Niche-driven evolution of metabolic and life-history strategies in natural and domesticated populations of Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>Variation of resource supply is one of the key factors that drive the evolution of life-history strategies, and hence the interactions between individuals. In the yeast <it>Saccharomyces cerevisiae</it>, two life-history strategies related to different resource utilization have been previously described in strains from different industrial origins. In this work, we analyzed metabolic traits and life-history strategies in a broader collection of yeast strains sampled in various ecological niches (forest, human body, fruits, laboratory and industrial environments).</p> <p>Results</p> <p>By analysing the genetic and plastic variation of six life-history and three metabolic traits, we showed that <it>S. cerevisiae </it>populations harbour different strategies depending on their ecological niches. On one hand, the forest and laboratory strains, referred to as extreme "ants", reproduce quickly, reach a large carrying capacity and a small cell size in fermentation, but have a low reproduction rate in respiration. On the other hand, the industrial strains, referred to as extreme "grasshoppers", reproduce slowly, reach a small carrying capacity but have a big cell size in fermentation and a high reproduction rate in respiration. "Grasshoppers" have usually higher glucose consumption rate than "ants", while they produce lower quantities of ethanol, suggesting that they store cell resources rather than secreting secondary products to cross-feed or poison competitors. The clinical and fruit strains are intermediate between these two groups.</p> <p>Conclusions</p> <p>Altogether, these results are consistent with a niche-driven evolution of <it>S. cerevisiae</it>, with phenotypic convergence of populations living in similar habitat. They also revealed that competition between strains having contrasted life-history strategies ("ants" and "grasshoppers") seems to occur at low frequency or be unstable since opposite life-history strategies appeared to be maintained in distinct ecological niches.</p

Invasion Pathway of the Ctenophore Mnemiopsis leidyi in the Mediterranean Sea

Gelatinous zooplankton outbreaks have increased globally owing to a number of human-mediated factors, including food web alterations and species introductions. The invasive ctenophore Mnemiopsis leidyi entered the Black Sea in the early 1980s. The invasion was followed by the Azov, Caspian, Baltic and North Seas, and, most recently, the Mediterranean Sea. Previous studies identified two distinct invasion pathways of M. leidyi from its native range in the western Atlantic Ocean to Eurasia. However, the source of newly established populations in the Mediterranean Sea remains unclear. Here we build upon our previous study and investigate sequence variation in both mitochondrial (Cytochrome c Oxidase subunit I) and nuclear (Internal Transcribed Spacer) markers in M. leidyi, encompassing five native and 11 introduced populations, including four from the Mediterranean Sea. Extant genetic diversity in Mediterranean populations (n = 8, Na = 10) preclude the occurrence of a severe genetic bottleneck or founder effects in the initial colonizing population. Our mitochondrial and nuclear marker surveys revealed two possible pathways of introduction into Mediterranean Sea. In total, 17 haplotypes and 18 alleles were recovered from all surveyed populations. Haplotype and allelic diversity of Mediterranean populations were comparable to populations from which they were likely drawn. The distribution of genetic diversity and pattern of genetic differentiation suggest initial colonization of the Mediterranean from the Black-Azov Seas (pairwise FST = 0.001–0.028). However, some haplotypes and alleles from the Mediterranean Sea were not detected from the well-sampled Black Sea, although they were found in Gulf of Mexico populations that were also genetically similar to those in the Mediterranean Sea (pairwise FST = 0.010–0.032), raising the possibility of multiple invasion sources. Multiple introductions from a combination of Black Sea and native region sources could be facilitated by intense local and transcontinental shipping activity, respectively

Creating opportunities through science symposia

For most marine scientists, unless we work in the field of fisheries development or at the interface of science and policy, it is rare to feel that we are making an impact on the lives of people in the wider community. Most research scientists at universities and government laboratories also have limited opportunity to engage with schools and the general public outside of once-a-year open days. But beyond the science and networking, conferences, especially international conferences, can provide a myriad of opportunities for us to redress both these issues in a way that enriches all. Here, we describe the programme of development-related activities that supported the 6th International Jellyfish Blooms Symposium, and their impact, and we urge it be used as a template for other scientific meetings in the future. Jellyfish are far more than merely an interesting find on the beach. On the one hand, when abundant, jellyfish can cause economic harm to the tourism, aquaculture, fisheries and energy sectors1, but on the other hand, they provide food for other animals, e.g. turtles, shelter for juvenile fish and a potential resource to exploit2. In recognition of their role in marine ecosystems, the international jellyfish community updates and renews itself at a conference every 3 years or so. The first meeting was held in the USA in January 2000 and after conferences in Australia, Argentina, Japan and Spain, Africa’s turn came in 2019, after Monty Graham (University of Southern Mississippi) convinced one of us (M.J.G.) to host the conference at the University of the Western Cape

A nonlinear mixed-effects approach for the mechanistic interpretation of time-series transcriptomics data

Mechanistic models are essential to unravel the molecular mechanisms driving cellular responses. However, the integration of high-throughput data with mechanistic knowledge is limited by the availability of scalable computational approaches able to disentangle biological and technical sources of variation. Results: We present an approach based on nonlinear mixed-effects modelling for the parameter estimation of large-scale mechanistic models from time-series transcriptomics data. It allows to factor out technical variability, to compensate for the limited number of conditions and time points by a population approach, and it incorporates mechanistic details to gain insight on the molecular causes of biological variability. We applied our approach for the biological interpretation of microarray and RNA-Seq gene expression profiles, with different levels of technical noise, but it is generalisable to numerous types of data. When integrated in a model describing the degradation kinetics of all cellular mRNAs, the data allowed to identify the targets of post-transcriptional regulatory mechanisms. Our approach paves the way for the interpretation of high-throughput biological data with more comprehensive mechanistic models. Availability: The Monolix script for estimation and output files are freely available at https://gitlab.inria. fr/tetienne/eccb_script, together with the microarray data. The RNA-Seq dataset is being prepared for publication (Roux et al., in preparation) and will be made available on demand upon acceptance of the article

Poly-phased fluid flow in the giant fossil pockmark of Beauvoisin, SE basin of France

The giant Jurassic-aged pockmark field of Beauvoisin developed in a 800 m wide depression for over 3.4 Ma during the Oxfordian; it formed below about 600 m water depth. It is composed of sub-sites organized in clusters and forming vertically stacked carbonate lenses encased in marls . This fine-scale study is focused on a detailed analysis of petrographical organization and geochemical signatures of crystals that grew up in early to late fractures of carbonate lenses, surrounding nodules, and tubes that fed them. The isotopic signature (C, O and Sr) shows that at least three different episodes of fluid migration participated to the mineralization processes. Most of the carbonates precipitated when biogenic seepage was active in the shallow subsurface during the Oxfordian. The second phase occurred relatively soon after burial during early Cretaceous and thermogenic fluids came probably from underlying Pliensbachian, Late Toarcian or Bajocian levels. The third phase is a bitumen-rich fluid probably related to these levels reaching the oil window during Mio-Pliocene. The fluids migrated through faults induced by the emplacement of Triassic-salt diapir of Propiac during the Late Jurassic and that remained polyphased drain structures over time

Repurposing Metformin in Nondiabetic People With HIV:Influence on Weight and Gut Microbiota

Background. People with HIV (PWH) taking antiretroviral therapy (ART) may experience weight gain, dyslipidemia, increased risk of non-AIDS comorbidities, and long-term alteration of the gut microbiota. Both low CD4/CD8 ratio and chronic inflammation have been associated with changes in the gut microbiota of PWH. The antidiabetic drug metformin has been shown to improve gut microbiota composition while decreasing weight and inflammation in diabetes and polycystic ovary syndrome. Nevertheless, it remains unknown whether metformin may benefit PWH receiving ART, especially those with a low CD4/CD8 ratio. Methods. In the Lilac pilot trial, we recruited 23 nondiabetic PWI I receiving ART for more than 2 years with a low CD4/CD8 ratio ( Results. Metformin decreased weight in PWH, and weight loss was inversely correlated with plasma levels of the satiety factor GDF-15. Furthermore, metformin changed the gut microbiota composition by increasing the abundance of anti-inflammatory bacteria such as butyrate-producing species and the protective Akkermansia muciniphila. Conclusions. Our study provides the first evidence that a 12-week metformin treatment decreased weight and favored anti-inflammatory bacteria abundance in the microbiota of nondiabetic ART-treated PWH. Larger randomized placebo-controlled clinical trials with longer metformin treatment will be needed to further investigate the role of metformin in reducing inflammation and the risk of non-AIDS comorbidities in ART-treated PWH

Artisanal and farmer bread making practices differently shape fungal species community composition in French sourdoughs

Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to the Kazachstania genus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence of Kazachstania humilis in sourdoughs made with artisanal-like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and non-sourdough strains were found for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities

La TD-GC×GC-HRTOFMS pour investiguer la fibrose pulmonaire chez des patients

Comprehensive two-dimensional gas chromatography has a great potential for exhaled breath analysis. The increased peak capacity and sensitivity, provided by the combination of two capillary columns of different stationary phases by means of a modulator, enable the chromatographic separation and detection of thousands of compounds from a complex matrix. For this reason, we carried out an exploratory study on SSc. Basically, breath samples were collected in 5L Tedlar® bags. Volatiles contained in the sampling bag were then transferred onto Tenax®GR/Carbopack™B thermal desorption tubes and finally released and separated into a Pegasus GC-HRT 4D through a mid-polar Rxi-624SilMS as first column (dimension) and a polar Stabilwax as second dimension. The exhaled breath of 32 patients and 30 healthy subjects was therefore analyzed. The high resolving power of this approach and the use of statistical models enabled the identification of 16 compounds discriminating SSC patients from healthy ones. However, further investigations had to be held to reach a better disease classification. In fact, the biomarkers highlighted here could be related to the scarring of the lungs making these non-specific to SSCs. The second phase of the study aims to go deeper in patient stratification. Three groups were investigated: 50 SSC patients, 50 SSC-fibrosis patients and 50 ILD ones. The samples were collected at Maastricht medical center and CHU of Liège. All samples were then analyzed in the OBiACHem lab. Currently, a classification model is under construction to stratify patients based on their fibrosis status

BREATHOMICS APPROACH TO INVESTIGATE SYSTEMIC SCLEROSIS USING THERMAL DESORPTION AND COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY HIGH-RESOLUTION TIME-OF-FLIGHT MASS SPECTROMETRY

Systemic sclerosis (SSc) is a chronic and heterogenous auto-immune disease of unknown origin characterized by fibrosis, inflammation, vascular damages, and involvement of internal organs. Organ involvement appears at the early stage of the disease[1,2]. Interstitial lung disease (ILD) is one of the most common types of pulmonary involvement, responsible for the disease severity, and leading to high morbidity and mortality. One of the challenges in SSc remains the early diagnosis of patients with a high risk of disease progression driving mortality[3]. There is an unmet need for biological markers enabling SSc early diagnosis, prognosis, disease progression monitoring, and improving patients’ classification for more targeted therapies. Ideally, new diagnostic methods for SSc should be simple, fast, accurate, and cost-effective. Comprehensive two-dimensional gas chromatography (GC×GC) has a great potential for exhaled breath analysis. The increased peak capacity and sensitivity of GC×GC, provided by the combination of two capillary columns of different stationary phases by means of a modulator, enable the chromatographic separation and detection of thousands of compounds from a complex matrix[4]. For this reason, we carried out an exploratory study on SSc[5]. Basically, breath samples were collected in 5L Tedlar® bags. Volatiles contained in the sampling bag were then transferred onto Tenax®GR/Carbopack™B thermal desorption tubes (Markes International Ltd., Llantrisant, UK) and finally released and separated into a Pegasus GC-HRT 4D (LECO Corporation, St Joseph, MI, USA) through a mid-polar Rxi-624SilMS (30 m × 0.25 mm × 1.4 μm) as first column (dimension) and a polar Stabilwax (2 m × 0.25 mm ×0.5μm) as second dimension. The exhaled breath of 32 patients and 30 healthy subjects was therefore analyzed. The high resolving power of this approach and the use of statistical models enabled the identification of 16 compounds discriminating SSC patients from healthy ones[5]. However, further investigations had to be held to reach a better disease classification. In fact, the biomarkers highlighted here could be related to the scarring (fibrosis) of the lungs making these non-specific to SSCs. The second phase of the study aims to go deeper in patient stratification. Three groups were investigated: 50 SSC patients, 50 SSC-fibrosis patients and 50 ILD ones. The samples were collected at Maastricht medical center and CHU of Liège. All samples were then analyzed in the OBiACHem lab. Currently, a classification model is under construction to stratify patients based on their fibrosis status. [1] E. Zanatta, V. Codullo, J. Avouac, Y.A.-J. bone spine, undefined 2020, Elsevier (2019). [2] O. Bonhomme, B. André, F. Gester, … D. de S.-, undefined 2019, Academic.Oup.Com (n.d.). [3] J. Guiot, M. Henket, B. Andre, M. Herzog, N. Hardat, M.S. Njock, C. Moermans, M. Malaise, R. Louis, Clin. Epigenetics 12 (2020). [4] D. Zanella, J. Focant, F.A. Franchina, Anal. Sci. Adv. 2 (2021) 213–224. [5] D. Zanella, J. Guiot, P.-H. Stefanuto, L. Giltay, M. Henket, F. Guissard, B. André, M. Malaise, J. Potjewijd, F. Schleich, R. Louis, J.-F. Focant, Anal. Bioanal. Chem. 2021 41314 413 (2021) 3813–3822