Development of New Methods for the (Q)SAR Applicability Domain Assessment: Using Structural Information in a Statistical Study of the Errors in Prediction

The main aim of (Q)SAR is to build models to evaluate and predict properties of molecules, such as biological and environmental effects, and physicochemical properties. These models are built using available experimental data, whose quality and quantity heavily affect their capability of obtaining reliable predictions for new chemicals. A dataset can be viewed as a "sampling" of the whole chemical space, if a sample is too small and / or too homogeneous, the model will inevitably have limitations in the type of chemicals it can predict. From the point of view of protecting the human health and the environment, it is preferable that a model is able to predict even a small number of chemicals, but with the highest possible reliability. The "coverage" issue can be overcome by integrating results from different models. In this perspective the importance of clearly defining the model's applicability domain is crucial to identify which model is most suitable for each chemical to assess. The definition of the applicability domain (AD) of (Q)SAR models is still an open research field. Several approaches have been proposed and implemented through years, including the use of structural features such as functional groups and atom-centered fragments. These features have also proven to be useful for an a priori definition of AD, making it independent from the specific algorithm chosen to develop the model. Within this study, the definition of (Q)SAR models' applicability domain has been investigated using structural features of different complexity: thresholds for chemical composition and molecular weight, chemical classes related to commonly well and badly predicted molecules, and statistically-extracted structural fragments to model the error in prediction. In the case studies considered, these approaches improved the AD definition provided by the model developers, supporting their integration within the definition of the models' applicability domain

Control hormonal del ciclo estral en bovinos y ovinos

The goal of this review is conducting a detailed and updated literature description of hormonal mechanisms that regulate the estrous cycle. Indeed, we know that estrous cycle is the time period from one heat to the beginning of the next one. The endocrine events during the estrous cycle are regulated by hypothalamus (through GnRH secretion), the pituitary (lh and fsh secretion), the follicles (estrogens and inhibin secretion), the corpus luteum (progesterone and oxytocin), and uterus (responsible for production of prostaglandin F2α). Within proestrus, a quick decrease in plasma progesterone levels precedes the estrus caused by releasing prostaglandin F2 α from endometrium. Such reduction of progesterone concentrations allows the ovulatory follicle to grow and secrete estradiol; so plasma estradiol binding to specific receptors in the hypothalamus can set off the neural mechanism that triggers behavioral changes associated with the estrus onset. During estrus, or heat, the female is receptive to the male and allows mating. A peak in estradiol levels occurs shortly after the estrus onset and induces the lh pre-ovulatory discharge, which in turn induces the ovulation and the beginning of luteinization process of theca and granulose cells. A new corpus luteum is developed during metestrus with a subsequent increase in progesterone serum concentration. This corpus completes its maturation during diestrus. If a viable embryo in the uterus, it sends a signal for maternal recognition of pregnancy whose recognition prevents luteolisis process and, subsequently, the beginning of a new estrus cycle during pregnancy.El objetivo de esta revisión de literatura es realizar una descripción detallada y actualizada de los mecanismos hormonales que regulan el ciclo estral. En efecto, sabemos que el ciclo estral es el tiempo comprendido desde un celo hasta el comienzo del siguiente. Los eventos endocrinos presentes durante el ciclo son regulados por el hipotálamo (mediante la secreción de GnRH), la hipófisis (secreción de lhy fsh), el folículo (secreta estrógenos e inhibina), el cuerpo lúteo (secreta progesterona y oxitocina) y el útero (productor de prostaglandina F2α). En el proestro una rápida disminución en los niveles de progesterona plasmática precede al estro, causada por la liberación de prostaglandina F2α desde el endometrio. La disminución en las concentraciones de progesterona permite al folículo ovulatorio crecer y secretar estradiol; la captación de estradiol plasmático por receptores específicos en el hipotálamo puede “disparar” el mecanismo neural que permite los cambios de comportamiento asociados con el inicio del celo. Durante el estro, la hembra es receptiva al macho y permite la cópula. Un pico en las concentraciones de estradiol aparece después del inicio del estro e induce la descarga preovulatoria de lh. Ésta induce la ovulación e inicia el proceso de luteinización de las células de la teca y la granulosa. Durante el metaestro, se desarrolla un nuevo cuerpo lúteo, las concentraciones séricas de progesterona inician su elevación hasta que, en el diestro, el cuerpo lúteo termina su proceso de maduración. Si existe un embrión viable en el útero, éste enviará señales de reconocimiento materno que frenará el proceso de luteólisis, evitando que el animal inicie un nuevo ciclo estral y mantenga así la vida del cuerpo lúteo durante la gestación

Heat shock response in PBMCs of Nellore cows after in vitro thermal stress

Abstract Adaptation is an important feature to be studied in animals when thinking about maintenance and raise of productivity. Although Nellore breed is widely disseminated in Brazil, the knowledge related to its thermotolerance in tropical climate conditions remains unknown. Hence, the aim of this study was to understand the Nellore breed cellular adaptation when exposed to heat shock in vitro, using peripheral blood mononuclear cells (PBMCs). The comprehension of the most expressed and sensible heat shock proteins in Bos taurus indicus may elucidate a molecular marker for genetic improvement related to thermotolerance. Previous to blood sampling, the physiological parameters of 16 cows were measured in order to classify them in efficient and non-efficient on heat loss. For this experiment, the blood was collected in three different heparin tubes by jugular venipuncture only in 10 cows, 5 efficient and 5 nonefficient, at morning. The molecular analyzes were performed in Physiology and Molecular Endocrinology Laboratory, Faculty of Veterinary Medicine and Animal Science, University of São Paulo. After sampling, each blood tube were placed in three different water bath devices calibrated for: 38°C, 40°C and 42°C for two consecutive hours. The PBMCs were separated, washed with hemolysis solution, the RNA extracted, the cDNA synthetized and performed the qPCR for the genes HSP60, HSP70 and HSP90. There was a maintenance on HSPs transcripts on 38°C and 40°C and a decrease on all HSPs transcripts at 42°C. Among all, the HSP70 was the most expressed at 38°C and 40°C, elucidating its protective importance. No difference was observed between gene expression and heat loss efficiency. In conclusion, the Nellore cell adaptability was confirmed by the maintenance of heat shock proteins 60, 70 and 90 kDa. The pathway for understanding responses involving thermotolerance is still long and requires more knowledge of cell signaling, either in vitro or in vivo conditions. Taken together, these informations may contribute in future keys for genetic selection of adapted animals

Follicular dynamics, corpus luteum growth and regression in multiparous buffalo cows and buffalo heifers

ABSTRACT Objective. Characterize the follicular dynamics and luteal growth and regression pattern of multiparous (MB) and heifer (BH) Murrah buffaloes in Colombian tropical conditions. Material and methods. Ten MB and ten BH were synchronized with a progesterone-releasing intravaginal device. No artificial insemination was performed during the estrous and daily ultrasound examinations were performed 15 days later to determine the number and diameter of the structures present in both ovaries in the subsequent natural estrous cycle. The Student’s T test was used to evaluate differences between MB and BH. All data are presented as mean ± standard deviation. Results. The length of the estrous cycle was 22.00±4.50 days for MB and 22.00±2.70 days for BH. Follicular growth occurs in one (n=1; 5.89%), two (n=14; 82.35%) or three waves (n=2; 11.76%). The first wave initiated the day after ovulation with the recruitment of 8.33±2.06 and 10.00±2.72 follicles in MB and BH, while the second wave started on day 11.00±2.00 and 10.50±2.82, presenting 8.37±2.26 and 8.00±1.51 follicles. The third wave began on day 16.21±3.10 showing 6.50±1.70 follicles, only BM had three waves. The maximum luteal diameter was 19.58±4.16 mm and 17.74±3.32 mm respectively. There were no significant differences between the groups for these variables. Conclusions. These results show that the follicular development in buffaloes occurs in waves, where two waves is the most common pattern, as previously reported by other authors

Oviductal transcriptional profiling of a bovine fertility model by next-generation sequencing

In cattle, the oviduct plays a fundamental role in the reproductive process. Oviductal functions are controlled by the ovarian sex steroids: estradiol and progesterone. Here, we tested the hypothesis that the exposure to contrasting sex steroid milieus differentially impacts the oviductal transcriptional profile. We manipulated growth of the pre-ovulatory follicle to obtain cows that ovulated a larger (LF group) or a smaller (SF group) follicle. The LF group presented greater proestrus/estrus concentrations of estradiol and metaestrus concentrations of progesterone (Gonella-Diaza et al. 2015 [1], Mesquita et al. 2014 [2]). Also, the LF group was associated with greater fertility in timed-artificial insemination programs (Pugliesi et al. 2016 [3]). Cows were slaughtered on day 4 of the estrous cycle and total RNA was extracted from ampulla and isthmus fragments and analyzed by RNAseq. The resulting reads were mapped to the bovine genome (Bos taurus UMD 3.1, NCBI). The differential expression analyses revealed that 325 and 367 genes in ampulla and 274 and 316 genes in the isthmus were up-regulated and down-regulated in LF samples, respectively. To validate the RNAseq results, transcript abundance of 23 genes was assessed by qPCR and expression patterns were consistent between the two techniques. A functional enrichment analysis was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Processes enriched in the LF group included tissue morphology changes (extracellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters). An overview of the gene expression data was deposited in the NCBI's Gene Expression Omnibus (GEO) and is accessible through the accession number GSE65681. In conclusion, differences in the peri-ovulatory sex steroid milieu modify the oviductal gene expression profiles. Such differences may be associated with the greater fertility of the LF cows. This dataset is useful for further investigations of the oviductal biology and the impact of sex-steroid on the female reproductive tract

Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle

In cattle, molecular control of oviduct receptivity to the embryo is poorly understood. Here, we used a bovine model for receptivity based on size of the pre-ovulatory follicle to compare oviductal global and candidate gene transcript abundance on day 4 of the estrous cycle. Growth of the pre-ovulatory follicle (POF) of Nelore (Bos indicus) cows was manipulated to produce two groups: large POF large corpus luteum (CL) group (LF-LCL; greater receptivity) and small POF-small CL group (SF-SCL). Oviductal samples were collected four days after GnRH-induced ovulation. Ampulla and isthmus transcriptome was obtained by RNA-seq, regional gene expression was assessed by qPCR, and PGR and ERa protein distribution was evaluated by immunohistochemistry. There was a greater abundance of PGR and ERa in the oviduct of LF-LCL animals thus indicating a greater availability of receptors and possibly sex steroids stimulated signaling in both regions. Transcriptomic profiles indicated a series of genes associated with functional characteristics of the oviduct that are regulated by the periovulatory sex steroid milieu and that potentially affect oviductal receptivity and early embryo development. They include tissue morphology changes (extra cellular matrix remodeling), cellular changes (proliferation), and secretion changes (growth factors, ions and metal transporters), and were enriched for the genes with increased expression in the LF-LCL group. In conclusion, differences in the periovulatory sex steroid milieu lead to different oviductal gene expression profiles that could modify the oviductal environment to affect embryo survival and development

Actions of DKK1 on the bovine embryo during the morula-to-blastocyst stage of development on pregnancy outcomes and placental hormone secretion after embryo transfer.

Edição dos abstracts da Annual Conference of the International Embryo Transfer Society, 48., Savannah, Geórgia, 2022

Measurement of the cross-section for b-jets produced in association with a Z boson at root s=7 TeV with the ATLAS detector ATLAS Collaboration

A measurement is presented of the inclusive cross-section for b-jet production in association with a Z boson in pp collisions at a centre-of-mass energy of root s = 7 TeV. The analysis uses the data sample collected by the ATLAS experiment in 2010, corresponding to an integrated luminosity of approximately 36 pb(-1). The event selection requires a Z boson decaying into high P-T electrons or muons, and at least one b-jet, identified by its displaced vertex, with transverse momentum p(T) > 25 GeV and rapidity vertical bar y vertical bar < 2.1. After subtraction of background processes, the yield is extracted from the vertex mass distribution of the candidate b-jets. The ratio of this cross-section to the inclusive Z cross-section (the average number of b-jets per Z event) is also measured. Both results are found to be in good agreement with perturbative QCD predictions at next-to-leading order