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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

Mechanism and recent updates on insulin-related disorders

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世界临床病例杂志 2023年第25期11卷 5840-5856页

作者： shashank Kumar Sabyasachi Senapati Neetu Bhattacharya Amit Bhattacharya shashank Kumar Maurya Hadiya Husain Jasvinder Singh Bhatti Abhay Kumar pandey Department of Biochemistry Central University of PunjabBathinda 151401PunjabIndia Department of Human Genetics and Molecular Medicine Central University of PunjabBathinda 151401PunjabIndia Department of Zoology Dyal Singh CollegeUniversity of DelhiNew Delhi 110003India Department of Zoology Ramjas CollegeUniversity of DelhiNew Delhi 110007India Department of Zoology University of DelhiNew Delhi 110007India Department of Zoology University of LucknowLucknow 226007India Department of Biochemistry University of AllahabadAllahabad(Prayagraj)211002India

Insulin,a small protein with 51 amino acids synthesized by pancreatic β-cells,is crucial to sustain glucose homeostasis at biochemical and molecular *** metabolic dysfunctions are related to insulin-mediated altered glucose *** of the significant pathophysiological conditions linked to the insulin associated disorder is diabetes mellitus(DM)(type 1,type 2,and gestational).Insulin resistance(IR)is one of the major underlying causes of metabolic disorders despite its association with several physiological *** syndrome(MS)is another pathophysiological condition that is associated with IR,hypertension,and ***,several other pathophysiological disorders/diseases are associated with the insulin malfunctioning,which include polycystic ovary syndrome,neuronal disorders,and *** are an uncommon type of pancreatic β-cell-derived neuroendocrine tumor that makes up 2% of all pancreatic *** revealed that different biochemical events,molecular signaling pathways,microRNAs,and microbiota act as connecting links between insulin disorder and associated pathophysiology such as DM,insuloma,neurological disorder,MS,and *** this review,we focus on the insulin-related disorders and the underlying mechanisms associated with the pathophysiology.

关键词： Insulin disorder Diabetes Metabolic syndrome Neurological disorder Obesity Cancer

Current therapeutic modalities and chemopreventive role of natural products in liver cancer:Progress and promise

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World Journal of Hepatology 2023年第1期15卷 1-18页

作者： Amit Kumar Singh Shiv Vardan Singh Ramesh Kumar shashank Kumar Sabyasachi Senapati Abhay K pandey Department of Botany Government Naveen Girls CollegeBalod(Hemchand Yadav University)DurgChattisgarhIndia Department of Biochemistry University of AllahabadPrayagraj 211002Uttar PradeshIndia Department of Biochemistry School of Basic and Applied SciencesCentral University of PunjabBathinda 151401PunjabIndia Department of Human Genetics and Molecular Medicine Central University of PunjabBathinda 151401PunjabIndia

Liver cancer is a severe concern for public health officials since the clinical cases are increasing each year,with an estimated 5-year survival rate of 30%–35%after *** carcinoma(HCC)constitutes a significant subtype of liver cancer(approximate75%)and is considered primary liver *** for liver cancer mainly depends on the stage of its progression,where surgery including,hepatectomy and liver transplantation,and ablation and radiotherapy are the prime *** advanced liver cancer,various drugs and immunotherapy are used as first-line treatment,whereas second-line treatment includes chemotherapeutic drugs from natural and synthetic *** and lenvatinib are first-line therapies,while regorafenib and ramucirumab are secondline *** metabolic and signaling pathways such as Notch,JAK/STAT,Hippo,TGF-β,and Wnt have played a critical role during HCC *** has also been implicated in liver ***-induced toxicity is a key obstacle in the treatment of liver cancer,necessitating the development of effective and safe medications,with natural compounds such as resveratrol,curcumin,diallyl sulfide,and others emerging as promising anticancer *** review highlights the current status of liver cancer research,signaling pathways,therapeutic targets,current treatment strategies and the chemopreventive role of various natural products in managing liver cancer.

关键词： Liver cancer Hepatocellular carcinoma Signaling pathways Therapeutic targets Natural products Chemopreventive

Self-referenced measurements of the dielectric properties of metals using terahertz time-domain spectroscopy via the excitation of surface plasmon-polaritons

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Photonics Research 2013年第4期1卷 148-153页

作者： shashank.pandey Shuchang Liu Barun Gupta Ajay Nahata Department of Electrical and Computer Engineering University of UtahSalt Lake CityUtah 84112USA

We present experimental measurements that show direct determination of the dielectric properties of various metals relevant to *** contrast to traditional measurements that typically rely on transmission and reflectance measurements,we launch surface plasmon-polaritons on a variety of different substrates and measure the propagation properties using terahertz time-domain ***,we find that the extracted values for the dielectric constant for these metals differ by orders of magnitude from published *** order to validate the obtained results,we separately measure the 1∕e decay length,both along the propagation direction and normal to the metal surface,and show that the results are fully self-consistent with experimental *** generality of the measurement technique makes it a useful tool to estimate the properties not only of planar conducting substrates but also a wide variety of more complex plasmonic structures.

关键词： spectroscopy. metals surface

Direct observation of Anderson localization in plasmonic terahertz devices

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Light(Science & Applications) 2016年第1期5卷 160-164页

作者： shashank.pandey Barun Gupta Sushil Mujumdar Ajay Nahata Department of Electrical and Computer Engineering University of UtahSalt Lake CityUT 84112USA Tata Institute for Fundamental Research Mumbai 400005India

We present the first experimental observation of Anderson localization in the terahertz frequency range using plasmonic *** accomplish this goal,we designed THz waveguides consisting of a one-dimensional array of rectangular apertures that were fabricated in a freestanding metal *** is introduced into the waveguide by offsetting the position of each aperture by a random distance within a prescribed *** example,for a waveguide with apertures spaced by 250μm in a periodic waveguide,10%disorder would correspond to the apertures being shifted by a random value between±25μm along the waveguide *** find that for disorder levels below 25%,there is only an increase in the propagation loss along the ***,for two specific waveguides with 25%disorder,we observe a spatially localized mode that lies just within the stop band of the device and exhibits a double-sided exponential spatial decay away from the maximum.

关键词： waveguide sided prescribed