Biology subjects

Ferraz, J. B. S.

Publications and source records attributed to Ferraz, J. B. S..

4 recordsLinked to original sources

bioRxiv2023

Assessment of Total Oocyte Transcripts Representation through Single Ooplasm Biopsy in Bovine with High Reliability

Understanding the entire transcriptional and epigenetic landscape is facilitated by the application of omics in a number of ways. Today, omic instruments are more affordable and easier to implement. In human research, for instance, single-omics are a reality and are used extensively to generate vast quantities of data. This method permits the comprehensive reconstruction of transcriptome and epigenetic markers removing bias from pooled samples. In tandem with the evolution of machines and protocols, algorithms and genome annotation have undergone continuous improvement. The genome annotation of domestic animals is inferior to that of humans, rodents, and less complex organisms. In the case of heifers, the reference is incomplete, with significant gaps and only a portion of the noncoding transcripts. The purpose of this study is to validate our compartmentalized single oocyte biopsy by comparing a small fraction of bovine oocytes, 1%, to the entire oocyte at the Metaphase II stage. In addition, we examined the use of four database sources (NCBI, ENSEMBL, UCSC, and NONCODE) to produce a merged non-redundant gene alignment and counting in order to enhance gene detection and normalization, resulting in a more accurate method to comprehend the entire landscape. This study is a continuation of our research titled "Retrospective model utilizing biopsies, granulosa cells, and polar body to predict oocyte competence in bovine" in which this method was used to retrospectively compare biopsy oocytes collected during the MII phase. With the addition of NONCODE information, gene normalization was significantly enhanced. In addition, our analysis identified 4560 noncoding genes from NONCODE references. ENSEMBL and NCBI have nearly the same number of annotated genes (16,423 vs. 17,804), but using ENSEMBL as a reference, 2356 genes were able to be normalized and identified. Proceeding to biopsy x oocyte analysis, we were able to detect a greater number of genes in oocytes than in biopsy, where the preponderance was from NONCODE sources (68). Despite these minor differences, the high correlation of expression between them (89%) was consistent and proved to be a valuable instrument for studying the oocyte without destroying it.

bioinformatics↗

bioRxiv2023

An exploratory data analysis from ovine and bovine RNA-seq identifies pathways and key genes related to cervical dilatation

The present study developed a review and exploration of data in public and already validated repositories. The main objective is to identify the pathways involved in ruminants cervical dilatation, which are conserved between cattle and sheep in the follicular and luteal phases of the reproductive cycle. In cattle, 1961 genes were found to be more expressed in the follicular phase and 1560 in the luteal phase. 24 genes were considered exclusively expressed from these 18 genes were in the follicular phase and 6 genes were in the luteal phase. In sheep, 2126 genes are more expressed in the follicular phase and 2469 genes are more expressed in the luteal phase. Hoxb genes were identified in both species and are correlated with the PI3K/Akt pathway. PI3K/Akt was also found in both cattle and sheep, appearing prominently in the follicular and luteal phases of both species. Our analyzes have pointed out that the PI3K/Akt pathway and the Hoxb genes appear in prominence, in modulating mechanisms that involve estrus alterations in the cervix. PI3K/Akt appears to be an important pathway in the cervical relaxation process.

genomics↗

bioRxiv2019

Factors affecting secondary sex characteristics in the yellowtail tetra Astyanax altiparanae

This work aimed to analyze factors affecting secondary sexual characteristics in the yellowtail tetra Astyanax altiparanae. For this, seventy-five specimens were first separated into three different size classes (small, medium and large groups) between two seasons, summer and winter. In all groups, male fish were consistently bigger in the summer. On the other hand, females from both seasons presented in media the same length into the length classes. Afterwards, we performed histological analyses of the gonads to first confirm the genus and investigate the phase of maturation of each animal. During the winter, most of the small animals were males (22), most of the large animals, females (23), and the medium size animals followed a tendency of 1:1 ratio (9 male: 16 female). In the summer, male were the majority in both small (20) and medium (20) size. Larger-size animals were female (23). Then, in order to analyze the influence of genus, phase of maturation, season of the year, the number, and length of the animals spinelets, we diaphanized, counted, and measured them in each animal. Our results demonstrated that the spinelets are a sexual secondary characteristic of male genus independently of the size, season and phase of maturation. However, some tendencies were observed. Males bigger than 48 mm always presented spinelets; their size are in media the double in summer in comparison to winter; and summer males presents more rays with spinelets in the summer. Curiously, the larger specimen sampled was a female presenting spinelets in five rays. Lastly, we performed the gonadectomization of the animals and hypothesized that gonad hormones will directly influence this characteristic. The gonadectomization only initially influence on the size and number of spinelets in the anal fin rays, since the thirty-day-gonadectomized animals presented few and smaller spinelets against the control ones. However, the spinelets normalized in ninety-day-gonadectomized specimens. Such a work showed spinelets can be considered a secondary sexual characteristic to distinct male from female and can be used in the management in specimens bigger than 48 mm, but cannot indicate fish sterility.\n\nSummary statementThis study elucidated whether the size, sex, environmental conditions, and gonadal development affect the development of spinelets, a bony structure presented in anal fins in mature fish. Additionally, gonadectomized fish were used to elucidate the effect of gonad on the rise of such structures. Interesting new data showed that such a secondary sex characteristic is influenced by sex, size, gonadal development, and season of the year, but spinelets arose even within gonadectomized fish; this suggests that such a structure is not indicative of sterility in this species.

physiology↗

bioRxiv2018

Systems biology reveals NR2F6 and TGFB1 as key regulators of feed efficiency in beef cattle

Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (100bp, pared-end). From the 17,354 expressed genes, 1,317 were prioritized by five selection categories (differentially expressed, harbouring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated to FE. Moreover, we indicated potential biomarkers of FE which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.

systems biology↗