scholarly journals Diauxic lags explain unexpected coexistence in multi-resource environments

2021 ◽  
Author(s):  
William Bloxham ◽  
Hyunseok Lee ◽  
Jeff Gore
Keyword(s):  
Environmental Changes ◽  
Common Mechanism ◽  
Large Set ◽  
Major Question ◽  
Acinetobacter Species ◽  
Multiple Resources ◽  
As Species ◽  
Slow Growing ◽  
Pseudomonas Aurantiaca ◽  
Slow Grower

How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly three times as frequently when the slow-grower is the fast-switcher. Our work illustrates a potentially common mechanism for the emergence of multi-resource coexistence despite single-resource competitive exclusions.

scholarly journals Soft Selective Sweep on Chemosensory Genes Correlates with Ancestral Preference for Toxic Noni in a Specialist Drosophila Population

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 32
Author(s):  
Erina A. Ferreira ◽  
Sophia Lambert ◽  
Thibault Verrier ◽  
Frédéric Marion-Poll ◽  
Amir Yassin
Keyword(s):  
Genetic Variation ◽  
Selective Sweep ◽  
Environmental Changes ◽  
Population Genomics ◽  
Morinda Citrifolia ◽  
Major Question ◽  
Host Plant Specialization ◽  
Chemosensory Genes ◽  
Combine Population

Understanding how organisms adapt to environmental changes is a major question in evolution and ecology. In particular, the role of ancestral variation in rapid adaptation remains unclear because its trace on genetic variation, known as soft selective sweep, is often hardly recognizable from genome-wide selection scans. Here, we investigate the evolution of chemosensory genes in Drosophila yakuba mayottensis, a specialist subspecies on toxic noni (Morinda citrifolia) fruits on the island of Mayotte. We combine population genomics analyses and behavioral assays to evaluate the level of divergence in chemosensory genes and perception of noni chemicals between specialist and generalist subspecies of D. yakuba. We identify a signal of soft selective sweep on a handful of genes, with the most diverging ones involving a cluster of gustatory receptors expressed in bitter-sensing neurons. Our results highlight the potential role of ancestral genetic variation in promoting host plant specialization in herbivorous insects and identify a number of candidate genes underlying behavioral adaptation.

scholarly journals Transcription-dependent spreading of canonical yeast GATA factor across the body of highly expressed genes

2017 ◽  
Author(s):  
Aria Ronsmans ◽  
Maxime Wery ◽  
Camille Gautier ◽  
Marc Descrimes ◽  
Evelyne Dubois ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase Ii ◽  
Cancer Progression ◽  
Transcription Initiation ◽  
Environmental Changes ◽  
The Body ◽  
Large Set ◽  
Gata Factor ◽  
Gata Factors ◽  
Gata Transcription Factors

AbstractGATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis. However, although their consensus binding sites have been well definedin vitro, thein vivoselectivity for recognition by GATA factors remains poorly characterized. Using ChIP-Seq, we identified the Dal80 GATA factor targets in yeast. Our data reveal Dal80 binding to a large set of promoters, sometimes independently of GATA sites. Strikingly, Dal80 was also detected across the body of promoter-bound genes, correlating with high, Dal80-sensitive expression. Mechanistic single-gene experiments showed that Dal80 spreading across gene bodies is independent of intragenic GATA sites but requires transcription elongation. Consistently, Dal80 co-purified with the post-initiation form of RNA Polymerase II. Our work suggests that GATA factors could play dual, synergistic roles during transcription initiation and post-initiation steps, promoting efficient remodeling of the gene expression program in response to environmental changes.Author SummaryGATA transcription factors are highly conserved among eukaryotes and play key roles in cancer progression and hematopoiesis. In budding yeast, four GATA transcription factors are involved in the response to the quality of nitrogen supply. We have determined the whole genome binding profile of one of them, Dal80, and revealed that it also binds across the body or promoter-bound genes. Our observation that ORF binding correlated with elevated transcription levels and exquisite Dal80 sensitivity suggests that GATA factors could play other, unexpected roles at post-initiation stages in eukaryotes.

Advective pathways of nutrients and key ecological substances in the Arctic

2021 ◽  
Author(s):  
Myriel Vredenborg ◽  
Benjamin Rabe ◽  
Sinhue Torres-Valdès
Keyword(s):  
Sea Ice ◽  
Arctic Ocean ◽  
Ocean Circulation ◽  
Environmental Changes ◽  
Marine Ecosystem ◽  
Ocean Model ◽  
The Arctic ◽  
Large Set ◽  
Sea Ice Extent ◽  
Near Surface

<p>The Arctic Ocean is undergoing remarkable environmental changes due to global warming. The rise in the Arctic near-surface air temperature during the past decades is more than twice as high as the global average, a phenomenon known as the “Arctic Amplification”. As a consequence the Arctic summer sea ice extent has decreased by more than 40 % in recent decades, and moreover a year-round sea ice loss in extent and thickness was recorded. By opening up of large areas formerly covered by sea ice, the exchange of heat, moisture and momentum between the ocean and the atmosphere intensified. This resulted in changes in the ocean circulation and the water masses impacting the marine ecosystem. We investigate these changes by using a large set of hydrographic and biogeochemical data of the entire Arctic Ocean. To better quantify the current changes in the Arctic ecosystem we will compare our observational data analysis with high-resolution biogeochemical atmosphere-ice-ocean model simulations.</p>

Rule of age and size at maturity of chum salmon (Oncorhynchus keta): implications of recent trends among Oncorhynchus spp.

2005 ◽  
Vol 62 (12) ◽  
pp. 2752-2759 ◽  
Author(s):  
Kentaro Morita ◽  
Shoko H Morita ◽  
Masa-aki Fukuwaka ◽  
Hiroyuki Matsuda
Keyword(s):  
Growth Rate ◽  
Chum Salmon ◽  
Environmental Changes ◽  
Pacific Salmon ◽  
Oncorhynchus Keta ◽  
Size At Maturity ◽  
Chum Salmon Oncorhynchus Keta ◽  
Realistic Modeling ◽  
Recent Trends ◽  
Slow Growing

In the last quarter of the 20th century, the size at maturity of many North Pacific salmon (Oncorhynchus spp.) populations decreased. During this same period, the age at maturity increased, implying that the growth rate of Pacific salmon decreased, probably owing to environmental changes. To elucidate these trends, we identified the rule of age and size at maturity of Japanese chum salmon (Oncorhynchus keta), which was that slow-growing salmon initiated maturation at an older age and smaller size than did fast-growing salmon. We then simulated the potential modification of age and size at maturity in response to changing growth rate using a size-structured model with age- and size-specific maturation rates. This showed that reducing the growth rate without assuming a genetic change was sufficient for realistic modeling of recent changes. In addition, the observed rule of age and size at maturity was consistent with the optimal age and size at maturity in terms of maximizing the fitness. Our results attributed the recent trends in chum salmon's increasing age and decreasing size at maturity to an adaptive phenotypic response to a reduced growth rate.

scholarly journals Characterization of the growth dynamics and biofilm formation of Staphylococcus epidermidis strains isolated from contaminated platelet units

2014 ◽  
Vol 63 (6) ◽  
pp. 884-891 ◽  
Author(s):  
Hamza Ali ◽  
Valerie S. Greco-Stewart ◽  
Michael R. Jacobs ◽  
Roslyn A. Yomtovian ◽  
Ineke G. H. Rood ◽  
...  
Keyword(s):  
Staphylococcus Epidermidis ◽  
Biofilm Formation ◽  
Growth Dynamics ◽  
Extracellular Polysaccharide ◽  
Lag Phase ◽  
Infectious Risk ◽  
Slow Growing ◽  
Growth Experiments ◽  
Slow Grower

Bacterial contamination of platelet concentrates (PCs) poses the highest transfusion-associated infectious risk, with Staphylococcus epidermidis being a predominant contaminant. Herein, the growth dynamics of 20 S. epidermidis strains in PCs and regular media were characterized. Strains were categorized as fast (short lag phase) or slow (long lag phase) growers in PCs. All strains were evaluated for the presence of the biofilm-associated icaAD genes by PCR, their capability to produce extracellular polysaccharide (slime) on Congo red agar plates and their ability to form surface-attached aggregates (biofilms) in glucose-supplemented trypticase soy broth (TSBg) using a crystal violet staining assay. A subset of four strains (two slow growers and two fast growers) was further examined for the ability for biofilm formation in PCs. Two of these strains carried the icAD genes, formed slime and produced biofilms in TSBg and PCs, while the other two strains, which did not carry icaAD, did not produce slime or form biofilms in TSBg. Although the two ica-negative slime-negative strains did not form biofilms in media, they displayed a biofilm-positive phenotype in PCs. Although all four strains formed biofilms in PCs, the two slow growers formed significantly more biofilms than the fast growers. Furthermore, growth experiments of the two ica-positive strains in plasma-conditioned platelet bags containing TSBg revealed that a slow grower isolate was more likely to escape culture-based screening than a fast grower strain. Therefore, this study provides novel evidence that links S. epidermidis biofilm formation with slow growth in PCs and suggests that slow-growing biofilm-positive S. epidermidis would be more likely to be missed with automate culture.

scholarly journals Adaptation strategies of coastal fishing communities as species shift poleward

2018 ◽  
Vol 76 (1) ◽  
pp. 93-103 ◽  
Author(s):  
Talia Young ◽  
Emma C Fuller ◽  
Mikaela M Provost ◽  
Kaycee E Coleman ◽  
Kevin St. Martin ◽  
...  
Keyword(s):  
Environmental Change ◽  
Environmental Changes ◽  
High Mobility ◽  
Interdisciplinary Approach ◽  
Adaptation Strategies ◽  
Fishing Communities ◽  
Data Set ◽  
Small Vessels ◽  
As Species ◽  
Trawl Fishing

Abstract In this period of environmental change, understanding how resource users respond to such changes is critical for effective resource management and adaptation planning. Extensive work has focused on natural resource responses to environmental changes, but less has examined the response of resource users to such changes. We used an interdisciplinary approach to analyse changes in resource use among commercial trawl fishing communities in the northwest Atlantic, a region that has shown poleward shifts in harvested fish species. We found substantial community-level changes in fishing patterns since 1996: southern trawl fleets of larger vessels with low catch diversity fished up to 400 km further north, while trawl fleets of smaller vessels with low catch diversity shrank or disappeared from the data set over time. In contrast, trawl fleets (of both large and small vessels) with higher catch diversity neither changed fishing location dramatically or nor disappeared as often from the data set. This analysis suggests that catch diversity and high mobility may buffer fishing communities from effects of environmental change. Particularly in times of rapid and uncertain change, constructing diverse portfolios and allowing for fleet mobility may represent effective adaptation strategies.

scholarly journals Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes

2000 ◽  
Vol 11 (12) ◽  
pp. 4241-4257 ◽  
Author(s):  
Audrey P. Gasch ◽  
Paul T. Spellman ◽  
Camilla M. Kao ◽  
Orna Carmel-Harel ◽  
Michael B. Eisen ◽  
...  
Keyword(s):  
Dna Microarrays ◽  
Environmental Changes ◽  
Osmotic Shock ◽  
Expression Patterns ◽  
Transcriptional Response ◽  
Yeast Cells ◽  
Large Set ◽  
Genomic Expression ◽  
Sequence Elements ◽  
Almost All

We explored genomic expression patterns in the yeastSaccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (∼ 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

scholarly journals A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance

2021 ◽  
Vol 118 (43) ◽  
pp. e2019060118
Author(s):  
Lufeng Dan ◽  
Yuze Li ◽  
Shuhua Chen ◽  
Jingbo Liu ◽  
Yu Wang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Environmental Changes ◽  
Growth Defect ◽  
Common Mechanism ◽  
Evolutionary Divergence ◽  
Resistance Mutations ◽  
Genetic Changes ◽  
Clonal Population ◽  
Reading Frame ◽  
Correct Reading

Most genetic changes have negligible reversion rates. As most mutations that confer resistance to an adverse condition (e.g., drug treatment) also confer a growth defect in its absence, it is challenging for cells to genetically adapt to transient environmental changes. Here, we identify a set of rapidly reversible drug-resistance mutations in Schizosaccharomyces pombe that are caused by microhomology-mediated tandem duplication (MTD) and reversion back to the wild-type sequence. Using 10,000× coverage whole-genome sequencing, we identify nearly 6,000 subclonal MTDs in a single clonal population and determine, using machine learning, how MTD frequency is encoded in the genome. We find that sequences with the highest-predicted MTD rates tend to generate insertions that maintain the correct reading frame, suggesting that MTD formation has shaped the evolution of coding sequences. Our study reveals a common mechanism of reversible genetic variation that is beneficial for adaptation to environmental fluctuations and facilitates evolutionary divergence.

Grenadiers of the World Oceans: Biology, Stock Assessment, and Fisheries

2008 ◽  
Keyword(s):  
Factor Analysis ◽  
Environmental Changes ◽  
Stock Assessment ◽  
Deep Ocean ◽  
Dynamic Factor ◽  
Population Declines ◽  
The North ◽  
The World ◽  
Long Time ◽  
Slow Growing

<em>Abstract.</em>—Roundnose grenadier <em>Coryphaenoides rupestris </em>and roughhead grenadier <em>Macrourus berglax </em>are well known slope species in the North Atlantic. Dramatic population declines in both species in Canadian waters of the Northwest Atlantic raised the question: was the decline a result of environmental changes or exploitation? Min–max autocorrelation factor analysis and dynamic factor analysis, two types of time series analysis, showed that a combination of factors acting on different temporal scales explained the trends in both species. Those in <em>Macrourus </em>were best explained by environmental factors operating on long time scales; those in <em>Coryphaenoides </em>were related to exploitation. Our results support the view that an unregulated deep-ocean fishery, as experienced by <em>Coryphaenoides, </em>has serious consequences for species that are slow-growing, long-lived, and late-maturing.

scholarly journals Circadian Rhythm in Adipose Tissue: Novel Antioxidant Target for Metabolic and Cardiovascular Diseases

Antioxidants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 968
Author(s):  
Andy W. C. Man ◽  
Ning Xia ◽  
Huige Li
Keyword(s):  
Oxidative Stress ◽  
Adipose Tissue ◽  
Circadian Rhythm ◽  
Cardiovascular Diseases ◽  
Cardiovascular Health ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Biological Clock ◽  
Common Mechanism ◽  
And Oxidative Stress

Obesity is a major risk factor for most metabolic and cardiovascular disorders. Adipose tissue is an important endocrine organ that modulates metabolic and cardiovascular health by secreting signaling molecules. Oxidative stress is a common mechanism associated with metabolic and cardiovascular complications including obesity, type 2 diabetes, and hypertension. Oxidative stress can cause adipose tissue dysfunction. Accumulating data from both humans and experimental animal models suggest that adipose tissue function and oxidative stress have an innate connection with the intrinsic biological clock. Circadian clock orchestrates biological processes in adjusting to daily environmental changes according to internal or external cues. Recent studies have identified the genes and molecular pathways exhibiting circadian expression patterns in adipose tissue. Disruption of the circadian rhythmicity has been suggested to augment oxidative stress and aberrate adipose tissue function and metabolism. Therefore, circadian machinery in the adipose tissue may be a novel therapeutic target for the prevention and treatment of metabolic and cardiovascular diseases. In this review, we summarize recent findings on circadian rhythm and oxidative stress in adipose tissue, dissect the key components that play a role in regulating the clock rhythm, oxidative stress and adipose tissue function, and discuss the potential use of antioxidant treatment on metabolic and cardiovascular diseases by targeting the adipose clock.

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