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An Improved Methodology to Overcome Key Issues in Human Fecal Metagenomic DNA Extraction

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Genomics, Proteomics & Bioinformatics 2016年第6期14卷 371-378页

作者： Jitendra Kumar Manoj Kumar shashank Gupta Vasim Ahmed Manu Bhambi Rajesh Pandey Nat singh Chauhan Department of Biochemistry Maharshi Dayanand UniversityRohtak 124001India Ayurgenomics Unit Translational Research and Innovative Science Through AyurgeomicsCouncil of Scientific and Industrial ResearchInstitute of Genomics and Integrative BiologyNew Delhi 110020India

Microbes are ubiquitously distributed in nature, and recent culture-independent studies have highlighted the significance of gut microbiota in human health and disease. Fecal DNA is the primary source for the majority of human gut microbiome studies. However, further improvement is needed to obtain fecal metagenomic DNA with sufficient amount and good quality but low host genomic DNA contamination. In the current study, we demonstrate a quick, robust, unbiased, and cost-effective method for the isolation of high molecular weight （〉 23 kb） metagenomic DNA （260/280 ratio 〉 1.8） with a good yield （55.8 ± 3.8 ng/mg of feces）. We also confirm that there is very low human genomic DNA contamination （eubacterial： human genomic DNA marker genes = 227.9：1） in the human feces. The newly-developed method robustly performs for fresh as well as stored fecal samples as demonstrated by 16s rRNA gene sequencing using 454 FLX＋. Moreover, 16s rRNA gene analysis indicated that compared to other DNA extraction methods tested, the fecal metagenomic DNA isolated with current methodology retains species richness and does not show microbial diversity biases, which is further confirmed by qPCR with a known quantity of spike-in genomes. Overall, our data highlight a protocol with a balance between quality, amount, user-friendliness, and cost effectiveness for its suitability toward usage for cultureindependent analysis of the human gut microbiome, which provides a robust solution to overcome key issues associated with fecal metagenomic DNA isolation in human gut microbiome studies.

关键词： Metagenomic DNAextraction Gut microbiome Human feces 16s rRNA

Implantable photoelectronic charging(I-PEC)for medical implants

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能源评论(英文) 2022年第2期1卷 60-69页

作者： Kai Wang sumanta Kumar Karan Mohan sanghadasa Congcong Wu shashank Priya Department of Materials science and Engineering Pennsylvania State UniversityUniversity ParkPA16802United States Materials Research Institute Pennsylvania State UniversityUniversity ParkPA16802United States U.s.Army Combat Capabilities Development Command Aviation&Missile Center Redstone ArsenalAlabama35898United States Key Laboratory for the Green Preparation and Application of Functional Materials Hubei Key Laboratory of Polymer MaterialsSchool of Materials Science and EngineeringHubei UniversityWuhan430062China

Medical implants with functionalities such as sensing,health monitoring,stimulation,diagnosis,and physiological treatment are rapidly *** the increasing functional sophistication and addition of modules such as data transmission,on-chip processing,and data storage,energy demand of the implantable system is also *** implantable energy harvester either to recharge or ultimately replace hazardous battery is essential to provide a long-term sustainable *** harvesting techniques using piezoelectric,thermoelectric,radio frequency power transmission,biofuel,and photoelectronic(or sometimes termed as“photovoltaic”in terms of solar light harvesting,i.e.,PV)conversion,have been attempted for the implantable,but these methods are currently limited by insufficient power output,large footprint,and low ***,the planar PV with potential of lighter weight,higher energy density,and higher efficiency,provides promising power solution for in-body medical *** this short review,we will discuss the potential opportunities and challenges associated with PV's for medical implants,covering materials,to devices,and to system level requirements.

关键词： photoelectron harvesting charging

Dietary phytochemicals and their role in cancer chemoprevention

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Journal of Cancer Metastasis and Treatment 2021年第1期7卷 709-712页

作者： shashank Kumar sanjay Gupta Molecular signaling and Drug Discovery Laboratory Department of BiochemistrySchool of Basic and Applied SciencesCentral University of PunjabBathinda 151401India Department of Urology Case Western Reserve UniversityClevelandOH 44106USA Department of Urology The Urology InstituteUniversity Hospitals Cleveland Medical CenterClevelandOH 44106USA Department of Nutrition Case Western Reserve UniversityClevelandOH 44106USA Divison of General Medical sciences Case Comprehensive Cancer CenterClevelandOH 44106USA Department of Urology Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandOH 44106USA.

Epidemiological studies suggest a close association between diet and cancer initiation,which provides evidence that the dietary components may be effectively developed as chemopreventive agents[1].These pieces of evidence are further supported by several case-control and cohort studies,which overwhelmingly support a converse association between the intake of phytochemicals and cancer risk[2,3].A number of clinical studies have been conducted demonstrating that dietary phytochemicals have the ability to inhibit tumorigenesis[4].Components presenting in fruit and vegetables termed“bioactive”phytochemicals belong to several classes of micronutrients,including flavonoids,polyphenols,and dietary *** components have the ability to reduce the cancer risk alone or by interactions between them.

关键词： prevention cancer dietary

Gankyrin: A potential target for drug therapy against hepatocellular carcinoma

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Journal of Biomedical science and Engineering 2012年第8期5卷 469-475页

作者： shashank Gandhi Veena Puri sanjeev Puri Center for system Biology and Bioinformatics U.I.E.A.S.T Panjab University Chandigarh India Department of Biotechnology University Institute of Engineering and Technology Panjab University Chandigarh India

Hepatocellular Carcinoma is a primary malignant tumor of the liver and gankyrin is an oncoprotein over-expressed in hepatocellular carcinoma. It has been found that Gankyrin protein reduces the level of p53 protein by increasing its ubiquitylation and degradation, following a MDM-2 mediated pathway. Interaction of gankyrin with MDM2 enhances the ubiquitylation of p53. Independent study of this protein molecule revealed that it is identical to the p28 subunit of the 26s proteasome, having seven similar alpha helical ankyrin repeats. Gankyrin also binds to the Tumor suppressor Protein (TsP) Retinoblastoma (RB), thereby accelerating its phosphorylation and proteasomal degradation. Blocking the expression of Gankyrin with MDM2 in cases of Hepatocellular Carcinoma (HCC) promoted apoptosis in cancer cells. Hence, Gankyrin can be used as a potential target for drug therapy against Hepatocellular Carcinoma.

关键词： Hepatocellular Carcinoma Murine Double Minute-2 p53 Tumor suppressor Protein Gankyrin

segmenting salient Objects in 3D Point Clouds of Indoor scenes Using Geodesic Distances

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Journal of signal and Information Processing 2013年第3期4卷 102-108页

作者： shashank Bhatia stephan K. Chalup school of Electrical Engineering and Computer science The University of Newcastle Callaghan 2308 NSW Australia.

Visual attention mechanisms allow humans to extract relevant and important information from raw input percepts. Many applications in robotics and computer vision have modeled human visual attention mechanisms using a bottom-up data centric approach. In contrast, recent studies in cognitive science highlight advantages of a top-down approach to the attention mechanisms, especially in applications involving goal-directed search. In this paper, we propose a top-down approach for extracting salient objects/regions of space. The top-down methodology first isolates different objects in an unorganized point cloud, and compares each object for uniqueness. A measure of saliency using the properties of geodesic distance on the object’s surface is defined. Our method works on 3D point cloud data, and identifies salient objects of high curvature and unique silhouette. These being the most unique features of a scene, are robust to clutter, occlusions and view point changes. We provide the details of the proposed method and initial experimental results.

关键词： saliency Detection 3D Image Analysis Image segmentation

Integrative taxonomy of the Plain-backed Thrush(Zoothera mollissima)complex(Aves,Turdidae)reveals cryptic species,including a new species

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Chinese Birds 2016年第1期7卷 2-39,1页

作者： Per Alstrom Pamela C.Rasmussen Chao Zhao Jingzi Xu shashank Dalvi Tianlong Cai Yuyan Guan Ruiying Zhang Mikhail V.Kalyakin Fumin Lei Urban Olsson Department of Animal Ecology Evolutionary Biology CentreUppsala University Key Laboratory of Zoological systematics and Evolution Institute of ZoologyChinese Academy of Sciences swedish species Information Centre Swedish University of Agricultural Sciences Department of Integrative Biology and MsU Museum Michigan State University Bird Group The Natural History Museum at Tring Cloud Mountain Conservation Department of Evolutionary Biology Evolutionary Biology CentreUppsala University Researchers for Wildlife Conservation F-21National Centre for Biological Sciences College of Life sciences University of Chinese Academy of Sciences Zoological Museum of Lomonosov Moscow state University systematics and Biodiversity Department of Biology and Environmental SciencesUniversity of Gothenburg

Background: The Plain-backed Thrush Zoothera mollissima breeds in the Himalayas and mountains of central China. It was long considered conspecific with the Long-tailed Thrush Zoothera dixoni, until these were shown to be broadly ***: We revise the Z. mollissima–Z. dixoni complex by integrating morphological, acoustic, genetic(two mitochondrial and two nuclear markers), ecological and distributional ***: In earlier field observations, we noted two very different song types of "Plain-backed" Thrush segregated by breeding habitat and elevation. Further integrative analyses congruently identify three groups: an alpine breeder in the Himalayas and sichuan, China("Alpine Thrush"); a forest breeder in the eastern Himalayas and northwest Yunnan(at least), China("Himalayan Forest Thrush"); and a forest breeder in central sichuan("sichuan Forest Thrush"). Alpine and Himalayan Forest Thrushes are broadly sympatric, but segregated by habitat and altitude, and the same is probably true also for Alpine and sichuan Forest Thrushes. These three groups differ markedly in morphology and songs. In addition, DNA sequence data from three non-breeding specimens from Yunnan indicate that yet another lineage exists("Yunnan Thrush"). However, we find no consistent morphological differences from Alpine Thrush, and its breeding range is unknown. Molecular phylogenetic analyses suggest that all four groups diverged at least a few million years ago, and identify Alpine Thrush and the putative "Yunnan Thrush" as sisters, and the two forest taxa as sisters. Cytochrome b divergences among the four Z. mollissima sensu lato(s.l.) clades are similar to those between any of them and Z. dixoni, and exceed that between the two congeneric outgroup species. We lectotypify the name Oreocincla rostrata Hodgson, 1845 with the Z. mollissima sensu stricto(s.s.) specimen long considered its type. No available name unambiguously pertains to the Himalayan Forest ***: The

关键词： systematics Morphology Bioacoustics Altitudinal distributions Genetic distances Undescribed taxa Zoothera dixoni Lectotypification Holotype

Resistance to second generation antiandrogens in prostate cancer: pathways and mechanisms

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Cancer Drug Resistance 2020年第4期3卷 742-761页

作者： shiv Verma Kumari sunita Prajapati Prem Prakash Kushwaha Mohd shuaib Atul Kumar singh shashank Kumar sanjay Gupta Department of Urology Case Western Reserve UniversityClevelandOH 44106USA The Urology Institute University Hospitals Cleveland Medical CenterClevelandOH 44106USA school of Basic and Applied sciences Department of Biochemistry and Microbial SciencesCentral University of PunjabBathinda 151001India Department of Nutrition Case Western Reserve UniversityClevelandOH 44106USA Divison of General Medical sciences Case Comprehensive Cancer CenterClevelandOH 44106USA Department of Urology Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandOH 44106USA

Androgen deprivation therapy targeting the androgens/androgen receptor(AR)signaling continues to be the mainstay treatment of advanced-stage prostate *** use of second-generation antiandrogens,such as abiraterone acetate and enzalutamide,has improved the survival of prostate cancer patients;however,a majority of these patients progress to castration-resistant prostate cancer(CRPC).The mechanisms of resistance to antiandrogen treatments are complex,including specific mutations,alternative splicing,and amplification of oncogenic proteins resulting in dysregulation of various signaling *** this review,we focus on the major mechanisms of acquired resistance to second generation antiandrogens,including AR-dependent and AR-independent resistance mechanisms as well as other resistance mechanisms leading to CRPC *** knowledge of resistance mechanisms to AR targeted treatments will lead to additional research on designing more effective therapies for advanced-stage prostate cancer.

关键词： Prostate cancer second-generation antiandrogens androgen receptor castration resistance prostate cancer

A Prospective, Multicentric, Post Marketing surveillance to Evaluate Efficacy & safety of Ranitidine HCl (150 & 300 mg IR/CR) in Indian Patients with Gastroesophageal Reflux Disease (PROGRADE)

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Open Journal of Gastroenterology 2023年第7期13卷 237-249页

作者： Akash shukla Anil Kumar Awasthi Ramesh Rao Dawesh Prakash Yadav Nilesh Nolkha Rajesh Pendlimari sanjiv Dua shrish Bhatnagar Ravindra Mote Ashish Birla Jay savai Kapil Mehta shashank salunke Department of Gastroenterology Gastro Universe Mumbai India Department of Medicine Ajanta Research Centre Ajanta Hospital & IVF Centre Lucknow India Departmentof Nephrology Sanjeevani Kidney Care Mumbai India Department of Gastroenterology Institute of Medical Sciences Banaras Hindu University Varanasi India Department of Rheumatology Wockhardt Hospitals Mumbai India Department of Gastroenterology Rajalakshmi Hospital and Research Center Bangalore India Department of General surgery SaiKripa Hospital Mumbai India Department of Gastroenterology Sparsh Child Care and Gastro Centre Lucknow India Department of Clinical Research Mediclin Clinical Research Mumbai India Department of Medical Affairs JB Chemicals & Pharmaceuticals Ltd. Mumbai India

Purpose: Ranitidine hydrochloride (HCl) remains an important medication for treating acid-peptic ailments such as Gastroesophageal reflux disease (GERD). The main objective of this Post Marketing surveillance (PMs) clinical study was to test the efficacy and safety of Ranitidine HCl in Indian patients suffering from GERD. Patients and Methods: Data of 2446 patients (1307 males;1121 females) from 21 centers across India were analyzed. Patients received either of the three treatments: Ranitidine HCl 150 mg twice a day (BID) (ARM-A), Ranitidine HCl 300 mg once daily (OD) or BID (ARM-B), and Ranitidine HCl 300 mg OD (ARM-C). Gastroesophageal Reflux Disease symptom Assessment scale (GsAs) score and Heartburn severity score were used to assess the drug’s efficacy. The adverse events reported by patients or investigators were analyzed to assess the safety profile of Ranitidine. Results: Of the 2446 subjects screened, 2428 were enrolled. There was a significant reduction in GsAs scores from baseline to the end of the study visit in all three ARMs. The GsAs scores reduced from 2.02 to 0.23 in ARM-A, 2.01 to 0.24 in ARM-B, and 2.07 to 0.26 in ARM-C patients. In ARM A, 72.82% had 24 hours heartburn-free days, and 66.89% had 7 consecutive heartburn-free days, which was more significant than the other two ARMs. 128 (5.27%) patients reported ADRs due to Ranitidine HCl at different doses. The most frequently reported ADR was constipation (17.18%), followed by oliguria (14.06%), cold (13.28%), and dysuria (12.5%). Of 128 ADRs, 113 (88.28%) were mild, and only 11 (8.59%) ADRs were related to the study drug. No severe ADRs were reported during the study. Conclusion: Ranitidine HCl 150/300 mg tablet was found to be an effective and safe H2-receptor antagonist for treating GERD in Indian Patients.

关键词： Ranitidine Hydrochloride GERD Heartburn H2-Receptor Antagonists

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一例罕见的感染性结肠炎

Gastroenterology Report 2016年第4期4卷 328-330,I0003页

作者： Aditya Kalakonda shashank Garg suraj Tandon Rakesh Vinayak sudhir Dutta state University of New York(sUNY)Upstate Medical University SyracuseNYUSA Department of Gastroenterology Sinai Hospital of BaltimoreBaltimoreMDUSA

Methicillin-resistant staphylococcus aureus(MRsA)is responsible for numerous infectious *** tract involvement is rather rare and only a handful of cases of MRsA colitis have been reported in North *** present a case of MRsA colitis in an adult without apparent risk *** computed tomography(CT)showed thickening of the sigmoid colon,indicative of colitis,and empiric therapy with ciprofloxacin and metronidazole was *** work-up for infection-including blood and stool cultures,and stool Clostridium difficile toxin assay-was *** patient’s clinical status improved but his diarrhea did not *** of stool culture demonstrated luxuriant growth of MRsA sensitive to *** vancomycin was administered and the patient’s symptoms promptly ceased.

关键词： methicillin-resistant staphylococcus aureus infectious colitis stool culture