Biology subjects

Herrera, C.

Publications and source records attributed to Herrera, C..

18 recordsLinked to original sources

bioRxiv2026

Pannexin 1 inhibition reduces tumorigenic properties of patient-derived glioblastoma cells through the HIPPO and Wnt signalling pathways

Glioblastoma (GBM) is the most common primary brain tumour, with a median survival of 12-18 months, highlighting a need for new treatment targets. We observed that pannexin 1 (PANX1), a channel-forming glycoprotein important in purinergic signalling, is upregulated in GBM compared to normal tissue and expressed throughout patient tumours. Western blot analysis of patient-derived GBM cell lines revealed significantly increased PANX1 expression in these primary lines compared to brain tissue and control glial cells. Bulk RNA-sequencing compared the gene expression of GBM cells devoid of PANX1 via CRISPR/Cas9 deletion (PANX1-KO) compared to controls. Gene Ontology and KEGG gene set analyses revealed PANX1-KO in GBM cells affects cell surface and cell junction components, processes, and pathways, including the HIPPO pathway, in addition to critically downregulating {beta}-catenin mRNA and other components of the Wnt pathway. The deletion of PANX1 resulted in a disruption of the {beta}-catenin protein and a dramatic reduction in migration and cell growth. Pharmacological inhibition of PANX1 in GBM cells with Probenecid (PBN) and Spironolactone (SPIR) demonstrated a significant reduction in live cell numbers and migration via scratch assay. Both blockers dramatically decreased F-actin filament formation, and the cellular localization of beta-catenin became more intracellular compared to controls. Xenografted GBM tumours showed a reduction in tumour cell viability by bioluminescent imaging and reduced hemorrhaging incidence when treated with PBN. These new insights support further investigation of PANX1 as a potential GBM therapeutic target and its role in multiple cancer signaling pathways that regulate this devastating disease.

cancer biology↗

bioRxiv2026

A Portable Fluorescence Platform for Decentralized One-Health mcr-1 Monitoring

Antimicrobial resistance (AMR) represents a major global health threat, with plasmid-borne mcr genes driving colistin resistance and exposing critical gaps in One-Health surveillance across human, animal, and environmental reservoirs. The most prevalent variant, mcr-1, remains difficult to monitor in resource-limited settings due to the lack of rapid, affordable, and field-deployable molecular tools. Here, we developed C12amcr, an integrated molecular toolbox that combines pre-amplification PCR with a fluorescent CRISPR-Cas12a assay targeting a conserved region of mcr-1 and a custom low-cost, hand-held 3D-printed portable fluorometer. Under optimized conditions, the assay achieved a limit of detection of 630 cells/mL. In poultry feces spiked with mcr-1-positive E. coli, C12amcr detected as few as 1,800 cells/mL. When tested on 22 community-derived E. coli isolates, the assay showed 100% concordance with both next-generation sequencing for mcr-1 detection and phenotypic colistin susceptibility testing by broth microdilution. The accompanying portable fluorometer performed equivalently to a laboratory microplate reader while enabling fully decentralized workflows compatible with portable PCR platforms. By integrating locally produced molecular reagents, straightforward protocols, and an accessible field-ready fluorescence reader, C12amcr overcomes key barriers to decentralized AMR surveillance and provides a practical, scalable solution for One-Health monitoring in resource-limited settings.

molecular biology↗

bioRxiv2026

Transgenerational imprint of subindividual variation: somatic epigenetic divergence within trees cascades into epigenetic and phenotypic pollen divergence

The evolutionary significance of somatic mosaicism created within plants by random epigenetic drift or localized responses to the environment will rest on its transgenerational implications. This paper tests whether the epigenetic mosaicism exhibited by individuals of a long-lived tree leaves some discernible "imprint" in the next gametophytic generation. Paired samples of leaves and pollen from five distinct branches within each of five wild-growing Pistacia terebinthus (Anacardiaceae) trees were characterized epigenetically using genome-wide DNA cytosine methylation level and multivariate epigenetic fingerprinting. Pollen grains were also characterized phenotypically by size and shape. Individual trees were somatically heterogeneous with regard to both cytosine methylation level and multilocus epigenetic fingerprints of leaf tissue, and within-tree variance in leaf epigenetic features exceeded among-tree variance. Phenotypic and epigenetic features of pollen differed significantly among branches of individual trees, and intraplant variation in phenotype and epigenetic fingerprints of pollen was predicted by intraplant variation in epigenetic features of leaves. Results provide evidence that intraindividual epigenetic heterogeneity arising in long-lived plants can leave its imprint into subsequent sporophyte generations via the production of epigenetically and phenotypically heterogeneous haploid gametophytes. Testable hypotheses for future epigenetic research on wild populations of non-model plants are suggested.

Plant Biology↗

bioRxiv2025

A novel post-translational modification of fimbriae drives pathogenicity in Klebsiella pneumoniae

Multi-drug resistant Gram-negative bacteria, including carbapenem-resistant Klebsiella pneumoniae (CRKp), are a public health emergency. The predominant CRKp sequence type worldwide is ST258. However, the factors underlying ST258s epidemic success are not well defined. The understudied two-component system CrrAB is a genomic feature of ST258 and has been hypothesized to contribute to its global dominance. Despite this, the molecular details underpinning CrrABs contribution to ST258 pathogenicity are not well understood. We used RNA-sequencing to identify the regulon of CrrA and found that CrrAB induces the expression of a novel gene, encoding Crr-regulated fimbriae modifying protein (CfmP). CfmP post-translationally modifies fimbriae to significantly increase host cell adhesion and high bacterial loads within the host, consequently increasing ST258 virulence. CrrAB also drives high antibiotic resistance in CRKp. Thus, our data places CrrAB at the intersection of virulence and antibiotic resistance supporting its function as an important regulatory system driving the pathogenicity of ST258.

microbiology↗

bioRxiv2025

Shedding light on day-night habitat use of oyster reefs by fish

Oyster reefs provide key ecosystem functions, including the provision of habitat for fish. While their importance in supporting fish assemblages is widely accepted, an assessment of intertidal oyster reefs at night remains a knowledge gap. Documenting habitat use at night could reveal new species reliant on these systems and help uncover diel fish movements among structured and unstructured habitats. We hypothesise that habitat use will interact with time and habitat, whereby differences in fish assemblages between oyster reef and unstructured habitats would be greater during the day. In this study, we used infrared-capable remote underwater video stations (RUVS) to sample paired intertidal oyster reefs and unstructured habitat during day and night. Assemblages using these habitats during the day do not match those at night, consistent with diel shifts observed in similar habitats. Consistent with our hypothesis, during the day oyster reefs had higher diversity and richness than unstructured habitat, whereas both habitats had low diversity and richness at night. The high relative abundance of piscivores in oyster reefs during the day suggests reefs create food webs that extend beyond benthic matter and sustain higher trophic levels. Nighttime abundances and diversity in oyster reefs dropped to levels similar to those of unstructured habitats during the day and night, likely a product of temporal niche partitioning and dynamic predation risks. Nighttime studies were important in documenting a wider suite of species and can thus provide a more complete understanding of fish-habitat interactions. Furthermore, this study used novel methods that enabled depth and size estimation from a single camera unit. While still in its infancy, this can serve as a force multiplier in monitoring intertidal habitats and lead towards a cost-effective method for standardising day/night abundance measurements and obtaining fish size estimates.

ecology↗

bioRxiv2025

Impaired envelope integrity in the absence of SanA is linked to increased Lipid II availability and an imbalance of FtsI and FtsW activities

In Gram-negative bacteria, the outer membrane (OM) acts in conjunction with the peptidoglycan (PG) cell wall as a barrier against physical, osmotic, and chemical environmental stressors including antibiotics. SanA, an inner membrane protein in Escherichia coli K-12, is required for vancomycin resistance at high temperatures (>42 {degrees}C) and impacts sodium dodecyl sulfate (SDS) resistance during stationary phase reached from carbon limitation. However, its function remains unknown. Here, we show that {Delta}sanA has a synthetic genetic interaction with {Delta}wecA, a mutation that increases the availability of the isoprenoid carrier for PG synthesis. Specifically, the {Delta}sanA {Delta}wecA strain demonstrated heightened SDS-EDTA sensitivity, activation of the Rcs stress response, and increased cell length. Further investigation tied the SDS-EDTA sensitivity to increased lipid II available for PG synthesis. Spontaneous suppressor mutants of this phenotype harbored point mutations in prc, which encodes tail specific protease, or ftsI, which encodes the cell division DD-transpeptidase, a target of Prc. We focused on the ftsI mutations and demonstrated that the ftsI mutations had increased cell length but nevertheless enhanced PG incorporation at the septum compared to the {Delta}sanA mutant, returning PG incorporation to wild-type levels. Moreover, other mutations affecting septal PG synthesis, but not divisome assembly, also suppressed the SDS-EDTA sensitivity. These findings suggest that, in the absence of SanA, increased lipid II availability perturbs the balance between septal PG synthesis, lateral PG elongation, and other envelope biogenesis pathways, which leads to increased OM permeability. IMPORTANCEThe Gram-negative cell envelope is a barrier that protects the cell from environmental stress. Therefore, the synthesis of each layer of this envelope needs to be closely coordinated throughout growth and division. Here, we investigated SanA, a protein in Escherichia coli K-12 that affects envelope permeability under cellular stress, including nutrient limitation and high temperature. We found that SanA plays a key role in maintaining the permeability barrier when precursor levels for peptidoglycan (PG) synthesis are elevated, linking envelope integrity to balanced septal PG production during cell division. Our results suggest that SanA modulates substrate availability to preserve envelope function, and that in its absence, imbalanced substrate flux to septal PG synthesis disrupts septum formation and compromises barrier integrity.

microbiology↗

bioRxiv2025

Randomized field trial of a therapeutic vaccine against Trypanosoma cruzi natural infection in dogs and correlates for efficacy

Background and AimsChagas disease, caused by Trypanosoma cruzi, is a vector-borne parasitic disease, with dogs acting as a major domestic host of the parasite. An immunotherapeutic vaccine would be an excellent tool to treat infections and prevent chronic cardiac disease in this host. Building on previous pre-clinical studies, we performed here the first randomized field trial of a vaccine against T. cruzi among client-owned dogs with natural infections. MethodsA total of 31 dogs with T. cruzi infection with diverse parasite strains were enrolled and received three doses of a vaccine composed of Tc24-C4 and TSA1-C4 recombinant proteins with MPLA (N=16) or saline control (N=15) and followed for up to six months to assess efficacy. ResultsBlood parasite burden and electrocardiographic (ECG) recordings as primary outcomes showed that therapeutic vaccination led to a significant decrease in parasite burden, prevented/stopped cardiac alterations and was safe. This clinical benefit was mediated by major changes in T cell activation and T cell receptor (TCR) repertoire, while antibody responses were minimally affected. In addition, vaccination also reprogrammed the ongoing trained immunity to reduce inflammation, suggesting a complex interplay between innate and T cells in its mechanism of action. ConclusionsThese results provide a strong support for the further development of a veterinary vaccine based on these antigens as well as a human therapeutic vaccine to prevent the progression of chronic cardiac disease from T. cruzi infection. Structured graphical abstractO_ST_ABSKey questionC_ST_ABSCan an immunotherapeutic vaccine against Trypanosoma cruzi control an ongoing infection and prevent the progression of chronic cardiac disease in naturally infected dogs? Key findingTherapeutic vaccination of chronically infected dogs led to a reduced blood parasite burden and prevented the progression of chronic cardiac disease (Primary outcomes). Correlates of vaccine efficacy included major changes in T cell repertoire/activation and changes in innate immunity to reduce inflammation. Take home messageImmunotherapeutic vaccination of dogs with natural infection with T. cruzi was safe and effective to control an ongoing infection with a broad diversity of parasite strains and prevented the progression of chronic cardiac disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/653529v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@17ce572org.highwire.dtl.DTLVardef@bba649org.highwire.dtl.DTLVardef@1a20405org.highwire.dtl.DTLVardef@1b61c7e_HPS_FORMAT_FIGEXP M_FIG C_FIG Translational perspectiveCurrent drug treatments for Chagas disease have major limitations due to significant adverse effects and a limited efficacy as chronic cardiac disease develops. A veterinary vaccine for dogs, a major domestic host of the parasite, would help reduce domestic transmission and improve dog health, as well as provide support for the development of a human immunotherapeutic vaccine to prevent the progression of chronic Chagasic cardiomyopathy.

microbiology↗

bioRxiv2024

The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners

Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections in the US and of preventable blindness worldwide. This obligate intracellular pathogen replicates within a membrane-bound inclusion, but how it acquires nutrients from the host while avoiding detection by the innate immune system is incompletely understood. C. trachomatis accomplishes this in part through the translocation of a unique set of effectors into the inclusion membrane, the inclusion membrane proteins (Incs). Incs are ideally positioned at the host-pathogen interface to reprogram host signaling by redirecting proteins or organelles to the inclusion. Using a combination of co-affinity purification, immunofluorescence confocal imaging, and proteomics, we characterize the interaction between an early-expressed Inc of unknown function, Tri1, and tumor necrosis factor receptor associated factor 7 (TRAF7). TRAF7 is a multi-domain protein with a RING finger ubiquitin ligase domain and a C-terminal WD40 domain. TRAF7 regulates several innate immune signaling pathways associated with C. trachomatis infection and is mutated in a subset of tumors. We demonstrate that Tri1 and TRAF7 specifically interact during infection and that TRAF7 is recruited to the inclusion. We further show that the predicted coiled-coil domain of Tri1 is necessary to interact with the TRAF7 WD40 domain. Finally, we demonstrate that Tri1 displaces the native TRAF7 binding partners, mitogen activated protein kinase kinase kinase 2 (MEKK2) and MEKK3. Together, our results suggest that by displacing TRAF7 native binding partners, Tri1 has the capacity to alter TRAF7 signaling during C. trachomatis infection. ImportanceChlamydia trachomatis is the leading cause of bacterial sexually transmitted infections in the US and preventable blindness worldwide. Although easily treated with antibiotics, the vast majority of infections are asymptomatic and therefore go untreated, leading to infertility and blindness. This obligate intracellular pathogen evades the immune response, which contributes to these outcomes. Here, we characterize the interaction between a C. trachomatis secreted effector, Tri1, and a host protein involved in innate immune signaling, TRAF7. We identified host proteins that bind to TRAF7 and demonstrate that Tri1 can displace these proteins upon binding to TRAF7. Remarkably, the region of TRAF7 to which these host proteins bind is often mutated in a subset of human tumors. Our work suggests a mechanism by which Tri1 may alter TRAF7 signaling and has implications not only in the pathogenesis of C. trachomatis infections, but also in understanding the role of TRAF7 in cancer.

microbiology↗

bioRxiv2024

First-in-class Transactivator-Free, Doxycycline-inducible IL-18-engineered CAR-T cells for relapsed/refractory B-cell lymphomas

BackgroundDespite their success treating type B cancers, Chimeric Antigen Receptor (CAR) T cells still showed limited efficacy in certain lymphomas and solid tumors. Reinforcing conventional CAR-T cells to release cytokines can improve their efficacy but also increase safety concerns. Several strategies have been developed to regulate their secretion using minimal promoters that are controlled by chimeric proteins harboring transactivators. However, these chimeric proteins can disrupt the normal physiology of target cells. MethodsCo-transduction with CAR19 and Lent-On-Plus-IL-18 LVs allowed for generating constitutive CAR/Dox-inducible IL-18 CAR-T cells that respond to ultra-low doses of doxycycline (iTRUCK19.18). iTRUCK19.18 were evaluated against an aggressive Burkitt lymphoma model in vitro and in vivo, against primary B-cell tumors and against a CD19-engineered pancreatic tumor model. Patient-derived iTRUCK19.18 cells were also generated. ResultsiTRUCK19.18 controlled IL-18 release through a dual mechanism dependent on doxycycline and T cell activation, thereby enhancing the safety profile. IL-18 release increased the activation state/proinflammatory profile of T cells in a doxycycline-dependent manner without altering cellular fitness, which was translated into an increased CAR-T cell antitumor activity against aggressive hematologic and solid tumor models. In a clinically relevant context, we generated patient-derived iTRUCK19.18 cells able to significantly increase elimination of primary B cells tumors under doxycycline. Furthermore, IL-18-releasing iTRUCK19.18 polarized pro-tumoral M2 macrophages towards an antitumoral phenotype (M1), suggesting the ability to modulate the tumor microenvironment. ConclusionWe have generated the first transactivator-free inducible TRUCKs from healthy donors and B-cell neoplasms patients. iTRUCK19-18 exhibit dual safety control mechanisms for IL-18 secretion and improved antitumoral activity against type-B neoplasms. Inducible IL-18 secretion not only enhanced T cell potency but could also change the tumor microenvironment to a more antitumoral state.

immunology↗

bioRxiv2023

Proteomics analysis reveals a role for E. coli polyphosphate kinase in membrane structure and polymyxin resistance during starvation

Polyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. In Escherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP ({Delta}ppk) during starvation to identify novel pathways regulated by PPK. In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and {Delta}ppk mutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, while{Delta} ppk mutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks. From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in {Delta}ppk mutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in {Delta}ppk cells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that {Delta}ppk mutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss of ppk restores polymyxin sensitivity in resistant strains carrying a constitutively active basR allele. Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.

molecular biology↗

bioRxiv2022

Bacterial Microbiome of Foreskin Tissue: Impact of Short-course PrEP and Host Inflammation

As part of the CHAPS randomized clinical trial, we sequenced a segment of the bacterial 16S rRNA gene from foreskin tissue of 144 adolescents from South Africa and Uganda collected during surgical penile circumcision after receipt of 1 to 2 doses of placebo, emtricitabine with tenofovir disoproxil fumarate, or emtricitabine with tenofovir alafenamide. We found a large proportion of Corynebacterium in addition to other anaerobic species. Cutibacterium acnes was more abundant among participants from South Africa than Uganda, though this made no difference in surgical recovery. We did not find a difference in bacterial populations by treatment received nor bacterial taxa that were differentially abundant between participants who received placebo versus active drug. Using RNAseq libraries from foreskin tissue of the same participants, we found negative correlations between the relative abundance of bacterial taxa and the expression of genes downstream of the innate response to bacteria and regulation of the inflammatory response. When participants were divided into clusters based on bacterial community composition, two main clusters emerged which were distinguished by high and low bacterial diversity. Random forest classification showed higher expression of NFATC3 and SELENOS and lower expression of STAP1 and NLRP6 in the higher diversity group compared to the lower. Our results show no difference in the tissue microbiome of the foreskin with short-course PrEP but that bacterial taxa were largely inversely correlated with gene expression, consistent with non-inflammatory colonization. Author SummaryWe investigated the bacterial community of the foreskin of the penis. Previous studies found increased inflammation with certain anaerobic bacteria from swabs taken under the foreskin, but we found that higher relative abundances of the bacteria were correlated with lower expression of inflammatory genes. We did not find different bacteria in participants who received medicine to prevent HIV. Understanding the relationship between bacteria and inflammation in the penis will help us to understand how interventions like penile circumcision reduce the risk of acquiring sexually transmitted infections such as HIV.

microbiology↗

bioRxiv2022

The coupling between healthspan and lifespan in Caenorhabditis depends on complex interactions between compound intervention and genetic background

Aging is characterized by declining health that results in decreased neuromuscular function and cellular resilience. The relationship between lifespan and health, and the influence of genetic background on that relationship, has important implications in the development of anti-aging interventions. Here we combined survival under thermal and oxidative stress with swimming performance, to evaluate health effects across a nematode genetic diversity panel for three compounds previously studied in the Caenorhabditis Intervention Testing Program - NP1, propyl gallate, and resveratrol. We show that oxidative stress resistance and thermotolerance vary with compound intervention, genetic background, and age. The effects of tested compounds on swimming locomotion, in contrast, are largely species-specific. Additionally, thermotolerance, but not oxidative stress or swimming ability, correlates with lifespan. Our results demonstrate the importance of assessing health and lifespan across genetic backgrounds in the effort to identify reproducible aging interventions.

physiology↗

bioRxiv2021

Bovine pangenome reveals trait-associated structural variation from diverse assembly inputs

Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. We generated haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified 90 thousand structural variants including 931 overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.

genomics↗

bioRxiv2021

NMR spectroscopy of a single mammalian embryo

The resolving power, chemical sensitivity and non-invasive nature of NMR has made it an established technique for in vivo studies of large organisms both for research and clinical applications. These features would clearly be beneficial at the nanoliter scale (nL), typical of early development of mammalian embryos, microtissues and organoids, the scale where the building blocks of complex organisms could be observed. However, the handling of such small samples (about 100 micrometers) and sensitivity issues have prevented the widespread adoption of NMR. Recently we have shown how these limitations can be overcome with ultra-compact single-chip probes. In this article we show that such probes have sufficient sensitivity to detect and resolve NMR signals from individual bovine pre-implantation embryos. In less than 1 hour these spherical samples of just 130-190 micrometers produce distinct spectral peaks, largely originating from lipids contained inside them. We further observe how the spectral features, namely the peak intensities, vary from one sample to another despite their optical and morphological similarities.

biochemistry↗

bioRxiv2021

HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells

Human immunodeficiency virus type 1 (HIV-1) replicates in CD4+ T cells leading to profound T cell loss, immunological dysfunction and AIDS. Determining how HIV-1 shapes the immunological niche in which it resides to create a permissive environment is central to informing efforts to limit pathogenesis, disturb viral reservoirs and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate CD4+ T cells in vitro in order to make them permissive to infection. This dramatically alters T cell biology, obscuring native virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient and productive infection of resting CD4+ T cells without the need for prior activation. Infection is preferential for resting memory T cells, is observed with both CXCR4-tropic virus and CCR5-tropic transmitter-founder viruses and results in virus production and onward spreading infection. Strikingly, we find that HIV-1 infection of resting memory CD4+ T cells primes for induction of a tissue-resident memory (TRM)-like phenotype evidenced by upregulation of TRM markers CD69/CXCR6 alongside co-expression of CD49a, PD-1, CD101 as well as transcription factor Blimp-1. Furthermore, we reveal that HIV-1 initiates a transcriptional program that overlaps with the core TRM transcriptional signature. This reprograming depends on the HIV-1 accessory protein Vpr. We propose that HIV-1 infection drives a CD4+ TRM-phenotype potentially sequestering infected cells within tissues to support viral replication and persistence.

microbiology↗

bioRxiv2020

Polymorphism and selection pressure of SARS-CoV-2 vaccine and diagnostic antigens: implications for immune evasion and serologic diagnostic performance

The ongoing SARS-CoV-2 pandemic has triggered multiple efforts for serological tests and vaccine development. Most of these tests and vaccines are based on the Spike glycoprotein (S) or the Nucleocapsid (N) viral protein. Conservation of these antigens among viral strains is critical to ensure optimum diagnostic test performance and broad protective efficacy, respectively. We assessed N and S antigen diversity from 17,853 SARS-CoV-2 genome sequences and evaluated selection pressure. Up to 6-7 incipient phylogenetic clades were identified for both antigens, confirming early variants of the S antigen and identifying new ones. Significant diversifying selection was detected at multiple sites for both antigens. Some sequence variants have already spread in multiple regions, in spite of their low frequency. In conclusion, the N and S antigens of SARS-CoV-2 are well conserved antigens, but new clades are emerging and may need to be included in future diagnostic and vaccine formulations.

microbiology↗

bioRxiv2018

Estimating the current burden of Chagas disease in Mexico: a systematic review of epidemiological surveys from 2006 to 2017

BackgroundIn Mexico, estimates of Chagas disease prevalence and burden vary widely. Updating surveillance data is therefore an important priority to ensure that Chagas disease does not remain a barrier to the development of Mexicos most vulnerable populations.\n\nMethodology/Principal FindingsThe aim of this systematic review was to analyze the literature on epidemiological surveys to estimate Chagas disease prevalence and burden in Mexico, during the period 2006 to 2017. A total of 2,764 articles were screened and 38 were retained for the final analysis. Epidemiological surveys have been performed in most of Mexico, but with variable geographic coverage. Based on studies reporting confirmed cases, i.e. using at least 2 serological tests, the national seroprevalence of Trypanosoma cruzi infection was 2.26% [95% Confidence Interval (CI) 2.12-2.41], suggesting that there are 2.71 million cases in Mexico. Studies focused on pregnant women, which may transmit the parasite to their newborn during pregnancy, reported a seroprevalence of 1.00% [95% CI 0.87-1.14], suggesting that there are 22,930 births from T. cruzi infected pregnant women per year, and 1,445 cases of congenitally infected newborns per year. Children under 18 years had a seropositivity rate of 1.49% [95% CI 1.20-1.85], which indicate ongoing transmission. Finally, cases of T. cruzi infection in blood donors have also been reported in most states, with a national seroprevalence of 0.51% [95% CI 0.49-0.53].\n\nConclusions/SignificanceOur analysis suggests a disease burden for T. cruzi infection higher than previously recognized, highlighting the urgency of establishing Chagas disease surveillance and control as a key national public health priority in Mexico, to ensure that it does not remain a major barrier to the economic and social development of the countrys most vulnerable populations.\n\nAuthor summaryIn Mexico, estimates of Chagas disease prevalence and burden vary widely due to the ecology and epidemiology of this disease resulting of many geographical, ecological, biological, and social interactions. Better data are thus urgently needed to help develop appropriate public health programs for disease control and patient care. In this study we analyzed published data on T. cruzi seroprevalence infection in Mexico between 2006 and 2017. This systematic review shows a national seroprevalence of T. cruzi infection of 2.26% [95%CI 2.12-2.41], with over 2.71 million cases in Mexico, which is higher than previously recognized. The presence of T. cruzi infection in specific subpopulations such as pregnant women, children and blood donors also informs on specific risks of infection and call for the implementation of well-established control interventions. This work confirms the place of Mexico as the country with the largest number of cases, highlighting the urgency of establishing Chagas disease control as a key national public health priority.

epidemiology↗

bioRxiv2018

A novel role of VisP and Wzz system during O-antigen assembly in Salmonella Typhimurium pathogenesis

Salmonella enterica serovars are associated with diarrhea and gastroenteritis and are a helpful model for understanding host-pathogen mechanisms. Salmonella Typhimurium regulates the distribution of O-antigen (OAg) and presents a trimodal distribution based on Wzy polymerase, WzzST (long chain length OAg, L-OAg) and WzzfepE (very long chain length OAg, VL-OAg) co-polymerases; however, several mechanisms regulating this process remain unclear. Here, we report that LPS modifications modulate the infectious process and that OAg chain length determination plays an essential role during infection. An increase in VL-OAg is dependent on Wzy polymerase, which is promoted by a growth condition resembling the environment of Salmonella-containing vacuoles (SCVs). The virulence and stress-related periplasmic protein (VisP) participates in OAg synthesis, as {Delta}visP presents a semirough OAg phenotype. The {Delta}visP mutant has greatly decreased motility and J774 macrophage survival in a colitis model of infection. Interestingly, the phenotype is restored after mutation of the wzzST or wzzfepE gene in a {Delta}visP background. Loss of both the visP and wzzST genes promotes an imbalance in flagellin secretion. L-OAg may function as a shield against host immune systems in the beginning of an infectious process, and VL-OAg protects bacteria during SCV maturation and facilitates intramacrophage replication. Taken together, these data highlight the roles of OAg length in generating phenotypes during S. Typhimurium pathogenesis and show the periplasmic protein VisP as a novel protein in the OAg biosynthesis pathway.\n\nAuthor summarySalmonella modifies its LPS, specifically the O-antigen length, to adapt itself to distinct intestinal environments. These LPS modifications may provide a way for this bacterium to avoid complement activation in the intestinal lumen, improving Salmonella pathogenesis. This process is essential for a successful infection, and our investigation into these specific details regarding LPS in this foodborne pathogen will elucidate different aspects of the host-pathogen association.

microbiology↗