria ◽  
Interaction Network ◽  
Higher Order ◽  
Competitive Interactions ◽  
Community Function ◽  
Strain Competition ◽  
Model Community

Microbial communities are typically incredibly diverse, and this diversity is thought to play a key role in community function. However, explaining how this diversity can be maintained is a major challenge in ecology. Temporal fluctuations and spatial structure in the environment likely play a key role, but it has also been suggested that the structure of interactions within the community may act as a stabilizing force for species diversity. In particular, if competitive interactions are non-transitive as in the classic rock-paper-scissors game, they can contribute to the maintenance of species diversity; on the other hand, if they are predominantly hierarchical, any observed diversity must be maintained via other mechanisms. Here, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. We find that the interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Moreover, in agreement with recently proposed community assembly rules, the full 20-strain competition resulted in extinction of all but three of the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community. The lack of non-transitivity and higher order interactions in vitro indicates that other factors, such as temporal or spatial heterogeneity, must be at play in enabling these strains to coexist in nature.

scholarly journals Structures of mouse and human GITR–GITRL complexes reveal unique TNF superfamily interactions

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Feng Wang ◽  
Bryant Chau ◽  
Sean M. West ◽  
Christopher R. Kimberlin ◽  
Fei Cao ◽  
...  
Keyword(s):  
T Cells ◽  
Cell Signaling ◽  
Tumor Necrosis ◽  
Immune Cell ◽  
Linear Chain ◽  
Tumor Necrosis Factor Receptor ◽  
Higher Order ◽  
Membrane Structures ◽  
Receptor Interface

AbstractGlucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) and GITR ligand (GITRL) are members of the tumor necrosis superfamily that play a role in immune cell signaling, activation, and survival. GITR is a therapeutic target for directly activating effector CD4 and CD8 T cells, or depleting GITR-expressing regulatory T cells (Tregs), thereby promoting anti-tumor immune responses. GITR activation through its native ligand is important for understanding immune signaling, but GITR structure has not been reported. Here we present structures of human and mouse GITR receptors bound to their cognate ligands. Both species share a receptor–ligand interface and receptor–receptor interface; the unique C-terminal receptor–receptor enables higher order structures on the membrane. Human GITR–GITRL has potential to form a hexameric network of membrane complexes, while murine GITR–GITRL complex forms a linear chain due to dimeric interactions. Mutations at the receptor–receptor interface in human GITR reduce cell signaling with in vitro ligand binding assays and minimize higher order membrane structures when bound by fluorescently labeled ligand in cell imaging experiments.

scholarly journals Do temperate tree species diversity and identity influence soil microbial community function and composition?

2017 ◽  
Vol 7 (19) ◽  
pp. 7965-7974 ◽  
Author(s):  
Rim Khlifa ◽  
Alain Paquette ◽  
Christian Messier ◽  
Peter B. Reich ◽  
Alison D. Munson
Keyword(s):  
Microbial Community ◽  
Species Diversity ◽  
Tree Species ◽  
Soil Microbial Community ◽  
Tree Species Diversity ◽  
Microbial Community Function ◽  
Soil Microbial ◽  
Community Function

In vitro measurements of the competitive interactions between two saprobic basidiomycetes on Typha latifolia

2005 ◽  
Vol 83 (11) ◽  
pp. 1523-1527 ◽  
Author(s):  
Michael J. Schulz ◽  
James F. Cahill, ◽  
Randolph S. Currah
Keyword(s):  
Relative Abundance ◽  
Typha Latifolia ◽  
The Other ◽  
Competitive Interactions ◽  
In Vitro Measurements ◽  
Leaf Tissues ◽  
Leaf Segments

Psathyrella typhae (Kalchbr.) Pearson & Dennis forms small basidiomata (mushrooms) and Sclerotium hydrophilum Saccardo in Rothert numerous minute sclerotia at the base of senescent shoots of Typha latifolia L. To assess how the two might compete in nature, isolates of these fungi were paired on autoclaved leaf segments of T. latifolia and incubated at 15 and 25 °C. The relative abundance of each species in the segments was determined by macerating the leaf tissues and then transferring fragments of macerate to microplates containing two types of media: one conclusively demonstrated the presence of P. typhae while the other demonstrated the presence of S. hydrophilum. Relative numbers of microplate wells showing positive reactions for each species on each medium indicated the proportion of the segment occupied following single and paired inoculations. These data demonstrated that competition was asymmetric, with P. typhae the stronger competitor at both temperatures, and uninhibited by the presence of S. hydrophilum. In contrast, S. hydrophilum was competitively excluded by P. typhae.

scholarly journals In vivo reconstitution finds multivalent RNA-RNA interactions as drivers of mesh-like condensates

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Weirui Ma ◽  
Gang Zheng ◽  
Wei Xie ◽  
Christine Mayr
Keyword(s):  
Surface Area ◽  
Protein Trafficking ◽  
Rna Binding ◽  
Interaction Network ◽  
Large Surface Area ◽  
High Propensity ◽  
Membrane Protein Trafficking ◽  
Protein Components

Liquid-like condensates have been thought to be sphere-like. Recently, various condensates with filamentous morphology have been observed in cells. One such condensate is the TIS granule network that shares a large surface area with the rough endoplasmic reticulum and is important for membrane protein trafficking. It has been unclear how condensates with mesh-like shapes, but dynamic protein components are formed. In vitro and in vivo reconstitution experiments revealed that the minimal components are a multivalent RNA-binding protein that concentrates RNAs that are able to form extensive intermolecular mRNA-mRNA interactions. mRNAs with large unstructured regions have a high propensity to form a pervasive intermolecular interaction network that acts as condensate skeleton. The underlying RNA matrix prevents full fusion of spherical liquid-like condensates, thus driving the formation of irregularly shaped membraneless organelles. The resulting large surface area may promote interactions at the condensate surface and at the interface with other organelles.

scholarly journals SCREENING OF SOIL BACTERIA FOR PLANT GROWTH PROMOTION ACTIVITIES IN VITRO

2016 ◽  
Vol 4 (1) ◽  
pp. 27 ◽  
Author(s):  
Edi Husen
Keyword(s):  
Plant Growth ◽  
Soil Bacteria ◽  
Phosphate Solubilization ◽  
Azotobacter Vinelandii ◽  
Growth Promotion ◽  
Nitrogenase Activity ◽  
Chelating Agent ◽  
Plant Growth Promoting Rhizobacteria ◽  
Iaa Production

Fourteen isolates of soil bacteria, including two known plant growth promoting rhizobacteria (PGPR) strains, Azotobacter vinelandii Mac 259 and Bacillus cereus UW 85, were tested in vitro. Parameters assessed were indoleacetic acid (IAA) production, phosphate solubilization, dinitrogen fixation, and siderophore (Fe-III chelating agent) production. IAA production was assayed colorimetrically using ferric chlorideperchloric acid reagent. Phosphate-solubilization and siderophore production were tested qualitatively by plating the bacteria in Pikovskaya and chrome azurol S agar, respectively. The ability to fix dinitrogen was measured based on nitrogenase activity of the bacteria by gas chromatography. The results showed that twelve isolates produced IAA, ranged from 2.09 to 33.28 µmol ml-1. The ability to solubilize precipitated phosphate was positively exhibited by four isolates (BS 58, BTS, TCaR 61, and BTCaRe 65). Seven isolates including Mac 259 positively produced siderophore. None of the isolates showed nitrogenase activity. Only one isolate (TS 3) did not exhibit any of the traits tested. Isolate TCeRe 60 and reference strain Mac 259 were found to have IAA- and siderophore-producing traits. Four P-solubilizing bacteria (BS 58, BTS, TCaR 61, and BTCaRe 65) were also IAA- and siderophore-producing bacteria. Potential use of these PGPR isolates needs further test in enhancing plant growth.

P4-298: Understanding the target and evaluating the consequences of gamma-secretase modulation from in vitro models to higher-order species

2013 ◽  
Vol 9 ◽  
pp. P814-P814
Author(s):  
Kathleen Wood ◽  
Nikolay Pozdnyakov ◽  
Emily Sylvain ◽  
Michael Marconi ◽  
Ashley Robshaw ◽  
...  
Keyword(s):  
In Vitro Models ◽  
Higher Order ◽  
Gamma Secretase

DECOMPOSITION OF CHLORO-SUBSTITUTED ALIPHATIC ACIDS BY SOIL BACTERIA

1957 ◽  
Vol 3 (2) ◽  
pp. 151-164 ◽  
Author(s):  
H. L. Jensen
Keyword(s):  
Amino Acids ◽  
Yeast Extract ◽  
Soil Bacteria ◽  
Basal Medium ◽  
Soil Extract ◽  
Taxonomic Position ◽  
Vitamin B ◽  
Selective Media ◽  
Aliphatic Acids

Three groups of bacteria capable of decomposing chloro-substituted aliphatic acids were isolated from soil by means of selective media. A group of Pseudomonas-like bacteria (A) decomposed monochloroacetate (and monobromoacetate) readily in media with yeast extract, peptone, or amino acids. They also decomposed α-monochloropropionate with moderate vigor, but had little effect on dichloro-acetate and -propionate, and none on trichloroacetate. A non-sporeforming bacterium of uncertain taxonomic position (B) was able to decompose trichloroacetate in media containing soil extract or vitamin B12, and also in basal medium when associated with vitamin B12-producing strains of Streptomyces. Dichloroacetate was only slightly attacked, and monochloroacetate and α-dichloropropionate not at all. A group of bacteria (C) apparently belonging to Agrobacterium decomposed α-dichloropropionate and dichloroacetate, but was less active towards α-monochloropropionate, and did not attack mono- and tri-chloroacetate. The organisms of groups B and C grew only feebly in ordinary media. The decomposition of monochloroacetate, trichloroacetate, and α-dichloropropionate in soil was accelerated by addition of cell suspensions of groups A, B, and C, respectively. The organisms seemed to be more active in the soil than in vitro.

Irinotecan Resistance – In Search of New Markers in CRC.

2021 ◽  
Author(s):  
Jakub Kryczka ◽  
Joanna Boncela
Keyword(s):  
Drug Resistance ◽  
Cell Lines ◽  
Expression Profiles ◽  
Resistance Mechanism ◽  
Interaction Network ◽  
In Vitro Study ◽  
Cancer Drug ◽  
New Genes

Abstract Colorectal cancer (CRC) is one of the most prominent causes of cancer death worldwide. Chemotherapeutic regimens consisting of different drugs combinations such as 5-fluorouracil, and oxaliplatin (FOLFOX) or irinotecan (FOLFIRI) have been proven successful in the treatment of CRC. However, chemotherapy often leads to the acquisition of cancer drug resistance followed by metastasis and in the aftermath therapeutic failure. The molecular mechanism responsible for drug resistance is still unclear. The systemic search for new biomarkers of this phenomenon may identify new genes and pathways. To understand the drug resistance mechanism in CRC, the in vitro study based on the molecular analysis of drug-sensitive cells lines vs drug-resistant cells lines has been used. In our study to bridge the gap between in vitro and in vivo study, we compared the expression profiles of cell lines and patient samples from the publicly available database to select the new candidate genes for irinotecan resistance. Using The Gene Expression Omnibus (GEO) database of CRC cell lines (HT29, HTC116, LoVo, and their respective irinotecan-resistant variants) and patient samples (GSE42387, GSE62080, and GSE18105) we compared the changes in the mRNA expression profile of the main genes involved in irinotecan body’s processing, such as transport out of the cells and metabolism. Furthermore, using a protein-protein interaction network of differently expressed genes between FOLFIRI resistant and sensitive CRC patients, we have selected top networking proteins (upregulated: NDUFA2, SDHD, LSM5, DCAF4, and COX10, downregulated: RBM8A, TIMP1, QKI, TGOLN2, and PTGS2). Our analysis provided several potential irinotecan resistance markers, previously not described as such.

scholarly journals Beyond direct neighbourhood effects: higher-order interactions improve modelling and predicting tree survival and growth

2020 ◽  
Author(s):  
Yuanzhi Li ◽  
Margaret M Mayfield ◽  
Bin Wang ◽  
Junli Xiao ◽  
Kamil Kral ◽  
...  
Keyword(s):  
Species Diversity ◽  
Temperate Forest ◽  
Species Coexistence ◽  
Biotic Interactions ◽  
Higher Order ◽  
Individual Level ◽  
Pairwise Interactions ◽  
Tree Survival ◽  
Survival And Growth ◽  
Tree Performance

Abstract It is known that biotic interactions are the key to species coexistence and maintenance of species diversity. Traditional studies focus overwhelmingly on pairwise interactions between organisms, ignoring complex higher-order interactions (HOIs). In this study, we present a novel method of calculating individual-level HOIs for trees, and use this method to test the importance of size- and distance-dependent individual-level HOIs to tree performance in a 25-ha temperate forest dynamic plot. We found that full HOIs-inclusive models improved our ability to model and predict the survival and growth of trees, providing empirical evidence that HOIs strongly influence tree performance in this temperate forest. Specifically, assessed HOIs mitigate the competitive direct effects of neighbours on survival and growth of focal trees. Our study lays a foundation for future investigations of the prevalence and relative importance of HOIs in global forests and their impact on species diversity.

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