Biology subjects

Pereira, S.

Publications and source records attributed to Pereira, S..

13 recordsLinked to original sources

bioRxiv2026

High-resolution HLA and MICA/MICB typing of the 1000 Genomes panel: a resource for precision medicine

High-resolution characterization of human leukocyte antigen (HLA) and MICA/MICB variation is important for transplantation, immunogenetics, and the interpretation of disease associations within the major histocompatibility complex (MHC). However, publicly available population reference datasets remain limited in their resolution and coverage of these loci. We performed high-resolution typing of the 1000 Genomes Phase 3 panel across 13 HLA and MIC loci, generating HLA genotypes for 2,486 individuals, extended HLA-A, -B, and -C allele assignments, and MICA/MICB genotypes for 2,393 individuals representing 25 populations and five continental super-populations. Concordance with previously reported HLA genotypes was 96.2-97.4% at two-field resolution, and independent retyping confirmed the present assignments for samples exhibiting reciprocal genotype discrepancies with an earlier dataset. Analysis of extended class I variation within defined assay boundaries revealed that most of the 78 common three-field HLA lineages were dominated by a single extended sequence group. However, eleven lineages exhibited substantial heterogeneity, with the predominant group accounting for less than 80% of observed copies. The distinguishing sequence differences were noncoding, involving intronic and 3' untranslated regions, and their distributions varied among ancestral populations. These findings identify recurrent, population-relevant variants for which functional consequences remain to be established. Population analyses demonstrated extensive allelic diversity at classical class I loci and DRB1, whereas the greatest between-population differentiation occurred at selected class II and DRB-linked loci. Most common alleles were shared among populations but differed substantially in frequency. Multilocus haplotypes revealed characteristic population-associated combinations of HLA and MIC alleles and provided the basis for predicting MIC genotypes from existing HLA typing. Using two-field HLA-B and HLA-C genotypes, five-fold cross-validation achieved exact genotype prediction accuracies of 77.3% for MICA and 53.6% for MICB, compared with 4.6% and 21.6%, respectively, without HLA information. Together, these results provide an extended-resolution HLA and MIC reference resource, demonstrate the limited routine utility of universal fourth-field typing while identifying specific variants for functional investigation, and establish the potential for recovering MIC variation from existing HLA-typed cohorts. The resource also supports future investigations of MHC variation underlying disease associations and transplantation outcomes.

genetics↗

bioRxiv2025

Circadian rhythms in sexual behavior and their influence on reproductive outcomes in mice

Circadian clocks coordinate mammalian reproductive physiology, and circadian misalignment (resulting from shift work, jet lag, etc.) is known to impair fertility. Despite the well-established links between clock function and reproductive success, it remains unclear whether male and female mice maintained under standard ad libitum feeding conditions exhibit circadian rhythms in the propensity for sexual behavior, and to what degree such timing influences reproductive outcomes. Using standardized mating paradigms in C57BL/6J mice, we identified a circadian rhythm in sexual behavior in both sexes, with peak sexual activity most often occurring at circadian time (CT) 13-16 and a trough at CT4-7. To test the functional significance of these rhythms, we conducted 1-hour mating trials across four cohorts of C57BL/6J mice with pairs of mice having either aligned (e.g. male CT16 peak and female CT16 peak) or misaligned (e.g. male CT16 peak and female CT4 nadir) sexual behavior phases and monitored mating outcomes via ultrasound. While pregnancies were almost as frequent across all four cohorts, the numbers of live offspring were significantly more frequent when both the male and female mated at their peak phases than when both mice mated at their troughs. Notably, mating specifically during the males behavioral peak increased the likelihood of successful delivery of pups, suggesting that male circadian phase is a key determinant of miscarriage vs successful birth. These findings establish a circadian rhythm in the propensity for sexual behavior under standard feeding and housing conditions and indicate that mating time--particularly relative to the males circadian peak--can influence reproductive success. This insight provides a foundation for translational studies that explore whether intercourse timed to the circadian rhythms of the couple might help to increase fertility chances.

physiology↗

bioRxiv2025

Fish spawning events stimulate trophic hotspots across freshwater food webs

1.0Mass reproductive events, where large numbers of organisms aggregate for synchronous reproduction, are often captivating and ecologically significant, boosting offspring survival and reducing time spent searching for mates. However, mass reproduction can also instigate cryptic but consequential responses across entire food webs. Reproductive materials are abundant and accessible resources that can attract mobile consumers from up to thousands of kilometers away. Yet, their consumption, especially in aquatic systems, is difficult to detect and rarely characterized. Here, we combine molecular techniques with acoustic telemetry, literature review, and extensive natural history observations to investigate the food web consequences of synchronized reproduction in freshwater fishes. First, we demonstrate that a common but underappreciated fish species, white sucker, creates a resource pulse used ubiquitously by consumers, from local invertebrates and fishes to mobile predatory fishes, birds, and terrestrial mammals. Spawning white sucker create trophic hotspots that attract consumers across trophic levels and ecosystems to feed on eggs, spawning adults, and aggregated egg predators. Then we show that egg provisioning and predation is widespread among north-temperate freshwater fish species, highlighting that resource pulses instigated by mass reproduction may play a critical but underappreciated role in freshwater and terrestrial ecosystems.

ecology↗

bioRxiv2025

The fecal microbiota transplantation from drug-naive schizophrenia patients distinctively changes gut microbiome and metabolic profiles in male and female mice

BackgroundEmerging evidence suggests a role for the gut microbiome in schizophrenia (SCZ) and antipsychotic-induced metabolic perturbations. Using human fecal microbiota transplantation (FMT) in mice, this study investigated the role of gut microbiome in metabolic changes related to SCZ and antipsychotic (olanzapine) treatment. Methods5-6 weeks old germ-free NIH Swiss mice of both sexes received microbiota from either SCZ patients (SCZ-FMT) or healthy controls (HC-FMT) followed by a diet with or without olanzapine for six-weeks. Food intake and body weight were monitored weekly, and an intraperitoneal glucose tolerance test and open field test were performed. Serum glucose, and insulin were measured. Gut microbiome characterization and short-chain fatty acids (SCFAs) quantification were performed in the cecal samples using 16S rRNA gene sequencing and gas chromatography-mass spectrometry, respectively. ResultsOlanzapine treatment decreased the locomotor activity in the open field test, irrespective of sex or microbiota. Female SCZ-FMT recipient mice exhibited insulin resistance compared to HC-FMT, irrespective of olanzapine treatment. Female SCZ-FMT mice showed significantly lower alpha-diversity compared to HC-FMT, whereas olanzapine treatment increased alpha-diversity. SCZ-FMT and olanzapine treatment differentially altered the microbial abundances, and metabolic pathways in male and female mice. Interestingly, cecal SCFAs, mainly acetate levels, were significantly decreased in female SCZ-FMT mice compared to HC-FMT, while olanzapine treatment increased acetate levels in male mice. Both male and female SCZ-FMT mice showed elevated levels of isovaleric acid compared to HC-FMT. ConclusionThese preliminary findings suggest that gut microbiome could be a predisposing factor contributing to the intrinsic risk of developing type 2 diabetes associated with SCZ in females. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/675957v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@8cfd10org.highwire.dtl.DTLVardef@3a6031org.highwire.dtl.DTLVardef@813428org.highwire.dtl.DTLVardef@87609e_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

neuroscience↗

bioRxiv2025

Protective effects of central leptin on whole-body energy homeostasis upon acute olanzapine exposure

Second-generation antipsychotic use is associated with severe metabolic side effects such as obesity and type 2 diabetes. Leptin is a hormone that is secreted by adipose tissue, and it acts on the brain to decrease body weight by reducing food intake and stimulating energy expenditure. Leptin also improves glucose and lipid metabolism. We examined the short-term impact of olanzapine, a commonly used second-generation antipsychotic, on the central leptin-mediated regulation of energy balance, lipid metabolism, and hypothalamic kinase activity. Male Sprague Dawley rats were given an acute intracerebroventricular (ICV, 3rd ventricle) injection of either leptin or vehicle, combined with subcutaneous olanzapine or vehicle. As expected, ICV leptin decreased food intake and importantly, olanzapine did not block this effect. Administration of leptin, olanzapine, or their combination reduced the average respiratory exchange ratio (RER) during the light cycle, which indicates that fat oxidation was increased. In the dark cycle, leptin decreased the average RER regardless of olanzapine administration, and in the presence of leptin, olanzapine did not affect the average RER. Leptin did not alter the olanzapine-induced increase in serum triglyceride concentrations. Olanzapine and central leptin treatment differentially activated hypothalamic kinases. In conclusion, regulation of food intake and fuel preference by central leptin is intact following acute olanzapine administration.

neuroscience↗

bioRxiv2024

Shifting Routes: Plant Specific Insert trafficking and function in Arabidopsis seedlings under abiotic stress

Due to plants inability to escape adverse conditions, they must adapt and adjust their endomembrane system through protein sorting and distribution. Cardosins A and B are key models for studying intracellular trafficking. They are aspartic proteinases in thistle flowers that mediate different vacuolar pathways despite sharing high sequence similarity, and both are responsive to stress conditions. The Plant Specific Insert (PSI) is a 100 amino acid domain found in these proteins. It is known that stress can impact protein sorting, shifting it from the conventional pathway (ER-Golgi) to a Golgi-independent route. In this work we assessed changes in the expression and localization of PSI from Cardosin B (PSI B) in Arabidopsis plants overexpressing PSI B-mCherry submitted to different abiotic stress conditions (saline, hydric, oxidative, metals). Aside from potential PSI B localization changes, we focused on characterizing the homozygous line, alongside assessing several biometric parameters and biochemical endpoints. The results revealed that the PSI B line responded differently depending on the stress conditions. Biometric and biochemical analyses emphasized the roles of PSI B in enhancing plant fitness and supporting adaptation to abiotic stress. Besides, confocal microscopy allowed us to find PSI B accumulation in Endoplasmic Reticulum-derived vesicles (ER bodies), indicating a shift from the common PSI B-mediated route. These findings underscore the role of PSI B in enhancing plant fitness and adaptation to abiotic stress through altered protein trafficking. HighlightPSI B has an active role in enhancing plant fitness, revealing its value in adaptation and tolerance to abiotic stress by adjusting its localization and trafficking under challenging environments.

plant biology↗

bioRxiv2024

PriMAT: A robust multi-animal tracking model for primates in the wild

O_LIDetection and tracking of animals is an important first step for automated behavioral studies using videos. Animal tracking is currently done mostly using deep learning frameworks based on keypoints, which show remarkable results in lab settings with fixed cameras, backgrounds, and lighting. However, multi-animal tracking in the wild presents several challenges such as high variability in background and lighting conditions, complex motion, and occlusion. C_LIO_LIWe propose a multi-animal tracking model, PriMAT, for nonhuman primates in the wild. The model learns to detect and track primates and other objects of interest from labeled videos or single images using bounding boxes instead of keypoints. Using bounding boxes significantly facilitates data annotation and robustness. Our one-stage model is conceptually simple but highly flexible, and we add a classification branch that allows us to train individual identification. C_LIO_LITo evaluate the performance of our model, we applied it in two case studies with Assamese macaques (Macaca assamensis) and redfronted lemurs (Eulemur rufifrons) in the wild. We show that with only a few hundred frames labeled with bounding boxes, we can achieve robust tracking results. Combining these results with the classification branch for the lemur videos, our model shows an accuracy of 84% in predicting lemur identities. C_LIO_LIOur approach presents a promising solution for accurately tracking and identifying animals in the wild, offering researchers a tool to study animal behavior in their natural habitats. Our code, models, training images, and evaluation video sequences are publicly available1, facilitating their use for animal behavior analyses and future research in this field. C_LI

animal behavior and cognition↗

bioRxiv2024

Development of novel tools for dissection of central versus peripheral dopamine D2-like receptor signaling in dysglycemia

Dopamine (DA) D2-like receptors in both the central nervous system (CNS) and the periphery are key modulators of metabolism. Moreover, disruption of D2-like receptor signaling is implicated in dysglycemia. Yet, the respective metabolic contributions of CNS versus peripheral D2-like receptors including D2 (D2R) and D3 (D3R) receptors remain poorly understood. To address this, we developed new pharmacological tools, D2-like receptor agonists with diminished and delayed blood-brain barrier capability, to selectively manipulate D2R/D3R signaling in the periphery. We designated bromocriptine methiodide (BrMeI), a quaternary methiodide analogue of D2/3R agonist and diabetes drug bromocriptine, as our lead compound based on preservation of D2R/D3R binding and functional efficacy. We then used BrMeI and unmodified bromocriptine to dissect relative contributions of CNS versus peripheral D2R/D3R signaling in treating dysglycemia. Systemic administration of bromocriptine, with unrestricted access to CNS and peripheral targets, significantly improved both insulin sensitivity and glucose tolerance in obese, dysglycemic mice in vivo. In contrast, metabolic improvements were attenuated when access to bromocriptine was restricted either to the CNS through intracerebroventricular administration or delayed access to the CNS via BrMeI. Our findings demonstrate that the coordinated actions of both CNS and peripheral D2-like receptors are required for correcting dysglycemia. Ultimately, the development of a first-generation of drugs designed to selectively target the periphery provides a blueprint for dissecting mechanisms of central versus peripheral DA signaling and paves the way for novel strategies to treat dysglycemia.

neuroscience↗

bioRxiv2023

Cardiac Molecular Analysis Reveals Aging-Associated Metabolic Alterations Promoting Glycosaminoglycans Accumulation Via Hexosamine Biosynthetic Pathway

Age is a prominent risk factor for cardiometabolic disease, and often leads to heart structural and functional changes. However, precise molecular mechanisms underlying cardiac remodeling and dysfunction resulting from physiological aging per se remain elusive. Understanding these mechanisms requires biological models with optimal translation to humans. Previous research demonstrated that baboons undergo age-related reduction in ejection fraction and increased heart sphericity, mirroring changes observed in humans. The goal of this study was to identify early cardiac molecular alterations that precede functional adaptations, shedding light on the regulation of age-associated changes. We performed unbiased transcriptomics of left ventricle (LV) samples from female baboons aged 7.5-22.1 years (human equivalent [~]30-88 years). Weighted-gene correlation network and pathway enrichment analyses were performed to identify potential age-associated mechanisms in LV, with histological validation. Myocardial modules of transcripts negatively associated with age were primarily enriched for cardiac metabolism, including oxidative phosphorylation, tricarboxylic acid cycle, glycolysis, and fatty-acid {beta}-oxidation. Transcripts positively correlated with age suggest upregulation of glucose uptake, pentose phosphate pathway, and hexosamine biosynthetic pathway (HBP), indicating a metabolic shift towards glucose-dependent anabolic pathways. Upregulation of HBP commonly results in increased glycosaminoglycan precursor synthesis. Transcripts involved in glycosaminoglycan synthesis, modification, and intermediate metabolism were also upregulated in older animals, while glycosaminoglycan degradation transcripts were downregulated with age. These alterations would promote glycosaminoglycan accumulation, which was verified histologically. Upregulation of extracellular matrix (ECM)-induced signaling pathways temporally coincided with glycosaminoglycan accumulation. We found a subsequent upregulation of cardiac hypertrophy-related pathways and an increase in cardiomyocyte width. Overall, our findings revealed a transcriptional shift in metabolism from catabolic to anabolic pathways that leads to ECM glycosaminoglycan accumulation through HBP prior to upregulation of transcripts of cardiac hypertrophy-related pathways. This study illuminates cellular mechanisms that precede development of cardiac hypertrophy, providing novel potential targets to remediate age-related cardiac diseases.

molecular biology↗

bioRxiv2023

Mesothelial cells exhibit characteristics of perivascular cells in an in vitro angiogenesis assay

Mesothelial cells have been shown to have remarkable plasticity towards mesenchymal cell types during development and in disease situations. Here, we have characterized the potential of mesothelial cells to undergo changes towards perivascular cells using an in vitro angiogenesis assay. We demonstrate that GFP-labelled mesothelial cells (GFP-MCs) aligned closely and specifically with endothelial networks formed when human dermal microvascular endothelial cells (HDMECs) were cultured in the presence of VEGF-A165 on normal human dermal fibroblasts (NHDFs) for a 7-day period. The co-culture with GFP-MCs had a positive effect on branch point formation indicating that the cells supported endothelial tube formation. We interrogated the molecular response of the GFP- MCs to the angiogenic co-culture by qRT-PCR and found that the pericyte marker Ng2 was upregulated when the cells were co-cultured with HDMECs on NHDFs, indicating a change towards a perivascular phenotype. When GFP-MCs were cultured on the NHDF feeder layer, they upregulated the epithelial-mesenchymal transition marker Zeb1 and lost their circularity while increasing their size, indicating a change to a more migratory cell type. We analysed the pericyte- like behavior of the GFP-MCs in a 3D cardiac microtissue (spheroid) with cardiomyocytes, cardiac fibroblasts and cardiac endothelial cells where the mesothelial cells showed alignment with the endothelial cells. These results indicate that mesothelial cells have the potential to adopt a perivascular phenotype and associate with endothelial cells to potentially support angiogenesis.

cell biology↗

bioRxiv2021

Ser/Thr phospho-regulation by PknB and Stp mediates bacterial quiescence and antibiotic persistence in Staphylococcus aureus

Staphylococcus aureus colonizes 30 to 50% of healthy adults and can cause a variety of diseases, ranging from superficial to life-threatening invasive infections such as bacteraemia and endocarditis. Often, these infections are chronic and difficult-to-treat despite adequate antibiotic therapy. Most antibiotics act on metabolically active bacteria in order to eradicate them. Thus, bacteria with minimized energy consumption resulting in metabolic quiescence, have increased tolerance to antibiotics. The most energy intensive process in cells - protein synthesis - is attenuated in bacteria entering into quiescence. Eukaryote-like serine/threonine kinases (STKs) and phosphatases (STPs) can fine-tune essential cellular processes, thereby enabling bacteria to quickly respond to environmental changes and to modulate quiescence. Here, we show that deletion of the only annotated functional STP, named Stp, in S. aureus leads to increased bacterial lag-phase and phenotypic heterogeneity under different stress challenges, including acidic pH, intracellular milieu and in vivo abscess environment. This growth delay was associated with reduced intracellular ATP levels and increased antibiotic persistence. Using phosphopeptide enrichment and mass spectrometry-based proteomics, we identified possible targets of Ser/Thr phosphorylation that regulate cellular processes and bacterial growth, such as ribosomal proteins including the essential translation elongation factor EF-G. Finally, we show that acid stress leads to a reduced translational activity in the stp deletion mutant indicating metabolic quiescence correlating with increased antibiotic persistence. One-sentence summaryPhospho-regulation mediates quiescence and antibiotic persistence in Staphylococcus aureus.

microbiology↗

bioRxiv2021

Analysis of mitochondrial genome methylation using Nanopore single-molecule sequencing

The level and the biological significance of mitochondrial DNA (mtDNA) methylation in human cells is a controversial topic. Using long-read third-generation sequencing technology, mtDNA methylation can be detected directly from the sequencing data, which overcomes previously suggested biases, introduced by bisulfite treatment-dependent methods. We investigated mtDNA from whole blood-derived DNA and established a workflow to detect CpG methylation with Nanopolish. In order to obtain native mtDNA, we adjusted a whole-genome sequencing protocol and performed ligation library preparation and Nanopore sequencing. To validate the workflow, 897bp of methylated and unmethylated synthetic DNA samples at different dilution ratios were sequenced and CpG methylation was detected. Interestingly, we observed that reads with higher methylation in the synthetic DNA did not pass Guppy calling, possibly affecting conclusions about DNA methylation in Nanopore sequencing. We detected in all blood-derived samples overall low-level methylation across the mitochondrial genome, with exceptions at certain CpG sites. Our results suggest that Nanopore sequencing is capable of detecting low-level mtDNA methylation. However, further refinement of the bioinformatical pipelines including Guppy failed reads are recommended.

genetics↗

bioRxiv2019

Pancreas-specific miR-216a regulates proliferation and endocrine and exocrine cell function in vivo

Pancreas is a vital organ composed of exocrine and endocrine cells that aid digestion of food and regulate blood glucose levels. Perturbations in the function of pancreatic cells leads to the development of life-burdening and/or threatening diseases such as diabetes and pancreatic cancer. Thus, it is critical to understand the molecular check-points that maintain normal pancreas physiology. MicroRNAs (miRNAs) are small non-coding RNAs involved in regulating gene expression in normal and diseased tissues. Several miRNAs have tissue-specific patterns consistent with crucial functions in many biological processes. Yet, there is limited knowledge about the role of pancreas-specific miRNAs in pancreatic pathologies. Here, we report that miR-216a is a conserved, pancreas-specific miRNA that is expressed in both endocrine and exocrine cells. Deletion of miR-216a in mice leads to reduced {beta}-cell mass and a reduction in islet size under both chow and high-fat diet feeding conditions. We show that inhibition of miR-216a increases apoptosis and decreases cell proliferation in {beta}- and exocrine cells. Smad7 is upregulated in miR-216a deficient islets and cell cycle and proliferation are among the most significantly regulated biological processes in miR-216 knockout pancreata. Re-introduction of miR-216a in the pancreatic cancer line, PANC-1, increases cell migration more than 2-fold. In vivo, deletion of miR-216a in the pancreatic cancer prone mouse line KrasG12D;Ptf1aCreER inhibits the propensity of pancreatic cancer precursor lesions. Our study identifies miR-216a as an important pancreas-specific miRNA which may have implications for both diabetes and pancreatic cancer.

physiology↗