Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Randomized Controlled Trial of Exercise and Nutrition Supplementation on Physical and Cognitive Function in Older Chinese Adults Aged 50 Years and Older
Woo, Jean ; Chan, Ruth ; Ong, Sherlin ; Bragt, Marjolijn ; Bos, Rolf ; Parikh, Panam ; Groot, Lisette C.P.G.M. de - \ 2019
Journal of the American Medical Directors Association (2019). - ISSN 1525-8610
cognitive function - Exercise - nutrition - older adults - physical performance - self-rated health

Objectives: To assess whether a 24-week multidomain lifestyle intervention including a nutritional milk supplement and an exercise program had any effect on physical and cognitive function, self-rated health, and health-related quality of life in older Chinese adults. Design: Randomized controlled trial. Setting and participants: Community-living people aged 50 years and older. Methods: 180 participants (mean age 61 ± 6 years) were randomized to 24 weeks of exercise plus nutrition supplementation or no intervention. The primary outcome was gait speed, with additional physical and cognitive function measures, self-rated health, and health-related quality of life as secondary outcomes. Information collected also included dietary intake by 3-day dietary records, and blood sampling for renal function, glycated hemoglobin, serum vitamin B12, 25-hydroxyvitamin D, and biochemical indices of bone turnover. Results: There was no significant group difference in the change of gait speed, muscle strength, muscle power, cardiovascular fitness, or cognitive function over time, either by intention-to-treat or per-protocol analysis. A significant time × group effect (P = .039) on self-rated health was detected, but there was no significant time or time × group difference in the change of physical and mental health-related quality of life measures over time. In addition, moderate physical activity level was greatly increased from baseline to 24 weeks in the intervention group compared with the control group. Conclusions and implications: A 24-week exercise and nutrition supplementation program among community-living people in late midlife to early old age improved self-rated health and the overall level of physical activity, without objective improvements in physical and cognitive function.

Addressing nutritional requirements of ageing consumers in Asia-recommendations from an expert workshop
Ong, Sherlin ; Woo, Jean ; Parikh, Panam ; Chan, Ruth ; Sun, Jianqin ; Mun, Chan Yoke ; Wee, Shiou Liang ; Thu, Nghiem Nguyet ; Thang, Pham ; Setiati, Siti ; Huang, Yi Chen ; Wahlqvist, Mark L. ; Bos, Rolf ; Groot, Lisette Cpgm de - \ 2019
Asia Pacific Journal of Clinical Nutrition 28 (2019)2. - ISSN 0964-7058 - p. 204 - 213.

The number of older persons in Asia is expected to triple by 2050. Ageing is associated with non-communicable chronic diseases, malnutrition, and geriatric syndromes, which influences the burden on the cost related to healthcare, health outcomes, and the quality of life. Experts in the field of older adult nutrition from Asia, Australia, and Europe were invited to participate in a two-day workshop to review the available data, current policies and programs for the ageing population in different countries of Asia to identify the gaps in knowledge and to develop recommendations for action. In Asia, most of the data pertaining to health status, nutritional status, and nutrient intake of the older persons were mainly obtained by conducting studies in nursing homes or hospitals and small cohort studies. There were limited country-specific data on this population. Moreover, the available data pertaining to different countries were difficult to compare due to differences in the reporting format and reference values used. Although nutrition initiatives and policies were realized and public education was conducted to support the older persons, most of these efforts targeted the general population rather than the older persons population segment. In healthcare management, a higher amount of education is required pertaining to the knowledge of nutritional requirements and appropriate feeding of the older persons to reduce underfeeding and its consequences. The expert group recommended the use of a systematic approach for reviewing data pertaining to different countries, initiatives, and programs to further evaluate the available data to underpin future research.

Correction to: Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Li ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abeçasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)7. - ISSN 0340-6717 - p. 789 - 791.

Every author has erroneously been assigned to the affiliation “62”. The affiliation 62 belongs to the author Graham Casey.

Airborne host–plant manipulation by whiteflies via an inducible blend of plant volatiles
Zhang, Peng Jun ; Wei, Jia Ning ; Zhao, Chan ; Zhang, Ya Fen ; Li, Chuan You ; Liu, Shu Sheng ; Dicke, Marcel ; Yu, Xiao Ping ; Turlings, Ted C.J. - \ 2019
Proceedings of the National Academy of Sciences of the United States of America 116 (2019)15. - ISSN 0027-8424 - p. 7387 - 7396.
Herbivore-induced plant volatiles - Jasmonic acid - Salicylic acid - Tomato - Whiteflies

The whitefly Bemisia tabaci is one of the world’s most important invasive crop pests, possibly because it manipulates plant defense signaling. Upon infestation by whiteflies, plants mobilize salicylic acid (SA)-dependent defenses, which mainly target pathogens. In contrast, jasmonic acid (JA)-dependent defenses are gradually suppressed in whitefly-infested plants. The down-regulation of JA defenses make plants more susceptible to insects, including whiteflies. Here, we report that this host–plant manipulation extends to neighboring plants via airborne signals. Plants respond to insect attack with the release of a blend of inducible volatiles. Perception of these volatiles by neighboring plants usually primes them to prepare for an imminent attack. Here, however, we show that whitefly-induced tomato plant volatiles prime SA-dependent defenses and suppress JA-dependent defenses, thus rendering neighboring tomato plants more susceptible to whiteflies. Experiments with volatiles from caterpillar-damaged and pathogen-infected plants, as well as with synthetic volatiles, confirm that whiteflies modify the quality of neighboring plants for their offspring via whitefly-inducible plant volatiles.

Disentangling the genetics of lean mass
Karasik, David ; Zillikens, M.C. ; Hsu, Yi Hsiang ; Aghdassi, Ali ; Akesson, Kristina ; Amin, Najaf ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Bochud, Murielle ; Borecki, Ingrid B. ; Broer, Linda ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos-Obando, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Chambers, John C. ; Chen, Zhao ; Cho, Nam H. ; Choi, Hyung Jin ; Chou, Wen Chi ; Cummings, Steven R. ; Groot, Lisette C.P.G.M. De; Jager, Phillip L. De; Demuth, Ilja ; Diatchenko, Luda ; Econs, Michael J. ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Eriksson, Joel ; Eriksson, Johan G. ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Gieger, Christian ; Grallert, Harald ; Gudnason, Vilmundur ; Lenore, Launer J. ; Hayward, Caroline ; Hofman, Albert ; Homuth, Georg ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Johnson, Toby ; Biffar, Reiner ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koller, Daniel L. ; Kooner, Jaspal S. ; Kraus, William E. ; Kritchevsky, Stephen ; Kutalik, Zoltán ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Lerch, Markus M. ; Lewis, Joshua R. ; Lill, Christina ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Livshits, Gregory ; Ljunggren, Östen ; Loos, Ruth J.F. ; Lorentzon, Mattias ; Luan, Jian An ; Luben, Robert N. ; Malkin, Ida ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Nethander, Maria ; Newman, Anne B. ; Oconnell, Jeffery R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Prince, Richard L. ; Psaty, Bruce M. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Rivadeneira, Fernando ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schipf, Sabine ; Shin, Chan Soo ; Smith, Albert V. ; Smith, Shad B. ; Soranzo, Nicole ; Spector, Timothy D. ; StanÄ Áková, Alena ; Stefansson, Kari ; Steinhagen-Thiessen, Elisabeth ; Stolk, Lisette ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorleifsson, Gudmar ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Uitterlinden, André G. ; Duijn, Cornelia M. Van; Schoor, Natasja M. Van; Vandenput, Liesbeth ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; J Wareham, Nicholas ; Waterworth, Dawn ; Weedon, Michael N. ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Yerges-Armstrong, Laura M. ; Yu, Lei ; Zhang, Weihua ; Zhao, Jing Hua ; Zhou, Yanhua ; Nielson, Carrie M. ; Harris, Tamara B. ; Demissie, Serkalem ; Kiel, Douglas P. ; Ohlsson, Claes - \ 2019
American Journal of Clinical Nutrition 109 (2019)2. - ISSN 0002-9165 - p. 276 - 278.
body composition - body fat - meta-Analysis of genome-wide association studies - metabolic profile - skeletal muscle

Background Lean body mass (LM) plays an important role in mobility and metabolic function. We previously identified five loci associated with LM adjusted for fat mass in kilograms. Such an adjustment may reduce the power to identify genetic signals having an association with both lean mass and fat mass. Objectives To determine the impact of different fat mass adjustments on genetic architecture of LM and identify additional LM loci. Methods We performed genome-wide association analyses for whole-body LM (20 cohorts of European ancestry with n = 38,292) measured using dual-energy X-ray absorptiometry) or bioelectrical impedance analysis, adjusted for sex, age, age 2, and height with or without fat mass adjustments (Model 1 no fat adjustment; Model 2 adjustment for fat mass as a percentage of body mass; Model 3 adjustment for fat mass in kilograms). Results Seven single-nucleotide polymorphisms (SNPs) in separate loci, including one novel LM locus (TNRC6B), were successfully replicated in an additional 47,227 individuals from 29 cohorts. Based on the strengths of the associations in Model 1 vs Model 3, we divided the LM loci into those with an effect on both lean mass and fat mass in the same direction and refer to those as "sumo wrestler" loci (FTO and MC4R). In contrast, loci with an impact specifically on LM were termed "body builder" loci (VCAN and ADAMTSL3). Using existing available genome-wide association study databases, LM increasing alleles of SNPs in sumo wrestler loci were associated with an adverse metabolic profile, whereas LM increasing alleles of SNPs in "body builder" loci were associated with metabolic protection. Conclusions In conclusion, we identified one novel LM locus (TNRC6B). Our results suggest that a genetically determined increase in lean mass might exert either harmful or protective effects on metabolic traits, depending on its relation to fat mass.

Genetic variant predictors of gene expression provide new insight into risk of colorectal cancer
Bien, Stephanie A. ; Su, Yu-Ru ; Conti, David V. ; Harrison, Tabitha A. ; Qu, Conghui ; Guo, Xingyi ; Lu, Yingchang ; Albanes, Demetrius ; Auer, Paul L. ; Banbury, Barbara L. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Brenner, Hermann ; Buchanan, Daniel D. ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chen, Sai ; Connolly, Charles M. ; Easton, Douglas F. ; Feskens, Edith J.M. ; Gallinger, Steven ; Giles, Graham G. ; Gunter, Marc J. ; Hampe, Jochen ; Huyghe, Jeroen R. ; Hoffmeister, Michael ; Hudson, Thomas J. ; Jacobs, Eric J. ; Jenkins, Mark A. ; Kampman, Ellen ; Kang, Hyun Min ; Kühn, Tilman ; Küry, Sébastien ; Lejbkowicz, Flavio ; Marchand, Loic Le; Milne, Roger L. ; Li, Christopher I. ; Lindblom, Annika ; Lindor, Noralane M. ; Martín, Vicente ; McNeil, Caroline E. ; Melas, Marilena ; Moreno, Victor ; Newcomb, Polly A. ; Offit, Kenneth ; Pharaoh, Paul D.P. ; Potter, John D. ; Qu, Chenxu ; Riboli, Elio ; Rennert, Gad ; Sala, Núria ; Schafmayer, Clemens ; Scacheri, Peter C. ; Schmit, Stephanie L. ; Severi, Gianluca ; Slattery, Martha L. ; Smith, Joshua D. ; Trichopoulou, Antonia ; Tumino, Rosario ; Ulrich, Cornelia M. ; Duijnhoven, Fränzel J.B. van; Guelpen, Bethany Van; Weinstein, Stephanie J. ; White, Emily ; Wolk, Alicja ; Woods, Michael O. ; Wu, Anna H. ; Abecasis, Goncalo R. ; Casey, Graham ; Nickerson, Deborah A. ; Gruber, Stephen B. ; Hsu, Li ; Zheng, Wei ; Peters, Ulrike - \ 2019
Human Genetics 138 (2019)4. - ISSN 0340-6717 - p. 307 - 326.
Genome-wide association studies have reported 56 independently associated colorectal cancer (CRC) risk variants, most of which are non-coding and believed to exert their effects by modulating gene expression. The computational method PrediXcan uses cis-regulatory variant predictors to impute expression and perform gene-level association tests in GWAS without directly measured transcriptomes. In this study, we used reference datasets from colon (n = 169) and whole blood (n = 922) transcriptomes to test CRC association with genetically determined expression levels in a genome-wide analysis of 12,186 cases and 14,718 controls. Three novel associations were discovered from colon transverse models at FDR ≤ 0.2 and further evaluated in an independent replication including 32,825 cases and 39,933 controls. After adjusting for multiple comparisons, we found statistically significant associations using colon transcriptome models with TRIM4 (discovery P = 2.2 × 10− 4, replication P = 0.01), and PYGL (discovery P = 2.3 × 10− 4, replication P = 6.7 × 10− 4). Interestingly, both genes encode proteins that influence redox homeostasis and are related to cellular metabolic reprogramming in tumors, implicating a novel CRC pathway linked to cell growth and proliferation. Defining CRC risk regions as one megabase up- and downstream of one of the 56 independent risk variants, we defined 44 non-overlapping CRC-risk regions. Among these risk regions, we identified genes associated with CRC (P < 0.05) in 34/44 CRC-risk regions. Importantly, CRC association was found for two genes in the previously reported 2q25 locus, CXCR1 and CXCR2, which are potential cancer therapeutic targets. These findings provide strong candidate genes to prioritize for subsequent laboratory follow-up of GWAS loci. This study is the first to implement PrediXcan in a large colorectal cancer study and findings highlight the utility of integrating transcriptome data in GWAS for discovery of, and biological insight into, risk loci.
A research roadmap for quantifying non-state and subnational climate mitigation action
Hsu, Angel ; Höhne, Niklas ; Kuramochi, Takeshi ; Roelfsema, Mark ; Weinfurter, Amy ; Xie, Yihao ; Lütkehermöller, Katharina ; Chan, Sander ; Corfee-Morlot, Jan ; Drost, Philip ; Faria, Pedro ; Gardiner, Ann ; Gordon, David J. ; Hale, Thomas ; Hultman, Nathan E. ; Moorhead, John ; Reuvers, Shirin ; Setzer, Joana ; Singh, Neelam ; Weber, Christopher ; Widerberg, Oscar - \ 2019
Nature Climate Change 9 (2019)1. - ISSN 1758-678X - p. 11 - 17.

Non-state and subnational climate actors have become central to global climate change governance. Quantitatively assessing climate mitigation undertaken by these entities is critical to understand the credibility of this trend. In this Perspective, we make recommendations regarding five main areas of research and methodological development related to evaluating non-state and subnational climate actions: defining clear boundaries and terminology; use of common methodologies to aggregate and assess non-state and subnational contributions; systematically dealing with issues of overlap; estimating the likelihood of implementation; and addressing data gaps.

Climate change opens new frontiers for marine species in the Arctic: Current trends and future invasion risks
Chan, Farrah T. ; Stanislawczyk, Keara ; Sneekes, A.C. ; Dvoretsky, Alexander ; Gollasch, Stephan ; Minchin, Dan ; David, Matej ; Jelmert, Anders ; Albretsen, Jon ; Bailey, Sarah A. - \ 2019
Global Change Biology 25 (2019)1. - ISSN 1354-1013 - p. 25 - 38.
alien species - aquaculture - climate warming - fisheries - invasion pathways - invasive species - knowledge gap - nonindigenous species - shipping - vessels
Climate change and increased anthropogenic activities are expected to elevate the potential of introducing nonindigenous species (NIS) into the Arctic. Yet, the knowledge base needed to identify gaps and priorities for NIS research and management is limited. Here, we reviewed primary introduction events to each ecoregion of the marine Arctic realm to identify temporal and spatial patterns, likely source regions of NIS, and the putative introduction pathways. We included 54 introduction events representing 34 unique NIS. The rate of NIS discovery ranged from zero to four species per year between 1960 and 2015. The Iceland Shelf had the greatest number of introduction events (n = 14), followed by the Barents Sea (n = 11), and the Norwegian Sea (n = 11). Sixteen of the 54 introduction records had no known origins. The majority of those with known source regions were attributed to the Northeast Atlantic and the Northwest
Pacific, 19 and 14 records, respectively. Some introduction events were attributed
to multiple possible pathways. For these introductions, vessels transferred the greatest number of aquatic NIS (39%) to the Arctic, followed by natural spread (30%) and aquaculture activities (25%). Similar trends were found for introductions attributed to a single pathway. The phyla Arthropoda and Ochrophyta had the highest number of recorded introduction events, with 19 and 12 records, respectively. Recommendations including vector management, horizon scanning, early detection, rapid response, and a pan‐Arctic biodiversity inventory are considered in this paper. Our study provides a comprehensive record of primary introductions of NIS for marine environments in the
circumpolar Arctic and identifies knowledge gaps and opportunities for NIS research and management. Ecosystems worldwide will face dramatic changes in the coming decades due to global change. Our findings contribute to the knowledge base needed to address two aspects of global change—invasive species and climate change.
Discovery of common and rare genetic risk variants for colorectal cancer
Huyghe, Jeroen R. ; Bien, Stephanie A. ; Harrison, Tabitha A. ; Kang, Hyun Min ; Chen, Sai ; Schmit, Stephanie L. ; Conti, David V. ; Qu, Conghui ; Jeon, Jihyoun ; Edlund, Christopher K. ; Greenside, Peyton ; Wainberg, Michael ; Schumacher, Fredrick R. ; Smith, Joshua D. ; Levine, David M. ; Nelson, Sarah C. ; Sinnott-armstrong, Nasa A. ; Albanes, Demetrius ; Alonso, M.H. ; Anderson, Kristin ; Arnau-Collell, Coral ; Arndt, Volker ; Bamia, Christina ; Banbury, Barbara L. ; Baron, John A. ; Berndt, Sonja I. ; Bézieau, Stéphane ; Bishop, D.T. ; Boehm, Juergen ; Boeing, Heiner ; Brenner, Hermann ; Brezina, Stefanie ; Buch, Stephan ; Buchanan, Daniel D. ; Burnett-hartman, Andrea ; Butterbach, Katja ; Caan, Bette J. ; Campbell, Peter T. ; Carlson, Christopher S. ; Castellví-Bel, Sergi ; Chan, Andrew T. ; Chang-Claude, Jenny ; Chanock, Stephen J. ; Chirlaque, Maria-Dolores ; Cho, Sang Hee ; Connolly, Charles M. ; Cross, Amanda J. ; Feskens, Edith J.M. ; Li, Li ; Huang, Wen-Yi - \ 2018
Nature Genetics 51 (2018). - ISSN 1061-4036 - p. 76 - 87.
To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10−8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.
Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce
Jurak, E. ; Suzuki, H. ; Erven, G. van; Gandier, J.A. ; Wong, P. ; Chan, K. ; Ho, C.Y. ; Gong, Y. ; Tillier, E. ; Rosso, M.N. ; Kabel, M.A. ; Miyauchi, S. ; Master, E.R. - \ 2018
BMC Genomics 19 (2018)1. - ISSN 1471-2164
Carbohydrate active enzymes - Hydrophobins - Lignocellulose conversions - Loosenins - Phanerochaete carnosa - Transcriptomics

BACKGROUND: The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative transcriptomic analysis of P. carnosa following growth on wood powder from one softwood (spruce; Picea glauca) and one hardwood (aspen; Populus tremuloides). P. carnosa was grown on each substrate for over one month, and mycelia were harvested at five time points for total RNA sequencing. Residual wood powder was also analyzed for total sugar and lignin composition. RESULTS: Following a slightly longer lag phase of growth on spruce, radial expansion of the P. carnosa colony was similar on spruce and aspen. Consistent with this observation, the pattern of gene expression by P. carnosa on each substrate converged following the initial adaptation. On both substrates, highest transcript abundances were attributed to genes predicted to encode manganese peroxidases (MnP), along with auxiliary activities from carbohydrate-active enzyme (CAZy) families AA3 and AA5. In addition, a lytic polysaccharide monooxygenase from family AA9 was steadily expressed throughout growth on both substrates. P450 sequences from clans CPY52 and CYP64 accounted for 50% or more of the most highly expressed P450s, which were also the P450 clans that were expanded in the P. carnosa genome relative to other white-rot fungi. CONCLUSIONS: The inclusion of five growth points and two wood substrates was important to revealing differences in the expression profiles of specific sequences within large glycoside hydrolase families (e.g., GH5 and GH16), and permitted co-expression analyses that identified new targets for study, including non-catalytic proteins and proteins with unknown function.

Zwitterionic polymer modified porous carbon for high performance and antifouling capacitive desalination
Zhang, Penghui ; Fritz, P.A. ; Schroen, C.G.P.H. ; Duan, Hongwei ; Boom, R.M. ; Chan-Park, M.B. - \ 2018
ACS Applied Materials and Interfaces 10 (2018)39. - ISSN 1944-8244 - p. 33564 - 33573.
Capacitive deionization (CDI) is an emerging technology for effective brackish water desalination to address fresh water scarcity. It is of great interest due to its high energy efficiency, environmental friendliness, and low-cost operation, compared with traditional desalination technologies. However, electrode fouling, caused by dissolved organic matter and resulting in reduction of electrode electrosorption capacity and device lifespan, is an impediment to practical application of CDI. Herein, we report a novel salty water desalination electrode with excellent antifouling properties. The antifouling electrode is prepared by coating zwitterionic polymer brushes, i.e., poly (sulfobetaine methacrylate) (SBMA), on porous carbon (PC) via surface-initiated atom transfer radical polymerization. The successful coating of zwitterionic polymer on PC surface is confirmed by TEM, SEM, XPS, TGA, and other characterizations. Coating with polySBMA did not affect the electrosorption capacity of PC electrodes and imparted antifouling properties (versus fouling by model foulant bovine serum albumin (BSA)) during long-term salt removal tests (100 desalination/regeneration cycles). This is an important step toward practical application of capacitive deionization technology for brackish water desalination.
Biocatalytic C=C Bond Reduction through Carbon Nanodot-Sensitized Regeneration of NADH Analogues
Kim, Jinhyun ; Lee, Sahng Ha ; Tieves, Florian ; Choi, Da Som ; Hollmann, Frank ; Paul, Caroline E. ; Park, Chan Beum - \ 2018
Angewandte Chemie-International Edition 57 (2018)42. - ISSN 1433-7851 - p. 13825 - 13828.
alkene hydrogenation - asymmetric catalysis - carbon nanodot - NADH analogues - photobiocatalysis

Light-driven activation of redox enzymes is an emerging route for sustainable chemical synthesis. Among redox enzymes, the family of Old Yellow Enzyme (OYE) dependent on the nicotinamide adenine dinucleotide cofactor (NADH) catalyzes the stereoselective reduction of α,β-unsaturated hydrocarbons. Here, we report OYE-catalyzed asymmetric hydrogenation through light-driven regeneration of NADH and its analogues (mNADHs) by N-doped carbon nanodots (N-CDs), a zero-dimensional photocatalyst. Our spectroscopic and photoelectrochemical analyses verified the transfer of photo-induced electrons from N-CDs to an organometallic electron mediator (M) for highly regioselective regeneration of cofactors. Light triggered the reduction of NAD+ and mNAD+s with the cooperation of N-CDs and M, and the reduction behaviors of cofactors were dependent on their own reduction peak potentials. The regenerated cofactors subsequently delivered hydrides to OYE for stereoselective conversions of a broad range of substrates with excellent biocatalytic efficiencies.

Prediagnostic serum Vitamin D levels and the risk of Crohn's disease and ulcerative colitis in european populations : A nested case-control study
Opstelten, Jorrit L. ; Chan, Simon S.M. ; Hart, Andrew R. ; Schaik, Fiona D.M. Van; Siersema, Peter D. ; Lentjes, Eef G.W.M. ; Khaw, Kay Tee ; Luben, Robert ; Key, Timothy J. ; Boeing, Heiner ; Bergmann, Manuela M. ; Overvad, Kim ; Palli, Domenico ; Masala, Giovanna ; Racine, Antoine ; Carbonnel, Franck ; Boutron-Ruault, Marie Christine ; Tjønneland, Anne ; Olsen, Anja ; Andersen, Vibeke ; Kaaks, Rudolf ; Kuhn, Tilman ; Tumino, Rosario ; Trichopoulou, Antonia ; Peeters, Petra H.M. ; Verschuren, W.M.M. ; Witteman, Ben J.M. ; Oldenburg, Bas - \ 2018
Inflammatory Bowel Diseases 24 (2018)3. - ISSN 1078-0998 - p. 633 - 640.
Crohn's disease - etiology - inflammatory bowel disease - ulcerative colitis - Vitamin D

Background A low vitamin D status has been put forward as a potential risk factor for the development of inflammatory bowel disease (IBD). This study investigated the association between prediagnostic circulating vitamin D concentrations and dietary intakes of vitamin D, and the risk of Crohn's disease (CD) and ulcerative colitis (UC). Methods Among 359,728 participants of the European Prospective Investigation into Cancer and Nutrition cohort, individuals who developed CD or UC after enrollment were identified. Each case was matched with2 controls by center, gender, age, date of recruitment, and follow-up time. At cohort entry, blood samples were collected and dietary vitamin D intakes were obtained from validated food frequency questionnaires. Serum 25-hydroxyvitamin D levels were measured using liquid chromatography-tandem mass spectrometry. Conditional logistic regression was performed to determine the odds of CD and UC. Results Seventy-two participants developed CD and 169 participants developed UC after a median follow-up of 4.7 and 4.1 years, respectively. Compared with the lowest quartile, no associations with the 3 higher quartiles of vitamin D concentrations were observed for CD (p trend = 0.34) or UC (p trend = 0.66). Similarly, no associations were detected when serum vitamin D levels were analyzed as a continuous variable. Dietary vitamin D intakes were not associated with CD (p trend = 0.39) or UC (p trend = 0.83). Conclusions Vitamin D status was not associated with the development of CD or UC. This does not suggest a major role for vitamin D deficiency in the etiology of IBD, although larger studies are needed to confirm these findings.

The Ozone Monitoring Instrument : Overview of 14 years in space
Levelt, Pieternel F. ; Joiner, Joanna ; Tamminen, Johanna ; Veefkind, J.P. ; Bhartia, Pawan K. ; Zweers, Deborah C.S. ; Duncan, Bryan N. ; Streets, David G. ; Eskes, Henk ; Der, Ronald A. Van; McLinden, Chris ; Fioletov, Vitali ; Carn, Simon ; Laat, Jos De; Deland, Matthew ; Marchenko, Sergey ; McPeters, Richard ; Ziemke, Jerald ; Fu, Dejian ; Liu, Xiong ; Pickering, Kenneth ; Apituley, Arnoud ; Abad, Gonzalo González ; Arola, Antti ; Boersma, Folkert ; Miller, Christopher Chan ; Chance, Kelly ; Graaf, Martin De; Hakkarainen, Janne ; Hassinen, Seppo ; Ialongo, Iolanda ; Kleipool, Quintus ; Krotkov, Nickolay ; Li, Can ; Lamsal, Lok ; Newman, Paul ; Nowlan, Caroline ; Suleiman, Raid ; Tilstra, Lieuwe Gijsbert ; Torres, Omar ; Wang, Huiqun ; Wargan, Krzysztof - \ 2018
Atmospheric Chemistry and Physics 18 (2018)8. - ISSN 1680-7316 - p. 5699 - 5745.
This overview paper highlights the successes of the Ozone Monitoring Instrument (OMI) on board the Aura satellite spanning a period of nearly 14 years. Data from OMI has been used in a wide range of applications and research resulting in many new findings. Due to its unprecedented spatial resolution, in combination with daily global coverage, OMI plays a unique role in measuring trace gases important for the ozone layer, air quality, and climate change. With the operational very fast delivery (VFD; direct readout) and near real-time (NRT) availability of the data, OMI also plays an important role in the development of operational services in the atmospheric chemistry domain.
A Pressure Test to Make 10 Molecules in 90 Days : External Evaluation of Methods to Engineer Biology
Casini, Arturo ; Chang, Fang Yuan ; Eluere, Raissa ; King, Andrew M. ; Young, Eric M. ; Dudley, Quentin M. ; Karim, Ashty ; Pratt, Katelin ; Bristol, Cassandra ; Forget, Anthony ; Ghodasara, Amar ; Warden-Rothman, Robert ; Gan, Rui ; Cristofaro, Alexander ; Borujeni, Amin Espah ; Ryu, Min Hyung ; Li, Jian ; Kwon, Yong Chan ; Wang, He ; Tatsis, Evangelos ; Rodriguez-Lopez, Carlos ; O'Connor, Sarah ; Medema, Marnix H. ; Fischbach, Michael A. ; Jewett, Michael C. ; Voigt, Christopher ; Gordon, D.B. - \ 2018
Journal of the American Chemical Society 140 (2018)12. - ISSN 0002-7863 - p. 4302 - 4316.
Centralized facilities for genetic engineering, or "biofoundries", offer the potential to design organisms to address emerging needs in medicine, agriculture, industry, and defense. The field has seen rapid advances in technology, but it is difficult to gauge current capabilities or identify gaps across projects. To this end, our foundry was assessed via a timed "pressure test", in which 3 months were given to build organisms to produce 10 molecules unknown to us in advance. By applying a diversity of new approaches, we produced the desired molecule or a closely related one for six out of 10 targets during the performance period and made advances toward production of the others as well. Specifically, we increased the titers of 1-hexadecanol, pyrrolnitrin, and pacidamycin D, found novel routes to the enediyne warhead underlying powerful antimicrobials, established a cell-free system for monoterpene production, produced an intermediate toward vincristine biosynthesis, and encoded 7802 individually retrievable pathways to 540 bisindoles in a DNA pool. Pathways to tetrahydrofuran and barbamide were designed and constructed, but toxicity or analytical tools inhibited further progress. In sum, we constructed 1.2 Mb DNA, built 215 strains spanning five species (Saccharomyces cerevisiae, Escherichia coli, Streptomyces albidoflavus, Streptomyces coelicolor, and Streptomyces albovinaceus), established two cell-free systems, and performed 690 assays developed in-house for the molecules.
Affordances of agricultural systems analysis tools : A review and framework to enhance tool design and implementation
Ditzler, Lenora ; Klerkx, Laurens ; Chan-Dentoni, Jacqueline ; Posthumus, Helena ; Krupnik, Timothy J. ; Ridaura, Santiago López ; Andersson, Jens A. ; Baudron, Frédéric ; Groot, Jeroen C.J. - \ 2018
Agricultural Systems 164 (2018). - ISSN 0308-521X - p. 20 - 30.
Bio-economic farm models - Farming systems analysis - Fuzzy cognitive mapping - Literature review - Role play and serious games - Stakeholder participation
The increasingly complex challenges facing agricultural systems require problem-solving processes and systems analysis (SA) tools that engage multiple actors across disciplines. In this article, we employ the theory of affordances to unravel what tools may furnish users, and how those affordances contribute to a tool's usefulness in co-design and co-innovation processes. Affordance is defined as a function provided by an object through an interaction with a user. We first present a conceptual framework to assess the affordances of SA tools. This framework is then applied in a literature review of three SA tools used in agricultural systems research (fuzzy cognitive mapping, bio-economic whole-farm models, and role play and serious games). Through this exercise, we extend the SA tool design and implementation dialogue by illuminating (i) links between lower-level affordances, tool design, and heuristic functioning, and (ii) the central role of use setting and facilitation in mobilizing higher-level, productive affordances. Based on our findings, we make five propositions for how SA tool design and implementation in participatory problem-solving settings can be improved.
Potential of conservation agriculture (CA) for climate change adaptation and food security under rainfed uplands of India : A transdisciplinary approach
Pradhan, Aliza ; Chan, Catherine ; Roul, Pravat Kumar ; Halbrendt, Jacqueline ; Sipes, Brent - \ 2018
Agricultural Systems 163 (2018). - ISSN 0308-521X - p. 27 - 35.
Analytic hierarchy process (AHP) - Conservation agriculture (CA) - Indian tribal farmers - Maize based cropping system - Rainfed agriculture - Soil quality - Transdisciplinary approach
Rainfed agro-ecosystems, the purported grey patches untouched by the Green Revolution or most technological advances, occupy a prominent position in Indian agriculture. Cropping intensities and crop yields are low and unstable in these areas due to unpredictable patterns of rainfall, a host of biotic and abiotic stresses and adherence to traditional farm practices. This precarious food security situation is especially dangerous in the central Indian tribal belt (also known as the poverty belt) which is a typical rainfed area dominated by tribal communities. More than 90% of the tribal people are totally dependent on agriculture and produce much of what they eat. Small land holdings and their low productivity, along with uncertainties in rainfall patterns, increases economic and social risks for these farmers. With degraded soils and unreliable weather patterns, return on investment is uncertain and likely to be much lower overall than under irrigated conditions with better soils. Under such conditions, one approach to achieve improved crop production is to minimize soil and other natural resource degradation by adopting a set of crop-nutrient-water-land system management practices, such as conservation agriculture (CA). To assess the effect of introduced technology under local ecological and socio-economic conditions, the study focused on two ecosystem services: a) provisional, and b) regulatory through five treatments consisting of farmers' traditional practice (FP) which was conventional tillage with broadcast of local variety maize (Zea mays L.); and four CA treatments viz., conventional tillage with sole cropped maize using line sowing of the improved maize cultivar 'Nilesh' (CT-M); conventional tillage with maize intercropped with the improved cowpea (Vigna unguiculata L. cultivar 'Hariyalli Bush') (CT-M + C); reduced tillage with sole cropped maize (MT-M); and reduced tillage with maize + cowpea (MT-M + C). After harvest of maize and cowpea, mustard was planted as a post rainy season crop and all the mustard plant residues were returned to their respective plots as residue cover except FP. Under provisional ecosystem services, performance of CA on crop yield, and profitability was assessed through maize equivalent yield and partial budget analysis, respectively. Results showed that reduced tillage combined with maize-cowpea intercropping (MT-M + C) followed by mustard residue retention had higher system productivity and net benefits, an increase of 200% and 230%, respectively over FP. Under regulatory ecosystem services, the soil quality was assessed through calculation of soil quality index (SQI) which was highest under MT-M + C followed by mustard residue retention and lowest under farmers' practices. In terms of CA treatment preference, 35% of the farmers indicated a strong preference for MT-M + C compared to 14% for FP. Combined, these results clearly demonstrate the potential of CA to simultaneously increase yield, diversify crop production and improve soil quality which should support a move towards sustainable intensification of crop production to improve future household income and food security. Additionally, using a transdisciplinary approach fully engaged all stakeholders in co-designing the CA treatments appropriate for the farmers and local environmental conditions leading to significant impacts on economic livelihoods, environmental sustainability and food security.
Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass
Zillikens, M.C. ; Demissie, Serkalem ; Hsu, Yi Hsiang ; Yerges-Armstrong, Laura M. ; Chou, Wen Chi ; Stolk, Lisette ; Livshits, Gregory ; Broer, Linda ; Johnson, Toby ; Koller, Daniel L. ; Kutalik, Zoltán ; Luan, J. ; Malkin, Ida ; Ried, Janina S. ; Smith, Albert V. ; Thorleifsson, Gudmar ; Vandenput, Liesbeth ; Hua Zhao, Jing ; Zhang, Weihua ; Aghdassi, Ali ; Åkesson, Kristina ; Amin, Najaf ; Baier, Leslie J. ; Barroso, Inês ; Bennett, David A. ; Bertram, Lars ; Biffar, Rainer ; Bochud, Murielle ; Boehnke, Michael ; Borecki, Ingrid B. ; Buchman, Aron S. ; Byberg, Liisa ; Campbell, Harry ; Campos Obanda, Natalia ; Cauley, Jane A. ; Cawthon, Peggy M. ; Cederberg, Henna ; Chen, Zhao ; Cho, Nam H. ; Jin Choi, Hyung ; Claussnitzer, Melina ; Collins, Francis ; Cummings, Steven R. ; Jager, Philip L. De; Demuth, Ilja ; Dhonukshe-Rutten, Rosalie A.M. ; Diatchenko, Luda ; Eiriksdottir, Gudny ; Enneman, Anke W. ; Erdos, Mike ; Eriksson, Johan G. ; Eriksson, Joel ; Estrada, Karol ; Evans, Daniel S. ; Feitosa, Mary F. ; Fu, Mao ; Garcia, Melissa ; Gieger, Christian ; Girke, Thomas ; Glazer, Nicole L. ; Grallert, Harald ; Grewal, Jagvir ; Han, Bok Ghee ; Hanson, Robert L. ; Hayward, Caroline ; Hofman, Albert ; Hoffman, Eric P. ; Homuth, Georg ; Hsueh, Wen Chi ; Hubal, Monica J. ; Hubbard, Alan ; Huffman, Kim M. ; Husted, Lise B. ; Illig, Thomas ; Ingelsson, Erik ; Ittermann, Till ; Jansson, John Olov ; Jordan, Joanne M. ; Jula, Antti ; Karlsson, Magnus ; Khaw, Kay Tee ; Kilpeläinen, Tuomas O. ; Klopp, Norman ; Kloth, Jacqueline S.L. ; Koistinen, Heikki A. ; Kraus, William E. ; Kritchevsky, Stephen ; Kuulasmaa, Teemu ; Kuusisto, Johanna ; Laakso, Markku ; Lahti, Jari ; Lang, Thomas ; Langdahl, Bente L. ; Launer, Lenore J. ; Lee, Jong Young ; Lerch, Markus M. ; Lewis, Joshua R. ; Lind, Lars ; Lindgren, Cecilia ; Liu, Yongmei ; Liu, Tian ; Liu, Youfang ; Ljunggren, Östen ; Lorentzon, Mattias ; Luben, Robert N. ; Maixner, William ; McGuigan, Fiona E. ; Medina-Gomez, Carolina ; Meitinger, Thomas ; Melhus, Håkan ; Mellström, Dan ; Melov, Simon ; Michaëlsson, Karl ; Mitchell, Braxton D. ; Morris, Andrew P. ; Mosekilde, Leif ; Newman, Anne ; Nielson, Carrie M. ; O'Connell, Jeffrey R. ; Oostra, Ben A. ; Orwoll, Eric S. ; Palotie, Aarno ; Parker, Stephen C.J. ; Peacock, Munro ; Perola, Markus ; Peters, Annette ; Polasek, Ozren ; Prince, Richard L. ; Räikkönen, Katri ; Ralston, Stuart H. ; Ripatti, Samuli ; Robbins, John A. ; Rotter, Jerome I. ; Rudan, Igor ; Salomaa, Veikko ; Satterfield, Suzanne ; Schadt, Eric E. ; Schipf, Sabine ; Scott, Laura ; Sehmi, Joban ; Shen, Jian ; Soo Shin, Chan ; Sigurdsson, Gunnar ; Smith, Shad ; Soranzo, Nicole ; Stančáková, Alena ; Steinhagen-Thiessen, Elisabeth ; Streeten, Elizabeth A. ; Styrkarsdottir, Unnur ; Swart, Karin M.A. ; Tan, Sian Tsung ; Tarnopolsky, Mark A. ; Thompson, Patricia ; Thomson, Cynthia A. ; Thorsteinsdottir, Unnur ; Tikkanen, Emmi ; Tranah, Gregory J. ; Tuomilehto, Jaakko ; Schoor, Natasja M. van; Verma, Arjun ; Vollenweider, Peter ; Völzke, Henry ; Wactawski-Wende, Jean ; Walker, Mark ; Weedon, Michael N. ; Welch, Ryan ; Wichmann, H.E. ; Widen, Elisabeth ; Williams, Frances M.K. ; Wilson, James F. ; Wright, Nicole C. ; Xie, Weijia ; Yu, Lei ; Zhou, Yanhua ; Chambers, John C. ; Döring, Angela ; Duijn, Cornelia M. van; Econs, Michael J. ; Gudnason, Vilmundur ; Kooner, Jaspal S. ; Psaty, Bruce M. ; Spector, Timothy D. ; Stefansson, Kari ; Rivadeneira, Fernando ; Uitterlinden, André G. ; Wareham, Nicholas J. ; Ossowski, Vicky ; Waterworth, Dawn ; Loos, Ruth J.F. ; Karasik, David ; Harris, Tamara B. ; Ohlsson, Claes ; Kiel, Douglas P. - \ 2017
Nature Communications 8 (2017)1. - ISSN 2041-1723 - 1 p.

A correction to this article has been published and is linked from the HTML version of this article.

Efficiency of conservation agriculture production systems for smallholders in rain-fed uplands of India: A transformative approach to food security
Chan, Catherine ; Sipes, Brent ; Ayman, Abouzeid ; Zhang, Xu ; LaPorte, Patricia ; Fernandes, Fellipe ; Pradhan, Aliza ; Chan-Dentoni, Jacqueline ; Roul, Pravat - \ 2017
Land 6 (2017)3. - ISSN 2073-445X
Conservation agriculture cropping system - Intercrop - Maize-based system - Technical efficiency - Transdisciplinary approach - Tribal villages

With challenges from global climate change, it is imperative to enhance food production using climate-smart technologies and maximize farm efficiency. Fifty-six households in Rudhiapada and Badamahulidiha, Odisha, India were selected to evaluate farmers' efficiency using conservation agriculture (CA) cropping system practices. Data envelopment analysis (DEA) and regression analysis were used to estimate farmer efficiency and the determinants of yield. Conventional tillage with the local maize cultivar was compared to reduced tillage with improved maize cultivar and maize intercropped with cowpea. Badamahulidiha outperformed Rudhiapada in yields for all cropping systems. This could be attributed to lower input use and exposure to NGO training. The current efficiency level of farmers' productivity was between 0.4 and 0.7. Inputs such as labor, seed, and fertilizers were found to be significant in increasing yield except for female labor and phosphate. This finding suggests conservation agriculture cropping system is female friendly. The conservation agriculture cropping systems improved maize yields by 60% to 70% when compared to conventional farming system. Combining conservation agriculture practices with improving efficiency of farmers in optimal use of the inputs can contribute substantially to productivity, thus enhancing food security and nutrition in the face of climate change in India and other tropical areas.

Healthcare entitlements for citizens and transborder mobile peoples in Southeast Asia
Ormond, Meghann ; Khoon, Chan Chee ; Verghis, Sharuna - \ 2017
In: Routledge Handbook of Southeast Asian Development / McGregor, Andrew, Law, Lisa, Miller, Fiona, Abington : Routledge - ISBN 9781138848535 - p. 186 - 197.
The health of a population is shaped by a complex interplay of economic, political, social, cultural and biological factors that transcend national borders. In this chapter, we consider how these factors work together within the Association of Southeast Asian Nations (ASEAN), a supra-national regional political space encompassing a population of over 600 million across ten countries. Specifically, we query how economic liberalization and corollary increases in the movement of people, goods and services are challenging and transforming entrenched ideas about who is entitled to and responsible for health and social care within and across ASEAN member states’ national borders.
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