2017
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PublicationArticle Ribosomal DNA ITS1, 5.8S and ITS2 secondary structure, nuclear DNA content and phytochemical analyses reveal distinctive characteristics of four subclades of Protasparagus(Wiley-Liss Inc., 2017) Partha Sarathi Saha; Mainak Sengupta; Sumita JhaThe use of ribosomal DNA (rDNA) internal transcribed spacer (ITS) primary sequence based phylogeny is a conventional practice to estimate the evolutionary interspecies relationship. However, analysis of the functional folding patterns and higher order secondary structures of ITS regions can provide additional important information regarding species relatedness and interspecies variations. In the present study, we provide the first detailed information on the rDNA ITS secondary structure diversity in the four subclades of the subgenus Protasparagus. Several angiospermic conserved motifs were identified in each of the ITS1, 5.8S and ITS2 secondary structures of the studied taxon. Topological comparison of the ITS1 secondary structures showed variations in the helix- IV regions. Moreover, presence of unique sequence motifs and differences in the internal loop structures were found to be subclade specific. The present study suggests that comprehensive analysis of the ITS1, 5.8S and ITS2 structural elements including helices, loops and bulges can be used as an important tool for species delimitation. The present study investigated the evolution of the secondary structure of ITS marker (its phylogenetic utility), genome size, base chromosome number and phytochemicals, and identified a putative polyploid event shared by a number of Protasparagus species. The phytochemical analysis of two important active compounds, i.e., shatavarin-IV and sarsasapogenin, also reveals their presence in all the studied taxa constitutively even at the subclade level. © 2016 Institute of Botany, Chinese Academy of SciencesPublicationArticle Choline metabolic pathway gene polymorphisms and risk for Down syndrome: An association study in a population with folate-homocysteine metabolic impairment(Nature Publishing Group, 2017) S.K. Jaiswal; K.K. Sukla; A. Chauhan; A.R. Lakhotia; A. Kumar; A.K. RaiBackground/objectives:Choline is an essential nutrient involved in one-carbon metabolism, but its role in mechanisms underlying meiotic non-disjunction is poorly known. The relationship between folate-homocysteine metabolic pathway gene polymorphism and Down syndrome (DS) risk has been widely analyzed, but there are limited reports on its correlation with choline metabolism. In the present case-control association study, we investigated the relationship of three single-nucleotide polymorphisms (SNPs) (phosphatidylethanolamine N-methyltransferase (PEMT) rs12325817, choline dehydrogenase (CHDH) rs12676 and homocysteine methyltransferase (BHMT) rs3733890) of choline metabolism with risk for DS.Subject/methods:Genotyping of 228 mothers of a down syndrome child (DSM) and 200 control mothers (CMs) for all SNPs was performed by PCR coupled with restriction fragment length polymorphism method.Results:A significantly increased risk for BHMT +742AA genotype with an odds ratio of 4.96 (95% confidence interval (CI): 1.66-14.88, P=0.0036) was observed. For PEMT rs12325817 and CHDH rs12676, no significant difference in allelic and genotypic frequencies was observed. In genotypic combination analysis considering PEMT -744GG/CHDH +432GG/BHMT +742GG as the reference combination, PEMT -744GC/CHDH +432GG/BHMT +742GG genotypic combination was significantly higher in DSM compared with that in CMs with an odds ratio of 2.061 (95% CI: 1.10-3.86, P=0.0342). We also observed an epistatic interaction between methylenetetrahydrofolate reductase (MTHFR) rs1801133 and choline metabolic pathway gene variants.Conclusions:Our findings indicate impaired choline metabolism showing a greater risk for DS, especially in a population associated with homocysteine-folate impairment. Further studies are required to confirm our findings. © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.PublicationArticle Vibrational investigations of guanine, thioguanine and their singly charged cations and anions(Scientific Publishers, 2017) R. Singh; R.A. YadavThe complete vibrational studies have been done with help of quantum mechanics for the neutral Guanine (Gua) and Thioguanine (TGua) molecules and their singly charged cations and anions employing the B3LYP/6-311++G** method. Neutral Thioguanine and cations of Guanine and Thioguanine show planar structures and belong to Cs point group symmetry while the neutral Guanine and anions of Guanine and Thioguanine possess non-planar structure with C1 point group symmetry. Vibrational studies of ionic radicals of Gua and its thio- derivative are not available in literatures. Such extensive studies have been attempted for the first time. The normal modes of all the species have been assigned on the basis using potential energy distributions (PEDs) using GAR2PED software. The PEDs have also been calculated to make a conspicuous assignment as animation available in GaussView is not a guarantee for correct normal mode assignment. Charge transfer occurs in the molecule have been shown by the calculated highest occupied molecular orbital—lowest unoccupied molecular orbital (HOMO–LUMO) energies. The mapping of electron density iso-surface with electrostatic potential, has been carried out to get the information about the size, shape, charge density distribution and site of chemical reactivity of the molecule. The electronic properties HOMO and LUMO energies have been measured. The energy gap from HOMO to LUMO of the Gua is 5.0547 eV and TGua 4.0743 eV. © 2016, Indian Association for the Cultivation of Science.PublicationArticle Overexpression of Withania somnifera SGTL1 gene resists the interaction of fungus Alternaria brassicicola in Arabidopsis thaliana(Academic Press, 2017) Manoj K. Mishra; M. Srivastava; G. Singh; S. Tiwari; A. Niranjan; N. Kumari; P. MisraHeterologus transformed Arabidopsis plants improved tolerance against abiotic stress by the modulation of glycosylation of sterols and sterol glycosides. It is due to enhanced activity of WsSGTL1 enzyme in different stresses. Presently, the effect of WsSGTL1 gene was investigated, focusing on interaction of A. brassicicola fungus on transgenic lines. Overexpressed lines showed restricted lesion, less spore counts and few electrolyte leakages. Biochemical study suggested that the transgenic lines had more glycosylated sterol/phenolic compounds. Relative expression of JA biosynthesis gene and phenylalanine ammonia lyase (PAL) showed enhanced expression. Photosynthesis and chlorophyll fluorescence imaging revealed that transgenic plants had minimum damage of photosynthetic apparatus because of minimum PSII destruction. © 2016 Elsevier LtdPublicationArticle Potassium ferricyanide-incorporated branched polyethylenimine as a potential scaffold for electrocatalytic reduction and amperometric sensing of nitrite(Springer Netherlands, 2017) Pankaj Kumar Rastogi; Vellaichamy Ganesan; Rupali Gupta; Preeti Singh; Piyush Kumar Sonkar; Dharmendra Kumar YadavAbstract: Anionic redox mediator-incorporated polymer scaffold on glassy carbon (GC) electrode has been used for the electrocatalytic determination of nitrite. The polymer based on branched polyethylenimine (BPEI) crosslinked with ethylene glycol diglycidyl ether (EGDE) (BPEI-EGDE) has been employed as the potent scaffold. BPEI-EGDE film on GC electrode has been used to immobilize anionic redox mediator [Fe(CN)6]3− by ion-exchange and utilized as the scaffold for the electrochemical determination of nitrite. The voltammetric analysis confirms the confinement of the redox mediator inside the polymer film. This polymeric scaffold, GC/BPEI-EGDE/[Fe(CN)6]3− exhibits a reversible redox response for [Fe(CN)6]3−/4− and retains its redox activity and stability even in strong acidic conditions. The redox mediator confined into the polymer scaffold catalyzes the reduction of nitrite. Significant enhancement in the cathodic current associated with the concomitant decrease in the anodic current was observed in the presence of nitrite. The electrocatalytic response of the scaffold was exploited for the amperometric sensing of nitrite at the potential of 450 mV. The polymer scaffold is highly sensitive (28.5 µA mM−1 cm−2) and it could detect nitrite at micromolar levels (detection limit is 4.8 µM). The scaffold has been successfully used for the real sample analysis and high selectivity, stability, and reproducibility have been achieved. Graphical Abstract: [Figure not available: see fulltext.] © 2016, Springer Science+Business Media Dordrecht.PublicationArticle Interleukin-6 and Interleukin-8 Levels Correlate with the Severity of Aplastic Anemia in Children(Lippincott Williams and Wilkins, 2017) Vineeta Gupta; Sushil Kumar; Rimjhim Sonowal; Surya K. SinghAim: The aim of this study was to evaluate the levels of interleukin (IL)-6 and IL-8 in patients with aplastic anemia and its correlation with severity of the disease. Materials and Methods: IL-6 and IL-8 levels were measured in 40 patients with aplastic anemia in the age group of 4 to 14 years. A total of 40 healthy children served as controls. Quantitative estimation of IL-6 and IL-8 was performed using a solid-phase sandwich ELISA kit. Results were presented as IL-6 and IL-8 concentrations in pg/mL. Patients received immunosuppressive therapy per the British Committee for Standards in Haematology Guidelines 2009. Results: Mean age of the patients was 9.78±2.74 years. IL-6 level of patients was elevated compared with controls (193.48±352.3 vs. 4.58±3.39; P<0.001). IL-8 levels were also significantly elevated in patients compared with controls (15.58±18.0 vs. 1.85±0.95; P<0.001). IL levels were also assessed in relation to severity of the disease. Levels were the highest in patients with very severe aplastic anemia (724.33±519.42), followed by severe aplastic anemia (80.51±66.28 pg/mL), and non-severe aplastic anemia (6.01±1.89). Differences were statistically significant. A similar trend was also observed for IL-8 levels, where the levels were 41.02±24.23, 11.34±8.0, and 1.67±0.71 for very severe aplastic anemia, severe aplastic anemia, and non-severe aplastic anemia, respectively. The differences were again statistically significant. IL levels were also correlated with the treatment outcome. Responders had lower levels compared with nonresponders, but the difference was not statistically significant (186.36±322.45 vs. 198.74±368.10). Levels of ILs decreased in responders, but were not comparable with that of controls 6 months after therapy. Conclusions: High levels of IL-6 and IL-8 were observed in children with aplastic anemia. Increased levels showed correlation with disease severity and therefore appear to play an important role in aplastic anemia. However, levels had no significant correlation with the treatment outcome. Copyright © 2017 Wolters Kluwer Health, Inc. All rights reserved.PublicationArticle Semilocal Convergence Analysis of S-iteration Process of Newton–Kantorovich Like in Banach Spaces(Springer Science and Business Media, LLC, 2017) Daya Ram Sahu; Jen Chih Yao; Vipin Kumar Singh; Satyendra KumarIn the present article, we establish a semilocal convergence theorem for the S-iteration process of Newton–Kantorovich like in Banach space setting for solving nonlinear operator equations and discuss its semilocal convergence analysis. We apply our result to solve the Fredholm-integral equations. © 2016, Springer Science+Business Media New York.PublicationArticle Effects of cryptogein gene on growth, phenotype and secondary metabolite accumulation in co-transformed roots and plants of Tylophora indica(Polish Academy of Sciences, 2017) Amrita Basu; Dipasree Roychowdhury; Raj Kumar Joshi; Sumita JhaTylophora indica, an indigenous medicinal plant, was transformed with the cryptogein gene to determine the effect of crypt gene on secondary metabolites in co-transformed roots and plants via Agrobacterium rhizogenes mediated transformation. The Ri crypt co-transformed roots and plants showed expression of crypt gene. Southern hybridization specifies that crypt gene has been transferred and positively integrated into the Ri crypt co-transformed plant. AFLP fingerprinting revealed high degree of genetic similarity among the Ri-transformed and Ri crypt co-transformed cultures. The expression of crypt gene stimulated phenolic compound accumulation in transformed root and plants while tylophorine content was comparable in Ri transformed and Ri crypt co-transformed root lines and plants. The Ri crypt co-transformed root lines showed significantly higher (p ≤ 0.05) phenolics production (caffeic acid, 1.8–2.9-fold; p-coumaric acid, 1.9-fold and ferulic acid, 1.5–2-fold) compared to Ri-transformed root lines. The roots of Ri crypt co-transformed plants showed a significantly (p ≤ 0.05) higher content of caffeic acid (1.19-fold) and ferulic acid (1.53-fold) than Ri-transformed plants. It is suggested that crypt-transformed plants can also be used as a tool to elucidate the biochemical basis of defense responses as phenolics are known to play a role in providing defense barriers to infection by pathogen. © 2016, Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków.PublicationArticle Development, Validation, and Verification of a Self-Assessment Tool to Estimate Agnibala (Digestive Strength)(SAGE Publications Ltd, 2017) Aparna Singh; Girish Singh; Kishor Patwardhan; Sangeeta GehlotAccording to Ayurveda, the traditional system of healthcare of Indian origin, Agni is the factor responsible for digestion and metabolism. Four functional states (Agnibala) of Agni have been recognized: regular, irregular, intense, and weak. The objective of the present study was to develop and validate a self-assessment tool to estimate Agnibala. The developed tool was evaluated for its reliability and validity by administering it to 300 healthy volunteers of either gender belonging to 18 to 40-year age group. Besides confirming the statistical validity and reliability, the practical utility of the newly developed tool was also evaluated by recording serum lipid parameters of all the volunteers. The results show that the lipid parameters vary significantly according to the status of Agni. The tool, therefore, may be used to screen normal population to look for possible susceptibility to certain health conditions. © 2016, © The Author(s) 2016.PublicationArticle Exploring Indus crop processing: combining phytolith and macrobotanical analyses to consider the organisation of agriculture in northwest India c. 3200–1500 bc(Springer New York LLC, 2017) Jennifer Bates; Ravindra Nath Singh; Cameron A. PetrieThis paper presents a preliminary study combining macrobotanical and phytolith analyses to explore crop processing at archaeological sites in Haryana and Rajasthan, northwest India. Current understanding of the agricultural strategies in use by populations associated with South Asia’s Indus Civilisation (3200–1900 bc) has been derived from a small number of systematic macrobotanical studies focusing on a small number of sites, with little use of multi-proxy analysis. In this study both phytolith and macrobotanical analyses are used to explore the organisation of crop processing at five small Indus settlements with a view to understanding the impact of urban development and decline on village agriculture. The differing preservation potential of the two proxies has allowed for greater insights into the different stages of processing represented at these sites: with macrobotanical remains allowing for more species-level specific analysis, though due to poor chaff presentation the early stages of processing were missed; however these early stages of processing were evident in the less highly resolved but better preserved phytolith remains. The combined analyses suggests that crop processing aims and organisation differed according to the season of cereal growth, contrary to current models of Indus Civilisation labour organisation that suggest change over time. The study shows that the agricultural strategies of these frequently overlooked smaller sites question the simplistic models that have traditionally been assumed for the time period, and that both multi-proxy analysis and rural settlements are deserving of further exploration. © 2016, The Author(s).