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Hasan, M. M.

Publications and source records attributed to Hasan, M. M..

At least 19 recordsLinked to original sources

CBAM-enhanced MaxViT-Tiny for gastrointestinal endoscopy image classification: Robustness, explainability, and external validation

Automated classification of the huge number of images generated during gastrointestinal (GI) endoscopy is required for reliable and interpretable diagnosis, but there is concern about the vulnerability of deep models to adversarial perturbations. In the current study, a MaxViT-Tiny backbone with a Convolutional Block Attention Module (CBAM) head is used for 8-class classification of the Kvasir endoscopic images. After deleting duplicate images, 3,996 images remained, which were split into a training set (70%), a validation set (15%) and a test set (15%); the model was compared with five backbones using the same CBAM head under three random seeds. The proposed model obtained the highest test accuracy of 94.33%, a macro F1 score of 0.9431, and a macro area under the receiver operating characteristic curve (AUC) of 0.9975, with a mean accuracy of 93.72 {+/-} 1.06% across all seeds. White-box FGSM, PGD, CW-L2, and MI-FGSM attacks greatly reduced the accuracy: after adversarial fine-tuning, the accuracy under FGSM was 74.17%, while the accuracy under PGD and MI-FGSM was below 4%, showing poor cross-attack generalization. A preliminary attack detector obtained an AUC of 0.857. Grad-CAM++, Score-CAM, and GradientSHAP sometimes identified clinically relevant regions, but also sometimes focused on non-anatomical artefacts. High accuracy on clean images, even with attention augmentation, therefore does not imply high accuracy on adversarial images or reliable explanations, and the model needs further verification on independent datasets and multi-centre validation before clinical use.

bioengineering↗

FlexAutoDock: A Flexible Platform for Automated Molecular Docking and Virtual Screening of Natural and Synthetic Compounds

Drug discovery (DD) is a complex, time-consuming, and resource-intensive process that involves the identification of therapeutic targets, selection of bioactive compounds, and extensive experimental validation. The discovery of promising therapeutic compounds from large libraries of phytochemicals and synthetic molecules remains a major challenge in modern drug development. Screening millions of compounds through conventional experimental approaches requires substantial time, cost, and computational resources. In recent years, in- silico molecular docking has emerged as an important computational approach for predicting interactions between small molecules and target proteins, thereby helping researchers prioritize promising compounds for further investigation. Several molecular docking webservers, including iScreen, SwissDock, CB-Dock2, DockThor, and MTiOpenScreen, have been developed to support virtual screening studies. However, many currently available platforms still face some important limitations. Most existing tools lack integrated repositories of medicinal plant-derived phytochemicals and organism-derived bioactive compounds, automated mapping between plants and their associated phytochemicals, and flexible ligand retrieval using chemical names, SMILES strings, PubChem CIDs, or drug names. In addition, many platforms require extensive manual protein and ligand preparation, provide limited support for AlphaFold-predicted protein structures, and lack efficient large-scale multi-target virtual screening. Most existing docking platforms offer limited support for interactive inspection of docked protein-ligand complexes, often requiring users to download the results and analyse them using external molecular visualization software. To address these limitations, we developed FlexAutoDock, an automated cloud-based molecular docking platform that provides a unified environment for protein-ligand docking and large-scale virtual screening. Unlike existing web servers, FlexAutoDock integrates curated repositories of medicinal plant- derived phytochemicals, organism-derived bioactive compounds, and synthetic compounds from the ZINC database while supporting flexible ligand acquisition through medicinal plant or organism selection, chemical names, SMILES strings, PubChem CIDs, and drug-name queries. The platform further streamlines the docking workflow through automated protein structure retrieval from the Protein Data Bank and AlphaFold databases, receptor and ligand preparation, chain-specific protein selection, blind and site-specific docking, interactive visualization of predicted protein-ligand complexes, and scalable multi-target virtual screening. The resulting platform enables rapid, flexible, and large-scale virtual screening while simplifying the molecular docking workflow, providing researchers with an accessible computational resource for accelerating early-stage drug discovery. FlexAutoDock offers a fast, reliable, and accessible computational platform for molecular docking and virtual screening, freely available to the scientific community at http://103.99.177.82:3000/.

bioinformatics↗

CRISPR-mediated Correction of Oncogenic AS-NMD in Splicing Factor Mutant Cancer

Alternative splicing coupled to nonsense-mediated mRNA decay (AS-NMD) evolved as a master regulator of gene expression. Dysregulated AS-NMD has been identified as the root of many human maladies, from developmental defects to deadly cancer. Poison exons (PEs) are highly conserved alternative exons that contain a premature termination codon and elicit AS-NMD when included in a transcript. Cancer cells often exploit the inclusion of PEs to downregulate tumor suppressors or the exclusion of PEs to upregulate oncoproteins. Therefore, PEs have drawn significant attention as a novel therapeutic avenue for cancer and other diseases. Here, we examine a therapeutic proof-of-concept for manipulating PE-mediated oncogenic AS-NMD using a CRISPR-based approach. Using paired guide RNA, we successfully deleted a PE of a tumor suppressor (EZH2) from the genome of SRSF2-mutated leukemia. This editing resulted in EZH2 mRNAs without a PE, escaped AS-NMD, and restored the protein expression. This subsequently reinstated H3K27 histone methylation and rescued defective chromatin regulation associated with impaired hematopoietic stem cell differentiation. Finally, we showed the preferential advantages of CRISPR over the antisense technology we recently developed targeting the PE of EZH2. Therefore, the CRISPR strategy shows compelling evidence as a therapeutic approach targeting PE in cancer and other human diseases.

cancer biology↗

Targeting EZH2 Oncogenic Splicing: Decoding the Regulatory Network and Antisense Correction

Recurrent mutations in splicing factors (SFs) have been established as crucial drivers of tumorigenesis in several types of blood cancer, and also common in a variety of solid tumors. Mutations change the RNA-binding preferences of SFs, promote global splicing alterations, and often generate erroneous mRNAs that are then degraded by nonsense-mediated mRNA decay (NMD). Consequently, several critical genes linked to hematopoiesis are dysregulated, leading to blood cancer. Although the field has progressed considerably in identifying aberrant genes and affected pathways, effective therapies have not yet emerged in SF-mutated cancers. To address this key gap, we instigated a gene-specific targeted strategy by unlocking the regulatory network. As a proof-of-concept, we scrutinized a tumor suppressor gene EZH2, which is a bona fide target in SRSF2-mutated cancer. We precisely defined splicing cis-elements in EZH2 transcripts and illustrated the dynamic choreography of regulatory proteins in the entire splicing and NMD catalytic pathways. We uncovered a highly coordinated cross-regulation between splicing and NMD promoted by mutant SRSF2 by enhancing the deposition of critical spliceosome- and NMD-associated factors, augmenting mRNA decay to ablate tumor suppression. We then designed antisense oligonucleotides (ASOs) targeting important regulatory sites. Our lead ASO successfully corrects aberrant splicing and NMD, restores the expression and function of EZH2, and partially rescues hematopoietic defects and cellular properties. Our study demonstrates that ASO pharmacology is an actionable strategy for clinical development, challenging the existing paradigms in SF-mutated cancers.

cancer biology↗

Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities

African men are disproportionately impacted by aggressive prostate cancer (PCa). Key to this disparity both genetic and environmental factors, alluding to epigenetic modifications. However, African-inclusive prostate tumour DNA methylation studies are lacking. Assembling a multi-geo-ancestral prostate tissue cohort, including men with (57 African, 48 European, 23 Asian) or without (65 African) PCa, we interrogate for genome-wide differential methylation. Overall, methylation appears to be driven by ancestry over geography (152 southern Africa, 41 Australia). African tumours show substantial heterogeneity, with universal hypermethylation indicating epigenetic silencing, encompassing PCa suppressor genes and enhancer-targeted binding motifs. Conversely, African tumour-associated heterochromatic hypomethylation suggests permissive chromatin remodelling, with developmental pathway activation via enhancer targets. Taken together, we show methylation aberrations favour metastatic growth, genomic instability and disease aggressiveness in African tumours, which we hypothesise is driven by extensive plasticity of intergenic regulatory regions.

genomics↗

Rejuvenated human amniotic fluid stem cells: a superior source of standardized induced mesenchymal stem cells for enhanced therapeutic applications

Human fetal mesenchymal stem cells (hfMSCs) present advantageous characteristics compared to their adult counterparts and have emerged as potent cells in the field of regenerative medicine. In the context of skeletal regeneration, human amniotic fluid stem cells (AFSCs) have been shown to improve the quality and structure of the bone extracellular matrix in an experimental model of severe osteogenesis imperfecta. However, primary hfMSCs undergo replicative senescence during in vitro expansion, along with a progressive decrease in plasticity and tissue repair potential. To overcome this challenge, we rejuvenated AFSC to pluripotency using non-integrative episomal reprogramming and subsequently re-derived the cells towards the mesoderm to obtain induced MSCs (iMSCs). We found that iMSCs have a slower proliferation rate compared to their parental cell line (40h{+/-}2h vs. 29h{+/-}5h) but retain the multipotency and differentiation potential characteristic of MSCs. Comparative genomic analysis revealed that iMSCs express higher levels of genes involved in maintaining stemness, cell signaling, adhesion and migration, as well as promoting osteoblast differentiation, whilst AFSC expressed higher levels of genes involved in cell proliferation. In addition, iMSCs secrete small extracellular vesicles (iEVs) that have the potential to stimulate fibroblast migration, a key process in tissue repair and wound healing. Together, these data suggest that resetting the epigenetic clock of primary hfMSCs may represent a promising strategy to address the limitations associated with primary cell use and enhance their therapeutic potential.

cell biology↗

Identification of potential inhibitors against Inosine 5'-Monophosphate Dehydrogenase of Cryptosporidium parvum through an integrated in silico approach

The protozoan parasite Cryptosporidium, found in several vertebrates, including humans, is the source of the global infection known as cryptosporidiosis, which manifests as acute gastroenteritis, abdominal pain, and diarrhea. Although infections in certain individuals have been linked to other species, Cryptosporidium parvum is the main cause of illnesses in humans. Lactate Dehydrogenase, Inosine 5'-Monophosphate Dehydrogenase (IMPDH), and several other targets have been identified by the genome sequencing of C. parvum. Bioactive phytochemicals derived from nature have enormous potential as anti-cryptosporidiosis agents. The study aimed to identify new anti-cryptosporidial agents that work against the IMPDH of the parasite by using integrated in silico approaches. In this study, a total of 24 bioactive phytochemicals were screened virtually through molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analyses. Four lead compounds were identified, including Brevelin A (-8.9 kcal/mol), Vernodalin (-8.7 kcal/mol), Luteolin (-8.6 kcal/mol), and Pectolinarigenin (-8.1 kcal/mol), against the IMPDH protein (PDB ID: 4IXH) from the parasite. All the lead compounds had excellent pharmacokinetic and pharmacodynamic characteristics. The toxicity analysis showed satisfactory results with no major side effects. All of the selected compounds showed no violation of Lipinskis rules of five, indicating the possibility of oral bioavailability as potential drug candidates. In the majority of cases, target class prediction-identified enzymes, as well as investigational and experimental drugs, have been found to have structural similarities to the lead compounds. With significant biochemical interactions, all of the targeted phytochemical compounds have demonstrated excellent pharmacokinetics and better bioavailabilities. The findings strongly recommend in vitro experimental studies to aid in the development of novel therapeutics against Cryptosporidium parvum.

bioinformatics↗

The prion-like protein Doppel: A soluble biomarker steering ovarian cancers peritoneal to circulatory dissemination

Detecting ovarian cancer (OC) early using existing biomarkers, e.g., cancer antigen 125 (CA125), is challenging due to its ubiquitous expression in many tissues. Doppel, a prion-like protein, expresses in male reproductive organ but absent in female reproductive systems and healthy tissues, but plays an important role in neoangiogenesis. Here, we have shown two platforms, soluble Doppel in sera/ascites and Doppel expressed circulating tumor cells (Dpl+CTC) in the whole blood, to detect subsets of epithelial OC (EOC). Increased level of Doppel in the sera of OC patients, in three different cohorts, confirm Doppel as OC specific biomarker. Serum Doppel level distinguishes EOC subtypes and early stages HGSOCs from non-cancerous conditions with high sensitivity and specificity. Stratifying the EOCs based on Doppel level, we categorized them into Doppel-high (Dplhi) and Doppel-low (Dpllow) groups. Using ascites-derived organoids and single cell sequencing of whole ascites of Dplhi and Dpllow patients, we identify that Doppel induces epithelial-mesenchymal transition (EMT) and creates an immunosuppressive microenvironment, respectively. Doppel levels in the sera/ascites correlate with the changes of Dpl+CTC number in whole blood, highlighting the association of Doppel-induced EMT with CTC dissemination in circulation. Thus, Doppel-based detection of EOC subtypes could be a promising platform as clinical biomarker and link Doppel-axis with OC dissemination.

cancer biology↗

Exploring Effector Protein Dynamics and Natural Fungicidal Potential in Rice Blast Pathogen Magnaporthe oryzae

Rice blast, caused by Magnaporthe oryzae, is a severe agricultural disease leading to significant global economic losses. Genetic and genomic investigations have identified crucial genes and pathways involved in its pathogenesis, particularly highlighting effector proteins like AvrPik variants and MAX proteins. These proteins interact with specific Pik alleles on rice chromosome 11, influencing host immune responses. This study focused on 35 plant-derived metabolites known for their antifungal properties, evaluating their potential as fungicidal agents against M. oryzae. Molecular docking analyses identified Hecogenin and Cucurbitacin E as highly effective binders to MAX40 and APIKL2A proteins, respectively, which are pivotal for fungal virulence and immune evasion. Molecular dynamics simulations further validated strong and stable interactions, affirming the therapeutic potential of these compounds. Additional assessments including Lipinskis rule of five criteria and toxicity predictions indicated their suitability for agricultural use. These findings underscore the promise of Hecogenin and Cucurbitacin E as lead candidates in developing novel fungicidal strategies against rice blast, offering prospects for enhanced crop protection and agricultural sustainability.

bioinformatics↗

A Novel Artificial Intelligence (AI) Method to Classify and Predict the Progression of Alzheimers Disease

PurposeThe objective of this study was to develop a novel AI-ensembled network based on the most important features and affected brain regions to accurately classify and exhibit the pattern of progression of the stages of Cognitive Impairment (CI). MethodsWe proposed a novel ensembled architecture, 3D ResNet-18 - RF (Random Forest), and used this network to categorize the stages of Alzheimers disease (AD). The residual unit (blocks of ResNet) was introduced to the 3D Convolutional Neural network (CNN) to solve the degradation problem. It was considered an innovative strategy since the combination with fine-tuning resulted in higher accuracy. This network was trained on selected features and affected brain regions. The structured magnetic resonance images (MRI) were collected from the Alzheimers Disease Neuroimaging Initiative (ADNI) dataset, and the random forest was used for determining the importance of the features and affected regions from the parcellated 170 regions of interest (ROIs) using Atlas, automated anatomical labeling 3(AAL-3). This framework classified five categories of AD and detected the progression pattern. ResultsThe proposed network showed promising results with a 66% F-1 score, 76% sensitivity, and 93.5% specificity, which outperformed the performance of conventional methods for categorizing five categories. Ventral Posterolateral and Pulvinar lateral regions were the regions most affected, indicating the progression from early MCI to AD. The five-fold validation accuracy for the developed model was 60.02%. ConclusionThe results showed that the gray matter to white matter ratio was the most significant feature, which also accurately predicted the progression pattern. The performance metrics fluctuated with different hyperparameters, but they never exceeded 0.05% of the estimated results, indicating the validity and originality of the suggested methodology.

bioinformatics↗

Pleotropic effects of a recessive COL1A2 mutation occurring in a mouse model of severe osteogenesis imperfecta

Approximately 85-90% of individuals with Osteogenesis Imperfecta (OI) have dominant pathogenic variants in the COL1A1 or COL1A2 genes. This leads to decreased or abnormal Collagen type I production. Subsequently, bone formation is strongly reduced, causing bone fragility and liability to fractures throughout life. OI is clinically classified in 5 types with the severity ranging from mild to lethal depending on the gene and the type and location of the OI-causative variant and the subsequent effect on (pro) collagen type I synthesis. However, the specific effects on the phenotype and function of osteoblasts are not fully understood. To investigate this, the OI murine model was used, with the oim/oim (OIM) mice closest resembling severely deforming OI type 3 in humans. We showed that in OIM, COL1 mutation results in a multifactorial inhibition of the osteogenic differentiation and maturation as well as inhibition of osteoclastogenesis. The phenotype of differentiated OIM osteoblasts also differs from that of wild type mature osteoblasts, with upregulated oxidative cell stress and autophagy pathways, possibly in response to the intracellular accumulation of type I collagen mRNA. The extracellular accumulation of defective type I collagen fibres contributes to activation of the TGF-{beta} signalling pathway and activates the inflammatory pathway. These effects combine to destabilise the balance of bone turnover, increasing bone fragility. Together, these findings identify the complex mechanisms underlying OI bone fragility in the OIM model of severe OI and can potentially enable identification of clinically relevant endpoints to assess the efficacy of innovative pro-osteogenic treatment for patients with OI.

genetics↗

Cryptosporidium Life Cycle Small Molecule Probing Implicates Translational Repression And An Apetala 2 Transcription Factor In Sexual Differentiation

The apicomplexan parasite Cryptosporidium is a leading cause of childhood diarrhea in developing countries. Current treatment options are inadequate and multiple preclinical compounds are being actively pursued as potential drugs for cryptosporidiosis. Unlike most apicomplexans, Cryptosporidium spp. sequentially replicate asexually and then sexually within a single host to complete their lifecycles. Anti-cryptosporidial compounds are generally identified or tested through in vitro phenotypic assays that only assess the asexual stages. Therefore, compounds that specifically target the sexual stages remain unexplored. In this study, we leveraged the ReFRAME drug repurposing library against a newly devised multi-readout imaging assay to identify small-molecule compounds that modulate sexual differentiation and maturation. mRNA-seq studies confirmed selective modulation of sexual differentiation for 10 hit compounds (9 inhibitors and 1 accelerator). The collective transcriptomic profiles of these compounds indicates that translational repression accompanies Cryptosporidium sexual differentiation, which we validated experimentally. Additionally, cross comparison of the RNA-seq data with promoter sequence analysis for stage-specific genes converged on a key role for an Apetala 2 (AP2) transcription factor (cgd2_3490) in sexual differentiation. Finally, drug annotation for the ReFRAME hits indicates that an elevated supply of energy equivalence in the host cell is critical for gamont formation.

microbiology↗

The mature N termini of Plasmodium effector proteins confer specificity of export

The intraerythrocytic malaria parasite Plasmodium falciparum exports hundreds of proteins into the host red blood cell (RBC). Most are targeted to the ER by a stretch of hydrophobic amino acids and cleaved further downstream at a conserved motif called the Protein Export Element (PEXEL) by the ER protease plasmepsin V (PM V). The mature effectors then travel through the secretory pathway to the parasitophorous vacuole (PV) that surrounds the parasite. There, PEXEL proteins are somehow recognized as export-destined proteins, as opposed to PV- resident proteins, and are selectively translocated out into the RBC. The mature N terminus appears to be important for export. There is conflicting data on whether PM V cleavage is needed for proper export, or whether any means of generating the mature N terminus would suffice. We replaced the PEXEL-containing N-terminal sequence of an exported GFP reporter with a signal peptide sequence and showed that precise cleavage by signal peptidase, generating the proper mature N terminus, yields export competence. Expressing a construct with only the native ER targeting signal without the PM V cleavage site dramatically decreased the amount of a mature PEXEL reporter, indicating that the hydrophobic stretch lacks an efficient cleavage signal. Therefore, the PEXEL motif functions as a specialized signal cleavage site when appropriately located after an ER targeting sequence. Our data suggest that PM V cleavage and RBC export are two independent events for PEXEL proteins. We also tested and rejected the hypothesis that an alpha-helical mature N terminus is necessary for export. ImportanceMalaria parasites export hundreds of proteins to the cytoplasm of the host red blood cells for their survival. A five amino acid sequence, called the PEXEL motif, is conserved among many exported proteins and is thought to be a signal for export. However, the motif is cleaved inside the endoplasmic reticulum of the parasite and mature proteins starting from the fourth PEXEL residue travel to the parasite periphery for export. We showed that the PEXEL motif is dispensable for export as long as identical mature proteins can be efficiently produced via alternative means in the ER. We also showed that the exported and non-exported proteins are differentiated at the parasite periphery based on their mature N termini, however, any discernible export signal within that region remained cryptic. Our study resolves a longstanding paradox in PEXEL protein trafficking.

microbiology↗

Intermittent Cytomegalovirus Infection Alters Neurobiological Metabolism and Induces Cognitive Deficits in Mice

Risk factors contributing to dementia are multifactorial. Pathogens as risk factors for dementia is largely correlative with few causal relationships. Here, we demonstrate that intermittent cytomegalovirus (CMV) infection in mice, mimicking human chronic infection and reactivation/reinfection events, alters blood brain barrier (BBB) metabolic pathways. An increase in basal mitochondrial function is observed in brain microvasculature endothelial cells (BMEC) at 12 months post infection but not at earlier time points and is accompanied by elevated levels of superoxide, indicative of oxidative stress. Further, these mice score lower in cognitive assays as compared to age-matched controls. Our data show that repeated systemic infection with CMV, alters BBB metabolic function and impacts cognition. These observations provide mechanistic insights through which pathogens contribute to the progression of pathologies associated with dementia. In BriefMechanistic evidence supporting an infectious etiology of dementia (e.g. Alzheimers Disease) are poorly defined. Harrison et al., show that intermittent infection with cytomegalovirus metabolically rewires the blood brain barrier and neighboring glial cells altering their function, resulting in decreased cognitive function.

neuroscience↗

Low temperature induced quiescence in parasitoids Trichogramma evanescens Westwood and Trichogramma chilonis Ishii reared on Plodia interpunctella (Hübner): Its utilization as quality control for mass rearing

Egg parasitoid, Trichogramma spp. is an important potential biological control agent for wide range of lepidopteran pests. Cold storage of host eggs has been proposed as a valuable technique for ensuring the release of sufficient parasitoid numbers whenever it is needed. Thus, the impact of low temperatures to induce quiescence in Trichogramma evanescens and Trichogramma chilonis was studied using eggs of Plodia interpunctella as hosts. Prepupae of the parasitoids Trichogramma evanescens and T.chilonis were stored for 15, 30, 45, 60 and 75 d at 4{degrees}C, following a 7 d period of acclimation at 10{degrees}C. Both parasitoid species seem to survive unfavorable temperature conditions by entering a state of quiescence. Parasitism, adult emergence, female proportion relative to male and F1 adult emergence were not affected by cold storage in either parasitoid for up to 30 d of storage. Parasitized host eggs of P. interpunctella can be stored for up to 60 d at 4{degrees}C for both parasitoids, but there was no emergence at 75 d. Results clearly show that there are specific intervals of cold storage during which the parasitoids can remain unaffected for relatively long periods of time. Although we observed some adverse effect in longevity and parasitism rates, the technique described here can be further utilized in mass rearing strategies of egg parasitoids for relatively long periods that will allow shipment and application in biological control programs.

zoology↗

LSTM-PHV: Prediction of human-virus protein-protein interactions by LSTM with word2vec

Viral infection involves a large number of protein-protein interactions (PPIs) between human and virus. The PPIs range from the initial binding of viral coat proteins to host membrane receptors to the hijacking of host transcription machinery. However, few interspecies PPIs have been identified, because experimental methods including mass spectrometry are time-consuming and expensive, and molecular dynamic simulation is limited only to the proteins whose 3D structures are solved. Sequence-based machine learning methods are expected to overcome these problems. We have first developed the LSTM model with word2vec to predict PPIs between human and virus, named LSTM-PHV, by using amino acid sequences alone. The LSTM-PHV effectively learnt the training data with a highly imbalanced ratio of positive to negative samples and achieved an AUC of 0.976 with an accuracy of 98.4% using 5-fold cross-validation. By using independent test dataset, we compared the LSTM-PHV with existing state-of-the-art PPI predictors including DeepViral. In predicting PPIs between human and unknown or new virus, the LSTM-PHV presented higher performance than the existing predictors when they were trained by multiple host protein-including datasets. LSTM-PHV learnt multiple host protein sequence contexts more efficiently than the DeepViral. Interestingly, learning of only sequence contexts as words presented remarkably high performances. Use of uniform manifold approximation and projection demonstrated that the LSTM-PHV clearly distinguished the positive PPI samples from the negative ones. We presented the LSTM-PHV online web server that is freely available at http://kurata35.bio.kyutech.ac.jp/.

bioinformatics↗

Spontaneous selection of Cryptosporidium drug resistance in a calf model of infection

The intestinal protozoan Cryptosporidium is a leading cause of diarrheal disease and mortality in young children. There is currently no fully effective treatment for cryptosporidiosis, which has stimulated interest in anticryptosporidial development over the last [~]10 years with numerous lead compounds identified including several tRNA synthetase inhibitors. In this study, we report the results of a dairy calf efficacy trial of the methionyl-tRNA (CpMetRS) synthetase inhibitor 2093 and the spontaneous emergence of drug resistance. Dairy calves experimentally infected with Cryptosporidium parvum initially improved with 2093 treatment, but parasite shedding resumed in two of three calves on treatment day five. Parasites shed by each recrudescent calf had different amino acid altering CpMetRS mutations, coding either an aspartate 243 to glutamate (D243E) or a threonine 246 to isoleucine (T246I) mutation. Transgenic parasites engineered to have either the D243E or T246I CpMetRS mutation using CRISPR/Cas9 grew normally but were highly 2093 resistant; the D243E and T246I mutant expressing parasites respectively had 2093 EC50S of 613- or 128-fold that of transgenic parasites with wild-type CpMetRS. In studies using recombinant enzymes, the D243E and T246I mutations shifted the 2093 IC50 by >170-fold. Structural modeling of CpMetRS based on an inhibitor-bound Trypanosoma brucei MetRS crystal structure suggested that the resistance mutations reposition nearby hydrophobic residues, interfering with compound binding while minimally impacting substrate binding. This is the first report of naturally emerging Cryptosporidium drug resistance, highlighting the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence. ImportanceCryptosporidium is a leading protozoan cause of diarrhea in young children with no reliable treatment. We report results of a dairy calf drug efficacy trial and the spontaneous emergence of drug resistance. Cryptosporidium parvum infected calves initially improved with drug treatment, but infection relapsed in two animals. Parasites shed by each recrudescent calf had mutations in the gene encoding the drug target that altered its amino acid sequence. Recapitulation of the drug target mutations by CRISPR/Cas9 genome editing resulted in highly drug-resistant parasites, and recombinant mutant enzymes were resistant to inhibition. This is the first report of naturally emerging Cryptosporidium drug resistance. There is a currently a great opportunity to impact public health with new drugs to treat cryptosporidiosis, and this report highlights the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence in order to realize their full potential. One-sentence summaryDrug-target point mutations mediating anticryptosporidial resistance spontaneously arose in the dairy calf C. parvum infection model.

microbiology↗

Screening and potent applicability analysis of commonly used pesticides against desert locust: an integrative entomo-informatics approach

The locust problem is a global threat for food security. Locusts can fly and migrate overseas within a zip and creating a large-scale devastation to the diversified agro-ecosystem. GIS based analysis showed the recent movement of locusts, among them Schistocerca gregaria and Locusta migratoria are predominant in Indian subcontinent and are found more notorious and devastating one. This devastation needs to be stopped to save human race from food deprivation. In our study, we screened some commonly used agricultural pesticides and strongly recommended three of them viz. biphenthrin, diafenthiuron and silafluofen which might be potential to control the desert locusts based on their binding affinity towards the locusts survival proteins. Our phylogenetic analysis reveals that these three recommended pesticides might also show potency to the other locust species as well as they are also way safer than the other commercially available pesticides. These proposed pesticides bioactive analogs from fungus and bacteria may also show efficacy as next generation controlling measures of locust as well as different kind of pests. These recommended pesticides are expected to be highly effective against locusts and needs to bring forward by the entomologists by performing experimental field trials. HighlightsO_LIGIS map unmasked the 2020 migratory pattern of locusts which now predominant towards Indian subcontinent. C_LIO_LIBiphenthrin, diafenthiuron and silafluofen showed maximum binding affinity. C_LIO_LIBiphenthrin and diafenthiuron were relatively safer than silafluofen. C_LIO_LIBioactive analogs from fungus and bacteria could be an alternative to control locusts. C_LIO_LIPesticides inhibition hotspots for desert locusts were unrevealed. C_LI

bioinformatics↗