Biology subjects

Ali, M. S.

Publications and source records attributed to Ali, M. S..

11 recordsLinked to original sources

bioRxiv2026

Genetic dissection of the obesity paradox in carotid atherosclerosis using a hyperlipidemic mouse cohort

BackgroundOverweight and obese individuals often exhibit lower mortality rates or better prognoses than lean or normal-weight individuals with stroke and other diseases, a phenomenon called the "obesity paradox". Carotid atherosclerosis is the primary cause of ischemic stroke, and body weight serves as a reliable surrogate for adiposity in mice. MethodsPhenotypic and genetic connections of carotid atherosclerosis with body weight were evaluated in 299 F2 mice derived from BALB/cJ and LP/J Apoe knockout (Apoe-/-) mice. F2 mice were fed a Western diet for 12 weeks. Atherosclerotic lesion sizes in left carotid arteries, body weight, coat color, plasma lipids, glucose, small dense LDL ApoB, and malondialdehyde were measured, and 11,000 single nucleotide polymorphism (SNP) markers were genotyped. ResultsCarotid lesion sizes inversely correlated with body weight in both sexes. Genome-wide scans identified two significant quantitative trait loci (QTLs) for carotid atherosclerosis on chromosomes (Chr) 6 and 15 in an additive sex model, and five QTLs on Chr 6, 7, 12, 13, and 15 in an interactive sex model. Adjusting for body weight variation downgraded Chr 15 QTL (Cath5) in both models, whereas other QTLs upgraded in the additive sex model and downgraded in the interactive sex model. Human syntenic region of Cath5 associated with carotid intima-medial thickness (cIMT) and waist-to-hip ratio (WHR). ConclusionsThese findings indicate that the obesity paradox in carotid atherosclerosis is partially driven by shared genetic components that exert opposing effects on adiposity and plaque development and act through sex-dependent mechanisms.

genetics↗

bioRxiv2026

Phosphorylation-mediated regulation of the essential splicing factor PUF60

PUF60 is a splicing factor related to the polypyrimidine-tract binding protein U2AF2. PUF60 is deleted in developmental disorders such as Verheij syndrome and amplified in approximately 8% of cancers. Thus, both increases and decreases in PUF60 expression can have profound physiological effects. However, little is known about how changes in PUF60 expression impact global splicing patterns. Here, we created a model system of CRISPRa/i in mouse stem cells (mESCs) to transcriptionally upregulate or downregulate Puf60. Our results uncovered extensive transcriptional, post-transcriptional, and post-translational regulation of Puf60 protein expression. We observed that Puf60 protein levels in normal mESCs drop dramatically at a critical cell density, leading to cell death. Puf60 is very essential in stem cells, and its repression causes cell death and impacts specific splicing events, including its own splicing autoregulation, providing valuable insights into the functional consequences of PUF60 dysregulation. Analysis of phosphoprotein data revealed phosphorylation of threonine at the N-terminus of PUF60. Our results showed that mutating threonine to glutamate downregulates the protein and alters its localization. Thus, our study reveals a novel regulatory mechanism of Puf60 phosphorylation that mediates its function and may be related to its frequent overexpression in cancer cells.

molecular biology↗

bioRxiv2025

Activin receptor type IIA/B blockade increases muscle mass and strength, but compromises glycemic control in mice

Short abstractO_ST_ABSPurposeC_ST_ABSBlocking the Activin receptor type IIA and B (ActRIIA/IIB) has clinical potential to increase muscle mass and improve glycemic control in obesity, cancer, and aging. However, the impact of blocking ActRIIA/IIB on strength, metabolic regulation and insulin action remains unclear. MethodsHere, we investigated the effect of short- (10 mg/kg once, 40h) or long-term (10 mg/kg twice weekly, 21 days) antibody targeting ActRIIA/IIB (ActRIIA/IIBab) in lean and diet-induced obese mice and engineered human muscle tissue. ResultsShort-term ActRIIA/IIB administration in lean mice increased insulin-stimulated glucose uptake in skeletal muscle by 76-105%. Despite this, ActRIIA/IIB-treated mice exhibited 33% elevated fasting blood glucose and glucose intolerance. Moreover, long-term ActRIIA/IIB treatment increased average muscle mass (20%) and reduced fat mass (-8%) in obese mice but did not change insulin-stimulated glucose uptake in skeletal muscle or adipose tissue, yet induced marked glucose intolerance, and increased hepatic glucose output in response to pyruvate. Concomitantly, long-term ActRIIA/IIBab treatment increased strength (30%) in mouse soleus muscle and prevented activin A-induced loss of tissue strength in engineered human muscle tissue. Surprisingly, long-term ActRIIA/IIBab treatment lowered volitional running (-250%). ConclusionOur findings demonstrate that, in accordance with human studies, ActRIIA/IIB blockade holds promise for increasing muscle mass, strength, and insulin sensitivity. However, contrary to the improved glycemic control in humans, ActRIIA/IIB blockade in mice causes severe glucose intolerance and lowers voluntary physical activity. Our study underscores the complex metabolic and functional consequences of ActRIIA/IIB blockade, and highlight species differences on glycemic control, which warrant further investigation.

molecular biology↗

bioRxiv2025

pH-Responsive Near Infrared Light Triggered Hydroxyapatite Nanoparticles for Targeted Photothermal Cancer Therapy

Photothermal therapy (PTT), which utilizes photothermal agents (PTAs) to induce localized hyperthermia within tumors upon light irradiation, has emerged as a promising cancer treatment strategy. However, low water solubility, poor in vivo circulation stability and a lack of tumor specificity of many common PTAs limit their applicability. To address these issues, we have developed a simple, yet highly potent, tumor-targeted nanotheranostic system that consists of lipid/PEG-coated hydroxyapatite nanoparticles (LHAPNs) encapsulating the near-infrared (NIR) photothermal dye IR106 (LHAPNIRs). The lipid coat serves to retain the encapsulated dye and prevent serum protein adsorption and macrophage recognition, which would otherwise destabilize the nanoparticles and hinder their tumor targeting efficiency. Additionally, the coat is functionalized with the tumor-acidity-triggered rational membrane (ATRAM) peptide for efficient and specific internalization into tumor cells in the mildly acidic microenvironment of tumors. The nanoparticles facilitated real-time fluorescence and thermal imaging of tumors and demonstrated potent NIR-light triggered anticancer activity in vitro and in vivo, without adversely affecting healthy tissue, leading to markedly prolonged survival. Our results demonstrate that the biocompatible and biodegradable ATRAM-functionalized LHAPNIRs (ALHAPNIRs) effectively combine dual-mode diagnostic imaging with targeted cancer PTT.

bioengineering↗

bioRxiv2024

Housing temperature dictates the systemic and tissue specific molecular responses to cancer in mice

Cancer cachexia is a metabolic condition affecting up to 80% of patients with cancer. Cachexia is mediated by reduced muscle and fat mass and impaired function, and it lowers survival for patients. With no approved drugs to treat cachexia, preclinical efforts focus on understanding the molecular mechanisms underlying this condition to reveal treatment targets. Housing laboratory mice at ambient temperature imposes cold stress, leading to induced thermogenic activity and consequent whole-body metabolic adaptations. Yet, the impact of housing temperature in in vivo preclinical cachexia remains unknown. We found that thermoneutral (TN) housing in C26 carcinoma-bearing (C26) mice affected lean and fat mass, but not muscle weight or force. TN housing improved glucose tolerance in C26 mice, while enhancing circulating abundance of FGF21 and IL-6. Thermogenic tissues, especially brown adipose tissue, exhibited housing temperature-dependent molecular responses to cancer in oxygen consumption, ATP levels and SERCA ATPase activity, which are all crucial for cancer-induced whole-body metabolic adaptations. We conclude that molecular and systemic adaptations to cancer in mice critically depend on housing temperature, which should be considered in the design and interpretation of preclinical cancer studies.

physiology↗

bioRxiv2024

Computational Transcriptomic and Comparative Genomic Analysis of dead box RNA Helicase gene AT2G45810 Expressed in Plants Arabidopsis thaliana

Arabidopsis thaliana is a short life cycle, small genome, and Brassicaceae family winter annual small flowering plants. It is popularly used as a model organism in genetics and plant biology research, and it is essential to understanding the molecular biology of many plant features, including light sensing and flower formation. It also plays a key role in the science of agronomy, and plant transcriptomics as well as genomics. When it comes to the development of multicellular creatures, transcriptional programs are crucial. The constantly active growth of different organ systems is supported by transcriptional programs. Arabidopsis embryos possess remarkable transcriptomes compared to other plant tissues comprising somatic embryo differentiation circumstances operating during plant embryogenesis. Here we show that the transcriptomic analysis of the genome dead box RNA helicase gene AT2G45810 of Arabidopsis thaliana Araport11 species which revealed the specific gene expression patterns of Arabidopsis tissue-specific information of developmental map, embryo, single cell, DNA damage, cellular interactions, pathway analysis, etc., through In Silico or computational approaches. In this particular study, we used the TAIR, Phytozome, and plant comparative genomics portal for retrieving and identification of specific genes of interest. Next, we used web-based Bar utoronto tools to visualize other data, including functional genomics. Their protein and gene expression tools facilitate the exploration of promoters, the identification of protein-protein interactions, the viewing of expression patterns as electronic fluorescent pictographs or heatmaps, and more.

developmental biology↗

bioRxiv2023

The Rho GTPase Rac1 mediates exercise training adaptations

Exercise training elicits tremendous health benefits; however, the molecular underpinnings are poorly understood. As one of the most regulated groups of proteins following acute exercise in human muscle, Rho GTPases are unexplored candidates for mediating the beneficial effects of exercise. The Rho GTPase Rac1 was activated during multiple exercise modalities and remained elevated hours after resistance exercise in human muscle. Inducible muscle-specific Rac1 knockout (Rac1 imKO) mice, displayed attenuated muscle protein synthesis, glycogen resynthesis and p38 MAPK signaling in recovery from contractions. Exercise training upregulated Rac1 protein content in human and mouse muscle. Overexpression of hyperactive Rac1 elevated reactive oxidant species production during exercise yet did not induce a trained muscle phenotype. In Rac1 imKO mice, the improvements in running capacity and muscle mass after exercise training were diminished. Using gain- and loss-of-function mouse models and human muscle biopsies, we identify Rac1 as a regulator of exercise training adaptions. HighlightsO_LIVarious exercise modalities activate Rac1 signaling in human skeletal muscle. C_LIO_LIHSP27, MNK1, and CREB are Rac1-dependent contraction-responsive targets in muscle. C_LIO_LIPost-contraction protein synthesis requires Rac1 but not NOX2. C_LIO_LIRac1-NOX2 signaling is necessary for post-contraction glycogen resynthesis. C_LIO_LIExercise training increases Rac1 protein content in human and mouse muscles. C_LIO_LIRac1 mediates critical adaptations to exercise training. C_LI

molecular biology↗

bioRxiv2023

Bacterial risk evaluation of widely consumed fast foods by the younger population in Bangladesh and its potential health effects

Food-borne illness is a significant public health concern in Bangladesh, especially among the younger generation. They often consume spicy street foods, such as Fusca, Hog plum bedfellow, and Chotpoti. These foods can be contaminated with harmful bacteria, which can cause various diseases, including diarrhea, cholera, and dysentery. This study investigated the microbiological quality of three commonly consumed street foods in Bangladesh. We collected samples of Fusca, Hog plum bedfellow, and Chotpoti from different vendors in Dhaka and analyzed them in a laboratory. We found that all three of the food samples were contaminated with a variety of bacteria, including Bacillus spp., Haemophilus spp., Salmonella spp., Klebsiella spp., Staphylococcus spp., and Streptococcus spp. Some of these bacteria, such as Haemophilus spp., were resistant to the antibiotic ciprofloxacin. Our findings suggest that there is a high risk of food-borne illness associated with the consumption of street foods in Bangladesh. We urge vendors and consumers to take steps to improve food safety, such as proper food handling and cooking and clean water and utensils.

microbiology↗

bioRxiv2022

AMPK is elevated in human cachectic muscle and prevents cancer-induced metabolic dysfunction in mice

BackgroundMetabolic dysfunction and cancer cachexia are associated with poor cancer prognosis, yet the molecular mechanisms causing cancer-induced metabolic dysfunction and cachexia remain to be defined. A key link between metabolic- and muscle mass-regulation is adenosine monophosphate-activated protein kinase (AMPK). As AMPK could be a potential treatment, it is important to determine the function for AMPK in cancer-associated metabolic dysfunction and cachexia. Here we determined the function of AMPK in cancer-associated metabolic dysfunction, insulin resistance, and cachexia. MethodsIn vastus lateralis muscle biopsies from pre-cachectic and cachectic patients with Non-Small-Cell Lung Carcinoma (NSCLC), AMPK signaling and expression were examined by immunoblotting. To investigate the role of muscle AMPK, male mice overexpressing a dominant-negative AMPK2 (kinase-dead) specifically in striated muscle (mAMPK-KD) were inoculated with Lewis Lung Carcinoma (LLC) cells. In a subsequent cohort, male LLC-tumor-bearing mice were treated with/without 5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR) to activate AMPK for 13 days. Littermate mice were used as control. Metabolic phenotyping of mice was performed via indirect calorimetry, body composition analyses, glucose- and insulin tolerance tests, tissue-specific 2-deoxy- glucose (2-DG) uptake, and immunoblotting. ResultsIn muscle from patients with NSCLC, we found increased expression of AMPK subunits 1, 2, {beta}2, {gamma}1, and {gamma}3; ranging from +27% to +79% compared to healthy control subjects. AMPK subunit expression correlated with indices of cachexia, including cross sectional area and weight loss. Tumor-bearing mAMPK-KD mice presented increased fat loss as well as glucose and insulin intolerance. LLC in mAMPK-KD mice displayed lower insulin-stimulated 2-DG uptake in skeletal muscle (quadriceps; -35%, soleus; -49%, EDL; -48%) and the heart (-29%) compared to non-tumor-bearing mice. In skeletal muscle, mAMPK-KD abrogated the tumor-induced increase in phosphorylation of TBC1D4thr642. Additionally, protein expression of TBC1D4 (+26%), pyruvate dehydrogenase (PDH, +94%), and PDH-kinases (PDKs, +45% to +100%), and glycogen synthase (+48%) were increased in skeletal muscle of tumor-bearing mice in an AMPK-dependent manner. Lastly, chronic AICAR treatment elevated hexokinase-II protein expression and normalized phosphorylation of p70S6Kthr389 (mTORC1 substrate) and ACCser212 (AMPK substrate) and rescued the cancer-induced insulin intolerance. ConclusionsUpregulated protein expression of AMPK subunits observed in skeletal muscle of (pre)cachectic patients with non-small-cell lung carcinoma. This seemed protective inferred by AMPK-deficient tumor-bearing mice being highly prone to developing metabolic dysfunction, which included the AMPK-dependent regulation of several proteins involved in glucose metabolism. These observations highlight the potential for targeting AMPK to counter cancer-associated metabolic dysfunction and cachexia. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/495096v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@7ff169org.highwire.dtl.DTLVardef@1c249aeorg.highwire.dtl.DTLVardef@736350org.highwire.dtl.DTLVardef@17d2be2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2020

Conditioned media from MCF7 and BT474 breast cancer cells induce insulin resistance in skeletal muscle myotubes

BackgroundMetabolic disorders are prevalent in women with breast cancer, increasing mortality and cancer recurrence rates. Despite clinical implications, the cause of breast cancer-associated metabolic dysfunction remains poorly understood. Skeletal muscle is crucial for insulin-stimulated glucose uptake, thus key to whole-body glucose homeostasis. In this study, we determined the effect of breast cancer cell-conditioned media on skeletal muscle glucose uptake in response to insulin. MethodL6 myotubes overexpressing myc-tagged GLUT4 (GLUT4myc-L6) were incubated with 40% conditioned media from tumorigenic MCF7 or BT474, or non-tumorigenic control MCF10A breast cells. Mass-spectrometry-based proteomics was applied to detect molecular rewiring in response to breast cancer in the muscle. Expression of myogenesis and inflammation markers, GLUT4 translocation, [3H]-2-deoxyglucose (2DG) uptake, and intramyocellular insulin signalling were determined. ResultsBreast cancer cell-conditioned media induced proteomic changes in pathways related to sarcomere organisation, actin filament binding, and vesicle trafficking, disrupted myogenic differentiation, activated an inflammatory response via NF-{kappa}B, and induced muscle atrophy. Basal and insulin-stimulated GLUT4 translocation and 2DG uptake were reduced in myotubes treated with breast cancer cell-conditioned media compared to the control. Insulin signalling via the Rho GTPase Rac1 was blocked in breast cancer-treated myotubes, while Akt-TBC1D4 signalling was unaffected. ConclusionConditioned media from MCF7 and BT474 breast cancer cells reduced skeletal muscle glucose uptake via inhibition of GLUT4 translocation and intramyocellular insulin signalling by selectively blocking Rac1 activation and inducing inflammation. These findings indicate that the rewiring of skeletal muscle proteome, inflammation, and insulin signalling could play a role in metabolic dysfunction in patients with breast cancer.

cancer biology↗

bioRxiv2019

Prevalence and risk factors profile of seropositive Toxoplasmosis gondii infection among apparently immunocompetent Sudanese women

ObjectivesToxoplasma gondii is an opportunistic parasite that cause a clinical manifestation known as toxoplasmosis. We investigated the prevalence and potential risk factors of T. gondii infection among women in Khartoum, Sudan. A sero-parasitological cross-sectional study included 100 women aging between 15-50 years old was conducted in Khartoum, Sudan between January - November 2018. Serum samples were collected and investigated for presence of anti-T. gondii immunoglobulins.\n\nResultsMean age of the women population included was 26.75{+/-}8.25 with a range between 15 and 50 years. Sero-prevalence of T. gondii antibodies was 27% (27/100) with a 95% confidence interval (CI) of 18.6 - 36.8%. Among seropositive population 81% (22/27), 15% (4/27) and 4% (1/27) were seropositive for IgG antibodies, IgM antibodies and both antibodies respectively. Age group 21-30 years old had the highest frequency of detected IgG (10/45) and IgM (3/45). Married women had the highest frequency of detected IgG or IgM, 18/79 and 3/79, respectively. Risk factors analysis showed a total of 37/100 participants were having direct contact with cats and 66/100 have a frequent raw meat consumption, neither direct cats contact nor raw meat consumption had statistically significant association with seropositivity to T. gondii (P. value =0.052 and 0.565, respectively).

microbiology↗