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https://www.readbyqxmd.com/read/28010773/biosynthesis-of-silver-nanoparticles-using-pre-hydrolysis-liquor-of-eucalyptus-wood-and-its-effective-antimicrobial-activity
#1
M Shivakumar, K L Nagashree, S Yallappa, S Manjappa, K S Manjunath, M S Dharmaprakash
Herein, we described for the first time, biosynthesis of silver nanoparticles (AgNPs) using pre-hydrolyzed liquor of Eucalyptus wood under ambient conditions. The pre-hydrolyzed liquor containing a high amount of metabolites such as polyphenols, hemicelluloses and its derivatives are mainly assisted for the reduction and stabilization process of Ag+ ions to AgNPs. The formation of AgNPs is monitored by recording the UV-vis spectrophotometer for surface plasmon resonance (SPR) peak observed at ∼415nm. The intensity of SPR increased linearly with increasing the reaction time at ambient condition...
February 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27975292/network-tools-for-the-analysis-of-proteomic-data
#2
David Chisanga, Shivakumar Keerthikumar, Suresh Mathivanan, Naveen Chilamkurti
Recent advancements in high-throughput technologies such as mass spectrometry have led to an increase in the rate at which data is generated and accumulated. As a result, standard statistical methods no longer suffice as a way of analyzing such gigantic amounts of data. Network analysis, the evaluation of how nodes relate to one another, has over the years become an integral tool for analyzing high throughput proteomic data as they provide a structure that helps reduce the complexity of the underlying data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975286/proteotypic-peptides-and-their-applications
#3
Shivakumar Keerthikumar, Suresh Mathivanan
Recent advances in mass spectrometry based proteomic techniques and publicly available large proteomic repositories are being exploited to characterize the proteome of multiple organisms. While humongous amount of proteomic data is being acquired and analyzed, many biological questions still remain unanswered. Proteotypic peptides which uniquely represent target proteins or a protein isoform are used as an alternative strategy for protein identification in the field of immunological methods and targeted proteomic techniques...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975284/unassigned-ms-ms-spectra-who-am-i
#4
Mohashin Pathan, Monisha Samuel, Shivakumar Keerthikumar, Suresh Mathivanan
Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975282/label-based-and-label-free-strategies-for-protein-quantitation
#5
Sushma Anand, Monisha Samuel, Ching-Seng Ang, Shivakumar Keerthikumar, Suresh Mathivanan
The precise quantification of changes between various physiological states in a biological system is highly complex in nature. Over the past few years, in combination with classical methods, mass spectrometry based approaches have become an indispensable tool in deciphering exact abundance of proteins in composite mixtures. The technique is now well established and employs both label-based and label-free quantitation strategies. Label-based quantitation methods utilize stable isotope labels which are incorporated within the peptides, introducing an expectable mass difference within the two or more experimental conditions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975280/proteomic-data-storage-and-sharing
#6
Shivakumar Keerthikumar, Suresh Mathivanan
With the advent of high-throughput genomic and proteomic techniques, there is a massive amount of multidimensional data being generated and has increased several orders of magnitude. But the amount of data that is cataloged in the central repositories and shared publicly with the scientific community does not correlate the same rate at which the data is generated. Here, in this chapter, we discuss various proteomics data repositories that are freely accessible to the researchers for further downstream meta-analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27975279/an-introduction-to-proteome-bioinformatics
#7
Shivakumar Keerthikumar
High-throughput techniques are indispensable for aiding basic and translational research. Among them, recent advances in proteomics techniques have allowed biomedical researchers to characterize the proteome of multiple organisms. This remarkable advancement have been well complemented by proteome bioinformatics methods and tools. Proteome bioinformatics refers to the study and application of informatics in the field of proteomics. This chapter provides an overview of computational strategies, methods, and techniques reported in this book for bioinformatics analysis of protein data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27969076/the-impact-of-il10-polymorphisms-and-shla-g-levels-on-the-risk-of-schizophrenia
#8
Ashwini Rajasekaran, Venkataram Shivakumar, Sunil V Kalmady, Janardhanan C Narayanaswamy, Manjula Subbana, Deepthi Venugopal, Anekal C Amaresha, Ganesan Venkatasubramanian, Monojit Debnath
Early life immune aberrations have strongly been associated with the risk of schizophrenia. Amongst them, inflammation induced neurodevelopmental origin has emerged as one of the widely recognized underlying mechanisms. Interleukin-10 (IL-10) is an important anti-inflammatory and immunoregulatory cytokine. It modulates the expression of another immuno-inhibitory molecule, Human Leukocyte Antigen-G (HLA-G), predominantly expressed at the feto-maternal interface. Under physiological conditions, IL-10 and HLA-G molecules regulate the feto-maternal immune homeostasis by limiting the inflammatory states and influence the outcome of pregnancy...
October 2016: Asian Journal of Psychiatry
https://www.readbyqxmd.com/read/27965082/analysis-of-whole-chloroplast-genomes-from-the-genera-of-the-clauseneae-the-curry-tribe-rutaceae-citrus-family
#9
Vikram S Shivakumar, Marc S Appelhans, Gabriel Johnson, Monica Carlsen, Elizabeth A Zimmer
The Clauseneae (Aurantioideae, Rutaceae) is a tribe in the Citrus family that, although economically important as it contains the culinary and medicinally-useful curry tree (Bergera koenigii), has been relatively understudied. Due to the recent significant taxonomic changes made to this tribe, a closer inspection of the genetic relationships among its genera has been warranted. Whole genome skimming was used to generate chloroplast genomes from six species, representing each of the four genera (Bergera, Clausena, Glycosmis, Micromelum) in the Clauseneae tribe plus one closely related outgroup (Merrillia), using the published plastome sequence of Citrus sinensis as a reference...
December 11, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/27943215/bioinformatics-tools-for-extracellular-vesicles-research
#10
Shivakumar Keerthikumar, Lahiru Gangoda, Yong Song Gho, Suresh Mathivanan
Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27931901/auditory-false-perception-in-schizophrenia-development-and-validation-of-auditory-signal-detection-task
#11
Harleen Chhabra, Selvaraj Sowmya, Vanteemar S Sreeraj, Sunil V Kalmady, Venkataram Shivakumar, Anekal C Amaresha, Janardhanan C Narayanaswamy, Ganesan Venkatasubramanian
Auditory hallucinations constitute an important symptom component in 70-80% of schizophrenia patients. These hallucinations are proposed to occur due to an imbalance between perceptual expectation and external input, resulting in attachment of meaning to abstract noises; signal detection theory has been proposed to explain these phenomena. In this study, we describe the development of an auditory signal detection task using a carefully chosen set of English words that could be tested successfully in schizophrenia patients coming from varying linguistic, cultural and social backgrounds...
December 2016: Asian Journal of Psychiatry
https://www.readbyqxmd.com/read/27891020/preventing-medico-legal-issues-in-clinical-practice
#12
REVIEW
Bevinahalli N Raveesh, Ragavendra B Nayak, Shivakumar F Kumbar
The medical profession is considered to be one of the noblest professions in the world. The practice of medicine is capable of rendering noble service to humanity provided due care, sincerity, efficiency, and professional skill is observed by the doctors. However, today, the patient-doctor relationship has almost diminished its fiduciary character and has become more formal and structured. Doctors are no longer regarded as infallible and beyond questioning. Corporatization of health care has made it like any other business, and the medical profession is increasingly being guided by the profit motive rather than that of service...
October 2016: Annals of Indian Academy of Neurology
https://www.readbyqxmd.com/read/27886364/ultrasound-guided-angioplasty-for-treatment-of-peripheral-stenosis-of-arteriovenous-fistula-a-single-center-experience
#13
Sunil Kumar, Nikhil Mahajan, Shivakumar S Patil, Navdeep Singh, Soham Dasgupta, Seetharam Tejavath, Sarbpreet Singh, Deepesh B Kenwar, Ashish Sharma, Mukut Minz
PURPOSE: In patients with end-stage renal disease, arteriovenous fistulas (AVFs) are the access of choice for hemodialysis but are often complicated by stenosis. We present single-center experience of 78 ultrasound-guided angioplasty procedures for treating peripheral stenoses of AVFs. METHODS: Between January 2013 and November 2015, 78 angioplasties were performed under ultrasound guidance in 53 patients with end-stage renal disease who were referred from dialysis centers with low flow rate, difficult cannulation, increased cannulation site bleeding, immature or thrombosed AVF...
November 22, 2016: Journal of Vascular Access
https://www.readbyqxmd.com/read/27872522/sentinel-lymph-node-biopsy-in-n0-neck-for-squamous-cell-carcinoma-of-oral-cavity-a-prospective-study
#14
K Shivakumar, Goel Vipin, Manjunath Suraj, B V Rajaram, Ramesh Rakesh, A Anuradha, K Hemanth
Oral cancers in India are very common. SLNB (sentinel lymph node biopsy) for the management of the cN0 neck provides proper staging with less morbidity. The study aims at assessment of the technical feasibility and accuracy of SLNB. Two by two table and Kappa statistic was used to compare SLN and END. In 14 cases out of 16 cases, SLN was identified. Sensitivity and specificity of 100 % were found. One hundred percent agreement was observed between SLN and END using kappa statistics. A meta-analysis of 19 studies showed 97...
December 2016: Indian Journal of Surgical Oncology
https://www.readbyqxmd.com/read/27832715/green-synthesis-of-selenium-nanoparticles-conjugated-clausena-dentata-plant-leaf-extract-and-their-insecticidal-potential-against-mosquito-vectors
#15
P Sowndarya, G Ramkumar, M S Shivakumar
Mosquitoes are major vectors for the transmission of many diseases like chikungunya, malaria, dengue, zika, etc. worldwide. In the present study, selenium nanoparticles (SeNPs) were synthesized from Clausena dentata and were tested for their larvicidal efficacy against the fourth-instar larvae of Anopheles stephensi, Aedes Aegypti, and Culex quinquefasciatus. The synthesized nanoparticles were characterized using UV-Vis spectroscopy, Fourier Transform Infrared Radiation (FTIR) spectroscopy, EDaX, and SEM. The results recorded from UV-Vis spectroscopy show the peak absorption spectrum at 420 nm...
November 10, 2016: Artificial Cells, Nanomedicine, and Biotechnology
https://www.readbyqxmd.com/read/27829754/a-randomized-triple-blind-clinical-trial-to-compare-the-effectiveness-of-topical-triamcinolone-acetonate-0-1-clobetasol-propionate-0-05-and-tacrolimus-orabase-0-03-in-the-management-of-oral-lichen-planus
#16
Shivakumar Sivaraman, Krishnamoorthy Santham, Aruldoss Nelson, Bijaykumar Laliytha, Pandian Azhalvel, John Hearty Deepak
BACKGROUND: Oral lichen planus (OLP) is believed to result from an abnormal T-cell mediated immune response. The most useful agent in the treatment is corticosteroids. The present study will be aimed at evaluation of therapeutic efficiency of two corticosteroids triamcinolone acetonate (0.1%) and clobetasol propionate with tacrolimus orabase (0.03%), an immunomodulator in the management of OLP. AIM: To compare the effectiveness of topical triamcinolone acetonate (0...
October 2016: Journal of Pharmacy & Bioallied Sciences
https://www.readbyqxmd.com/read/27821372/ninhydrin-sodium-molybdate-chromogenic-analytical-probe-for-the-assay-of-amino-acids-and-proteins
#17
Shivakumar Anantharaman, Nagaraja Padmarajaiah, Naef Ghllab Saeed Al-Tayar, Ashwinee Kumar Shrestha
A sensitive method has been proposed for the quantification of amino acids and proteins using ninhydrin and sodium molybdate as chromogenic substrates in citrate buffer of pH5.6. A weak molybdate-hydrindantin complex plays the role in the formation of Ruhemann's purple. The linear response for the amino acid, amino acid mixture and Bovine serum albumin is between 0.999 and 66.80μM, 1.52 and 38μM and 5 and 100μg/L, respectively. The molar absorptivity of the individual amino acid by the proposed reaction extends from 0...
February 15, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/27798154/icos-ligand-triggering-impairs-osteoclast-differentiation-and-function-in-vitro-and-in-vivo
#18
Casimiro L Gigliotti, Elena Boggio, Nausicaa Clemente, Yogesh Shivakumar, Erika Toth, Daniele Sblattero, Patrizia D'Amelio, Giovanni C Isaia, Chiara Dianzani, Junji Yagi, Josè M Rojo, Annalisa Chiocchetti, Renzo Boldorini, Michela Bosetti, Umberto Dianzani
Osteoblasts, osteocytes, and osteoclasts (OCs) are involved in the bone production and resorption, which are crucial in bone homeostasis. OC hyperactivation plays a role in the exaggerated bone resorption of diseases such as osteoporosis, rheumatoid arthritis, and osteolytic tumor metastases. This work stems from the finding that OCs can express B7h (ICOS-Ligand), which is the ligand of the ICOS T cell costimulatory molecule. Because recent reports have shown that, in endothelial, dendritic, and tumor cells, B7h triggering modulates several activities of these cells, we analyzed the effect of B7h triggering by recombinant ICOS-Fc on OC differentiation and function...
October 19, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27789139/design-synthesis-and-evaluation-of-2s-4r-ketoconazole-sulfonamide-analogs-as-potential-treatments-for-metabolic-syndrome
#19
Benjamin E Blass, Pravin Iyer, Magid Abou-Gharbia, Wayne E Childers, John C Gordon, Mercy Ramanjulu, George Morton, Premkumar Arumugam, Joshodeep Boruwa, John Ellingboe, Sayan Mitra, Rajashekar Reddy Nimmareddy, Shalini Paliwal, Jamallamudi Rajasekhar, Savithiri Shivakumar, Pratima Srivastava, Raghuram S Tangirala, Konda Venkataramanaiah, Mahesh Yanamandra
Metabolic Syndrome, also referred to as 'Syndrome X' or 'Insulin Resistance Syndrome,' remains a major, unmet medical need despite over 30years of intense effort. Recent research suggests that there may be a causal link between this condition and abnormal glucocorticoid processing. Specifically, dysregulation of the hypothalamic-pituitary-adrenocortical (HPA) axis leads to increased systemic cortisol concentrations. Cushing' syndrome, a disorder that is also typified by a marked elevation in levels of cortisol, produces clinical symptomology that is similar to those observed in MetS, and they can be alleviated by decreasing circulating cortisol concentrations...
December 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27765065/extending-gene-ontology-in-the-context-of-extracellular-rna-and-vesicle-communication
#20
Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B Gerstein, Andrew F Hill, Robert R Kitchen, Jan Lötvall, Tushar Patel, Dena C Procaccini, Peter Quesenberry, Joel Rozowsky, Robert L Raffai, Aleksandra Shypitsyna, Andrew I Su, Clotilde Théry, Kasey Vickers, Marca H M Wauben, Suresh Mathivanan, Aleksandar Milosavljevic, Louise C Laurent
BACKGROUND: To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts relevant to the exRNA domain. By extending GO in this manner, the exRNA data/metadata will be more easily annotated and queried because it will be based on a shared set of terms and relationships relevant to extracellular research. METHODS: By following a consensus-building process, we have worked with several academic societies/consortia, including ERCC, ISEV, and ASEMV, to identify and approve a set of exRNA and extracellular vesicle-related terms and relationships that have been incorporated into GO...
April 12, 2016: Journal of Biomedical Semantics
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