Biology subjects

Hossain, M. A.

Publications and source records attributed to Hossain, M. A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Population dynamics of fruit flies (Diptera: Tephritidae) in a semirural area under subtropical monsoon climate of Bangladesh

Fruit flies belonging to Tephritidae family are highly destructive agricultural pests, posing a significant threat to various fruits and vegetables grown in Bangladesh. A comprehensive year-round survey was conducted at Atomic Energy Research Establishment (AERE) campus located in the central region of Bangladesh. Three types of male lures (methyl eugenol, cue-lure and zingerone) were used to detect and assess the diversity of pest fruit fly species. A total of seventeen species of Tephritidae fruit flies were detected in this survey. The Bactrocera carambolae fruit fly has been discovered for the first time in our survey area, indicating spread of its range towards the north-west region from its previous detection sites (Chattogram and Sylhet Divisions) in Bangladesh. Among the detected pest species, we identified six abundant species: Bactrocera dorsalis, Zeugodacus cucurbitae, Zeugodacus tau, Bactrocera rubigina, Bactrocera zonata, and Dacus longicornis. The most abundant species was the polyphagous fruit pest B. dorsalis, comprising 76.83% of all captured flies. The species Z. cucurbitae was the second most abundant, representing 13.82% of the total trapped flies. The fitted curve to survey data using Gaussian mixture model revealed the existence of overlapped subgroups in the population of B. dorsalis and Z. cucurbitae. In addition, our statistical analysis of the six abundant Tephritidae fruit fly species revealed correlation of population dynamics with several factors including temperature, rainfall, humidity, photoperiod, and fruiting time of host plant species in the selected area.

ecology↗

bioRxiv2024

Effect of different lining paper materials and infusions on oviposition preference of Aedes aegypti (Diptera: Culicidae) gravid mosquitoes

Aedes aegypti (Linnaeus) mosquito is a vector, responsible for increasing global public health concerns due to its rapid geographical spread and increasing vectorial capacity. Understanding the breeding behavior of Ae. aegypti is crucial to control this vector and thereby limiting the spread of diseases. To study this mosquito breeding in the laboratories and ovitraps, different types of lining-papers, surrounding inner surface of a container along with different types of added infusions, are used. Lining-papers serve as surfaces for oviposition and infusions provide the essential environment for nurturing. The types of oviposition surfaces and infusions used in laboratory rearing facilities or ovitraps influence oviposition preference, changing the breeding behavior of Ae. aegypti gravid mosquitoes. This study presents a comparative study on oviposition preferences for six different types of lining-papers and six different types of infusions in a bioassay cage. ANOVA analysis shows a significant effect on oviposition preference of different types of lining-papers that served as oviposition surfaces. The highest oviposition activity was observed for the agri seed germination paper-75 lining-paper when normal tap water infusion was used. Likewise, statistical analysis shows that when a plain printing offset paper 80 GSM lining-paper was used, a highly statistically significant effect on oviposition preference is observed for different types of infusions used in the oviposition cups.

animal behavior and cognition↗

bioRxiv2024

Heli-SMACC: Helicase-targeting SMAll Molecule Compound Collection

Helicases have emerged as promising targets for the development of antiviral drugs; however, the family remains largely undrugged. To support the focused development of viral helicase inhibitors we identified, collected, and integrated all chemogenomics data for all available helicases from the ChEMBL database. After thoroughly curating and enriching the data with relevant annotations we have created a derivative database of helicase inhibitors which we dubbed Heli-SMACC (Helicase-targeting SMAll Molecule Compound Collection). The current version of Heli-SMACC contains 20,432 bioactivity entries for viral, human, and bacterial helicases. We have selected 30 compounds with promising viral helicase activity and tested them in a SARS-CoV-2 NSP13 ATPase assay. Twelve compounds demonstrated ATPase inhibition and a consistent dose-response curve. The Heli-SMACC database may serve as a reference for virologists and medicinal chemists working on the development of novel helicase inhibitors. Heli-SMACC is publicly available at https://smacc.mml.unc.edu. HighlightsO_LIWe created a curated Helicase-Targeting SMAll Molecule Compound Collection (Heli-SMACC). C_LIO_LIHeli-SMACC covers 29 human, viral, and bacterial helicases. C_LIO_LITwelve of thirty selected compounds demonstrated inhibitory activity in a SARS-CoV-2 NSP13 ATPase Assay. C_LIO_LIHeli-SMACC is freely available online at https://smacc.mml.unc.edu. C_LI TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/602122v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@8e098forg.highwire.dtl.DTLVardef@115cb2borg.highwire.dtl.DTLVardef@1cd9da3org.highwire.dtl.DTLVardef@2870a6_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of Chikungunya nsP2 Cysteine Protease with Anti-alphavirus Activity

Despite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic {beta}-aminomethyl vinyl sulfone RA-0002034 (1a) is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad spectrum antiviral activity. Analogs of 1a that varied each of three regions of the molecule were synthesized to establish structure-activity relationships for inhibition of Chikungunya (CHIKV) nsP2 protease and viral replication. The covalent warhead was highly sensitive to modifications of the sulfone or vinyl substituents. However, numerous alterations to the core 5-membered heterocycle and its aryl substituent were well tolerated and several analogs were identified that enhanced CHIKV nsP2 binding. For example, the 4-cyanopyrazole analog 8d exhibited a kinact/Ki ratio >10,000 M-1s-1. 3-Arylisoxazole was identified an isosteric replacement for the 5-membered heterocycle, which circumvented the intramolecular cyclization that complicated the synthesis of pyrazole-based inhibitors like 1a. The accumulated structure-activity data was used to build a ligand-based model of the enzyme active site, which can be used to guide the design of covalent nsP2 protease inhibitors as potential therapeutics against alphaviruses.

cell biology↗

bioRxiv2024

Structures of the human transcription factor brachyury offer insights into DNA recognition, and identify small molecule binders for the development of degraders for cancer therapy

The transcription factor brachyury is a member of the T-Box family of transcription factors. It is active during embryogenesis and is required for the formation of the posterior mesoderm and the notochord in vertebrates. Aside from its role in embryogenesis, brachyury plays an essential role in tumour growth of the rare chordoma bone cancer and is implicated in other solid tumours. Given that brachyury is minimally expressed in healthy tissues, these findings suggest that brachyury is a potential therapeutic target in cancer. Unfortunately, as a ligandless transcription factor, brachyury has historically been considered undruggable. To investigate direct targeting of brachyury by small molecules, we initially determined the structure of human brachyury both in complex with its cognate DNA and in the absence of DNA. Analysis of these structures provided insights into brachyury DNA binding and the structural context of the G177D variant which is strongly associated with chordoma risk. We used these structures to perform a crystallographic fragment screen of brachyury and identify hotspot regions on numerous pockets on the brachyury surface. Finally, we have performed follow-up chemistry on fragment hits and describe the structure-based progression of a thiazole-containing chemical series. Excitingly, we have produced brachyury binders with low {micro}M potency that can serve as starting point for further medicinal chemistry efforts. These data show that brachyury is ligandable and provides an example of how crystallographic fragment screening may be used to find ligands to target protein classes that are traditionally difficult to address using other approaches.

molecular biology↗

bioRxiv2024

Spatial Profiling of Metals through Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging

The spatial-omic analysis of biomolecules such as nucleic acids, lipids, metabolites, and proteins is advancing the study of biological systems and processes in a physio-pathological context. Here, we describe an innovative matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) method to detect metals within biological tissues using instrumentation that is widely available in research and clinical laboratories. We characterize the spatial distribution of metals in diverse settings including mouse embryogenesis, genetic disorders leading to abnormal metal accumulation, and preclinical testing for improved platinum-based chemotherapy delivery through focused ultrasound across the blood-brain barrier. Spatial metal profiling will advance research studies and the clinical analysis of metal-related diseases, enabling more precise use of metal-based therapies and advances in diverse scientific fields beyond biomedicine. One-Sentence SummarySpatial metallomic profiling maps native metals or those coordinated to xenobiotics, antibodies, and biomolecules in tissues.

cancer biology↗

bioRxiv2024

Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC50 of 58 {+/-} 17 nM, and further analysis with time-dependent inhibition studies yielded a kinact/KI of 6.4 x 103 M-1s-1. LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic. Significance StatementChikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.

biochemistry↗

bioRxiv2023

Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh

The spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in the Mycobacterium tuberculosis rpoB gene. While some of these infrequent mutations show lower fitness in vitro than more common mutations, their in vivo fitness is currently unknown. We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44% of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderline rpoB mutations and those with common rpoB mutations. We found a relatively low percentage of transmission clustering in the dataset (34.8%) but no difference in clustering between different types of rpoB mutations. Compensatory mutations in rpoA, rpoB, and rpoC were associated with higher levels of transmission clustering as were lineages 2, 3, and 4 relative to lineage 1. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster. Our findings show that although borderline rpoB mutations have lower in vitro growth potential this does not translate into lower transmission potential or in vivo fitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities. Data summaryWGS reads are available in the European Nucleotide Archive (PRJEB39569). In addition, WGS reads, as well as pDST and clinical data, are included in the ReSeqTB data platform and are accessible on registration at https://platform.reseqtb.org/. Custom scripts for clustering are available at https://github.com/conmeehan/pathophy.

genomics↗

bioRxiv2022

SGC-CLK-1 (CAF-170) a chemical probe for the Cdc2-Like kinases CLK1, CLK2, and CLK4

Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2 and 4. Here, we present the synthesis, selectivity, and potential binding site of this compound - SGC-CLK-1. We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine rich (SR) protein phosphorylation, but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.

cancer biology↗

bioRxiv2022

SGC-CAMKK2-1: A chemical probe for CAMKK2

The serine/threonine protein kinase calcium/calmodulin-dependent protein kinase kinase 2 (CAMKK2) plays critical roles in a range of biological processes. Despite its importance, only a handful of inhibitors of CAMKK2 have been disclosed. Having a selective small molecule tool to interrogate this kinase will help demonstrate that CAMKK2 inhibition can be therapeutically beneficial. Herein, we disclose SGC-CAMKK2-1, a selective chemical probe that targets CAMKK2.

cancer biology↗

bioRxiv2022

A host defense peptide mimetic, brilacidin, potentiates caspofungin antifungal activity against human pathogenic fungi

A. fumigatus is the main etiological agent of a group of heterogeneous diseases called aspergillosis of which the most lethal form is the invasive pulmonary aspergillosis (IPA). Fungicidal azoles and amphotericin B are the first line defense against A. fumigatus, but fungistatic echinocandins, such as caspofungin (CAS), can be used as salvage therapy for IPA. Here, we screened repurposing libraries and identified several compounds that potentiate CAS activity against A. fumigatus, including the host defense peptide mimetic, brilacidin (BRI). BRI converts CAS into a fungicidal drug and potentiates voriconazole (VOR) against A. fumigatus. BRI increases the ability of both CAS and VOR to control A. fumigatus biofilm growth. BRI depolarizes the A. fumigatus cell membrane leading to disruption of membrane potential. By using a combination of protein kinase inhibitors and screening of a catalytic subunit null mutant library, we identified the mitogen activated protein kinase (MAPK) MpkA and the phosphatase calcineurin as mediators of the synergistic action of BRI. These results suggest the most likely BRI mechanism of action for CAS potentiation is the inhibition of A. fumigatus cell wall integrity (CWI) pathway. BRI potentiates CAS activity against C. albicans, C. auris, and C. neoformans. Interestingly, BRI overcomes the CAS-acquired resistance in both A. fumigatus and C. albicans and the CAS-intrinsic resistance in C. neoformans. BRI also has an additive effect on the activity of posaconazole (POSA) against several Mucorales fungi. Cell toxicity assays and fungal burden studies in an immunosuppressed murine model of IPA showed that BRI combined with CAS is not toxic to the cells and significantly clears A. fumigatus lung infection, respectively. Our results indicate that combinations of BRI and antifungal drugs in clinical use are likely to improve the treatment outcome of IPA and other fungal infections.

microbiology↗

bioRxiv2022

Genomic diversity and molecular epidemiology of a multidrug resistant Pseudomonas aeruginosa DMC30b isolated from hospitalized burn patient in Bangladesh

ObjectivesPseudomonas aeruginosa is a key opportunistic pathogen causing a wide range of community- and hospital-acquired infections in immunocompromised or catheterized patients. Here, we report the complete genome sequence of a multidrug resistant (MDR) P. aeruginosa DMC30b in order to elucidate the genetic diversity, molecular epidemiology, and underlying mechanisms for antimicrobial resistance and virulence. MethodsP. aeruginosa DMC30b was isolated from septic wound swab of a severe burn patient. Whole-genome sequencing (WGS) was performed under Ion Torrent platform. The genome was annotated using the SPAdes v. 3.12.01 in an integrated Genome Analysis Platform (IonGAP) for Ion Torrent sequence data. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). In-silico predictions of antimicrobial resistance genes (ARGs), virulence factor genes (VFGs) and metabolic functional potentials were performed using different curated bioinformatics tools. ResultsP. aeruginosa DMC30b was classified as MDR and belongs to sequence type 244 (ST244). The complete genome size is 6,994,756 bp with a coverage of 76.76x, G+C content of 65.7% and a BUSCO (Benchmarking Universal Single-Copy Orthologs) score of 100. The genome of P. aeruginosa DMC30b harboured two plasmids (e,g., IncP-6 plasmid p10265-KPC; 78,007 bp and ColRNAI_pkOIISD1; 9,359 bp), 35 resistomes (ARGs) conferring resistance to 18 different antibiotics (including four beta-lactam classes), and 214 VFGs. It was identified as the 167th ST244 strain among [~] 5,800 whole-genome sequences of P. aeruginosa available in the NCBI database. ConclusionP. aeruginosa DMC30b belongs to ST244 and was identified as the 167th such isolate to be submitted to NCBI, and the first complete ST244 genome from Bangladesh. The complete genome data with high genetic diversity and underlying mechanisms for antimicrobial resistance and virulence of P. aeruginosa DMC30b (ST244) will aid in understanding the evolution and phylogeny of such high-risk clones and provide a solid basis for further research on MDR or extensively drug resistant strains.

microbiology↗

bioRxiv2022

Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: insights from machine learning and bioinformatics approaches

SARS-CoV-2 continues to spread and evolve worldwide, despite intense efforts to develop multiple vaccines and therapeutic options against COVID-19. Moreover, the precise role of SARS-CoV-2 in the pathophysiology of the nasopharyngeal tract (NT) is still unfathomable. Therefore, we used the machine learning methods to analyze 22 RNA-seq datasets from COVID-19 patients (n=8), recovered individuals (n=7), and healthy individuals (n=7) to find disease-related differentially expressed genes (DEGs). In comparison to healthy controls, we found 1960 and 153 DEG signatures in COVID-19 patients and recovered individuals, respectively. We compared dysregulated DEGs to detect critical pathways and gene ontology (GO) connected to COVID-19 comorbidities. In COVID-19 patients, the DEG- miRNA and DEG-transcription factors (TFs) interactions network analysis revealed that E2F1, MAX, EGR1, YY1, and SRF were the most highly expressed TFs, whereas hsa-miR-19b, hsa-miR-495, hsa-miR-340, hsa-miR-101, and hsa-miR-19a were the overexpressed miRNAs. Three chemical agents (Valproic Acid, Alfatoxin B1, and Cyclosporine) were abundant in COVID-19 patients and recovered individuals. Mental retardation, mental deficit, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs. Finally, we detected DEGs impacted by SARS-CoV-2 infection and mediated by TFs and miRNA expression, indicating that SARS-CoV-2 infection may contribute to various comorbidities. These pathogenetic findings can provide some crucial insights into the complex interplay between COVID-19 and the recovery stage and support its importance in the therapeutic development strategy to combat against COVID-19 pandemic. IMPORTANCEDespite it has now been over two years since the beginning of the COVID-19 pandemic, many crucial questions about SARS-CoV-2 infection and the different COVID-19 symptoms it causes remain unresolved. An intriguing question about COVID-19 is how SARS-CoV-2 interplays with the host during infection and how SARS-CoV-2 infection can cause so many disease symptoms. Our analysis of three different datasets (COVID-19, recovered, and healthy) revealed significantly higher DEGs in COVID-19 patients than recovered humans and healthy controls. Some of these DEGs were found to be co-expressed in both COVID-19 patients. They recovered humans supporting the notion that DEGs level is directly correlated with the viral load, disease progression, and different comorbidities. The protein-protein interaction consisting of 24 nodes and 72 edges recognized eight hub-nodes as potential hub-proteins (i.e., RPL4, RPS4X, RPL19, RPS12, RPL19, EIF3E, MT-CYB, and MT-ATP6). Protein-chemical interaction analysis identified three chemical agents (e.g., Valproic Acid, Alfatoxin B1, and Cyclosporine) enriched in COVID-19 patients and recovered individuals. Mental retardation, mental deficiency, intellectual disability, muscle hypotonia, micrognathism, and cleft palate were the significant diseases associated with COVID-19 by sharing DEGs.

bioinformatics↗

bioRxiv2022

Metagenomic analysis reveals the abundance and diversity of opportunistic fungal pathogens in the nasopharyngeal tract of COVID-19 patients

The nasopharyngeal tract (NT) of human is a habitat of a diverse microbial community that work together with other gut microbes to maintain the host immunity. In our previous study, we reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome (bacteria, archaea and commensal respiratory viruses) but increases the abundance of pathobionts. This study aimed to assess the possible changes in the resident fungal diversity by the inclusion of opportunistic fungi due to the infection of SARS-CoV-2 in the NT of humans. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNAseq-based metagenomics analyses. Our results indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of NT fungi with a high inclusion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct microbiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species in the NT of COVID-19 patients. Importantly, 16% commensal fungal species found in the Healthy control were not detected in either COVID-19 patients or when they were recovered from the COVID-19. Pairwise Spearmans correlation test showed that several altered metabolic pathways had significant positive correlations (r > 0.5, p < 0.01) with dominant fungal species detected in three metagenomes. Taken together, our results indicate that SARS-CoV-2 infection causes significant dysbiosis of fungal microbiome and alters some metabolic pathways and expression of genes in the NT of human. Findings of our study might be helpful for developing microbiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients. Author summaryThe SARS-CoV-2 is a highly transmissible and pathogenic betacoronavirus that primarily enters into the human body through NT to cause fearsome COVID-19 disease. Recent high throughput sequencing and downstream bioinformatic analyses revealed that microbiome dysbiosis associated with SARS-CoV-2 infection are not limited to bacteria, and fungi are also implicated in COVID-19 development in susceptible individuals. This study demonstrates that SARS-CoV-2 infection results in remarkable depletion of NT commensal fungal microbiomes with inclusion of various opportunistic fungal pathogens. We discussed the role of these altered fungal microbiomes in the pathophysiology of the SARS-CoV-2 infection. Our results suggest that dysbiosis in fungal microbiomes and associated altered metabolic functional pathways (or genes) possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. Thus, the identifiable changes in the diversity and composition of the NT fungal population and their related genomic features demonstrated in this study might lay a foundation for better understanding of the underlying mechanism of co-pathogenesis, and the ongoing development of therapeutic agents including antifungal drugs for the resolution of COVID-19 pandemic.

microbiology↗

bioRxiv2022

B cells discriminate HIV-1 Envelope protein affinities by sensing antigen binding association rates

HIV-1 Envelope (Env) proteins designed to induce neutralizing antibody responses allow study of the role of affinities (equilibrium dissociation constant, KD) and kinetic rates (association/dissociation rates) on B cell antigen recognition. It is unclear whether affinity discrimination during B cell activation is based solely on Env protein binding KD, and whether B cells discriminate between proteins of similar affinities but that bind with different kinetic rates. Here we used a panel of Env proteins and Ramos B cell lines expressing IgM BCRs with specificity for CD4 binding-site broadly neutralizing (bnAb) or a precursor antibody to study the role of antigen binding kinetic rates on both early (proximal/distal signaling) and late events (BCR/antigen internalization) in B cell activation. Our results support a kinetic model for B cell activation in which Env protein affinity discrimination is based not on overall KD, but on sensing of association rate and a threshold antigen-BCR half-life.

immunology↗

bioRxiv2021

Exploring of bacterial blight resistance in landraces, mining of resistant gene(s) and genetic divergence of resistant germplasm through molecular markers and quantitative traits.

Bacterial blight, one of the oldest and severe diseases of rice poses a major threat towards global rice production and food security. Thereafter, sustainable management of this disease has given paramount importance globally. In the current study, we explored 792 landraces to evaluate their disease reaction status against three highly virulent strains (BXo69, BXo87 and BXo93) of Xanthomonas oryzae pv. oryzae (Xoo). Subsequently, we intended to identify the possible candidate resistant (R) genes responsible for the resistant reaction using six STS markers correspond to Xa4, xa5, Xa7, xa13, Xa21 and Xa23 genes and finally, we evaluated morphological and molecular diversity of the potential bacterial blight resistant germplasm using quantitative traits and ISSR markers. Based on pathogenicity test, a single germplasm was found as highly resistant while, 33 germplasm were resistant and 40 were moderately resistant. Further molecular study on these 74 germplasm divulged that 41 germplasm carried Xa4 gene, 15 carried xa5 gene, 62 carried Xa7 gene, 33 carried xa13 gene, and 19 carried Xa23 gene. Only a single germplasm consisted of Xa21 gene. Interestingly, we found a wide range of gene combinations ranged from 2 to 4 genes among the germplasm resistant to bacterial blight and G3 genotype (Acc. No. 4216; highly resistant) having Xa4, Xa7, xa13, Xa21 and G43 genotype (Acc. No. 1523; resistant) having Xa4, xa5, xa13 and Xa23 gene combination being the most effective against all the Xoo strains. Nonetheless, UPGMA dendrogram and heatmap analysis based on quantitative traits identified two important clusters viz. cluster-III and cluster-VIII with multiple desired traits However, genetic similarity based on ISSR marker data pointed out 3 germplasm, namely, G20 (Acc. No. 4004; contained Xa4, Xa7, xa13 genes), G17 (Acc. No. 3981; contained Xa7, xa13 genes) and G6 (Acc. No. 991; contained Xa4, Xa7, xa13, Xa23 genes) having comparatively lower genetic similarity (0.30, 0.37 and 0.38, respectively) with elite variety BRRI dhan28. Notably, Mantle test of molecular and morphological data indicated that there was a positive correlation (r = 0.113) between them. The outcome of this study would enrich and diversify the rice gene pool and would be useful for the development of durable bacterial blight resistant varieties.

plant biology↗

bioRxiv2021

Protein crosslinking as a therapeutic strategy for SOD1-related ALS

Mutations in the gene encoding Cu-Zn superoxide dismutase 1 (SOD1) cause a subset of familial amyotrophic lateral sclerosis (fALS). One effect of these mutations is that SOD1, which is normally a stable dimer, dissociates into toxic monomers. Considerable research efforts have been devoted to developing compounds that stabilize the dimer of fALS SOD1 variants, but these have not yet resulted in an approved drug. We demonstrate that a cyclic thiosulfinate cross-linker can stabilize prevalent disease-causing SOD1 variants. The degree of stabilization afforded by cyclic thiosulfinates (up to 24 {degrees}C) is unprecedented. We show this compound works rapidly in vivo with a half-life of ~3 days. The efficacy, low toxicity, and pharmacodynamics of cross-linker mediated stabilization make it a promising therapeutic approach for SOD1-related fALS. Significance statementCyclic thiosulfinate S-XL6 enables the kinetic stabilization of ALS-associated SOD1 variants, in vivo.

neuroscience↗

bioRxiv2021

Structural insights into the modes of relaxin-binding and tethered-agonist activation of RXFP1 and RXFP2

Our poor understanding of the mechanism by which the peptide-hormone H2 relaxin activates its G protein coupled receptor, RXFP1 and the related receptor RXFP2, has hindered progress in its therapeutic development. Both receptors possess large ectodomains, which bind H2 relaxin, and contain an N-terminal LDLa module that is essential for receptor signalling and postulated to be a tethered agonist. Here, we show that a conserved motif (GDxxGWxxxF), C-terminal to the LDLa, is critical for receptor activity. Importantly, this motif adopts different structures in RXFP1 and RXFP2, suggesting distinct activation mechanisms. For RXFP1, the motif is flexible, weakly associates with the LDLa, and requires H2 relaxin binding to stabilize an active conformation. Conversely, the GDxxGWxxxF motif in RXFP2 is more closely associated with the LDLa, forming an essential binding interface for H2 relaxin. These differences in the activation mechanism will aid drug development targeting these receptors.

biophysics↗