35 results on '"Ambrose B"'
Search Results
2. CHARMM-DYES : Parameterization of fluorescent dyes for use with the CHARMM force field
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Shaw, R.A., Johnston-Wood, T., Ambrose, B., Craggs, T.D., and Hill, J.G.
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Quantitative Biology::Biomolecules - Abstract
We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments to resolve the dynamics of proteins and nucleic acids at the nanoscale. However, little is known about the accuracy of the theoretical approximations used in determining the dynamics from the spectroscopic data. Molecular dynamics simulations can provide valuable insights into these dynamics at an atomistic level, but this requires accurate parameters for the dyes. The complex structure of the dyes and the importance of this in determining their spectroscopic properties mean that parameters generated by analogy to existing parameters do not give meaningful results. Through validation relative to quantum chemical calculation and experiments, the new parameters are shown to significantly outperform those that can be generated automatically, giving better agreement in both the charge distributions and structural properties. These improvements, in particular with regard to orientation of the dipole moments on the dyes, are vital for accurate simulation of FRET processes.
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- 2020
3. The smfBox is an open-source platform for single-molecule FRET
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Ambrose, B., Baxter, J.M., Cully, J., Willmott, M., Steele, E.M., Bateman, B.C., Martin-Fernandez, M.L., Cadby, A., Shewring, J., Aaldering, M., and Craggs, T.D.
- Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET’s broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community.
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- 2020
4. Regional Conformational Flexibility Couples Substrate Specificity and Scissile Phosphate Diester Selectivity in Human Flap Endonuclease 1
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Bennet, I., Finger, L.D., Baxter, N.J., Ambrose, B., Hounslow, A., Thompson, M.J., Exell, J.C., Shahari, N.N.B.M., Craggs, T.D., Waltho, J.P., and Grasby, J.A.
- Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5′-terminus/flap through the arch and recognition of a single nucleotide 3′-flap by the α2–α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2–α3 loop are disordered without substrate. Disorder within the arch explains how 5′-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1–DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1–DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
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- 2018
5. State of the climate in 2016
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Aaron-Morrison, A. P., Ackerman, S. A., Adams, N. G., Adler, R. F., Albanil, A., Alfaro, E. J., Allan, R., Alves, L. M., Amador, J. A., Andreassen, L. M., Arendt, A., Arévalo, J., Arndt, D. S., Arzhanova, N. M., Aschan, M. M., Azorin-Molina, C., Banzon, V., Bardin, M. U., Barichivich, J., Baringer, M. O., Barreira, S., Baxter, S., Bazo, J., Becker, A., Bedka, K. M., Behrenfeld, M. J., Bell, G. D., Belmont, M., Benedetti, A., Bernhard, G., Berrisford, P., Berry, D. I., Bettolli, M. L., Bhatt, U. S., Bidegain, M., Bill, B. D., Billheimer, S., Bissolli, P., Blake, E. S., Blunden, J., Bosilovich, M. G., Boucher, O., Boudet, D., Box, J. E., Boyer, T., Braathen, G. O., Bromwich, D. H., Brown, R., Bulygina, O. N., Burgess, D., Calderón, B., Camargo, S. J., Campbell, J. D., Cappelen, J., Carrasco, G., Carter, B. R., Chambers, D. P., Chandler, E., Christiansen, H. H., Christy, J. R., Chung, D., Chung, E. S., Cinque, K., Clem, K. R., Coelho, C. A., Cogley, J. G., Coldewey-Egbers, M., Colwell, S., Cooper, O. R., Copland, L., Cosca, C. E., Cross, J. N., Crotwell, M. J., Crouch, J., Davis, S. M., Eyto, E., Jeu, R. A. M., Laat, J., Degasperi, C. L., Degenstein, D., Demircan, M., Derksen, C., Destin, D., Di Girolamo, L., Di Giuseppe, F., Diamond, H. J., Dlugokencky, E. J., Dohan, K., Dokulil, M. T., Dolgov, A. V., Dolman, A. J., Domingues, C. M., Donat, M. G., Dong, S., Dorigo, W. A., Dortch, Q., Doucette, G., Drozdov, D. S., Ducklow, H., Dunn, R. J. H., Durán-Quesada, A. M., Dutton, G. S., Ebrahim, A., Elkharrim, M., Elkins, J. W., Espinoza, J. C., Etienne-Leblanc, S., Evans, T. E., Famiglietti, J. S., Farrell, S., Fateh, S., Fausto, R. S., Fedaeff, N., Feely, R. A., Feng, Z., Fenimore, C., Fettweis, X., Fioletov, V. E., Flemming, J., Fogarty, C. T., Fogt, R. L., Folland, C., Fonseca, C., Fossheim, M., Foster, M. J., Fountain, A., Francis, S. D., Franz, B. A., Frey, R. A., Frith, S. M., Froidevaux, L., Ganter, C., Garzoli, S., Gerland, S., Gobron, N., Goldenberg, S. B., Gomez, R. S., Goni, G., Goto, A., Grooß, J. U., Gruber, A., Guard, C. C., Gugliemin, M., Gupta, S. K., Gutiérrez, J. M., Hagos, S., Hahn, S., Haimberger, L., Hakkarainen, J., Hall, B. D., Halpert, M. S., Hamlington, B. D., Hanna, E., Hansen, K., Hanssen-Bauer, I., Harris, I., Heidinger, A. K., Heikkilä, A., Heil, A., Heim, R. R., Hendricks, S., Hernández, M., Hidalgo, H. G., Hilburn, K., Ho, S. P. B., Holmes, R. M., Hu, Z. Z., Huang, B., Huelsing, H. K., Huffman, G. J., Hughes, C., Hurst, D. F., Ialongo, I., Ijampy, J. A., Ingvaldsen, R. B., Inness, A., Isaksen, K., Ishii, M., Jevrejeva, S., Jiménez, C., Jin, X., Johannesen, E., John, V., Johnsen, B., Johnson, B., Johnson, G. C., Jones, P. D., Joseph, A. C., Jumaux, G., Kabidi, K., Kaiser, J. W., Kato, S., Kazemi, A., Keller, L. M., Kendon, M., Kennedy, J., Kerr, K., Kholodov, A. L., Khoshkam, M., Killick, R., Kim, H., Kim, S. J., Kimberlain, T. B., Klotzbach, P. J., Knaff, J. A., Kobayashi, S., Kohler, J., Korhonen, J., Korshunova, N. N., Kovacs, K. M., Kramarova, N., Kratz, D. P., Kruger, A., Kruk, M. C., Kudela, R., Kumar, A., Lakatos, M., Lakkala, K., Lander, M. A., Landsea, C. W., Lankhorst, M., Lantz, K., Lazzara, M. A., Lemons, P., Leuliette, E., L’heureux, M., Lieser, J. L., Lin, I. I., Liu, H., Liu, Y., Locarnini, R., Loeb, N. G., Lo Monaco, C., Long, C. S., López Álvarez, L. A., Lorrey, A. M., Loyola, D., Lumpkin, R., Luo, J. J., Luojus, K., Lydersen, C., Lyman, J. M., Maberly, S. C., Maddux, B. C., Malheiros Ramos, A., Malkova, G. V., Manney, G., Marcellin, V., Marchenko, S. S., Marengo, J. A., Marra, J. J., Marszelewski, W., Martens, B., Martínez-Güingla, R., Massom, R. A., Mata, M. M., Mathis, J. T., May, L., Mayer, M., Mazloff, M., Mcbride, C., Mccabe, M. F., Mccarthy, M., Mcclelland, J. W., Mcgree, S., Mcvicar, T. R., Mears, C. A., Meier, W., Meinen, C. S., Mekonnen, A., Menéndez, M., Mengistu Tsidu, G., Menzel, W. P., Merchant, C. J., Meredith, M. P., Merrifield, M. A., Metzl, N., Minnis, P., Miralles, D. G., Mistelbauer, T., Mitchum, G. T., Monselesan, D., Monteiro, P., Montzka, S. A., Morice, C., Mote, T., Mudryk, L., Mühle, J., Mullan, A. B., Nash, E. R., Naveira-Garabato, A. C., Nerem, R. S., Newman, P. A., Nieto, J. J., Noetzli, J., O’neel, S., Osborn, T. J., Overland, J., Oyunjargal, L., Parinussa, R. M., Park, E. H., Parker, D., Parrington, M., Parsons, A. R., Pasch, R. J., Pascual-Ramírez, R., Paterson, A. M., Paulik, C., Pearce, P. R., Pelto, M. S., Peng, L., Perkins-Kirkpatrick, S. E., Perovich, D., Petropavlovskikh, I., Pezza, A. B., Phillips, D., Pinty, B., Pitts, M. C., Pons, M. R., Porter, A. O., Primicerio, R., Proshutinsky, A., Quegan, S., Quintana, J., Rahimzadeh, F., Rajeevan, M., Randriamarolaza, L., Razuvaev, V. N., Reagan, J., Reid, P., Reimer, C., Rémy, S., Renwick, J. A., Revadekar, J. V., Richter-Menge, J., Riffler, M., Rimmer, A., Rintoul, S., Robinson, D. A., Rodell, M., Rodríguez Solís, J. L., Romanovsky, V. E., Ronchail, J., Rosenlof, K. H., Roth, C., Rusak, J. A., Sabine, C. L., Sallée, J. B., Sánchez-Lugo, A., Santee, M. L., Sawaengphokhai, P., Sayouri, A., Scambos, T. A., Schemm, J., Schladow, S. G., Schmid, C., Schmid, M., Schmidtko, S., Schreck, C. J., Selkirk, H. B., Send, U., Sensoy, S., Setzer, A., Sharp, M., Shaw, A., Shi, L., Shiklomanov, A. I., Shiklomanov, N. I., Siegel, D. A., Signorini, S. R., Sima, F., Simmons, A. J., Smeets, C. J. P. P., Smith, S. L., Spence, J. M., Srivastava, A. K., Stackhouse, P. W., Stammerjohn, S., Steinbrecht, W., Stella, J. L., Stengel, M., Stennett-Brown, R., Stephenson, T. S., Strahan, S., Streletskiy, D. A., Sun-Mack, S., Swart, S., Sweet, W., Talley, L. D., Tamar, G., Tank, S. E., Taylor, M. A., Tedesco, M., Teubner, K., Thoman, R. L., Thompson, P., Thomson, L., Timmermans, M. L., Maxim Timofeyev, Tirnanes, J. A., Tobin, S., Trachte, K., Trainer, V. L., Tretiakov, M., Trewin, B. C., Trotman, A. R., Tschudi, M., As, D., Wal, R. S. W., A, R. J., Schalie, R., Schrier, G., Werf, G. R., Meerbeeck, C. J., Velicogna, I., Verburg, P., Vigneswaran, B., Vincent, L. A., Volkov, D., Vose, R. S., Wagner, W., Wåhlin, A., Wahr, J., Walsh, J., Wang, C., Wang, J., Wang, L., Wang, M., Wang, S. H., Wanninkhof, R., Watanabe, S., Weber, M., Weller, R. A., Weyhenmeyer, G. A., Whitewood, R., Wijffels, S. E., Wilber, A. C., Wild, J. D., Willett, K. M., Williams, M. J. M., Willie, S., Wolken, G., Wong, T., Wood, E. F., Woolway, R. I., Wouters, B., Xue, Y., Yamada, R., Yim, S. Y., Yin, X., Young, S. H., Yu, L., Zahid, H., Zambrano, E., Zhang, P., Zhao, G., Zhou, L., Ziemke, J. R., Love-Brotak, S. E., Gilbert, K., Maycock, T., Osborne, S., Sprain, M., Veasey, S. W., Ambrose, B. J., Griffin, J., Misch, D. J., Riddle, D. B., Young, T., Macias Fauria, M, Blunden, J, Arndt, D, Earth and Climate, Faculty of Earth and Life Sciences, Clinical Developmental Psychology, Climate Change and Landscape Dynamics, and Molecular Cell Physiology
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Meteor (satellite) ,Atmospheric Science ,010504 meteorology & atmospheric sciences ,0208 environmental biotechnology ,02 engineering and technology ,01 natural sciences ,020801 environmental engineering ,Geography ,13. Climate action ,Climatology ,SDG 13 - Climate Action ,SDG 14 - Life Below Water ,0105 earth and related environmental sciences - Abstract
In 2016, the dominant greenhouse gases released into Earth's atmosphere-carbon dioxide, methane, and nitrous oxide-continued to increase and reach new record highs. The 3.5 +/- 0.1 ppm rise in global annual mean carbon dioxide from 2015 to 2016 was the largest annual increase observed in the 58-year measurement record. The annual global average carbon dioxide concentration at Earth's surface surpassed 400 ppm (402.9 +/- 0.1 ppm) for the first time in the modern atmospheric measurement record and in ice core records dating back as far as 800000 years. One of the strongest El Nino events since at least 1950 dissipated in spring, and a weak La Nina evolved later in the year. Owing at least in part to the combination of El Nino conditions early in the year and a long-term upward trend, Earth's surface observed record warmth for a third consecutive year, albeit by a much slimmer margin than by which that record was set in 2015. Above Earth's surface, the annual lower troposphere temperature was record high according to all datasets analyzed, while the lower stratospheric temperature was record low according to most of the in situ and satellite datasets. Several countries, including Mexico and India, reported record high annual temperatures while many others observed near-record highs. A week-long heat wave at the end of April over the northern and eastern Indian peninsula, with temperatures surpassing 44 degrees C, contributed to a water crisis for 330 million people and to 300 fatalities. In the Arctic the 2016 land surface temperature was 2.0 degrees C above the 1981-2010 average, breaking the previous record of 2007, 2011, and 2015 by 0.8 degrees C, representing a 3.5 degrees C increase since the record began in 1900. The increasing temperatures have led to decreasing Arctic sea ice extent and thickness. On 24 March, the sea ice extent at the end of the growth season saw its lowest maximum in the 37-year satellite record, tying with 2015 at 7.2% below the 1981-2010 average. The September 2016 Arctic sea ice minimum extent tied with 2007 for the second lowest value on record, 33% lower than the 1981-2010 average. Arctic sea ice cover remains relatively young and thin, making it vulnerable to continued extensive melt. The mass of the Greenland Ice Sheet, which has the capacity to contribute similar to 7 m to sea level rise, reached a record low value. The onset of its surface melt was the second earliest, after 2012, in the 37-year satellite record. Sea surface temperature was record high at the global scale, surpassing the previous record of 2015 by about 0.01 degrees C. The global sea surface temperature trend for the 21st century-to-date of +0.162 degrees C decade(-1) is much higher than the longer term 1950-2016 trend of +0.100 degrees C decade(-1). Global annual mean sea level also reached a new record high, marking the sixth consecutive year of increase. Global annual ocean heat content saw a slight drop compared to the record high in 2015. Alpine glacier retreat continued around the globe, and preliminary data indicate that 2016 is the 37th consecutive year of negative annual mass balance. Across the Northern Hemisphere, snow cover for each month from February to June was among its four least extensive in the 47-year satellite record. Continuing a pattern below the surface, record high temperatures at 20-m depth were measured at all permafrost observatories on the North Slope of Alaska and at the Canadian observatory on northernmost Ellesmere Island. In the Antarctic, record low monthly surface pressures were broken at many stations, with the southern annular mode setting record high index values in March and June. Monthly high surface pressure records for August and November were set at several stations. During this period, record low daily and monthly sea ice extents were observed, with the November mean sea ice extent more than 5 standard deviations below the 1981-2010 average. These record low sea ice values contrast sharply with the record high values observed during 2012-14. Over the region, springtime Antarctic stratospheric ozone depletion was less severe relative to the 1991-2006 average, but ozone levels were still low compared to pre-1990 levels. Closer to the equator, 93 named tropical storms were observed during 2016, above the 1981-2010 average of 82, but fewer than the 101 storms recorded in 2015. Three basins-the North Atlantic, and eastern and western North Pacific-experienced above-normal activity in 2016. The Australian basin recorded its least active season since the beginning of the satellite era in 1970. Overall, four tropical cyclones reached the Saffir-Simpson category 5 intensity level. The strong El Nino at the beginning of the year that transitioned to a weak La Nina contributed to enhanced precipitation variability around the world. Wet conditions were observed throughout the year across southern South America, causing repeated heavy flooding in Argentina, Paraguay, and Uruguay. Wetter-than-usual conditions were also observed for eastern Europe and central Asia, alleviating the drought conditions of 2014 and 2015 in southern Russia. In the United States, California had its first wetter-than-average year since 2012, after being plagued by drought for several years. Even so, the area covered by drought in 2016 at the global scale was among the largest in the post-1950 record. For each month, at least 12% of land surfaces experienced severe drought conditions or worse, the longest such stretch in the record. In northeastern Brazil, drought conditions were observed for the fifth consecutive year, making this the longest drought on record in the region. Dry conditions were also observed in western Bolivia and Peru; it was Bolivia's worst drought in the past 25 years. In May, with abnormally warm and dry conditions already prevailing over western Canada for about a year, the human-induced Fort McMurray wildfire burned nearly 590000 hectares and became the costliest disaster in Canadian history, with $3 billion (U.S. dollars) in insured losses.
- Published
- 2017
6. Evaluation of Three Proprietary Slow-Release Oxytocin Formulations on Corpus Luteum (CL) Function in Mares
- Author
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Vanderwall, D.K., primary, Kinney, D.L., additional, Mason, H., additional, Ambrose, B., additional, and Rigas, J., additional
- Published
- 2018
- Full Text
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7. The MERLIN Induction Voltage Adder radiographic accelerator
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Thomas, K., primary, Beech, P, additional, Clough, S, additional, Moodhoo, R, additional, Stevens, A, additional, Wales, K, additional, Sinclair, M, additional, Buck, J, additional, Burscough, J, additional, Davis, K, additional, Hindle, A, additional, White, A, additional, Nicholls, J, additional, Traylen, D, additional, Bryant, P, additional, Ewing, C, additional, Younger, C, additional, Jones, S, additional, Grant, D, additional, Jones, A, additional, Goude, D, additional, Williams, R, additional, Threadgold, J, additional, Nesbitt, J, additional, Kilminster, P, additional, Holmes, H, additional, Shaw, R, additional, Bell, M, additional, Ambrose, B, additional, Soulsby, J, additional, Fraser, S, additional, Gray, A, additional, Huckle, I, additional, Page, A, additional, Seward, H, additional, Toury, M, additional, and Hourdin, L, additional
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- 2017
- Full Text
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8. The governance of urban green spaces in selected EU-cities : Policies, Practices, Actors, Topics
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Buizer, I.M., Elands, B.H.M., Mattijssen, T.J.M., Jagt, A.P.N., Ambrose, B., Geroházi, E., and Santos, E.
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management of urban green areas ,Alterra - Centrum Landschap ,public green areas ,groenbeheer ,WASS ,stadsomgeving ,urban environment ,Forest and Nature Conservation Policy ,groene infrastructuur ,Landscape Centre ,green infrastructure ,governance ,participation ,Bos- en Natuurbeleid ,openbaar groen ,participatie - Abstract
In a time of continuing urbanization, there is an increasing focus on developing attractive and healthy urban environments. Green spaces, ranging from woodlands and parks to allotment gardens and green roofs, provide a range of ecosystem services that contribute to better cities (Lovell and Taylor, 2013). The Green Infrastructure and Urban Biodiversity for Sustainable Urban Development and the Green Economy project (GREEN SURGE in brief), funded under the EU’s 7th Framework Programme for research, will identify, develop and test ways of linking green spaces, biodiversity, people and the green economy in order to meet the major urban challenges related to land use conflicts, climate change adaptation, demographic changes and human health and well being. The contents of this report are based on work conducted in Work Package 6, one of the eight Work Packages of GREEN SURGE. Work Package 6 focuses on governance arrangements for urban green spaces. In this report, we discuss the findings of the GREEN SURGE Work Package 6 Tier 1 research on identifying and conceptualising innovative participatory governance arrangements in regards to the management of urban green infrastructure.
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- 2015
9. Diagnostic analysis of the Canary Current System of West Africa: the need for a paradigm shift to proactive natural resource management
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Isimemen Osemwegie, Katelene da Cruz Delgado, Abdul Wahid Arimiyaw, Ambrose Bockarie Kanneh, Christian Tchègoun Todota, Amy Faye, and Felicia Olufunmilayo Akinyemi
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Anthropogenic disturbance ,Canary Current Large Marine Ecosystem ,Climate change ,Land-based pollution ,Productivity ,Oceanography ,GC1-1581 - Abstract
Large exports of land-based contaminants to the ocean exacerbate the effects of climate change, pollute ocean waters, disrupt biogeochemical cycles, harm marine organisms, and consequently jeopardise food security and the livelihoods of ocean-dependent communities. The Canary Current Large Marine Ecosystem (CCLME) is characterised by a mix of the Atlantic Ocean basin waters, reverse flow from the Mediterranean Sea, and inland waters from adjacent countries. This biodiversity-rich ecosystem is a source of ecosystem goods and services that provide sustenance for populations in the coastal states of West Africa and beyond. However, with the ocean surface warming, ocean productivity and fisheries’ outputs have declined across multiple trophic levels. Therefore, in this diagnostic study based on a systematic literature review (publications from 2009 to 2020), we (a) provide an integrative assessment of the CCLME with the exception of Morocco, in the context of the modular large marine ecosystem framework using the categories ‘environmental’ (productivity, fish and fisheries, pollution, and ecosystem health) and ‘non-environmental’ (socioeconomic and governance), and (b) identify knowledge gaps and data scarce regions. The key drivers of change in the CCLME were identified as fishing pressure, land-based pollution, coastal habitat loss, and climate change. Productivity, land-based pollution, and ecosystem health were priority areas for data collection in the CCLME, with data deficiencies particularly apparent in The Gambia and Guinea. Therefore, to mitigate further degradation and accelerate progress toward sustainable management of the CCLME, research should be conducted in these priority areas of data deficiency. Furthermore, as most drivers of change in this ecosystem are related to weak management and a lack of regulatory enforcement, we recommend effective implementation, monitoring, and enforcement of existing national and transboundary regulations, as well as ecosystem-based human-centred management approaches, as proactive strategies for decoupling anthropogenic disturbances from climate change and optimising the productivity of the CCLME.
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- 2022
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10. Ozdravljenik. U blizini agitatora. Novi organon. Politika. Religijski napredak.
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Ambrose Bierce and Stefan Elezović
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Social Sciences ,History of scholarship and learning. The humanities ,AZ20-999 - Abstract
OZDRAVLJENIK Šta! "Van opasnosti?" Može li uobražena dama Ili nagnuti farisej prestati klevetati? Neće li me izdaja više milovati po ruci, Niti mržnja vrebati me oko vrata? – Nezahvalnost, uz otkazane beneficije, Nije zatvorila puni dlan da napravi pesnicu? Hoće li se zavist ne uzvraćati Za vrline na koje se bilo uzaludno ugledati?
- Published
- 2022
11. Association Between Electronic Cigarette Use and Openness to Cigarette Smoking Among US Young Adults
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Coleman, B. N., primary, Apelberg, B. J., additional, Ambrose, B. K., additional, Green, K. M., additional, Choiniere, C. J., additional, Bunnell, R., additional, and King, B. A., additional
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- 2014
- Full Text
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12. Understanding the role of incentives for achieving and sustaining viral suppression: A qualitative sub-study of a financial incentives trial in Uganda.
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Carol S Camlin, Kara Marson, Alex Ndyabakira, Monica Getahun, Devy Emperador, Ambrose Byamukama, Dalsone Kwarisiima, Harsha Thirumurthy, and Gabriel Chamie
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Medicine ,Science - Abstract
BackgroundViral suppression among people living with HIV (PLHIV) is essential for protecting health and preventing HIV transmission, yet globally, rates of viral suppression are sub-optimal. Interventions to improve HIV prevention and care cascade outcomes remain vital. Financial incentives hold promise for improving these outcomes, yet to date, clinical trial results have been mixed.MethodsThis qualitative sub-study, embedded in a trial (NCT02890459) in Uganda to test whether incentives are effective for achieving viral suppression in PLHIV, sought to enhance our understanding of the factors that influence this outcome. Forty-nine (n = 49) PLHIV, purposely sampled to balance across gender, study arm, and viral suppression status, were interviewed to explore barriers and motivations for care engagement, adherence, and viral suppression, and attributions for decision-making, including perceived influence of incentives on behaviors.ResultsWhile many participants with undetectable viral load (VL) who received incentives said the incentives motivated their ART adherence, others expressed intrinsic motivation for adherence. All felt that incentives reduced burdens of transport costs, lost income due to time spent away from work, and food insecurity. Incentives may have activated attention and memory for some, as excitement about anticipating incentives helped them adhere to medication schedules. In comparison, participants who were randomized to receive incentives but had detectable VL faced a wider range, complexity and severity of challenges to care engagement. Notably, their narratives included more accounts of poor treatment in clinics, food insecurity, and severe forms of stigma. With or without incentives, adherence was reinforced through experiencing restored health due to ART, social support (especially from partners), and good quality counseling and clinical care.ConclusionsIn considering why incentives sometimes fail to achieve behavior change, it may be helpful to attend to the full set of factors- psychological, interpersonal, social and structural- that militate against the behavior change required to achieve behavioral outcomes. To be effective, incentives may need to be combined with other interventions to address the spectrum of barriers to care engagement.
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- 2022
- Full Text
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13. Leveraging incentives to increase HIV testing uptake among men: qualitative insights from rural Uganda
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Alex Ndyabakira, Monica Getahun, Ambrose Byamukama, Devy Emperador, Stella Kabageni, Kara Marson, Dalsone Kwarisiima, Gabriel Chamie, Harsha Thirumurthy, Diane Havlir, Moses R. Kamya, and Carol S. Camlin
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HIV testing ,Men ,Economic incentives ,Lottery ,Loss aversion ,Sub Saharan Africa ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background Few studies have explored how economic incentives influence behavioral outcomes. This study aimed to identify pathways of action of an incentives-based intervention to increase men’s participation in HIV testing. Methods The qualitative study was embedded in a randomized-controlled trial that compared effectiveness of gain-framed, loss-framed and lottery-based incentives to increase HIV testing among men. Following testing at a community health campaign, 60 in-depth interviews were conducted with men systematically sampled on the basis of age, incentive group, and campaign attendance. Data were coded deductively and inductively for thematic content analysis. Results Incentives addressed men’s structural, interpersonal and individual-level barriers to testing: offered at convenient locations, incentives offset costs of testing, in lost wages, which are exacerbated when livelihoods required mobility. Interpersonal barriers included anticipated stigma/fear of disclosure, social obligations, and negative peer influences. Providing incentives in public settings provided “social proof” that prizes could be won, and facilitated social support and positive norms by promoting testing with trusted others. Incentives had little influence when men appraised prize values to be low, disbelieved they would win a prize, or were already intrinsically motivated to test. Yet, incentives provided a behavioral ‘cue to action’ for many men who perceived themselves to be susceptible to HIV and perceived HIV disease to be severe, acting as secondary motivator for testing that “sweetened the deal”. Conclusion Incentives can be an important ‘lever’ to promote men’s healthy behaviors in resource-poor settings. HIV testing in convenient, public settings, when paired with incentives, provides multiple pathways to stimulate men’s testing uptake. Trial registration Registered with ClinicalTrials.gov on 08/10/2016, ID: NCT02890459. The first participant was enrolled on 11th April 2016.
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- 2019
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14. The determinants of crop yields in Uganda: what is the role of climatic and non-climatic factors?
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Terence Epule Epule, James D. Ford, Shuaib Lwasa, Benon Nabaasa, and Ambrose Buyinza
- Subjects
Crop yields ,Climatic drivers ,Non-climatic drivers ,Uganda ,Agriculture ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Abstract Background It is widely accepted that crop yields will be affected by climate change. However, the role played by climate in affecting crop yields vis-a-vis non-climatic stresses, is often unclear, limiting decision choices around efforts to promote increased production in light of multiple stresses. Results This study quantifies the role of climatic and non-climatic factors affecting multiple crop yields in Uganda, utilizing a systematic approach which involves the use of a two-stage multiple linear regression to identify and characterize the most important drivers of crop yield, examine the location of the key drivers, identify the socio-economic implications of the drivers and identify policy options to enhance agricultural production. We find that non-climatic drivers of crop yields such as forest area dynamics (p = 0.012), wood fuel (p = 0.032) and usage of tractors (0.041) are more important determinants of crop yields than climatic drivers such as precipitation, temperature and CO2 emissions from forest clearance. Climatic drivers are found to multiply existing risks facing production, the significance of which is determined by variability and inadequate distribution of precipitation over the crop growing seasons. Conclusion The significance and validity of these results is observed in an f-statistic of 50 for the final optimized model when compared to the initial model with an f-statistic of 19.3. Research and agricultural policies have to be streamlined to include not only the climatic elements but also the non-climatic drivers of global, regional and national agricultural systems.
- Published
- 2018
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15. Knowledge and practice of testicular self-examination among secondary students at Ntare School in Mbarara District, South western Uganda
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Catherine Atuhaire, Ambrose Byamukama, Rosaline Yumumkah Cumber, and Samuel Nambile Cumber
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knowledge ,practice ,testicular ,self-examination ,uganda ,Medicine - Abstract
INTRODUCTION: Testicular self-examination (TSE) is a screening technique that involves inspection of the appearance and palpation of the testes to detect any changes from the normal. Globally, the incidence of cancer has increased among which is testicular cancer (TC). Data on this topic among male secondary school adolescents in Uganda is limited therefore this study sought to assess the knowledge and practice of testicular self-examination among secondary students at Ntare School, Mbarara District in south western Uganda. The objective of the study is to assess the knowledge and practice of testicular self-examination among secondary students at Ntare School in Mbarara district, south western Uganda. METHODS: we conducted a descriptive cross-sectional quantitative study among 165 students. Recruitment was made using simple random sampling technique. Respondents were selected among advanced level (A level) male students studying at Ntare School in Mbarara district, south western Uganda. Structured self-administered questionnaires was used for data collection.
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- 2019
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16. Weather Forecasts for Pastoralism in a Changing Climate: Navigating the Data Space in North Eastern Uganda
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Shuaib Lwasa, Ambrose Buyinza, and Benon Nabaasa
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pastoralism ,climate shocks ,weather forecasts ,resilience ,traditional systems ,Science (General) ,Q1-390 - Abstract
Efforts to support the building of resilient pastoralism have been stepped up in Uganda through a number of activities. One of the activity is the provision of seasonal and medium-range climate forecasts to enable decisions concerning livestock herding. Seasonal weather forecasts are critical but there are challenges of timeliness and usability of the forecasts. The challenges are associated with the multiplicity of information sources, methods for data integration and dissemination channels. Institutions including public and Civil Society Organizations usually invest in collecting weather and other data which should be accessible. Often times this data remains hoarded necessitating other organizations to collect similar data. The inter-institutional relations notwithstanding, the lack of data sharing leads to minimal data available for open access. This paper illustrates that this challenge can be addressed by using combined multiple methods to elicit data on weather and other biophysical conditions for pastoralism in Karamoja. In this paper we additionally analyse the opportunities and challenges of using multiple sources of pastoral-relevant data to couple with weather information in support of herding decisions. Building resilient pastoralism that utilizes pasture and water availability will have to utilize available data. It is evident that more robust approaches for data sharing at global, regional and local levels are needed to understand how pastoralists can respond to climate shocks and changes. The paper illustrates the use of a multifaceted-methods approach including open data to develop climate forecast information for risk-reduction oriented information for decision-making. Integration of this data provides insights on how pastoralists have long adapted to a variable and changing climate, the methods and processes of adaptation to losses and damages from the climate shocks.
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- 2017
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17. Viologen-Cucurbit[7]uril Based Polyrotaxanated Covalent Organic Networks: A Metal Free Electrocatalyst for Oxygen Evolution Reaction.
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Ambrose B, Madhu R, Ramamurthy K, Kathiresan M, and Kundu S
- Abstract
Viologen-based covalent organic networks represent a burgeoning class of materials distinguished by their captivating properties. Here, supramolecular chemistry is harnessed to fabricate polyrotaxanated ionic covalent organic polymers (iCOP) through a Schiff-base condensation reaction under solvothermal conditions. The reaction between 1,1'-bis(4-aminophenyl)-[4,4'-bipyridine]-1,1'-diium dichloride (DPV-NH
2 ) and 1,3,5-triformylphloroglucinol (TPG) in various solvents yields an iCOP-1 and iCOP-2. Likewise, employing cucurbit[7]uril (CB[7]) in the reaction yielded polyrotaxanated iCOPs, denoted as iCOP-CB[7]-1 and iCOP-CB[7]-2. All four iCOPs exhibit exceptional stability under the acidic and basic conditions. iCOP-CB[7]-2 displays outstanding electrocatalytic Oxygen Evolution Reaction (OER) performance, demanding an overpotential of 296 and 332 mV at 10 and 20 mA cm-2 , respectively. Moreover, the CB[7] integrated iCOP-2 exhibits a long-term stable nature for 30 h in 1 m KOH environment. Further, intrinsic activity studies like TOF show a 4.2-fold increase in generation of oxygen (O2 ) molecules than the bare iCOP-2. Also, it is found that iCOP-CB[7]-2 exhibits a high specific (19.48 mA cm-2 ) and mass activity (76.74 mA mg-1 ) at 1.59 V versus RHE. Operando-EIS study evident that iCOP-CB[7]-2 commences OER at a relatively low applied potential of 1.5 V versus RHE. These findings pave the way for a novel approach to synthesizing various mechanically interlocked molecules through straightforward solvothermal conditions., (© 2024 Wiley‐VCH GmbH.)- Published
- 2024
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18. Evaluation of the complexation behaviour among functionalized diphenyl viologens and cucurbit[7] and [8]urils.
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Ambrose B, Sathyaraj G, and Kathiresan M
- Abstract
The complexation behaviour of Diphenyl viologens (DPVs) with Cucurbit[n]urils (CB[n]) was evaluated in detail and the results were reported. In this work, we present the synthesis of various DPVs functionalised with electron withdrawing and electron donating groups (EWGs & EDGs) and investigate their complexation behaviour with CB[7] and CB [8]. Carboxylic acid functionalized DPV's (DPV-COOH) complexation with CB[8] gives additional insights, i.e., indicates hydrogen bonding plays an effective role in the complexation. The formation of a 2:2 quaternary complex of DPV-COOH/CB[8] under neutral pH conditions was supported by various analytical techniques. The complexation of DPVs with CB[7] specifies that irrespective of the functional group attached, they all form a 1:2 ternary complex, but the findings elaborate that the pattern followed in the complexation depends on the EW or EDG attached to the DPVs. The competition experiments conducted between functionalized DPVs and CB[7], CB[8] shows that they have more affinity towards CB[8] than CB[7] because of the better macrocyclic confinement effect of CB[8], as confirmed using UV-Vis spectroscopy. The binding affinity among EWG and EDG functionalised DPVs with CB[8] concludes EDG functionalised DPVs show better affinity towards CB[8], because they can form a charge transfer complex inside the CB[8] cavity. Exploring these host-guest interactions in more complex biological or environmental settings and studying their impact on the functionality of DPVs could be an exciting avenue for future research., (© 2024. The Author(s).)
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- 2024
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19. A new twist on PIFE: photoisomerisation-related fluorescence enhancement.
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Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda DS, Steffen FD, Cordes T, Magennis SW, and Lerner E
- Subjects
- Fluorescence Resonance Energy Transfer, DNA chemistry, Proteins chemistry
- Abstract
PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate of cis / trans photoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules., (Creative Commons Attribution license.)
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- 2023
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20. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity.
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Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, and Martienssen RA
- Abstract
We present the genome of the living fossil, Wollemia nobilis , a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia , like other conifers, is susceptible to Phytophthora , and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts., Competing Interests: Competing interests: The authors declare no competing interests.
- Published
- 2023
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21. Enhanced Electrochemical Performance of Hybrid Solid Polymer Electrolytes Encompassing Viologen for All-Solid-State Lithium Polymer Batteries.
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Angulakhsmi N, Ambrose B, Sathya S, Kathiresan M, Lingua G, Ferrari S, Gowd EB, Wang W, Shen C, Elia GA, Gerbaldi C, and Stephan AM
- Abstract
Hybrid solid polymer electrolytes (HSPE) comprising poly(ethylene oxide) (PEO), LiTFSI, barium titanate (BaTiO
3 ), and viologen are prepared by a facile hot press. The physical properties of the HSPE membranes are studied by using small-angle and wide-angle X-ray scattering, thermogravimetric analysis, differential scanning calorimetry, and tensile strength. The prepared hybrid solid polymer electrolytes are also investigated by means of ionic conductivity and transport number measurements. The employed analyses collectively reveal that each additive in the PEO host contributes to a specific property: LiTFSI is essential in providing ionic species, while BaTiO3 and viologen enhance the thermal stability, ionic conductivity, and transport number. The enhanced value in the Li+ -transport number of HSPE are presumably attributed to the electrostatic attraction of TFSI anions and the positive charges of viologen. Synergistically, the added BaTiO3 and viologen improve the electrochemical properties of HSPE for the applications in all-solid-state-lithium polymer batteries., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)- Published
- 2023
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22. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.
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Agam G, Gebhardt C, Popara M, Mächtel R, Folz J, Ambrose B, Chamachi N, Chung SY, Craggs TD, de Boer M, Grohmann D, Ha T, Hartmann A, Hendrix J, Hirschfeld V, Hübner CG, Hugel T, Kammerer D, Kang HS, Kapanidis AN, Krainer G, Kramm K, Lemke EA, Lerner E, Margeat E, Martens K, Michaelis J, Mitra J, Moya Muñoz GG, Quast RB, Robb NC, Sattler M, Schlierf M, Schneider J, Schröder T, Sefer A, Tan PS, Thurn J, Tinnefeld P, van Noort J, Weiss S, Wendler N, Zijlstra N, Barth A, Seidel CAM, Lamb DC, and Cordes T
- Subjects
- Reproducibility of Results, Molecular Conformation, Laboratories, Fluorescence Resonance Energy Transfer methods, Proteins chemistry
- Abstract
Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology., (© 2023. The Author(s).)
- Published
- 2023
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23. Predictors of E-cigarette and Cigarette Use Trajectory Classes from Early Adolescence to Emerging Adulthood Across Four Years (2013-2017) of the PATH Study.
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Stanton CA, Tang Z, Sharma E, Seaman E, Gardner LD, Silveira ML, Hatsukami D, Day HR, Cummings KM, Goniewicz ML, Limpert J, Everard C, Bansal-Travers M, Ambrose B, Kimmel HL, Borek N, Compton WM, Hyland AJ, and Pearson JL
- Subjects
- Humans, Adolescent, Male, Young Adult, Adult, Longitudinal Studies, Tobacco Use, Nicotiana, Electronic Nicotine Delivery Systems, Tobacco Products, Substance-Related Disorders
- Abstract
Introduction: This study examines predictors of trajectories of cigarette and e-cigarette use among a cohort of US adolescents transitioning into young adulthood. Comparing trajectories of each tobacco product is important to determine if different intervention targets are needed to prevent progression to daily use., Methods: Latent trajectory class analyses identified cigarette and e-cigarette use (never, ever excluding past 12-month, past 12-month (excluding past 30-day (P30D)), P30D 1-5 days, P30D 6+ days) trajectory classes, separately, among US youth (12-17; N = 10,086) using the first 4 waves (2013-2017) of data from the nationally representative PATH Study. Weighted descriptive analyses described the class characteristics. Weighted multinomial logistic regression analyses examined demographic, psychosocial, and behavioral predictors of class membership., Results: Younger adolescents 12-15 years had lower tobacco use compared to 16-17 year olds and less stable classes. In the 16-17 year group, there were five unique trajectories of cigarette smoking, including a Persistent High Frequency class. Four e-cigarette use trajectories were identified; but not a persistent use class. Shared predictors of class membership for cigarettes and e-cigarettes included mental health problems, other tobacco use, marijuana use, and poorer academic achievement. Male sex and household tobacco use were unique e-cigarette trajectory class predictors., Conclusions: There was no evidence that initiation with e-cigarettes as the first product tried was associated with cigarette progression (nor cigarettes as first product and e-cigarette progression). Interventions should focus on well-established risk factors such as mental health and other substance use to prevent progression of use for both tobacco products., Implications: Using nationally representative data and definitions of use that take into account frequency and recency of use, longitudinal 4-year trajectories of e-cigarette and cigarette use among US adolescents transitioning into young adulthood were identified. Results among 16-17-year olds revealed a class of persistent high frequency cigarette smoking that was not identified for e-cigarette use. Cigarette use progression was not associated with e-cigarettes as the first product tried. Risk factors for progression of use of both products included mental health and other substance use, which are important prevention targets for both tobacco products., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco.)
- Published
- 2023
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24. Making Precise and Accurate Single-Molecule FRET Measurements using the Open-Source smfBox.
- Author
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Abdelhamid MAS, Rhind-Tutt AV, Ambrose B, and Craggs TD
- Subjects
- DNA, Diffusion, Fluorescence Resonance Energy Transfer, Nanotechnology
- Abstract
The smfBox is a recently developed cost-effective, open-source instrument for single-molecule Förster Resonance Energy Transfer (smFRET), which makes measurements on freely diffusing biomolecules more accessible. This overview includes a step-by-step protocol for using this instrument to make measurements of precise FRET efficiencies in duplex DNA samples, including details of the sample preparation, instrument setup and alignment, data acquisition, and complete analysis routines. The presented approach, which includes how to determine all the correction factors required for accurate FRET-derived distance measurements, builds on a large body of recent collaborative work across the FRET Community, which aims to establish standard protocols and analysis approaches. This protocol, which is easily adaptable to a range of biomolecular systems, adds to the growing efforts in democratising smFRET for the wider scientific community.
- Published
- 2021
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25. Exposure to Nicotine and Toxicants Among Dual Users of Tobacco Cigarettes and E-Cigarettes: Population Assessment of Tobacco and Health (PATH) Study, 2013-2014.
- Author
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Smith DM, Christensen C, van Bemmel D, Borek N, Ambrose B, Erives G, Niaura R, Edwards KC, Stanton CA, Blount BC, Wang L, Feng J, Jarrett JM, Ward CD, Hatsukami D, Hecht SS, Kimmel HL, Travers M, Hyland A, and Goniewicz ML
- Subjects
- Adult, Biomarkers urine, Cigarette Smoking adverse effects, Cigarette Smoking epidemiology, Female, Humans, Male, Metals, Heavy urine, Middle Aged, Nitrosamines urine, Polycyclic Aromatic Hydrocarbons urine, Pyrenes urine, Smokers, Nicotiana, United States, Vaping epidemiology, Cigarette Smoking urine, Electronic Nicotine Delivery Systems, Health Behavior, Nicotine urine, Tobacco Products adverse effects, Vaping urine
- Abstract
Introduction: Concurrent use of tobacco cigarettes and e-cigarettes ("dual use") is common among tobacco users. Little is known about differences in demographics and toxicant exposure among subsets of dual users., Aims and Methods: We analyzed data from adult dual users (current every/some day users of tobacco cigarettes and e-cigarettes, n = 792) included in the PATH Study Wave 1 (2013-2014) and provided urine samples. Samples were analyzed for biomarkers of exposure to nicotine and selected toxicants (tobacco-specific nitrosamine NNK [NNAL], lead, cadmium, naphthalene [2-naphthol], pyrene [1-hydroxypyrene], acrylonitrile [CYMA], acrolein [CEMA], and acrylamide [AAMA]). Subsets of dual users were compared on demographic, behavioral, and biomarker measures to exclusive cigarette smokers (n = 2411) and exclusive e-cigarette users (n = 247)., Results: Most dual users were predominant cigarette smokers (70%), followed by daily dual users (13%), non-daily concurrent dual users (10%), and predominant vapers (7%). Dual users who smoked daily showed significantly higher biomarker concentrations compared with those who did not smoke daily. Patterns of e-cigarette use had little effect on toxicant exposure. Dual users with high toxicant exposure were generally older, female, and smoked more cigarettes per day. Dual users who had low levels of biomarkers of exposure were generally younger, male, and smoked non-daily., Conclusions: In 2013-2014, most dual users smoked cigarettes daily and used e-cigarettes occasionally. Cigarette smoking appears to be the primary driver of toxicant exposure among dual users, with little-to-no effect of e-cigarette use on biomarker levels. Results reinforce the need for dual users to stop smoking tobacco cigarettes to reduce toxicant exposure., Implications: With considerable dual use of tobacco cigarettes and e-cigarettes in the United States, it is important to understand differences in toxicant exposure among subsets of dual users, and how these differences align with user demographics. Findings suggest most dual users smoke daily and use e-cigarettes intermittently. Low exposure to toxicants was most common among younger users, males, and intermittent smokers; high exposure to toxicants was most common among older users, females, and heavier cigarette smokers. Results underscore the heterogeneity occurring within dual users, and the need to quit smoking cigarettes completely in order to reduce toxicant exposure., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Research on Nicotine and Tobacco. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2021
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26. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.
- Author
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Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CA, and Weiss S
- Subjects
- Molecular Biology instrumentation, Single Molecule Imaging instrumentation, Fluorescence Resonance Energy Transfer methods, Molecular Biology methods, Single Molecule Imaging methods
- Abstract
Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current 'state of the art' from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of 'soft recommendations' about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage 'open science' practices., Competing Interests: EL, AB, JH, BA, VB, SB, RB, HS, TC, TC, AD, JD, JF, RG, IG, TH, CH, GH, NH, SH, SH, TH, AI, CJ, AK, HK, TL, NL, TL, EL, EM, JM, XM, SM, DN, TP, EP, YR, NR, BS, HS, CT, RV, DL, CS, SW No competing interests declared
- Published
- 2021
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27. CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field.
- Author
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Shaw RA, Johnston-Wood T, Ambrose B, Craggs TD, and Hill JG
- Abstract
We present CHARMM-compatible force field parameters for a series of fluorescent dyes from the Alexa, Atto, and Cy families, commonly used in Förster resonance energy transfer (FRET) experiments. These dyes are routinely used in experiments to resolve the dynamics of proteins and nucleic acids at the nanoscale. However, little is known about the accuracy of the theoretical approximations used in determining the dynamics from the spectroscopic data. Molecular dynamics simulations can provide valuable insights into these dynamics at an atomistic level, but this requires accurate parameters for the dyes. The complex structure of the dyes and the importance of this in determining their spectroscopic properties mean that parameters generated by analogy to existing parameters do not give meaningful results. Through validation relative to quantum chemical calculation and experiments, the new parameters are shown to significantly outperform those that can be generated automatically, giving better agreement in both the charge distributions and structural properties. These improvements, in particular with regard to orientation of the dipole moments on the dyes, are vital for accurate simulation of FRET processes.
- Published
- 2020
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28. The smfBox is an open-source platform for single-molecule FRET.
- Author
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Ambrose B, Baxter JM, Cully J, Willmott M, Steele EM, Bateman BC, Martin-Fernandez ML, Cadby A, Shewring J, Aaldering M, and Craggs TD
- Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET's broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community.
- Published
- 2020
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29. A review on chemical and electrochemical methodologies for the sensing of biogenic amines.
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Kannan SK, Ambrose B, Sudalaimani S, Pandiaraj M, Giribabu K, and Kathiresan M
- Subjects
- Amino Acids, Biogenic Amines, Meat, Fermented Foods, Meat Products analysis
- Abstract
Biogenic amines (BA) are biomolecules of low molecular weight with organic basic functionalities (amine group) that are formed by the microbial decarboxylation of amino acids of fermented food/beverages. Hence BAs are an important indicator in estimating the freshness and quality of meat, seafood, and industrial food products with high protein content. The reaction of BAs with nitrites available in certain meat products forms nitrosoamine, a carcinogenic compound. Hence BAs are in general considered to be a food hazard and monitoring the level of BAs in food samples becomes crucial as their high concentrations may lead to health problems. This review offers an overview of the available chemical and electrochemical methods that are typically used for the sensing of BAs in food samples. Certain compounds are known to selectively interact with BAs via chemical or non-covalent interactions and these interactions are often accompanied by fluorescence or visible color changes (sometimes visual detection) that could be monitored/assessed using a fluorescence spectrophotometer or UV-vis spectrophotometer (colorimetric methods). The colorimetric methods are limited by sensitivity and selectivity as they are based on straight-forward chemical reactions. In the case of electrochemical sensing of BAs, mediators are often used which undergo oxidation/reduction to produce intermediates that could interact with BAs accompanied by changes in their electrochemical potential. Overall, this review summarizes the available chemical and electrochemical strategies towards the sensing of BAs with a discussion on further prospects.
- Published
- 2020
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30. Estimating the Potential Public Health Impact of Prohibiting Characterizing Flavors in Cigars throughout the US.
- Author
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L Rostron B, G Corey C, Holder-Hayes E, and K Ambrose B
- Subjects
- Cigar Smoking trends, Humans, United States epidemiology, Cigar Smoking mortality, Flavoring Agents analysis, Public Health, Tobacco Products statistics & numerical data
- Abstract
Flavored cigar use is common among cigar smokers, particularly those at younger ages. Several US localities have implemented policies restricting the sale of flavored tobacco products, including cigars. We estimated the population health benefits of removal of flavored cigars throughout the US in terms of reductions in cigar smoking-attributable mortality due to increased cessation and reductions in cigar smoking prevalence due to decreased initiation and continuing use. Monte Carlo simulation was used to estimate possible ranges for these values. We used published estimates of cigar use and attributable mortality in the US, as well as prior study conclusions on the effect of local and national flavor restriction policies. We estimated that removal of flavored cigars would result in approximately 800 (90% prediction interval = 400-1200) fewer cigar smoking-attributable deaths in the US each year and 112,000 fewer cigar smokers (90% prediction interval = 76,000-139,000) in each cohort of 18 year olds. The removal of characterizing flavors in cigars sold in the US is thus projected to have substantial public health benefits over time.
- Published
- 2019
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31. Evaluation of a Proprietary Slow-Release Oxytocin Formulation on Corpus Luteum Function in Mares.
- Author
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Sarnecky BA, Vanderwall DK, Mason HM, Kirschner SM, Ambrose B, and Parker TL
- Subjects
- Animals, Estrus, Female, Ovulation, Progesterone, Corpus Luteum, Horses physiology, Oxytocin
- Abstract
Prolonging function of the corpus luteum (CL) is a method of suppressing estrus that relies on continued secretion of endogenous progesterone to keep mares out of heat naturally. The use of oxytocin treatment to prolong CL function is gaining increasing use, and the most common treatment protocol involves administration of 60 units of oxytocin intramuscularly (IM) once daily on days 7-14 after ovulation (eight daily treatments). Although that protocol induces prolonged CL function in ≥70% of treated mares, the need for daily administration is a drawback to its use. Therefore, the objective of this study was to evaluate the efficacy of a proprietary slow-release oxytocin formulation (SR-OT) for prolonging CL function that requires only two treatments. Mares were examined via transrectal palpation and ultrasonography to determine the day of ovulation (day 0) and then randomly assigned to a nontreated control group and an SR-OT treatment group (n = 8 mares/group). Mares in the treated group received 1.0 mL of SR-OT containing 2,400 IU oxytocin IM once on day 7 and again on day 10 after ovulation. Jugular blood samples were collected on day 0 and then every Monday, Wednesday, and Friday for 50 days for determination of the serum progesterone concentration. Mares were classified as having prolonged CL function if their progesterone concentration remained >1.0 ng/mL continuously for at least 30 days. Corpus luteum function was prolonged in 0/8 (0%) control mares and 6/8 (75%) of the SR-OT-treated mares (P < .01). The demonstrated efficacy of this two-injection, SR-OT protocol represents a 75% reduction in the number of oxytocin treatments compared with daily administration of oxytocin from day 7-14, making it a more practical treatment protocol., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
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32. Comparison of Nicotine and Toxicant Exposure in Users of Electronic Cigarettes and Combustible Cigarettes.
- Author
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Goniewicz ML, Smith DM, Edwards KC, Blount BC, Caldwell KL, Feng J, Wang L, Christensen C, Ambrose B, Borek N, van Bemmel D, Konkel K, Erives G, Stanton CA, Lambert E, Kimmel HL, Hatsukami D, Hecht SS, Niaura RS, Travers M, Lawrence C, and Hyland AJ
- Subjects
- Adult, Biomarkers urine, Cross-Sectional Studies, Female, Humans, Male, Metals urine, Middle Aged, Polycyclic Aromatic Hydrocarbons urine, United States epidemiology, Inhalation Exposure analysis, Nicotine urine, Nitrosamines urine, Smoking epidemiology, Smoking urine, Vaping epidemiology, Vaping urine
- Abstract
Importance: Use of electronic cigarettes (e-cigarettes) is increasing. Measures of exposure to known tobacco-related toxicants among e-cigarette users will inform potential health risks to individual product users., Objectives: To estimate concentrations of tobacco-related toxicants among e-cigarette users and compare these biomarker concentrations with those observed in combustible cigarette users, dual users, and never tobacco users., Design, Setting, and Participants: A population-based, longitudinal cohort study was conducted in the United States in 2013-2014. Cross-sectional analysis was performed between November 4, 2016, and October 5, 2017, of biomarkers of exposure to tobacco-related toxicants collected by the Population Assessment of Tobacco and Health Study. Participants included adults who provided a urine sample and data on tobacco use (N = 5105)., Exposures: The primary exposure was tobacco use, including current exclusive e-cigarette users (n = 247), current exclusive cigarette smokers (n = 2411), and users of both products (dual users) (n = 792) compared with never tobacco users (n = 1655)., Main Outcomes and Measures: Geometric mean concentrations of 50 individual biomarkers from 5 major classes of tobacco product constituents were measured: nicotine, tobacco-specific nitrosamines (TSNAs), metals, polycyclic aromatic hydrocarbons (PAHs), and volatile organic compounds (VOCs)., Results: Of the 5105 participants, most were aged 35 to 54 years (weighted percentage, 38%; 95% CI, 35%-40%), women (60%; 95% CI, 59%-62%), and non-Hispanic white (61%; 95% CI, 58%-64%). Compared with exclusive e-cigarette users, never users had 19% to 81% significantly lower concentrations of biomarkers of exposure to nicotine, TSNAs, some metals (eg, cadmium and lead), and some VOCs (including acrylonitrile). Exclusive e-cigarette users showed 10% to 98% significantly lower concentrations of biomarkers of exposure, including TSNAs, PAHs, most VOCs, and nicotine, compared with exclusive cigarette smokers; concentrations were comparable for metals and 3 VOCs. Exclusive cigarette users showed 10% to 36% lower concentrations of several biomarkers than dual users. Frequency of cigarette use among dual users was positively correlated with nicotine and toxicant exposure., Conclusions and Relevance: Exclusive use of e-cigarettes appears to result in measurable exposure to known tobacco-related toxicants, generally at lower levels than cigarette smoking. Toxicant exposure is greatest among dual users, and frequency of combustible cigarette use is positively correlated with tobacco toxicant concentration. These findings provide evidence that using combusted tobacco cigarettes alone or in combination with e-cigarettes is associated with higher concentrations of potentially harmful tobacco constituents in comparison with using e-cigarettes alone.
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- 2018
- Full Text
- View/download PDF
33. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.
- Author
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Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, and Hugel T
- Abstract
This paper was originally published under standard Springer Nature copyright. As of the date of this correction, the Analysis is available online as an open-access paper with a CC-BY license. No other part of the paper has been changed.
- Published
- 2018
- Full Text
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34. Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.
- Author
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Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Rezaei Adariani S, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, Gebhardt C, Götz M, Gouridis G, Gratton E, Ha T, Hao P, Hanke CA, Hartmann A, Hendrix J, Hildebrandt LL, Hirschfeld V, Hohlbein J, Hua B, Hübner CG, Kallis E, Kapanidis AN, Kim JY, Krainer G, Lamb DC, Lee NK, Lemke EA, Levesque B, Levitus M, McCann JJ, Naredi-Rainer N, Nettels D, Ngo T, Qiu R, Robb NC, Röcker C, Sanabria H, Schlierf M, Schröder T, Schuler B, Seidel H, Streit L, Thurn J, Tinnefeld P, Tyagi S, Vandenberk N, Vera AM, Weninger KR, Wünsch B, Yanez-Orozco IS, Michaelis J, Seidel CAM, Craggs TD, and Hugel T
- Subjects
- Reproducibility of Results, Fluorescence Resonance Energy Transfer methods, Laboratories standards
- Abstract
Single-molecule Förster resonance energy transfer (smFRET) is increasingly being used to determine distances, structures, and dynamics of biomolecules in vitro and in vivo. However, generalized protocols and FRET standards to ensure the reproducibility and accuracy of measurements of FRET efficiencies are currently lacking. Here we report the results of a comparative blind study in which 20 labs determined the FRET efficiencies (E) of several dye-labeled DNA duplexes. Using a unified, straightforward method, we obtained FRET efficiencies with s.d. between ±0.02 and ±0.05. We suggest experimental and computational procedures for converting FRET efficiencies into accurate distances, and discuss potential uncertainties in the experiment and the modeling. Our quantitative assessment of the reproducibility of intensity-based smFRET measurements and a unified correction procedure represents an important step toward the validation of distance networks, with the ultimate aim of achieving reliable structural models of biomolecular systems by smFRET-based hybrid methods.
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- 2018
- Full Text
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35. Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1.
- Author
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Bennet IA, Finger LD, Baxter NJ, Ambrose B, Hounslow AM, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP, and Grasby JA
- Subjects
- Catalytic Domain, Cations, Divalent chemistry, DNA chemistry, DNA metabolism, Flap Endonucleases metabolism, Fluorescence Resonance Energy Transfer, Humans, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Phosphates chemistry, Protein Conformation, Protein Structure, Secondary, Substrate Specificity, Flap Endonucleases chemistry
- Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap through the arch and recognition of a single nucleotide 3'-flap by the α2-α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2-α3 loop are disordered without substrate. Disorder within the arch explains how 5'-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1-DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1-DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
- Published
- 2018
- Full Text
- View/download PDF
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