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Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.

Defensins are a prominent family of antimicrobial peptides. They play sophisticated roles in the defense against pathogens in all living organisms, but few works address their expression under different conditions and plant tissues. The present work prospected defensins of Manihot esculenta Crantz, popularly known as cassava. Five defensin candidates (MeDefs) were retrieved from the genome sequences and characterized. Considering chromosome distribution, only MeDef1 and 2 occupy adjacent positions in the same chromosome arm. All 3D structures had antiparallel ß-sheets, an α-helix, and amphipathic residues distributed throughout the peptides with a predominance of cationic surface charge. MeDefs expression was validated by RT-qPCR, including two stress types (biotic: fungus Macrophomina pseudophaseolina, and abiotic: mechanical injury) and a combination of both stresses (fungus+injury) in three different tissues (root, stem, and leaf). For this purpose, ten reference genes (RGs) were tested, and three were chosen to characterize MeDef expression. MeDef3 was up-regulated at roots in all stress situations tested. MeDef1 and MeDef5 were induced in leaves under biotic and abiotic stresses, but not in both stress types simultaneously. Only MeDef2 was down-regulated in the stem tissue also with biotic/abiotic combined stresses. These results indicate that although defensins are known to be responsive to pathogen infection, they may act as preformed defense or, still, have tissue or stress specificities. Aspects of their structure, stability and evolution are also discussed.

In the present study, we aimed to identify morphological and molecular changes of in vivo and in vitro-produced goat embryos submitted to cryopreservation. In vivo embryos were recovered by transcervical technique from superovulated goats, whereas in vitro produced embryos were produced from ovaries collected at a slaughterhouse. Embryos were frozen by two-steps slow freezing method, which is defined as freezing to -32 °C followed by transfer to liquid nitrogen. Morphological evaluation of embryos was carried out by assessing blastocoel re-expansion rate and the total number of blastomeres. The expression profile of candidate genes related to thermal and oxidative stress, apoptosis, epigenetic, and implantation control was measured using RT-qPCR based SYBR Green system. In silico analyses were performed to identify conserved genes in goat species and protein-protein interaction networks were created. In vivo-produced embryos showed greater blastocoel re-expansion and more blastomere cells (P 0.05). The expression level of CTP2 and HSP90 genes from in vitro cryopreserved embryos was higher than their in vivo counterparts. Unlikely, no significant difference was observed in the transcription level of SOD gene between groups. The high similarity of CPT2 and HSP90 proteins to their orthologs among mammals indicates that they share conserved functions. In summary, cryopreservation negatively affects the morphology and viability of goat embryos produced in vitro and changes the CPT2 and HSP90 gene expression likely in response to the in vitro production process.

Pluripotency-associated transcription factors (PATFs) are involved in several cellular processes, such as transcription initiation, cellular metabolism, and cell fate determination in preimplantation embryos. Despite growing understanding of PATFs in pluripotent human and mouse cells, their roles in other species or cell types remain limited. The work aimed to determine the transcript availability of OCT4 and four non-canonical PATFs (NAC1, NR0B1, RONIN, and ZFP281) in goat ovaries, eggs, and cumulus cells. Goat ovaries were collected at slaughterhouses and cumulus-oocyte complexes (COC) were retrieved from 3 to 6 mm follicles. The COCs were subject to in vitro maturation in TCM-199 medium containing 2 mM l-glutamine, 5.0 μg mL−1 FSH, 10% FBS, and antibiotics at 38.5 °C with saturated humidity and 5% CO2 during 24 h. Gene activity was detected by both conventional reverse transcription quantitative polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR). In silico analysis were carried out for protein physical properties, phenetic analysis, and protein domains within goat, mouse, and human PATF orthologs. Products of all five PATFs analyzed (NAC1, NR0B1, OCT4, RONIN, and ZFP281) were detected in goat eggs, but NR0B1 was not detected in the ovary. Surprisingly, NR0B1, RONIN, and ZFP281 were also expressed in cumulus cells. All PATFs and their binding partners (i.e., OCT4-SOX2, RONIN HCF1, and NANOG-NR0B1-ZFP281-NAC1) showed similar protein size, molecular weight, and isoelectric point among species. The phenetic analysis clustered more closely goat and human proteins for OCT4, SOX2, NANOG, and NR0B1. Finally, both DNA-binding and transactivation domains were also highly conserved among species, particularly between goats and humans, suggesting that these PATFs may have conserved functions and similar target genes. In conclusion, non-canonical PATFs have distinctive transcript abundance in goat eggs and cumulus cells, while in silico approaches suggest that these genes may play similar roles to their mouse and human orthologs.

Almost 48 years after the gene-for-gene interaction model was proposed by Flor, NBS-LRR resistance (R) genes are still the focus of intense research interest. Also called NB-LRR, NB-ARC, NLR (Nucleotide Binding Domain and Leucine-rich Repeat), this group regards the largest R gene class, accounting for more than half of the plant R genes, with an impressing number and structural diversity, especially in angiosperms. With the omics advent, especially genomics and transcriptomics, an emergence of the so-called NLRomics came out, allowing the annotation and comparative analysis of NBS-LRR members at functional and structural level on a previously unfeasible scale. The present chapter provides a retrospective of studies involving NBS-LRR genes and proteins, including information on mechanisms of action, regulation, patterns of expression, subcellular localization, origin, diversification, and evolution in plants. Aspects of plant-pathogen coevolution are discussed, as well as resistance-breaking mechanisms reported in the literature. Main databases compiling NBS-LRR genes are discussed, and a routine for their annotation and structural analysis is presented. Practical implications of NBS-LRR molecules are considered, together with aspects about existing limitations and their potential biotechnological applications.

SummaryPluripotency-associated transcription factors (PATFs) modulate gene expression during early mammalian embryogenesis. Despite a strong understanding of PATFs during mouse embryogenesis, limited progress has been made in ruminants. This work aimed to describe the temporal expression of eight PATFs during both sheep and cattle preimplantation development. Transcript availability of PATFs was evaluated by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in eggs, cleavage-stage embryos, morulae, and blastocysts. Transcripts of five genes were detected in all developmental stages of both species (KLF5, OCT4, RONIN, ZFP281, and ZFX). Furthermore, CMYC was detected in all cattle samples but was found from cleavage-stage onwards in sheep. In contrast, NR0B1 was detected in all sheep samples but was not detected in cattle morulae. GLIS1 displayed the most significant variation in temporal expression between species, as this PATF was only detected in cattle eggs and sheep cleavage-stage embryos and blastocysts.In silicoanalysis suggested that cattle and sheep PATFs share similar size, isometric point and molecular weight. A phenetic analysis showed two patterns of PATF clustering between cattle and sheep, among several mammalian species. In conclusion, the temporal expression of pluripotency-associated transcription factors differs between sheep and cattle, suggesting species-specific regulation during preimplantation development.

Introduction: During evolution, plants developed defense mechanisms against pathogen attack, including an infinity of molecular processes that are triggered by pathogen exposure, such as resistance gene synthesis (R). The NBS-LRR gene family is known as one of the most representative families in the R gene class, in which its protein domains are related to one form of plant defense mechanisms. Objective: To identify and characterize candidate sequences of the NBS-LRR gene family in the Vitis vinifera genome. Methodology: Initially, a seed sequence was selected from those curated in the NBS-LRR family and deposited in the UniProt database. This sequence was aligned via tBLASTn against the V. vinifera genome deposited in the NCBI, by adopting a cut-off of e-value ≥ e-10. The sequences were annotated, translated and had its conserved protein domains identified by both ORF Finder and CD-search tools, respectively. Finally, the prediction of the isoelectric point was performed, and the molecular weight was also estimated using the JVirGel 2.0 software. Moreover, the subcellular localization was carried out by the Cell-PLoc 2.0 software. Results and Discussion: A total of 40 candidate sequences were retrieved that are related to the gene of interest. The translated proteins showed a variation from 338 to 944 aa in size. A total of 33 complete NBS domains were found, from which 16 sequences had a whole RX-CC_like domain, while only two sequences have a full-length LRR domain. The candidate proteins had an isoelectric point from 5.25 to 9.46, a molecular weight varying from 38.47 and 108.14 kDa. All proteins showed cytoplasmatic subcellular localization, from which, 21 % also displayed an cellular membrane localization, in agreement with the data described in the literature. Conclusions: The results described here can contribute to a better understanding of the molecular characteristics of the NBS-LRR gene family and their role in defense mechanisms of grapevines to pathogens.