Biology subjects

Azam, M.

Publications and source records attributed to Azam, M..

7 recordsLinked to original sources

bioRxiv2026

Dissecting the genetic basis of DUS characters in Pakistani wheat varieties

Distinctness, Uniformity and Stability (DUS) testing is fundamental to varietal characterization and the protection of Plant Breeders Rights (PBRs), but conventional DUS assessment relies predominantly on morphological characteristics whose expression may be influenced by environmental conditions, developmental stage and observer-related variation. Integrating character-specific molecular markers with conventional DUS assessment may therefore improve the reproducibility and genetic resolution of varietal identification. This study investigated the genetic architecture of DUS characteristics in a panel of 102 historical and modern Pakistani wheat varieties using genome-wide association studies (GWAS). Phenotypic variation was evaluated using distribution, correlation and hierarchical clustering analyses, while the germplasm was genotyped using a wheat genotyping-by-targeted sequencing platform. After quality filtering, 21,670 high-quality single-nucleotide polymorphisms (SNPs) were retained for analyses of genetic diversity, population structure, linkage disequilibrium (LD) and marker-trait associations. Population structure analysis indicated extensive admixture, with cross-entropy supporting K = 9 ancestral components, whereas hierarchical genetic clustering separated the germplasm into five broad groups. The first three principal components explained 8.09%, 7.20% and 5.39% of the total genetic variation, respectively. GWAS using BLINK and FarmCPU identified significant associations for several diagnostically important DUS characteristics. Growth habit was strongly associated with SNP 1B_129176704, with an additional signal on chromosome 5B. Shattering showed its strongest association at 1D_445256324, accompanied by several closely linked SNPs in the same region and a secondary significant locus at 7B_703502819. Flag leaf length was associated with a cluster of SNPs on chromosome 6A, while tiller density showed a major association with 5D_205488820. These findings demonstrate substantial phenotypic and genetic diversity within Pakistani wheat germplasm and identify genomic regions that merit validation as character-specific molecular tools to complement conventional DUS testing and PBR implementation.

plant biology↗

bioRxiv2024

Enhanced intracranial aneurysm development in a rat model of polycystic kidney disease.

BackgroundPolycystic kidney disease (PKD) patients have a high intracranial aneurysms (IAs) incidence and risk of rupture. The mechanisms that make PKD patients more vulnerable to IA disease are still not completely understood. The PCK rat is a well-known PKD model and has been extensively used to study cyst development and kidney damage. Here, we used this rat model to study IA induction and vulnerability. MethodsIAs were induced in wild-type (WT) and PCK rats and their incidence was followed. Variation in the anatomy of the circle of Willis was studied in PCK rats and PKD patients. The expression of tight junction proteins was examined by immunohistochemistry in rats and in human ruptured and unruptured IAs from patients enrolled in the @neurIST study. ResultsAn increased frequency of fatal aortic dissection was unexpectedly observed in PCK rats after IA induction, which was due to modifications in the elastic architecture of the aorta in combination with the induced hypertension. Interestingly, IAs developed faster in PCK rats compared to WT rats. Variations in the anatomy of the circle of Willis were identified in PCK rats and PKD patients, a risk factor that may (in part) explain the higher IA incidence found in these groups. At 2-weeks after induction, the endothelium of IAs from PCK rats showed a decrease in the tight junction proteins zonula occludens-1 and claudin-5. This decrease in tight junction proteins was also observed in the endothelium of human ruptured IAs compared to unruptured IAs, making it a potential marker of IA wall vulnerability. ConclusionsOur study showed that PCK rats are more sensitive to IA induction. Variations in the anatomy of the circle of Willis and impaired regulation of tight junction proteins might put PCK rats and PKD patients more at risk of developing vulnerable IAs.

pathology↗

bioRxiv2024

A Comprehensive Evaluation of Large Language Models in Mining Gene Interactions and Pathway Knowledge

BackgroundUnderstanding complex biological pathways, including gene-gene interactions and gene regulatory networks, is critical for exploring disease mechanisms and drug development. Manual literature curation of biological pathways is useful but cannot keep up with the exponential growth of the literature. Large-scale language models (LLMs), notable for their vast parameter sizes and comprehensive training on extensive text corpora, have great potential in automated text mining of biological pathways. MethodThis study assesses the effectiveness of 21 LLMs, including both API-based models and open-source models. The evaluation focused on two key aspects: gene regulatory relations (specifically, activation, inhibition, and phosphorylation) and KEGG pathway component recognition. The performance of these models was analyzed using statistical metrics such as precision, recall, F1 scores, and the Jaccard similarity index. ResultsOur results indicated a significant disparity in model performance. Among the API-based models, ChatGPT-4 and Claude-Pro showed superior performance, with an F1 score of 0.4448 and 0.4386 for the gene regulatory relation prediction, and a Jaccard similarity index of 0.2778 and 0.2657 for the KEGG pathway prediction, respectively. Open-source models lagged their API-based counterparts, where Falcon-180b-chat and llama1-7b led with the highest performance in gene regulatory relations (F1 of 0.2787 and 0.1923, respectively) and KEGG pathway recognition (Jaccard similarity index of 0.2237 and 0. 2207, respectively). ConclusionLLMs are valuable in biomedical research, especially in gene network analysis and pathway mapping. However, their effectiveness varies, necessitating careful model selection. This work also provided a case study and insight into using LLMs as knowledge graphs.

bioinformatics↗

bioRxiv2023

Development of novel genetically-encoded fluorescent probes to track ceramides during phagocytosis

Ceramides regulate phagocytosis, however their exact function remains poorly understood. Here we sought 1) to develop genetically encoded fluorescent tools for imaging ceramide, and 2) to use them to examine ceramide dynamics during phagocytosis. Fourteen EGFP fusion constructs based on four known ceramide-binding domains were generated and screened. While most constructs localized to the nucleus or cytosol, three based on the CA3 ceramide-binding domain of KSR1 localized to plasma membrane or endolysosomes. C-terminally-tagged CA3 with a vector-based (C-KSR) or glycine-serine linker (C-KSR-GS) responded sensitively and similarly to ceramide depletion and accumulation using a panel of ceramide modifying drugs, whereas N-terminally tagged CA3 (N-KSR) responded differently to a subset of treatments. Lipidomic and liposome microarray analysis suggested that, instead, N-KSR preferentially binds to glucosyl-ceramide. Additionally, the three probes showed distinct dynamics during phagocytosis. Despite partial lysosomal degradation, C-KSR robustly accumulated at the plasma membrane during phagocytosis, whereas N-KSR becomes cytoplasmic at later timepoints. Moreover, weak recruitment of C-KSR-GS to endoplasmic reticulum and phagosomes was enhanced by overexpression of the endoplasmic reticulum proteins STIM1 and Sec22b, and was more salient in dendritic cells. The data suggest these novel probes can be used to analyze sphingolipid dynamics and function in living cells.

cell biology↗

bioRxiv2022

The SNARE Sec22b regulates phagosome maturation by promoting ORP8-mediated PI(4)P exchange at ER-phagosome contact sites.

The precise control of phagosome maturation is critical for innate and adaptive immunity, determining whether phagocytosed material is destroyed or used to present antigens. We observed previously that non-fusogenic contacts between the endoplasmic reticulum (ER) and phagosomes, called membrane contact sites (MCS), are tethered by the calcium regulator STIM1 and fine-tune phagosomal maturation. The secretory pathway SNARE protein Sec22b has been implicated in controlling phagocytosis, phagosome maturation and antigen presentation, though its effects are controversial, and its mechanism of action poorly understood. Recently, Sec22b was shown to tether MCS at the plasma membrane without mediating membrane fusion. Here, we show that Sec22b localizes to and regulates the frequency of ER-phagosome contacts independently of STIM proteins. Sec22b knockdown and overexpression of a an MCS-disrupting mutant Sec22b-P33 induced only mild or no effect on global and local calcium signalling. However, Sec22b knockdown altered phagosomal phospholipids including PI(3)P, PI(4)P and PS, but not PI(4,5)P2. Increased PI(4)P in shSec22b cells was rescued by re-expression of Sec22b or the artificial MCS tether MAPPER but not the P33 mutant. Moreover, Sec22b co-precipitated and was co-recruited to phagosomes with the PS/PI(4)P lipid exchange protein ORP8. Expression of wild-type, but not mutant ORP8, also rescued phagosomal PI(4)P. Concordantly, Sec22b, MAPPER and ORP8 but not P33 or the ORP8 mutant decreased phagolysosome fusion in shSec22b cells. These results clarify a novel mechanism through which Sec22b controls phagosome maturation and beg a reassessment of the relative contribution of Sec22b-mediated fusion versus tethering to phagosome biology.

cell biology↗

bioRxiv2021

Momelotinib is a highly potent inhibitor of FLT3-mutant AML

Kinase activating mutation in FLT3 is the most frequent genetic lesion associated with poor prognosis in acute myeloid leukemia (AML). Therapeutic response to FLT3 tyrosine kinase inhibitor (TKI) therapy is dismal, and many patients relapse even after allogenic stem cell transplantation. Despite the introduction of more selective FLT3 inhibitors, remissions are short-lived, and patients show progressive disease after an initial response. Acquisition of resistance-conferring genetic mutations and growth factor signaling are two principal mechanisms that drive relapse. FLT3 inhibitors targeting both escape mechanisms could lead to a more profound and lasting clinical responses. Here we show that the JAK2 inhibitor, momelotinib, is an equipotent type-1 FLT3 inhibitor. Momelotinib showed potent inhibitory activity on both mouse and human cells expressing FLT3-ITD, including clinically relevant resistant mutations within the activation loop at residues, D835, D839, and Y842. Additionally, momelotinib efficiently suppressed the resistance mediated by FLT3 ligand (FL) and hematopoietic cytokine activated JAK2 signaling. Interestingly, unlike gilteritinib, momelotinib inhibits the expression of MYC in leukemic cells. Consequently, concomitant inhibition of FLT3 and downregulation of MYC by momelotinib treatment showed better efficacy in suppressing the leukemia in a preclinical murine model of AML. Altogether, these data provide evidence that momelotinib is an effective type-1 dual JAK2/FLT3 inhibitor and may offer an alternative to gilteritinib. Its ability to impede the resistance conferred by growth factor signaling and activation loop mutants suggests that momelotinib treatment could provide a deeper and durable response; thus, warrants its clinical evaluation. Key pointsO_LIMomelotinib shows high efficacy against FLT3 mutated AML cells including quizartinib-resistant activation loop variants. C_LIO_LIMomelotinib effectively suppresses intrinsic resistance conferred by FLT3 ligand and hematopoietic cytokines (GM-CSF and IL3). C_LI

cancer biology↗

bioRxiv2019

Animal model and therapeutic prospects for left ventricular hypertrophy and associated renal complication

Cardiac and renal dysfunction often co-occur and considerably worsen the prognosis leading to difficulty in therapy in left ventricular hypertrophy (LVH). The aim of this study was to elucidate changes in expression of human ortholog genes of hypertension, vascular and cardiac remodeling and hypertensive nephropathy phenotypes under normal, disease and gasotransmitter, H2S (hydrogen sulphide) and NO (nitric oxide) and combined (H2S+NO), treatment of rat myocardium and renal tissues. LVH rat models were generated and were treated with H2S and NO. Relative gene expression was quantified. Heart and renal physical indices were significantly modified under individual as well as combined H2S+NO treatment in control and LVH rats. Expression analysis revealed, hypertension, vascular remodeling genes ACE, TNF and IGF1, mRNAs to be significantly increased (P<0.05) in myocardia and kidneys of LVH rats, while individual and combined H2S+NO treatment reduced gene expression to normal/near to normal values. The cardiac remodeling genes MYH7, TGF{beta}, SMAD4 and BRG1 expression were significantly up-regulated (P<0.05) in the myocardia of LVH and combined H2S+NO treatment, which recovered the normal/near to normal expression more effectively as compared to individual treatments. Interestingly, individual as well as combined H2S and NO treatment significantly decreased PKD1 expression in renal tissue, which was significantly up-regulated in LVH rats (P<0.05). The reduction in hemodynamic parameters and cardiac indices as well as alteration in gene expression on treatment in LVH rat model indicates important therapeutic potential of combined treatment with H2S+NO gasotransmitters in hypertension and cardiac hypertrophy associated with renal complications.

pharmacology and toxicology↗