Diversity of bacterial communities in wetlands of Calakmul Biosphere Reserve: a comparative analysis between conserved and semi-urbanized zones in pre-Mayan Train era.

BACKGROUND: The Calakmul Biosphere Reserve (CBR) is known for its rich animal and plant biodiversity, yet its microbial communities remain largely unknown. The reserve does not possess permanent bodies of water; nevertheless, seasonal depressions associated with fractures create wetlands, known locally as aguadas. Given the recent construction of the Maya train that crosses the CRB, it is essential to assess the biodiversity of its microorganisms and recognize their potential as a valuable source of goods. This evaluation is pivotal in mitigating potential mismanagement of the forest ecosystem. To enhance comprehension of microbial communities, we characterized the microbiota in three different wetlands. Ag-UD1 and Ag-UD2 wetlands are located in a zone without human disturbances, while the third, Ag-SU3, is in a semi-urbanized zone. Sampling was carried out over three years (2017, 2018, and 2019), enabling the monitoring of spatiotemporal variations in bacterial community diversity. The characterization of microbiome composition was conducted using 16S rRNA metabarcoding. Concurrently, the genomic potential of select samples was examined through shotgun metagenomics. RESULTS: Statistical analysis of alpha and beta diversity indices showed significant differences among the bacterial communities found in undisturbed sites Ag-UD1 and Ag-UD2 compared to Ag-SU3. However, no significant differences were observed among sites belonging to the undisturbed area. Furthermore, a comparative analysis at the zone level reveals substantial divergence among the communities, indicating that the geographic location of the samples significantly influences these patterns. The bacterial communities in the CBR wetlands predominantly consist of genera from phyla Actinobacteria, Acidobacteria, and Proteobacteria. CONCLUSION: This characterization has identified the composition of microbial communities and provided the initial overview of the metabolic capacities of the microbiomes inhabiting the aguadas across diverse conservation zones. The three sites exhibit distinct microbial compositions, suggesting that variables such as chemical composition, natural and anthropogenic disturbances, vegetation, and fauna may play a pivotal role in determining the microbial structure of the aguadas. This study establishes a foundational baseline for evaluating the impact of climatic factors and human interventions on critical environments such as wetlands.

The Importance of Structural Water in HDAC8 for Correct Binding Pose Applied for Drug Design of Anticancer Molecules.

AIMS: Validating the docking procedure and maintaining the structural water molecules at HDAC8 catalytic site. BACKGROUND: Molecular docking simulations play a significant role in Computer-Aided Drug Design, contributing to the development of new molecules. To ensure the reliability of these simulations, a validation process called "self-docking or re-docking" is employed, focusing on the binding mode of a ligand co-crystallized with the protein of interest. OBJECTIVE: In this study, several molecular docking studies were conducted using five X-ray structures of HDAC8-ligand complexes from the PDB. METHODS: Ligands initially complexed with HDAC8 were removed and re-docked onto the free protein, revealing a poor reproduction of the expected binding mode. In response to this, we observed that most HDAC8-ligand complexes contained one to two water molecules in the catalytic site, which were crucial for maintaining the cocrystallized ligand. RESULTS: These water molecules enhance the binding mode of the co-crystallized ligand by stabilizing the proteinligand complex through hydrogen bond interactions between ligand and water molecules. Notably, these interactions are lost if water molecules are removed, as is often done in classical docking methodologies. Considering this, molecular docking simulations were repeated, both with and without one or two conserved water molecules near Zn+2 in the catalytic cavity. Simulations indicated that replicating the native binding pose of co-crystallized ligands on free HDAC8 without these water molecules was challenging, showing greater coordinate displacements (RMSD) compared to those including conserved water molecules from crystals. CONCLUSION: The study highlighted the importance of conserved water molecules within the active site, as their presence significantly influenced the successful reproduction of the ligands' native binding modes. The results suggest an optimal molecular docking procedure for validating methods suitable for filtering new HDAC8 inhibitors for future experimental assays.

Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules.

Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions. To date, only four molecular analyses have been conducted on the group and they failed to resolve the relationships of the main lineages and even recovering the non-monophyly of the three genera. These studies were limited to a few Sanger loci or phylogenomic analyses with at most seven ingroup samples. To increase phylogenetic resolution in this little-understood and poorly studied group, we present the most comprehensive phylogenomic study of Ricinulei to date leveraging the Arachnida ultra-conserved element probe set. With a data set of 473 loci across 96 ingroup samples, analyses resolved a monophyletic Neotropical clade consisting of four main lineages. Two of them correspond to the current genera Cryptocellus and Pseudocellus while topology testing revealed one lineage to likely be a phylogenetic reconstruction artefact. The fourth lineage, restricted to Northwestern, Andean South America, is consistent with the Cryptocellus magnus group, likely corresponding to the historical genus Heteroricinoides. Since we did not sample the type species for this old genus, we do not formally re-erect Heteroricinoides but our data suggest the need for a thorough morphological re-examination of Neotropical Ricinulei.

A computational pipeline elucidating functions of conserved hypothetical Trypanosoma cruzi proteins based on public proteomic data.

The proteome is complex, dynamic, and functionally diverse. Functional proteomics aims to characterize the functions of proteins in biological systems. However, there is a delay in annotating the function of proteins, even in model organisms. This gap is even greater in other organisms, including Trypanosoma cruzi, the causative agent of the parasitic, systemic, and sometimes fatal disease called Chagas disease. About 99.8% of Trypanosoma cruzi proteome is not manually annotated (unreviewed), among which>25% are conserved hypothetical proteins (CHPs), calling attention to the knowledge gap on the protein content of this organism. CHPs are conserved proteins among different species of various evolutionary lineages; however, they lack functional validation. This study describes a bioinformatics pipeline applied to public proteomic data to infer possible biological functions of conserved hypothetical Trypanosoma cruzi proteins. Here, the adopted strategy consisted of collecting differentially expressed proteins between the epimastigote and metacyclic trypomastigotes stages of Trypanosoma cruzi; followed by the functional characterization of these CHPs applying a manifold learning technique for dimension reduction and 3D structure homology analysis (Spalog). We found a panel of 25 and 26 upregulated proteins in the epimastigote and metacyclic trypomastigote stages, respectively; among these, 18 CHPs (8 in the epimastigote stage and 10 in the metacyclic stage) were characterized. The data generated corroborate the literature and complement the functional analyses of differentially regulated proteins at each stage, as they attribute potential functions to CHPs, which are frequently identified in Trypanosoma cruzi proteomics studies. However, it is important to point out that experimental validation is required to deepen our understanding of the CHPs.

Habitat specialization predicts demographic response and vulnerability of floodplain birds in Amazonia.

The annual flooding cycle of Amazonian rivers sustains the largest floodplains on Earth, which harbour a unique bird community. Recent studies suggest that habitat specialization drove different patterns of population structure and gene flow in floodplain birds. However, the lack of a direct estimate of habitat affinity prevents a proper test of its effects on population histories. In this work, we used occurrence data, satellite images and genomic data (ultra-conserved elements) from 24 bird species specialized on a variety of seasonally flooded environments to classify habitat affinities and test its influence on evolutionary histories of Amazonian floodplain birds. We demonstrate that birds with higher specialization in river islands and dynamic environments have gone through more recent demographic expansion and currently have less genetic diversity than floodplain generalist birds. Our results indicate that there is an intrinsic relationship between habitat affinity and environmental dynamics, influencing patterns of population structure, demographic history and genetic diversity. Within the floodplains, historical landscape changes have had more severe impacts on island specialists, making them more vulnerable to current and future anthropogenic changes, as those imposed by hydroelectric dams in the Amazon Basin.

Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped, plus-stranded RNA virus responsible for the Coronavirus Disease 2019 (COVID-19). Patients infected with COVID-19 may be asymptomatic or have symptoms ranging from mild manifestations to severe cases of the disease that could lead to death. The SARS-CoV-2 genome encodes 4 structural proteins, including the Spike protein (S), the Nucleocapsid protein (N), Membrane protein (M) and, the Envelope protein (E). The N protein forms a major component of the ribonucleoprotein complex within the virus particle and play a vital role in its transcription and replication. Nevertheless, the S protein was the most important protein in the development of vaccines against COVID-19. However, the decrease in number of registered immunizations against the disease and the rapid drop in neutralizing antibody titers together with looser preventive measures for virus transmission, favored the rapid appearance of new variants of concerns (VOCs) that primarily show mutations in the S protein. This fact makes the N protein a good candidate for the development of diagnostic tests, due to its stability, amino acid conservation, high immunogenicity, and the smaller likelihood of mutation. With the aim of developing a new diagnostic kit based on the N protein, we evaluated the humoral response in female Wistar rats against this target. Three constructions of the N protein were used to inoculate the animals: the full-length protein (Cfull), the N- (NTD), and the C-terminal (CTD) portion of the protein. The immunizations induced the animal's immune response, with specific polyclonal IgG antibodies against the Cfull protein and its fragments. There were not non-specific bind to the protein used as negative control. Anti-Cfull antibodies demonstrated high efficiency in binding to the NTD protein and the antibodies present in the anti-CTD and anti-NTD sera have recognized the Cfull protein, but they were not able to recognize the NTD and CTD proteins, respectively. Our results indicate an efficient protocol for obtaining high antibody titers against the N recombinant protein of SARS-CoV-2 and its fragments highlighting the Cfull protein, which can be used in the development of new diagnostic kits.

Environmental filters explain the ecomorphological patterns of stream fish in the southern Amazon

ABSTRACT The ecomorphology reflects morphological variations that may indicate significant ecological processes. In this study, the influence of environmental variables on the ecomorphological composition of stream fish was tested. The study was developed in ten streams within a conservation area in the Juruena River sub-basin, in Mato Grosso state, Brazil. The sampling occurred during the drought period in July 2012. The fish were sampled with simple sieves and trawl nets. We analyzed 17 variables of the physical habitat and 14 morphological indices based on morphometric measurements of the fish. In total, 753 specimens were collected, comprising four orders, 14 families, and 27 species. Only fine sediments influenced the ecomorphological composition of the fish assemblages. This substrate variable acted as a filter for the ecomorphology of fish that usually inhabit slow waters, have a morphology adapted towards a good stabilization capacity and maneuverability, fins capable of large and rapid impulses, and that feed close to the surface. Our results can contribute to the understanding of the ecological processes that drive the composition of fish assemblages in conserved Amazonian streams.

RESUMO A ecomorfologia reflete variações morfológicas que podem indicar processos ecológicos significativos. Neste estudo, testamos a influência de variáveis ambientais na composição ecomorfológica de peixes de riachos. O estudo foi desenvolvido em dez riachos em uma área de conservação na sub-bacia do Rio Juruena, estado de Mato Grosso, Brasil. A amostragem ocorreu durante o período de estiagem em julho de 2012. Os peixes foram amostrados com redes de peneira e redes de arrasto. Foram analisadas 17 variáveis do habitat físico e 14 índices morfológicos baseados em medidas morfométricas dos peixes. No total, foram coletados 753 exemplares de quatro ordens, 14 famílias e 27 espécies. Apenas sedimentos finos influenciaram a composição ecomorfológica das assembleias de peixes. Esta variável de substrato funcionou como um filtro para a ecomorfologia de peixes que normalmente habitam águas lentas, têm uma morfologia adaptada a uma boa capacidade de estabilização e manobrabilidade, nadadeiras capazes de impulsos grandes e rápidos, e que se alimentam junto à superfície. Nossos resultados podem contribuir para a compreensão dos processos ecológicos que estruturam as assembléias de peixes em riachos amazônicos conservados.

Old and cold: Diverse phylogenomic datasets support an ancient transantarctic dispersive route on the scorpion family Bothriuridae in temperate Gondwana.

In this contribution we try to unveil the diversification process of Bothriuridae in temperate Gondwana through dated phylogenomic analyses using UCE and transcriptomics, and including in the analyses species of genera Urophonius and Cercophonius, the most closely related genera of Bothriuridae from South America and Australia respectively. Additionally we explored the hypothesis that the winter activity period of some species of Urophonius, as well as the cold environmental preferences of this genus, could be related to the climatic conditions of the time frame and area in which it evolved. Genus Urophonius was recovered as sister group to Cercophonius using amino acids and UCE. The time frame obtained for the split between South American and Australian bothriurids is 94 Ma., which suggests a dispersal event through temperate Gondwana, before the final breakup of the land bridge of South America-Antarctica-Australia ca. 35 Ma. The split between summer and winter species of Urophonius, taking place at 64 Ma, is considered representative to the turnover time from the summer activity period to the winter activity period in some species of the genus. This time frame is compatible with a period of global warming of the late Cretaceous greenhouse episode that could have triggered this change.

Addition of grape marc improves the silage of aerial parts of cassava plant / La adición de orujo mejora el ensilaje de las partes aéreas de la planta de yuca / A adição de bagaço de uva melhora a silagem da parte aérea da mandioca

Abstract Background: Although it is possible to preserve the aerial part of cassava in the form of silage, as demonstrated in previous studies, its low dry matter content can result in undesirable fermentation and increased effluent losses during silage, leading to a reduction in the final quality of the silage. A possible way to get around this problem would consist in mixing this silage with dehydrated by-products from the agroindustry. Objective: To evaluate the addition of dehydrated grape marc (DGM) to a silage of aerial parts of cassava (Manihot esculenta, Crantz) on the chemical composition, degradability and in vitro gas production of silage. Methods: A completely randomized experimental design was used, with two treatments: (I) silage of the aerial part of cassava without additive; (II) silage of the aerial part of cassava added with 10% dehydrated grape marc (DGM) in the natural matter, as an additive. After 30 days of fermentation, silages were evaluated to estimate the contents of dry matter (DM), crude protein (CP), ether extract (EE), neutral detergent fiber (NDF), total digestible nutrients (TDN), as well as pH, in vitro degradability, and cumulative gas production by semi-automatic in vitro gas production. Results: Addition of DGM did not affect CP, EE, NDF, nor TDN levels in silage. The DGM, however, promoted an increase in DM content (32.61 vs 30.31%) and a reduction in pH (4.00 vs 4.75) of the silage. The silage that received DGM presented higher degradability coefficients of soluble and potentially degradable fractions, which led to higher values of potential and effective degradability. Similarly, DGM promoted a reduction in particle colonization time (6.74 vs 10.01 h) and increased cumulative gas production (62.03 vs 57.82 mL/g DM). Conclusion: Addition of 10% dehydrated grape marc in the silage of aerial parts of cassava can be useful to reduce pH and increase dry matter contents of the silage.

Resumen Antecedentes: Si bien es posible preservar la parte aérea de la yuca en forma de ensilaje, como se demostró en estudios anteriores, el bajo contenido de materia seca puede resultar en fermentaciones indeseables y mayores pérdidas de efluentes durante el ensilaje, levando a una reducción en la calidad final del ensilaje. Una de las formas de solucionar este problema sería el ensilaje mixto de la parte aérea de la yuca con subproductos deshidratados de la agroindustria. Objetivo: Evaluar el efecto de la adición de bagazo de uva deshidratado (BUD) a la parte aérea del ensilaje de yuca (Manihot esculenta, Crantz) sobre la composición química, degradabilidad y producción de gas in vitro del ensilado. Métodos: El diseño experimental utilizado fue completamente al azar y los tratamientos consistieron en: (I) ensilado de brotes de yuca sin aditivos; (II) ensilaje de la parte aérea de yuca con 10% de BUD en materia natural, como aditivo. Luego de 30 días de fermentación, los ensilajes fueron evaluados para materia seca (MS), proteína cruda (PC), extracto de éter (EE), fibra detergente neutra (FDN), nutrientes digestibles totales (NDT), pH, degradabilidad in vitro y producción acumulada de gas mediante la técnica de producción de gas in vitro semiautomática. Resultados: La adición de BUD no cambió los contenidos de PB, EE, FDN y NDT del ensilaje. Sin embargo, BUD promovió un aumento en el contenido de MS (32,61 vs 30,31%) y una reducción en el pH (4,00 vs 4,75) del ensilaje. El ensilado que recibió la BUD mostró mayores coeficientes de degradabilidad de las fracciones solubles y potencialmente degradables, lo que resultó en mayores valores de degradabilidad potencial y efectiva. De manera similar, BUD promovió una reducción en el tiempo de colonización de partículas (6,74 vs 10,01 h) y un aumento en la producción acumulada de gas (62,03 vs 57,82 mL/g MS). Conclusiones: La adición de 10% de bagazo de uva deshidratado al ensilaje de la parte aérea de yuca puede ser útil para reducir el pH y aumentar el contenido de materia seca del ensilaje.

Resumo Antecedentes: Embora seja possível preservar a parte aérea da mandioca na forma de silagem, conforme demonstrado em estudos anteriores o baixo teor de matéria seca, pode resultar em fermentação indesejável e aumento das perdas de efluentes durante a silagem, levando à redução da qualidade final da silagem. Uma das formas de contornar esse problema seria a silagem mista da parte aérea da mandioca com subprodutos desidratados da agroindústria. Objetivo: Avaliar o efeito da adição do bagaço desidratado de uva (BDU) na ensilagem da parte aérea de mandioca (Manihot esculenta, Crantz) sobre a composição química, degradabilidade e produção de gases in vitro da silagem. Métodos: O delineamento experimental utilizado foi inteiramente casualizado e os tratamentos constituíram-se por: (I) silagem da parte aérea da mandioca sem aditivo; (II) silagem da parte aérea da mandioca com 10% de bagaço desidratado de uva (BDU) na matéria natural, como aditivo. Após 30 dias de fermentação, as silagens foram avaliadas quanto aos teores de matéria seca (MS), proteína bruta (PB), extrato etéreo (EE), fibra em detergente neutro (FDN), nutrientes digestíveis totais (NDT), pH, degradabilidade in vitro e produção cumulativa de gases por meio da técnica semiautomática de produção de gases in vitro. Resultados: A adição do BDU não alterou os teores de PB, EE, FDN e NDT da silagem. No entanto, o BDU promoveu aumento no teor de MS (32,61 vs 30,31%) e redução no pH (4,00 vs 4,75) da silagem. A silagem que recebeu o BDU apresentou maiores coeficientes de degradabilidade das frações solúvel e potencialmente degradável, o que acarretou em maiores valores de degradabilidade potencial e efetiva. Do mesmo modo, o BDU promoveu uma redução no tempo de colonização da partícula (6,74 vs 10,01 h) e um aumento na produção cumulativa de gás (62,03 vs 57,82 mL/g MS). Conclusões: A adição de 10% do bagaço desidratado de uva na silagem da parte aérea de mandioca pode ser útil para reduzir o pH e aumentar os teores de matéria seca da silagem.

CoCoView - A codon conservation viewer via sequence logos.

Sequence logos are a simple way to display a set of aligned sequences, and they are useful to identify conserved patterns. Since their introduction, several tools have been developed for generating these representations at the single residue level (amino acids or nucleotides). We have developed a tool to build sequence logos of protein-coding sequences at the codon level, allowing more accurate analysis of coding-sequences as they represent synonymous and non-synonymous changes instead of showing only changes that imply on amino acid substitutions. We built CoCoView on top of the Logomaker Python API. It creates codon sequence logos from a multiple sequence alignment of protein-coding sequences. Some properties of the data and the generated logos can be controlled by the end-users, such as data redundancy, plot type and alphabet color. • Split aligned sequences into codon positions; • For each position compute codon frequency and information content; • Use the computed information to plot the graphic.

Immunoinformatics-based characterization of immunogenic CD8 T-cell epitopes for a broad-spectrum cell-mediated immunity against high-risk human papillomavirus infection.

Human papillomavirus (HPV) represents the most prevalent sexually transmitted infectious agent worldwide. Vaccination has been an approach successfully used as a prophylactic measure against this infectious agent in patients without previous contact with the genotypes present in the vaccine. In this work, we use a computational approach to predict CD8 T cell epitopes from HPV proteins to promote cell-mediated immunity. We evaluated immunogenicity, conservation, toxicity, stability and population coverage of epitopes. Finally, a molecular docking analysis was performed to confirm the stability of the complexes formed. We identified 17 epitopes with affinity for several HLA alleles, covering 5 binding supermotifs (A2, A3, A24, B62 and B57). The analyses showed that these epitopes have a high population coverage and are highly conserved among several HPV genotypes. Seven of them (NWKNFFSTTWE1594-603, KVSAFQYRVFRVL163-74, LQFIFQLCKL1372-380, RVFRVQLPDPNKL170-81, FNKPYWLHRL1307-315, FITCVDTTRL1330-338 and HLRREQIFARL1248-257) were 100% conserved. Finally, molecular docking confirmed the stability of the complexes by means of a large network of hydrogen bonds formed and the calculated low bonding energy. The epitopes identified in this study are potential candidates as components of therapeutic vaccines and we suggest that these epitopes can be used in future studies aiming to activate antigen-specific CD8 T cells.

Babesia bovis AMA-1, MSA-2c and RAP-1 contain conserved B and T-cell epitopes, which generate neutralizing antibodies and a long-lasting Th1 immune response in vaccinated cattle.

Vaccines against bovine babesiosis must, ideally, induce a humoral immune response characterized by neutralizing antibodies against conserved epitopes and a cellular Th1 immune response. In Babesia bovis, proteins such as AMA-1, MSA-2c, and RAP-1 have been characterized and antibodies against these proteins have shown a neutralizing effect, demonstrating the implication of B and T-cell epitopes in the immune response. There is evidence of the existence of B and T-cell epitopes in these proteins, however, it remains to be defined, the presence of conserved peptides in strains from around the world containing B and T-cell epitopes, and their role in the generation of a long-lasting immunity. The aim in this paper was to identify peptides of Babesia bovis AMA-1, MSA-2c, and RAP-1 that elicit a neutralizing and long-lasting Th1 immune response. Peptides containing B-cell epitopes of AMA-1, MSA-2c and RAP-1, were identified. The immune response generated by each peptide was characterized in cattle. All peptides tested induced antibodies that recognized intraerythrocytic parasites, however, only 5 peptides generated neutralizing antibodies in vitro: P2AMA-1 (6.28%), P3MSA-2c (10.27%), P4MSA-2c (10.42%), P1RAP-1 (32.45%), and P4RAP-1 (36.98%). When these neutralizing antibodies were evaluated as a pool, the inhibition percentage of invasion increased to 52.37%. When the T cellular response was evaluated, two peptides: P3MSA2c and P2AMA1 induced a higher percentage (>70%) of activated CD4 +/CD45RO+ T cells than unstimulated cells. Additionally, both peptides induced the production of gamma interferon (IFN-) in PBMCs from vaccinated cattle after one year proving the implication of a long-lasting Th1 immune response. In conclusion, we identified conserved peptides containing B and T-cell epitopes in antigens of B. bovis that elicit a Th1 immune response and showed evidence that peptides from the same protein elicit different immune responses, which has implication for vaccine development in bovine babesiosis.

Evolutionary and structural constraints influencing apolipoprotein A-I amyloid behavior.

Apolipoprotein A-I (apoA-I) has a key function in the reverse cholesterol transport. However, aggregation of apoA-I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural consequences introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA-I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation-prone regions (APRs) present in apoA-I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA-I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA-I. Structural properties of full-length apoA-I models suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Compared to silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha-helix bundle with the concomitant exposure of APR1 to the solvent, suggesting an insight into the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA-I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region.

Phylogenomic systematics of the spotted skunks (Carnivora, Mephitidae, Spilogale): Additional species diversity and Pleistocene climate change as a major driver of diversification.

Four species of spotted skunks (Carnivora, Mephitidae, Spilogale) are currently recognized: Spilogale angustifrons, S. gracilis, S. putorius, and S. pygmaea. Understanding species boundaries within this group is critical for effective conservation given that regional populations or subspecies (e.g., S. p. interrupta) have experienced significant population declines. Further, there may be currently unrecognized diversity within this genus as some taxa (e.g., S. angustifrons) and geographic regions (e.g., Central America) never have been assessed using DNA sequence data. We analyzed species limits and diversification patterns in spotted skunks using multilocus nuclear (ultraconserved elements) and mitochondrial (whole mitogenomes and single gene analysis) data sets from broad geographic sampling representing all currently recognized species and subspecies. We found a high degree of genetic divergence among Spilogale that reflects seven distinct species and eight unique mitochondrial lineages. Initial divergence between S. pygmaea and all other Spilogale occurred in the Early Pliocene (~ 5.0 million years ago). Subsequent diversification of the remaining Spilogale into an "eastern" and a "western" lineage occurred during the Early Pleistocene (~1.5 million years ago). These two lineages experienced temporally coincident patterns of diversification at ~0.66 and ~0.35 million years ago into two and ultimately three distinct evolutionary units, respectively. Diversification was confined almost entirely within the Pleistocene during a timeframe characterized by alternating glacial-interglacial cycles, with the origin of this diversity occurring in northeastern Mexico and the southwestern United States of America. Mitochondrial-nuclear discordance was recovered across three lineages in geographic regions consistent with secondary contact, including a distinct mitochondrial lineage confined to the Sonoran Desert. Our results have direct consequences for conservation of threatened populations, or species, as well as for our understanding of the evolution of delayed implantation in this enigmatic group of small carnivores.

Heterogeneity of Genetic Admixture Determines SLE Susceptibility in Mexican.

Systemic Lupus Erythematosus (SLE) is an autoimmune inflammatory disorder for which Major Histocompatibility Complex (MHC) genes are well identified as risk factors. SLE patients present different clinical phenotypes, which are partly explained by admixture patterns variation among Mexicans. Population genetic has insight into the high genetic variability of Mexicans, mainly described through HLA gene studies with anthropological and biomedical importance. A prospective, case-control study was performed. In this study, we recruited 146 SLE patients, and 234 healthy individuals were included as a control group; both groups were admixed Mexicans from Mexico City. The HLA typing methods were based on Next Generation Sequencing and Sequence-Based Typing (SBT). The data analysis was performed with population genetic programs and statistical packages. The admixture estimations based on HLA-B and -DRB1 revealed that SLE patients have a higher Southwestern European ancestry proportion (48 ± 8%) than healthy individuals (30 ± 7%). In contrast, Mexican Native American components are diminished in SLE patients (44 ± 1%) and augmented in Healthy individuals (63 ± 4%). HLA alleles and haplotypes' frequency analysis found variants previously described in SLE patients from Mexico City. Moreover, a conserved extended haplotype that confers risk to develop SLE was found, the HLA-A∗29:02∼C∗16:01∼B∗44:03∼DRB1∗07:01∼DQB1∗02:02, pC = 0.02, OR = 1.41. Consistent with the admixture estimations, the origin of all risk alleles and haplotypes found in this study are European, while the protection alleles are Mexican Native American. The analysis of genetic distances supported that the SLE patient group is closer to the Southwestern European parental populace and farthest from Mexican Native Americans than healthy individuals. Heterogeneity of genetic admixture determines SLE susceptibility and protection in Mexicans. HLA sequencing is helpful to determine susceptibility alleles and haplotypes restricted to some populations.

Nutritional value, total dry matter losses, effluent production and pollutant potential in Brachiaria brizantha cv. Paiaguás grass / [Valor nutricional, perdas totais de matéria seca, produção e potencial poluidor de efluentes em silagem de Brachiaria brizantha cv. Paiaguás]

The objective of the present study was to evaluate losses, production and polluting potential of the effluent, nutritional value and aerobic stability of silages of Brachiaria brizantha cv. Paiaguás grass, in different particle sizes and compaction density in silage. Three theoretical particle sizes (TTP 5; 8 and 12mm) and three compaction densities (DC 550; 600 and 650kg/m3) were evaluated, distributed in a factorial design (3 x 3), with four repetitions. The highest volume of effluent was found in silages with higher compaction densities (600 and 650kg/m3) and lower TTP (5 and 8mm). The highest chemical oxygen demand and biochemical oxygen demand were registered in the treatment with TTP of 5mm and higher DC (600 and 650kg/m3). Greater in vitro digestibility of DM was verified in the silage chopped at 5 and 8mm. There was no break in aerobic stability for 216 hours. Silage with a low compaction density 550kg/m3 and processing with a theoretical particle size of 12mm reduces effluent losses. In general, the nutritional value of Paiaguás grass was not influenced by the treatments. Different particle sizes and compaction density did not change the aerobic stability of silages.(AU)

Objetivou-se avaliar perdas, produção e potencial poluidor do efluente, valor nutricional e estabilidade aeróbia de silagens do capim Brachiaria brizantha cv. Paiaguás, em diferentes tamanhos de partícula e densidade de compactação na ensilagem. Foram avaliados três tamanhos teóricos de partícula (TTP 5; 8 e 12mm) e três densidades de compactação (DC 550; 600 e 650kg/m3), distribuídos em arranjo fatorial (3 x 3), com quatro repetições. O maior volume de efluente foi verificado nas silagens com maiores densidades de compactação (600 e 650kg/m3) e menores TTP (5 e 8mm). As maiores demanda química de oxigênio e demanda bioquímica de oxigênio foram registradas no tratamento com TTP de 5mm e nas maiores DC (600 e 650kg/m3). Maior digestibilidade in vitro da MS (média de 57,2%) foi verificada na silagem picada a 5 e 8mm. Não houve quebra da estabilidade aeróbia durante 216 horas. A ensilagem com baixa densidade de compactação (550kg/m3) e o processamento com tamanho teórico de partículas 12mm reduzem as perdas por efluente. O valor nutricional da silagem de capim-paiaguás, em geral, não foi influenciado pelos tratamentos. Diferentes tamanhos de partícula e densidade de compactação não alteraram a estabilidade aeróbia das silagens.(AU)

Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus.

Zika virus (ZIKV), without a vaccine or an effective treatment approved to date, has globally spread in the last century. The infection caused by ZIKV in humans has changed progressively from mild to subclinical in recent years, causing epidemics with greater infectivity, tropism towards new tissues and other related symptoms as a product of various emergent ZIKV-host cell interactions. However, it is still unknown why or how the RNA genome structure impacts those interactions in differential evolutionary origin strains. Moreover, the genomic comparison of ZIKV strains from the sequence-based phylogenetic analysis is well known, but differences from RNA structure comparisons have barely been studied. Thus, in order to understand the RNA genome variability of lineages of various geographic distributions better, 410 complete genomes in a phylogenomic scanning were used to study the conservation of structured RNAs. Our results show the contemporary landscape of conserved structured regions with unique conserved structured regions in clades or in lineages within circulating ZIKV strains. We propose these structures as candidates for further experimental validation to establish their potential role in vital functions of the viral cycle of ZIKV and their possible associations with the singularities of different outbreaks that lead to ZIKV populations to acquire nucleotide substitutions, which is evidence of the local structure genome differentiation.

Dry matter intake and milk production of grazing dairy cows supplemented with corn silage or a total mixed ration offered ad libitum in a subtropical area.

This study aimed to evaluate the feeding choice, dry matter (DM) intake, and milk production of dairy cows that strip grazed on a mixed perennial species pasture receiving different supplementation strategies. The treatments were without supplementation (WS) or with supplementation of either corn silage (CS) or a total mixed ration (TMR) based on CS and concentrates, in a subtropical area. The supplements were provided ad libitum after the afternoon milking. Twelve Holstein × Jersey cows in mid-lactation (133 ± 43 days in milk) were divided into six groups (two cows/group) and distributed in accordance with a replicated 3 × 3 Latin square design, with three 21 day periods (15 adaptation days and 6 evaluation days). The total DM intake, milk production, milk fat, and milk protein production were greater in the TMR treatment than in the WS and CS treatments and were similar between the WS and CS treatments. The herbage DM intake and proportion of time spent grazing were greater in the CS treatment than in the TMR treatment. CS supplementation did not affect the total DM intake or milk production/cow, whereas TMR supplementation greatly improved the total DM intake and milk production of the dairy cows grazing on mixed perennial species.

Objections to the proposition of the new genera Protaetiibacter and Pseudolysinimonas.

Our principal conclusions state that Lysinimonas kribbensis and Lysinimonas soli strains, actually constitute a single coherent group at 16S rRNA gene level, and Protaetiibacter intestinalis is phylogenetically and genomically consistent with the genus Leifsonia and its nomenclature must be amended.

Isolation, social stress, low socioeconomic status and its relationship to immune response in Covid-19 pandemic context.

The coronavirus disease 2019 (COVID-19) outbreak was first reported December 2019, in Wuhan, China, and has since spread worldwide. Social distancing or isolation measures were taken to mitigate the pandemic. Furthermore, stress and low socioeconomic status in humans confer increased vulnerability to morbidity and mortality, what can be biologically observed. This condition tends to remain during the Covid-19 pandemic. Social disruption stress (SDR) raises important questions regarding the functioning of the immune system, and the release of several stress hormones. A molecular pattern, conserved transcriptional response to adversity (CTRA), is thought to have evolved to defend against physical injury during periods of heightened risk. Chronic CTRA activation could leave an organism vulnerable to viral infections, leading to increased pro-inflammatory gene expression and a suppression of anti-viral gene expression. The activation of such transcriptional status is related to conditions of social stress through either hostile human contact, or increased predatory vulnerability due to separation from the social group and also low socioeconomic status. This review aims to point out questions for government officials, researchers and health professionals to better target their actions during a pandemic and encourage studies for a better understanding of these characteristics.