Biology subjects

Ali, S.

Publications and source records attributed to Ali, S..

3 recordsLinked to original sources

bioRxiv2018

Stage specific classification of DEGs via statistical profiling and network analysis reveals potential biomarker associated with various stages of TB

BackgroundTuberculosis (TB) is a deadly transmissible disease that can infect almost any body-part of the host but is mostly infect the lungs. It is one of the top 10 causes of death worldwide. In the 30 high TB burden countries, 87% of new TB cases occurred in 2016. Seven countries: India, Indonesia, China, Philippines, Pakistan, Nigeria, and South Africa accounted for 64% of the new TB cases. To stop the infection and progression of the disease, early detection of TB is important. In our study, we used microarray data set and compared the gene expression profiles obtained from blood samples of patients with different datasets of Healthy control, Latent infection, Active TB and performed network-based analysis of DEGs to identify potential biomarker.\n\nObjectivesWe want to observe the transition of genes from normal condition to different stages of the TB and identify, annotate those genes/pathways/processes that play key role in the progression of TB disease during its cyclic interventions in human body.\n\nResultsWe identified 319 genes that are differentially expressed in various stages of TB (Normal to LTTB, Normal to Active TB and LTTB to active TB) and allocated to pathways from multiple databases which comprised of curated class of associated genes. These pathways importance was then evaluated according to the no. of DEGs present in the pathway and these genes show the broad spectrum of processes that take part in every state. In addition, we studied the regulatory networks of these classified genes, network analysis does consider the interactions between genes (specific for TB) or proteins provide us new facts about TB disease, which in turn can be used for potential biomarkers identification. We identified total 29 biomarkers from various comparison groups of TB stages in which 14 genes are over expressed as host responses against pathogen, but 15 genes are down regulated that means these genes has allowed the process of host defense to cease and give time to pathogen for its progression.\n\nConclusionsThis study revealed that gene-expression profiles can be used to identify and classified the genes on stage specific pattern among normal, LTTB and active TB and network modules associated with various stages of TB were elucidated, which in turn provided a basis for the identification of potential pathways and key regulatory genes that may be involved in progression of TB disease.

systems biology↗

bioRxiv2018

Retronasal Habituation: Characterization and Impact on Flavor Perception using Time-Intensity

Olfactory habituation results from prolonged exposure to an odor, leading to perceptual changes defined by several characteristics. To date, human habituation research has focused on orthonasal olfaction which is perceived externally while ignoring internal routes of odor perception related to flavor. In our study, we conducted two experiments to characterize retronasal olfactory habituation and measured its impact on flavor perception. In Experiment 1, 22 participants rhythmically breathed a food odor (lime), non-food odor (lavender), and blank (propylene glycol) that was presented using an orally-adhered strip, while rating the odor intensity using the time-intensity procedure. After a 10-minute exposure, the participants ate a lime-flavored gummy and rated the lime flavor. In Experiment 2, the same procedure was performed for a low-level lime odor, a simple (lime oil) and complex (lime oil + sucrose + citric acid) beverage as the flavor stimuli. Our results demonstrated two known principles of habituation for retronasally presented odors: 1) prolonged exposure lead to decreased perception, 2) weaker stimuli lead to more rapid habituation. Additionally, we found that the non-food odor habituated slower than the food odor; however, the participants seemed to recover simultaneously upon food and beverage consumption leading to no change in flavor perception.

neuroscience↗

bioRxiv2017

Quantitative variation and evolution of spatially explicit morphogen expression in Drosophila

Robustness in development allows for the accumulation of neutral genetically based variation in expression, and here will be termed genetic stochasticity . This largely neutral variation is potentially important for both evolution and complex disease phenotypes. However, it has generally only been investigated as variation exhibited in the response to large genetic perturbations. In addition, work on variation in gene expression has similarly generally been limited to being spatial, or quantitative, but because of technical restrictions not both. Here we bridge these gaps by investigating replicated quantitative spatial gene expression using rigorous statistical models, in different genotypes, sexes, and species (Drosophila melanogaster and D. simulans). Using this type of quantitative approach with developmental data allows for effective comparison among conditions, including health versus disease. We apply this approach to the morphogenetic furrow, a wave of differentiation that sweeps across the developing eye disc. Within the morphogenetic furrow, we focus on four conserved morphogens, hairy, atonal, hedgehog, and Delta. Hybridization chain reaction quantitatively measures spatial gene expression, co-staining for all four genes simultaneously and with minimal effort. We find considerable variation in the spatial expression pattern of these genes in the eye between species, genotypes, and sexes. We also find that there has been evolution of the regulatory relationship between these genes. Lastly, we show that the spatial interrelationships of these genes evolved between species in the morphogenetic furrow. This is essentially the first population genetics of development as we are able to evaluate wild type differences in spatial and quantitative gene expression at the level of genotype, species and sex.

developmental biology↗