Biology subjects

Sivakumar, S.

Publications and source records attributed to Sivakumar, S..

5 recordsLinked to original sources

bioRxiv2018

PUMILIO hyperactivity drives premature aging of Norad-deficient mice

Although numerous long noncoding RNAs (lncRNAs) have been identified, our understanding of their roles in mammalian physiology remains limited. Here we investigated the physiologic function of the conserved lncRNA Norad in vivo. Deletion of Norad in mice results in genomic instability and mitochondrial dysfunction, leading to a dramatic multi-system degenerative phenotype resembling premature aging. Loss of tissue homeostasis in Norad-deficient animals is attributable to augmented activity of PUMILIO proteins, which act as post-transcriptional repressors of target mRNAs to which they bind. Norad is the preferred RNA target of PUMILIO2 (PUM2) in mouse tissues and, upon loss of Norad, PUM2 hyperactively represses key genes required for mitosis and mitochondrial function. Remarkably, enforced Pum2 expression fully phenocopies Norad deletion, resulting in rapid-onset aging-associated phenotypes. These findings provide new insights and open new lines of investigation into the roles of noncoding RNAs and RNA binding proteins in normal physiology and aging.

molecular biology↗

bioRxiv2018

Antiviral viral compound from Streptomyces ghanaensis like strain against white spot syndrome virus (WSSV) of shrimp

Actinomycetes isolates collected from different environments were screened for antiviral activity against WSSV. One isolate designated as CAHSH-2 showed antiviral activity against WSSV at the concentration of 0.2 mg per shrimp. The laboratory trial of determining antiviral activity of ethyl acetate extract (EtOAcE) of CAHSH-2 against WSSV was carried out 21 times since 2014. CAHSH-2 isolate which showed antiviral activity was characterized and identified as Streptomyces ghanaensis like strain. Among the five fractions obtained from EtOAcE of potential actinomycetes isolate, F1 was found to have strong antiviral activity. The F1A and F1B sub-fractions from F1 fraction were subjected to GC-MS, FTIR, 1H and 13C NMR analyses and, the compounds identified were di-n-octyl phthalate and bis (2-methylheptyl) phthalate, respectively. Among these compounds, di-n-octyl phthalate showed strong antiviral activity against WSSV. Molecular docking studies revealed that di-n-octyl phthalate was found to have high binding affinity with VP26 and VP28 proteins of WSSV, whereas the bis (2-methylheptyl) phthalate showed low binding affinity with VP26 and VP28. The antiviral activity of EtOAcE of actinomycetes against WSSV was confirmed by PCR, RT-PCR, Western blot and ELISA. The EA extract of active isolate was found to be non-toxic to Artemia, post-larvae and adult Litopenaeus vannamei.\n\nImportanceWhite spot syndrome virus (WSSV) is an important shrimp viral pathogen and responsible for huge economic loss to shrimp culture industry worldwide including India. The global loss due to WSSV has been estimated about USD 10 billion and the loss continues at the same extent even now. Various strategies have been followed to prevent or control diseases of aquatic animals. In spite of various preventive and control strategies, WSSV has been still persisting for more than two decades. No control strategies have so far been evolved to put a break to WSSV. In this situation, an attempt was made in the present work to screen some actinomycetes isolates for antiviral activity against WSSV. Among these isolates, one isolate identified as Streptomyces ghanaensis like isolate CAHSH-2 showed activity against WSSV. This article gives the information about the antiviral compound against WSSV and the mechanism of viral inhibition.

molecular biology↗

bioRxiv2017

Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Metaanalysis of transcriptional subtypes

Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a 5-year survival rate of < 5% and median overall survival of typically six months from diagnosis. Recent transcriptional studies of PDAC have provided several competing stratifications of the disease. However, the development of therapeutic strategies will depend on a unique and coherent classification of PDAC. Here, we use an integrative meta-analysis of four different PDAC gene expression studies to derive the consensus PDAC classification. Despite the fact that immunotherapies have yet to have an impact in treatment of PDAC, the gene expression signatures that stratify PDAC across studies are immunologic. We define these as \"adaptive\", \"innate\" and \"immune-exclusion\" immunologic signatures, which are prognostic across independent cohorts. An appreciation of the immune composition of PDAC with prognostic significance is an opportunity to understand distinct immune escape mechanisms in development of the disease and design novel immune-oncology therapeutic strategies to overcome current barriers.

cancer biology↗

bioRxiv2017

PHOSPHATASE-REGULATED RECRUITMENT OF THE SPINDLE AND KINETOCHORE ASSOCIATED (SKA) COMPLEX TO KINETOCHORES

Kinetochores move chromosomes on dynamic spindle microtubules and regulate cell cycle progression by signaling the spindle checkpoint. The Spindle and Kinetochore-Associated (Ska) Complex, a hexamer composed of two copies of Ska1, Ska2 and Ska3, participates in both roles. The mitotic kinases, Cdk1, Aurora B, Plk1, Mps1 and Bub1 play key, overlapping tasks in regulating chromosome movement and checkpoint signaling. However, roles for the phosphatases that oppose these kinases are more poorly defined. Recently, we showed that Ska1 is important for recruiting protein phosphatase 1 (PP1) to kinetochores. Here we show that PP1 and protein phosphatase 2A (PP2A) both promote accumulation of Ska at kinetochores. Depletion of PP1 or PP2A by siRNA reduces Ska binding at kinetochores, impairs alignment of chromosomes to the spindle midplane, and causes metaphase delay or arrest, phenotypes also seen after depletion of Ska. Tethering of PP1 to the kinetochore protein Nuf2 promotes Ska recruitment to kinetochores, and reduces mitotic defects seen after Ska depletion. We propose that kinetochore-associated phosphatases generate a positive feedback cycle to reinforce Ska complex accumulation and function at kinetochores.\n\nSUMMARY STATEMENTPhosphatases reinforce recruitment of the Ska complex at kinetochores to stabilize microtubule attachment and oppose spindle checkpoint signaling.

cell biology↗

bioRxiv2017

Evaluation of pre-analytical factors affecting plasma DNA analysis

Pre-analytical factors can significantly affect circulating cell-free DNA (cfDNA) analysis. However, there are few robust methods to rapidly assess sample quality and the impact of pre-analytical processing. To address this gap and to evaluate effects of DNA extraction methods and blood collection tubes on cfDNA yield and fragment size, we developed a multiplexed droplet digital PCR (ddPCR) assay with 5 short and 4 long amplicons targeting single copy genomic loci (mean amplicon size: 71 bp and 471 bp respectively). Using this assay, we compared performance of 7 cfDNA extraction kits and found cfDNA yield and fragment size varies significantly between them. We also compared 3 blood collection protocols used to collect plasma samples from 23 healthy volunteers (EDTA tubes processed within 1 hour and Cell-free DNA BCT tubes at ambient temperature processed within 24 hours and 72 hours of collection). To assess whether cell-stabilizing preservative in BCT tubes introduced noise in cfDNA, we performed digital targeted sequencing. We found no significant differences in cfDNA yield, fragment size and background sequencing noise between these protocols. In 219 clinical samples tested for quality using the ddPCR assay, cfDNA fragment size was significantly shorter in plasma samples immediately processed for ctDNA analysis compared to archived samples, suggesting background DNA contributed by lysed peripheral blood cells. In summary, we describe a multiplexed ddPCR approach that enables cfDNA quality assessment and could inform the design of future circulating tumor DNA studies.\n\nGene namesNone

genomics↗