Examining the effects of green revolution led agricultural expansion on net ecosystem service values in India using multiple valuation approaches
Sannigrahi, Srikanta ; Pilla, Francesco ; Zhang, Qi ; Chakraborti, Suman ; Wang, Ying ; Basu, Bidroha ; Basu, Arunima Sarkar ; Joshi, P.K. ; Keesstra, Saskia ; Roy, P.S. ; Sutton, Paul C. ; Bhatt, Sandeep ; Rahmat, Shahid ; Jha, Shouvik ; Singh, Laishram Kanta - \ 2021
Journal of Environmental Management 277 (2021). - ISSN 0301-4797
Ecology - Ecosystem service value - Green revolution - India - Land use change - Value transfer
Ecosystem Services (ESs) are bundles of natural processes and functions that are essential for human well-being, subsistence, and livelihoods. The ‘Green Revolution’ (GR) has substantial impact on the agricultural landscape and ESs in India. However, the effects of GR on ESs have not been adequately documented and analyzed. This leads to the main hypothesis of this work – ‘the incremental trend of ESs in India is mainly prompted by GR led agricultural innovations that took place during 1960 - 1970’. The analysis was carried out through five successive steps. First, the spatiotemporal Ecosystem Service Values (ESVs) in Billion US$ for 1985, 1995, and 2005 were estimated using several value transfer approaches. Second, the sensitivity and elasticity of different ESs to land conversion were carried out using coefficient of sensitivity and coefficient of elasticity. Third, the Geographically Weighted Regression model was performed using five explanatory factors, i.e., total crop area, crop production, crop yield, net irrigated area, and cropping intensity, to explore the cumulative and individual effects of these driving factors on ESVs. Fourth, Multi-Layer Perceptron based Artificial Neural Network was employed to estimate the normalized importance of these explanatory factors. Fifth, simple and multiple linear regression modeling was done to assess the linear associations between the driving factors and the ESs. During the observation periods, cropland, forestland and water bodies contributed to 80%–90% of ESVs, followed by grassland, mangrove, wetland and urban built-up. In all three evaluation years, the highest estimated ESVs among the nine ES categories was provided by water regulation, followed by soil formation and soil-water retention, biodiversity maintenance, waste treatment, climate regulation, and greenhouse gas regulation. Among the five explanatory factors, total crop area, crop production, and net irrigated area showed strong positive associations with ESVs, while cropping intensity exhibited a negative association. Therefore, the study reveals a strong association between GR led agricultural expansion and ESVs in India. This study suggests that there should be an urgent need for formulation of rigorous ecosystem management strategies and policies to preserve ecological integrity and flow of uninterrupted ESs and to sustain human well-being.
RPS5 interacts with the rabbit hemorrhagic disease virus 3' extremities region and plays a role in virus replication
Guo, Hongyuan ; Zhu, Jie ; Miao, Qiuhong ; Qi, Ruibin ; Tang, Aoxing ; Liu, Chuncao ; Yang, Hongzao ; Yuan, Ligang ; Liu, Guangqing - \ 2020
Veterinary Microbiology 249 (2020). - ISSN 0378-1135
Rabbit hemorrhagic disease virus - RNA-protein interaction - RPS5 - Viral replication
Rabbit hemorrhagic disease virus (RHDV), a member of Caliciviridae family, causes a highly contagious disease in rabbits. The RHDV replication mechanism is poorly understood due to the lack of a suitable culture system in vitro. This study identified RHDV 5' and 3' extremities (Ex) RNA binding proteins from the rabbit kidney cell line RK-13 based on a pull-down assay by applying a tRNA scaffold streptavidin aptamer. Using mass spectrometry (MS), several host proteins were discovered which interact with RHDV 5' and 3' Ex RNA. The ribosomal protein S5 (RPS5) was shown to interact with RHDV 3' Ex RNA directly by RNA-pulldown and confocal microscopy. To further investigate the role of RPS5 in RHDV replication, small interfering RNAs for RPS5 and RPS5 eukaryotic expression plasmids were used to change the expression level of RPS5 in RK-13 cells and the results showed that the RHDV replication and translation levels were positively correlated with the expression level of RPS5. It was also verified that RPS5 promoted RHDV replication by constructing RPS5 stable overexpression cell lines and RPS5 knockdown cell lines. In summary, it has been identified that RPS5 interacted with the RHDV 3' Ex RNA region and played a role in virus replication. These results will help to understand the mechanism of RHDV replication.
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Kuhn, Jens H. ; Adkins, Scott ; Alioto, Daniela ; Alkhovsky, Sergey V. ; Amarasinghe, Gaya K. ; Anthony, Simon J. ; Avšič-Županc, Tatjana ; Ayllón, María A. ; Bahl, Justin ; Balkema-Buschmann, Anne ; Ballinger, Matthew J. ; Bartonička, Tomáš ; Basler, Christopher ; Bavari, Sina ; Beer, Martin ; Bente, Dennis A. ; Bergeron, Éric ; Bird, Brian H. ; Blair, Carol ; Blasdell, Kim R. ; Bradfute, Steven B. ; Breyta, Rachel ; Briese, Thomas ; Brown, Paul A. ; Buchholz, Ursula J. ; Buchmeier, Michael J. ; Bukreyev, Alexander ; Burt, Felicity ; Buzkan, Nihal ; Calisher, Charles H. ; Cao, Mengji ; Casas, Inmaculada ; Chamberlain, John ; Chandran, Kartik ; Charrel, Rémi N. ; Chen, Biao ; Chiumenti, Michela ; Choi, Ryong ; Clegg, J.C.S. ; Crozier, Ian ; Graça, John V. da; Bó, Elena Dal; Dávila, Alberto M.R. ; Torre, Juan Carlos de la; Lamballerie, Xavier de; Swart, Rik L. de; Bello, Patrick L. Di; Paola, Nicholas Di; Serio, Francesco Di; Dietzgen, Ralf G. ; Digiaro, Michele ; Dolja, Valerian V. ; Dolnik, Olga ; Drebot, Michael A. ; Drexler, Jan Felix ; Dürrwald, Ralf ; Dufkova, Lucie ; Dundon, William G. ; Duprex, W.P. ; Dye, John M. ; Easton, Andrew J. ; Ebihara, Hideki ; Elbeaino, Toufic ; Ergünay, Koray ; Fernandes, Jorlan ; Fooks, Anthony R. ; Formenty, Pierre B.H. ; Forth, Leonie F. ; Fouchier, Ron A.M. ; Freitas-Astúa, Juliana ; Gago-Zachert, Selma ; Gāo, George Fú ; García, María Laura ; García-Sastre, Adolfo ; Garrison, Aura R. ; Gbakima, Aiah ; Goldstein, Tracey ; Gonzalez, Jean Paul J. ; Griffiths, Anthony ; Groschup, Martin H. ; Günther, Stephan ; Guterres, Alexandro ; Hall, Roy A. ; Hammond, John ; Hassan, Mohamed ; Hepojoki, Jussi ; Hepojoki, Satu ; Hetzel, Udo ; Hewson, Roger ; Hoffmann, Bernd ; Hongo, Seiji ; Höper, Dirk ; Horie, Masayuki ; Hughes, Holly R. ; Hyndman, Timothy H. ; Jambai, Amara ; Jardim, Rodrigo ; Jiāng, Dàohóng ; Jin, Qi ; Jonson, Gilda B. ; Junglen, Sandra ; Karadağ, Serpil ; Keller, Karen E. ; Klempa, Boris ; Klingström, Jonas ; Kobinger, Gary ; Kondō, Hideki ; Koonin, Eugene V. ; Krupovic, Mart ; Kurath, Gael ; Kuzmin, Ivan V. ; Laenen, Lies ; Lamb, Robert A. ; Lambert, Amy J. ; Langevin, Stanley L. ; Lee, Benhur ; Lemos, Elba R.S. ; Leroy, Eric M. ; Li, Dexin ; Lǐ, Jiànróng ; Liang, Mifang ; Liú, Wénwén ; Liú, Yàn ; Lukashevich, Igor S. ; Maes, Piet ; Marciel de Souza, William ; Marklewitz, Marco ; Marshall, Sergio H. ; Martelli, Giovanni P. ; Martin, Robert R. ; Marzano, Shin Yi L. ; Massart, Sébastien ; McCauley, John W. ; Mielke-Ehret, Nicole ; Minafra, Angelantonio ; Minutolo, Maria ; Mirazimi, Ali ; Mühlbach, Hans Peter ; Mühlberger, Elke ; Naidu, Rayapati ; Natsuaki, Tomohide ; Navarro, Beatriz ; Navarro, José A. ; Netesov, Sergey V. ; Neumann, Gabriele ; Nowotny, Norbert ; Nunes, Márcio R.T. ; Nylund, Are ; Økland, Arnfinn L. ; Oliveira, Renata C. ; Palacios, Gustavo ; Pallas, Vicente ; Pályi, Bernadett ; Papa, Anna ; Parrish, Colin R. ; Pauvolid-Corrêa, Alex ; Pawęska, Janusz T. ; Payne, Susan ; Pérez, Daniel R. ; Pfaff, Florian ; Radoshitzky, Sheli R. ; ul Rahman, Aziz ; Ramos-González, Pedro L. ; Resende, Renato O. ; Reyes, Carina A. ; Rima, Bertus K. ; Romanowski, Víctor ; Robles Luna, Gabriel ; Rota, Paul ; Rubbenstroth, Dennis ; Runstadler, Jonathan A. ; Ruzek, Daniel ; Sabanadzovic, Sead ; Salát, Jiří ; Sall, Amadou Alpha ; Salvato, Maria S. ; Sarpkaya, Kamil ; Sasaya, Takahide ; Schwemmle, Martin ; Shabbir, Muhammad Z. ; Shí, Xiǎohóng ; Shí, Zhènglì ; Shirako, Yukio ; Simmonds, Peter ; Širmarová, Jana ; Sironi, Manuela ; Smither, Sophie ; Smura, Teemu ; Song, Jin Won ; Spann, Kirsten M. ; Spengler, Jessica R. ; Stenglein, Mark D. ; Stone, David M. ; Straková, Petra ; Takada, Ayato ; Tesh, Robert B. ; Thornburg, Natalie J. ; Tomonaga, Keizō ; Tordo, Noël ; Towner, Jonathan S. ; Turina, Massimo ; Tzanetakis, Ioannis ; Ulrich, Rainer G. ; Vaira, Anna Maria ; Hoogen, Bernadette van den; Varsani, Arvind ; Vasilakis, Nikos ; Verbeek, Martin ; Wahl, Victoria ; Walker, Peter J. ; Wang, Hui ; Wang, Jianwei ; Wang, Xifeng ; Wang, Lin Fa ; Wèi, Tàiyún ; Wells, Heather ; Whitfield, Anna E. ; Williams, John V. ; Wolf, Yuri I. ; Wú, Zhìqiáng ; Yang, Xin ; Yáng, Xīnglóu ; Yu, Xuejie ; Yutin, Natalya ; Zerbini, Murilo ; Zhang, Tong ; Zhang, Yong Zhen ; Zhou, Guohui ; Zhou, Xueping - \ 2020
Archives of Virology (2020). - ISSN 0304-8608
In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Genome-wide Modeling of Polygenic Risk Score in Colorectal Cancer Risk
Thomas, Minta ; Sakoda, Lori C. ; Hoffmeister, Michael ; Rosenthal, Elisabeth A. ; Lee, Jeffrey K. ; Duijnhoven, Franzel J.B. van; Platz, Elizabeth A. ; Wu, Anna H. ; Dampier, Christopher H. ; Chapelle, Albert de la; Wolk, Alicja ; Joshi, Amit D. ; Burnett-Hartman, Andrea ; Gsur, Andrea ; Lindblom, Annika ; Castells, Antoni ; Win, Aung Ko ; Namjou, Bahram ; Guelpen, Bethany Van; Tangen, Catherine M. ; He, Qianchuan ; Li, Christopher I. ; Schafmayer, Clemens ; Joshu, Corinne E. ; Ulrich, Cornelia M. ; Bishop, D.T. ; Buchanan, Daniel D. ; Schaid, Daniel ; Drew, David A. ; Muller, David C. ; Duggan, David ; Crosslin, David R. ; Albanes, Demetrius ; Giovannucci, Edward L. ; Larson, Eric ; Qu, Flora ; Mentch, Frank ; Giles, Graham G. ; Hakonarson, Hakon ; Hampel, Heather ; Stanaway, Ian B. ; Figueiredo, Jane C. ; Huyghe, Jeroen R. ; Minnier, Jessica ; Chang-Claude, Jenny ; Hampe, Jochen ; Harley, John B. ; Visvanathan, Kala ; Curtis, Keith R. ; Offit, Kenneth ; Li, Li ; Marchand, Loic Le; Vodickova, Ludmila ; Gunter, Marc J. ; Jenkins, Mark A. ; Slattery, Martha L. ; Lemire, Mathieu ; Woods, Michael O. ; Song, Mingyang ; Murphy, Neil ; Lindor, Noralane M. ; Dikilitas, Ozan ; Pharoah, Paul D.P. ; Campbell, Peter T. ; Newcomb, Polly A. ; Milne, Roger L. ; MacInnis, Robert J. ; Castellví-Bel, Sergi ; Ogino, Shuji ; Berndt, Sonja I. ; Bézieau, Stéphane ; Thibodeau, Stephen N. ; Gallinger, Steven J. ; Zaidi, Syed H. ; Harrison, Tabitha A. ; Keku, Temitope O. ; Hudson, Thomas J. ; Vymetalkova, Veronika ; Moreno, Victor ; Martín, Vicente ; Arndt, Volker ; Wei, Wei Qi ; Chung, Wendy ; Su, Yu Ru ; Hayes, Richard B. ; White, Emily ; Vodicka, Pavel ; Casey, Graham ; Gruber, Stephen B. ; Schoen, Robert E. ; Chan, Andrew T. ; Potter, John D. ; Brenner, Hermann ; Jarvik, Gail P. ; Corley, Douglas A. ; Peters, Ulrike ; Hsu, Li - \ 2020
American Journal of Human Genetics 107 (2020)3. - ISSN 0002-9297 - p. 432 - 444.
cancer risk prediction - colorectal cancer - machine learning - polygenic risk score
Accurate colorectal cancer (CRC) risk prediction models are critical for identifying individuals at low and high risk of developing CRC, as they can then be offered targeted screening and interventions to address their risks of developing disease (if they are in a high-risk group) and avoid unnecessary screening and interventions (if they are in a low-risk group). As it is likely that thousands of genetic variants contribute to CRC risk, it is clinically important to investigate whether these genetic variants can be used jointly for CRC risk prediction. In this paper, we derived and compared different approaches to generating predictive polygenic risk scores (PRS) from genome-wide association studies (GWASs) including 55,105 CRC-affected case subjects and 65,079 control subjects of European ancestry. We built the PRS in three ways, using (1) 140 previously identified and validated CRC loci; (2) SNP selection based on linkage disequilibrium (LD) clumping followed by machine-learning approaches; and (3) LDpred, a Bayesian approach for genome-wide risk prediction. We tested the PRS in an independent cohort of 101,987 individuals with 1,699 CRC-affected case subjects. The discriminatory accuracy, calculated by the age- and sex-adjusted area under the receiver operating characteristics curve (AUC), was highest for the LDpred-derived PRS (AUC = 0.654) including nearly 1.2 M genetic variants (the proportion of causal genetic variants for CRC assumed to be 0.003), whereas the PRS of the 140 known variants identified from GWASs had the lowest AUC (AUC = 0.629). Based on the LDpred-derived PRS, we are able to identify 30% of individuals without a family history as having risk for CRC similar to those with a family history of CRC, whereas the PRS based on known GWAS variants identified only top 10% as having a similar relative risk. About 90% of these individuals have no family history and would have been considered average risk under current screening guidelines, but might benefit from earlier screening. The developed PRS offers a way for risk-stratified CRC screening and other targeted interventions.
Impact of plastic mulch film debris on soil physicochemical and hydrological properties
Qi, Yueling ; Beriot, Nicolas ; Gort, Gerrit ; Huerta Lwanga, Esperanza ; Gooren, Harm ; Yang, Xiaomei ; Geissen, Violette - \ 2020
Environmental Pollution 266 (2020). - ISSN 0269-7491
Agricultural soil - Biodegradable plastic - Microplastics - Plastic pollution - Soil quality
The plastic mulch films used in agriculture are considered to be a major source of the plastic residues found in soil. Mulching with low-density polyethylene (LDPE) is widely practiced and the resulting macro- and microscopic plastic residues in agricultural soil have aroused concerns for years. Over the past decades, a variety of biodegradable (Bio) plastics have been developed in the hope of reducing plastic contamination of the terrestrial ecosystem. However, the impact of these Bio plastics in agroecosystems have not been sufficiently studied. Therefore, we investigated the impact of macro (around 5 mm) and micro (<1 mm) sized plastic debris from LDPE and one type of starch-based Bio mulch film on soil physicochemical and hydrological properties. We used environmentally relevant concentrations of plastics, ranging from 0 to 2% (w/w), identified by field studies and literature review. We studied the effects of the plastic residue on a sandy soil for one month in a laboratory experiment. The bulk density, porosity, saturated hydraulic conductivity, field capacity and soil water repellency were altered significantly in the presence of the four kinds of plastic debris, while pH, electrical conductivity and aggregate stability were not substantially affected. Overall, our research provides clear experimental evidence that microplastics affect soil properties. The type, size and content of plastic debris as well as the interactions between these three factors played complex roles in the variations of the measured soil parameters. Living in a plastic era, it is crucial to conduct further interdisciplinary studies in order to have a comprehensive understanding of plastic debris in soil and agroecosystems.
Sel1L-Hrd1 ER-associated degradation maintains β cell identity via TGF-β signaling
Shrestha, Neha ; Liu, Tongyu ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Li, Xin ; Zhang, Maria ; Tang, Chih-Hang Anthony ; Hu, Chih-Chi Andrew ; Liu, Chengyang ; Naji, Ali ; Liu, Ming ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling - \ 2020
The Journal of Clinical Investigation 130 (2020)7. - ISSN 0021-9738 - p. 3499 - 3510.
β Cell apoptosis and dedifferentiation are 2 hotly debated mechanisms underlying β cell loss in type 2 diabetes; however, the molecular drivers underlying such events remain largely unclear. Here, we performed a side-by-side comparison of mice carrying β cell-specific deletion of ER-associated degradation (ERAD) and autophagy. We reported that, while autophagy was necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex was required for the maintenance of β cell maturation and identity. Using single-cell RNA-Seq, we demonstrated that Sel1L deficiency was not associated with β cell loss, but rather loss of β cell identity. Sel1L-Hrd1 ERAD controlled β cell identity via TGF-β signaling, in part by mediating the degradation of TGF-β receptor 1. Inhibition of TGF-β signaling in Sel1L-deficient β cells augmented the expression of β cell maturation markers and increased the total insulin content. Our data revealed distinct pathogenic effects of 2 major proteolytic pathways in β cells, providing a framework for therapies targeting distinct mechanisms of protein quality control
ER-associated degradation is required for the maintenance of β cell identity via TGFβ signaling
Shrestha, Neha ; Liu, T. ; Ji, Yewei ; Reinert, Rachel B. ; Torres, Mauricio ; Zhang, M. ; Tang, C.A. ; Hu, C.A. ; Liu, Chengyang ; Naji, Ali ; Lin, Jiandie D. ; Kersten, Sander ; Arvan, Peter ; Qi, Ling ; Hooiveld, Guido - \ 2020
Wageningen University & Research
Mus musculus - GSE143757 - PRJNA601502
β cell apoptosis and dedifferentiation are two hotly-debated mechanisms underlying β cell loss in type 2 diabetes (T2D); however, the molecular drivers underlying such events remain largely unclear. Here, by performing a side-by-side comparison of mice carrying β cell-specific deletion of endoplasmic reticulum (ER)-associated degradation (ERAD) and autophagy, we report that while autophagy appears necessary for β cell survival, the highly conserved Sel1L-Hrd1 ERAD protein complex is required for the maintenance of β cell maturation and identity. Notably, SEL1L expression is significantly reduced in human T2D islets compared to healthy human islets. At the single cell level, we demonstrate that Sel1L deficiency is not associated with β cell loss, but rather loss of β cell identity. Mechanistically, we find that Sel1L-Hrd1 ERAD controls β cell identity via TGFβ signaling, in part by mediating the degradation of TGF-β receptor 1 (TGFβRI). Inhibition of TGFβ signaling in Sel1L-deficient β cells augments the expression of β cell maturation markers and increases the total insulin content. Our data reveal profound but distinct pathogenic effects of two major proteolytic pathways in β cells, providing a new framework for therapies targeting distinct mechanisms of protein quality control
Fatty acids in the de novo lipogenesis pathway and incidence of type 2 diabetes : A pooled analysis of prospective cohort studies
Imamura, Fumiaki ; Fretts, Amanda M. ; Marklund, Matti ; Ardisson Korat, Andres V. ; Yang, Wei Sin ; Lankinen, Maria ; Qureshi, Waqas ; Helmer, Catherine ; Chen, Tzu An ; Virtanen, Jyrki K. ; Wong, Kerry ; Bassett, Julie K. ; Murphy, Rachel ; Tintle, Nathan ; Yu, Chaoyu Ian ; Brouwer, Ingeborg A. ; Chien, Kuo Liong ; Chen, Yun Yu ; Wood, Alexis C. ; Gobbo, Liana C. Del; Djousse, Luc ; Geleijnse, Johanna M. ; Giles, Graham G. ; Goede, Janette de; Gudnason, Vilmundur ; Harris, William S. ; Hodge, Allison ; Hu, Frank ; Koulman, Albert ; Laakso, Markku ; Lind, Lars ; Lin, Hung Ju ; McKnight, Barbara ; Rajaobelina, Kalina ; Riserus, Ulf ; Robinson, Jennifer G. ; Samieri, Cecilia ; Senn, Mackenzie ; Siscovick, David S. ; Soedamah-Muthu, Sabita S. ; Sotoodehnia, Nona ; Sun, Qi ; Tsai, Michael Y. ; Tuomainen, Tomi Pekka ; Uusitupa, Matti ; Wagenknecht, Lynne E. ; Wareham, Nick J. ; Wu, Jason H.Y. ; Micha, Renata ; Lemaitre, Rozenn N. - \ 2020
PLOS Medicine 17 (2020)6. - ISSN 1549-1676 - p. e1003102 - e1003102.
BACKGROUND: De novo lipogenesis (DNL) is the primary metabolic pathway synthesizing fatty acids from carbohydrates, protein, or alcohol. Our aim was to examine associations of in vivo levels of selected fatty acids (16:0, 16:1n7, 18:0, 18:1n9) in DNL with incidence of type 2 diabetes (T2D). METHODS AND FINDINGS: Seventeen cohorts from 12 countries (7 from Europe, 7 from the United States, 1 from Australia, 1 from Taiwan; baseline years = 1970-1973 to 2006-2010) conducted harmonized individual-level analyses of associations of DNL-related fatty acids with incident T2D. In total, we evaluated 65,225 participants (mean ages = 52.3-75.5 years; % women = 20.4%-62.3% in 12 cohorts recruiting both sexes) and 15,383 incident cases of T2D over the 9-year follow-up on average. Cohort-specific association of each of 16:0, 16:1n7, 18:0, and 18:1n9 with incident T2D was estimated, adjusted for demographic factors, socioeconomic characteristics, alcohol, smoking, physical activity, dyslipidemia, hypertension, menopausal status, and adiposity. Cohort-specific associations were meta-analyzed with an inverse-variance-weighted approach. Each of the 4 fatty acids positively related to incident T2D. Relative risks (RRs) per cohort-specific range between midpoints of the top and bottom quintiles of fatty acid concentrations were 1.53 (1.41-1.66; p < 0.001) for 16:0, 1.40 (1.33-1.48; p < 0.001) for 16:1n-7, 1.14 (1.05-1.22; p = 0.001) for 18:0, and 1.16 (1.07-1.25; p < 0.001) for 18:1n9. Heterogeneity was seen across cohorts (I2 = 51.1%-73.1% for each fatty acid) but not explained by lipid fractions and global geographical regions. Further adjusted for triglycerides (and 16:0 when appropriate) to evaluate associations independent of overall DNL, the associations remained significant for 16:0, 16:1n7, and 18:0 but were attenuated for 18:1n9 (RR = 1.03, 95% confidence interval (CI) = 0.94-1.13). These findings had limitations in potential reverse causation and residual confounding by imprecisely measured or unmeasured factors. CONCLUSIONS: Concentrations of fatty acids in the DNL were positively associated with T2D incidence. Our findings support further work to investigate a possible role of DNL and individual fatty acids in the development of T2D.
Can pedotransfer functions based on environmental variables improve soil total nutrient mapping at a regional scale?
Song, Xiao Dong ; Rossiter, David G. ; Liu, Feng ; Wu, Hua Yong ; Zhao, Xiao Rui ; Cao, Qi ; Zhang, Gan Lin - \ 2020
Soil & Tillage Research 202 (2020). - ISSN 0167-1987
Digital soil mapping - Random forest - Regression analysis - Total nitrogen - Total phosphorus - Total potassium
Numerous pedotransfer functions (PTFs) have been developed to predict the soil properties of interest from other soil properties and, less commonly, from environmental variables. However, only a few PTFs have been developed to predict soil nutrients using environmental variables and to extrapolate them to characterize spatial soil variations at a regional scale. In this study, we attempted to develop PTFs for the total nitrogen (TN), total phosphorus (TP) and total potassium (TK) concentrations in three typical pedo-climatic areas of China (Fujian Province, Jiangsu Province and Qilian Mountains) with diverse climate, terrain and soil types. A series of linear PTFs were developed to quantify the effect of terrain and climate on the predictive relations between the soil nutrients and other measured soil properties and environmental variables. In addition, digital soil mapping (DSM) based on the random forest (RF) technique was performed to test the hypothesis that the best-fit PTFs could be extrapolated, based on soil maps and environmental variables, to describe regional soil variations in the soil nutrients. The root mean square errors (RMSEs) of the best-fit PTFs for TN, TP and TK ranged from 0.21 to 0.79 g kg−1, 0.20 to 0.58 g kg−1, and 3.68 to 5.00 g kg−1, respectively. Different RMSEs were produced by DSM, namely 0.37-1.89 g kg−1, 0.19−0.56 g kg−1 and 3.79-4.83 g kg−1 for TN, TP and TK, respectively. PTFs provided a sound basis for database compilation if the soil properties were highly correlated. However, the extrapolation of best-fit PTFs to regional scales yielded greater errors than those produced by DSM. The comparison results reveal the limitations of PTFs and suggest that their performance could be improved by using environmental covariates or by fitting data in areas with relatively homogeneous soil landscapes. The DSM techniques may provide satisfactory alternatives to predict soil data at both regional and plot scales.
Litter cover promotes biocrust decomposition and surface soil functions in sandy ecosystem
Wu, Gao Lin ; Zhang, Meng Qi ; Liu, Yu ; López‐Vicente, Manuel - \ 2020
Geoderma 374 (2020). - ISSN 0016-7061
Ecological restoration - Sandy ecosystem - Soil crust - Soil nutrient - Soil organic matter - Soil particle size
Ecological restoration of sandy inland ecosystems is important for achieving global sustainability. In the world's semi-arid regions, soil crusts play crucial roles in maintaining ecosystem functioning. However, the true extent of soil quality improvement during the development of crusts is an issue not solved. In this study, four development stages of natural soil crusts, i.e., physical crusts (PC), biocrusts (BC), litter covered biocrusts (LBC) and litter crusts (LC) were selected in a semi-arid sandy ecosystem, along with a bare sandy land (BSL) as control area, to evaluate soil physicochemical properties at different soil depths. The coverage of litter (mainly leaves of Populus simonii) increased soil moisture and reduced soil bulk density. Compared with BC, the content of total soil organic matter (SOM) decreased in LBC by 13.83% and increased in LC by 36.57%. In contrast with BC, LC promoted a significant increase in soil nutrients, such as total nitrogen (30.30%), total phosphorus (46.89%) and available potassium (34.40%) in the topsoil layer (0–2 cm). Besides, LC contained higher clay and silt contents (10.47% and 29.81%) and lower sand content (−1.02%) than BC. In the 0–10 cm soil layer, the D (fractal dimension of the soil particle size distribution) of LC was the largest, with a value 5.71%, 6.1%, 2.44% and 0.93% higher than D in BSL, PC, BC and LBC, respectively. These findings reveal that litter covering facilitate the disintegration of BC, which further forms LC, and these processes clearly promote the enhancement of soil quality under sandy semi-arid conditions. Our findings are particularly important for predicting the transformation processes of sandy soil crusts and are of interest in ecological restoration programs.
A DMP-triggered in vivo maternal haploid induction system in the dicotyledonous Arabidopsis
Zhong, Yu ; Chen, Baojian ; Li, Mengran ; Wang, Dong ; Jiao, Yanyan ; Qi, Xiaolong ; Wang, Min ; Liu, Zongkai ; Chen, Chen ; Wang, Yuwen ; Chen, Ming ; Li, Jinlong ; Xiao, Zijian ; Cheng, Dehe ; Liu, Wenxin ; Boutilier, K.A. ; Liu, Chenxu ; Chen, Shaojiang - \ 2020
Nature Plants 6 (2020). - ISSN 2055-026X - p. 466 - 472.
Doubled haploid technology using inducer lines carrying mutations in ZmPLA1/MTL/NLD and ZmDMP1–4 has revolutionized traditional maize breeding. ZmPLA1/MTL/NLD is conserved in monocots and has been used to extend the system from maize to other monocots5–7, but no functional orthologue has been identified in dicots, while ZmDMP-like genes exist in both monocots and dicots4,8,9. Here, we report that loss-of-function mutations in the Arabidopsis thaliana ZmDMP-like genes AtDMP8 and AtDMP9 induce maternal haploids, with an average haploid induction rate of 2.1 ± 1.1%. In addition, to facilitate haploid seed identification in dicots, we established an efficient FAST-Red fluorescent marker-based haploid identification system that enables the identification of haploid seeds with >90% accuracy. These results show that mutations in DMP genes also trigger haploid induction in dicots. The conserved expression patterns and amino acid sequences of ZmDMP-like genes in dicots suggest that DMP mutations could be used to develop in vivo haploid induction systems in dicots.
Border-row proportion determines strength of interspecific interactions and crop yields in maize/peanut strip intercropping
Wang, Ruonan ; Sun, Zhanxiang ; Zhang, Lizhen ; Yang, Ning ; Feng, Liangshan ; Bai, Wei ; Zhang, Dongsheng ; Wang, Qi ; Evers, Jochem B. ; Liu, Yang ; Ren, Jianhong ; Zhang, Yue ; Werf, Wopke van der - \ 2020
Field Crops Research 253 (2020). - ISSN 0378-4290
border-row effect - relative yield total - row configuration - strip cropping - yield components
Strip intercropping enables increases in yields and ecological services in agriculture. Crop yields of species grown in strip intercropping are often related to the yield responses (increases or decreases) in the outer rows of the strips: the border rows. This suggests that the yield response can be modulated by changing the proportion of border rows in the field. Here we studied the relationship between component species yields and proportion of border rows in strip intercrops of maize (Zea mays L.) and peanut (Arachis hypogaea Linn.). We tested four different intercrops with equal proportions of maize and peanut but a different number of rows per strip: M2P2 (2 rows maize intercropped with 2 rows peanut), M4P4, M6P6, M8P8, and sole maize (SM) and sole peanut (SP). The border-row proportions were 1, 0.5, 0.33 and 0.25 for the intercropping M2P2 to M8P8, respectively, and 0 for the pure stands. Yield responded positively to the proportion of border rows for maize, but negatively for peanut, confirming the dominance of maize in this system. Kernel number per ear of maize and pod number per plant of peanut were the main yield components that responded to the border-row proportion. Across three years, relative maize yield (yield in intercropping divided by yield in monoculture), varied from 0.76 in M2P2 to 0.56 in M8P8, while relative peanut yield varied from 0.19 in M2P2 to 0.39 in M8P8. Relative yield total was not significantly different from one in any of the mixtures. Yield of intercropped maize in border rows was 48% higher than in inner rows and the sole crop, in part due to a significantly higher kernel number per ear (13%). Yield of intercropped peanut in border rows was on average 29% lower than in inner rows and 48% lower than in sole peanut. Yield responses in border rows were independent from the border-row proportion. The results show that relative crop yields responded strongly to variation in border-row proportion resulting from variation in strip width from 1 to 4 m. Strip width thus provides a mechanism to control the strength of interspecific plant interactions and relative yields in strip intercropping.
Regulation of endoplasmic reticulum-mitochondria contacts and mitochondrial dynamics by Sel1L-Hrd1 ERAD during thermogenesis
Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
GSE145895 - PRJNA608688 - Mus musculus
Organelles such as endoplasmic reticulum (ER) and mitochondria interact with each other at specialized domains on the ER known as mitochondria-associated membranes (MAMs). Here, using three-dimensional high-resolution imaging techniques, we show that the Sel1LHrd1 protein complex, the most conserved branch of ER-associated protein degradation (ERAD), exerts a profound impact on ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover and hence the abundance of the MAM protein sigma receptor 1 (SigmaR1). Sel1L or Hrd1 deficiency in brown adipocytes impairs dynamic interaction between ER and mitochondria, leading to the formation of pleomorphic “megamitochondria” and, in some cases with penetrating ER tubule(s), in response to acute cold challenge. Mice with ERAD deficiency are cold sensitive and exhibit mitochondrial dysfunction in brown adipocytes. Mechanistically, endogenous SigmaR1 is targeted for proteasomal degradation by Sel1L-Hrd1 ERAD, whose accumulation in ERAD-deficient cells leads to mitofusin 2 (Mfn2) oligomerization, thereby linking ERAD to mitochondrial dynamics. Our study identifies Sel1L-Hrd1 ERAD as a critical determinant of ER-mitochondria contacts, thereby regulating mitochondrial dynamics and thermogenesis.
Endoplasmic reticulum-associated degradation regulates mitochondrial dynamics in brown adipocytes
Zhou, Zhangsen ; Torres, Mauricio ; Sha, Haibo ; Halbrook, Christopher J. ; Bergh, Françoise van den; Reinert, Rachel B. ; Yamada, Tatsuya ; Wang, Siwen ; Luo, Yingying ; Hunter, Allen H. ; Wang, Chunqing ; Sanderson, Thomas H. ; Liu, Meilian ; Taylor, Aaron ; Sesaki, Hiromi ; Lyssiotis, Costas A. ; Wu, Jun ; Kersten, Sander ; Beard, Daniel A. ; Qi, Ling - \ 2020
Science 368 (2020)6486. - ISSN 0036-8075 - p. 54 - 60.
The endoplasmic reticulum (ER) engages mitochondria at specialized ER domains known as mitochondria-associated membranes (MAMs). Here, we used three-dimensional high-resolution imaging to investigate the formation of pleomorphic “megamitochondria” with altered MAMs in brown adipocytes lacking the Sel1L-Hrd1 protein complex of ER-associated protein degradation (ERAD). Mice with ERAD deficiency in brown adipocytes were cold sensitive and exhibited mitochondrial dysfunction. ERAD deficiency affected ER-mitochondria contacts and mitochondrial dynamics, at least in part, by regulating the turnover of the MAM protein, sigma receptor 1 (SigmaR1). Thus, our study provides molecular insights into ER-mitochondrial cross-talk and expands our understanding of the physiological importance of Sel1L-Hrd1 ERAD.
Examining the effects of forest fire on terrestrial carbon emission and ecosystem production in India using remote sensing approaches
Sannigrahi, Srikanta ; Pilla, Francesco ; Basu, Bidroha ; Basu, Arunima Sarkar ; Sarkar, Konika ; Chakraborti, Suman ; Joshi, Pawan Kumar ; Zhang, Qi ; Wang, Ying ; Bhatt, Sandeep ; Bhatt, Anand ; Jha, Shouvik ; Keesstra, Saskia ; Roy, P.S. - \ 2020
Science of the Total Environment 725 (2020). - ISSN 0048-9697
Burn indices - Carbon emission - Forest fire - Greenhouse gas emission - Net primary productivity - Remote sensing
Remote sensing techniques are effectively used for measuring the overall loss of terrestrial ecosystem productivity and biodiversity due to forest fires. The current research focuses on assessing the impacts of forest fires on terrestrial ecosystem productivity in India during 2003–2017. Spatiotemporal changes of satellite remote sensing derived burn indices were estimated for both fire and normal years to analyze the association between forest fires and ecosystem productivity. Two Light Use Efficiency (LUE) models were used to quantify the terrestrial Net Primary Productivity (NPP) of the forest ecosystem using the open-source and freely available remotely sensed data. A novel approach (delta NPP/delta burn indices) is developed to quantify the effects of forest fires on terrestrial carbon emission and ecosystem production. During 2003–2017, the forest fire intensity was found to be very high (>2000) across the eastern Himalayan hilly region, which is mostly covered by dense forest and thereby highly susceptible to wildfires. Scattered patches of intense forest fires were also detected in the lower Himalayan and central Indian states. The spatial correlation between the burn indices and NPP were mainly negative (−0.01 to −0.89) for the fire-prone states as compared to the other neighbouring regions. Additionally, the linear approximation between the burn indices and NPP showed a positive relation (0.01 to 0.63), suggesting a moderate to high impact of the forest fires on the ecosystem production and terrestrial carbon emission. The present approach has the potential to quantify the loss of ecosystem productivity due to forest fires.
A global database of soil nematode abundance and functional group composition
Hoogen, Johan van den; Geisen, Stefan ; Wall, Diana H. ; Wardle, David A. ; Traunspurger, Walter ; Goede, Ron G.M. de; Adams, Byron J. ; Ahmad, Wasim ; Ferris, Howard ; Bardgett, Richard D. ; Bonkowski, Michael ; Campos-Herrera, Raquel ; Cares, Juvenil E. ; Caruso, Tancredi ; Brito Caixeta, Larissa de; Chen, Xiaoyun ; Costa, Sofia R. ; Creamer, Rachel ; Cunha e Castro, José Mauro da; Dam, Marie ; Djigal, Djibril ; Escuer, Miguel ; Griffiths, Bryan S. ; Gutiérrez, Carmen ; Hohberg, Karin ; Kalinkina, Daria ; Kardol, Paul ; Kergunteuil, Alan ; Korthals, Gerard ; Krashevska, Valentyna ; Kudrin, Alexey A. ; Li, Qi ; Liang, Wenju ; Magilton, Matthew ; Marais, Mariette ; Martín, José Antonio Rodríguez ; Matveeva, Elizaveta ; Mayad, El Hassan ; Mzough, E. ; Mulder, Christian ; Mullin, Peter ; Neilson, Roy ; Nguyen, Duong T.A. ; Nielsen, Uffe N. ; Okada, Hiroaki ; Rius, Juan Emilio Palomares ; Pan, Kaiwen ; Peneva, Vlada ; Pellissier, Loïc ; Silva, Julio Carlos Pereira da; Pitteloud, Camille ; Powers, Thomas O. ; Powers, Kirsten ; Quist, Casper W. ; Rasmann, Sergio ; Moreno, Sara Sánchez ; Scheu, Stefan ; Setälä, Heikki ; Sushchuk, Anna ; Tiunov, Alexei V. ; Trap, Jean ; Vestergård, Mette ; Villenave, Cecile ; Waeyenberge, Lieven ; Wilschut, Rutger A. ; Wright, Daniel G. ; Keith, Aidan M. ; Yang, Jiuein ; Schmidt, Olaf ; Bouharroud, R. ; Ferji, Z. ; Putten, Wim H. van der; Routh, Devin ; Crowther, Thomas W. - \ 2020
Scientific Data 7 (2020)1. - ISSN 2052-4463
As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
Examining effects of climate change and land use dynamic on biophysical and economic values of ecosystem services of a natural reserve region
Sannigrahi, Srikanta ; Zhang, Qi ; Joshi, P.K. ; Sutton, Paul C. ; Keesstra, Saskia ; Roy, P.S. ; Pilla, Francesco ; Basu, Bidroha ; Wang, Ying ; Jha, Shouvik ; Paul, Saikat Kumar ; Sen, Somnath - \ 2020
Journal of Cleaner Production 257 (2020). - ISSN 0959-6526
CA-Markov - Climate change - Ecosystem services - InVEST - Land use - Sundarbans
Ecosystem Service Valuation (ESV) is a process of evaluating and quantifying the monetary values of ESs and their functions. Using both biophysical and spatially explicit integrated models, biophysical and monetary values of key Ecosystem Services (ESs) were estimated in the Sundarbans Biosphere Region (SBR), India. Quantification was made both in time series (1982–2017) and individual years (1973, 1988, 2003, 2013, 2018, 2025, 2035, 2045) to understand the impact of climate change and land-use dynamics on the long-term ecological status of the region. The monetary and biophysical values of the ESs were then obtained from Net Primary Productivity (NPP) models, Integrated Valuation of Ecosystem Services and Trade-offs (InVEST), and Cellular Automata Markov Chain Model (CA-Markov). NPP increased significantly during the first half period (1982–1999), but significantly declined during the second period (2000–2017). The highest estimated ESVs (US$ ha−1) was found for habitat service (30780), nutrient cycling (12626), and gas regulation (7224.81), whereas, lower ESVs were approximated for water regulation (347.81), raw material production (777.82) and waste treatment (13.57) services. Among the nine ESs evaluated, climate regulation, gas regulation, and disturbance regulation were the most important regulating services of the SBR. The combined effects of climate change and land-use dynamics on ESs are much stringent in a vulnerable region like the SBR. Most of the regulating services were closely associated with the fluctuation of land use land cover input. Thus, land management policies and land reform strategies that will encourage the conversion of productive land, especially the highly productive mangrove forest, for the development or any other financial benefits, would disturb the ideal human-nature balance of this ecosystem. The outcomes of this study also provide an important reference to the land administrators, researchers, and decision-makers to comprehend the expected social-ecological juxtaposition in a protected natural reserve region like the Sundarbans.
Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite
Qi, Wanhe ; Taherzadeh, Mohammad J. ; Ruan, Yunjie ; Deng, Yale ; Chen, Ji Shuang ; Lu, Hui Feng ; Xu, Xiang Yang - \ 2020
Bioresource Technology 305 (2020). - ISSN 0960-8524
Bacterial community - Fungal community - PBS/Bamboo composite - RAS effluent treatment - Solid-phase denitrification
This study explored the denitrification performance of solid-phase denitrification (SPD) systems packed with poly (butylene succinate)/bamboo powder composite to treat synthetic aquaculture wastewater under different salinity conditions (0‰ Vs. 25‰). The results showed composite could achieve the maximum denitrification rates of 0.22 kg (salinity, 0‰) and 0.34 kg NO3 −-N m−3 d−1 (salinity, 25‰) over 200-day operation. No significant nitrite accumulation and less dissolved organic carbon (DOC) release (<15 mg/L) were found. The morphological and spectroscopic analyses demonstrated the mixture composites degradation. Microbial community analysis showed that Acidovorax, Simplicispira, Denitromonas, SM1A02, Marinicella and Formosa were the dominant genera for denitrifying bacteria, while Aspergillus was the major genus for denitrifying fungus. The co-network analysis also indicated the interactions between bacterial and fungal community played an important role in composite degradation and denitrification. The outcomes provided a potential strategy of DOC control and cost reduction for aquaculture nitrate removal by SPD.
Responses of ecosystem services to natural and anthropogenic forcings: A spatial regression based assessment in the world's largest mangrove ecosystem
Sannigrahi, Srikanta ; Zhang, Qi ; Pilla, Francesco ; Joshi, Pawan Kumar ; Basu, Bidroha ; Keesstra, Saskia ; Roy, P.S. ; Wang, Ying ; Sutton, Paul C. ; Chakraborti, Suman ; Paul, Saikat Kumar ; Sen, Somnath - \ 2020
Science of the Total Environment 715 (2020). - ISSN 0048-9697
Biophysical and economic valuation - Climate change - Data dimensionality - Ecosystem services - Spatial regression - Sundarbans
Most of the Earth's Ecosystem Services (ESs) have experienced a decreasing trend in the last few decades, primarily due to increasing human dominance in the natural environment. Identification and categorization of factors that affect the provision of ESs from global to local scales are challenging. This study makes an effort to identify the key driving factors and examine their effects on different ESs in the Sundarbans region, India. We carry out the analysis following five successive steps: (1) quantifying biophysical and economic values of ESs using three valuation approaches; (2) identifying six major driving forces on ESs; (3) categorizing principal data components with dimensionality reduction; (4) constructing multivariate regression models with variance partitioning; (5) implementing six spatial regression models to examine the causal effects of natural and anthropogenic forcings on ESs. Results show that climatic factors, biophysical factors, and environmental stressors significantly affect the ESs. Among the six driving factors, climate factors are highly associated with the ESs variation and explain the maximum model variances (R2 = 0.75–0.81). Socioeconomic (R2 = 0.44–0.66) and development (R2 = 27–0.44) factors have weak to moderate effects on the ESs. Furthermore, the joint effects of the driving factors are much higher than their individual effects. Among the six spatial regression models, Geographical Weighted Regression (GWR) performs the most accurately and explains the maximum model variances. The proposed hybrid valuation method aggregates biophysical and economic estimates of ESs and addresses methodological biases existing in the valuation process. The presented framework can be generalized and applied to other ecosystems at different scales. The outcome of this study could be a reference for decision-makers, planners, land administrators in formulating a suitable action plan and adopting relevant management practices to improve the overall socio-ecological status of the region.
Nationwide assessment of persistent halogenated compounds (PHCs) in farmed golden pompano of China
Cheng, Bo ; Peng, Feng Jiao ; Liu, Qiao Rong ; Ke, Chang Liang ; Liu, Qi ; Pan, Chang Gui - \ 2020
Food Chemistry 313 (2020). - ISSN 0308-8146
Golden pompano - Health risk - Organochlorine pesticides (OCPs) - Persistent halogenated compounds (PHCs) - Polychlorinated biphenyls (PCBs)
Persistent halogenated compounds (PHCs) contamination has become a major concern over the world. Here we investigated occurrence, spatial distributions, congener profiles, as well as health risks of PHCs in farmed golden pompano in China using gas chromatography/mass spectrometry (GC/MS). The concentrations of PCBs, PBDEs and OCPs were in the range of 0.78–4.79 ng/g wet weight (ww), not detected (nd)-1.14 ng/g ww and 1.1–38.8 ng/g ww, respectively. Furthermore, ρ,ρ′-DDT, ο,ρ′-DDT and PCB 101 were the dominant PHC contaminants. The estimated daily intakes of PHCs through consumption of golden pompano were up to 12.86 and 131.34 ng/kg body weight/day based on the mean and 95th concentrations determined in golden pompano, respectively. Risk-based analysis indicates that target PHCs in golden pompano would not pose risks to human. Our study presents the first report of a nationwide survey of PHCs contamination in farmed golden pompano in China.