Biology subjects

Mohammed, A. I.

Publications and source records attributed to Mohammed, A. I..

6 recordsLinked to original sources

bioRxiv2026

Mutagenesis study of a Bacteriophytochrome - insights for the development of labels for optical imaging.

Bacteriophytochromes (BphPs) find increasing interest as near-infrared (NIR) labels for imaging. Applications range from whole animal imaging to cell-to super-resolution microscopy. Here we present a comprehensive study of a BphP from Rhizobium etli (ReBphP) allowing mutant-based insights into BphP photophysics. This is complemented by QM/MM-optimized deep-learning structure predictions of ReBphP and variants in their photoswitched states, rationalizing the effects of variants. Pertaining to imaging, based on our study we identify a bright and far red-shifted BphP for imaging in mammalian cells as well as a fluorescent photoswitching BphP. Utilizing the latter, we introduce photoswitching fluorescence background suppression for in vivo whole animal fluorescence imaging achieving higher contrast over background than possible utilizing non-switching labels.

biochemistry↗

bioRxiv2020

Distinct Neuronal Populations Contribute to Trace Conditioning and Extinction Learning in the Hippocampal CA1

Trace conditioning and extinction learning depend on the hippocampus, but it remains unclear how ongoing neural activities in the hippocampus are modulated during different learning processes. To explore this question, we performed calcium imaging in a large number of individual CA1 neurons during both trace eye-blink conditioning and subsequent extinction learning in mice. Using trial-averaged calcium fluorescence analysis, we found direct evidence that in real time, as learning emerges, distinct populations of CA1 cells contribute to trace conditioned learning versus extinction learning. Furthermore, we examined network connectivity by calculating co-activity between CA1 neuron pairs, and found that CA1 network connectivity is different between conditioning and extinction and between correct versus incorrect behavioral responses during trace conditioned learning. However, the overall connectivity density remains constant across these behavioral conditions. Together, our results demonstrate that distinct populations of CA1 neurons, forming different sub-networks with unique connectivity patterns, encode different aspects of learning.

neuroscience↗

bioRxiv2019

Identification of Six novel missense single nucleotide polymorphisms in MAOA gene predisposing to aggressive behavior. Bioinformatics study.

BackgroundAn astonishing observation is that aggressive behavior is actually a highly heritable. Recent experimental work and behavior research has linked individual variation in a functional polymorphism of the monoamine oxidase-A gene (MAOA) to the occurrence of anger-driven aggression. Aggressive antisocial and violent behavior has become a regularly debated topic in the scientific community; the impending question is what is the source of aggressive behavior, is it genetic or environmental or is it just an individual choice. This study aims to analyses the SNPs found in MAOA gene and it is possible association to aggressive behavior. MethodVarious bioinformatics software (SIFT, PolyPhen-2, PROVEAN, SNAP22, SNP&GO and PMut)is used to analyses the SNPs within the MAOA gene to study the structural and functional implication on the associated protein, which is further clarified using chimera software. Then gene-gene interaction is studied with geneMANIA software. Furthermore, conservation and annotation studies were done through the ConSurf server and Variant Effect Predictor (VEP) respectively. ResultSix missense SNPs were found to affect the structural and functional prospect of MAOA protein. ConclusionGenetic mutation within MAOA is likely to be associated with aggressive behavior; this will enrich future management and screening possibilities for this behavior.

bioinformatics↗

bioRxiv2019

In silico analysis of CDC73 gene revealing 11 novel SNPs associated with Jaw Tumor Syndrome

Back groundhyperparathyroidism-jaw tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the effect of SNPs on CDC73 structure and function using different bioinformatics tools.\n\nMethodComputational analysis using eight different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, PMut and Imutant were used to identify the impact on the structure and/or function of CDC73 gene that might be causing jaw tumour.\n\nResultsFrom (733) SNPs identified in the CDC73 gene we found that only Eleven were deleterious to the function and structure of protein and expected to cause syndrome.\n\nConclusionEleven substantial genetic/molecular aberrations in CDC73 gene were identified that could serve as actionable targets for chemotherapeutic intervention in patients whose disease is no longer surgically curable.

bioinformatics↗

bioRxiv2019

In silico analysis of coding SNPs and 3′-UTR associated miRNAs in DCAF17 gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome

BackgroundWoodhouse-Sakati Syndrome refers to a group of inherited disorders characterized by alopecia, hypogonadism, diabetes mellitus, hypothyroidism and progressive extrapyramidal signs. The aim of this study is to identify the pathogenic SNPs in the DCAF17 gene with their related mciroRNAs and their effect on the structure and function of the protein.\n\nMaterial and MethodsWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. After that we defined the miRNAs founded in the 3'-UTR region on the DCAF17 gene and studied the annotations relative to it.\n\nResultsTen deleterious SNPs out of 339 were found to have a damaging effect on the protein structure and function, with one significant micoRNA in the 3'-UTR region.\n\nConclusionThis was the first in silico analysis of DCAF17 gene, in which 10 novel mutations were found using different bioinformatics tools that could be used as a diagnostic markers for Woodhouse-Sakati syndrome, with one relevant microRNA that can regulate the function of the protein.

bioinformatics↗

bioRxiv2017

Striatal cholinergic receptor activation causes a rapid, selective, & state-dependent rise in corticostriatal β activity.

Cortico-basal ganglia-thalamic (CBT) {beta} oscillations (15-30 Hz) are elevated in Parkinsons disease and correlated with movement disability. To date, no experimental paradigm outside of loss of dopamine has been able to specifically elevate {beta} oscillations in the CBT loop. Here, we show that activation of striatal cholinergic receptors selectively increased {beta} oscillations in mouse striatum and motor cortex. In individuals showing simultaneous {beta} increases in both striatum and M1, {beta} partial directed coherence (PDC) increased from striatum to M1 (but not in the reverse direction). In individuals that did not show simultaneous {beta} increases, {beta} PDC increased from M1 to striatum (but not in the reverse direction), and M1 was characterized by persistent {beta}-HFO phase-amplitude coupling. Finally, the direction of {beta} PDC distinguished between {beta} subbands. This suggests: (1) striatal cholinergic tone exerts state-dependent and frequency-selective control over CBT {beta} power and coordination; (2) ongoing rhythmic dynamics can determine whether elevated {beta} oscillations are expressed in striatum and M1; (3) altered striatal cholinergic tone differentially modulates distinct {beta} subbands.

neuroscience↗