Miracle-dz/UniFAR-FTUs huggingface dataset:
Standing genetic variation in FRIGIDA mediates experimental evolution of flowering time in Arabidopsis

The role of standing genetic variation in adaptive evolution remains unclear. Although there has been much progress in identifying candidate genes that underlie adaptive traits, we still lack direct evidence that natural allelic variation in these genes can actually mediate adaptive evolution. In this study, we investigate the role of natural allelic variation in two candidate flowering time genes, in response to selection for early flowering in Arabidopsis thaliana: FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). We performed artificial selection for early flowering under ‘spring‐’ and ‘winter‐annual’ growth conditions using an outbred population of A. thaliana produced by intermating 19 natural accessions. FRI and FLC are involved in A. thaliana's response to winter conditions, and nonfunctional and weak alleles at these loci are know to reduce flowering time, particularly under spring‐annual conditions. Our results provide direct evidence that natural allelic variation in FRI can provide rapid and predictable adaptive evolution in flowering time under spring‐annual conditions. We observed a strong response to selection, in terms of reducing flowering time, in both growth conditions (~2 standard deviation reduction). Concomitantly, the frequency of functional FRI alleles under spring‐annual conditions was reduced by 68%, in agreement with predicted changes. No significant changes in allele frequencies were observed in FRI in the winter‐annual growth condition or in FLC for either growth conditions. These results indicate that changes in flowering time are mediated by different genetic factors under spring‐ and winter‐annual growth conditions, and that other loci must also be contributing to the response to selection.
Mono(2-Ethylhexyl) Phthalate Accelerates Early Folliculogenesis and Inhibits Steroidogenesis in Cultured Mouse Whole Ovaries and Antral Follicles1

ABSTRACT Humans are ubiquitously exposed to di(2-ethylhexyl) phthalate (DEHP), which is an environmental toxicant present in common consumer products. DEHP potentially targets the ovary through its metabolite mono(2-ethylhexyl) phthalate (MEHP). However, the direct effects of MEHP on ovarian folliculogenesis and steroidogenesis, two processes essential for reproductive and nonreproductive health, are unknown. The present study tested the hypotheses that MEHP directly accelerates early folliculogenesis via overactivation of phosphatidylinositol 3-kinase (PI3K) signaling, a pathway that regulates primordial follicle quiescence and activation, and inhibits the synthesis of steroid hormones by decreasing steroidogenic enzyme levels. Neonatal ovaries from CD-1 mice were cultured for 6 days with vehicle control, DEHP, or MEHP (0.2–20 μg/ml) to assess the direct effects on folliculogenesis and PI3K signaling. Further, antral follicles from adult CD-1 mice were cultured with vehicle control or MEHP (0.1–10 μg/ml) for 24–96 h to establish the temporal effects of MEHP on steroid hormones and steroidogenic enzymes. In the neonatal ovaries, MEHP, but not DEHP, decreased phosphatase and tensin homolog levels and increased phosphorylated protein kinase B levels, leading to a decrease in the percentage of germ cells and an increase in the percentage of primary follicles. In the antral follicles, MEHP decreased the mRNA levels of 17alpha-hydroxylase-17,20-desmolase, 17beta-hydroxysteroid dehydrogenase, and aromatase leading to a decrease in testosterone, estrone, and estradiol levels. Collectively, MEHP mediates the effect of DEHP on accelerated folliculogenesis via overactivating PI3K signaling and inhibits steroidogenesis by decreasing steroidogenic enzyme levels.
‘Conceptualizing’ the Endometrium: Identification of Conceptus-Derived Proteins During Early Pregnancy in Cattle1

ABSTRACT The aim of this study was to identify conceptus-derived proteins, in addition to IFNT, that may facilitate pregnancy recognition in cattle. Analysis of the protein content of the uterine luminal fluid (ULF) from cyclic heifers on Day 16 by nano liquid chromatography tandem mass spectrometry identified 334 proteins. Comparison of these data with 299 proteins identified in the ULF of pregnant heifers on Day 16 identified 85 proteins only present in the ULF of pregnant heifers. Analysis of Day 16 conceptus-conditioned culture medium revealed the presence of 1005 proteins of which 30 proteins were unique to ULF from Day 16 pregnant heifers. Of these 30 proteins, 12 had mRNA expression values at least 2-fold higher in abundance (P < 0.05) in the conceptus compared to the endometrium (ARPC5L, CAPG, CKMT1, CSTB, HSPA8, HSPE1, LGALS3, MSN, NUTF2, P4HB, PRKAR2A, TKT) as determined by RNA sequencing. In addition, genes that have a significant biological interaction with the proteins (ACO2, CKMT1, CSTB, EEF2, GDI1, GLB1, GPLD1, HNRNPA1, HNRNPA2B1, HNRNPF, HSPA8, HSPE1, IDH2, KRT75, LGALS3, MSN, NUTF2, P4HB, PRKAR2A, PSMA4, PSMB5, PSMC4, SERPINA3, TKT) were differentially expressed in the endometrium of pregnant compared to cyclic heifers during the pregnancy recognition period (Days 16–18). These results indicate that 30 proteins unique to ULF from pregnant heifers and produced by short-term in vitro cultured Day 16 conceptuses could potentially be involved in facilitating the interactions between the conceptus and the endometrium during the pregnancy recognition period.
Effects of Endocrine-Disrupting Chemicals on the Ovary1

ABSTRACT Endocrine-disrupting chemicals (EDCs) are found abundantly in the environment, resulting in daily human exposure. This is of concern because many EDCs are known to target the female reproductive system and, more specifically, the ovary. In the female, the ovary is the key organ responsible for reproductive and endocrine functions. Exposure to EDCs is known to cause many reproductive health problems such as infertility, premature ovarian failure, and abnormal sex steroid hormone levels. Some EDCs and their effects on adult ovarian function have been studied extensively over the years, whereas the effects of others remain unclear. This review covers what is currently known about the effects of selected EDCs (bisphenol A, methoxychlor, 2,3,7,8-tetrachlorodibenzo-p-dioxin, phthalates, and genistein) on the adult ovary and the mechanisms by which they act upon the ovary, focusing primarily on their effects on folliculogenesis and steroidogenesis. Furthermore, this review discusses future directions needed to better understand the effects of EDCs, including the need to examine the effects of multiple and more consistent doses and to study different mechanisms of action.
Force Spectroscopy of the Plasmodium falciparum Vaccine Candidate Circumsporozoite Protein Suggests a Mechanically Pliable Repeat Region*

The most effective vaccine candidate of malaria is based on the Plasmodium falciparum circumsporozoite protein (CSP), a major surface protein implicated in the structural strength, motility, and immune evasion properties of the infective sporozoites. It is suspected that reversible conformational changes of CSP are required for infection of the mammalian host, but the detailed structure and dynamic properties of CSP remain incompletely understood, limiting our understanding of its function in the infection. Here, we report the structural and mechanical properties of the CSP studied using single-molecule force spectroscopy on several constructs, one including the central region of CSP, which is rich in NANP amino acid repeats (CSPrep), and a second consisting of a near full-length sequence without the signal and anchor hydrophobic domains (CSPΔHP). Our results show that the CSPrep is heterogeneous, with 40% of molecules requiring virtually no mechanical force to unfold (<10 piconewtons (pN)), suggesting that these molecules are mechanically compliant and perhaps act as entropic springs, whereas the remaining 60% are partially structured with low mechanical resistance (∼70 pN). CSPΔHP having multiple force peaks suggests specifically folded domains, with two major populations possibly indicating the open and collapsed forms. Our findings suggest that the overall low mechanical resistance of the repeat region, exposed on the outer surface of the sporozoites, combined with the flexible full-length conformations of CSP, may provide the sporozoites not only with immune evasion properties, but also with lubricating capacity required during its navigation through the mosquito and vertebrate host tissues. We anticipate that these findings would further assist in the design and development of future malarial vaccines.
Defective Human Sperm Cells Are Associated with Mitochondrial Dysfunction and Oxidant Production1

ABSTRACT Infertility affects about 15% of couples of reproductive age. The male factor is involved in nearly 50% of infertility cases. Defective human sperm function has been associated with evidence of high levels of reactive oxygen species (ROS) and a resultant loss of fertilizing potential in vivo and in vitro. Analogous to what has been observed in somatic cells, mitochondria are likely the major sources of ROS in sperm cells. In this study, we analyzed mitochondrial function using high-resolution respirometry, ROS production, and footprints of oxidative and nitrative stress processes in intact human sperm cells. We showed that mitochondrial dysfunction (measured through the respiratory control ratio) was correlated with a decrease in human sperm motility. The samples analyzed presented nitro-oxidative modifications of proteins, such as protein 3-nitrotyrosine, that were observed mainly in the mid-piece (where mitochondria are localized) and in the sperm head. Semen samples presenting lower percentage of motile sperm showed higher amounts of nitro-oxidative protein modifications than those with larger quantities of motile sperm. When spermatozoa were exposed to inhibitors of the respiratory mitochondrial function, in the presence of a nitric oxide flux, sperm produced potent nitro-oxidative species (i.e., peroxynitrite). This effect was observed in more than 90% of intact living sperm cells and in sperm mitochondrial fractions. These data suggest that dysfunctional mitochondria in sperm cells produce oxidants that may contribute to male infertility. These data provide the rationale for testing the potential of compounds that improve sperm mitochondrial function to treat male infertility.
A quantitative review of heterozygosity–fitness correlations in animal populations

The ease of obtaining genotypic data from wild populations has renewed interest in the relationship between individual genetic diversity and fitness‐related traits (heterozygosity–fitness correlations, or HFC). Here we present a comprehensive meta‐analysis of HFC studies using powerful multivariate techniques which account for nonindependence of data. We compare these findings with those from univariate techniques, and test the influence of a range of factors hypothesized to influence the strength of HFCs. We found small but significantly positive effect sizes for life‐history, morphological, and physiological traits; while theory predicts higher mean effect sizes for life‐history traits, effect size did not differ consistently with trait type. Newly proposed measures of variation were no more powerful at detecting relationships than multilocus heterozygosity, and populations predicted to have elevated inbreeding variance did not exhibit higher mean effect sizes. Finally, we found evidence for publication bias, with studies reporting weak, nonsignificant effects being under‐represented in the literature. In general, our review shows that HFC studies do not generally reveal patterns predicted by population genetic theory, and are of small effect (less than 1% of the variance in phenotypic characters explained). Future studies should use more genetic marker data and utilize sampling designs that shed more light on the biological mechanisms that may modulate the strength of association, for example by contrasting the strength of HFCs in mainland and island populations of the same species, investigating the role of environmental stress, or by considering how selection has shaped the traits under investigation.
L-Carnitine and Pyruvate Are Prosurvival Factors During the Storage of Stallion Spermatozoa at Room Temperature1

ABSTRACT The spermatozoa of many stallions do not tolerate being cooled, restricting the commercial viability of these animals and necessitating the development of a chemically defined room temperature (RT) storage medium. This study examined the impact of two major modulators of oxidative phosphorylation, pyruvate (Pyr) and L-carnitine (L-C), on the storage of stallion spermatozoa at RT. Optimal concentrations of Pyr (10 mM) and L-C (50 mM) were first identified and these concentrations were then used to investigate the effects of these compounds on sperm functionality and oxidative stress at RT. Mitochondrial and cytosolic reactive oxygen species, along with lipid peroxidation, were all significantly suppressed by the addition of L-C (48 h MitoSOX Red negative: 46.2% vs. 26.1%; 48 and 72 h dihydroethidium negative: 61.6% vs. 43.1% and 64.4% vs. 46.9%, respectively; 48 and 72 h 4-hydroxynonenal negative: 37.1% vs. 23.8% and 41.6% vs. 25.7%, respectively), while the Pyr + L-C combination resulted in significantly higher motility compared to the control at 72 h (total motility: 64.2% vs. 39.4%; progressive motility: 34.2% vs. 15.2%). In addition, supplementation with L-C significantly reduced oxidative DNA damage at 72 h (9.0% vs. 15.6%). To investigate the effects of L-C as an osmolyte, comparisons were made between media that were osmotically balanced with NaCl, choline chloride, or L-C. This analysis demonstrated that spermatozoa stored in the L-C balanced medium had significantly higher total motility (55.0% vs. 39.0%), rapid motility (44.0% vs. 25.7%), and ATP levels (70.9 vs. 12.8 ng/ml) following storage compared with the NaCl treatment, while choline chloride did not significantly improve these parameters compared to the control. Finally, mass spectrometry was used to demonstrate that a combination of Pyr and L-C produced significantly higher acetyl-L-carnitine production than any other treatment (6.7 pg/106 spermatozoa vs. control at 4.0 pg/106 spermatozoa). These findings suggest that Pyr and L-C could form the basis of a novel, effective RT storage medium for equine spermatozoa.
Developmental Programming: Does Prenatal Steroid Excess Disrupt the Ovarian VEGF System in Sheep?1

ABSTRACT Prenatal testosterone (T), but not dihydrotestosterone (DHT), excess disrupts ovarian cyclicity and increases follicular recruitment and persistence. We hypothesized that the disruption in the vascular endothelial growth factor (VEGF) system contributes to the enhancement of follicular recruitment and persistence in prenatal T-treated sheep. The impact of T/DHT treatments from Days 30 to 90 of gestation on VEGFA, VEGFB, and their receptor (VEGFR-1 [FLT1], VEGFR-2 [KDR], and VEGFR-3 [FLT4]) protein expression was examined by immunohistochemistry on Fetal Days 90 and 140, 22 wk, 10 mo (postpubertal), and 21 mo (adult) of age. Arterial morphometry was performed in Fetal Day 140 and postpubertal ovaries. VEGFA and VEGFB expression were found in granulosa cells at all stages of follicular development with increased expression in antral follicles. VEGFA was present in theca interna, while VEGFB was present in theca interna/externa and stromal cells. All three receptors were expressed in the granulosa, theca, and stromal cells during all stages of follicular development. VEGFR-3 increased with follicular differentiation with the highest level seen in the granulosa cells of antral follicles. None of the members of the VEGF family or their receptor expression were altered by age or prenatal T/DHT treatments. At Fetal Day 140, area, wall thickness, and wall area of arteries from the ovarian hilum were larger in prenatal T- and DHT-treated females, suggestive of early androgenic programming of arterial differentiation. This may facilitate increased delivery of endocrine factors and thus indirectly contribute to the development of the multifollicular phenotype.
Bisphenol A and Related Alkylphenols Exert Nongenomic Estrogenic Actions Through a G Protein-Coupled Estrogen Receptor 1 (Gper)/Epidermal Growth Factor Receptor (Egfr) Pathway to Inhibit Meiotic Maturation of Zebrafish Oocytes1

ABSTRACT Xenobiotic estrogens, such as bisphenol A (BPA), disrupt a wide variety of genomic estrogen actions, but their nongenomic estrogen actions remain poorly understood. We investigated nongenomic estrogenic effects of low concentrations of BPA and three related alkylphenols on the inhibition of zebrafish oocye maturation (OM) mediated through a G protein-coupled estrogen receptor 1 (Gper)-dependent epidermal growth factor receptor (Egfr) pathway. BPA (10–100 nM) treatment for 3 h mimicked the effects of estradiol-17beta (E2) and EGF, decreasing spontaneous maturation of defolliculated zebrafish oocytes, an effect not blocked by coincubation with actinomycin D, but blocked by coincubation with a Gper antibody. BPA displayed relatively high binding affinity (15.8% that of E2) for recombinant zebrafish Gper. The inhibitory effects of BPA were attenuated by inhibition of upstream regulators of Egfr, intracellular tyrosine kinase (Src) with PP2, and matrix metalloproteinase with ilomastat. Treatment with an inhibitor of Egfr transactivation, AG1478, and an inhibitor of the mitogen-activated protein kinase (MAPK) 3/1 pathway, U0126, increased spontaneous OM and blocked the inhibitory effects of BPA, E2, and the selective GPER agonist, G-1. Western blot analysis showed that BPA (10–200 nM) mimicked the stimulatory effects of E2 and EGF on Mapk3/1 phosphorylation. Tetrabromobisphenol A, 4-nonylphenol, and tetrachlorobisphenol A (5–100 nM) also inhibited OM, an effect blocked by cotreatment with AG1478, as well as with the GPER antagonist, G-15, and displayed similar binding affinities as BPA to zebrafish Gper. The results suggest that BPA and related alkylphenols disrupt zebrafish OM by a novel nongenomic estrogenic mechanism involving activation of the Gper/Egfr/Mapk3/1 pathway.
Highly infectious symbiont dominates initial uptake in coral juveniles

The majority of reef‐building corals acquire their obligate algal symbionts (Symbiodinium) from the environment. However, factors shaping the initial establishment of coral–algal symbioses, including parental effects, local environmental conditions and local availability of symbionts, are not well understood. This study monitored the uptake and maintenance of Symbiodinium in juveniles of two common corals, Acropora tenuis and Acropora millepora, that were reciprocally explanted between sites where adult colonies host different types of Symbiodinium. We found that coral juveniles were rapidly dominated by type D Symbiodinium, even though this type is not found in adult colonies (including the parental colonies) in four out of the five study populations. Furthermore, type D Symbiodinium was found in less than one‐third of a wide range of coral species (n > 50) sampled at the two main study sites, suggesting that its dominance in the acroporid juveniles is not because it is the most abundant local endosymbiotic type. Moreover, dominance by type D was observed irrespective of the light intensity to which juveniles were exposed in a field study. In summary, despite its relatively low abundance in coral assemblages at the study sites and irrespective of the surrounding light environment, type D Symbiodinium is the main symbiont type initially acquired by juveniles of A. millepora and A. tenuis. We conclude that during early ontogeny in these corals, there are few barriers to the uptake of Symbiodinium types which differ from those found in parental colonies, resulting in dominance by a highly infectious and potentially opportunistic symbiont.
Acrosomal Swelling Is Triggered by cAMP Downstream of the Opening of Store-Operated Calcium Channels During Acrosomal Exocytosis in Human Sperm1

ABSTRACT Acrosomal exocytosis in mammalian sperm is a regulated secretion with unusual characteristics. One of its most striking features is the postfusion loss of the outer acrosomal membrane and the overlying plasma membrane as hybrid vesicles. We have previously reported in human sperm that, by preventing the release of calcium from the acrosome, the exocytic process can be arrested at a stage where the acrosomes are profusely swollen, with invaginations of the outer acrosomal membrane. In this report, we show by transmission electron microcopy swelling with similar characteristics without arresting the exocytic process. Acrosomal swelling was observed when secretion was promoted by pharmacological and physiological inducers of the acrosome reaction that trigger exocytosis by different mechanisms. We show that progesterone- and thapsigargin-induced swelling depended on a calcium influx from the extracellular medium through store-operated calcium channels. However, calcium was dispensable when sperm were stimulated with cAMP analogs. KH7, an inhibitor of the soluble adenylyl cyclase, blocked progesterone-induced swelling. Our results indicate that swelling is a required process for acrosomal exocytosis triggered by activation of an adenylyl cyclase downstream of the opening of store-operated calcium channels.
Molecular road ecology: exploring the potential of genetics for investigating transportation impacts on wildlife

Transportation infrastructures such as roads, railroads and canals can have major environmental impacts. Ecological road effects include the destruction and fragmentation of habitat, the interruption of ecological processes and increased erosion and pollution. Growing concern about these ecological road effects has led to the emergence of a new scientific discipline called road ecology. The goal of road ecology is to provide planners with scientific advice on how to avoid, minimize or mitigate negative environmental impacts of transportation. In this review, we explore the potential of molecular genetics to contribute to road ecology. First, we summarize general findings from road ecology and review studies that investigate road effects using genetic data. These studies generally focus only on barrier effects of roads on local genetic diversity and structure and only use a fraction of available molecular approaches. Thus, we propose additional molecular applications that can be used to evaluate road effects across multiple scales and dimensions of the biodiversity hierarchy. Finally, we make recommendations for future research questions and study designs that would advance molecular road ecology. Our review demonstrates that molecular approaches can substantially contribute to road ecology research and that interdisciplinary, long‐term collaborations will be particularly important for realizing the full potential of molecular road ecology.