Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficiency of mating, artificial insemination or resynchronisation at different times after first timed artificial insemination in postpartum Nellore cows to produce crossbred calves

The objective of this trial was to evaluate different post-timed artificial insemination (TAI) reproductive managements in postpartum beef cows to produce crossbred calves from artificial insemination (AI). Nellore cows (n = 607), with 45 days postpartum, were inseminated at a fixed time, using a protocol that included an intravaginal progesterone-releasing device along with oestradiol benzoate, prostaglandin, equine chorionic gonadotropin, and oestradiol cypionate, followed TAI 48 h post-device removal. Four post-TAI treatments were evaluated: in CONTROL (T1, n = 161), cows were exposed to Nellore clean-up bulls until the end of the breeding season (75 days). In OBSERVATION (T2, n = 132), heat detection was performed for 15–25 days post-TAI, followed by AI. In RESYNC22 (T3, n = 157) and RESYNC30 (T4, n = 157), resynchronisation started after 22 or 30 days, following second TAI at Day 32 or 40 days after first TAI. In T2, T3 and T4, after the second AI, cows were exposed to Nellore clean-up bulls until the end of the breeding season (75 days). The pregnancy rate (PR) for the first TAI did not differ (54.6%, 53.0%, 59.2%, and 51.6% for CONTROL, OBSERVATION, RESYNC 22, and RESYNC 30, respectively; P = 0.66), and no difference was observed for the second TAI (RESYNC 22 = 45.31% and RESYNC30 = 46.05%; P = 0.137), in the PR at the end of the breeding season (86.33%, 86.36%, 78.98%, and 81.52%, P = 0.43), or embryonic losses (4.54%, 2.85%, 6.45% and 7.40%, respectively; P = 0.61), but the percentage of crossbred pregnancy was higher in groups with resynchronisation (RESYNC22 and RESYNC30) than CONTROL and OBSERVATION (98.38%, 90.62%, 63.30%, 78.95%, P < 0.001). In conclusion, resynchronisation programs of 22 or 30 days are more efficient to produce AI products, and the final pregnancy rate is similar among the treatments, differing only in the amount of calves produced by AI.
Lost in translation: egg transcriptome reveals molecular signature to predict developmental success and novel maternal-effect genes

Background Good quality or developmentally competent eggs result in high survival of progeny. Previous research has shed light on factors that determine egg quality, however, large gaps remain. Initial development of the embryo relies on maternally-inherited molecules, such as transcripts, deposited in the egg, thus, they would likely reflect egg quality. We performed transcriptome analysis on zebrafish fertilized eggs of different quality from unrelated, wildtype couples to obtain a global portrait of the egg transcriptome to determine its association with developmental competence and to identify new candidate maternal-effect genes. Results Fifteen of the most differentially expressed genes (DEGs) were validated by quantitative real-time PCR. Gene ontology analysis showed that enriched terms included ribosomes and translation. In addition, statistical modeling using partial least squares regression and genetics algorithm also demonstrated that gene signatures from the transcriptomic data can be used to predict reproductive success. Among the validated DEGs, otulina and slc29a1a were found to be increased in good quality eggs and to be predominantly localized in the ovaries. CRISPR/Cas9 knockout mutants of each gene revealed remarkable subfertility whereby the majority of their embryos were unfertilizable. The Wnt pathway appeared to be dysregulated in the otulina knockout-derived eggs. Conclusions Our novel findings suggested that even in varying quality of eggs due to heterogeneous causes from unrelated wildtype couples, gene signatures exist in the egg transcriptome, which can be used to predict developmental competence. Further, transcriptomic profiling revealed two new potential maternal-effect genes that have essential roles in vertebrate reproduction.
Differences in seed dormancy associated with the domestication of Cucurbita maxima: elucidation of some mechanisms behind this response

Abstract This work presents the results of physiological studies developed to understand modifications linked to the reduction of seed dormancy provoked by domestication processes. The experiments performed compared wild and domesticated Cucurbita subspecies and their hybrids developed by reciprocal crossings. Seeds of two accessions of the wild subspecies presented dormancy, but it was largely reduced in seeds from the domesticated genotype, and partially reverted in hybrids, especially in those obtained when the domesticated genotype was used as the mother plant. In addition, naked embryos of all subspecies did not display dormancy when incubation was performed at 28°C, but embryo germination was progressively reduced only in the wild genotype under decreasing incubation temperatures (22 and 16°C). In the embryos, abscisic acid (ABA) concentrations were similar in both domesticated and wild subspecies, whereas in the seed coat, it was threefold higher in the wild subspecies. The naked embryos from the wild subspecies were far more responsive to ABA than those from the domesticated subspecies. These results indicate that dormancy in the wild subspecies is imposed by the seed coat tissues and that this effect is mediated by their high ABA content and the sensitivity of the embryos to ABA. These physiological aspects were apparently removed by domestication along with the temperature-dependent response for germination.
Relocating bleached Platygyra sinensis facilitates recovery from thermal stress during a minor bleaching event

Abstract The recovery of bleached corals is crucial in ensuring the persistence of the coral reef ecosystem function. This study investigated whether relocating bleached Platygyra sinensis colonies was a viable measure to accelerate their recovery. During a mild bleaching event in 2014, eight bleached colonies of P. sinensis were relocated from an affected reef at Sultan Shoal, Singapore, to a reef at Kusu that was less impacted. Another eight colonies at Sultan Shoal were tagged as controls. After five months, 88% of relocated bleached colonies at Kusu showed full recovery whereas only 25% of the control bleached colonies at Sultan Shoal had recovered. The differential coral recovery among the two sites was most likely due to lower seawater temperatures and faster water flow at Kusu, which helped to mitigate the effects of thermal stress on the bleached corals. This relocation study demonstrated that relocating bleached P. sinensis to sites with more favourable environmental conditions is a viable approach to reduce bleaching impacts for this species.
Ordering geniculate input into primary visual cortex

Precise point-to-point connectivity is the basis of ordered maps of the visual field in the brain. One point in the visual field is represented at one locus in the dLGN and one locus in primary visual cortex. A fundamental problem in the development of most sensory systems is the creation of the topographic projections which underlie these maps. Mechanisms ranging from ordered ingrowth of fibres, through chemical guidance of axons to sculpting of the map from an early exuberant input have been proposed. However, we know little about how ordered maps are created beyond the first relay. What we do know is that a topological mismatch requires the exchange of neighbours in the geniculo-cortical projection and that manipulating the input to the primary relay can affect the geniculo-cortical topography. Taking advantage of the immaturity of the newborn hamster’s visual system, I studied the generation of an ordered map in primary visual cortex during the time of target innervation in normal and manipulated animals. I also investigated the patterning of neuronal activity prior to natural eye-opening. Paired injections of retrograde fluorescent tracers into visual cortex reveal that geniculate fibres are highly disordered at the time of invasion of the cortical plate. Topography in the geniculo-cortical projection emerges out of an unordered projection to area 17 in the first postnatal week. Furthermore, I show that manipulating the peripheral input can alter the topographic map which arises out of the early scatter. Removal of one eye at birth appears to slow the process of geniculo-cortical map formation ipsilateral to the remaining eye and at the end of the second postnatal week, a double projection between thalamus and cortex has formed. If retinal activity is blocked during this time, this double projection does not emerge. The results implicate retinal activity as the signal that induces the development of a different topographic order in the geniculo-cortical projection. It is generally believed that visual experience can influence development only after eye-opening. However, the final part of my thesis shows that neurons in the developing visual cortex of the ferret can not only be visually driven at least 10 days before natural eye-opening, but are also selective for differently oriented gratings presented through the closed eye-lid . Thus, visually-driven neuronal activity could influence development much earlier than previously assumed in many developmental studies.
The evolutionary approach to history: sociocultural phylogenetics

This paper on cultural or sociocultural evolution begins with a discussion of the Darwinian-inspired evolutionary approach to history. It then outlines modern evolutionary phylogenetic methods borrowed from Biology but now used extensively in the social sciences and humanities. We provide examples of how language trees may be inferred; phylogenetic comparative methods that use language trees to answer questions about aspects of geographical, social, political, cultural or economic organization; and phylogenetic investigations of material culture and oral traditions.The conclusion is drawn that culture does indeed “descend with modification”.
The potential for Probiotic Bacteria from milkfish intestine in reducing mercury metals in skimmed milk media

Mercury (Hg) is one of the heavy metals that is harmful to humans. The accumulation of mercury in the body is generally derived from food. Several types of bacteria from intestine of milkfish are known to reduce mercury concentration. People can take advantage of this bacterial ability by eating it through probiotic foods. This research conducted to figure out the potential for probiotic bacteria from milkfish intestine in reducing mercury. Isolation from probiotic bacteria from milkfish intestine conducted with grown the isolates in MRSA medium with addition of 1% CaCO3. Twelve isolate were obtained from milkfish intestine. Mercury resistance tested was performed by measuring cell density using a spectrophotometer at concentrations of 10, 15 and 20 ppm respectively in skim milk media. Probiotic tests (gastric acid, bile salts and antimicrobial activity) for MRSB media was also conducted. Results showed that seven isolate were resistant to mercury in all concentrations and potential as probiotics. All resistant isolate then tested for skim milk media with addition of 5, 10, 20 ppm mercury acetate respectively. Result showed that only one isolated was able to reduce the concentration of mercury (Hg) in all variations on concentration and potential as mercury reducer probiotic bacteria.
Systematic Review on Effects of Diet on Gut Microbiota in Relation to Metabolic Syndromes

The microbiota is a complex ecosystem of microbes, the bulk of which reside mainly in the colon, and has been shown to be significantly influenced by the diet. The biological functions of the microbiota have been strongly linked to health and disease, including the development of metabolic syndrome (MetS). The aim of this paper was to review current literature on the effects of the diet on gut microbiota in relation to the development of MetS through the following objectives: (i) to determine how the diet influences the composition and functions of the microbiota; (ii) evaluate evidence of how this is linked with development obesity and biomarkers of MetS; (iii) investigate the significance of diet-microbiota interactions in relation to obesity and MetS. Multiple databases were used to find and collate relevant literatures. The main findings highlight that a plant-based diet, rich in indigestible carbohydrate was strongly associated with a richer, more diverse microbiota profile compared to a high-energy, high-fat Western diet. Studies in mice have indicated that weight gain can be induced via inoculation of an obese-type microbiota without changes in dietary intake. Additionally, polyphenols appear to interact with the microbiota, producing metabolites which have shown to possess more health potential than their precursors. Unabsorbed polyphenols also seem to beneficially modulate the microbiota, resulting in positive health outcomes. More in vivo human studies are necessary to conclude the significance of the microbiota and mechanisms of action in the development of MetS. With this knowledge, there may be potential to manipulate the gut microbiota toward the generation of desired health outcomes as an alternative to pharmaceuticals.
Combinatorial RNAi strategies against HIV-1 and other escape-prone viruses

: RNA interference (RNAi) is an evolutionarily conserved mechanism in which double-stranded RNA (dsRNA) induces sequence-specific gene silencing. RNAi as a gene suppression tool holds great promise for basic research and multiple applications. RNAi strategies with a single inhibitor have received much attention and some are currently being tested in clinical trials as potential drug for infectious diseases, cancer and genetic disorders. Although very successful, such an RNAi mono-therapy is not always sufficient. For example, several proteins should be silenced simultaneously for the elucidation of cross-talk between signalling pathways. Furthermore, development of a durable RNAi therapy for viral infections and cancer may also require the use of multiple inhibitors, as this may prevent the selection of virus variants or cancer cells that escape from the RNAi therapy by mutation of the target gene. Therefore, several combinatorial RNAi strategies have been developed and recent reports demonstrated the potency of this approach by targeting multiple viral genes or oncogenes. At the same time, combinatorial RNAi may also increase the risk of saturation of the endogenous RNAi pathway and off-target effects. This review summarizes the latest experimental advances in combinatorial RNAi research and gene therapy approaches, in particular against escape-prone viruses, like the human immunodeficiency virus type 1 (HIV-1).
Variability in β-catenin pulse dynamics in a stochastic cell fate decision in C. elegans

During development, cell fate decisions are often highly stochastic, but with the frequency of the different possible fates tightly controlled. To understand how signaling networks control the cell fate frequency of such random decisions, we studied the stochastic decision of the Caenorhabditis elegans P3.p cell to either fuse to the hypodermis or assume vulva precursor cell fate. Using time-lapse microscopy to measure the single-cell dynamics of two key inhibitors of cell fusion, the Hox gene LIN-39 and Wnt signaling through the β-catenin BAR-1, we uncovered significant variability in the dynamics of LIN-39 and BAR-1 levels. Most strikingly, we observed that BAR-1 accumulated in a single, 1-4 hour pulse at the time of the P3.p cell fate decision, with strong variability both in pulse slope and time of pulse onset. We found that the time of BAR-1 pulse onset was delayed relative to the time of cell fusion in mutants with low cell fusion frequency, linking BAR-1 pulse timing to cell fate outcome. Overall, a model emerged where animal-to-animal variability in LIN-39 levels and BAR-1 pulse dynamics biases cell fate by modulating their absolute level at the time cell fusion is induced. Our results highlight that timing of cell signaling dynamics, rather than its average level or amplitude, could play an instructive role in determining cell fate. Article summary We studied the stochastic decision of the Caenorhabditis elegans P3.p cell to either fuse to the hypodermis or assume vulva precursor cell fate. We uncovered significant variability in the dynamics of LIN-39/Hox and BAR-1/β-catenin levels, two key inhibitors of cell fusion. Surprisingly, we observed that BAR-1 accumulated in a 1-4 hour pulse at the time of the P3.p cell fate decision, with variable pulse slope and time of pulse onset. Our work suggests a model where animal-to-animal variability in LIN-39 levels and BAR-1 pulse dynamics biases cell fate by modulating their absolute level at the time cell fusion is induced.
Soil fertility management and its impact on mustard aphid, Lipaphis erysimi (Kaltenbach) (Hemiptera: Aphididae)

Abstract Maize-mustard cropping sequence is the most adopted cropping pattern in the rainfed belt of Jammu region, Jammu & Kashmir, India. Mustard is attacked by aphids, flea beetles, saw flies and painted bugs, among which aphids are of great economic importance. An experiment was conducted to assess the impact of various organic and inorganic fertilizers / pesticides on mustard aphid, Lipaphis erysimi (Kaltenbach) (Hemiptera: Aphididae). During 2009–2010 and 2010–2011, mustard was sown applying Farm Yard Manure, Neem cake, Adhatoda vasica twigs, Di Ammonium Phosphate and Muriate of Potash (MOP) at different rates and their impact on mustard aphid incidence was studied. The lowest aphid population was noticed in MOP at 80 kg/ha. This was followed by MOP at 40 kg/ha or Neem cake at 5 quintals/ha. The aphid incidence was highest in plots treated with higher dose of DAP at 120 kg/ha (117.97 aphids per ten cm twig), showing the adverse impact of application of higher dose of nitrogenous fertilizer. Application of neem cake also acted as fertilizer and recorded highest yield of 7.34 q/ha along with MOP at 80 kg/ha (7.34 q/ha). The impact of application of various organic and inorganic fertilizers on available soil nutrients, was also recorded after the completion of two year experiment during 2010–2011 (post harvest soil samples).
First Record of Keeled Plump Bush-Cricket (Isophya costata Brunner von Wattenwyl, 1878) (Orthoptera, Tettigoniidae) in Slovakia

Abstract Keeled Plump Bush-cricket Isophya costata is one of ten orthopteran species of European Community interest (Annex II and IV of Habitats Directive), endemic to the Pannonian Basin in Central Europe. It was discovered for the first time in Slovakia in June 2017, in southwestern area of the country (the site Devínske jazero, 48.2722°N / 16.9404°E, 134 m a.s.l.), in continental flooded meadows. The presence of the species in this new site is copying the northern edge of its area. New data of species distribution, its habitat, accompanying orthopteran species are described and main threats and conservation measures of the species are discussed.
Lignocellulosic‐based bioenergy and water quality parameters: a review

High rates of crop residue removal as biofuel feedstocks could increase losses of nonpoint source pollutants, negatively affecting water quality. An alternative to residue removal can be growing dedicated bioenergy crops such as warm season grasses (WSGs) and short‐rotation woody crops (SRWCs). Yet, our understanding of the implications of growing dedicated bioenergy crops on water quality is limited. Thus, we (i) synthesized and compared the impacts of crop residue removal, WSGs, and SRWCs on water quality parameters (i.e., sediment and nutrient runoff, and nutrient leaching) and (ii) identified research gaps for growing dedicated energy crops. Literature indicates that residue removal at rates >50% (residue retention up to 4.71 Mg ha−1) can increase runoff by 5–15 mm, sediment loss by 0.2–7 Mg ha−1, NO3–N by 0.58–1 kg ha−1, and sediment‐associated C by 0.3–57 kg ha−1 per rainstorm event compared to no residue removal. Crop residue removal may also increase nutrient leaching. Studies on the impacts of growing WSGs as dedicated bioenergy crops at field scale on water quality parameters are few. However, WSGs when used as conservation buffers reduce losses of sediment by 66–97%, nutrients by 21–94%, and contaminants by 9–98%. This suggests that if WSGs were grown as dedicated bioenergy crops at larger scales, they could reduce losses of nonpoint source pollutants. Literature indicates that SRWCs can consistently reduce NO3–N leaching. More modeled than field data are available, warranting further field research on (i) field data collection from WSGs and SRWCs from marginal lands, (ii) growing monoculture or polyculture of WSGs, and (iii) large‐scale production of energy crops. Overall, dedicated bioenergy crops, particularly WSGs, can reduce losses of nonpoint source pollutants compared to residue removal and be an important strategy to improve water quality if grown at larger scales.
Partitioning kin groups of broodstock in the critically endangered Chinese sturgeon, Acipenser sinensis Gray 1835

Pedigrees of broodstock with unknown relationship of the critically endangered Chinese sturgeon, Acipenser sinensis, was evaluated using microsatellite markers to facilitate genetic management in restocking programs with small broodstock size. We characterized the distributions of relatedness values to reconstruct kin groups in four hatchery families with known pedigrees using microsatellites. The distributions of relatedness values for kin classes were used for partitioning full sibling groups of wild A. sinensis broodstock kept in two hatcheries, resulted in 13 full sibling clusters, four of which containing 62% of all the wild individuals. This indicates high probability of choosing close related breeder pairs in random mating, thus selective breeding is necessary to minimize inbreeding and maintain genetic diversity. This study provides a useful tool for genetic management in conservation programs of A. sinensis in aim of preserving self-sustained wild populations.
A Functional Genomics Approach for Characterizing the Role of Six Transcription Factors in Muscle Development

Proper development of skeletal muscle occurs through a highly complex process where activation and repression of genes are essential. Control of this process is regulated by timely and spatial expression of specific transcription factors (TFs). Six1 and Six4 are homeodomain TFs known to be essential for skeletal muscle development in mice. Using the C2C12 cell line, a model for skeletal muscle differentiation, I used a functional genomics approach, employing siRNA specific to both these TFs, to characterize their role in skeletal myogenesis. To identify the genes that are regulated by both these TFs, gene expression profiling by microarray of cells treated with siRNA against Six1 and/or Six4 was performed. The knock-down of these TFs caused lower expression of markers of terminal differentiation genes in addition to an impairment of myoblast fusion and differentiation. Interestingly, transcript profiling of cells treated with siRNA against myogenin revealed that several of the Six1 and Six4 target genes are also regulated by myogenin. Through a combination of bioinformatic analyses it was also found that specific knock-down of Six4 causes an upregulation of genes involved in mitosis and the cell cycle. In summary, these results show that Six1 and Six4 can both independently regulate different genes, but can also cooperate together with other TFs where they play an important role in the proper regulation of skeletal