Biology subjects

Ali, A.

Publications and source records attributed to Ali, A..

130 records · Page 8Linked to original sources

bioRxiv2018

Comparing the metabolic fates of BALB/c mice maintained on cafeteria-style diets with differential nutritive values

Cafeteria (CAF) diet-fed rodents are shown to provide a robust model of metabolic syndrome and human obesity. The carbohydrate/fat-rich food-items provided to the CAF-diet-model more closely approximate the ultra-processed human diet. However, most of the previous studies applied the commercially available rodent chow-diet for the comparative analyses and labeled it as a healthy-diet. The presented work aims to extend the knowledge on CAF-diet model by exposing the mice to human foods with different nutritional values. Our major goal was to study the metabolic fates of mice maintained on human food-items, which depending upon on their macronutrient compositions are categorized as healthy or unhealthy. BALB/c mice were randomly allocated to one of the three dietary intervention groups, standard chow diet; high-sugar/high-fat-cafeteria (HSHF-CAF) diet; or low-sugar/low-fat-cafeteria (LSLF-CAF) diet, for 5 weeks. The differences in multiple metabolic parameters (including food-/energy /macronutrient-intake, body-weight gain rate, organ-to-body weight ratios, plasma lipid profiles, adipocyte physiology, lipid deposition in metabolic tissues and ectopic fat storage in heart and kidney) were compared among the three intervention groups. We did not observe hyperphagia in mice maintained on CAF-diets. Nonetheless, the CAF-diet-fed mice displayed increased weight-gain-rate, adiposity, and adipocyte hypertrophy when compared to the chow-fed mice. However, the mice maintained on the two cafeteria-style diets displayed similar metabolic profiles, with HSHF-CAF-group displaying slightly higher weight-gain-rate. The HSHF-CAF-and LSLF-CAF-diet induced comparable adiposity in BALB/c mice. Further studies, with longer dietary intervention periods, are required to elucidate the effects of differential CAF-diets on the metabolic health of mice.

biochemistry↗

bioRxiv2018

Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was [≥] 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

genomics↗

bioRxiv2018

Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

bioinformatics↗

bioRxiv2017

Cardio- and neurometabolic effects of lower-body pressure supported exercise in obese non-diabetic women: Resetting autonomic imbalance?

BackgroundOvernutrition and underactivity cause most chronic disease via inflammation and stress. Life-style changes such as diet is largely unsuccessful and exercise is painful, uncomfortable and difficult for people with diabesity, cardiorespiratory and joint diseases and cognitive decline affecting their ability to ambulate and adhere to exercise guidelines. Diets or exercise causing weight loss are stressful and trigger numerous redundant counter regulatory mechanisms defending lean body mass, explaining failures to sustain these behaviors. In this hypothesis-generating pilot study we used a NASA-developed weight supporting lower-body positive pressure (LBPP) treadmill providing comfortable low-amount, low intensity walking, challenging current exercise guidelines.\n\nMethodsSixteen nondiabetic, untrained, Black volunteer women (BMI 28-50), age 18-56 years were studied by anthropometry, analyses of energy expenditure and blood chemistry: oral glucose tolerance tests (OGTT) with insulin, C-peptide, GLP-1 and FFA and fasting lipids, cytokines, adipokines and appetitive peptides, before and after 10 weeks of twice weekly 30-minute weight supported LBPP treadmill sessions.\n\nResultsWe found novel baseline associations between gluco- and neuro-regulatory peptides and plasma lipids, inflammatory cytokines and appetitive hormones related to neurogenesis, mood and energy balance. Post-study, independent of body weight or energy expended there were significant decreases in OGTT plasma insulin (p=0.002) and GLP-1 (p=0.060) and fasting triglycerides (p=0.029), ghrelin (p=0.008) and changes in most molecules including increased leptin and beta-endorphin. Correlations between changes among different classes of peptides were highly significant, notably leptin - adiponectin, and beta-endorphin - oxytocin and orexin A. We propose synergy between low-amount, low-intensity exercise at levels below thresholds of increased sympathetic tone, and baro-physiological effects of LBPP normalizing parasympathetic tone.\n\nConclusionBrief, low-dose, lower-body positive-pressure weight-supported treadmill exercise improved cardiometabolic fitness and exhibited favorable changes in neuro-regulatory peptides without weight loss in inner-city obese Black women.

physiology↗