Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth and abscisic acid responses of Medicago sativa to water stress at different growth stages

A pot experiment was conducted in a greenhouse with three alfalfa ( Medicago sativa ) cultivars, Aohan, Zhongmu No.1 and Sanditi, to examine the morphological and physiological responses of alfalfa to water stress. The response of alfalfa to water stress at different growth stages was generally similar, but varied among cultivars. At the branching, ﬂ owering and podding stages, the shoot biomasses of Aohan and Zhongmu No.1 were greatly affected by, and responded quickly to, water stress. The shoot biomass of Sanditi was not affected by mild water stress, but had a slight response to moderate and severe water stress. The root/shoot ratios in Aohan and Zhongmu No.1 were more sensitive to water stress than in Sanditi, with the root/shoot ratio in Aohan increasing most signi ﬁ cantly. At ﬂ owering, the root/shoot ratio was the highest and the effect of water stress the greatest. The abscisic acid (ABA) concentration in the roots of Aohan and Zhongmu No.1 increased under water stress, while in Sanditi there was only a slight or delayed response of ABA concentration.
Whole genome scan reveals the multigenic basis of recent tidal marsh adaptation in a sparrow

Natural selection acts on functional molecular variation to create local adaptation, the “good fit” we observe between an organism’s phenotype and its environment. Genomic comparisons of lineages in the earliest stages of adaptive divergence have high power to reveal genes under natural selection because molecular signatures of selection on functional loci are maximally detectable when overall genomic divergence is low. We conducted a scan for local adaptation genes in the North American swamp sparrow (Melospiza georgiana), a species that includes geographically connected populations that are differentially adapted to freshwater vs. brackish tidal marshes. The brackish tidal marsh form has rapidly evolved tolerance for salinity, a deeper bill, and darker plumage since colonizing coastal habitats within the last 15,000 years. Despite their phenotypic differences, background genomic divergence between these populations is very low, rendering signatures of natural selection associated with this recent coastal adaptation highly detectable. We recovered a multigenic snapshot of ecological selection via a whole genome scan that revealed robust signatures of selection at 31 genes with functional connections to bill shape, plumage melanism and salt tolerance. As in Darwin’s finches, BMP signaling appears responsible for changes in bill depth, a putative magic trait for ecological speciation. A signal of selection at BNC2, a melanocyte transcription factor responsible for human skin color saturation, implicates a shared genetic mechanism for sparrow plumage color and human skin tone. Genes for salinity tolerance constituted the majority of adaptive candidates identified in this genome scan (23/31) and included vasoconstriction hormones that can flexibly modify osmotic balance in tune with the tidal cycle by influencing both drinking behavior and kidney physiology. Other salt tolerance genes had potential pleiotropic effects on bill depth and melanism (6/31), offering a mechanistic explanation for why these traits have evolved together in coastal swamp sparrows, and in other organisms that have converged on the same “salt marsh syndrome”. As a set, these candidates capture the suite of physiological changes that coastal swamp sparrows have evolved in response to selection pressures exerted by a novel and challenging habitat.
Effect of a Yeast Cell Wall Preparation on Cecal and Ovarian Colonization With Salmonella enteritidis in Commercial Layers

SUMMARY Salmonella enteritidis (S.E.) was the most common serotype in human infections in 2016. Various yeast products have been shown to inhibit colonization of chickens by Salmonella and could be a useful adjunct in an S.E. control strategy. This study sought to determine whether feeding a yeast cell wall product (Celmanax SCP) at 100 ppm to commercial layer pullets either from 1 d to 17 wk or from 10 to 17 wk would affect S.E. colonization of both the digestive tract and ovaries. At 16 wk of age, the pullets were orally challenged with 1.8 × 109 CFU S.E. and then ceca and ovaries were assayed at 1 wk post challenge for S.E. prevalence and load. The colonization level was very high in the ceca with many counts too numerous to count (>106 most probable number (MPN)/g, TNTC). A censored regression model was used to account for the large number of TNTC samples from each treatment group. Both of the Celmanax SCP‐treated groups had an estimated marginal mean log10 MPN that was numerically lower than that of the untreated challenged positive control group by about 1.5 log10, and while this difference approached significance, it was not significant at the 5% level (P = 0.056). Although the proportion of isolates that exceeded the upper limit of the MPN assay was numerically lower for the group fed Celmanax SCP from day 1 (25.5%) than for the group fed Celmanax SCP from 10 wk (43.8%), or the untreated challenged positive control (47.9%), this difference again approached but did not achieve significance at the 5% level (P = 0.060). Also, there was no significant difference between challenged treatment groups with respect to ovary Salmonella prevalences (P = 0.322).
Visual features contribute differently to preferences for different item categories

Low-level visual features have been known to play a role in value-based decision-making. However, thus far, mainly single features were tested on one type of item using one method of measurement. Here, we test the contribution of low-level visual features on three items types: fractal-art images, faces, and snack food items. We test the role of visual features on preferences using both subjective ratings and choices. We show that low-level visual features contribute to value-based decision-making even after controlling for higher level configural features of faces like eye-distance and market features of snacks like calories. Importantly, we show that while low-level visual features consistently contribute to value-based decision-making, different features contribute to different types of items when using different measurement methods. Our study highlights the necessity of using multiple item types and multiple measurement methods to construct a unifying framework regarding the contribution of low-level features to value-based decision-making.
Phenolic Substances in Beer: Structural Diversity, Reactive Potential and Relevance for Brewing Process and Beer Quality.

For the past 100 years, polyphenol research has played a central role in brewing science. The class of phenolic substances comprises simple compounds built of 1 phenolic group as well as monomeric and oligomeric flavonoid compounds. As potential anti- or prooxidants, flavor precursors, flavoring agents and as interaction partners with other beer constituents, they influence important beer quality characteristics: flavor, color, colloidal, and flavor stability. The reactive potential of polyphenols is defined by their basic chemical structure, hydroxylation and substitution patterns and degree of polymerization. The quantitative and qualitative profile of phenolic substances in beer is determined by raw material choice. During the malting and brewing process, phenolic compounds undergo changes as they are extracted or enzymatically released, are subjected to heat-induced chemical reactions or are precipitated with or adsorbed to hot and cold trub, yeast cells and stabilization agents. This review presents the current state of knowledge of the composition of phenolic compounds in beer and brewing raw materials with a special focus on their fate from raw materials throughout the malting and brewing process to the final beer. Due to high-performance analytical techniques, new insights have been gained on the structure and function of phenolic substance groups, which have hitherto received little attention. This paper presents important information and current studies on the potential of phenolics to interact with other beer constituents and thus influence quality parameters. The structural features which determine the reactive potential of phenolic substances are discussed.
dispRity: A modular R package for measuring disparity

Biological data is multivariate in essence: many traits in organisms covary with each other in space and time. This causes biologists to either reduce these to a manageable number of variables or, increasingly, to use multivariate toolkits. One such toolkit is based on creating a multidimensional space where the variables are the axes. It is then possible to measure diverse aspects of the distribution of some observation (e.g. species) in this space. For example, if studying morphology, one can create a morphospace for two groups of species, measure the volume occupied by each of these groups and then test whether these two volumes are significantly different or not. There are as many definitions of these multidimensional spaces, metrics and tests as there are questions that can be tackled with such methods. Many of these methods are implemented in specific software or r packages. However, the definition of the space, metric and test is often dependent on the software/package and authors points of view or specific questions. This can unfortunately hamper researchers’ ability to apply different methods that best suits their specific questions. Here I present the dispRity package, a flexible R package for performing multidimensional analysis. It allows users to define each step of the analysis (whether it is the space, the metric or the test) through a highly modular architecture where each definition can be passed as a function. It also provides a tidy interface through the dispRity object, allowing users to easily run reproducible multivariate analysis. The dispRity package also comes with an extend manual regularly updated following users’ questions or suggestions. Furthermore, the package contains some simulation tools (e.g to simulate complex multidimensional space or morphological data). Finally, it also contains a suite of utility functions to work with dispRity objects aimed at helping users to develop their own multidimensional metrics and/or tests.
Control and manipulation of angiogenesis in the primate ovarian follicle

of Thesis The ovary is one of the most plastic tissues in the body undergoing constant serial remodelling throughout its reproductive lifetime, during both folliculogenesis and the formation and regression of the corpus luteum. The process of follicle growth and selection is intimately associated with the de novo establishment of vasculature supporting the developing follicles. Blood vessels are recruited from the ovarian stroma to form vascular sheaths surrounding each developing follicle supplying steroid hormone precursors, oxygen and nutrients to the expanding follicle. During folliculogenesis only the theca of the developing follicle becomes vascularised, the granulosa cells remaining avascular until ovulation at which point the basement membrane that has been separating the granulosa and theca breaks down. After ovulation the granulosa cells become heavily vascularised during the process of luteinisation and the formation of the corpus luteum. Angiogenesis, the growth of new blood vessels from the pre-existing vasculature, requires the degradation of the established vessels followed by endothelial cell proliferation and finally stabilisation of the new vessels. Recently, techniques to quantify angiogenesis, identify putative molecular regulators, and inhibit them in vivo have become available. The work in this thesis applies these advances to the following questions: 1) What is the effect of the inhibition of the gonadotrophins, using a gonadotrophin releasing hormone (GnRH) antagonist, on follicular angiogenesis? The hypothesis being tested was that follicular angiogenesis would be dependent on follicle stimulating hormone (FSH) / luteinising hormone (LH) and be severely inhibited by GnRH antagonist treatment. In vivo follicular angiogenesis was assessed by quantitative immunocytochemistry of bromodeoxyuridine and the endothelial cell marker CD31. The effect of treatment on follicular development and angiogenesis at the molecular level was assessed by in situ hybridisation of mRNA for vascular endothelial growth factor (VEGF) and aromatase. The results suggest that while VEGF expression in the preovulatory follicle is under gonadotrophic control, it is not dependent on normal gonadotrophin secretion in tertiary follicles, indicating that there are other paracrine factors regulating VEGF expression in the
A new genus for Cirolana troglexuma Botosaneanu & Iliffe, 1997, an anchialine cave dwelling cirolanid isopod (Crustacea, Isopoda, Cirolanidae) from the Bahamas

Cirolana troglexuma Botosaneanu & Iliffe, 1997 is redescribed and a Lucayalana Bruce & Brix, gen. n. established for the species. In total 38 specimens were collected from Hatchet Bay Cave, Eleuthera. Specimens on which previous records of L. troglexuma (from Exuma Cays, Cat Island, and Eleuthera) were based have been re-examined when possible. The diagnostic identifying characters and purported apomorphies for Lucayalana gen. n. are: frontal lamina short, narrow, less than 7% width of labrum, not extending to anterior margin of head; pleonite 3 extending posteriorly to posterior of pleonite 5, laterally overlapping pleonites 4 and 5; ventrally broad, forming a strong ventrally directed blade; pereopods 1–3 merus inferior margin RS not molariform. Mitochondrial COI and 16S loci and the nuclear 18S locus data show that all specimens are the one species. Comparison to additional cirolanid COI sequence data Subterranean Biology 21: 57–92 (2017) doi: 10.3897/subtbiol.21. 11181 http://subtbiol.pensoft. net Copyright Niel L. Bruce et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. RESEARCH ARTICLE Subterranean Biology Published by The International Society for Subterranean Biology A peer-reviewed open-access journal
Post-translational modifications regulatory networks : evolution, mechanisms et implications

One of the most important challenges in systems biology is to understand how cells respond to genetic and environmental perturbations. Here we show that the yeast DHFRPCA, coupled with high-resolution growth profiling (DHFR-qPCA), is a straightforward assay to study the modulation of protein-protein interactions (PPIs) in vivo as a response to genetic, metabolic and drug perturbations. Using the canonical Protein Kinase A (PKA) pathway as a test system, we show that changes in PKA activity can be measured in living cells as a modulation of the interaction between its regulatory (Bcy1) and catalytic (Tpk1, Tpk2) subunits in response to changes in carbon metabolism, caffeine and methyl methanesulfonate (MMS) treatments and to modifications in the dosage of its enzymatic regulators, the phosphodiesterases. Our results show that the DHFR-qPCA is easily implementable and amenable to high-throughput. The DHFR-qPCA will pave the way to the study of the effects of drug, genetic and environmental perturbations on in vivo PPI networks, thus allowing the exploration of new spaces of the eukaryotic interactome.
Single cell functional genomics reveals the importance of mitochondria in cell-to-cell variation in proliferation, drug resistance and mutation outcome

Mutations frequently have outcomes that differ across individuals, even when these individuals are genetically identical and share a common environment. Moreover, individual microbial and mammalian cells can vary substantially in their proliferation rates, stress tolerance, and drug resistance, with important implications for the treatment of infections and cancer. To investigate the causes of cell-to-cell variation in proliferation, we developed a high-throughput automated microscopy assay and used it to quantify the impact of deleting >1,500 genes in yeast. Mutations affecting mitochondria were particularly variable in their outcome. In both mutant and wild-type cells mitochondria state – but not content – varied substantially across individual cells and predicted cell-to-cell variation in proliferation, mutation outcome, stress tolerance, and resistance to a clinically used anti-fungal drug. These results suggest an important role for cell-to-cell variation in the state of an organelle in single cell phenotypic variation.
The role of genetics, growth habit, and cultural practices in the mitigation of Fusarium head blight

Abstract: Field trials were conducted under natural infection and artificial inoculation from 2012 to 2014 at seven sites across the Canadian prairies to determine genetic and management effects on Fusarium head blight (FHB) in wheat production systems. A system of management, which consisted of (1) a control of no fungicide was compared with (2) the seed treatment (ST) thiamethoxam + difenoconazole + metalaxyl-M + S-isomer, (3) an in-crop foliar fungicide (tebuconazole + prothioconazole), or (4) ST + foliar fungicide, was integrated with four wheat cultivars of contrasting growth habits and levels of FHB resistance. Results indicated the cultivars expressing improved FHB resistance, Carberry (spring wheat) and Emerson (winter wheat), were superior over susceptible cultivars, Harvest (spring wheat) and CDC Falcon (winter wheat), in reducing Fusarium-damaged kernel (FDK) and deoxynivalenol (DON) levels, and displayed higher yield under high Fusarium pressure. Winter wheat displayed higher overall yield, with Emerson producing the highest and most stable yields across environments. Application of foliar fungicide, with or without the ST, increased grain yield, seed mass, and test weight; and lowered FDK and DON. Seed treatment alone increased test weight, spring plant density of both winter wheat varieties, and kernel weight in Emerson. A management strategy of foliar fungicide and (or) ST + foliar fungicide generally produced higher yields with greater stability, particularly for susceptible cultivars in high FHB environments. The results of this study reinforce that integration of FHB-resistant cultivars with appropriate cultural practices is required to reduce the risk of FHB and optimize grain yield, and is further enhanced with a winter vs. spring growth habit.
The effect of light conditions on interpreting oil composition engineering in Arabidopsis seeds

Abstract Arabidopsis thaliana is the most developed and utilized model plant. In particular, it is an excellent model for proof‐of‐concept seed oil engineering studies because it accumulates approximately 37% seed oil by weight, and it is closely related to important Brassicaceae oilseed crops. Arabidopsis can be grown under a wide variety of conditions including continuous light; however, the amount of light is strongly correlated with total seed oil accumulation. In addition, many attempts to engineer novel seed oil fatty acid compositions in Arabidopsis have reported significant reductions in oil accumulation; however, the relative reduction from the nontransgenic controls varies greatly within the literature. A set of experiments were conducted to systematically analyze the effect of light conditions (including day/night cycle vs. continuous light, and different light intensities) on the relative accumulation of seed oil between three different transgenic lines producing novel hydroxy fatty acids and their nontransgenic background. Oil content was measured per seed and as a percentage of seed weight. Our results indicate the relative amount of seed oil between transgenic lines and nontransgenic controls is dependent on both the light conditions and the type of oil content measurement utilized. In addition, the light conditions effect the relative accumulation of the novel fatty acids between various transgenic lines. Therefore, the success of novel fatty acid proof‐of‐concept engineering strategies on both oil accumulation and fatty acid composition in Arabidopsis seeds should be considered in light of the select growth and measurement conditions prior to moving engineering strategies into crop plants.
Acidic pH-dependent depletion of Mycobacterium tuberculosis thiol pools potentiates antibiotics and oxidizing agents

Mycobacterium tuberculosis (Mtb) must sense and adapt to immune pressures such as acidic pH and reactive oxygen species (ROS) during pathogenesis. The goal of this study was to isolate compounds that inhibit acidic pH resistance, thus defining virulence pathways that are vulnerable to chemotherapy. Here we report that the acidic pH-dependent compound AC2P36 depletes intracellular thiol pools, sensitizes Mtb to killing by acidic pH, and potentiates the bactericidal activity of isoniazid, clofazimine, and oxidizing agents. We show that the pHdependent activity of AC2P36 is associated with metabolic stress at acidic pH and a pHdependent accumulation of intracellular ROS. Mechanism of action studies show that AC2P36 directly depletes Mtb thiol pools. These data support a model where chemical depletion of Mtb thiol pools at acidic pH enhances sensitivity to oxidative damage, resulting in bacterial killing and potentiation of antibiotics.
Functional genetic studies of symbiotic genes in Medicago truncatula indicate a role for a CCAAT-box transcription factor in rhizobial infection

ABSTRACT Legumes form mutualistic associations with nitrogen-fixing bacteria and arbuscular mycorrhizal (AM) fungi which increases nutrient availability to the plant. Nodulation is generally restricted to legumes and has co-opted genes required for the AM symbiosis. As a result, both associations share common genes and have analogous infection strategies, including the early lipochitooligosaccharide (LCO) signals that plants perceive from the symbionts. In order to discover novel genes required for both these symbioses, I used both forward and reverse genetic approaches. A forward genetic screen in Medicago truncatula revealed an H+-ATPase mutant Mtha1 with a defective arbuscule phenotype. The reverse screen investigated several candidates previously identified as having enhanced expression in the nodule inception mutant during nodulation that were also expressed in AM-colonized roots. Four of these genes were chosen for further study. The first, a novel AM-specific gene, BiFunctional Protein (BFP) has a predicted a role in lipid modification. Phylogenetic analysis revealed that BFP was restricted to AM host plants including a member of the liverworts, Marchantia paleacea. BFP expression during AM interactions in M. truncatula was found to be dependent on the common symbiotic gene DOES NOT MAKE INFECTIONS 3. AM colonization assays using mutants for BFP in M. truncatula and Oryza sativa were inconclusive. Three CCAAT-Binding Factor transcription factors were also studied (CBF1, CBF2 and CBF3). Promoter-reporter studies revealed that these genes are also expressed during rhizobial infection of wild type plants. While the M. truncatula cbf1 mutant did not exhibit a consistent nodulation phenotype, mutant analysis for CBF3, showed it is required for normal infection during root hair colonisation of rhizobia in M. truncatula. Based on these results and a further analysis of expression data and published work, I propose a model in which CBF3 forms a complex with NF-YA1 and NF-YC2 during early responses to LCOs during nodulation.