Biology subjects

Bloch, I.

Publications and source records attributed to Bloch, I..

11 recordsLinked to original sources

bioRxiv2025

CladeOScope-GSA: A Tool for Predicting Functional Gene Interactions via Phylogenetic Profiling

Understanding gene function and protein network dynamics is a key challenge in biology and human health. In the light of the exponential growth in genomic data, phylogenetic profiling methods became more powerful in analysing thousands of genomes to uncover evolutionary associations and predict functional interactions [1,2,4,13,14,16,18,23,24,26]. It is based on the well-supported hypothesis that genes that work together are subject to similar evolutionary pressures and therefore their conservation patterns across phylogeny are correlated. We introduce CladeOScope-GSA, a web-based tool designed for phylogeny-aware analysis of gene sets across extensive comparative genomics datasets. By integrating clade-focused normalized phylogenetic profiling (NPP) with interactive visualization, CladeOScope-GSA enables researchers to identify evolutionary patterns within user-defined gene sets. Building upon the infrastructure of the original CladeOScope visualization platform, the addition of statistical gene set analysis, expanded phylogenetic and genomic data, enhanced visualization, and improved statistical tools represent a significant advancement in the tools capabilities. We demonstrate its utility through case studies spanning 1905 species, showcasing how CladeOScope-GSA empowers researchers to extract biological insights from complex comparative datasets. The web tool is accessible at https://tabachlab.shinyapps.io/CladeOScope

evolutionary biology↗

bioRxiv2024

Combining radio-telemetry and radar measurements to test optimal foraging in an aerial insectivore bird

Optimal foraging theory posits that foragers adjust their movements based on prey abundance to optimize food intake. While extensively studied in terrestrial and marine environments, aerial foraging has remained relatively unexplored due to technological limitations. This study, uniquely combining BirdScan-MR1 radar and the ATLAS biotelemetry system, investigates the foraging dynamics of Little Swifts (Apus affinis) in response to insect movements over Israels Hula Valley. Insect Movement Traffic Rate (MoTR) substantially varied across days, strongly influencing swift movement. On days with high MoTR, swifts exhibited reduced flight distance, increased colony visit rate, and earlier arrivals at the breeding colony, reflecting a dynamic response to prey availability. However, no significant effects were observed in total foraging duration, flight speed, or daily route length. Notably, as insect abundance increased, inter-individual distances decreased. These findings suggest that Little Swifts optimize their foraging behavior in relation to aerial insect abundance, likely influencing reproductive success and population dynamics. The integration of radar technology and biotelemetry systems provides a unique perspective on the interactions between aerial insectivores and their prey, contributing to a comprehensive understanding of optimal foraging strategies in diverse environments.

ecology↗

bioRxiv2024

Pesticide chemical leads inhibiting protein-protein interactions

Pesticides, especially herbicides, have revolutionized agriculture by providing energy-efficient solutions for pest control that replaces labor-intensive cultivation methods. However, the widespread evolution of pesticide resistance poses a significant challenge to current agriculture. Most pesticides function by binding to specific pockets on target enzymes, enabling a single mutation to confer resistance. An alternative approach is the disruption of protein-protein interactions (PPI), thus for resistance to occur, it requires complementary mutations on both interacting partners. Despite extensive efforts, no herbicides with new modes of action have been commercialized for decades. Thus, we focused on the discovery and design of small molecule inhibitors that target the interface of the PPI complex of O-acetylserine sulfhydrylase (OASS) and serine acetyltransferase (SAT), key plant enzymes involved in the biosynthesis of the essential amino acid cysteine. Using in silico filtering techniques on a virtual library of 30 million small molecules, we identified initial hits capable of binding OASS and interfering with its interaction with a peptide derived from SAT. Subsequently, we conducted chemical optimizations to evaluate biophysical enzyme disruption, followed by cellular and in-planta activity in plants. These new compounds described herein can serve as promising starting points for further optimization as herbicides acting on a new mode of action.

biochemistry↗

bioRxiv2023

Conversion of methionine biosynthesis in E. coli from trans- to direct-sulfurylation enhances extracellular methionine levels

Methionine is an essential amino acid in mammals and a critical metabolite in all organisms. As such, various applications, including food, feed, and pharmaceuticals, necessitate the addition of L-methionine. Although amino acids and other metabolites are commonly produced through bacterial fermentation, high-yield biosynthesis of L-methionine remains a significant challenge due to the strict cellular regulation of the biosynthesis pathway. As a result, methionine is produced primarily synthetically, resulting in a racemic mixture of D,L-methionine. This study aimed to enhance methionine bio-production yields in E. coli by replacing its highly regulated trans-sulfurylation pathway with the more common direct-sulfurylation pathway used by other bacteria. To this end, we generated an auxotroph E. coli strain (MG1655) by simultaneously deleting metA and metB genes and complementing them with metX and metY from different bacteria. Complementation of the genetically modified E. coli with metX/metY from Cyclobacterium marinum or Deinococcus geothermalis, together with the deletion of the global repressor metJ and overexpression of the transporter YjeH, resulted in a substantial increase of up to 126 and 160-fold methionine relative to the wild-type strain, respectively, and accumulation of up to 700 mg/L using minimal MOPS medium and 2 ml culture. Our findings provide a method to study methionine biosynthesis and a chassis for enhancing L-methionine production by fermentation. HighlightsO_LIReplacement of E. coli metA and metB with metX and metY recovered its growth C_LIO_LIThe engineered E. coli has a 160-fold increase in extracellular methionine levels C_LIO_LISelection of different metX and metY leads to varying growth rates and enhanced methionine levels C_LI

biochemistry↗

bioRxiv2022

Production and secretion of recombinant proteins using the endotoxin-free, Gram-negative bacterium Sphingobium japonicum

Gram-negative bacteria are common and efficient protein expression systems, yet their outer membrane endotoxins can elicit undesirable toxic effects, limiting their applicability for parenteral therapeutic applications, e.g., production of vaccine components. In the bacterial genus Sphingomonas from the Alphaproteobacteria class, lipopolysaccharide (LPS) endotoxins are replaced with non-toxic glycosphingolipids (GSL), rendering it an attractive alternative for therapeutic protein production. To explore the use of Sphingomonas as a safe expression system for production of proteins for therapeutic applications, in this study, Sphingobium japonicum (SJ) injected live into embryonated hen eggs proved safe and nontoxic. Multimeric viral polypeptides derived from Newcastle disease virus (NDV) designed for expression in SJ, yielded soluble proteins which were specifically recognized by antibodies raised against the whole virus. In addition, native signal peptides (SP) motifs identified using whole-genome computerized analysis and coupled to secreted proteins in SJ induced secretion of Amy and mCherry gene products. Relative to the same genes expressed without an SP, SP 104 increased secretion of Amy (3.7-fold) and mCherry (16.3-fold) proteins and yielded accumulation of up to 80{micro}g/L of the later in the culture medium. Taken together, the presented findings demonstrate the potential of this unique LPS-free Gram-negative bacterial family to serve as an important tool for protein expression for both research and biotechnological purposes, including for the development of novel vaccines. ImportanceThe Gram-negative, LPS-free Sphingomonas genus can serve as an effective and safe platform for therapeutic protein expression and secretion and bears potential as a live bacteria delivery system for protein vaccines.

molecular biology↗

bioRxiv2021

Protection against avian coronavirus conferred by oral vaccination with live bacteria secreting LTB-fused viral proteins

The devastating impact of infectious bronchitis (IB) triggered by the IB virus (IBV), on poultry farms is generally curbed by livestock vaccination with live attenuated or inactivated vaccines. Yet, this approach is challenged by continuously emerging variants and by time limitations of vaccine preparation techniques. This work describes the design and evaluation of an anti-IBV vaccine comprised of E. coli expressing and secreting viral spike 1 subunit (S1) and nucleocapsid N-terminus and C-terminus polypeptides fused to heat-labile enterotoxin B (LTB) (LS1, LNN, LNC, respectively). Following chicken oral vaccination, anti-IBV IgY levels and cellular-mediated immunity as well as protection against virulent IBV challenge, were evaluated 14 days following the booster dose. Oral vaccination induced IgY levels that exceeded those measured following vaccination with each component separately. Following exposure to inactivated IBV, splenocytes isolated from chicks orally vaccinated with LNN or LNC -expressing bacteria, showed a higher percentage of CD8+ cells as compared to splenocytes isolated from chicks vaccinated with wild type or LTB-secreting E. coli and to chicks subcutaneously vaccinated. Significant reduction in viral load and percent of shedders in the vaccinated chicks was evident starting 3 days following challenge with 107.5 EID50/ml virulent IBV. Taken together, orally delivered LTB-fused IBV polypeptide-expressing bacteria induced virus-specific IgY antibody production and was associated with significantly shorter viral shedding on challenge with a live IBV. The proposed vaccine design and delivery route promise an effective and rapidly adaptable means of protecting poultry farms from devastating IB outbreaks. HighlightsO_LIMucosal vaccination was shown particularly beneficial against respiratory viruses. C_LIO_LIAn anti-IBV vaccine composed of three IBV polypeptides fused to LTB was designed. C_LIO_LIVaccine composed of bacteria secreting polypeptides was orally delivered. C_LIO_LIVaccine induced specific immune responses and shortened viral shedding duration. C_LI

immunology↗

bioRxiv2021

Oral subunit SARS-CoV-2 vaccine induces systemic neutralizing IgG, IgA and cellular immune responses and can boost neutralizing antibody responses primed by an injected vaccine

The rapid spread of the COVID-19 pandemic, with its devastating medical and economic impacts, triggered an unprecedented race toward development of effective vaccines. The commercialized vaccines are parenterally administered, which poses logistic challenges, while adequate protection at the mucosal sites of virus entry is questionable. Furthermore, essentially all vaccine candidates target the viral spike (S) protein, a surface protein that undergoes significant antigenic drift. This work aimed to develop an oral multi-antigen SARS-CoV-2 vaccine comprised of the receptor binding domain (RBD) of the viral S protein, two domains of the viral nucleocapsid protein (N), and heat-labile enterotoxin B (LTB), a potent mucosal adjuvant. The humoral, mucosal and cell-mediated immune responses of both a three-dose vaccination schedule and a heterologous subcutaneous prime and oral booster regimen were assessed in mice and rats, respectively. Mice receiving the oral vaccine compared to control mice showed significantly enhanced post-dose-3 virus-neutralizing antibody, anti-S IgG and IgA production and N-protein-stimulated IFN-{gamma} and IL-2 secretion by T cells. When administered as a booster to rats following parenteral priming with the viral S1 protein, the oral vaccine elicited markedly higher neutralizing antibody titres than did oral placebo booster. A single oral booster following two subcutaneous priming doses elicited serum IgG and mucosal IgA levels similar to those raised by three subcutaneous doses. In conclusion, the oral LTB-adjuvanted multi-epitope SARS-CoV-2 vaccine triggered versatile humoral, cellular and mucosal immune responses, which are likely to provide protection, while also minimizing technical hurdles presently limiting global vaccination, whether by priming or booster programs. HighlightsO_LIMigVax-101 is a multi-epitope oral vaccine for SARS-CoV-2. C_LIO_LIMigVax-101 elicits neutralizing IgG and IgA production and cellular responses in mice C_LIO_LIMigVax-101 serves as an effective booster in rats to a parenteral anti-S1 vaccine. C_LI

immunology↗

bioRxiv2021

Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome

Inactivating mutations in the Methyl-CpG Binding Protein 2 (MECP2) gene are the main cause of Rett syndrome (RTT). Despite extensive research into MECP2 function, no treatments for RTT are currently available. Here we use an evolutionary genomics approach to construct an unbiased MECP2 gene network, using 1,028 eukaryotic genomes to prioritize proteins with strong co-evolutionary signatures with MECP2. Focusing on proteins targeted by FDA approved drugs led to three promising candidates, two of which were previously linked to MECP2 function (IRAK, KEAP1) and one that was not (EPOR). We show that each of these compounds has the ability to rescue different phenotypes of MECP2 inactivation in cultured human neural cell types, and appear to act on Nuclear Factor Kappa B (NF-{kappa}B) signaling in inflammation. This study highlights the potential of comparative genomics to accelerate drug discovery, and yields potential new avenues for the treatment of RTT. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/431162v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1d7e0f8org.highwire.dtl.DTLVardef@1f2c602org.highwire.dtl.DTLVardef@1a5dd7dorg.highwire.dtl.DTLVardef@7071c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2020

Conserved interactions required for in vitro inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6,900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50M concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.

microbiology↗

bioRxiv2020

Conservation motifs - a novel evolutionary-based classification of proteins

Cross-species protein conservation patterns, as directed by natural selection, are indicative of the interplay between protein function, protein-protein interaction and evolution. Since the beginning of the genomic era, proteins were characterized as either conserved or not conserved. This simple classification became archaic and cursory once data on protein orthologs became available for thousands of species. To enrich the language used to describe protein conservation patterns, and to understand their biological significance, we classified 20,294 human proteins against 1096 species. Analyses of the conservation patterns of human proteins in different eukaryotic clades yielded extremely variable and rich patterns that had never been characterized or studied before. Using mathematical classifications, we defined seven conservation motifs: Steps, Critical, Lately Developed, Plateau, Clade Loss, Trait Loss and Gain, which describe the evolution of human proteins. Overall, our work offers novel terms for conservation patterns and defines a new language intended to comprehensively describe protein evolution. This novel terminology enables the classification of proteins based on evolution, reveals aspects of protein evolution, and improves the understanding of protein functions.

evolutionary biology↗

bioRxiv2018

Objective Evaluation of Multiple Sclerosis Lesion Segmentation using a Data Management and Processing Infrastructure

We present a study of multiple sclerosis segmentation algorithms conducted at the international MICCAI 2016 challenge. This challenge was operated using a new open-science computing infrastructure. This allowed for the automatic and independent evaluation of a large range of algorithms in a fair and completely automatic manner. This computing infrastructure was used to evaluate thirteen methods of MS lesions segmentation, exploring a broad range of state-of-the-art algorithms, against a high-quality database of 53 MS cases coming from four centers following a common definition of the acquisition protocol. Each case was annotated manually by an unprecedented number of seven different experts. Results of the challenge highlighted that automatic algorithms, including the recent machine learning methods (random forests, deep learning, ...), are still trailing human expertise on both detection and delineation criteria. In addition, we demonstrate that computing a statistically robust consensus of the algorithms performs closer to human expertise on one score (segmentation) although still trailing on detection scores.

neuroscience↗