Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm trading and sex roles in the hermaphroditic opisthobranch sea slug Navanax inermis : eager females or opportunistic males?

The sea slug Navanax inermis (Gastropoda, Opisthobranchia) is a well-known example of a simultaneous hermaphrodite in which mating partners trade sperm. According to previous work by others, sperm trading follows from a general preference for the female role when the expected variance in reproductive success in the male role is higher and the risk of failure therefore larger. However, this view contradicts theoretical and empirical studies of other systems, which predict a general preference for the male role; sperm trading is assumed to follow from the fact that individuals benefit from sperm receipt as a nutritional compensation for sperm investment. In this study, we investigate the behaviour of N. inermis in more detail. In addition to observations of regular pairs, we also paired individuals with a partner that had been isolated for 33 days in order to induce changes in sex-role preference in the non-isolated partner. We also collected all clutches produced throughout the study to check for signs of infertility as a consequence of allosperm depletion. Fertility of field-collected and isolated individuals suggested that sperm depletion occurs under natural conditions and may be caused by a lack of partners. Although this argues in favour of female preference, low mating rates both reduce variance in male reproductive success and remove the intent to use sperm for nutritional purposes, thus eliminating the conditions under which both hypotheses are intended to operate. The observational data indicate that animals are eager to mate as males, particularly at the beginning of a mating session. Intromissions lasted longer when a simultaneous intromission was received from the partner. Increases in intromission were recorded in non-isolated individuals with partners which were previously isolated and therefore more attractive as females. This response would not have been expected were the female role the preferred one. A summary of the arguments concerning preference for either gender suggests some preference for the male role, but indicates that sexual preferences may actually change or become neutral within an individual, even in the course of a mating session. Overall, our results clearly confirm previously published observations of sperm trading in N. inermis . © 2003 The Linnean Society of London . Biological Journal of the Linnean Society, 2003, 78 , 105 - 116. ADDITIONAL KEYWORDS: sexual conflict ‐ sexual selection ‐ Gastropoda ‐ reciprocity ‐ gamete trading ‐ sperm trading ‐ egg trading.
THE GENERALITY OF FIELD EXPERIMENTS: INTERACTIONS BETWEEN LOCAL AND BROAD-SCALE PROCESSES

Linking the results of localized field experiments to generalities about the role of specific processes is essential in ecology. Comparative studies conducted at multiple locations enable the general importance of processes to be assessed. However, spatial or temporal variation in the strength of local ecological relationships frequently makes it difficult to draw general conclusions, as increasing the extent of a study is likely to increase the physical and biological heterogeneity. To unravel the influence of differences in wave climate on local ecological interactions among adult and juvenile sandflat bivalves, an experiment was conducted at three sites in each of three harbors in the North Island of New Zealand. The selected sites covered a range of wind-wave exposures but were all mid-intertidal sandflats with macrobenthic communities dominated by bivalves. Four treat- ments were used: additions of 0, 15, 45, and 110 adults of the tellinid bivalve Macomona liliana. At each site a DOBIE wave gauge was used to provide time-series data on wave orbital speed at the seabed over the 35-d duration of the experiment. Significant experiment x location interactions indicated site-dependent variation in the strength and direction of treatment effects. However, multiple regression models based on site environmental char- acteristics were very successful in explaining differences between sites in the strength of experimental treatment effects (66-99% of the variance explained). We used the cube of the orbital wave velocity at the seabed (U3) as an index of energy dissipation by waves. Both the site average and maximum U3 were important variables explaining location- dependent treatment effects. Average U} increased the strength of the negative effects of experimental additions of adult Macomona on juvenile bivalves, presumably by increasing the opportunity for juvenile bivalves to be resuspended by small waves and transported away from areas with high adult densities. Maximum U3 decreased the strength of the experimental effects, probably by increasing the purely passive transport of juveniles with sediment bedload and thus obliterating patterns in the distribution of juvenile bivalves relative to adult Macomona. Hence, different aspects of the wave climate influenced adult- juvenile interactions in different ways. Ambient density of adult Macomona around the experimental sites was also an important factor. This multisite experiment confirmed the importance of local adult-juvenile interactions and suggested ways in which these inter- actions are influenced by local environmental characteristics. Where the influence of such broad-scale variables can be identified, linking broad-scale information to small-scale stud- ies that identify mechanisms can increase the generality of ecological experiments.
Effects of paclitaxel and cisplatin on in vitro ovarian follicle development

Introduction Despite its importance in pre-chemotherapy counselling, specific reproductive toxicological information about cisplatin and paclitaxel is very rare. This study aimed to investigate the concentrations at which cisplatin and paclitaxel, alone or combined, affect the in vitro development of ovarian follicles. Their differential effects on the oocytes and surrounding granulosa cells was also evaluated. Material and methods Ovarian follicles were cultured in vitro using gonadotropins and treated with 10–8–10–10 M of cisplatin, paclitaxel, or both. At day 13, granulosa cells and oocytes were retrieved and used for imaging and functional analyses. Results Follicular survival and growth was significantly suppressed in all treatment groups at 10–9 M or higher concentrations, and additive effects were observed in the combination group (p < 0.01). Oocyte-specific genes such as growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) were more suppressed in the paclitaxel group than in the cisplatin group. Granulosa cell-specific gene suppression and its electron microscopic alteration were more prominent in the cisplatin group than in the paclitaxel group. X-linked inhibitor of apoptosis protein (XIAP) expression of granulosa cells was also further down-regulated in the cisplatin group. Conclusions These data provide an insight into the critical concentrations regarding in vitro follicular development and the differential effects of chemotherapeutic effects on oocytes and granulosa cells. Further studies are necessary to develop more efficient pre-chemotherapeutic fertility-sparing medical treatment that can evade oocyte-specific damage.
Autoinhibition of Casein Kinase I ε (CKIε) Is Relieved by Protein Phosphatases and Limited Proteolysis*

Casein kinase I ε (CKIε) is a member of the CKI gene family, members of which are involved in the control of SV40 DNA replication, DNA repair, and cell metabolism. The mechanisms that regulate CKIε activity and substrate specificity are not well understood. We report that CKIε, which contains a highly phosphorylated 123-amino acid carboxyl-terminal extension not present in CKIα, is substantially less active than CKIα in phosphorylating a number of substrates including SV40 large T antigen and is unable to inhibit the initiation of SV40 DNA replication. Two mechanisms for the activation of CKIε have been identified. First, limited tryptic digestion of CKIε produces a protease-resistant amino-terminal 39-kDa core kinase with several-fold enhanced activity. Second, phosphatase treatment of CKIε activates CKIε 5–20-fold toward T antigen. Similar treatment of a truncated form of CKIε produced only a 2-fold activation. Notably, this activation was transient; reautophosphorylation led to a rapid down-regulation of the kinase within 5 min. Phosphatase treatment also activated CKIε toward the novel substrates IκBα and Ets-1. These mechanisms may serve to regulate CKIε and related forms of CKI in the cell, perhaps in response to DNA damage.
Resistance of winter wheat varieties registered in the Czech Republic to mycotoxin accumulation in grain following inoculation with Fusarium culmorum

Resistance of 35 winter wheat varieties to the accumulation of mycotoxins deoxynivalenol (DON) and zearalenone (ZEA) in grain was evaluated in field trials lasting three years (2004, 2005, 2006) after artificial inoculation with Fusarium culmorum . Data on DON and ZEA content were supplemented by symptom scores and determination of % of Fusarium damaged grains and % reductions of thousand grain weight and grain weight per spike due to infection. The conditions of experimental years highly influenced the performance of all characters. The highest production of DON occurred in 2006 at a high temperature and high moisture con - tent during the infection period. Moderate resistance to the accumulation of DON (at the level of Swiss variety Arina) was detected in the varieties Apache, Samanta, Simila and Alana. Another six varieties (Rheia, Banquet, Ludwig, Rapsodia, Dromos and Globus) also showed relatively low average DON content, but a higher fluctua - tion in experimental years. DON content was positively related to ZEA content and significant correlations were also detected between DON content and the examined disease severity traits. In all years the earlier varieties showed lower DON accumulation than later varieties, but the effects of genotype earliness on the other traits, including ZEA content, were not often significant (not similar under different conditions). The obtained results could help to improve the classification of varieties from these aspects, which is desirable for recommendation on their use in practice and breeding.
The control of glycogen metabolism in yeast

Two interconvertible forms of glycogen synthase and glycogen phosphorylase, one active (a) or the other less active (b), were predominantly present in a thermosensitive adenylate-cyclase-deficient mutant that had been preincubated at the restrictive temperature of 35°C, either in the presence or in the absence of glucose. Glycogen phosphorylase was at least 20-fold less active after incubation of the cells in the presence of glucose, but this residual activity had kinetic properties identical to those of the active form of enzyme, obtained after incubation in the absence of glucose; this suggests that the b form might be completely inactive and that the low activity measured after glucose treatment must be attributed to a residual amount of phosphorylase a. By contrast, the kinetic properties of the two forms of glycogen synthase were very different. When measured in the absence of glucose 6-phosphate, the two forms of enzyme had a similar affinity for UDP-Glc but differed essentially by their Vmax. Glucose 6-phosphate had no effect on synthase a, but increased both Vmax and Km, of synthase b; these effects, however, were in great part counteracted by sulfate and by inorganic phosphate, the latter also having the property of increasing the Km, of the a form, without affecting Vmax. It was estimated that at physiological concentrations of substrates and effectors, synthase a was about 20-fold more active than synthase b. When an extract of cells that had been preincubated in the absence of glucose was gel-filtered and then incubated at 30°C, phosphorylase was progressively fully inactivated and synthase was partially activated; these reactions were severalfold faster and, in the case of glycogen synthase, more complete in the presence of 10 mM glucose 6-phosphate. When a gel-filtered extract of cells that had been preincubated in the presence of glucose was incubated at 30°C in the presence of ATP-Mg and EGTA, phosphorylase became activated and synthase was inactivated; the first of these two reactions was severalfold stimulated by micromolar concentrations of Ca2+, whereas both reactions were completely inhibited by 10 mM glucose 6-phosphate and only slightly and irregularly stimulated by cyclic AMP.
The Heating Microenvironment: Intercellular Cross Talk Within Thermogenic Adipose Tissue

Adipose tissue serves as the body’s primary energy storage site; however, findings in recent decades have transformed our understanding of the multifaceted roles of this adaptable organ. The ability of adipose tissue to undergo energy expenditure through heat generation is termed adaptive thermogenesis, a process carried out by thermogenic adipocytes. Adipocytes are the primary parenchymal cell type in adipose tissue, yet these cells are sustained within a rich stromal vascular microenvironment comprised of adipose stem cells and progenitors, immune cells, neuronal cells, fibroblasts, and endothelial cells. Intricate cross talk between these diverse cell types is essential in regulating the activation of thermogenic fat, and the past decade has shed significant light on how this intercellular communication functions. This review will draw upon recent findings and current perspectives on the sophisticated repertoire of cellular and molecular features that comprise the adipose thermogenic milieu.
Patient-derived glioblastoma cells (GBM) exhibit distinct biomechanical profiles associated with altered activity in the cytoskeleton regulatory pathway

Glioblastoma multiforme (GBM) is the most commonly diagnosed brain cancer in adults, characterized by rapid proliferation and aggressive invasion into the stroma. Advances in our understanding of the molecular subtypes of GBM have provided attractive druggable targets. However, the high degree of heterogeneity both among patients and within individual tumors has proven a significant challenge for the development of effective therapies. We hypothesized that this heterogeneity is also represented in the mechanical phenotypes of GBM, as the physical properties of tumor tissue strongly influence elements of tumor progression including cell cycle regulation, migration, and therapeutic resistance. To assess these phenotypes, we employed optical trap-based active microrheology to determine the viscoelastic properties of patient-derived GBM cells in 3D hydrogels mimicking the brain ECM. We found that each GBM cell line had a distinct rheological profile as a function of treatment status, and cell lines could be further characterized by strong power law dependence describing intracellular viscoelastic behavior. Single-cell phenotyping according to power law dependence was able to identify subpopulations of cells within the treatment-resistant line. Finally, proteomic analysis indicated that altered mechanical profiles were associated with differential cytoskeletal regulation, particularly in actin - and myosin-binding pathways. This work suggests that evaluating mechanical properties may serve as a valuable strategy for the further stratification of these tumors, and encourages the investigation of cytoskeleton regulation as a potential therapeutic target for GBM.
Probabilistic Ranking Of Microbiomes Plus Taxa Selection to discover and validate microbiome function models for multiple litter decomposition studies

The overwhelming complexity of microbiomes makes it difficult to decipher functional relationships between specific microbes and ecosystem properties. While machine learning analyses have demonstrated an impressive ability to correlate microbial community composition with macroscopic functions, mechanisms that dictate model predictions are often unknown, and predictions often lack an assigned metric of uncertainty. In this study, we apply Bayesian networks to build on prior feature selection analyses and construct easy-to-interpret probabilistic models, which accurately predict levels of dissolved organic carbon (DOC) from the relative abundance of soil bacteria (16S rRNA gene profiles). In addition to standard cross-validation, we show that a Bayesian network model trained using samples from a pine litter decomposition study accurately predicts DOC of samples from an independent oak litter decomposition study, suggesting that mechanisms driving variation in soil carbon storage may be conserved across different types of decomposing plant litter. Furthermore, the structure of the resulting Bayesian network model defines a minimal set of highly informative taxa, whose abundances directly constrain the probability of high or low DOC conditions. Significant accuracy of the Bayesian network model with independent data sets supports the validity of the identified relationships between taxa abundance and DOC. Summary Understanding the interplay between microbiomes and the environments they inhabit is a daunting task. While recent advances in gene sequencing technology provide a means of profiling the relative abundance of microbial species, the resulting data are noisy, sparse, and limited to small sample sizes. Despite these challenges, machine learning approaches have demonstrated a promising ability to discover patterns linking the microbiome with macroscopic behavior. However, most machine learning models applied to microbiome data do not estimate prediction uncertainty and provide little insight regarding how predictions are made. In this study, we couple machine learning approaches for feature reduction with Bayesian networks to model the relationship between the soil microbiome and dissolved organic carbon (DOC). We show that Bayesian networks are accurate and provide a transparent link between microbial abundance and DOC. To validate Bayesian networks, we demonstrate accurate predictions for held-out testing data and with data from independent decomposition experiments.
Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle

Adult muscles and their associated stem cells retain functional positional memory based on developmental origin. Muscle stem cells (satellite cells) are distributed throughout the body and have heterogeneous properties among muscles. However, functional topographical genes in satellite cells of adult muscle remain unidentified. Here, we show that expression of Homeobox-A (Hox-A) cluster genes accompanied with DNA hypermethylation of the Hox-A locus was robustly maintained in both somite-derived muscles and their associated satellite cells in adult mice, which recapitulates their embryonic origin. Somite-derived satellite cells were clearly separated from cells derived from cranial mesoderm in Hoxa10 expression. Hoxa10 inactivation led to genomic instability and mitotic catastrophe in somite-derived satellite cells in mice and human. Satellite cell–specific Hoxa10 ablation in mice resulted in a decline in the regenerative ability of somite-derived muscles, which were unobserved in cranial mesoderm–derived muscles. Thus, our results show that Hox gene expression profiles instill the embryonic history in satellite cells as positional memory, potentially modulating region-specific pathophysiology in adult muscles.
Resveratrol shortens the chronological lifespan of Saccharomyces cerevisiae by a pro-oxidant mechanism

Resveratrol consumption has linked with normalization of the risk factors of some diseases such as colon cancer and type 2 diabetes. The antioxidant phenotype caused by resveratrol has recognized as a key piece in the health benefits exerted by this phytochemical. Although the antioxidant activity showed by resveratrol has attributed at the molecule per se, recent evidence indicates that the antioxidant effect occasioned by resveratrol could be associated with a pro-oxidant mechanism. The hypothesis that resveratrol inhibits complex III of the electron transport chain as its main target suggests that resveratrol increases reactive oxygen species (ROS) generation produces via reverse electron transport. This idea also explains that cells respond to the oxidative damage caused by resveratrol, inducing their antioxidant systems. The free radical theory of aging postulates that organisms age due to the accumulation of the harmful effects of ROS in cells. For these reasons, we hypothesize that resveratrol shortens the chronological life span (CLS) of Saccharomyces cerevisiae due to a pro-oxidant activity. Herein, we provide evidence that 100 μM resveratrol supplementation at 5% glucose: 1) shorted the CLS of CTT1 and YAP1 genes deleted strains; 2) decreased the H2O2 release in the WT strain, and maintain unaltered the H2O2 release in the ctt1Δ strain; 3) lessened exponential growth of ctt1Δ strain, which was reverted with the adding of GSH; 4) increased catalase activity in the WT strain, a phenotype that was not observed in the ctt1Δ strain. Altogether, these results indicate that resveratrol decreases CLS by a pro-oxidant mechanism.
A novel sialic acid-binding adhesin present in multiple species contributes to the pathogenesis of Infective endocarditis

Bacterial binding to platelets is a key step in the development of infective endocarditis (IE). Sialic acid, a common terminal carbohydrate on host glycans, is the major receptor for streptococci on platelets. So far, all defined interactions between streptococci and sialic acid on platelets are mediated by serine rich repeat proteins (SRRPs). However, we identified Streptococcus oralis subsp. oralis IE-isolates that bind sialic acid but lack SRRPs. In addition to binding sialic acid, some SRRP-negative isolates also bind the cryptic receptor β-1,4-linked galactose through a yet unknown mechanism. Using comparative genomics, we identified a novel sialic acid-binding adhesin, here named AsaA (associated with sialic acid adhesion A), present in IE-isolates lacking SRRPs. We demonstrated that S. oralis subsp. oralis AsaA is required for binding to platelets in a sialic acid-dependent manner. AsaA comprises a non-repeat region (NRR), consisting of a FIVAR/CBM and two Siglec-like and Unique domains, followed by 31 DUF1542 domains. When recombinantly expressed, Siglec-like and Unique domains competitively inhibited binding of S. oralis subsp. oralis and directly interacted with sialic acid on platelets. We further demonstrated that AsaA impacts the pathogenesis of S. oralis subsp. oralis in a rabbit model of IE. Additionally, we found AsaA orthologues in other IE-causing species and demonstrated that the NRR of AsaA from Gemella haemolysans blocked binding of S. oralis subsp. oralis, suggesting that AsaA contributes to the pathogenesis of multiple IE-causing species. Finally, our findings provide evidence that sialic acid is a key factor for bacterial-platelets interactions in a broader range of species than previously appreciated, highlighting its potential as a therapeutic target. Authors summary Infective endocarditis (IE) is typically a bacterial infection of the heart valves that causes high mortality. Infective endocarditis can affect people with preexisting lesions on their heart valves (Subacute-IE). These lesions contain platelets and other host factors to which bacteria can bind. Growth of bacteria and accumulation of host factors results in heart failure. Therefore, the ability of bacteria to bind platelets is key to the development of IE. Here, we identified a novel bacterial protein, AsaA, which helps bacteria bind to platelets and contributes to the development of disease. Although this virulence factor was characterized in Streptococcus oralis, a leading cause of IE, we demonstrated that AsaA is also present in several other IE-causing bacterial species and is likely relevant to their ability to cause disease. We showed that AsaA binds to sialic acid, a terminal sugar present on platelets, thereby demonstrating that sialic acid serves as a receptor for a wider range of IE-causing bacteria than previously appreciated, highlighting its potential as a therapeutic target.