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Abstract Do all birds' sex chromosomes follow the same canonical one-way direction of evolution? We combined cytogenetic and genomic approaches to analyze the process of the W chromosomal differentiation in two selected Passeriform species, named the Pale-breasted Thrush Turdus leucomelas and the Rufous-bellied thrush T. rufiventris. We characterized the full catalog of satellite DNAs (satellitome) of T. leucomelas, and the 10 TleSatDNA classes obtained together with 16 microsatellite motifs were in situ mapped in both species. Additionally, using Comparative Genomic Hybridization (CGH) assays, we investigated their intragenomic variations. The W chromosomes of both species did not accumulate higher amounts of both heterochromatin and repetitive sequences. However, while T. leucomelas showed a heterochromatin-poor W chromosome with a very complex evolutionary history, T. rufiventris showed a small and partially heterochromatic W chromosome that represents a differentiated version of its original autosomal complement (Z chromosome). The combined approach of CGH and sequential satDNA mapping suggest the occurrence of a former W-autosomal translocation event in T. leucomelas, which had an impact on the W chromosome in terms of sequence gains and losses. At the same time, an autosome, which is present in both males and females in a polymorphic state, lost sequences and integrated previously W-specific ones. This putative W-autosomal translocation, however, did not result in the emergence of a multiple-sex chromosome system. Instead, the generation of a neo-W chromosome suggests an unexpected evolutionary trajectory that deviates from the standard canonical model of sex chromosome evolution.

Abstract Multiple sex chromosomes usually arise from chromosomal rearrangements which involve ancestral sex chromosomes. There is a fundamental condition to be met for their long-term fixation: the meiosis must function, leading to the stability of the emerged system, mainly concerning the segregation of the sex multivalent. Here, we sought to analyze the degree of differentiation and meiotic pairing properties in the selected fish multiple sex chromosome system present in the wolf-fish Hoplias malabaricus (HMA). This species complex encompasses seven known karyotype forms (karyomorphs) where the karyomorph C (HMA-C) exhibits a nascent XY sex chromosomes from which the multiple X1X2Y system evolved in karyomorph HMA-D via a Y-autosome fusion. We combined genomic and cytogenetic approaches to analyze the satellite DNA (satDNA) content in the genome of HMA-D karyomorph and to investigate its potential contribution to X1X2Y sex chromosome differentiation. We revealed 56 satDNA monomers of which the majority was AT-rich and with repeat units longer than 100 bp. Seven out of 18 satDNA families chosen for chromosomal mapping by fluorescence in situ hybridization (FISH) formed detectable accumulation in at least one of the three sex chromosomes (X1, X2 and neo-Y). Nine satDNA monomers showed only two hybridization signals limited to HMA-D autosomes, and the two remaining ones provided no visible FISH signals. Out of seven satDNAs located on the HMA-D sex chromosomes, five mapped also to XY chromosomes of HMA-C. We showed that after the autosome-Y fusion event, the neo-Y chromosome has not substantially accumulated or eliminated satDNA sequences except for minor changes in the centromere-proximal region. Finally, based on the obtained FISHpatterns, we speculate on the possible contribution of satDNA to sex trivalent pairing and segregation.

Abstract Background Crocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time. Results Alligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement. Conclusions Alligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

Pacu (Piaractus mesopotamicus) is one of the main native fish species for aquaculture in South America. Genomic selection is essential for developing desirable traits in pacu production, but genotyping at high densities of SNP markers can be costly for producers. Cost-effective genotyping strategies involving genotype imputation can facilitate the broader adoption of genomic selection for this species. Then, the main objective of this study was to evaluate imputation accuracies by adopting different SNP densities (9 K, 7 K, 5 K, 2 K, 1 K, and 0.5 K) from the commercial Axiom® 30 K SerraSNP array of pacu. When genotype imputation was performed between densities of 9 K to 1 K, the average accuracies ranged from 0.97 (SD 0.06) to 0.90 (SD 0.12) at the SNP level and from 0.98 (SD 0.04) to 0.92 (SD 0.06) when considering the genotyped individuals. For the density of 0.5 K, low accuracy values were recorded, and less than 40 % of the SNPs showed high imputation accuracies (R2 ≥ 0.80). Additionally, a large proportion of low and variable imputation accuracies were observed at the extremities of chromosomes when the 0.5 K density was assessed. Based on 15,166 (91.1 %) imputed SNPs with high accuracy, a 1 K SNP array was developed and validated using the Agriseq® tGBS platform. The high accuracy results presented in this study can serve as a basis for selecting genotyping strategies aimed at reducing the costs associated with implementing genetic improvement programs in pacu.

Climate trends and weather indicators are used in several research fields due to their importance in statistical modeling, frequently used as covariates. Usually, climate indicators are available as grid files with different spatial and time resolutions. The availability of a time series of climate indicators compatible with administrative boundaries is scattered in Brazil, not fully available for several years, and produced with diverse methodologies. In this paper, we propose time series of climate indicators for the Brazilian municipalities produced using zonal statistics derived from the ERA5-Land reanalysis indicators. As a result, we present datasets with zonal statistics of climate indicators with daily data, covering the period from 1950 to 2022.

Abstract Scarce genomic resources have limited the development of breeding programs for serrasalmid fish Colossoma macropomum (tambaqui) and Piaractus mesopotamicus (pacu), the key native freshwater fish species produced in South America. The main objectives of this study were to design a dense SNP array for this fish group and to validate its performance on farmed populations from several locations in South America. Using multiple approaches based on different populations of tambaqui and pacu, a final list of 29,575 and 29,612 putative SNPs was selected, respectively, to print an Axiom AFFYMETRIX (THERMOFISHER) SerraSNP array. After validation, 74.17% (n = 21,963) and 71.25% (n = 21,072) of SNPs were classified as polymorphic variants in pacu and tambaqui, respectively. Most of the SNPs segregated within each population ranging from 14,199 to 19,856 in pacu; and from 15,075 to 20,380 in tambaqui. Our results indicate high levels of genetic diversity and clustered samples according to their hatchery origin. The developed SerraSNP array represents a valuable genomic tool approaching in-depth genetic studies for these species.

Eukaryotic genomes are usually enriched in repetitive DNA sequences, which can be classified as dispersed or tandemly repeated elements. Satellite DNAs are noncoding monomeric sequences organized in a head-to-tail fashion that are generally located on the subtelomeric and/or pericentromeric heterochromatin. In general, a single species incorporates a diverse group of satellite DNA families, which collection is called satellitome. Here, we characterized three new satellitomes from distinct characid fish (Psalidodon fasciatus, P. bockmanni, and Astyanax lacustris) using a combination of genomic, cytogenetic, and bioinformatic protocols. We also compared our data with the available satellitome of P. paranae. We described 57 satellite DNA (satDNA) families of P. fasciatus (80 variants), 50 of P. bockmanni (77 variants), and 33 of A. lacustris (54 variants). Our analyses demonstrated that several sequences were shared among the analyzed species, while some were restricted to two or three species. In total, we isolated 104 distinctive satDNA families present in the four species, of which 10 were shared among all four. Chromosome mapping revealed that the clustered satDNA was mainly located in the subtelomeric and pericentromeric areas. Although all Psalidodon species demonstrated the same pattern of clusterization of satDNA, the number of clusters per genome was variable, indicating a high dynamism of these sequences. In addition, our results expand the knowledge of the As51 satellite DNA family, revealing that P. bockmanni and P. paranae exhibited an abundant variant of 39 bp, while P. fasciatus showed a variant of 43 bp. The majority of satDNAs in the satellitomes analyzed here presented a common library repetitive sequence in Psalidodon and Astyanax, with abundance variations in each species, as expected for closely related groups. In addition, we concluded that the most abundant satDNA in Psalidodon (As51) passed through a diversification process in this group, resulting in new variants exclusive of Psalidodon.

The identification of fish species using traditional methods is generally based only on morphological characteristics and these methods are currently under review. This kind of identification of hybrid fishes solely based on their morphologies may be unreliable, especially when the samples include juveniles and post-F1 lineage fishes. Therefore, in the present study, we used molecular markers to accurately identify the fish species of economic interest that are used as materials in the projects developed in research institutions. We evaluated six lots of fishes sampled from different research centers, containing a total of 84 specimens acquired from private fish farms that were considered to be the representatives of pure species. Genetic analyses of all the specimens revealed that, globally, 22 samples (26.2%) were interspecific hybrids, while 20 (90.9%) samples were surprisingly characterized as post-F1 hybrids. This result confirms that hybrids are sold in markets without adequate labeling and also indicates the lack of proper control of the commercialization and management of stocks and products in fish farms. In addition, we determined that molecular diagnosis was an extremely effective and necessary method to test the reliability of biological materials currently used in scientific research.

This study reports the first cytogenetic characterization of the Amazonian catfish Leiarius marmoratus (“jandiá”) and its F1 (first generation or interspecific) hybrid “cachandiá” with Pseudoplatystoma reticulatum (“cachara”). A diploid number of 56 chromosomes and a single argyrophilic nucleolus organizer region (Ag-NOR) in the short arm of two sub-telocentric chromosomes were observed for both L. marmoratus and P. reticulatum, but with differences in the karyotype formula and the size of the chromosome pair with NORs. The hybrid showed 2n = 56 chromosomes with an intermediate karyotype when compared to the parental species. A single Ag-NOR was maintained in the hybrid but located in two chromosomes with marked differences in size and presenting intraindividual variation in NOR activity (nucleolar dominance). For L. marmoratus and the hybrid, heterochromatic bands were predominately distributed in the terminal, centromeric, and sub-centromeric regions of some chromosomes and 5S rDNA sites located in two distinct sub-telocentric chromosomes, which was the same pattern than previously described for P. reticulatum in other studies. These results corroborated the lack of hybrid chromosomal homology, with chromosomes originating from L. marmoratus and from P. reticulatum. Results showed that chromosome morphology might be insufficient to account for a clear discrimination of hybrids from the parental lineages, however, Ag-NOR can help for the identification of hybrid fishes. The current study provides insights into the chromosomal features of L. marmoratus, and its hybrid, and contributes novel information about the rich biodiversity of fishes in South America.

Abstract Astronomy is entering an era of mega-data that will render conventional research methods as well as data and visual analytics tools ineffective. The Square Kilometre Array (SKA) drives one of the most significant big data challenges of the next decades. South Africa, China and India are partners in the global SKA collaboration and host recently completed, next generation radio astronomy facilities. South Africa, Brazil, China and India are involved in the Large Synoptic Survey Telescope (LSST), which represents a complementary mega-data challenge, vastly increasing the current data volume of optical surveys, and providing critical multi-wavelength data set for SKA analytics. Russian researchers are also engaged in radio astronomy and multi-wavelength, multi-messenger projects driving increasing volumes of observational data. This project brings together teams leading programs in data innovation in each partner country to collaborate on the development of new technologies and systems to meet the big data challenge of SKA pathfinder facilities and the multi-wavelength projects that are critical to the advance of astronomy. In so doing we will prototype and demonstrate scalable big data technologies for the new big data era, and establish a BRICS multinational federated data intensive cloud network for collaborative programs in data intensive astronomy.

Arapaima, pirarucu or paiche (Arapaima gigas) is one of the largest freshwater fish in the world, and has a long history of commercial exploitation in the Amazon region. To estimate levels of genetic variability and historical and recent connectivity in Arapaima, we examined variation in eleven microsatellite DNA markers in individuals from 22 localities in Brazil, Colombia, and Peru. The results of analysis of molecular variance, Bayesian clustering and discriminant analysis of principal components showed that Arapaima in our samples represents two major populations, one in the Amazonas and one in the Araguaia-Tocantins River basins. The Amazonas population is further structured by isolation-by-distance with the hydrologically largely unconnected Amapá locality representing the eastern-most extreme of this continuum; gene flow predominates at distances of less than 1500 km with localities separated by over 2000 km dominated by genetic drift and effectively forming different populations. We saw no evidence of multiple species of Arapaima in the Amazonas basin, and analysis of pairwise genetic divergence (FST) with Mantel tests and correlograms indicated that this largest population exhibits a large-scale pattern of isolation-by-distance, with which results from MIGRATE-N agreed. The degree and significance of genetic divergence indicates that most sampled localities represent demographically independent sub-populations, although we did identify several recent migration events between both proximal and more distant localities. The levels of genetic diversity were heterogeneous across sites, including low genetic diversity, effective population sizes, and evidence of genetic bottlenecks in several places. On average the levels of gene diversity and rarefied allelic richness were higher for localities along the Amazonas mainstem than in the tributaries, despite these being the areas of highest fishing pressure, while the lowest values were found in tributary headwaters, where landscape modification is a significant threat. We recommend that managers consider the regional and local threats to these populations and tailor strategies accordingly, strategies which should ensure the ability of young A. gigas to disperse through floodplain corridors to maintain genetic diversity among otherwise sedentary adult sub-populations.

B chromosomes have attracted the attention of Neotropical fish cytogeneticists in recent years, both for their remarkable occurrence in this group and also because of the interest in studies of the genetic structure and role played in the genome of these organisms. The aim of this study was to report the first occurrence of supernumerary chromosomes in Prochilodus argenteus (Agassiz, 1829), this being the fifth carrier species among thirteen within the genus Prochilodus (Agassiz, 1829). The extra elements identified in this species are small sized heterochromatic chromosomes characterized by a low mitotic instability index, being very similar to other supernumerary chromosomes described in the species of the genus Prochilodus. Morphology, structure and dispersion of the supernumerary genomic elements which occur in species of this genus are discussed aiming to better understand aspects involved the origin of supernumerary chromosomes and the differentiation process and relationships among species of this family.

Cytogenetic studies were developed in Prochilodus lineatus (Valenciennes 1836), describing an interesting system of small supernumerary chromosomes. The purpose of this work is to study the frequency and morphology of B chromosomes in individuals from the parental line and the inheritance patterns of these elements in individuals obtained from controlled crosses in the species P. lineatus. The transmission rate of B chromosomes revealed a kB=0.388 for the acrocentric type, a kB=0.507 for the metacentric type and a kB=0.526 for the submetacentric type. The obtained results raise hypothesis that B-acrocentric chromosomes are involved in an extinction process in this species, while the metacentric and submetacentric supernumerary elements comprises a neutral mechanism and follows a Mendelian transmission rate.

The aim of this study was to characterize cytogenetically one population of the fish Moenkhausia sanctaefilomenae (Steindachner, 1907), with emphasis on the analysis of B chromosomes. The nucleolar activity in the B microchromosomes was characterized, and an analysis of mitotic instability of these microchromosomes was accomplished. The results showed a diploid chromosome number of 50 chromosomes. In all individuals, we observed the presence of B microchromosomes with intra- and inter-individual variability. The analysis of the nucleolus organizing regions (NORs) by silver nitrate staining demonstrated multiple NORs. We observed active sites of ribosomal DNA in the B microchromosomes, with a frequency of 20% in the analyzed cells, which shows gene activity in these chromosomal elements. The analysis of constitutive heterochromatin patterns showed that the B microchromosomes are heterochromatic or euchromatic, which demonstrates differentiation of DNA composition between these genomic elements. The calculation of the mitotic instability index implied that B chromosomes in this species might be in a final stage of instability.

A ascite quilosa é uma complicação rara após procedimentos cirúrgicos e trauma abdominal, apresentando elevada morbidade e difícil manejo. Nos casos refratários ao tratamento clínico habitual, o tratamento cirúrgico se impõe, apesar da baixa taxa de sucesso. Dois casos são apresentados: o primeiro paciente foi vítima de trauma abdominal contuso e o segundo foi submetido a hernioplastia hiatal a Nissen videolaparoscópica, ambos evoluindo com ascite quilosa que necessitou de tratamento cirúrgico através da ligadura do ducto torácico, junto aos pilares diafragmáticos. Os pacientes evoluíram com melhora clínica e ausência de ascite após 24 meses de seguimento.Chylous ascites is a rare complication after abdominal procedures and blunt abdominal trauma, associated with high morbidity and difficult management. When clinical treatment fails, surgical intervention is necessary, despite the limited success rate. Two cases are reported: the first patient had a blunt abdominal trauma and the second patient underwent laparoscopic Nissen fundoplication; both developed chylous ascites and required surgical treatment with suture repair of the thoracic duct, close to the diaphragm. There was clinical improvement and ascites was absent at a 24-month follow-up.

Nuclear and mitochondrial genes were used as molecular markers for verifying the iden-tity of fish fillets marketed as pintado (Pseudoplatystoma corruscans). Based on THE polymorphisms of nuclear DNA (RAG2, globin, and EF1 genes) and mitochondrial regions (16S), we examined whether the fillets originated from inbred species of pintado or from hybrids derived from crosses between cachara (P. reticulatum) and pintado. Nuclear genes from both species were detected in the analyzed fillets (n = 29). This clearly iden-tified these fish as interspecific hybrids (or F1/first filial generation) of the type “cacha-pinta,” resulting from a cross between female cachara and male pintado. These results demonstrate that monitoring fish fillet trading is crucial for detecting discrepancies between the marketed species and related information declared on the label. Species that are frequently hybridized, such as pintado and cachara, require special attention.

Introduction: The escalation of multidrug-resistant organism (MDRO) infections post-liver transplantation (LT) poses significant risks, with MDRO colonization amplifying infection susceptibility. Environmental disinfection is crucial in curbing healthcare- associated infections (HAI). Hydrogen peroxide vapor (HPV) technology offers promise, yet its impact on MDRO infections and patient outcomes remains unclear. Methods: A cohort study enrolled 58 deceased adult LT recipients, comparing outcomes before and after routine HPV implementation. HPV disinfection followed terminal cleaning in surgical rooms and intensive care unit (ICU) boxes. Pathogen data included pre-transplant and post-discharge MDRO colonization. Clinical data covered recipient characteristics, disease severity, and donor-recipient relationships. Statistical analyses assessed associations and outcomes. Results: Twenty-seven patients were in the before-HPV group, 24 in the after-HPV group. Demographic and clinical characteristics were comparable between groups. HPV implementation significantly increased the likelihood of negative control swabs (odds ratio 2.33). Klebsiella pneumoniae carbapenemase was the most frequent pathogen, with surgical site infections being the primary site. Patients with negative swabs had shorter hospital stays (mean difference 10.54 days), notably diverging around the 8th day of hospitalization. HAI frequency and 90-day mortality were significantly lower in patients with negative swabs. Conclusion: HPV technology effectively reduced MDRO colonization in LT recipients. Negative swabs correlated with shorter hospital stays and lower HAI frequency, impacting 90-day mortality positively. Despite challenges in HPV implementation, its efficacy in reducing MDRO colonization suggests a valuable tool in infection control strategies for vulnerable populations like LT recipients.

Abstract Background Different patterns of sex chromosome differentiation are seen in Palaeognathae birds, a lineage that includes the ratites (Struthioniformes, Rheiformes, Apterygiformes, Casuariiformes, and the sister group Tinamiformes). While some Tinamiform species have well-differentiated W chromosomes, both Z and W of all the flightless ratites are still morphologically undifferentiated. Here, we conducted a comprehensive analysis of the ZW differentiation in birds using a combination of cytogenetic, genomic, and bioinformatic approaches. The whole set of satDNAs from the emu (Dromaius novaehollandiae) was described and characterized. Furthermore, we examined the in situ locations of these satDNAs alongside several microsatellite repeats and carried out Comparative Genomic Hybridizations in two related species: the greater rhea (Rhea americana) and the tataupa tinamou (Crypturellus tataupa). Results From the 24 satDNA families identified (which represent the greatest diversity of satDNAs ever uncovered in any bird species), only three of them were found to accumulate on the emu’s sex chromosomes, with no discernible accumulation observed on the W chromosome. The W chromosomes of both the greater rhea and the emu did not exhibit a significant buildup of either C-positive heterochromatin or repetitive DNAs, indicating their large undifferentiation both at morphological and molecular levels. In contrast, the tataupa tinamou has a highly differentiated W chromosome that accumulates several DNA repeats. Conclusion The findings provide new information on the architecture of the avian genome and an inside look at the starting points of sex chromosome differentiation in birds.

Abstract In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disease progression. The simian immunodeficiency virus (SIV) infecting nonhuman primates (NHP) is widely used as a model for the study of the human immunodeficiency virus (HIV) both because they are evolutionarily linked and because they share physiological and anatomical similarities that are largely explored to understand the disease progression. The HIHISIV database was developed to support researchers to integrate and evaluate the large number of transcriptional data associated with the presence/absence of the pathogen (SIV or HIV) and the host response (NHP and human). The datasets are composed of microarray and RNA-Seq gene expression data that were selected, curated, analyzed, enriched, and stored in a relational database. Six query templates comprise the main data analysis functions and the resulting information can be downloaded. The HIHISIV database, available at https://hihisiv.github.io , provides accurate resources for browsing and visualizing results and for more robust analyses of pre-existing data in transcriptome repositories.