Shajahan Anver

University College London | UCL · Department of Genetics, Evolution and Environment (GEE)

Chromatin regulatory proteins affect diverse developmental and environmental response pathways via their influence on nuclear processes such as the regulation of gene expression. Through a genome-wide genetic screen, we implicate a novel protein called X-chromosome-associated protein 5 (Xap5) in chromatin regulation. We show that Xap5 is a chromati...

Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Employing comparative transcriptomics of six Arabidopsis thaliana accessions and three addition...

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed...

Genomes produce widespread long non-coding RNAs (lncRNAs) of largely unknown functions. We characterize aal1 (ageing-associated lncRNA), which is induced in quiescent fission yeast cells. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression prolongs their lifespan, indicating that aal1 acts in tra...

The NotebookLM podcast for our paper "Ageing-associated long non-coding RNA extends lifespan and reduces translation in non-dividing cells" https://notebooklm.google.com/notebook/e29e205c-dd2b-4124-a3a6-8b4eafd89dae/audio

tRNAs are evolutionarily ancient molecular decoders essential for protein translation. In eukaryotes, tRNAs and other short, noncoding RNAs are transcribed by RNA polymerase (Pol) III, an enzyme that promotes ageing in yeast, worms, and flies. Here, we show that a partial reduction in Pol III activity specifically disrupts tRNA levels. This effect...

Genomes produce widespread long non-coding RNAs (lncRNAs) of largely unknown functions. We characterize aal1 (aging-associated lncRNA) which is induced in quiescent cells of fission yeast. Deletion of aal1 shortens the chronological lifespan of non-dividing cells, while ectopic overexpression of aal1 prolongs their lifespan, indicating that this ln...

The circadian oscillator allows organisms to synchronize their cellular and physiological activities with diurnal environmental changes. In plants, the circadian clock is primarily composed of multiple transcriptional-translational feedback loops. Regulators of post-transcriptional events, such as pre-mRNA splicing factors, are also involved in con...

The circadian oscillator allows organisms to synchronize their cellular and physiological activities with diurnal environmental changes. In plants, the circadian clock is primarily composed of multiple transcriptional-translational feedback loops. Regulators of post-transcriptional events, such as pre-mRNA splicing factors, are also involved in con...

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed...

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analysed...

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analyzed...

Plants recognize surrounding microbes by sensing microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). Despite their significance for microbial control, the evolution of PTI responses remains largely uncharacterized. Here, by employing comparative transcriptomics of six Arabidopsis thaliana accessions and three...

Postdoctoral research that I initated and completed halway through when I was at Max Plank Institute and completed by Thomas and Frederickson.

ggplot2 is an R package capable of plotting various graphs useful for scientists especially for visualizing data and for presentations. I just uploaded my notes hoping might be useful for someone. Include options to plot various graphs, adding error bars, annotating texts, colour/ add gene name by significance etc.

What you need are two or more lists of names to draw venndiagrams. The code shows how to draw venndiagrams with expression data in R including extracting gene lists from expression data, prepare objectives and define colours.

Highthrougput omics data visualization almost always involves clustering. Clustering and plotting heatmaps help to visulaize the data beyond numbers and help to see structure and associations in the data. The script summarises few popular ways of plotting heatmaps, clustering and extracting clusters in R. To get an in depth understanding in Basic p...

Time course RNAseq data could be analysed with various packages including limma and edgeR. maSigPro, a bioconductor package (https://bioconductor.org/packages/release/bioc/html/maSigPro.html; doi: 10.1093/bioinformatics/btu333) is bit different than the others and useful to see genes which sufficiently changes overtime. This lines of code is my exp...

XCT is potentially placed in a central hub(s) which sense(s) the external environmental ques and regulates the signalling to regulate growth and development. https://www.arabidopsis.org/servlets/TairObject?type=publication&id=501746629

X-chromosome associated protein 5 (Xap5) functions at the chromatin level http://events.biomedcentral.com/epigenetics-chromatin/

Significance Pathogens cause disease by deploying virulence effectors that interfere with various host targets, whereas plants counteract pathogen virulence when invoking a potent immunity known as effector-triggered immunity (ETI). Little is known about the mechanism underlying this molecular battle between plant immunity and pathogen virulence. W...

Immune signaling networks must be tunable to alleviate fitness costs associated with immunity and, at the same time, robust against pathogen interferences. How these properties mechanisti-cally emerge in plant immune signaling networks is poorly understood. Here, we discovered a molecular mechanism by which the model plant species Arabidopsis thali...

The phytohormone ethylene is implicated in diverse biological processes including resistance against pathogens. Ethylene production in plants is enhanced in response to pathogen infection. Activated ethylene signaling contributes positively or negatively to resistance depending on enemies and environmental conditions. In some cases, reported roles...

URL: https://search.proquest.com/docview/1513591402 ABSTRACT: Circadian systems are widespread in nature and enable the organisms that posses these endogenous systems to anticipate environmental changes and therefore allow them to take full advantage of their phenotypic/developmental plasticity. Since current plant clock models are not complete en...

XAP5 Circadian Time Keeper (XCT) is Essential under Temperature Stress A key aspect to plants’ success is the ability to fine tune growth and development both in anticipation of predictable changes such as day-night cycles and in response to variable environmental conditions. XCT is a gene involved in such environmental adaptation, as mutants wer...

To uncover new components of the Arabidopsis thaliana circadian system, seeds were mutagenized with EMS and plants were screened for altered free-running rhythms. One short period mutant identified in this screen has an alteration with in the XAP CIRCADIAN TIME KEEPER (XCT) gene, resulting in both circadian clock and photomorphogenic phenotypes. xc...

http://abstracts.aspb.org/pb2010/public/M09/M0903.html

It is claimed that hydroponically grown plants are superior in yield and resistance to pests and diseases. Although these attributes are explained on the basis of the principles of plant physiology, no specific research has been done to understand the physiological basis of such statements. Moreover, result of many molecular biology related experim...

As the demand for herbal medicines is growing at an increasing rate, it has become essential to commercially cultivate medicinal plants to enhance safety and quality of the herbs and to prevent biodiversity and habitat loss because larger proportion of medicinal plants comes from the wild. In this study biological and economical feasibility of hydr...