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Rai, R.

Publications and source records attributed to Rai, R..

24 records · Page 2Linked to original sources

Optimal Time Lags from Causal Prediction Model Help Stratify and Forecast Nervous System Pathology

Traditional clinical approaches diagnose disorders of the nervous system using standardized observational criteria. Although aiming for homogeneity of symptoms, this method often results in highly heterogeneous disorders. A standing question thus is how to automatically stratify a given random cohort of the population, such that treatment can be better tailored to each clusters symptoms, and severity of any given group forecasted to provide neuroprotective therapies. In this work we introduce new methods to automatically stratify a random cohort of the population composed of healthy controls of different ages and patients with different disorders of the nervous systems. Using a simple walking task and measuring micro-fluctuations in their biorhythmic motions, we combine non-linear causal network connectivity analyses in the temporal and frequency domains with stochastic mapping. The methods define a new type of internal motor timings. These are amenable to create personalized clinical interventions tailored to self-emerging clusters signaling fundamentally different types of gait pathologies. We frame our results using the principle of reafference and operationalize them using causal prediction, thus renovating the theory of internal models for the study of neuromotor control.

neuroscience↗

Spelling changes and fluorescent tagging with prime editing vectors for plants

Prime editing (PE) is a recent adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase (RT) fusion and a guide RNA (pegRNA) amended with template and primer binding site (PBS) sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of PE in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for PE in dicots and monocots, their validation in Nicotiana benthamiana, rice and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.

plant biology↗

Antagonistic roles of NOT1 paralogues in the timing of gene expression in Plasmodium falciparum

NOT1 is the scaffold of the CCR4-NOT complex, a highly conserved multi-protein complex that regulates gene expression in eukaryotes. As opposed to most eukaryotes in which NO1 is encoded by a single gene, malaria parasites, Plasmodium falciparum, carry two NOT1 paralogues, PfNOT1.1 and PfNOT1.2. Here we showed that the two PfNOT1 proteins function as mutually exclusive scaffolds within the PfCCR4-NOT protein complexes that are abundantly located in the parasite cytoplasm. Intriguingly, the two PfNOT1 paralogues appear to have directly opposing functions in regulation of mRNA abundance across the P. falciparum IDC, in which PfNTO1.1 and PfNOT1.2 induces and suppresses transcript abundance during their active transcription, respectively. Targeted disruption of either of the PfNOT1 gene causes defective growth and lower invasion rates presumably due to the deregulation the P. falciparum IDC transcriptional cascade. We also demonstrate that the regulatory function of both PfNOT1.1 and PfNOT1.2 are related to another PfCCR4-NOT subunit, PfCaf1, which indicates their activity during post-transcriptional regulation. Indeed RNA decay studies suggest the active role of both PfNOT1 proteins in regulation of mRNA stability in a directly opposing manner. Author summaryCCR4-NOT complex is a highly conserved multi-protein complex that regulates gene expression in eukaryotes. NOT1 serves as the scaffold of the complex and plays important roles in gene regulation both transcriptionally and post-transcriptionally. As opposed to other eukaryotes, P. falciparum encodes two paralogues of PfNOT1, raising the question as to the significance to possess an additional copy of PfNOT1 in the parasite. Here we described antagonistic regulatory functions of two PfNOT1 paralogues in gene expression during the 48-hour intraerythrocytic developmental cycle. We also reported that their regulatory functions are predominantly post-transcriptional and proposed a model in which distinct PfCCR4-NOT complexes defined by mutually exclusive PfNOT1 scaffolds differentially regulate PfCAF1 function in mRNA decay. This study highlights the importance of post-transcriptional regulation in P. falciparum and provides novel insights into mechanisms of gene regulation in this organism. The unique presence of two PfNOT1 paralogues may also open avenues for the development of new drug targets for anti-malarial control.

molecular biology↗

Wiskott Aldrich syndrome protein regulates non-selective autophagy and mitochondrial homeostasis in human myeloid cells

The actin cytoskeletal regulator Wiskott Aldrich syndrome protein (WASp) has been implicated in maintenance of the autophagy-inflammasome axis in innate murine immune cells. Here, we show that WASp deficiency is associated with impaired rapamycin-induced autophagosome formation and trafficking to lysosomes in primary human monocyte-derived macrophages (MDMs). WASp reconstitution in vitro and in WAS patients following clinical gene therapy restores autophagic flux and is dependent on the actin-related protein complex ARP2/3. Induction of mitochondrial damage with CCCP, as a model of selective autophagy, also reveals a novel ARP2/3-dependent role for WASp in formation of sequestrating actin cages and maintenance of mitochondrial network integrity. Furthermore, mitochondrial respiration is suppressed in WAS patient MDMs and unable to achieve normal maximal activity when stressed, indicating profound intrinsic metabolic dysfunction. Taken together, we provide evidence of new and important roles of human WASp in autophagic processes and immunometabolic regulation, which may mechanistically contribute to the complex WAS immunophenotype.

physiology↗

A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate

The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host susceptibility (S) genes important for disease. Clade III SWEET genes are major S genes for bacterial blight. The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed. However, strains that defeat both resistance genes individually were recently reported in India and Thailand. To gain insight into the mechanism(s), we completely sequenced the genome of one such strain from each country and examined the encoded TALEs. Strikingly, the two strains are clones, sharing nearly identical TALE repertoires, including a TALE known to activate SWEET11 strongly enough to be effective even when diminished by xa5. We next investigated SWEET gene induction by the Indian strain. The Indian strain induced no clade III SWEET in plants harbouring xa13, indicating a pathogen adaptation that relieves dependence on these genes for susceptibility. The findings open a door to mechanistic understanding of the role SWEET genes play in susceptibility and illustrate the importance of complete genome sequence-based monitoring of Xoo populations in developing varieties with effective disease resistance.

pathology↗

Epigenetic analysis identifies factors driving racial disparity in prostate cancer

Prostate cancer (PCa) is the second most leading cause of death in men worldwide. African American men (AA) represent more aggressive form of PCa as compared to Caucasian (CA) counterparts. Evidence suggests that genetic and other biological factors could account for the observed racial disparity. We analyzed the cancer genome atlas (TCGA) dataset (2015) for existing epigenetic variation in AA and CA prostate cancer patients, and carried out Reduced Representation Bisulphite Sequencing (RRBS) analysis to identify global methylation changes in AA and CA prostate cancer patients. The TCGA dataset analysis revealed that the epigenetic heterogeneity could be categorized into 4 classes, where AA associated primarily to methylation cluster 1 (p value 0.048), and CA associated to methylation cluster 3 (p value 0.000146). We identified enrichment of Wnt signaling genes in both AA and CA, however they were differentially activated in terms of canonical and non-canonical Wnt signaling pathway activation. This was further validated using the GenomeDx expression data. Our RRBS data also suggested distinct methylation patterns in AA compared to CA, and in part validated our TCGA findings. Survival analysis using the RRBS data suggested hypomethylated genes to be significantly associated with recurrence of prostate cancer in CA (p=6.07x10-6) as well as in AA (p=0.0077). Overall, the observed racial disparity in the molecular mechanism involved in the pathogenesis of prostate cancer suggests diverse heterogeneity that potentially could affect survival and should be considered during prognosis and treatment.

cancer biology↗