Biology subjects

Islam, S.

Publications and source records attributed to Islam, S..

4 recordsLinked to original sources

bioRxiv2018

Phosphorylation of the alpha2 glycine receptor induces an extracellular conformational change and slows the rise and decay rates of glycinergic synaptic currents

The 2 glycine receptor (GlyR) is a pentameric ligand-gated anion channel that plays a key role in cortical interneuron migration and in the differentiation of cortical progenitor cells into functional neurons. It also mediates tonic inhibitory chloride currents in adult forebrain neurons. Disruption of 2 GlyR gene expression or receptor function results in the aberrant functioning of neuronal circuits which contributes to the pathophysiology of schizophrenia, autism and epilepsy. This implicates the 2 GlyR as a possible therapeutic target for a range of neurological disorders. However, despite its therapeutic potential, little is known about the mechanisms by which 2 GlyRs are functionally modulated. To address this, we investigated whether the 2 GlyR is modulated by phosphorylation at a serine residue (S341) within the same PKA consensus sequence (R-E-S-R) that houses the 3 GlyR S346 residue that is known to be phosphorylated by PKA. Resolving this question might uncover a novel means of physiologically, pathologically or therapeutically modulating 2 GlyRs. We show using voltage-clamp fluorometry that forskolin-induced phosphorylation of S341 induces a conformational change in the glycine binding site. We also employed glycinergic artificial synapses to demonstrate that the S341E phospho-mimetic mutation slows the rise and decay rates of 2-mediated glycinergic inhibitory postsynaptic currents. These results suggest that PKA phosphorylation alters the structural and functional properties of the 2 GlyR. This information may help to identify new mechanisms by which 2 GlyRs may be pathologically modified or therapeutically targeted for the treatment of neurological disorders.

neuroscience↗

bioRxiv2018

Wheat avenin-like protein and its significant Fusarium Head Blight resistant functions

Wheat Avenin-like proteins (TaALP) are atypical storage proteins belonging to the Prolamin superfamily. Previous studies on ALPs have focused on the proteins positive effects on dough strength, whilst no correlation has been made between TaALPs and the plant immune system. Here, we performed genome-wide characterization of ALP encoding genes in bread wheat. In silico analyses indicated the presence of critical peptides in TaALPs that are active in the plant immune system. Pathogenesis-related nucleotide motifs were also identified in the putative promoter regions of TaALP encoding genes. RT-PCR was performed on TaALP and previously characterised pathogenesis resistance genes in developing wheat caryopses under control and Fusarium graminearum infection conditions. The results showed that TaALP and NMT genes were upregulated upon F. graminearum inoculation. mRNA insitu hybridization showed that TaALP genes were expressed in the embryo, aleurone and sub-aleurone layer cells. Seven TaALP genes were cloned for the expression of recombinant proteins in Escherichia coli, which displayed significant inhibitory function on F. graminearum under anti-fungal tests. In addition, FHB index association analyses showed that allelic variations of two ALP genes on chromosome 7A were significantly correlated with FHB symptoms. Over-expression of an ALP gene on chromosome 7A showed an enhanced resistance to FHB. Yeast two Hybridization results revealed that ALPs have potential proteases inhibiting effect on metacaspases and beta-glucosidases. A vital infection process related pathogen protein, F. graminearum Beta-glucosidase was found to interact with ALPs. Our study is the first to report a class of wheat storage protein or gluten protein with biochemical functions. Due to its abundance in the grain and the important multi-functions, the results obtained in the current study are expected to have a significant impact on wheat research and industry.

molecular biology↗

bioRxiv2017

De novo discovery of structural motifs in RNA 3D structures through clustering

As functional components in three-dimensional conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures; second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin, and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch, and ribozyme.

bioinformatics↗

bioRxiv2017

Molecular analysis of the midbrain dopaminergic niche during neurogenesis

Midbrain dopaminergic (mDA) neurons degenerate in Parkinsons disease and are one of the main targets for cell replacement therapies. However, a comprehensive view of the signals and cell types contributing to mDA neurogenesis is not yet available. By analyzing the transcriptome of the mouse ventral midbrain at a tissue and single-cell level during mDA neurogenesis we found that three recently identified radial glia types 1-3 (Rgl1-3) contribute to different key aspects of mDA neurogenesis. While Rgl3 expressed most extracellular matrix components and multiple ligands for various pathways controlling mDA neuron development, such as Wnt and Shh, Rgl1-2 expressed most receptors. Moreover, we found that specific transcription factor networks explain the transcriptome and suggest a function for each individual radial glia. A network controlling neurogenesis was found in Rgl1, progenitor maintenance in Rgl2 and the secretion of factors forming the mDA niche by Rgl3. Our results thus uncover a broad repertoire of developmental signals expressed by each midbrain cell type during mDA neurogenesis. Cells identified for their emerging importance are Rgl3, a niche cell type, and Rgl1, a neurogenic progenitor that expresses ARNTL, a transcription factor that we find is required for mDA neurogenesis.

systems biology↗