Massive Sequencing Research Articles

HTLV-1 Infection and Cervicovaginal Susceptibility to High-Risk HPV: Findings from Women Living with HTLV-1 in Salvador, Brazil

Persistent oncogenic HPV infection is strongly associated with cervical cancer. Studies have suggested a higher prevalence of HPV in women living with HTLV-1. This study aimed to determine whether HTLV-1 infection is associated with cervicovaginal HPV infection and to characterize HPV types according to oncogenic risk. Vaginal fluid samples were subjected to HPV diagnosis via PCR, and positive samples were subjected to Sanger sequencing and massive sequencing. Papanicolaou smears were examined using light microscopy to identify cell abnormalities. Among the 155 women screened, 79 were HTLV-1-infected and 76 were uninfected. HPV PCR identified 23 positive samples (15/79 vs. 8/76; p = 0.13). Twenty-three HPV types were identified, of which only types 31, 54, and 58 were present in both groups. When the number of HPV58 infections in each group was compared, women with HTLV-1 had a higher prevalence (8/79 versus 1/76; p = 0.03). In total, 61.9% of HTLV-1-infected women had at least one high-risk or probable high-risk HPV type (p = 0.12). Cytopathological findings were not significantly different between the groups. Further research is needed to determine whether HTLV-1 infection affects HPV progression and cervical cancer development and to assess the potential benefits of vaccination for women living with HTLV-1.

Global Protein Interactome Mapping in Rice Using Barcode-Indexed PCR Coupled with HiFi Long-Read Sequencing.

Establishing the protein-protein interaction network sheds light on functional genomics studies by providing insights from known counterparts. However, the rice interactome has barely been studied due to the lack of massive, reliable, and cost-effective methodologies. Here, the development of a barcode-indexed PCR coupled with HiFi long-read sequencing pipeline (BIP-seq) is reported for high throughput Protein Protein Interaction (PPI)identification. BIP-seq is essentially built on the integration of library versus library Y2H mating strategy to facilitate the efficient acquisition of random PPI colonies, semi-mechanized dual barcode-indexed yeast colony PCR for the large-scale indexed amplification of bait and prey cDNAs, and massive pac-bio sequencing of PCR amplicon pools. It is demonstrated that BIP-seq could map over 15 000 high-confidence (≈62.5% could be verified by Bimolecular fluorescence Complementation (BiFC)) rice PPIs within 2 months, outperforming the other reported methods. In addition, the obtained 23 032 rice PPIs, including 22,665 newly identified PPIs, greatly expanded the current rice PPI dataset, provided a comprehensive overview of the rice PPIs networks, and could be a valuable asset in facilitating functional genomics research in rice.

Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods.

Pyogenic liver abscesses (PLAs) are serious infections in which doctors often fail in identifying the causative agent due to microbiological limitations. These limitations in detecting uncommon pathogens complicate the treatment and recovery. Molecular techniques, like massive sequencing, enable the detection of uncommon pathogens and highlight the shortcomings of traditional cultures. The aim of this work was to characterise the bacterial composition of PLAs through massive sequencing of the V3-V4 hypervariable region of the 16S rRNA gene in cases where conventional culture methods were negative. Purulent material was collected from three patients with PLAs at Hospital Juárez de México. Classical and molecular microbiological cultures were performed in parallel. Metagenomic DNA was extracted and massively sequenced (16S rRNA gene) using the Illumina MiSeq platform. A bioinformatic analysis was performed to determine the diversity at six different taxa levels and the relative abundances. The culture methods were not sufficient to detect the causative agent of the PLAs. However, the massive sequencing revealed the causative agents of the monomicrobial and polymicrobial infectious foci, with Gardnerella vaginalis, Lactobacillus iners, and Prevotella timonensis as the dominant bacteria. The massive sequencing revealed the presence of unusual pathogens that traditional culture failed to detect. There is an immediate need for molecular or comprehensive microbiological culture techniques to search for unusual bacteria in the diagnosis of PLAs.

Genetic predisposition to polyposis syndromes.

Hereditary polyposis syndromes are significant contributors to colorectal cancer (CRC). These syndromes are characterized by the development of various types and numbers of polyps, distinct inheritance patterns, and extracolonic manifestations. This review explores these syndromes with a focus on their genetic characteristics. Advances in diagnostics, particularly the identification of pathogenic germline variants through massive sequencing technologies, have enhanced our understanding of the genetic alterations associated with polyp formation and CRC risk. Identifying pathogenic variants beyond traditional diagnostic criteria improves the management and surveillance of these syndromes. Genetic diagnosis not only refines patient treatment and surveillance, but also informs relatives of potential risks, enabling appropriate management. However, challenges persist in determining the pathogenicity of newly discovered mutations due to their low prevalence. This review covers hereditary polyposis syndromes, from well-established to newly recognized types, providing insights into their genetic landscapes and highlighting the need for tailored surveillance based on genotype.

Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data

Genomic variants causing abnormal splicing play important roles in genetic disorders and cancer development. Among them, variants that cause the formation of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs). To leverage massive transcriptome sequence data such as those available from the Sequence Read Archive, we develop a novel framework to screen for SSCVs solely using transcriptome data. We apply it to 322,072 publicly available transcriptomes and identify 30,130 SSCVs. Among them, 5121 SSCVs affect disease-causing variants. By utilizing this extensive collection of SSCVs, we reveal the characteristics of Alu exonization via SSCVs, especially the hotspots of SSCVs within Alu sequences and their evolutionary relationships. We discover novel gain-of-function SSCVs in the deep intronic region of the NOTCH1 gene and demonstrate that their activation can be suppressed using splice-switching ASOs. Collectively, we provide a systematic approach for automatically acquiring a registry of SSCVs, which facilitates the elucidation of novel biological mechanisms underlying splicing and serves as a valuable resource for drug discovery. The catalogs of SSCVs identified in this study are accessible on the SSCV DB (https://sscvdb.io).

RNA control of reverse transcription in a diversity-generating retroelement.

Diversity-generating retroelements (DGRs) create massive protein sequence variation (up to 1030)1 in ecologically diverse microorganisms. A recent survey identified around 31,000 DGRs from more than 1,500 bacterial and archaeal genera, constituting more than 90 environment types2. DGRs are especially enriched in the human gut microbiome2,3 and nano-sized microorganisms that seem to comprise most microbial life and maintain DGRs despite reduced genomes4,5. DGRs are also implicated in the emergence of multicellularity6,7. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for complementary DNA synthesis to be carried out by a complex of the DGR reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Here we show through cryogenic electron microscopy that this RNA envelops bRT and lies over the barrel-shaped Avd, forming an intimate ribonucleoprotein. An abundance of essential interactions in the ribonucleoprotein precisely position an RNA homoduplex in the bRT active site for initiation of reverse transcription. Our results explain how the surrounding RNA primes complementary DNA synthesis, promotes processivity, terminates polymerization and strictly limits mutagenesis to specific proteins through mechanisms that are probably conserved in DGRs belonging to distant taxa.

Hidden Places for Foodborne Bacterial Pathogens and Novel Approaches to Control Biofilms in the Meat Industry.

Biofilms are of great concern for the meat industry because, despite the implementation of control plans, they remain important hotspots of contamination by foodborne pathogens, highlighting the need to better understand the ecology of these microecosystems. The objective of this paper was to critically survey the recent scientific literature on microbial biofilms of importance for meat safety and quality, also pointing out the most promising methods to combat them. For this, the databases PubMed, Scopus, Science Direct, Web of Science, and Google Scholar were surveyed in a 10-year time frame (but preferably papers less than 5 years old) using selected keywords relevant for the microbiology of meats, especially considering bacteria that are tolerant to cleaning and sanitization processes. The literature findings showed that massive DNA sequencing has deeply impacted the knowledge on the species that co-habit biofilms with important foodborne pathogens (Listeria monocytogenes, Salmonella, pathogenic Escherichia coli, and Staphylococcus aureus). It is likely that recalcitrant commensal and/or spoilage microbiota somehow protect the more fastidious organisms from harsh conditions, in addition to harboring antimicrobial resistance genes. Among the members of background microbiota, Pseudomonas, Acinetobacter, and Enterobacteriales have been commonly found on food contact and non-food contact surfaces in meat processing plants, in addition to less common genera, such as Psychrobacter, Enhydrobacter, Brevundimonas, and Rothia, among others. It has been hypothesized that these rare taxa may represent a primary layer in microbial biofilms, offering better conditions for the adhesion of otherwise poor biofilm formers, especially considering their tolerance to cold conditions and sanitizers. Taking into consideration these findings, it is not only important to target the foodborne pathogens per se in cleaning and disinfection plans but the use of multiple hurdles is also recommended to dismantle the recalcitrant structures of biofilms. In this sense, the last part of this manuscript presents an updated overview of the antibiofilm methods available, with an emphasis on eco-friendly approaches.

Characterization and identification of Pseudomonas sp. AW4, an arsenic-resistant and plant growth-promoting bacteria isolated from the soybean (Glycine max L.) rhizosphere.

Pseudomonas sp. AW4 is a highly arsenic (As) resistant bacterium with plant growth promoting properties, originally isolated from the soybean (Glycine max L.) rhizosphere. In order to safely use this isolate in diverse bioformulations, its characterization needs to be completed and a reliable identification must be provided. In the present work, we analyzed the morpho-physiological, biochemical and genomic characteristics of Pseudomonas sp. AW4. Identification of the isolate varied according to the parameters analyzed, mainly biochemical and physiological tests or individual genes and phylogenetic analyses. In this regard, we performed massive sequencing of its genome, in order to consistently complete its characterization and identification. Pseudomonas sp. AW4 formed a monophyletic clade with P. urmiensis SWRI10, presenting 3.08% of unique genes against this reference isolate. More than 70% of AW4 genes were also shared with P. oryziphila strain 1257 NZ and with P. reidholzensis strain CCOS 865. The search for genes related to As resistance evidenced the presence of the operon arsHRBC. Taken together, results of the present work allow identification of this bacterium as Pseudomonas urmiensis AW4 and open up a number of opportunities to study this strain and understand the mechanisms of arsenic resistance and plant growth promotion.

Evidence of habitat specificity in sponge microbiomes from Antarctica

BackgroundMarine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.ResultsOur study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.ConclusionsThis study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.

Playing for 3D Human Recovery.

Image- and video-based 3D human recovery (i.e., pose and shape estimation) have achieved substantial progress. However, due to the prohibitive cost of motion capture, existing datasets are often limited in scale and diversity. In this work, we obtain massive human sequences by playing the video game with automatically annotated 3D ground truths. Specifically, we contribute GTA-Human, a large-scale 3D human dataset generated with the GTA-V game engine, featuring a highly diverse set of subjects, actions, and scenarios. More importantly, we study the use of game-playing data and obtain five major insights. First, game-playing data is surprisingly effective. A simple frame-based baseline trained on GTA-Human outperforms more sophisticated methods by a large margin. For video-based methods, GTA-Human is even on par with the in-domain training set. Second, we discover that synthetic data provides critical complements to the real data that is typically collected indoor. We highlight that our investigation into domain gap provides explanations for our data mixture strategies that are simple yet useful, which offers new insights to the research community. Third, the scale of the dataset matters. The performance boost is closely related to the additional data available. A systematic study on multiple key factors (such as camera angle and body pose) reveals that the model performance is sensitive to data density. Fourth, the effectiveness of GTA-Human is also attributed to the rich collection of strong supervision labels (SMPL parameters), which are otherwise expensive to acquire in real datasets. Fifth, the benefits of synthetic data extend to larger models such as deeper convolutional neural networks (CNNs) and Transformers, for which a significant impact is also observed. We hope our work could pave the way for scaling up 3D human recovery to the real world.

Genetic basis of hypertriglyceridemia.

The development of massive sequencing techniques and guidelines for assessing the pathogenicity of variants are allowing us the identification of new cases of familial chylomicronemia syndrome (FCS) mostly in the LPL gene, less frequently in GPIHBP1 and APOA5, and with even fewer cases in LMF1 and APOC2. From the included studies, it can be deduced that, in cases with multifactorial chylomicronemia syndrome (MCS), both loss-of-function variants and common variants in canonical genes for FCH contribute to the manifestation of this other form of chylomicronemia. Other common and rare variants in other triglyceride metabolism genes have been identified in MCS patients, although their real impact on the development of severe hypertriglyceridemia is unknown. There may be up to 60 genes involved in triglyceride metabolism, so there is still a long way to go to know whether other genes not discussed in this monograph (MLXIPL, PLTP, TRIB1, PPAR alpha or USF1, for example) are genetic determinants of severe hypertriglyceridemia that need to be taken into account.

Should the Faecal Microbiota Composition Be Determined to Certify a Faecal Donor?

Faecal microbiota transplantation (FMT) is considered a safe and effective therapy for recurrent Clostridioides difficile infection. It is the only current clinical indication for this technique, although numerous clinical research studies and trials propose its potential usefulness for treating other pathologies. Donor selection is a very rigorous process, based on a personal lifestyle interview and the absence of known pathogens in faeces and serum, leading to only a few volunteers finally achieving the corresponding certification. However, despite the high amount of data generated from the ongoing research studies relating microbiota and health, there is not yet a consensus defining what is a "healthy" microbiota. To date, knowledge of the composition of the microbiota is not a requirement to be a faecal donor. The aim of this work was to evaluate whether the analysis of the composition of the microbiota by massive sequencing of 16S rDNA could be useful in the selection of the faecal donors. Samples from 10 certified donors from Mikrobiomik Healthcare Company were collected and sequenced using 16S rDNA in a MiSeq (Illumina) platform. Alpha (Chao1 and Shannon indices) and beta diversity (Bray-Curtis) were performed using the bioinformatic web server Microbiome Analyst. The differences in microbial composition at the genera and phyla levels among the donors were evaluated. The microbial diversity metric by alpha diversity indexes showed that most donors exhibited a similar microbial diversity and richness, whereas beta diversity by 16S rDNA sequencing revealed significant inter-donor differences, with a more stable microbial composition over time in some donors. The phyla Bacillota and Bacteroidota were predominant in all donors, while the density of other phyla, such as Actinomycota and Pseudomonota, varied among individuals. Each donor exhibited a characteristic genera distribution pattern; however, it was possible to define a microbiome core consisting of the genera Agathobacter, Eubacterium, Bacteroides, Clostridia UCG-014 and Akkermansia. Conclusions: The results suggest that donor certification does not need to rely exclusively on their microbiota composition, as it is unique to each donor. While one donor showed greater microbial diversity and richness, clear criteria for microbial normality and health have yet to be established. Therefore, donor certification should focus more on clinical and lifestyle aspects.

Feasibility of successive hydrogen and methane production: Effects of temperature and organic loads on energy potential and microbial dynamics

This study aims to assess the co-digestion of Cassava Wastewater (CW) and glycerol in a two-stage process using fluidized bed reactors (AFBR), verifying the effect of organic loading rate (OLR) and temperature (mesophilic [SMR] and thermophilic [STR]) in sequential reactors on CH4 production. The OLR ranged from 1.2 to 15 g COD.L−1.d−1 and the hydraulic retention time (HRT) was set at 20 h. The mesophilic sequential reactor (MSR) (average temperature of 30 °C) showed greater tolerance to high OLR and its best MPR was 101.12 mL of CH4.d−1.L−1 h−1, obtained at a OLR of 15 g COD.L−1.d−1). The maximum yield was 341.10 mL of CH4.g−1CODcons, found at the OLR of 1.2 g COD.L−1.d−1. The sequential thermophilic reactor (STR) showed the maximum yield and MPR of 333.03 mL of CH4.g−1CODcons (1.2 g COD.L−1.d−1) and 58.84 mL of CH4.d− 1.L−1 h−1 (12 g COD.L−1.d−1), respectively. Through the massive sequencing analysis of the 16S rRNA gene, it was possible to observe a greater diversity of microorganisms in the TSR than in the MSR. A predominance of acetoclastic microorganisms was observed, with the genera Methanobacterium, Methanosarcina and Methanobrevibacter being the most abundant in both reactors. The two-stage system composed of mesophilic acidogenic reactor + MSR was more suitable for the co-digestion of CW and glycerol than the acidogenic reactor + TSR. These results support the notion of standard operating conditions at the industrial plant, where the cassava processing process is carried out at room temperature (25–30 °C).

Changes in the Composition and Diversity of the Intestinal Microbiota Associated with Carbohydrate Consumption in Type 2 Diabetes Mellitus Patients.

Type 2 diabetes mellitus (T2DM) is a multifactorial disease, influenced by dietary and environmental factors that can modify the intestinal microbiota. The aim of this study was to evaluate changes in the composition and diversity of the intestinal microbiota associated with carbohydrate (CHO) consumption in T2DM patients. Forty patients participated, with and without T2DM. Fecal samples were collected for the characterization of microbial diversity from the massive sequencing of the 16S rRNA gene. Carbohydrate consumption was quantified using the Frequency Consumption Foods questionnaire (FCF), the groups were categorized according to Body Mass Index (BMI) and BMI + CHO consumption. The group without T2DM showed normal biochemical and anthropometric parameters, although they had a high carbohydrate consumption compared to the group with T2DM. At the phylum level, there were differences in relative abundance; the control overweight group (CL-OW > CHO) and T2DM-Normal Weight > CHO patients had increased Bacteroides and decreased Firmicutes. In contrast, the CL-OW > CHO and T2DM-OW < CHO patients, showed reduced Bacteroidetes and an elevated amount of Firmicutes. At the genus level, the differences were in the relative abundance of Roseburia, Clostridium_IV, Prevotella, and Sporobacter, associated with the consumption of carbohydrates. The groups that consumed high amounts of carbohydrates, regardless of whether they had diabetes mellitus or were overweight, had a significantly reduced proportion of Faecalibacterium, an altered proportion of Bacteroides. The high consumption of carbohydrates showed considerable modifications in the composition and diversity of the bacterial communities.

Data normalization of plasma miRNA profiling from patients with COVID-19

When using the reverse-transcription quantitative polymerase chain reaction (RT-qPCR) technique for quantitative assessment of microRNA (miRNA) expression, normalizing data using a stable endogenous gene is essential; however, no universally adequate reference gene exists. Therefore, in this study, we aimed to determine, via the RNA-Seq technique, the most adequate endogenous normalizer for the expression assessment of plasma miRNAs in patients with coronavirus disease 2019 (COVID-19). Two massive sequencing procedures were performed (a) to identify differentially expressed miRNAs between patients with COVID-19 and healthy volunteers (n = 12), and (b) to identify differentially expressed miRNAs between patients with severe COVID-19 and those with mild COVID-19 (n = 8). The endogenous normalizer candidates were selected according to the following criteria: (1) the miRNA must have a fold regulation = 1; (2) the miRNA must have a p-value > 0.990; and (3) the miRNAs that were discovered the longest ago should be selected. Four miRNAs (hsa-miR-34a-3p, hsa-miR-194-3p, hsa-miR-17-3p, and hsa-miR-205-3p) met all criteria and were selected for validation by RT-qPCR in a cohort of 125 patients. Of these, only hsa-miR-205-3p was eligible endogenous normalizers in the context of COVID-19 because their expression was stable between the compared groups.

Carrier frequency and incidence estimation of deficiency of adenosine deaminase 2 in the Chinese population based on massive exome sequencing data

Deficiency of adenosine deaminase 2 (DADA2) is an autosomal recessive autoinflammatory disease characterised by early onset stroke, recurrent fever, and diverse vascular pathologies, caused by loss-of-function homozygous or compound heterozygous variants of ADA2. This research aimed to determine the carrier frequency and expected incidence of DADA2 in China, using massive exome sequencing (ES) data. A total of 50 likely pathogenic/pathogenic variants (LP/PVs) were identified among 69,413 Chinese individuals, including 20 novel and rare variants (<0.0022 % allele frequency), expanding the known spectrum of PVs in ADA2. The overall carrier frequency in the Chinese population was 1.05 % (732/69,413) and the estimated incidence of DADA2 was approximately one in 92,251 individuals. The present study provides an accurate estimation of the prevalence of DADA2 in China, supporting genetic counseling, early diagnosis treatment, and prognostic evaluation.

Characterisation of the metagenome of Peruvian Pisco grapes from Ica and Arequipa for the development of their regional identity

Pisco grapes and their associated microbiome are the fundamental inputs for the production of Pisco; thus, knowledge of the varietal and regional differences between microbiota is of high value due to contribute to the distinctiveness and quality of the Pisco. To this end, the metagenomics can be applied for an in-depth exploration of the berry microbiome. The aim of this work was to characterise the metagenome of Peruvian Pisco grapes from Ica and Arequipa, thereby contributing to their regional identities. Sixteen composite samples of berries from the protected designation of origin regions of Ica and Arequipa were analysed for both bacteria and fungi via massive sequencing. Ralstonia, Gluconobacter, Pantoea, Tatumella, Bradyrhizobium, Komagataeibacter and some unclassified species from the Orbaceae family were identified as the predominant genera of bacteria, and Cladosporium, Starmerella, Pichia, Hanseniaspora, Wallemia, Claviceps, Alternaria and some unclassified species from the Saccharomycetales order or other orders within the Ascomycota division as the predominant fungi as well as its richness and diversity. As has been shown elsewhere in the literature regarding wine, we have proven here that the terroir of Pisco depends on the composition of the microbiome and is affected by edaphoclimatic factors and cultivation practices. These exploratory results will contribute to a better understanding of the terroir of Pisco, thus providing fundamental knowledge for its regional identity.

How marine are Marine Stramenopiles (MAST)? A cross-system evaluation.

Marine Stramenopiles (MAST) were first described two decades ago through ribosomal RNA gene (rRNA gene) sequences from marine surveys of microbial eukaryotes. MAST comprise several independent lineages at the base of the Stramenopiles. Despite their prevalence in the ocean, the majority of MAST diversity remains uncultured. Previous studies, mainly in marine environments, have explored MAST's cell morphology, distribution, trophic strategies, and genomics using culturing-independent methods. In comparison, less is known about their presence outside marine habitats. Here, we analyse the extensive EukBank dataset to assess the extent to which MAST can be considered marine protists. Additionally, by incorporating newly available rRNA gene sequences, we update Stramenopiles phylogeny, identifying three novel MAST lineages. Our results indicate that MAST are primarily marine with notable exceptions within MAST-2 and MAST-12, where certain subclades are prevalent in freshwater and soil habitats. In the marine water column, only a few MAST species, particularly within clades -1, -3, -4, and -7, dominate and exhibit clear latitudinal distribution patterns. Overall, the massive sequencing dataset analysed in our study confirms and partially expands the previously described diversity of MASTs groups and underscores the predominantly marine nature of most of these uncultured lineages.

Boron depletion in Galactic early B-type stars reveals two different main sequence star populations

Context. The evolution and fate of massive stars are thought to be affected by rotationally induced internal mixing. The surface boron abundance is a sensitive tracer of this in early B-type main sequence stars. Aims. We test current stellar evolution models of massive main sequence stars which include rotational mixing through a systematic study of their predicted surface boron depletion. Methods. We construct a dense grid of rotating single star models using MESA, for which we employ a new nuclear network which follows all the stable isotopes up to silicon, including lithium, beryllium, boron, as well as the radioactive isotope aluminium-26. We also compile the measured physical parameters of the 90 Galactic early B-type stars with boron abundance information. We then compare each observed stars with our models through a Bayesian analysis, which yields the mixing efficiency parameter with which the star is reproduced the best, and the probability that it is represented by the stellar models. Results. We find that about two-thirds of the sample stars are well represented by the stellar models, with the best agreement achieved for a rotational mixing efficiency of ∼50% compared to the widely adopted value. The remaining one third of the stars, of which many are strongly boron depleted slow rotators, are largely incompatible with our models, for any rotational mixing efficiency. We investigate the observational incidence of binary companions and surface magnetic fields, and discuss their evolutionary implications. Conclusions. Our results confirm the concept of rotational mixing in radiative stellar envelopes. On the other hand, we find that a different boron depletion mechanism, and likely a different formation path, is required to explain about one-third of the sample stars. The large spread in the surface boron abundances of these stars may hold a clue to understanding their origin.

Calidad de los fenotipos humanos en pacientes con discapacidad intelectual con estudios de secuenciación de exoma en un hospital pediátrico peruano

Introduction. Massive sequencing and the Human Phenotype Ontology have revolutionized genetic diagnosis, allowing for a clearer understanding of diseases. The phenotypes described in medical records can be specific or general, the more detailed and specific the description, the higher the quality of the information. Objectives. To determine the relationship between the quality of human phenotypes in patients with intellectual disability and the findings from massive sequencing test at the Instituto Nacional de Salud del Niño. Methods. We analyzed 124 patients with intellectual disabilities with exome sequencing. The quality of human phenotypes was evaluated using different quality index. Results. A total of 278 human phenotype terms were identified. Phenotypic precision improved after filtering, highlighting the importance of specific phenotypic descriptions (from 103 to 86 unique terms). The specificity index of the dataset was lower in the group with variants of uncertain significance compared to the group with pathogenic variants (0 vs. 0.05). The most frequent phenotypes were psychomotor delay (12.9% - 15.9%) and microcephaly (4.5% - 5.2%). Conclusions. The importance of evaluating the quality of human phenotypes is highlighted. The presence of uncertain variants suggests a genotype-phenotype complexity, emphasizing the need for greater clarity in genetic interpretation. Consistency in confidence intervals and the specificity index of the dataset underscores the competence of local medical-genetic personnel.