Excess of power during electrochemical loading : materials, electrochemical conditions and techniques

"Notes on The ENEA-University of Missouri NRL-SRI International Research Activities." ENEA, University of Missouri, NRL and SRI are cooperating within the frame of an International Program. The research field is on Metal Hydrogen Systems for Energy Applications and is oriented to develop nanostructured materials to be used into electrochemical devices and to study the Fleischmann and Pons Effect. Progress in material science and improvement in controlling the effect is presented

A novel class of miniature inverted repeat transposable elements (MITEs) that contain hitchhiking (GTCY)n microsatellites

The movement of miniature inverted repeat transposable elements (MITEs) modifies genome structure and function. We describe the microsatellite-associated interspersed nuclear element 2 (MINE-2), that integrates at consensus WTTTT target sites, creates dinucleotide TT target site duplications (TSDs), and forms predicted MITE-like secondary structures; a 5\u27 subterminal inverted repeat (SIR; AGGGTTCCGTAG) that is partially complementary to a 5\u27 inverted repeat (IR; ACGAAGCCCT) and 3\u27-SIRs (TTACGGAACCCT). A (GTCY)(n) microsatellite is hitchhiking downstream of conserved 5\u27MINE-2 secondary structures, causing flanking sequence similarity amongst mobile microsatellite loci. Transfection of insect cell lines indicates that MITE-like secondary structures are sufficient to mediate genome integration, and provides insight into the transposition mechanism used by MINE-2s

Genome Desertification in Eutherians: Can Gene Deserts Explain the Uneven Distribution of Genes in Placental Mammalian Genomes?

The evolution of genome size as well as structure and organization of genomes belongs among the key questions of genome biology. Here we show, based on a comparative analysis of 30 genomes, that there is generally a tight correlation between the number of genes per chromosome and the length of the respective chromosome in eukaryotic genomes. The surprising exceptions to this pattern are placental mammalian genomes. We identify the number and, more importantly, the uneven distribution of gene deserts among chromosomes, i.e., long (>500 kb) stretches of DNA that do not encode for genes, as the main contributing factor for the observed anomaly of eutherian genomes. Gene-rich placental mammalian chromosomes have smaller proportions of gene deserts and vice versa. We show that the uneven distribution of gene deserts is a derived character state of eutherians. The functional and evolutionary significance of this particular feature of eutherian genomes remains to be explained

Chromogenic and Fluorogenic Probes for the Detection of Illicit Drugs

[EN] The consumption of illicit drugs has increased exponentially in recent years and has become a problem that worries both governments and international institutions. The rapid emergence of new compounds, their easy access, the low levels at which these substances are able to produce an effect, and their short time of permanence in the organism make it necessary to develop highly rapid, easy, sensitive, and selective methods for their detection. Currently, the most widely used methods for drug detection are based on techniques that require large measurement times, the use of sophisticated equipment, and qualified personnel. Chromo- and fluorogenic methods are an alternative to those classical procedures.We thank the Spanish Government [projects MAT2015-64139-C4-1-R and AGL2015-70235-C2-2-R (MINECO/FEDER)] and the Generalitat Valenciana (project PROMETEOII/2014/047) for support. S.E.S thanks the Ministerio de Economia y Competitividad for his Juan de la Cierva contract. B.L.T and E.G. thank the Spanish Government for their predoctoral grants. L.P. also thanks the Universitat Politecnica de Valencia for his predoctoral grant.Garrido-García, EM.; Pla, L.; Lozano-Torres, B.; El Sayed Shehata Nasr, S.; Martínez-Máñez, R.; Sancenón Galarza, F. (2018). Chromogenic and Fluorogenic Probes for the Detection of Illicit Drugs. ChemistryOpen. 7(5):401-428. https://doi.org/10.1002/open.201800034S40142875Komoroski, E. M., Komoroski, R. A., Valentine, J. L., Pearce, J. M., & Kearns, G. L. (2000). The Use of Nuclear Magnetic Resonance Spectroscopy in the Detection of Drug Intoxication. Journal of Analytical Toxicology, 24(3), 180-187. doi:10.1093/jat/24.3.180Drugs of Abuse: A DEA Resource Guide 2017World Drug Report 2017European Drug Report: Trends and Developments 2017Namera, A., Nakamoto, A., Saito, T., & Nagao, M. (2011). Colorimetric detection and chromatographic analyses of designer drugs in biological materials: a comprehensive review. Forensic Toxicology, 29(1), 1-24. doi:10.1007/s11419-010-0107-9Namera, A., Kawamura, M., Nakamoto, A., Saito, T., & Nagao, M. (2015). Comprehensive review of the detection methods for synthetic cannabinoids and cathinones. Forensic Toxicology, 33(2), 175-194. doi:10.1007/s11419-015-0270-0Kidwell, D. A., Holland, J. C., & Athanaselis, S. (1998). Testing for drugs of abuse in saliva and sweat. Journal of Chromatography B: Biomedical Sciences and Applications, 713(1), 111-135. doi:10.1016/s0378-4347(97)00572-0Cappelle, D., De Doncker, M., Gys, C., Krysiak, K., De Keukeleire, S., Maho, W., … Neels, H. (2017). A straightforward, validated liquid chromatography coupled to tandem mass spectrometry method for the simultaneous detection of nine drugs of abuse and their metabolites in hair and nails. Analytica Chimica Acta, 960, 101-109. doi:10.1016/j.aca.2017.01.022Koster, R. A., Alffenaar, J.-W. C., Greijdanus, B., VanDerNagel, J. E. L., & Uges, D. R. A. (2014). Fast and Highly Selective LC-MS/MS Screening for THC and 16 Other Abused Drugs and Metabolites in Human Hair to Monitor Patients for Drug Abuse. Therapeutic Drug Monitoring, 36(2), 234-243. doi:10.1097/ftd.0b013e3182a377e8Li, Y., Uddayasankar, U., He, B., Wang, P., & Qin, L. (2017). Fast, Sensitive, and Quantitative Point-of-Care Platform for the Assessment of Drugs of Abuse in Urine, Serum, and Whole Blood. Analytical Chemistry, 89(16), 8273-8281. doi:10.1021/acs.analchem.7b01288De la Asunción-Nadal, V., Armenta, S., Garrigues, S., & de la Guardia, M. (2017). Identification and determination of synthetic cannabinoids in herbal products by dry film attenuated total reflectance-infrared spectroscopy. Talanta, 167, 344-351. doi:10.1016/j.talanta.2017.02.026Risoluti, R., Materazzi, S., Gregori, A., & Ripani, L. (2016). Early detection of emerging street drugs by near infrared spectroscopy and chemometrics. Talanta, 153, 407-413. doi:10.1016/j.talanta.2016.02.044Andreou, C., Hoonejani, M. R., Barmi, M. R., Moskovits, M., & Meinhart, C. D. (2013). Rapid Detection of Drugs of Abuse in Saliva Using Surface Enhanced Raman Spectroscopy and Microfluidics. ACS Nano, 7(8), 7157-7164. doi:10.1021/nn402563fHe, S., Liu, D., Wang, Z., Cai, K., & Jiang, X. (2011). Utilization of unmodified gold nanoparticles in colorimetric detection. Science China Physics, Mechanics and Astronomy, 54(10), 1757-1765. doi:10.1007/s11433-011-4486-7Substance Abuse (Depressants or Sedative-Hypnotic Drugs) 2014Zhai, D., Agrawalla, B. K., Eng, P. S. F., Lee, S.-C., Xu, W., & Chang, Y.-T. (2013). Development of a fluorescent sensor for an illicit date rape drug – GBL. Chemical Communications, 49(55), 6170. doi:10.1039/c3cc43153cZhai, D., Tan, Y. Q. E., Xu, W., & Chang, Y.-T. (2014). Development of a fluorescent sensor for illicit date rape drug GHB. Chemical Communications, 50(22), 2904. doi:10.1039/c3cc49603aBaumes, L. A., Buaki Sogo, M., Montes-Navajas, P., Corma, A., & Garcia, H. (2010). A Colorimetric Sensor Array for the Detection of the Date-Rape Drug γ-Hydroxybutyric Acid (GHB): A Supramolecular Approach. Chemistry - A European Journal, 16(15), 4489-4495. doi:10.1002/chem.200903127Wang, W., Dong, Z.-Z., Yang, G., Leung, C.-H., Lin, S., & Ma, D.-L. (2017). A long-lived iridium(iii) chemosensor for the real-time detection of GHB. Journal of Materials Chemistry B, 5(15), 2739-2742. doi:10.1039/c6tb03396bMorris, J. A. (2007). Modified Cobalt Thiocyanate Presumptive Color Test for Ketamine Hydrochloride. Journal of Forensic Sciences, 52(1), 84-87. doi:10.1111/j.1556-4029.2006.00331.xMerck Manual Drug Information 2014Argente-García, A., Jornet-Martínez, N., Herráez-Hernández, R., & Campíns-Falcó, P. (2017). A passive solid sensor for in-situ colorimetric estimation of the presence of ketamine in illicit drug samples. Sensors and Actuators B: Chemical, 253, 1137-1144. doi:10.1016/j.snb.2017.07.183ELMOSALLAMY, M. A. F., & AMIN, A. S. (2014). New Potentiometric and Spectrophotometric Methods for the Determination of Dextromethorphan in Pharmaceutical Preparations. Analytical Sciences, 30(3), 419-425. doi:10.2116/analsci.30.419Mohseni, N., & Bahram, M. (2016). Mean centering of ratio spectra for colorimetric determination of morphine and codeine in pharmaceuticals and biological samples using melamine modified gold nanoparticles. Anal. Methods, 8(37), 6739-6747. doi:10.1039/c6ay02091gSAKAI, T., & OHNO, N. (1986). Spectrophotometric determination of stimulant drugs in urine by color reaction with tetrabromophenolphthalein ethyl ester. Analytical Sciences, 2(3), 275-279. doi:10.2116/analsci.2.275Sakai, T., & Ohno, N. (1987). Improved determination of methamphetamine, ephedrine and methylephedrine in urine by extraction-thermospectrometry. The Analyst, 112(2), 149. doi:10.1039/an9871200149Argente-García, A., Jornet-Martínez, N., Herráez-Hernández, R., & Campíns-Falcó, P. (2016). A solid colorimetric sensor for the analysis of amphetamine-like street samples. Analytica Chimica Acta, 943, 123-130. doi:10.1016/j.aca.2016.09.020Guler, E., Yilmaz Sengel, T., Gumus, Z. P., Arslan, M., Coskunol, H., Timur, S., & Yagci, Y. (2017). Mobile Phone Sensing of Cocaine in a Lateral Flow Assay Combined with a Biomimetic Material. Analytical Chemistry, 89(18), 9629-9632. doi:10.1021/acs.analchem.7b03017Choodum, A., Parabun, K., Klawach, N., Daeid, N. N., Kanatharana, P., & Wongniramaikul, W. (2014). Real time quantitative colourimetric test for methamphetamine detection using digital and mobile phone technology. Forensic Science International, 235, 8-13. doi:10.1016/j.forsciint.2013.11.018Choodum, A., Kanatharana, P., Wongniramaikul, W., & NicDaeid, N. (2015). A sol–gel colorimetric sensor for methamphetamine detection. Sensors and Actuators B: Chemical, 215, 553-560. doi:10.1016/j.snb.2015.03.089Moreno, D., Greñu, B. D. de, García, B., Ibeas, S., & Torroba, T. (2012). A turn-on fluorogenic probe for detection of MDMA from ecstasy tablets. Chemical Communications, 48(24), 2994. doi:10.1039/c2cc17823kFu, Y., Shi, L., Zhu, D., He, C., Wen, D., He, Q., … Cheng, J. (2013). Fluorene–thiophene-based thin-film fluorescent chemosensor for methamphetamine vapor by thiophene–amine interaction. Sensors and Actuators B: Chemical, 180, 2-7. doi:10.1016/j.snb.2011.10.031He, M., Peng, H., Wang, G., Chang, X., Miao, R., Wang, W., & Fang, Y. (2016). Fabrication of a new fluorescent film and its superior sensing performance to N-methamphetamine in vapor phase. Sensors and Actuators B: Chemical, 227, 255-262. doi:10.1016/j.snb.2015.12.048Lozano-Torres, B., Pascual, L., Bernardos, A., Marcos, M. D., Jeppesen, J. O., Salinas, Y., … Sancenón, F. (2017). Pseudorotaxane capped mesoporous silica nanoparticles for 3,4-methylenedioxymethamphetamine (MDMA) detection in water. Chemical Communications, 53(25), 3559-3562. doi:10.1039/c7cc00186jHe, C., He, Q., Deng, C., Shi, L., Fu, Y., Cao, H., & Cheng, J. (2011). Determination of Methamphetamine Hydrochloride by highly fluorescent polyfluorene with NH2-terminated side chains. Synthetic Metals, 161(3-4), 293-297. doi:10.1016/j.synthmet.2010.11.038Masseroni, D., Biavardi, E., Genovese, D., Rampazzo, E., Prodi, L., & Dalcanale, E. (2015). A fluorescent probe for ecstasy. Chemical Communications, 51(64), 12799-12802. doi:10.1039/c5cc04760aReviriego, F., Navarro, P., García-España, E., Albelda, M. T., Frías, J. C., Domènech, A., … Ortí, E. (2008). Diazatetraester 1H-Pyrazole Crowns as Fluorescent Chemosensors for AMPH, METH, MDMA (Ecstasy), and Dopamine. Organic Letters, 10(22), 5099-5102. doi:10.1021/ol801732tYamada, H., Ikeda-Wada, S., & Oguri, K. (1999). Highly Specific and Convenient Color Reaction for Methylenedioxymethamphetamine and Related Drugs Using Chromotropic Acid. Application as a Drug Screening Test. JOURNAL OF HEALTH SCIENCE, 45(6), 303-308. doi:10.1248/jhs.45.303Matsuda, K., Fukuzawa, T., Ishii, Y., & Yamada, H. (2007). Color reaction of 3,4-methylenedioxyamphetamines with chromotropic acid: its improvement and application to the screening of seized tablets. Forensic Toxicology, 25(1), 37-40. doi:10.1007/s11419-007-0022-xRouhani, S., & Haghgoo, S. (2015). A novel fluorescence nanosensor based on 1,8-naphthalimide-thiophene doped silica nanoparticles, and its application to the determination of methamphetamine. Sensors and Actuators B: Chemical, 209, 957-965. doi:10.1016/j.snb.2014.12.035Maue, M., & Schrader, T. (2005). A Color Sensor for Catecholamines. Angewandte Chemie International Edition, 44(15), 2265-2270. doi:10.1002/anie.200462702Maue, M., & Schrader, T. (2005). A Color Sensor for Catecholamines. Angewandte Chemie, 117(15), 2305-2310. doi:10.1002/ange.200462702Mosnaim, A. D., & Inwang, E. E. (1973). A spectrophotometric method for the quantification of 2-phenylethylamine in biological specimens. Analytical Biochemistry, 54(2), 561-577. doi:10.1016/0003-2697(73)90388-6Wang, D., Liu, T.-J., Zhang, W.-C., Zhang, W.-C., Slaven IV, W. T., & Li, C.-J. (1998). Enantiomeric discrimination of chiral amines with new fluorescent chemosensors. Chemical Communications, (16), 1747-1748. doi:10.1039/a802855iEl-Didamony, A. M., & Gouda, A. A. (2010). A novel spectrofluorimetric method for the assay of pseudoephedrine hydrochloride in pharmaceutical formulations via derivatization with 4-chloro-7-nitrobenzofurazan. Luminescence, 26(6), 510-517. doi:10.1002/bio.1261Mazina, J., Aleksejev, V., Ivkina, T., Kaljurand, M., & Poryvkina, L. (2012). Qualitative detection of illegal drugs (cocaine, heroin and MDMA) in seized street samples based on SFS data and ANN: validation of method. Journal of Chemometrics, 26(8-9), 442-455. doi:10.1002/cem.2462Sefah, K., Shangguan, D., Xiong, X., O’Donoghue, M. B., & Tan, W. (2010). Development of DNA aptamers using Cell-SELEX. Nature Protocols, 5(6), 1169-1185. doi:10.1038/nprot.2010.66Shi, Q., Shi, Y., Pan, Y., Yue, Z., Zhang, H., & Yi, C. (2014). Colorimetric and bare eye determination of urinary methylamphetamine based on the use of aptamers and the salt-induced aggregation of unmodified gold nanoparticles. Microchimica Acta, 182(3-4), 505-511. doi:10.1007/s00604-014-1349-8Mao, K., Yang, Z., Du, P., Xu, Z., Wang, Z., & Li, X. (2016). G-quadruplex–hemin DNAzyme molecular beacon probe for the detection of methamphetamine. RSC Advances, 6(67), 62754-62759. doi:10.1039/c6ra04912eShlyahovsky, B., Li, D., Weizmann, Y., Nowarski, R., Kotler, M., & Willner, I. (2007). Spotlighting of Cocaine by an Autonomous Aptamer-Based Machine. Journal of the American Chemical Society, 129(13), 3814-3815. doi:10.1021/ja069291nWang, F., Freage, L., Orbach, R., & Willner, I. (2013). Autonomous Replication of Nucleic Acids by Polymerization/Nicking Enzyme/DNAzyme Cascades for the Amplified Detection of DNA and the Aptamer–Cocaine Complex. Analytical Chemistry, 85(17), 8196-8203. doi:10.1021/ac4013094Wang, J., Song, J., Wang, X., Wu, S., Zhao, Y., Luo, P., & Meng, C. (2016). An ATMND/SGI based label-free and fluorescence ratiometric aptasensor for rapid and highly sensitive detection of cocaine in biofluids. Talanta, 161, 437-442. doi:10.1016/j.talanta.2016.08.039Huang, J., Chen, Y., Yang, L., Zhu, Z., Zhu, G., Yang, X., … Tan, W. (2011). Amplified detection of cocaine based on strand-displacement polymerization and fluorescence resonance energy transfer. Biosensors and Bioelectronics, 28(1), 450-453. doi:10.1016/j.bios.2011.05.038Zhang, C., & Johnson, L. W. (2009). Single Quantum-Dot-Based Aptameric Nanosensor for Cocaine. Analytical Chemistry, 81(8), 3051-3055. doi:10.1021/ac802737bEmrani, A. S., Danesh, N. M., Ramezani, M., Taghdisi, S. M., & Abnous, K. (2016). A novel fluorescent aptasensor based on hairpin structure of complementary strand of aptamer and nanoparticles as a signal amplification approach for ultrasensitive detection of cocaine. Biosensors and Bioelectronics, 79, 288-293. doi:10.1016/j.bios.2015.12.025Roncancio, D., Yu, H., Xu, X., Wu, S., Liu, R., Debord, J., … Xiao, Y. (2014). A Label-Free Aptamer-Fluorophore Assembly for Rapid and Specific Detection of Cocaine in Biofluids. Analytical Chemistry, 86(22), 11100-11106. doi:10.1021/ac503360nGuler, E., Bozokalfa, G., Demir, B., Gumus, Z. P., Guler, B., Aldemir, E., … Coskunol, H. (2016). An aptamer folding-based sensory platform decorated with nanoparticles for simple cocaine testing. Drug Testing and Analysis, 9(4), 578-587. doi:10.1002/dta.1992Ribes, À., Xifré -Pérez, E., Aznar, E., Sancenón, F., Pardo, T., Marsal, L. F., & Martínez-Máñez, R. (2016). Molecular gated nanoporous anodic alumina for the detection of cocaine. Scientific Reports, 6(1). doi:10.1038/srep38649Marsal, L. F., Vojkuvka, L., Formentin, P., Pallarés, J., & Ferré-Borrull, J. (2009). Fabrication and optical characterization of nanoporous alumina films annealed at different temperatures. Optical Materials, 31(6), 860-864. doi:10.1016/j.optmat.2008.09.008Oroval, M., Coronado-Puchau, M., Langer, J., Sanz-Ortiz, M. N., Ribes, Á., Aznar, E., … Martínez-Máñez, R. (2016). Surface Enhanced Raman Scattering and Gated Materials for Sensing Applications: The Ultrasensitive Detection ofMycoplasmaand Cocaine. Chemistry - A European Journal, 22(38), 13488-13495. doi:10.1002/chem.201602457Stojanovic, M. N., de Prada, P., & Landry, D. W. (2000). Fluorescent Sensors Based on Aptamer Self-Assembly. Journal of the American Chemical Society, 122(46), 11547-11548. doi:10.1021/ja0022223Stojanovic, M. N., de Prada, P., & Landry, D. W. (2001). Aptamer-Based Folding Fluorescent Sensor for Cocaine. Journal of the American Chemical Society, 123(21), 4928-4931. doi:10.1021/ja0038171Stojanovic, M. N., & Landry, D. W. (2002). Aptamer-Based Colorimetric Probe for Cocaine. Journal of the American Chemical Society, 124(33), 9678-9679. doi:10.1021/ja0259483Liu, Y., & Zhao, Q. (2017). Direct fluorescence anisotropy assay for cocaine using tetramethylrhodamine-labeled aptamer. Analytical and Bioanalytical Chemistry, 409(16), 3993-4000. doi:10.1007/s00216-017-0349-zZhou, Z., Du, Y., & Dong, S. (2011). Double-Strand DNA-Templated Formation of Copper Nanoparticles as Fluorescent Probe for Label-Free Aptamer Sensor. Analytical Chemistry, 83(13), 5122-5127. doi:10.1021/ac200120gShi, Y., Dai, H., Sun, Y., Hu, J., Ni, P., & Li, Z. (2013). Fluorescent sensing of cocaine based on a structure switching aptamer, gold nanoparticles and graphene oxide. The Analyst, 138(23), 7152. doi:10.1039/c3an00897eZhang, Y., Sun, Z., Tang, L., Zhang, H., & Zhang, G.-J. (2016). Aptamer based fluorescent cocaine assay based on the use of graphene oxide and exonuclease III-assisted signal amplification. Microchimica Acta, 183(10), 2791-2797. doi:10.1007/s00604-016-1923-3Zhang, J., Wang, L., Pan, D., Song, S., Boey, F. Y. C., Zhang, H., & Fan, C. (2008). Visual Cocaine Detection with Gold Nanoparticles and Rationally Engineered Aptamer Structures. Small, 4(8), 1196-1200. doi:10.1002/smll.200800057Li, Y., Ji, X., & Liu, B. (2011). Chemiluminescence aptasensor for cocaine based on double-functionalized gold nanoprobes and functionalized magnetic microbeads. Analytical and Bioanalytical Chemistry, 401(1), 213-219. doi:10.1007/s00216-011-5064-6Zou, R., Lou, X., Ou, H., Zhang, Y., Wang, W., Yuan, M., … Liu, Y. (2012). Highly specific triple-fragment aptamer for optical detection of cocaine. RSC Advances, 2(11), 4636. doi:10.1039/c2ra20307cZhang, S., Wang, L., Liu, M., Qiu, Y., Wang, M., Liu, X., … Yu, R. (2016). A novel, label-free fluorescent aptasensor for cocaine detection based on a G-quadruplex and ruthenium polypyridyl complex molecular light switch. Analytical Methods, 8(18), 3740-3746. doi:10.1039/c6ay00231eTang, Y., Long, F., Gu, C., Wang, C., Han, S., & He, M. (2016). Reusable split-aptamer-based biosensor for rapid detection of cocaine in serum by using an all-fiber evanescent wave optical biosensing platform. Analytica Chimica Acta, 933, 182-188. doi:10.1016/j.aca.2016.05.021Wang, L., Musile, G., & McCord, B. R. (2017). An aptamer-based paper microfluidic device for the colorimetric determination of cocaine. ELECTROPHORESIS, 39(3), 470-475. doi:10.1002/elps.201700254Liu, J., & Lu, Y. (2006). Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angewandte Chemie International Edition, 45(1), 90-94. doi:10.1002/anie.200502589Liu, J., & Lu, Y. (2006). Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles. Angewandte Chemie, 118(1), 96-100. doi:10.1002/ange.200502589He, M., Li, Z., Ge, Y., & Liu, Z. (2016). Portable Upconversion Nanoparticles-Based Paper Device for Field Testing of Drug Abuse. Analytical Chemistry, 88(3), 1530-1534. doi:10.1021/acs.analchem.5b04863Qiu, L., Zhou, H., Zhu, W., Qiu, L., Jiang, J., Shen, G., & Yu, R. (2013). A novel label-free fluorescence aptamer-based sensor method for cocaine detection based on isothermal circular strand-displacement amplification and graphene oxide absorption. New Journal of Chemistry, 37(12), 3998. doi:10.1039/c3nj00594aArslan, M., Yilmaz Sengel, T., Guler, E., Gumus, Z. P., Aldemir, E., Akbulut, H., … Yagci, Y. (2017). Double fluorescence assay via a β-cyclodextrin containing conjugated polymer as a biomimetic material for cocaine sensing. Polymer Chemistry, 8(21), 3333-3340. doi:10.1039/c7py00420fMao, K., Yang, Z., Li, J., Zhou, X., Li, X., & Hu, J. (2017). A novel colorimetric biosensor based on non-aggregated Au@Ag core–shell nanoparticles for methamphetamine and cocaine detection. Talanta, 175, 338-346. doi:10.1016/j.talanta.2017.07.011Ma, D.-L., Wang, M., He, B., Yang, C., Wang, W., & Leung, C.-H. (2015). A Luminescent Cocaine Detection Platform Using a Split G-Quadruplex-Selective Iridium(III) Complex and a Three-Way DNA Junction Architecture. ACS Applied Materials & Interfaces, 7(34), 19060-19067. doi:10.1021/acsami.5b05861Du, Y., Li, B., Guo, S., Zhou, Z., Zhou, M., Wang, E., & Dong, S. (2011). G-Quadruplex-based DNAzyme for colorimetric detection ofcocaine: Using magnetic nanoparticles as the separation and amplification element. The Analyst, 136(3), 493-497. doi:10.1039/c0an00557fZhang, K., Wang, K., Zhu, X., Zhang, J., Xu, L., Huang, B., & Xie, M. (2014). Label-free and ultrasensitive fluorescence detection of cocaine based on a strategy that utilizes DNA-templated silver nanoclusters and the nicking endonuclease-assisted signal amplification method. Chem. Commun., 50(2), 180-182. doi:10.1039/c3cc47418fZhou, J., Ellis, A. V., Kobus, H., & Voelcker, N. H. (2012). Aptamer sensor for cocaine using minor groove binder based energy transfer. Analytica Chimica Acta, 719, 76-81. doi:10.1016/j.aca.2012.01.011Drug Facts 2016Baudot, P., & Andre, J.-C. (1983). A Low-Cost Differential Fluorimeter for the Detection and Determination of LSD in Illicit Preparations. Journal of Analytical Toxicology, 7(2), 69-71. doi:10.1093/jat/7.2.69Mohseni, N., Bahram, M., & Baheri, T. (2017). Chemical nose for discrimination of opioids based on unmodified gold nanoparticles. Sensors and Actuators B: Chemical, 250, 509-517. doi:10.1016/j.snb.2017.04.145Shcherbakova, E. G., Zhang, B., Gozem, S., Minami, T., Zavalij, P. Y., Pushina, M., … Anzenbacher, P. (2017). Supramolecular Sensors for Opiates and Their Metabolites. Journal of the American Chemical Society, 139(42), 14954-14960. doi:10.1021/jacs.7b0637

Designing an artefact for sharing and reusing teaching practices in Higher Education institutions : an exploratory study

Knowledge management (KM) is considered as a significant source of success in many organisations, specifically higher education institutions. Instructors generate a considerable amount of valuable teaching-related knowledge that should be identified and shared among communities of instructors to enhance informal learning and deliver better quality teaching. However, many universities are facing difficulties in documenting, sharing and applying the teaching experiences gained by instructors. In the field of KM, a vast amount of research exists focusing on the activities of sharing knowledge, disregarding the importance of knowledge application and reuse. This research aims to close this gap by designing a system enabling instructors to share and apply teaching experiences. Therefore, we have followed a design research approach to explore meta-requirements by conducting an investigative study with instructors who work in Saudi universities. Through our exploratory study, we identified three challenges that might prevent instructors from sharing and reusing knowledge using the current communication channels: lack of access to experts and expertise, lack of structured knowledge, and lack of motivation. To overcome these challenges, a new artefact will be designed based on the resulting meta-requirements to ensure effective sharing and reuse of teaching experiences

Big Genomes Facilitate the Comparative Identification of Regulatory Elements

The identification of regulatory sequences in animal genomes remains a significant challenge. Comparative genomic methods that use patterns of evolutionary conservation to identify non-coding sequences with regulatory function have yielded many new vertebrate enhancers. However, these methods have not contributed significantly to the identification of regulatory sequences in sequenced invertebrate taxa. We demonstrate here that this differential success, which is often attributed to fundamental differences in the nature of vertebrate and invertebrate regulatory sequences, is instead primarily a product of the relatively small size of sequenced invertebrate genomes. We sequenced and compared loci involved in early embryonic patterning from four species of true fruit flies (family Tephritidae) that have genomes four to six times larger than those of Drosophila melanogaster. Unlike in Drosophila, where virtually all non-coding DNA is highly conserved, blocks of conserved non-coding sequence in tephritids are flanked by large stretches of poorly conserved sequence, similar to what is observed in vertebrate genomes. We tested the activities of nine conserved non-coding sequences flanking the even-skipped gene of the teprhitid Ceratis capitata in transgenic D. melanogaster embryos, six of which drove patterns that recapitulate those of known D. melanogaster enhancers. In contrast, none of the three non-conserved tephritid non-coding sequences that we tested drove expression in D. melanogaster embryos. Based on the landscape of non-coding conservation in tephritids, and our initial success in using conservation in tephritids to identify D. melanogaster regulatory sequences, we suggest that comparison of tephritid genomes may provide a systematic means to annotate the non-coding portion of the D. melanogaster genome. We also propose that large genomes be given more consideration in the selection of species for comparative genomics projects, to provide increased power to detect functional non-coding DNAs and to provide a less biased view of the evolution and function of animal genomes

Exploring the functional role of the CHRM2 gene in human cognition: results from a dense genotyping and brain expression study

<p>Abstract</p> <p>Background</p> <p>The <it>CHRM2 </it>gene, located on the long arm of chromosome 7 (7q31-35), is involved in neuronal excitability, synaptic plasticity and feedback regulation of acetylcholine release, and has been implicated in higher cognitive processing. The aim of this study is the identification of functional (non)coding variants underlying cognitive phenotypic variation.</p> <p>Methods</p> <p>We previously reported an association between polymorphisms in the 5'UTR regions of the <it>CHRM2 </it>gene and intelligence.. However, no functional variants within this area have currently been identified. In order to identify the relevant functional variant(s), we conducted a denser coverage of SNPs, using two independent Dutch cohorts, consisting of a children's sample (N = 371 ss; mean age 12.4) and an adult sample (N= 391 ss; mean age 37.6). For all individuals standardized intelligence measures were available. Subsequently, we investigated genotype-dependent <it>CHRM2 </it>gene expression levels in the brain, to explore putative enhancer/inhibition activity exerted by variants within the muscarinic acetylcholinergic receptor.</p> <p>Results</p> <p>Using a test of within-family association two of the previously reported variants – rs2061174, and rs324650 – were again strongly associated with intelligence (<it>P </it>< 0.01). A new SNP (rs2350780) showed a trend towards significance. SNP rs324650, is located within a short interspersed repeat (SINE). Although the function of short interspersed repeats remains contentious, recent research revealed potential functionality of SINE repeats in a gene-regulatory context. Gene-expression levels in post-mortem brain material, however were not dependent on rs324650 genotype.</p> <p>Conclusion</p> <p>Using a denser coverage of SNPs in the <it>CHRM2 </it>gene, we confirmed the 5'UTR regions to be most interesting in the context of intelligence, and ruled out other regions of this gene. Although no correlation between genomic variants and gene expression was found, it would be interesting to examine allele-specific effects on CHRM2 transcripts expression in much more detail, for example in relation to transcripts specific halve-life and their relation to LTP and memory.</p

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

<p>Abstract</p> <p>Background</p> <p>The black tiger shrimp (<it>Penaeus monodon</it>) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the <it>P. monodon </it>genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the <it>P. monodon </it>genome were obtained for repetitive and protein-coding sequence analyses.</p> <p>Results</p> <p>We found that microsatellite sequences were highly abundant in the <it>P. monodon </it>genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, <it>via </it>self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, <it>i.e</it>., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the <it>P. monodon </it>genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the <it>P. monodon </it>genome.</p> <p>Conclusions</p> <p>The redundancy of various repeat types in the <it>P. monodon </it>genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.</p

Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution

Genetic Analysis of Genome-Scale Recombination Rate Evolution in House Mice

The rate of meiotic recombination varies markedly between species and among individuals. Classical genetic experiments demonstrated a heritable component to population variation in recombination rate, and specific sequence variants that contribute to recombination rate differences between individuals have recently been identified. Despite these advances, the genetic basis of species divergence in recombination rate remains unexplored. Using a cytological assay that allows direct in situ imaging of recombination events in spermatocytes, we report a large (∼30%) difference in global recombination rate between males of two closely related house mouse subspecies (Mus musculus musculus and M. m. castaneus). To characterize the genetic basis of this recombination rate divergence, we generated an F2 panel of inter-subspecific hybrid males (n = 276) from an intercross between wild-derived inbred strains CAST/EiJ (M. m. castaneus) and PWD/PhJ (M. m. musculus). We uncover considerable heritable variation for recombination rate among males from this mapping population. Much of the F2 variance for recombination rate and a substantial portion of the difference in recombination rate between the parental strains is explained by eight moderate- to large-effect quantitative trait loci, including two transgressive loci on the X chromosome. In contrast to the rapid evolution observed in males, female CAST/EiJ and PWD/PhJ animals show minimal divergence in recombination rate (∼5%). The existence of loci on the X chromosome suggests a genetic mechanism to explain this male-biased evolution. Our results provide an initial map of the genetic changes underlying subspecies differences in genome-scale recombination rate and underscore the power of the house mouse system for understanding the evolution of this trait