bioRxiv Science⌕ Search

Biology subjects

Torres, A.

Publications and source records attributed to Torres, A..

At least 19 recordsLinked to original sources

Experimental flowering order shapes priority effects in plant-pollinator interactions

Climate change is disrupting life's seasonal rhythms, altering the timing of key phenophases and reshaping how communities assemble. Beyond shifting flowering times, climate change can modify the extent of floral overlap and the sequence in which species bloom, generating novel assemblages with uncertain consequences for plant-pollinator interactions. Here, we ask whether flowering order generates priority effects in plant-pollinator communities, much like germination order does in plant communities. We tested how flowering order influences bee foraging behaviour and plant reproductive success in two co-flowering species, Hypochaeris radicata and Campanula rotundifolia, using a greenhouse experiment in which we manipulated the sequence of floral availability while allowing bees to forage repeatedly. We quantified changes in visit frequency, interspecific switches, handling time, and seed production. Our findings reveal priority effects in bee foraging that were strong enough to affect plant fitness: both species received more visits when flowering earlier than their co-occurring counterpart, and seed production declined when species flowered later. Overall, our results show that flowering order is an underappreciated driver of plant-pollinator interactions, suggesting that climate-driven phenological shifts could alter priority-effect dynamics with broader implications for community assembly. Key questions remain: How will climate-driven phenological shifts rearrange flowering sequences, and how will these priority effects emerge in more diverse communities in the wild? Our controlled experiment reveals strong flowering-order effects, underscoring the need to evaluate how widespread and impactful such dynamics are under accelerating climate change.

ecology↗

Dopamine dynamics in human anterior cingulate cortex during Pavlovian-instrumental conflict

Dopamine is believed to modulate not only instrumental learning about the link between states, actions, and outcomes but also reflexive behaviours, such as a Pavlovian bias to approach in rewarding states and freeze in aversive ones. We studied these dual roles in the human brain, by combining intracranial dopamine recordings from the anterior cingulate cortex (ACC)-- a region implicated in behavioural and cognitive control -- with a motivational Go/NoGo task involving conflict between instrumental and Pavlovian action selection. We found evidence that dopamine in the ACC is involved in evaluating whether Pavlovian responding should guide behaviour. This computational motif was observed across multiple task events, including in response to rewards and punishments, and in analyses based on a reinforcement learning model. Our results indicate that dopamine supports learning at the more abstract level of behavioural policies in addition to the more concrete levels of states and actions.

neuroscience↗

Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis

tRNAs play a critical role in protein synthesis, influencing mRNA translation dynamics to shape proteomes. Emerging evidence links dysregulated tRNA activity to cancer progression, with tRNA-Arg-TCT identified as an oncogenic driver when ectopically overexpressed in non-malignant cells. The requirement of endogenous tRNA-Arg-TCT in cancer biology, however, remains untested. Moreover, considering that the tRNA-Arg-TCT family comprises six genes in humans, the importance of an individual tRNA isodecoder in cancer remains unknown. Here, we find elevated levels of tRNA-Arg-TCT-4-1 isodecoder are associated with poor patient prognosis across multiple cancer types. We demonstrate that, using different antisense RNA strategies, specific inhibition of tRNA-Arg-TCT-4-1 suppresses the growth of glioblastoma (GBM) and liposarcoma (LPS) cancer cells. Mechanistically, we find that tRNA-Arg-TCT-4-1 inhibition leads to a codon-biased remodeling of mRNA translation and the proteome, preferentially suppressing expression of growth-promoting genes and pathways encoded by mRNAs enriched in arginine AGA codons. Strikingly, intratumoral delivery of an antisense oligonucleotide (ASO) targeting tRNA-Arg-TCT-4-1 suppresses tumor growth and extends survival in mouse xenograft experiments performed using either a human LPS cell line or a patient-derived soft tissue sarcoma model. This study provides a foundation for targeting tRNA dysregulation as a novel therapeutic approach for cancer. One Sentence SummaryThis study identifies tRNA-Arg-TCT-4-1 as a new anti-cancer therapeutic target and demonstrates that an antisense oligonucleotide (ASO) targeting this tRNA effectively suppresses tumorigenesis and extends survival in mouse xenograft models.

cancer biology↗

Stress-Survival Pathway Profiling Reveals MCM10 as a Candidate Biomarker of Hispanic Colorectal Cancer Disparities

BackgroundColorectal cancer (CRC) remains the second leading cause of cancer mortality in the U.S., with significant racial and ethnic disparities in incidence, survival, and mortality rates. The rising incidence of early-onset CRC and the frequent presentation at advanced stages of CRC among the Hispanics makes this an important ethnic group to study. A deeper understanding of the complex interplay between molecular, genetic, and environmental factors is critical for developing targeted therapies to reduce the prevalence in specific racial and ethnic groups, such as Hispanics. This study explores the role of stress-survival pathway (SSP) genes in early-onset and late-stage CRC, primarily focusing on disparities between Hispanics and Non-Hispanic Whites (NHWs). Additionally, this study investigates the role of MCM10, in contributing to CRC disparities among the Hispanic populations with an emphasis of early-onset and late-stage CRC Hispanics. MethodsOne of our previous studies had identified some SSP protein coding genes associated with CRC. The transcript and protein level expressions of these genes were validated in CRC cell lines, cDNA arrays, and tissue microarrays, using qRT-PCR and immunohistochemistry, respectively. The transcript level expressions of differentially expressed SSP genes were further evaluated in Hispanic and NHWs tumor tissues, including early onset and late-stage cohorts. Additionally, we performed cellular, physiological, and functional assays to explore the role of MCM10 in tumor progression, before and after siRNA mediated knockdown of MCM10. High-throughput transcriptomic and proteomic analyses were performed to reveal the underlying molecular mechanism. ResultsWe observed the differential expressions of twelve SSP genes in CRC cell lines, at the transcript level; that of ten genes in early and late stages using cDNA arrays, and nine genes at the protein levels using tissue microarrays and immunohistochemistry. Hispanic CRC samples showed differential expression of all nine SSP genes compared to NHWs, in early-onset, and late-stage CRC, with all genes being upregulated other than CDK4 and PRDX4 in late-stage CRC and CDK4 in early-onset CRC. Our functional study demonstrated that MCM10 knockdown in CRC cell lines significantly reduced cell proliferation, growth, invasion, and migration by inducing cell cycle arrest, apoptosis, and reactive oxygen species pathways. The integrative RNA-sequencing and proteomics study identified that PPFIA1 could be associated with MCM10 mediated cancer progression. The role of MCM10 and PPFIA1 in cancer progression has also been validated by CRISPR-Cas9 mediated MCM10 knock out, using a Hispanic CRC patient derived organoid. ConclusionThe differential expression of SSP genes suggest a potential molecular contribution to CRC disparities in the Hispanic population. The essential oncogenic role of MCM10 and its axis with PPFIA1 was identified; this could lead to a new avenue for therapeutics targeting the MCM10-PPFIA1 axis, thereby, combating early-onset and advanced-stage CRC in this high-risk ethnic group. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/698057v2_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@11528c8org.highwire.dtl.DTLVardef@288d15org.highwire.dtl.DTLVardef@466703org.highwire.dtl.DTLVardef@150890_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

Targeting Pseudomonas aeruginosa Ventilator-associated pneumonia with a non-antibiotic and biolfilm-disrupting Live Biotherapeutic: Preclinical Safety and Efficacy study

Background.Ventilator-associated pneumonia (VAP) is the second most common hospital-acquired infection and is associated with high morbidity and mortality. The insertion of the endotracheal tube (ETT) compromises the hosts bronchial defenses and facilitates the formation of microbial biofilms and VAP. Although antibiotics remain the cornerstone treatment, their efficacy is often compromised by poor biofilm penetration and the prevalence of multidrug-resistant bacteria. This reveals the need to develop novel non-antibiotic therapeutic strategies. We engineered a non-pathogenic strain of the pulmonary bacteria Mycoplasma pneumoniae CV2 to express anti-biofilm and bactericidal enzymes (VAP platform). The therapeutic effect was validated in a murine model of Pseudomonas aeruginosa infection and ex vivo in ETTs of patients with P. aeruginosa-induced VAP. Methods.We evaluated the safety of an improved version of CV2 (CV8, Mycochassis) in a miniature pig model, and its efficacy with the VAP therapeutic platform (CV8_VAP) in a piglet model of P. aeruginosa-induced VAP. CV8_VAP was administered via intralobe instillation or nebulization. We assessed the platforms ability to degrade biofilms formed on ETTs in vivo and its impact on the airway microbiota. We evaluated bacterial load in the lungs, inflammatory responses, histopathological and the clinical outcomes to provide a comprehensive characterization of therapeutic efficacy and safety. Findings.VAP platform reduced biofilm thickness and P. aeruginosa load in ETTs and lungs, with the nebulized route showing enhanced efficacy. CV8_VAP contributed on microbiome diversity restoration. Inflammatory markers in the lung were markedly decreased, suggesting a local immunomodulatory effect. Interpretation.These findings support that CV8_VAP as a promising, non-antibiotic therapeutic strategy for treating VAP caused by P. aeruginosa. Funding.The project that gave rise to these results has received funding from "La Caixa" Foundation (HR18-00058), and the European Research Council under the European Unions Horizon 2020 research and innovation program (670216).

synthetic biology↗

Stress granule component TIA-1 is a specific negative regulator of the non-canonical NLRP3 inflammasome.

Inflammasomes are cytosolic signaling hubs assembled upon pathogen- or damage associated molecular patterns (PAMP and DAMP) sensing by innate immune pattern recognition receptors (PRR). Lipopolysaccharide (LPS) present on the cell wall of gram-negative bacteria is a PAMP that activates caspase 11 (CASP11) dependent nucleotide-binding oligomerization domain-like receptor pyrin domain-containing 3 (NLRP3) inflammasome (known as non-canonical NLRP3 inflammasome) leading to pyroptosis. Several host factors are shown to promote non-canonical NLRP3 inflammasome activation by making LPS readily available for recognition by CASP11. Here, we report T-cell intracellular antigen-1 (TIA1), an RNA binding protein as a negative regulator of non-canonical NLRP3 inflammasome. Using bone marrow-derived macrophages (BMDMs), we demonstrated that the loss of TIA1 led to an increase in caspase-1 (CASP1) activity in response to cytosolic LPS. A previous study had demonstrated that mice lacking Tia1 are more susceptible to LPS mediated endotoxic shock. Our results provide a potential explanation for this observation by showing loss of TIA1 increases non-canonical NLRP3 inflammasome activation resulting in increased inflammation and pathogenesis during LPS mediated endotoxic shock. Further, TIA1 mediated inhibition of non-canonical NLRP3 inflammasome is independent of TIA1s regulatory role in gene transcription as well as its role in stress granule assembly. TIA1 is also dispensable for activation of the canonical NLRP3 inflammasome as well as AIM2 and NLRC4 inflammasomes. While, the exact mechanism by which TIA1 inhibits non-canonical inflammasome activation remains to be elucidated, our finding that TIA1 is a negative regulator indicates the presence of undiscovered regulatory mechanisms. Future studies will focus on unraveling these mechanisms for developing anti-inflammatory drugs that exploit non-canonical inflammasome activity modulation.

immunology↗

UITOTO: a new software for molecular diagnoses in species descriptions

Millions of species remain undescribed, and each eventually will require a species description that includes a diagnosis. However, no software currently exists that fully integrates the derivation and validation of state-specific and contrastive molecular diagnoses. Here we introduce UITOTO which addresses this gap and facilitates the identification, testing, and visualization of Diagnostic Molecular Combinations (DMCs). The software uses a weighted random sampling algorithm based on the Jaccard Index for building candidate DMCs. It then selects DMCs with the highest specificity stability, meeting user-defined thresholds for exclusive character states. If multiple optimal DMCs are identified, UITOTO derives a majority-consensus DMC. To verify whether the newly generated DMCs are contrastive, UITOTO includes a validation module that tests DMCs against database sequences, efficiently handling up to hundreds of thousands of aligned or unaligned sequences. In this manuscript we propose and assess UITOTOs performance with DMCs obtained from other software (e.g., MOLD) for three large empirical datasets: i) Megaselia (Diptera: Phoridae: 69 species, 2,229 training and 30,289 testing barcodes); ii) Mycetophilidae, (Diptera: 118 species, 1,456 training and 60,349 testing barcodes); and iii) European Lepidoptera (49 species, 591 training and 21,483 testing barcodes). Based on several classification metrics (e.g., Accuracy, F1 Score), UITOTOs DMCs outcompete DMCs obtained with other software. We furthermore provide guidelines for generating molecular diagnoses and facilitate obtaining DMCs by providing a user-friendly Shiny App GUI and a module for obtaining publication-quality DMC visualizations in RStudio. Overall, our study confirms that the biggest challenge for generating molecular and morphological diagnoses is similar, i.e., balancing specificity and length. Short diagnoses often lack specificity, while excessively long DMCs are often so specific that they do not accommodate intraspecific variation.

bioinformatics↗

Urban crops demonstrate comparable potential for organic carbon storage as natural ecosystems.

Urban greenspaces, encompassing parks, golf courses, roundabouts, and urban crops, have potential to offset urban carbon footprints by storing soil organic carbon (SOC). This study analyzed particulate organic carbon (POC) and mineral-associated organic carbon (MAOC) stocks in topsoil across 27 Iberian cities, comparing urban greenspaces with natural ecosystems under varying climatic and edaphic conditions. Results revealed that urban greenspaces store comparable SOC stocks to natural ecosystems, with MAOC stocks being more dominant and stable across land-use types. POC stocks showed variability, particularly lower in roundabouts and parks compared to natural ecosystems, but remained similar in golf courses and urban crops. SOC fractions correlated inversely with mean annual temperature (MAT), emphasizing the need for cooling strategies in urban areas to preserve stable carbon pools. While MAOC exhibited saturation at higher SOC levels, POC showed a linear increase. This study highlights the importance of tailored management practices to enhance carbon storage in urban soils for climate change mitigation.

biochemistry↗

TILLCANN: A TILLING platform in Cannabis sativa for mutation discovery and crop improvement

Cultivation of Cannabis sativa is increasing because of its therapeutic value and recognition as a multi-purpose and sustainable crop. Targeting Induced Local Lesions in Genomes (TILLING) is a versatile reverse genetics approach that unlocks induced variation through mutagenesis to accelerate the development of new cultivars and contribute to the functional validation of genes. Increasingly efficient next-generation sequencing technologies and genomic resources have combined to make TILLING by sequencing (TbyS) an attractive technique that can be applied in cannabis. Here we describe the development of a mutagenesis protocol for C. sativa and the development of the TILLCANN platform composed of 1,633 M2 families. As a demonstration of the functionality of the platform, we used TbyS to perform a high throughput screening of novel mutations in amplicons for genes associated with important agronomic and biochemical traits in a set of 512 M2 families. We confirmed 14 of the identified mutations and calculated an average mutation frequency range of 1/263 to 1/320 kb. We found that heterozygous mutants in the cannabis homologue of Class II TEOSINTE BRANCHED 1/CYCLOIDEA/PCF (TCP4) are linked to alterations in leaf number and morphology. We expect that the novel genetic variability unlocked in the TILLCANN platform for performing forward or reverse genetic screens can significantly boost breeding programs geared toward both medicinal cannabis and industrial hemp. Gene & accession numbersRaw sequencing data generated in this study was deposited at the European Nucleotide Archive with accession numbers xxx and xxx. Genes and accession numbers discussed within this manuscript correspond to the Cannabis sativa cs10 genome assembly deposited in National Center for Biotechnology Information with accession number GCA_900626175.2.

plant biology↗

Serum metabolomics signatures after an acute bout of combined traditional or high-intensity tactical training in young males and females

Exercise is a multipotent stimulus that results in large-scale dynamic changes to the systemic molecular profile. Alternative exercise prescriptions and doses would be expected to result in distinct signatures due to differences in duration and intensity. We tested two novel combined endurance and resistance exercise regimens to better understand how differing prescriptions alter the acute metabolomics response at multiple timepoints up to 24h post-exercise. Serum metabolomics for n=37 untrained individuals was analyzed for participants completing traditional combined exercise [TRAD; n = 20 (11M/9F)] or high-intensity tactical training [HITT; n= 17 (8M/9F)] before exercise (pre), and immediately (h0), 3 and 24 h post-exercise (h3 and h24, respectively). We found minimal metabolites had a group by time interaction (2 with FDR < 0.10; 31 with nominal p < 0.05;), but both stimuli resulted in large-scale within-group changes to the circulating metabolome. TRAD consistently had greater numbers of differentially abundant metabolites (FDR < 0.10) as compared to HITT at h0 (431 vs. 333), h3 (435 vs. 331) and h24 (168 vs. 76). The major metabolite classes altered were related to key energy substrates for both groups at h0 (e.g., glucose, pyruvate) and energy replenishment for h3 and h24 (e.g., 12,13 diHOME, palmitoylcarnitine, free fatty acids). In summary, our data are the first to describe the acute changes in the circulating metabolome following combined endurance and resistance exercise. Additionally, we show the two distinct doses of combined exercise led to generally similar patterns of responses, with the longer duration TRAD dose resulting in a higher magnitude of change.

physiology↗

Liquid-like condensates that bind actin can polymerize and bundle actin filaments

Liquid-like protein condensates perform diverse physiological functions. Previous work showed that VASP, a processive actin polymerase, forms condensates that polymerize and bundle actin. To minimize their curvature, filaments accumulated at the inner condensate surface, ultimately deforming the condensate into a rod-like shape, filled with a bundle of parallel filaments. Here we show that this behavior does not require proteins with specific polymerase activity. Specifically, we found that condensates composed of Lamellipodin, a protein that binds actin but is not an actin polymerase, were also capable of polymerizing and bundling actin filaments. To probe the minimum requirements for condensate-mediated actin bundling, we developed an agent-based computational model. Guided by its predictions, we hypothesized that any condensate-forming protein that binds actin could bundle filaments through multivalent crosslinking. To test this idea, we added an actin-binding motif to Eps15, a condensate-forming protein that does not normally bind actin. The resulting chimera formed condensates that drove efficient actin polymerization and bundling. Collectively, these findings broaden the family of proteins that could organize cytoskeletal filaments to include any actin-binding protein that participates in protein condensation.

biophysics↗

Differential Expression Analysis of Cannabis sativa response to thermotherapy of Hops Latent Viroid (HLVd) infection and clearance of the viroid in Tissue Culture Micropropagation

Increased farming and cultivation of Cannabis sativa is rapidly pushing Cannabis (Cannabis sativa L.) towards becoming a commercial agricultural commodity. Large-scale cultivation facilities maintain thousands of clonal varieties of recreational and medicinal cannabis and there is a strong market-driven motivation to maintain a commercial pipeline of clean healthy vigorously growing plants free of pathogens. However, mass production and high-capacity cultivation create an environment that is susceptible to highly transmissible pathogens and infectious entities such as Hop Latent Viroid (HLVd). From nurseries to cultivation facilities, its become increasingly important to maintain a routine testing regimen and ensure cultivation facilities are HLVd-free environments. One method to address the problem of infected plants is to perform thermotherapy on C. sativa explants under tissue culture conditions and isolate clean tissue to multiply productive and healthy mature plants. We carried out a novel thermotherapy method using tissue culture in 5 varieties of type III cannabis that were HLVd positive to document the degree of success of the treatment at the RNA level. We observed that following thermotherapy treatment we were able to decrease the level of HLVd positive tests in select varieties and observed some varieties were highly susceptible and unable to clear the viroid. Plants were tested using a one-step RT-qPCR method, developed and validated, in part, along with this work, and present the results as well as an exploratory transcriptome analysis of an internally developed variety, AnnaLee, which tested negative for HLVd following thermotherapy treatment, and explore possible genes of interest for viroid infection, clearance, and mitigation. Author SummaryRT-qPCR and transcriptome analysis of Hops latent viroid (HLVd) in infected and non-infected Cannabis varieties. A thermotherapy procedure was conducted on HLVd infected Cannabis sativa meristem tissue maintained through tissue culture micropropagation techniques. Total RNA was isolated from the cultured plantlet stocks and evaluated by a real-time reverse transcriptase assay for HLVd. Infection status post thermotherapy was assessed, and viroid-free plants were maintained and subsequently tested. A single thermotherapy-treated cultivar, Anna Lee was selected for transcriptomics, and an analysis of the genes that were differentially regulated in infected and non-infected treated plants is discussed.

plant biology↗

Chitosan induces salicylic acid local and systemically in banana plants and reduces colonization by the pathogen Fusarium oxysporum f. sp. cubense TR4

Banana (Musa spp.) is essential for food security. For its clonality is highly susceptible to pests and diseases. The wilt fungus Fusarium oxysporum f. sp. cubense Tropical Race 4 (FocTR4) threatens banana production worldwide. We notice that chitosan protects banana from biotic stress. Chitosan, a plant defence elicitor with antimicrobial activity, triggers salicylic acid (SA) and methyl salicylate biosynthesis and induces systemic acquired resistance (SAR) genes, mainly flavin-dependent monooxygenase 1 (FMO1), in banana. Chitosan promotes root exudation of SA and emission of methyl salicylate (MeSA). Banana germplasm, Petit Naine, Gros Michel, Enzirabahima, Yangambi Km5 and Foconah banana differ in their response to chitosan. Chitosan induces, in Foc resistant Yangambi Km5, ca. 7-fold FMO1. Preventive chitosan treatments together with the endophytic biocontrol fungus Pochonia chlamydosporia strain 123 reduce (ca. 4-fold) colonization of banana roots by FocTR4. Therefore, chitosan and beneficial endophytes can help to manage sustainably FocTR4 in banana.

plant biology↗

Mining threats in high-level biodiversity conservation policies

Amid a global infrastructure boom, there is increasing recognition of the ecological impacts of the extraction and consumption of construction minerals, mainly as concrete. Recent research highlights the significant and expanding threat these minerals pose to global biodiversity. To what extent is this pressure acknowledged in biodiversity conservation policy? We investigate how high-level national and international biodiversity conservation policies, including the 2011-2020 and post-2020 biodiversity strategies, the national biodiversity strategies and action plans, and the assessments of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, address mining threats with a special focus on construction minerals. We find that mining appears rarely in national targets, but more frequently in national strategies with greater coverage of aggregates mining than limestone mining, yet it is dealt with superficially in most countries. We then outline an 8-point strategy to reduce the biodiversity impacts of construction minerals, which comprises actions such as targeting, reporting, and monitoring systems, the evidence-base around mining impacts on biodiversity, and the behavior of financial agents and businesses. Implementing these measures can pave the way for a more sustainable approach to construction mineral use and safeguard biodiversity.

ecology↗

The FMRF-NH2 Gated Sodium Channel of Biomphalaria glabrata: Localization and Expression Following Infection by Schistosoma mansoni

The neglected tropical disease schistosomiasis impacts the lives of over 700 million people globally. Schistosoma mansoni, the trematode parasite that causes the most common type of schistosomiasis, requires planorbid pond snails of the genus Biomphalaria to support its larval development and transformation to the form that can infect humans. A greater understanding of neural signaling systems that are specific to the Biomphalaria intermediate host could lead to novel strategies for parasite or snail control. This study characterized a Biomphalaria glabrata neural receptor that is gated by the molluscan neuropeptide FMRF-NH2. The Biomphalaria glabrata FMRF-NH2 gated sodium channel (Bgl-FaNaC) amino acid sequence was highly conserved with FaNaCs found in related gastropods, especially the planorbid Planorbella trivolvis (91% sequence identity). In common with the P. trivolvis FaNaC, the B. glabrata receptor exhibited a low affinity (EC50: 3 x 10-4 M) and high specificity for the FMRF-NH2 agonist. Its expression in the central nervous system, detected by immunohistochemistry and in situ hybridization, was widespread, with the protein localized mainly to neuronal fibers and the mRNA confined to cell bodies. Colocalization was observed with the FMRF-NH2 tetrapeptide precursor in some neurons associated with male mating behavior. At the mRNA level, Bgl-FaNaC expression in the visceral and left parietal ganglia decreased at 20 days post infection by S. mansoni and in the shedding phase. Altered FMRF-NH2 signaling could be vital for parasite survival and proliferation in its snail intermediate host.

neuroscience↗

Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

The application of B-cell epitope identification for the development of therapeutic antibodies is well established but consuming in terms of time and resources. For this reason, in the last few years, the immunoinformatic community has developed several computational predictive tools. While relatively successful, most of these tools only use a few properties of the candidate region to determine their likelihood of being a true B-cell epitope. However, this likelihood is influenced by a wide variety of protein features, including the presence of glycosylated residues in the neighbourhood of the candidate epitope, the subcellular location of the protein region or the three-dimensional information about their surface accessibility in the parental protein. In this study we created Brewpitopes, an integrative pipeline to curate computational predictions of B-cell epitopes by accounting for all the aforementioned features. To this end, we implemented a set of rational filters to mimic the conditions for the in vivo antibody recognition to enrich the B-cell epitope predictions in actionable candidates. To validate Brewpitopes, we analyzed the SARS-CoV-2 proteome. In the S protein, Brewpitopes enriched the initial predictions in 5-fold on epitopes with neutralizing potential (p-value < 2e-4). Other than S protein, 4 out of 16 proteins in the proteome contain curated B-cell epitopes and hence, have also potential interest for viral neutralization, since mutational escape mainly affects the S protein. Our results demonstrate that Brewpitopes is a powerful pipeline for the rapid prediction of refined B-cell epitopes during public health emergencies. Statement of significanceWe have created Brewpitopes, a new pipeline that integrates additional important features such as glycosylation or structural accessibility, to curate B-cell epitope more likely to be functional in vivo. We have also validated Brewpitopes against SARS-CoV-2 not only for S protein but also for the entire viral proteome demonstrating that is a rapid and reliable epitope predictive tool to be implemented in present or future public health emergencies. Brewpitopes has identified 7 SARS-CoV-2 epitopes in S and epitopes allocated in 4 other proteins. Overall, offering an accurate selection of epitopes that might be scaled up to the production of new antibodies.

bioinformatics↗

Evolution, Expansion and Characterization of Cannabinoid Synthase Gene Family in Cannabis Sativa

We are working toward a complete functional and genomic characterization of the cannabinoid synthase family in Cannabis (itself part of the larger Berberine Bridge Enzyme family). This clade, which is unique to Cannabis, includes four main subclades that appear to have arisen by a series of gene duplications. We have functionally characterized three cannabinoid synthases, in addition to the three already characterized, so that now all four subclades contain at least one characterized enzyme. The previously uncharacterized Clade C enzymes have relatively low activity and produce CBCA as their primary product. In addition, we report genomic characterization to better understand the structure and high level of copy number variation in this family. We report a pattern of shared regions immediately upstream of the cannabinoid synthase genes that suggests a specific sequence of breakpoints, and hence gene duplication events. We present a model of gene family expansion to account for the observed data, along with evidence that this expansion occurred under selective pressure. This work adds to our understanding of both the high level of variability in this family and the origin of THCA in type III plants lacking a functional THCAS gene.

genomics↗

Epigenetic alterations in gut and brain of adult rats after oral administration of miR-320-3p and miR-375-3p at mid-lactation, and preventive potential of miR-320-3p on early weaning stress.

AimTo investigate if the artificial delivery of microRNAs naturally present in the breastmilk can impact the gut and brain of young rats according to weaning. MethodsAnimals from a new transgenic rat line expressing green-fluorescent protein in the endocrine lineage (cholecystokinin expressing cells) received at Day-12, near neural diversification, a single oral bolus of mir-320-3p or miR-375-3p, embedded in DiOleyl-Succinyl-Paromomycin (DOSP), and were further early (Day-15) or regularly (Day-30) weaned. Relevant miRNA (miR-320-3p, miR-375-3p, miR-375-5p, miR-16-5p, miR-132-3p, miR-504), polr3d, hspb6, inflammation, enteroendocrine, and circadian clock-related mRNAs, chromatin complexes, and duodenal cell density were assayed at 8h post-inoculation and at Day-45. ResultsThe miR-320-3p/DOSP induced immediate effects on H3K4me3 chromatin complexes with polr3d promoter (p<0.05) but no long-term effects. On regular weaning, at Day-45, both miR-320-3p and 375-3p were down-regulated in the stomach, up-regulated in the hypothalamus (p<0.001) but only miR-320-3p was up-regulated in the duodenum. After early weaning, the miR-320-3p and miR-375-3p levels were down-regulated in the stomach and the duodenum, but up-regulated in the hypothalamus and the hippocampus. Combining miR-320-3p/DOSP with early weaning enhanced miR-320-3p and chromogranin A expression in the duodenum. In the hippocampus, the miR-504 was down-regulated for both sexes, but in the brain stem, up regulated only for females, along with miR-320-3p and miR-16-5p levels. In the hypothalamus, clock levels were up regulated for both sexes. In the miR-375-3p/DOSP group, the density of enteroendocrine duodenal cells increased. The long-term effect of miR-375-3p/DOSP was more limited, according to the fourfold lower number of predicted targets than with miR-320-3p. ConclusionAddressing oral miRNA-320-3p loads to duodenal cell lineage is paving the way for the design of new therapeutics, manipulating long term consequences of early life stress.

genetics↗