Spencermartinsiella nicolii sp. nov., a potential opportunistic pathogenic yeast species isolated from rotting wood in Brazil.

Nineteen isolates representing a candidate for a novel yeast species belonging to the genus Spencermartinsiella were recovered from rotting wood samples collected at different sites in Atlantic Rainforest and Amazonian Forest ecosystems in Brazil. Similarity search of the nucleotide sequence of the intergenic spacer (ITS)-5.8S and large subunit D1/D2 regions of the ribosomal gene cluster showed that this novel yeast is closely related to Spencermartinsiella cellulosicola. The isolates differ by four nucleotide substitutions in the D1/D2 domain and six substitutions and 31 indels in the ITS region from the holotype of S. cellulosicola. Phylogenomic analysis based on 1474 single-copy orthologues for a set of Spencermartinsiella species whose whole genome sequences are available confirmed that the novel species is phylogenetically close to S. cellulosicola. The low average nucleotide identity value of 83% observed between S. cellulosicola and the candidate species confirms that they are distinct. The novel species produced asci with hemispherical ascospores. The name Spencermartinsiella nicolii sp. nov. is proposed. The holotype is CBS 14238T. The MycoBank number is MB855027. Interestingly, the D1/D2 sequence of the S. nicolii was identical to that of an uncultured strain of Spencermartinsiella causing systemic infection in a male adult crocodile (Crocodylus niloticus). The characterization of some virulence factors and antifungal susceptibility of S. nicolii isolates suggest that this yeast may be an opportunistic pathogen for animals, including humans; the isolates grow at 37 °C.

DNA lesions that block transcription induce the death of Trypanosoma cruzi via ATR activation, which is dependent on the presence of R-loops.

Trypanosoma cruzi is the etiological agent of Chagas disease and a peculiar eukaryote with unique biological characteristics. DNA damage can block RNA polymerase, activating transcription-coupled nucleotide excision repair (TC-NER), a DNA repair pathway specialized in lesions that compromise transcription. If transcriptional stress is unresolved, arrested RNA polymerase can activate programmed cell death. Nonetheless, how this parasite modulates these processes is unknown. Here, we demonstrate that T. cruzi cell death after UV irradiation, a genotoxic agent that generates lesions resolved by TC-NER, depends on active transcription and is signaled mainly by an apoptotic-like pathway. Pre-treated parasites with α-amanitin, a selective RNA polymerase II inhibitor, become resistant to such cell death. Similarly, the gamma pre-irradiated cells are more resistant to UV when the transcription processes are absent. The Cockayne Syndrome B protein (CSB) recognizes blocked RNA polymerase and can initiate TC-NER. Curiously, CSB overexpression increases parasites' cell death shortly after UV exposure. On the other hand, at the same time after irradiation, the single-knockout CSB cells show resistance to the same treatment. UV-induced fast death is signalized by the exposition of phosphatidylserine to the outer layer of the membrane, indicating a cell death mainly by an apoptotic-like pathway. Furthermore, such death is suppressed in WT parasites pre-treated with inhibitors of ataxia telangiectasia and Rad3-related (ATR), a key DDR kinase. Signaling for UV radiation death may be related to R-loops since the overexpression of genes associated with the resolution of these structures suppress it. Together, results suggest that transcription blockage triggered by UV radiation activates an ATR-dependent apoptosis-like mechanism in T. cruzi, with the participation of CSB protein in this process.

Exploring the hidden hot world of long non-coding RNAs in thermophilic fungus using a robust computational pipeline.

Long noncoding RNAs (lncRNAs) are versatile RNA molecules recently identified as key regulators of gene expression in response to environmental stress. Our primary focus in this study was to develop a robust computational pipeline for identifying structurally identical lncRNAs across replicates from publicly available bulk RNA-seq datasets. In order to demonstrate the effectiveness of the pipeline, we utilized the transcriptome of the thermophilic fungus Thermothelomyces thermophilus and assessed the expression pattern of lncRNAs in conjunction with Heat Shock Proteins (HSP), a well-known protein family critical for the cell's response to high temperatures. Our findings demonstrate that the identification of structurally identical transcripts among replicates in this thermophilic fungus ensures the reliability and accuracy of RNA studies, contributing to the validity of biological interpretations. Furthermore, the majority of lncRNAs exhibited a distinct expression pattern compared to HSPs. Our study contributes to advancing the understanding of the biological mechanisms comprising lncRNAs in thermophilic fungi.

Spathaspora marinasilvae sp. nov., a xylose-fermenting yeast isolated from galleries of passalid beetles and rotting wood in the Amazonian rainforest biome.

Four yeast isolates were obtained from rotting wood and galleries of passalid beetles collected in different sites of the Brazilian Amazonian Rainforest in Brazil. This yeast produces unconjugated allantoid asci each with a single elongated ascospore with curved ends. Sequence analysis of the internal transcribed spacer-5.8 S region and the D1/D2 domains of the large subunit ribosomal RNA (rRNA) gene showed that the isolates represent a novel species of the genus Spathaspora. The novel species is phylogenetically related to a subclade containing Spathaspora arborariae and Spathaspora suhii. Phylogenomic analysis based on 1884 single-copy orthologs for a set of Spathaspora species whose whole genome sequences are available confirmed that the novel species represented by strain UFMG-CM-Y285 is phylogenetically close to Sp. arborariae. The name Spathaspora marinasilvae sp. nov. is proposed to accommodate the novel species. The holotype of Sp. marinasilvae is CBS 13467 T (MycoBank 852799). The novel species was able to accumulate xylitol and produce ethanol from d-xylose, a trait of biotechnological interest common to several species of the genus Spathaspora.

SARS-CoV-2 Selectively Induces the Expression of Unproductive Splicing Isoforms of Interferon, Class I MHC, and Splicing Machinery Genes.

RNA processing is a highly conserved mechanism that serves as a pivotal regulator of gene expression. Alternative processing generates transcripts that can still be translated but lead to potentially nonfunctional proteins. A plethora of respiratory viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), strategically manipulate the host's RNA processing machinery to circumvent antiviral responses. We integrated publicly available omics datasets to systematically analyze isoform-level expression and delineate the nascent peptide landscape of SARS-CoV-2-infected human cells. Our findings explore a suggested but uncharacterized mechanism, whereby SARS-CoV-2 infection induces the predominant expression of unproductive splicing isoforms in key IFN signaling, interferon-stimulated (ISGs), class I MHC, and splicing machinery genes, including IRF7, HLA-B, and HNRNPH1. In stark contrast, cytokine and chemokine genes, such as IL6 and TNF, predominantly express productive (protein-coding) splicing isoforms in response to SARS-CoV-2 infection. We postulate that SARS-CoV-2 employs an unreported tactic of exploiting the host splicing machinery to bolster viral replication and subvert the immune response by selectively upregulating unproductive splicing isoforms from antigen presentation and antiviral response genes. Our study sheds new light on the molecular interplay between SARS-CoV-2 and the host immune system, offering a foundation for the development of novel therapeutic strategies to combat COVID-19.

Unveiling overlooked pathways: The uric acid catabolism genes in the human genome.

In hominids, including Homo sapiens, uric acid is the end product of purine catabolism. In contrast, other placental mammals further degrade uric acid to (S)-allantoin by enzymes such as urate oxidase (uricase), HIU hydrolase (HIUase), and OHCU decarboxylase. Some organisms, such as frogs and fish, hydrolyze (S)-allantoin to allantoate and eventually to (S)-ureidoglycolate and urea, while marine invertebrates convert urea to ammonium. In H. sapiens, mutations in the uricase gene led to a reduction in the selective pressure for maintaining the integrity of the genes encoding the other enzymes of the purine catabolism pathway, resulting in an accumulation of uric acid. The hyperuricemia resulting from this accumulation is associated with gout, cardiovascular disease, diabetes, and preeclampsia. Many commonly used drugs, such as aspirin, can also increase uric acid levels. Despite the apparent absence of these enzymes in H. sapiens, there appears to be production of transcripts for uricase (UOX), HIUase (URAHP), OHCU decarboxylase (URAD), and allantoicase (ALLC). While some URAHP transcripts are classified as long non-coding RNAs (lncRNAs), URAD and ALLC produce protein-coding transcripts. Given the presence of these transcripts in various tissues, we hypothesized that they may play a role in the regulation of purine catabolism and the pathogenesis of diseases associated with hyperuricemia. Here, we specifically investigate the unique aspects of purine catabolism in H. sapiens, the effects mutations of the uricase gene, and the potential regulatory role of the corresponding transcripts. These findings open new avenues for research and therapeutic approaches for the treatment of hyperuricemia and related diseases.

Weight-drop model as a valuable tool to study potential neurobiological processes underlying behavioral and cognitive changes secondary to mild traumatic brain injury.

The pathophysiology of post-traumatic brain injury (TBI) behavioral and cognitive changes is not fully understood, especially in its mild presentation. We designed a weight drop TBI model in mice to investigate the role of neuroinflammation in behavioral and cognitive sequelae following mild TBI. C57BL/6 mice displayed depressive-like behavior at 72 h after mild TBI compared with controls, as indicated by a decrease in the latency to first immobility and climbing time in the forced swim test. Additionally, anxiety-like behavior and hippocampal-associated spatial learning and memory impairment were found in the elevated plus maze and in the Barnes maze, respectively. Levels of a set of inflammatory mediators and neurotrophic factors were analyzed at 6 h, 24 h, 72 h, and 30 days after injury in ipsilateral and contralateral hemispheres of the prefrontal cortex and hippocampus. Principal components analysis revealed two principal components (PC), which represented 59.1% of data variability. PC1 (cytokines and chemokines) expression varied between both hemispheres, while PC2 (neurotrophic factors) expression varied only across the investigated brain areas. Our model reproduces mild TBI-associated clinical signs and pathological features and might be a valuable tool to broaden the knowledge regarding mild TBI pathophysiology as well as to test potential therapeutic targets.

Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic markings.

COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, that regulates the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic markings in leukocytes favorably regulates central components of COVID-19 physiopathology.

Actividades ligninolíticas y producción de basidiomas de Ganoderma lucidum en cultivo sólido suplementado con manganeso / Ligninolytic activities and production of Ganoderma lucidum basidiomes in solid culture supplemented with manganese

RESUMEN Ganoderma lucidum es un basidiomiceto de pudrición blanca estudiado especialmente por sus atributos medicinales. No obstante, la información sobre la suplementación de los medios de cultivo con metales como Zn, Li, Mn, Cu es escasa aun conociendo que la presencia de metales en los sustratos mejora las características de los basidiomas obtenidos e incrementa su productividad. El objetivo fue evaluar las actividades enzimáticas lacasa (Lc) y manganeso peroxidasa (MnP), la fructificación y eficiencia biológica (EB) de G. lucidum en cultivos sólidos formulados con residuos agroindustriales (aserrín de roble, cascarilla de café, salvado de maíz) suplementados con dos niveles de sal de manganeso II (0,05 % y 0,1 % p/p) y una formulación sin adición de la sal de manganeso. Las actividades enzimáticas se determinaron durante 98 días del ciclo productivo, con toma de muestras semanales. El tratamiento uno (0,05 % p/p de MnSO4H2O) suministró la mayor EB del cultivo con 25,90 ± 2,12 % y los mayores títulos de actividades ligninolíticas en el tiempo con 0,7299 UE/g s.s. de MnP a los 35 días de fermentación y 4,1 760 UE/g s.s para la actividad de Lc a los 42 días de proceso con relación a los tratamientos dos y control. Asimismo, hubo una disminución del ciclo de cultivo del hongo para los tratamientos uno (83 días) y dos (95 días) en comparación con el tratamiento control (117 días). Los resultados de este trabajo son promisorios para cultivadores industriales de G. lucidum, ya que la suplementación de los sustratos con Mn incrementa la productividad de los cultivos.

ABSTRACT Ganoderma lucidum is a white rot basidiomycete specially studied for its medicinal attributes. However, the information on the supplementation of the substrate with metals such as Zn, Li, Mn, Cu and others is scarce. Even knowing that the presence of metals in the substrates improves the characteristics of the basidiomes produced and increases their productivity. The objective was to evaluate the enzymatic activities laccase (Lc) and manganese peroxidase (MnP). The fructification and biological efficiency (BE) of G. lucidum in solid culture formulated with agroindustrial residues, (oak sawdust, coffee husk, bran corn) supplemented with two levels of manganese II salt, (0.05 % and 0.1 % w/ w) and a formulation without addition of manganese II salt. Enzymatic activities were determined during 98 days of the production cycle, with weekly sampling. Treatment one (0.05 % w/w MnSO4.H2O) provided the highest BE of the culture with 25.90 ± 0.54% and the highest titers of ligninolytic activities, in the time with 0.7299 EU/g d.s for MnP at 35 days of fermentation and 4.1760 EU/g d.s for Lc activity at 42 days of process, in relation to treatments two and control. Likewise, there was a decrease in the fungus culture cycle for treatments one (83 days) and two (95 days) compared to the control treatment (117 days). The results of this work are promising for industrial growers of G. lucidum, since the supplementation of the substrates with Mn increase the productivity of the cultures.

AIM2 as a putative target in acute kidney graft rejection.

Acute rejection (AR) is a process triggered via the recognition of grafted organ-derived antigens by the immune system, which could present as a life-threatening condition. In the context of a kidney transplant, despite improvement with immunosuppressive therapies, AR maintains a significant incidence of 10%, and currently available drugs generally act in similar and canonical pathways of lymphocyte activation. This prompted the research for different approaches to identify potential novel targets that could improve therapeutic interventions. Here, we conducted a transcriptome analysis comparing groups of acute rejection (including T cell-mediated rejection and antibody-mediated rejection) to stable grafts that included differentially expressed genes, transcription factor and kinase enrichment, and Gene Set Enrichment Analysis. These analyses revealed inflammasome enhancement in rejected grafts and AIM2 as a potential component linked to acute rejection, presenting a positive correlation to T-cell activation and a negative correlation to oxidative phosphorylation metabolism. Also, the AIM2 expression showed a global accuracy in discerning acute rejection grafts (area under the curve (AUC) = 0.755 and 0.894, p < 0.0001), and meta-analysis comprising different studies indicated a considerable enhancement of AIM2 in rejection (standardized mean difference (SMD) = 1.45, [CI 95%, 1.18 to 1.71]), especially for T cell-mediated rejection (TCMR) (SMD = 2.01, [CI 95%, 1.58 to 2.45]). These findings could guide future studies of AIM2 as either an adjuvant target for immunosuppression or a potential biomarker for acute rejection and graft survival.

Metformin Treatment Modulates Long Non-Coding RNA Isoforms Expression in Human Cells.

Long noncoding RNAs (lncRNAs) undergo splicing and have multiple transcribed isoforms. Nevertheless, for lncRNAs, as well as for mRNA, measurements of expression are routinely performed only at the gene level. Metformin is the first-line oral therapy for type 2 diabetes mellitus and other metabolic diseases. However, its mechanism of action remains not thoroughly explained. Transcriptomic analyses using metformin in different cell types reveal that only protein-coding genes are considered. We aimed to characterize lncRNA isoforms that were differentially affected by metformin treatment on multiple human cell types (three cancer, two non-cancer) and to provide insights into the lncRNA regulation by this drug. We selected six series to perform a differential expression (DE) isoform analysis. We also inferred the biological roles for lncRNA DE isoforms using in silico tools. We found the same isoform of an lncRNA (AC016831.6-205) highly expressed in all six metformin series, which has a second exon putatively coding for a peptide with relevance to the drug action. Moreover, the other two lncRNA isoforms (ZBED5-AS1-207 and AC125807.2-201) may also behave as cis-regulatory elements to the expression of transcripts in their vicinity. Our results strongly reinforce the importance of considering DE isoforms of lncRNA for understanding metformin mechanisms at the molecular level.

Tecnología Biofloc: Perspectivas de Aplicación en Procesos de Producción Piscícola Sostenible / Biofloc Technology: Application Perspectives in Sustainable Fish Production Processes / Tecnologia Biofloc: Perspectivas de Aplicação em Processos Sustentáveis de Produção de Peixes

Resumen Introducción: la tecnología Biofloc, es un proceso de biorremediación que permite minimizar el intercambio de agua y su uso en los sistemas de acuicultura. Objetivo: presentar tendencias de las publicaciones científicas acerca de la tecnología Biofloc para producción piscícola, utilizando las herramientas de análisis bibliométrico. Materiales y métodos: se empleó la base de datos Web of Science, con una ecuación de búsqueda y procesamiento de la información apoyada por las herramientas BibExcel y VOSviewer. Se realizó un análisis sistemático en los documentos recuperados, teniendo en cuenta: tipo de cultivo, tiempo experimental, rendimiento de crecimiento y proteico, densidad poblacional, calidad del agua, características microbiológicas y fisiológicas del cultivo. Se determinaron categorías en las cuales están definidos los estudios con relación a la tecnología y los principales desafíos identificados en la aplicación de la tecnología. Resultados: se encontraron 258 documentos, el 94,12 % correspondieron a artículos de investigación. La productividad fue mayor en 2014 y 2016. La Universidad Federal de Santa Catarina y la Universidad Federal de Rio Grande FURG en Brasil tienen la mayor producción. En coautorías se identificaron 18 nodos. El 59,3 % de los documentos reportaron investigaciones con camarón y el 18,99 % con tilapia. Los mejores tiempos de producción estuvieron en los rangos de 41-50 días (12,4 %), 21-30 días (11,24 %) y 51-60 días (9,68 %). La relación C: N no fue reportada en el 92,6 % de los trabajos. Sin embargo, el 3,48 % reportaron relaciones de 15:1 y el 1,16 % de 20:1. Las principales categorías fueron rendimiento (44,18 %) y productividad (26,35 %). Conclusiones: la tecnología Biofloc representa una oportunidad para la sustentabilidad en prácticas acuícolas de especies. Se evidenció un crecimiento gradual en los procesos de investigación en los últimos años; los principales estudios están relacionados con el rendimiento en cuanto a crecimiento y optimización de los procesos de conversión proteica en los cultivos analizados bien sean individuales o en policultivo.

Abstract Introduction: Biofloc technology is a bioremediation process that allows minimizing the exchange of water and its use in aquaculture systems. Objective: to present trends in scientific publications about Biofloc technology for fish production, using bibliometric analysis tools. Materials and methods: the Web of Science database was used, with a search equation and information processing supported by the BibExcel and VOSviewer tools. A systematic analysis was carried out on the recovered documents, considering type of culture, experimental time, growth and protein yield, population density, water quality, microbiological and physiological characteristics of the crop. Categories were determined in which the studies related to technology and the main challenges identified in the application of technology are defined. Results: 258 documents were found, 94.12 % corresponded to research articles. Productivity was higher in 2014 and 2016. The Federal University of Santa Catarina and Federal University of Rio Grande FURG in Brazil have the highest production. In co-authorship, 18 nodes were identified. 59.3 °% of the documents reported investigations with shrimp and 18.99 % with tilapia. The best production times were in the ranges of 41-50 days (12.4 %), 2130 days (11.24 %) and 51-60 days (9.68 %). The C:N ratio was not reported in 92.6 % of the studies. However, 3.48 % reported ratios of 15:1 and 1.16 % of 20:1. The main categories were performance (44.18 %) and productivity (26.35 %). Conclusions: Biofloc technology represents an opportunity for sustainability in species aquaculture practices. A gradual growth in research processes was evidenced in recent years; the main studies are related to the performance in terms of growth and optimization of the protein conversion processes in the analyzed crops, whether individual or in polyculture.

Resumo Introdução: a tecnologia Biofloc é um processo de biorremediação que permite minimizar as trocas de água e seu uso em sistemas de aquicultura. Objetivo: apresentar tendências em publicações científicas sobre a tecnologia Biofloc para produção de peixes, utilizando ferramentas de análise bibliométrica. Materiais e métodos: foi utilizada a base de dados Web of Science, com equação de busca e processamento de informações apoiado pelas ferramentas BibExcel e VOSviewer. Foi efetuada uma análise sistemática dos documentos recuperados, tendo em consideração: tipo de cultura, tempo experimental, crescimento e rendimento protéico, densidade populacional, qualidade da água, características microbiológicas e fisiológicas da cultura. Foram definidas categorias nas quais são definidos os estudos relacionados à tecnologia e os principais desafios identificados na aplicação da tecnologia. Resultados: foram encontrados 258 documentos, 94,12 % correspondiam a artigos de pesquisa. A produtividade foi maior em 2014 e 2016. A Universidade Federal de Santa Catarina e a Universidade Federal do Rio Grande FURG no Brasil têm a maior produção. Em coautoria, 18 nós foram identificados. 59,3 °% dos documentos relataram investigações com camarão e 18,99 % com tilápia. Os melhores tempos de produção ficaram nas faixas de 4150 dias (12, %), 21-30 dias (11,24 %) e 51-60 dias (9,68 %). A relação C: N não foi relatada em 92,6 % dos estudos. No entanto, 3,48 % relataram proporções de 15:1 e 1,16 % de 20:1. As principais categorias foram desempenho(44,18 %) e produtividade (26,35 %). Conclusões: A tecnologia Biofloc representa uma oportunidade para a sustentabilidade nas práticas de aquicultura de espécies. Um crescimento gradual nos processos de pesquisa foi evidenciado nos últimos anos; Os principais estudos estão relacionados com o desempenho em termos de crescimento e otimização dos processos de conversão de proteínas nas culturas analisadas, sejam individuais ou em policultura.

The evolution of knowledge on genes associated with human diseases.

Thousands of biomedical scientific articles, including those describing genes associated with human diseases, are published every week. Computational methods such as text mining and machine learning algorithms are now able to automatically detect these associations. In this study, we used a cognitive computing text-mining application to construct a knowledge network comprising 3,723 genes and 99 diseases. We then tracked the yearly changes on these networks to analyze how our knowledge has evolved in the past 30 years. Our systems approach helped to unravel the molecular bases of diseases and detect shared mechanisms between clinically distinct diseases. It also revealed that multi-purpose therapeutic drugs target genes that are commonly associated with several psychiatric, inflammatory, or infectious disorders. By navigating this knowledge tsunami, we were able to extract relevant biological information and insights about human diseases.

Network analysis of ten thousand genomes shed light on Pseudomonas diversity and classification.

The growth of sequenced bacterial genomes has revolutionized the assessment of microbial diversity. Pseudomonas is a widely diverse genus, containing more than 254 species. Although type strains have been employed to estimate Pseudomonas diversity, they represent a small fraction of the genomic diversity at a genus level. We used 10,035 available Pseudomonas genomes, including 210 type strains, to build a genomic distance network to estimate the number of species through community identification. We identified taxonomic inconsistencies with several type strains and found that 25.65 % of the Pseudomonas genomes deposited on Genbank are misclassified. The phylogenetic tree using single-copy genes from representative genomes in each species cluster in the distance network revealed at least 14 Pseudomonas groups, including the P. alcaligenes group proposed here. We show that Pseudomonas is likely an admixture of different genera and should be further divided. This study provides an overview of Pseudomonas diversity from a network and phylogenomic perspective that may help reduce the propagation of mislabeled Pseudomonas genomes.

Phylogenetic analysis and population structure of Pseudomonas alloputida.

The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.

Transcriptional landscape of PTEN loss in primary prostate cancer.

BACKGROUND: PTEN is the most frequently lost tumor suppressor in primary prostate cancer (PCa) and its loss is associated with aggressive disease. However, the transcriptional changes associated with PTEN loss in PCa have not been described in detail. In this study, we highlight the transcriptional changes associated with PTEN loss in PCa. METHODS: Using a meta-analysis approach, we leveraged two large PCa cohorts with experimentally validated PTEN and ERG status by Immunohistochemistry (IHC), to derive a transcriptomic signature of PTEN loss, while also accounting for potential confounders due to ERG rearrangements. This signature was expanded to lncRNAs using the TCGA quantifications from the FC-R2 expression atlas. RESULTS: The signatures indicate a strong activation of both innate and adaptive immune systems upon PTEN loss, as well as an expected activation of cell-cycle genes. Moreover, we made use of our recently developed FC-R2 expression atlas to expand this signature to include many non-coding RNAs recently annotated by the FANTOM consortium. Highlighting potential novel lncRNAs associated with PTEN loss and PCa progression. CONCLUSION: We created a PCa specific signature of the transcriptional landscape of PTEN loss that comprises both the coding and an extensive non-coding counterpart, highlighting potential new players in PCa progression. We also show that contrary to what is observed in other cancers, PTEN loss in PCa leads to increased activation of the immune system. These findings can help the development of new biomarkers and help guide therapy choices.

DNA Topoisomerase 3α Is Involved in Homologous Recombination Repair and Replication Stress Response in Trypanosoma cruzi.

DNA topoisomerases are enzymes that modulate DNA topology. Among them, topoisomerase 3α is engaged in genomic maintenance acting in DNA replication termination, sister chromatid separation, and dissolution of recombination intermediates. To evaluate the role of this enzyme in Trypanosoma cruzi, the etiologic agent of Chagas disease, a topoisomerase 3α knockout parasite (TcTopo3α KO) was generated, and the parasite growth, as well as its response to several DNA damage agents, were evaluated. There was no growth alteration caused by the TcTopo3α knockout in epimastigote forms, but a higher dormancy rate was observed. TcTopo3α KO trypomastigote forms displayed reduced invasion rates in LLC-MK2 cells when compared with the wild-type lineage. Amastigote proliferation was also compromised in the TcTopo3α KO, and a higher number of dormant cells was observed. Additionally, TcTopo3α KO epimastigotes were not able to recover cell growth after gamma radiation exposure, suggesting the involvement of topoisomerase 3α in homologous recombination. These parasites were also sensitive to drugs that generate replication stress, such as cisplatin (Cis), hydroxyurea (HU), and methyl methanesulfonate (MMS). In response to HU and Cis treatments, TcTopo3α KO parasites showed a slower cell growth and was not able to efficiently repair the DNA damage induced by these genotoxic agents. The cell growth phenotype observed after MMS treatment was similar to that observed after gamma radiation, although there were fewer dormant cells after MMS exposure. TcTopo3α KO parasites showed a population with sub-G1 DNA content and strong γH2A signal 48 h after MMS treatment. So, it is possible that DNA-damaged cell proliferation due to the absence of TcTopo3α leads to cell death. Whole genome sequencing of MMS-treated parasites showed a significant reduction in the content of the multigene families DFG-1 and RHS, and also a possible erosion of the sub-telomeric region from chromosome 22, relative to non-treated knockout parasites. Southern blot experiments suggest telomere shortening, which could indicate genomic instability in TcTopo3α KO cells owing to MMS treatment. Thus, topoisomerase 3α is important for homologous recombination repair and replication stress in T. cruzi, even though all the pathways in which this enzyme participates during the replication stress response remains elusive.

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation.

RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory formation. However, whether additional RNA modifications may be playing a role in neuronal functions and in response to environmental queues is largely unknown. Here we characterize the biochemical function and cellular dynamics of two human RNA methyltransferases previously associated with neurological dysfunction, TRMT1 and its homolog, TRMT1-like (TRMT1L). Using a combination of next-generation sequencing, LC-MS/MS, patient-derived cell lines and knockout mouse models, we confirm the previously reported dimethylguanosine (m2,2G) activity of TRMT1 in tRNAs, as well as reveal that TRMT1L, whose activity was unknown, is responsible for methylating a subset of cytosolic tRNAAla(AGC) isodecoders at position 26. Using a cellular in vitro model that mimics neuronal activation and long term potentiation, we find that both TRMT1 and TRMT1L change their subcellular localization upon neuronal activation. Specifically, we observe a major subcellular relocalization from mitochondria and other cytoplasmic domains (TRMT1) and nucleoli (TRMT1L) to different small punctate compartments in the nucleus, which are as yet uncharacterized. This phenomenon does not occur upon heat shock, suggesting that the relocalization of TRMT1 and TRMT1L is not a general reaction to stress, but rather a specific response to neuronal activation. Our results suggest that subcellular relocalization of RNA modification enzymes may play a role in neuronal plasticity and transmission of information, presumably by addressing new targets.

From In-Person to the Online World: Insights Into Organizing Events in Bioinformatics.

Bioinformatics is a fast-evolving research field, requiring effective educational initiatives to bring computational knowledge to Life Sciences. Since 2017, an organizing committee composed of graduate students and postdoctoral researchers from the Universidade Federal de Minas Gerais (Brazil) promotes a week-long event named Summer Course in Bioinformatics (CVBioinfo). This event aims to diffuse bioinformatic principles, news, and methods mainly focused on audiences of undergraduate students. Furthermore, as the advent of the COVID-19 global pandemic has precluded in-person events, we offered the event in online mode, using free video transmission platforms. Herein, we present and discuss the insights obtained from promoting the Online Workshop in Bioinformatics (WOB) organized in November 2020, comparing it to our experience in previous in-person editions of the same event.