Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumanniicomplex

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes isolated from their functional contexts. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and micro-synteny conservation analyses. This allowed to delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with, or are found preferentially in, the pathogenic ACB clade. They unveil, at an unprecedented resolution, the genetic makeup that coincides with the manifestation of the pathogenic phenotype in the last common ancestor of the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. Specifically, we could show that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. They disclose promising routes for future therapeutic strategies.

Using the Hurst Exponent and Entropy Measures to Predict Effective Transmissibility in Empirical Series of Malaria Incidence

We analyze the empirical series of malaria incidence, using the concepts of autocorrelation, Hurst exponent and Shannon entropy with the aim of uncovering hidden variables in those series. From the simulations of an agent model for malaria spreading, we first derive models of the malaria incidence, the Hurst exponent and the entropy as functions of gametocytemia, measuring the infectious power of a mosquito to a human host. Second, upon estimating the values of three observables—incidence, Hurst exponent and entropy—from the data set of different malaria empirical series we predict a value of the gametocytemia for each observable. Finally, we show that the independent predictions show considerable consistency with only a few exceptions which are discussed in further detail.

Shedding Light on Autophagy During Human Tuberculosis. A Long Way to Go

Immunity against Mycobacterium tuberculosis (Mtb) is highly complex, and the outcome of the infection depends on the role of several immune mediators with particular temporal dynamics on the host microenvironment. Autophagy is a central homeostatic mechanism that plays a role on immunity against intracellular pathogens, including Mtb. Enhanced autophagy in macrophages mediates elimination of intracellular Mtb through lytic and antimicrobial properties only found in autolysosomes. Additionally, it has been demonstrated that standard anti-tuberculosis chemotherapy depends on host autophagy to coordinate successful antimicrobial responses to mycobacteria. Notably, autophagy constitutes an anti-inflammatory mechanism that protects against endomembrane damage triggered by several endogenous components or infectious agents and precludes excessive inflammation. It has also been reported that autophagy can be modulated by cytokines and other immunological signals. Most of the studies on autophagy as a defense mechanism against Mycobacterium have been performed using murine models or human cell lines. However, very limited information exists about the autophagic response in cells from tuberculosis patients. Herein, we review studies that face the autophagy process in tuberculosis patients as a component of the immune response of the human host against an intracellular microorganism such as Mtb. Interestingly, these findings might contribute to recognize new targets for the development of novel therapeutic tools to combat Mtb. Actually, either as a potential successful vaccine or a complementary immunotherapy, efforts are needed to further elucidate the role of autophagy during the immune response of the human host, which will allow to achieve protective and therapeutic benefits in human tuberculosis.

ETUDE DE LA NUISANCE DES MOUSTIQUES EN MILIEU UNIVERSITAIRE DE LA FACULTE DES SCIENCES ET TECHNIQUES, BAMAKO, MALI

Mosquitoes are potentially harmful and vectors of pathogens. They compromise the rest and well-being of humans and animals. The main goal of this study is to determine the composition of mosquitoes responsible of human biting at the Faculty of Sciences and Technics of Bamako-Mali. Longitudinal monitoring with monthly cross-sectional visit was carried out from September to December 2019, in order to collect the endophilic and endophagic mosquitoes. The spray-catch was used as a collection methodin 21 rooms selected randomly at the FST. Mosquitoes were identified morphologically andthen by PCR. ELISA-CSP test was used for Plasmodium infection index and the ELISA blood-meal test was to determine mosquitoes blood origin. In total, 802 mosquitoes were collected: 794Culex and 8Anopheles. There were 200 males and 602 females. Female mosquitoes were separated by gonotrophic stages: 231 unfed, 223 fed, 80 semi-gravid and 68 gravid. Up to 34% of Culex and 67% of Anopheles had a preference for human blood, but no female tested positive for Plasmodium infection. This result would be due to the small number of Anopheles captured. An. coluzzii is the only Anopheles species collected.This study shows that mosquitoes are linked to serious problems of nuisance and risk of pathogens transmission in the university. They highly prefer to feed on human host.

Prediction of Human proteins having interactions with HPV16 proteins using virus and host sequence motifs.

Background: Human Papillomavirus (HPV) infection has been found to be the major cause of cancer of cervical region, in females. Genome of HPV codes for 6 functional proteins E1, E2, E4, E5, E6 and E7. These proteins play different roles in development of HPV infection and its progression towards cervical cancer. The interactions of HPV proteins with human DNA and proteins occurs in the presence of short linear peptide motifs on these proteins, have similar sequence to those found on proteins in human cells. Methods: After identification of human motifs in HPV proteins, by use of ELM resource, their counter domains were found from PROSITE. The proteins of human proteome containing these counter domains were predicted as the proteins having possibility of interactions with HPV proteins. Results: we predicted 9468 human proteins for having interactions with HPV proteins. Our predicted proteins were enriched with the host proteins having possibility of being interacted by HPV proteins. 10% of our predicted proteins were already reported to be affected by one or more HPV proteins. The list of predicated proteins can be utilized to find out the connectivity between the virus HPV and human host. It can also be used to determine the pathways involved in pathogenesis of HPV leading towards the cervical cancer Conclusion: The list of predicated proteins can be utilized to find out the connectivity between the virus HPV and human host. It can also be used to determine the pathways involved in pathogenesis of HPV leading towards the cervical cancer.

IL-21 signaling promotes early dissemination of KSHV infection in B lymphocytes

Kaposi’s sarcoma-associated herpesvirus (KSHV) extensively manipulates the host immune system and the cytokine milieu, and cytokines are known to influence the progression of KSHV-associated diseases. However, the precise role of cytokines in the early stages of KSHV infection remains undefined. Here, using our unique model of KSHV infection in tonsil lymphocytes, we investigate the influence of host cytokines on the establishment of KSHV infection in B cells. Our data demonstrate that KSHV manipulates the host cytokine microenvironment during early infection and susceptibility generally associated with downregulation of multiple cytokines. However, we show that IL-21 signaling promotes KSHV infection by promoting both plasma cell numbers and increasing KSHV infection in plasma cells. Our data reveal that IL-21 producing T cells, particularly Th17/Tc17 and central memory CD8+ T cells may represent immunological factors that modulate host-level susceptibility to KSHV infection. These results suggest that IL-21 plays a significant role in the early stages of KSHV infection in the human immune system and may represent a novel mechanism to be further explored in the context of preventing KSHV transmission.Author SummaryVery little is known about how KSHV is transmitted and how it initially establishes infection in a new human host and this lack of information limits our ability to prevent KSHV-associated cancers by limiting its person-to-person transmission. Saliva is thought to be the primary route of person-to-person transmission for KSHV, making the tonsil a likely first site for KSHV replication in a new human host. In particular, the tonsil is likely to be the first place KSHV is able to enter B cells, which are thought to be a major site of persistent infection. Our previous work identified plasma cells as a highly targeted cell type in early KSHV infection in cultured cells from human tonsil. In this study, we show that the human cytokine IL-21 promotes both overall KSHV infection and the establishment of infection in plasma cells. We also investigate the immunological mechanisms underlying this effect. Our results demonstrate that IL-21 and IL-21-producing cells are a novel factor that influences the initial establishment of KSHV infection in humans.

Investigating the human host - ssRNA virus interaction landscape using the SMEAGOL toolbox

Viruses are intracellular parasites that need their host cell to reproduce. Consequently, they have evolved numerous mechanisms to exploit the molecular machinery of their host cells, including the broad spectrum of host RNA-binding proteins (RBPs). However, the RBP interactome of viral genomes and the consequences of these interactions for infection are still to be mapped for most RNA viruses. To facilitate these efforts we have developed SMEAGOL, a fast and user-friendly toolbox to analyze the enrichment or depletion of RBP binding motifs across RNA sequences (https://github.com/gruber-sciencelab/SMEAGOL). To shed light on the interaction landscape of RNA viruses with human host cell RBPs at a large scale, we applied SMEAGOL to 197 single-stranded RNA (ssRNA) viral genome sequences. We find that the majority of ssRNA virus genomes are significantly enriched or depleted in binding motifs for human RBPs, suggesting selection pressure on these interactions. Our analysis provides an overview of potential virus - RBP interactions, covering the majority of ssRNA viral genomes fully sequenced to date, and represents a rich resource for studying host interactions vital to the virulence of ssRNA viruses. Our resource and the SMEAGOL toolbox will support future studies of virus / host interactions, ultimately feeding into better treatments.

Successful Profiling of Plasmodium falciparum var Gene Expression in Clinical Samples via a Custom Capture Array

Malaria parasites display antigens on the surface of infected red blood cells in the human host that facilitate attachment to blood vessels, contributing to the severity of infection. These antigens are highly variable, allowing the parasite to evade the immune system.

Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage to the Human ACE2 Receptor Binding: A Structural Insight

The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these “variants of concern” has increased viral transmissibility or immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (Kappa and Delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants.