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Long non-coding RNA modifies chromatin

Alka Saxena, Piero Carninci
2011 Bioessays  
Saxena and P.  ...  Saxena and P. Carninci Review essays  ... 
doi:10.1002/bies.201100084 pmid:21915889 pmcid:PMC3258546 fatcat:3lot6vmwwza7dlqedjeamhcfva

Electrochemical Study of Cu2+, Ni2+, Co2+ and Mn2+ Complexes with Dithiodipropionic Acid

1984 Zenodo  
Department of Chemistry, Malaviya Regional Engineering College, Jaipur-302 017 Manuscript received 25 July1983, revised 12 December 1983, accepted 11 February 1984 The interaction of metalion (CU2+, Ni2+ , Co2+ and Mn2+) with dithiodipropionic acid bas been investigated by potentiometric and conductometric titration techniques. Two chelates having 1 : 1 and 1 : 2 mono-ratios of metal to ligand are formed simultaneously over the pH range 3.3-5.3. Their stability constants have been determined by
more » ... applying Calvin and Melchior's extension of Bjerrum's method and refined by alternative methods viz., least square treatment, correction term and convergence formulae. The values of overall \(\bigtriangleup\)G, \(\bigtriangleup\)H and \(\bigtriangleup\)S accompanying tbe complexation reactions are also evaluated at 30o
doi:10.5281/zenodo.6319895 fatcat:d3tj2mx2fjcunjyq4u4hc5cwwi

piRNAs Warrant Investigation in Rett Syndrome: An Omics Perspective

Alka Saxena, Dave Tang, Piero Carninci
2012 Disease Markers  
Mutations in the MECP2 gene are found in a large proportion of girls with Rett Syndrome. Despite extensive research, the principal role of MeCP2 protein remains elusive. Is MeCP2 a regulator of genes, acting in concert with co-activators and co-repressors, predominantly as an activator of target genes or is it a methyl CpG binding protein acting globally to change the chromatin state and to supress transcription from repeat elements? If MeCP2 has no specific targets in the genome, what causes
more » ... e differential expression of specific genes in the Mecp2 knockout mouse brain? We discuss the discrepancies in current data and propose a hypothesis to reconcile some differences in the two viewpoints. Since transcripts from repeat elements contribute to piRNA biogenesis, we propose that piRNA levels may be higher in the absence of MeCP2 and that increased piRNA levels may contribute to the mis-regulation of some genes seen in the Mecp2 knockout mouse brain. We provide preliminary data showing an increase in piRNAs in the Mecp2 knockout mouse cerebellum. Our investigation suggests that global piRNA levels may be elevated in the Mecp2 knockout mouse cerebellum and strongly supports further investigation of piRNAs in Rett syndrome.
doi:10.1155/2012/396737 pmid:22976001 pmcid:PMC3810717 fatcat:qjx4b3ssgndzhdnb2y2d4kwvmi

Modified Two Phase Clocked Adiabatic Static CMOS Logic

Swati Dhamani, Alka Agarwal, Praveer Saxena
2014 International Journal of Computer Applications  
In the past decade, various adiabatic logic techniques have been proposed by various authors. One of the widely known adiabatic logic style is Two Phase Clocked Adiabatic Static CMOS Logic (2PASCL). The logic circuits based on 2PASCL suffer from floating output node due to alternate hold phase in its operation. Keeping a node floating for a long time may result in erroneous node voltage. In this paper a technique to reduce the floating node problem associated with 2PASCL is introduced. Modified
more » ... 2PASCL is used to design a 2-input NAND gate, a 2-input NOR gate and 1-bit full adder at 45nm technology parameters provided by predictive technology and the circuits are simulated using HSPICE. The 2-input NAND gate designed with Modified 2PASCL is compared with the NAND gates designed with 2PASCL and Static CMOS in terms of average power consumed by them for different values of load capacitance and input frequency. NAND gates are also compared in terms of propagation delay, power delay product and the transistor count to implement them. It is observed that the NAND gate based on Modified 2PASCL offer up to 80.3% power saving in comparison to NAND gate based on static CMOS and also exhibit least power delay product. General Terms Adiabatic Logic, Charge Recycling.
doi:10.5120/16437-6158 fatcat:gv6ft5tfdrhg3hxqinsfz66jhy

'Engaging in an argumentative discourse'- narratives from biology classrooms

Astha Saxena, Alka Behari
2015 European Journal of Science and Mathematics Education  
The present paper delves into the classroom dynamics of Biology classrooms taking into account teaching learning processes associated with some of the ethical issues in Biological Sciences. Argumentation and debate appear to be the major transactional approaches adopted by teachers for dealing with these issues. The classroom discourses emanating from teacher student conversations have been analysed on four planes, viz., ethical, social context, interactional context and personal agency of the
more » ... eacher. Toulmin's method of argument analysis has been used in order to analyse the level of arguments of both teachers and their students. The findings reveal significant differences on all the four planes at K-12 and Undergraduate levels and, have implications for building upon teachers' pedagogical content knowledge (PCK) with respect to ethical issues.
doi:10.30935/scimath/9418 fatcat:qqceybexcjhhre5bfnp2akbffy

Comprehensive rural epilepsy surveillance programme in Uttarakhand state of India

Deepak Goel, Alka Agarwal, JS Dhanai, VD Semval, V Mehrotra, V Saxena, B Maithili
2009 Neurology India  
doi:10.4103/0028-3886.53274 pmid:19587489 fatcat:xccelq2ofzco7pvygkcr7yjfsa

Adaptive Spline Based PLL for Synchronization and Power Quality Improvement in Distribution System

Alka Singh, Hemant Saxena, Jitendra Nath Rai
2020 IET Generation, Transmission & Distribution  
A new type of non-linear adaptive phase-locked loop (PLL) has been proposed here, which is based on spline interpolation. The study discusses the method of cubic spline, which is used to extract the fundamental voltage component, its phase angle and frequency. Test results under varying grid conditions viz. normal and distorted conditions such as the presence of harmonics, noise, phase and frequency variations etc. are presented for the developed PLL. An application of the proposed PLL to power
more » ... quality improvement of grid current using shunt active power filter is further discussed here. The study demonstrates that the spline-based controller can be effectively employed as a PLL and to achieve improvement in the power quality of a three-phase, three-wire power distribution system.
doi:10.1049/iet-gtd.2019.0662 fatcat:dkkxsdgk35bopo6nndwtcta5hy

Kinetics of Discharge of Zinc(ll) and Nickel(ll) Ions at the D.M.E. in Dithiodipropionic Acid

1984 Zenodo  
Department of Chemistry, l\Ialaviya Regional Engineering College, Jaipur-301 017 Manuscript f'eceived 30 811ptemb6f' 1982, f'tn:i"d 7 January 198<1, accepted 15 August 198lo Kinetics of Discharge of Zinc(ll) and Nickel(ll) Ions at the D.M.E. in Dithiodipropionic Acid
doi:10.5281/zenodo.6334609 fatcat:dtwpu3z7izenlhw3vy3gnbxcau

Acute hepatic failure in India: A perspective from the East

Subrat K Acharya, Subrat K Panda, Alka Saxena, S Datta Gupta
2000 Journal of Gastroenterology and Hepatology  
doi:10.1046/j.1440-1746.2000.02073.x pmid:10847431 fatcat:4wxsetxjmbgtvm6kkrc7lntv64

Relationship between phyto-chemicals in Mentha piperita and their Antibacterial Activity

Madhu Prakash Srivastava, Kanchan Awasthi, Pratibha Kumari, Alka Saxena
2019 G-journal of environmental science and technology  
A plant with as diverse a role as Peppermint leaves is a versatile resource for all forms of life. The plant extracts have active compounds in the form of alkaloids, glycosides, lactones and steroids. All these active compounds have immunomodulatory and physiological roles of different types, thereby demonstrating the diverse versatility of the plant. Studies need to be conducted with aspects of how the active compounds actually interact with the living systems and affects the
more » ... relationships Aqueous extract of Peppermint leaves were extracted by aqueous method. In the qualitative phytochemical testing presence of various secondary metabolites were found in aqueous extract of Peppermint leaves were Alkaloid, Flavonoids, Tannins and Saponin. In the quantitative analysis carbohydrate was found in) Peppermint leaves sugar conc. is found (470 μg/ml). Antimicrobial activity was also quite good, in Peppermint leaves respectively against Escherichia coli and Staphylococcus aureus. The study demonstrates that the Mentha piperita contains the presence of different bioactive compounds having the potential as herbal drug.
doaj:97f86ccc52a6486e9e8ad2115c235413 fatcat:bsf4shf2wnfvbbnmhunaakmmxy

Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain

Alka Saxena, Akiko Wagatsuma, Yukihiko Noro, Takenobu Kuji, Atsuko Asaka-Oba, Akira Watahiki, Cecile Gurnot, Michela Fagiolini, Takao Hensch, Piero Carninci
2012 BioTechniques  
Efficient isolation of specific, intact, living neurons from the adult brain is problematic due to the complex nature of the extracellular matrix consolidating the neuronal network. Here, we present significant improvements to the protocol for isolation of pure populations of neurons from mature postnatal mouse brain using fluorescence activated cell sorting (FACS). The 10-fold increase in cell yield enables cell-specific transcriptome analysis by protocols such as nano-CAGE and RNA seq. The
more » ... malian brain consists of a variety of projection neurons, local interneurons, glial cells and extracellular matrix factors entangled in a complex network. Mature neurons are severely damaged by enzymatic dissociation and mechanical trituration, causing extensive cell death thus hampering downstream analyses. Collection of pure neuronal subtypes for RNA extraction and expression profiling has, therefore, been challenging, especially in the case of adult brain tissue. Gene expression profiling of isolated neuronal sub-types has the power to provide a catalog of genes expressed in neuronal sub-populations. Such catalogs would not only provide the means to understand normal neuronal development and function, but also permit distinctions between healthy and diseased states, establish biomarkers for diagnostic and prognostic applications, and facilitate the design of targeted molecular therapies (1, 2).
doi:10.2144/0000113878 pmid:22668417 pmcid:PMC3696583 fatcat:yvnzkyfzuzdibi2bx7gjmsj4da

Characterization of the RNA polymerase II and III complexes in Leishmania major

Santiago Martínez-Calvillo, Alka Saxena, Amanda Green, Aaron Leland, Peter J. Myler
2007 International Journal of Parasitology  
Transcription of protein-coding genes in Leishmania major and other trypanosomatids differs from that in most eukaryotes and bioinformatic analyses have failed to identify several components of the RNA polymerase (RNAP) complexes. To increase our knowledge about this basic cellular process, we used tandem affinity purification (TAP) to identify subunits of RNAP II and III. Mass spectrometric analysis of the complexes co-purified with TAP-tagged LmRPB2 (encoded by LmjF31.0160) identified seven
more » ... AP II subunits: RPB1, RPB2, RPB3, RPB5, RPB7, RPB10 and RPB11. With the exception of RPB10 and RPB11, and the addition of RPB8, these were also identified using TAP-tagged constructs of one (encoded by LmjF34.0890) of the two LmRPB6 orthologues. The latter experiments also identified the RNAP III subunits RPC1 (C160), RPC2 (C128), RPC3 (C82), RPC4 (C53), RPC5 (C37), RPC6 (C34), RPC9 (C17), RPAC1 (AC40) and RPAC2 (AC19). Significantly, the complexes precipitated by TAP-tagged LmRPB6 did not contain any RNAP I-specific subunits, suggesting that, unlike in other eukaryotes, LmRPB6 is not shared by all three polymerases but is restricted to RNAP II and III, while the LmRPB6z (encoded by LmjF25.0140) isoform is limited to RNAP I. Similarly, we identified peptides from only one (encoded by LmjF18.0780) of the two RPB5 orthologues and one (LmjF13.1120) of the two RPB10 orthologues, suggesting that LmRPB5z (LmjF18.0790) and LmRPB10z (LmjF13.1120) are also restricted to RNAP I. In addition to these RNAP subunits, we also identified a number of other proteins that co-purified with the RNAP II and III complexes, including a potential transcription factor, several histones, an ATPase involved in chromosome segregation, an endonuclease, four helicases, RNA splicing factor PTSR-1, at least two RNA binding proteins and several proteins of unknown function.
doi:10.1016/j.ijpara.2006.11.019 pmid:17275824 pmcid:PMC2939717 fatcat:o2yoifvzejg7rmxmi7uip2h4ue

Genes associated with neuropsychiatric disease increase vulnerability to abnormal deep grey matter development [article]

Harriet Cullen, Michelle Krishnan, Saskia Selzam, Gareth Ball, Alessia Visconti, Alka Saxena, Serena Counsell, Jo Hajnal, Gerome Breen, Robert Plomin, A David Edwards
2018 bioRxiv   pre-print
Neuropsychiatric disease has polygenic determinants but is often precipitated by environmental pressures, including adverse perinatal events. However, the way in which genetic vulnerability and early-life adversity interact remains obscure. Preterm birth is associated with abnormal brain development and psychiatric disease. We hypothesised that the extreme environmental stress of premature extra-uterine life could contribute to neuroanatomic abnormality in genetically vulnerable individuals.
more » ... hods: We combined Magnetic Resonance Imaging (MRI) and genome-wide single nucleotide polymorphism (SNP) data from 194 infants, born before 33 weeks of gestation, to test the prediction that: the characteristic deep grey matter abnormalities seen in preterm infants are associated with polygenic risk for psychiatric illness. Summary statistics from a meta-analysis of SNP data for five psychiatric disorders were used to compute individual polygenic risk scores (PRS). The variance explained by the PRS in the relative volumes of four deep grey matter structures (caudate nucleus, thalamus, subthalamic nucleus and lentiform nucleus) was estimated using linear regression both for the full, mixed-ancestral, cohort and a subsample of European infants. Results: The PRS was negatively associated with: lentiform volume in the full cohort (β=-0.24, p=8x10 -4 ) and the European subsample (β=-0.24, p=8x10 -3 ); and with subthalamic nuclear volume in the full cohort (β=-0.18, p=0.01) and the European subsample (β=-0.26, p=3x10 -3 ). Conclusions: Genetic variants associated with neuropsychiatric disease increase vulnerability to abnormal deep grey matter development and are associated with neuroanatomic changes in the perinatal period. This suggests a mechanism by which perinatal adversity leads to later neuropsychiatric disease in genetically predisposed individuals.
doi:10.1101/342394 fatcat:eunpyxdhuzdu5cu4ktmickynae


Vikash Sharma, Saurabh Singh, Arushi Dixit, Alka Saxena
2020 International journal of research in pharmacy and chemistry  
doi:10.33289/ijrpc.10.1.2020.10(3) fatcat:6jhlu76wknafzi3pmv2li3sxsa

Site-specific DICER and DROSHA RNA products control the DNA-damage response

Sofia Francia, Flavia Michelini, Alka Saxena, Dave Tang, Michiel de Hoon, Viviana Anelli, Marina Mione, Piero Carninci, Fabrizio d'Adda di Fagagna
2012 Nature  
Non-coding RNAs (ncRNAs) are involved in an increasing number of cellular events 1 . Some ncRNAs are processed by DICER and DROSHA ribonucleases to give rise to small doublestranded RNAs involved in RNA interference (RNAi) 2 . The DNA-damage response (DDR) is a signaling pathway that originates from the DNA lesion and arrests cell proliferation 3 . So far, DICER or DROSHA RNA products have not been reported to control DDR activation. Here we show that DICER and DROSHA, but not downstream
more » ... s of the RNAi pathway, are necessary to activate DDR upon oncogene-induced genotoxic stress and exogenous DNA damage, as studied also by DDR foci formation in mammalian cells and zebrafish and by checkpoint assays. DDR foci are sensitive to RNase A treatment, and DICER-and DROSHA-dependent RNA products are required to restore DDR foci in treated cells. Through RNA deep sequencing and studies of DDR activation at an inducible unique DNA double-strand break (DSB), we demonstrate that DDR foci formation requires site-specific DICER-and DROSHA-dependent small RNAs, named DDRNAs, which act in a MRE11-RAD50-NBS1 (MRN) complex-dependent manner. Chemically synthesized or in vitro-generated by DICER cleavage, DDRNAs are sufficient to restore DDR in RNase A-treated cells, also in the absence of other cellular RNAs. Our results describe an unanticipated direct role of a novel class of ncRNAs in the control of DDR activation at sites of DNA damage. § Corresponding author: IFOM Foundation -The FIRC Institute of Molecular Oncology Foundation via Adamello 16, Author Contributions A.S., D.T. and P.C. planned, generated and analysed the genomics data as in S20 a-e, S21, S22b, S23. M. d. H. performed statistical analysis of the genomics data. A.S., P.C. also edited the manuscript. M.M. and V.A. generated data in S14 and S15. F.M. generated data shown in 2b; 3d, e; 4b; S14 d, f; S2 b, e; S3 e; S4b; S5 f, g; S6 b-d; S7 d; S9; S13 d-f; S17 f, g; S18 a,b; S19; S20 g,h; S22a and generated RNA for deep sequencing; contributed to: S16a; S5 d, e; S11 c, d and edited the manuscript. S.F.
doi:10.1038/nature11179 pmid:22722852 pmcid:PMC3442236 fatcat:gel5q5l6tneyjavbua7lf2tcby
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