Altered microRNA composition in the uterine lumen fluid in cattle (Bos taurus) pregnancies initiated by artificial insemination or transfer of an in vitro produced embryo.

BACKGROUND: MicroRNAs (miRNAs) are presented in the uterine lumen of many mammals, and in vitro experiments have determined that several miRNAs are important for the regulation of endometrial and trophoblast functions. Our aim was to identify and contrast the miRNAs present in extracellular vesicles (EVs) in the uterine lumen fluid (ULF) at the onset of attachment in cattle pregnancies (gestation d 18) initiated by artificial insemination (AI) or by the transfer of an in vitro-produced blastocyst (IVP-ET). A third group had no conceptus after the transfer of an IVP embryo. RESULTS: The abundance of 263 annotated miRNAs was quantified in the EVs collected from ULF. There was an increase in the transcript abundance of 20 miRNAs in the ULF EVs from the AI pregnant group, while 4 miRNAs had a lower abundance relative to the group not containing a conceptus. Additionally, 4 miRNAs were more abundant in ULF EVs in the AI pregnant group relative to IVP-ET group (bta-mir-17, bta-mir-7-3, MIR7-1, MIR18A). Specific miRNAs in the ULF EVs were co-expressed with messenger RNAs expressed in extra-embryonic tissues and endometrium, including genes that are known to be their targets. CONCLUSIONS: The results provide biological insights into the participation of miRNAs in the regulation of trophoblast proliferation and differentiation, as well as in endometrium receptivity. The knowledge that in vitro cultured embryos can contribute to the altered abundance of specific miRNAs in the uterine lumen can lead to the development of corrective approaches to reduce conceptus losses during the first month of pregnancy in cattle.

Subacute and chronic toxic hepatopathy in cattle grazing pasture with Crotalaria spectabilis.

This report describes subacute and chronic toxic hepatopathy in cattle due to Crotalaria spectabilis poisoning. A total of 200 male Nellore cattle were introduced into a paddock contaminated with C. spectabilis. After spending 20 days grazing in this area, 6 cattle became ill and died. The remaining 194 cattle were moved to non-contaminated pasture in a nearby farm and, 45 days after arrival, 15 cattle became ill and died. Three affected cattle were necropsied. The main clinical changes consisted of anorexia, isolation from the herd, weight loss, jaundice, recumbency, and death. The primary lesions were observed in the liver. Subacutely poisoned cattle had slightly firm livers with an accentuated lobular pattern. Histologically, hepatocyte loss with dilated sinusoids, hepatomegalocytosis, and fibrosis was observed. Cattle with chronic disease had small, pale, firm livers with an irregular hepatic capsular surface. Microscopic changes included hepatocyte loss, hepatomegalocytosis, bile duct proliferation, and fibrosis.

Accurate Flow Decomposition via Robust Integer Linear Programming.

Minimum flow decomposition (MFD) is a common problem across various fields of Computer Science, where a flow is decomposed into a minimum set of weighted paths. However, in Bioinformatics applications, such as RNA transcript or quasi-species assembly, the flow is erroneous since it is obtained from noisy read coverages. Typical generalizations of the MFD problem to handle errors are based on least-squares formulations or modelling the erroneous flow values as ranges. All of these are thus focused on error handling at the level of individual edges. In this paper, we interpret the flow decomposition problem as a robust optimization problem and lift error-handling from individual edges to solution paths. As such, we introduce a new minimum path-error flow decomposition problem, for which we give an Integer Linear Programming formulation. Our experimental results reveal that our formulation can account for errors significantly better, by lowering the inaccuracy rate by 30-50% compared to previous error-handling formulations, with computational requirements that remain practical.

A simplified laboratory approach for isolating M. oryzae spores from rice samples infected with multiple pathogens.

A method for separating M. oryzae from rice samples infected with multiple pathogens using basic laboratory equipment is described. We conducted a series of experiments to obtain a single spore of M. oryzae. This method can also be used to isolate spores from other fungal species.

Identification of novel cattle (Bos taurus) genes and biological insights of their function in pre-implantation embryo development.

BACKGROUND: Appropriate regulation of genes expressed in oocytes and embryos is essential for acquisition of developmental competence in mammals. Here, we hypothesized that several genes expressed in oocytes and pre-implantation embryos remain unknown. Our goal was to reconstruct the transcriptome of oocytes (germinal vesicle and metaphase II) and pre-implantation cattle embryos (blastocysts) using short-read and long-read sequences to identify putative new genes. RESULTS: We identified 274,342 transcript sequences and 3,033 of those loci do not match a gene present in official annotations and thus are potential new genes. Notably, 63.67% (1,931/3,033) of potential novel genes exhibited coding potential. Also noteworthy, 97.92% of the putative novel genes overlapped annotation with transposable elements. Comparative analysis of transcript abundance identified that 1,840 novel genes (recently added to the annotation) or potential new genes were differentially expressed between developmental stages (FDR < 0.01). We also determined that 522 novel or potential new genes (448 and 34, respectively) were upregulated at eight-cell embryos compared to oocytes (FDR < 0.01). In eight-cell embryos, 102 novel or putative new genes were co-expressed (|r|> 0.85, P < 1 × 10-8) with several genes annotated with gene ontology biological processes related to pluripotency maintenance and embryo development. CRISPR-Cas9 genome editing confirmed that the disruption of one of the novel genes highly expressed in eight-cell embryos reduced blastocyst development (ENSBTAG00000068261, P = 1.55 × 10-7). CONCLUSIONS: Our results revealed several putative new genes that need careful annotation. Many of the putative new genes have dynamic regulation during pre-implantation development and are important components of gene regulatory networks involved in pluripotency and blastocyst formation.

Non-Alcoholic Fatty Liver Disease Induced by Feeding Medium-Chain Fatty Acids Upregulates Cholesterol and Lipid Homeostatic Genes in Skeletal Muscle of Neonatal Pigs.

Non-alcoholic fatty liver disease (NAFLD) is a range of disorders characterized by lipid accumulation in hepatocytes. Although this spectrum of disorders is associated with adult obesity, recent evidence suggests that this condition could also occur independently of obesity, even in children. Previously, we reported that pigs fed a formula containing medium-chain fatty acids (MCFAs) developed hepatic steatosis and weighed less than those fed an isocaloric formula containing long-chain fatty acids (LCFAs). Our objective was to determine the association between NAFLD and the skeletal muscle transcriptome in response to energy and lipid intake. Neonatal pigs were fed one of three formulas: a control formula (CONT, n = 6) or one of two isocaloric high-energy formulas containing either long (LCFA, n = 6) or medium (MCFA, n = 6) chain fatty acids. Pigs were fed for 22 d, and tissues were collected. Body weight at 20 and 22 d was greater for LCFA-fed pigs than their CONT or MCFA counterparts (p < 0.005). Longissimus dorsi weight was greater for LCFA compared with MCFA, while CONT was intermediate (p < 0.05). Lean gain and protein deposition were greater for LCFA than for CONT and MCFA groups (p < 0.01). Transcriptomic analysis revealed 36 differentially expressed genes (DEGs) between MCFA and LCFA, 53 DEGs between MCFA and CONT, and 52 DEGs between LCFA and CONT (FDR < 0.2). Feeding formula high in MCFAs resulted in lower body and muscle weights. Transcriptomics data suggest that the reduction in growth was associated with a disruption in cholesterol metabolism in skeletal muscles.

Reproductive biology as a tool to elucidate taxonomic delimitation: How different can two highly specialized subspecies of Parodia haselbergii (cactaceae) be?

Reproductive isolation is one of the mechanisms of speciation. The two currently accepted subspecies of Parodia haselbergii (P. haselbergii subsp. haselbergii and P. haselbergii subsp. graessneri) were studied regarding flower traits, phenology, breeding systems and pollination. In addition, a principal component analysis with 18 floral characters and germination tests under controlled conditions were performed for both taxa. Pollination was studied in the field, in two localities of Southern Brazil. Pollinators were recorded through photos and film. Breeding system experiments were performed by applying controlled pollinations to plants excluded from pollinators. Both taxa mostly differ in asynchronous flowering periods, floral traits (including floral part measurements and nectar concentration) and pollinators. The flowers of both subspecies are functionally protogynous and perform remarkably long lifespans (≥ 15 days), both traits being novelties for Cactaceae. Whereas the reddish flowers of P. haselbergii subsp. haselbergii (nectar concentration: ca. 18%) are pollinated by hummingbirds of Thalurania glaucopis, the greenish flowers of P. haselbergii subsp. graessneri (nectar concentration: ca. 29%) are pollinated by Augochlora bees (Halictidae). Both subspecies are self-compatible, yet pollinator-dependent. The principal component analysis evidenced that both subspecies are separated, regarding flower traits. The seeds of both subspecies performed differently in the germination tests, but the best results were recovered at 20 °C and germination considerably decreased around 30 °C. In conclusion, all these results support that both taxa are in reproductive isolation, and can be treated as different species.

Multiple karyotype differences between populations of the Hoplias malabaricus (Teleostei; Characiformes), a species complex in the gray area of the speciation process.

Neotropical fishes exhibit remarkable karyotype diversity, whose evolution is poorly understood. Here, we studied genetic differences in 60 individuals, from 11 localities of one species, the wolf fish Hoplias malabaricus, from populations that include six different "karyomorphs". These differ in Y-X chromosome differentiation, and, in several cases, by fusions with autosomes that have resulted in multiple sex chromosomes. Other differences are also observed in diploid chromosome numbers and morphologies. In an attempt to start understanding how this diversity was generated, we analyzed within- and between-population differences in a genome-wide sequence data set. We detect clear genotype differences between karyomorphs. Even in sympatry, samples with different karyomorphs differ more in sequence than samples from allopatric populations of the same karyomorph, suggesting that they represent populations that are to some degree reproductively isolated. However, sequence divergence between populations with different karyomorphs is remarkably low, suggesting that chromosome rearrangements may have evolved during a brief evolutionary time. We suggest that the karyotypic differences probably evolved in allopatry, in small populations that would have allowed rapid fixation of rearrangements, and that they became sympatric after their differentiation. Further studies are needed to test whether the karyotype differences contribute to reproductive isolation detected between some H. malabaricus karyomorphs.

Enterococcus faecalis-derived adenine enhances enterohaemorrhagic Escherichia coli Type 3 Secretion System-dependent virulence.

Interactions between microbiota and enteric pathogens can promote colonization resistance or enhance pathogenesis. The pathobiont Enterococcus faecalis increases enterohaemorrhagic E. coli (EHEC) virulence by upregulating Type 3 Secretion System (T3SS) expression, effector translocation, and attaching and effacing (AE) lesion formation on enterocytes, but the mechanisms underlying this remain unknown. Using co-infection of organoids, metabolomics, supplementation experiments and bacterial genetics, here we show that co-culture of EHEC with E. faecalis increases the xanthine-hypoxanthine pathway activity and adenine biosynthesis. Adenine or E. faecalis promoted T3SS gene expression, while transcriptomics showed upregulation of adeP expression, which encodes an adenine importer. Mechanistically, adenine relieved High hemolysin activity (Hha)-dependent repression of T3SS gene expression in EHEC and promoted AE lesion formation in an AdeP-dependent manner. Microbiota-derived purines, such as adenine, support multiple beneficial host responses; however, our data show that this metabolite also increases EHEC virulence, highlighting the complexity of pathogen-microbiota-host interactions in the gut.

Foliar Spraying with ZnSO4 or ZnO of Vitis vinifera cv. Syrah Increases the Synthesis of Photoassimilates and Favors Winemaking.

Zinc enrichment of edible food products, through the soil and/or foliar application of fertilizers, is a strategy that can increase the contents of some nutrients, namely Zn. In this context, a workflow for agronomic enrichment with zinc was carried out on irrigated Vitis vinifera cv. Syrah, aiming to evaluate the mobilization of photoassimilates to the winegrapes and the consequences of this for winemaking. During three productive cycles, foliar applications were performed with ZnSO4 or ZnO, at concentrations ranging between 150 and 1350 g.ha-1. The normal vegetation index as well as some photosynthetic parameters indicated that the threshold of Zn toxicity was not reached; it is even worth noting that with ZnSO4, a significant increase in several cases was observed in net photosynthesis (Pn). At harvest, Zn biofortification reached a 1.2 to 2.3-fold increase with ZnSO4 and ZnO, respectively (being significant relative to the control, in two consecutive years, with ZnO at a concentration of 1350 g.ha-1). Total soluble sugars revealed higher values with grapes submitted to ZnSO4 and ZnO foliar applications, which can be advantageous for winemaking. It was concluded that foliar spraying was efficient with ZnO and ZnSO4, showing potential benefits for wine quality without evidencing negative impacts.

Variations in dietary patterns of living sloths revealed by finite element analysis of jaws.

Although extinct sloths exhibited a wide range of dietary habits, modes of locomotion, and occupied various niches across the Americas, modern sloths are considered quite similar in their habits. The dietary habits of living sloths can be directly observed in the wild, and understanding the mechanical behavior of their jaws during chewing through finite element analysis (FEA) provides a valuable validation tool for comparative analysis with their extinct counterparts. In this study, we used FEA to simulate the mechanical behavior of sloth mandibles under lateral mastication loads, using it as a proxy for oral processing. Our research focused on the six extant sloth species to better understand their diets and validate the use of FEA for studying their extinct relatives. We found that all living sloths have the predominancy of low-stress areas in their mandibles but with significant differences. Choloepus didactylus had larger high-stress areas, which could be linked to a reduced need for processing tougher foods as an opportunistic generalist. Bradypus variegatus and Choloepus hoffmanni are shown to be similar, displaying large low-stress areas, indicating greater oral processing capacity in a seasonal and more competitive environment. Bradypus torquatus, Bradypus pygmaeus, and Bradypus tridactylus exhibited intermediary processing patterns, which can be linked to a stable food supply in more stable environments and a reduced requirement for extensive oral processing capacity. This study sheds light on extant sloths' dietary adaptations and has implications for understanding the ecological roles and evolutionary history of their extinct counterparts.

Anti-Ha Antisynthetase Syndrome: A Case Report.

Anti-synthetase syndrome (ASyS) is a rare systemic autoimmune myopathy characterized by the involvement of muscles, lungs, and joints, in addition to Raynaud's phenomenon, "mechanics' hand," and fever. Laboratory ASyS is defined by the positivity of anti-aminoacyl-tRNA synthetase autoantibodies, of which anti-Jo-1 is the most common. Herein, we reported an ASyS defined by an anti-Ha autoantibody, which has rarely been described in the literature. Moreover, to the best of our knowledge, we reported the first case of anti-Ha ASyS in Brazil.

Pre- and Postharvest Strategies for Pleurotus ostreatus Mushroom in a Circular Economy Approach.

Mushroom cultivation presents a viable solution for utilizing agro-industrial byproducts as substrates for growth. This process enables the transformation of low-economic-value waste into nutritional foods. Enhancing the yield and quality of preharvest edible mushrooms, along with effectively preserving postharvest mushrooms, stands as a significant challenge in advancing the industry. Implementing pre- and postharvest strategies for Pleurotus ostreatus (Jacq.) P. Kumm (oyster mushroom) within a circular economy framework involves optimizing resource use, minimizing waste, and creating a sustainable and environmentally friendly production system. This review aimed to analyze the development and innovation of the different themes and trends by bibliometric analysis with a critical literature review. Furthermore, this review outlines the cultivation techniques for Pleurotus ostreatus, encompassing preharvest steps such as spawn production, substrate preparation, and the entire mushroom growth process, which includes substrate colonization, fruiting, harvesting, and, finally, the postharvest. While novel methodologies are being explored for maintaining quality and extending shelf-life, the evaluation of the environmental impact of the entire mushroom production to identify areas for improvement is needed. By integrating this knowledge, strategies can be developed for a more sustainable and circular approach to Pleurotus ostreatus mushroom cultivation, promoting environmental stewardship and long-term viability in this industry.

Prone positioning in awake patients without ventilatory support does not alter major clinical outcomes in severe COVID-19: results from a retrospective observational cohort study, systematic review and meta-analysis.

OBJECTIVES: During the Coronavirus disease (COVID-19) pandemic, clinicians recommended awake-prone positioning (APP) to avoid the worst outcomes. The objectives of this study were to investigate if APP reduces intubation, death rates, and hospital length of stay (HLOS) in acute COVID-19. METHODS: We performed a retrospective cohort with non-mechanically ventilated patients hospitalized in a reference center in Manaus, Brazil, 2020. Participants were stratified into APP and awake-not-prone positioning (ANPP) groups. Also, we conducted a systematic review and performed a meta-analysis to understand if this intervention had different outcomes in resource-limited settings (PROSPERO CRD42023422452). RESULTS: A total of 115 participants were allocated into the groups. There was no statistical difference between both groups regarding time to intubation (HR: 0.861; 95CI: 0.474-1.1562; p=0.622) and time to death (HR: 1.666; 95CI: 0.939-2.951; p=0.081). APP was not significantly associated with reduced HLOS. A total of 86 articles were included in the systematic review, of which 76 (88,3%) show similar findings after APP. Also, low/middle, and high-income countries were similar regarding such outcomes. CONCLUSION: APP in COVID-19 does not present clinical improvement that affects mortality, intubation rate and HLOS. The lack of a prone position protocol, obtained through a controlled study, is necessary. After 3 years, APP benefits are still inconclusive.

Novel Dihydropteridinone Derivatives As Potent Inhibitors of the Understudied Human Kinases Vaccinia-Related Kinase 1 and Casein Kinase 1δ/ε.

Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.

Higher abundance of 2-dehydro-d-gluconate in the plasma of sub-fertile or infertile Bos taurus heifers.

Infertility or subfertility impacts approximately 5% and 15% of dairy and beef heifers (Bos taurus), respectively. Heifers that do not produce a calf within an optimum window of time have a significant negative impact on the profitability and sustainability of the cattle industry. Selection of heifers based on their fertility potential remains a challenge yet to be resolved. Here, we tested the hypothesis that heifers of different fertility potential have differing metabolome signatures in their plasma. We obtained blood from Bos taurus heifers at their first artificial insemination and processed the samples to separate the plasma. The heifers were classified based on their reproductive outcome as fertile (pregnant and delivered a calf after their first artificial insemination (AI)) or sub-fertile (Angus heifers: no pregnancy after two AI and exposure to a bull; Holstein heifers: no pregnancy by the third AI). We tested the relative abundance of 140 metabolites obtained from 22 heifers (Angus fertile n = 5, Angus sub-fertile n = 7, Holstein fertile N = 5, Holstein sub-fertile N = 5). The metabolite 2-Dehydro-D-gluconate (C6H10O7) was significantly more abundant in the plasma of sub-fertile heifers in both breeds (1.4-fold, false discovery rate < 0.1). In the context that a small proportion of circulating metabolites in the plasma were quantified in this study, the results show that the metabolomic profile in the blood stream may be associated with heifer fertility potential.

During the development of heifers for cow replacement, producers must invest substantial resources in each animal for over 15 mo. While the use of resources is equivalent across heifers being developed on a farm, a substantial proportion of the animals will not produce a calf (approximately 5% and approximately 15% of dairy and beef heifers, respectively). In this study, we identified one metabolite with higher abundance in the plasma of dairy and beef heifers with low chances of producing a calf by 25 mo of age.

Lactobacillus acidophilus LA-5 Ameliorates Inflammation and Alveolar Bone Loss Promoted by A. actinomycetemcomitans and S. gordonii in Mice and Impacts Oral and Gut Microbiomes.

The benefits of probiotics on dysbiotic microbiomes and inflammation are dependent on the tested strain, host factors, and the resident microbiome. There is limited knowledge on the effects of probiotics in A. actinomycetemcomitans-associated periodontitis. Thus, Lactobacillus acidophilus LA5 (LA5) was orally inoculated for 30 days in C57Bl/6 mice infected with A. actinomycetemcomitans JP2 (Aa) and S. gordonii (Sg). Alveolar bone loss, gingival gene expression, and oral and gut microbiomes were determined. LA5 controlled bone loss in Aa+Sg-infected mice, downregulated the expression of Il-1ß and upregulated Il-10 in gingival tissues, and altered the oral and gut microbiomes. LA5 increased the diversity of the oral microbiome of Aa+Sg infected mice, and Aa+Sg and Aa+Sg+LA5 oral or gut microbiomes clustered apart. LA5 induced shifts in Aa+Sg infected mice by increasing the abundance of Muribaculaceae and decreasing Bifidobacteriaceae in the oral cavity and increasing the abundance of Verrucomicrobiae and Eggerthellales in the gut. In conclusion, LA5 oral administration controls experimental Aa-associated periodontitis by altering inflammatory gene expression and the oral and gut microbiomes.

Exploring mitochondrial targeting: an innovative fluorescent probe reveals Nernstian potential and partitioning combination.

This study introduces a paradigm-shifting approach to optimize mitochondrial targeting. Employing a new fluorescent probe strategy, we unravel a combined influence of both Nernst potential (Ψ) and partitioning (P) contributions. Through the synthesis of new benz[e]indolinium-derived probes, our findings redefine the landscape of mitochondrial localization by optimizing the efficacy of mitochondrial probe retention in primary cortical neurons undergoing normoxia and oxygen-glucose deprivation. This methodology not only advances our understanding of subcellular dynamics, but also holds promise for transformative applications in biomedical research and therapeutic development.

Protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes.

The use of CRISPR-Cas9 ribonucleoproteins has revolutionized manipulation of genomes. Here, we present a protocol for the electroporation of CRISPR-Cas for DNA and RNA targeting in Bos taurus zygotes. First, we describe steps for production and preparation of presumptive zygotes for electroporation. The first electroporation introduces ribonucleoproteins formed by Cas9D10A with two guide RNAs to target DNA, and the second introduces the same ribonucleoprotein complex to target DNA plus Cas13a with one guide RNA to target RNAs. For complete details on the use and execution of this protocol, please refer to Nix et al.1.