Bioresour Technol , IF:7.539 , 2019 Jan , V272 : P489-500 doi: 10.1016/j.biortech.2018.10.079
Microbial community evolution and fate of antibiotic resistance genes along six different full-scale municipal wastewater treatment processes.
State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.; State Key Joint Laboratory of Environmental Simulation and Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Water Pollution Control, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. Electronic address: yswei@rcees.ac.cn.; Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark.; Department of Environmental Engineering, Technical University of Denmark, Copenhagen Lyngby 2800, Denmark.
The evolution of microbial community and the fate of ARGs along different full-scale wastewater treatment processes (i.e., Anaerobic-Anoxic-Oxic, Oxidation Ditch, and Cyclic Activated Sludge System) were investigated in this study. We found that the sludges of bioreactors treating similar influent showed the similar microbial communities, independent of the treatment technologies. The horizontal gene transfer (HGT) mainly occurred in aeration tank rather that anaerobic/anoxic tank. More co-occurrence of potential pathogens and ARGs was found in wastewater than in sludge. Microbial biomass was the key driver for the fate of ARGs in wastewater, while mobile genetic elements (MGEs) was the key factor for the fate of ARGs in sludge. Combination of wastewater characteristics, microbial diversity, microbial biomass, and MGEs contributed to the variation of ARGs. Finally, it was found that enhanced nutrients removal process and tertiary treatment would benefit ARGs removal.
PMID: 30391842
J Environ Manage , IF:5.647 , 2019 Jan , V229 : P27-37 doi: 10.1016/j.jenvman.2018.06.051
Exploring the dynamics of research collaborations by mapping social networks in invasion science.
Department of Conservation Ecology and Entomology and Centre for Invasion Biology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa. Electronic address: babrahams@sun.ac.za.; Department of Conservation Ecology and Entomology and Centre for Invasion Biology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; Natural Resources and the Environment, Council for Scientific and Industrial Research, PO Box 320, Stellenbosch 3599, South Africa.; Department of Conservation Ecology and Entomology and Centre for Invasion Biology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa.
Moving towards more integrative approaches within the invasion sciences has been recognized as a means of improving linkages between science, policy, and practice. Yet despite the recognition that biological invasions pose complex social-ecological challenges, the invasion literature poorly covers social-ecological or distinctly integrative research. Various initiatives and investments have been made towards building research capacity and conducting more integrative research aimed at improving the management of biological invasions. Using a combination of social network and thematic analysis approaches, and the South African Working for Water (WfW) program as a case study for the management of invasive species, we identify and explore the roles of core authors in shaping collaboration networks and research outputs, based on bibliographic records. We found that research produced under the auspices of WfW is authored by a handful of core authors, conducting primarily ecologically-focused research, with social research significantly underrepresented. Core authors identified in this study play an essential role in mediating relationships between researchers, in addition to potentially controlling access to those seeking to form collaborations, maintaining network cohesion and connectivity across institutional and disciplinary boundaries. Research projects should be designed to span disciplines and institutions if they are to adequately address complex challenges.
PMID: 29934131
Mol Ecol , IF:5.163 , 2019 Jan , V28 (2) : P365-378 doi: 10.1111/mec.14924
Non-random association patterns in a plant-mycorrhizal fungal network reveal host-symbiont specificity.
Department of Botany, University of Tartu, Tartu, Estonia.
Arbuscular mycorrhizal (AM) fungi are obligate plant symbionts that have important functions in most terrestrial ecosystems, but there remains an incomplete understanding of host-fungus specificity and the relationships between species and functional groups of plants and AM fungi. Here, we aimed to provide a comprehensive description of plant-AM fungal interactions in a biodiverse semi-natural grassland. We sampled all plant species in a 1,000-m(2) homogeneous plot of dry calcareous grassland in two seasons (summer and autumn) and identified root-colonizing AM fungi by SSU rDNA sequencing. In the network of 33 plant and 100 AM fungal species, we found a significant effect of both host plant species and host plant functional group on AM fungal richness and community composition. Comparison with network null models revealed a larger-than-random degree of partner selectivity among plants. Grasses harboured a larger number of AM fungal partners and were more generalist in partner selection, compared with forbs. More generalist partner association and lower specialization were apparent among obligately, compared with facultatively, mycorrhizal plant species and among locally more abundant plant species. This study provides the most complete data set of co-occurring plant and AM fungal taxa to date, showing that at this particular site, the interaction network is assembled non-randomly, with moderate selectivity in associations between plant species and functional groups and their fungal symbionts.
PMID: 30403423
Mol Ecol , IF:5.163 , 2019 Jan , V28 (2) : P293-306 doi: 10.1111/mec.14893
Geospatial variation in co-occurrence networks of nitrifying microbial guilds.
Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Uppsala, Sweden.
Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N-products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two-step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia-oxidizing bacteria (AOB) and archaea (AOA) and nitrite-oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field-scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44-hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co-occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module-connecting versus module-hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.
PMID: 30307658
Nutrients , IF:4.546 , 2019 Jan , V11 (1) doi: 10.3390/nu11010108
Synergistic Effects of Sanghuang(-)Danshen Bioactives on Arterial Stiffness in a Randomized Clinical Trial of Healthy Smokers: An Integrative Approach to in silico Network Analysis.
Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea. ynlim@ewha.ac.kr.; Department of Neurology, Ewha Womans University School of Medicine, Seoul 07985, Korea. knstar@ewha.ac.kr.; Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Korea. wchwang.kr@gmail.com.; Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul 01811, Korea. jiyeonk@seoultech.ac.kr.; Department of Bio and Brain Engineering, KAIST, Daejeon 34141, Korea. dhlee@kaist.ac.kr.; Department of Neurology, Eunpyeong St. Mary's Hospital, The Catholic University of Korea, Seoul 06591, Korea. brain930@gmail.com.; Department of Nutritional Science and Food Management, Ewha Womans University, Seoul 03760, Korea. orank@ewha.ac.kr.
The vascular endothelium is a favorite early target of cardiovascular risk factors, including cigarette smoking. Here, we investigated the synergistic effects of Sanghuang(-)Danshen (SD) bioactives on vascular stiffness in a controlled clinical trial of healthy chronic smokers (n = 72). Relative to placebo, 4-week SD consumption at 900 mg/day improves pulse wave velocity (p = 0.0497), reduces systolic blood pressure (peripheral, p = 0.0008; brachial, p = 0.0046; and ankle, p = 0.0066), and increases endothelial nitric oxide synthase activation (p < 0.0001). We then mapped all differential markers obtained from the clinical data, Affymetrix microarray, and (1)H NMR metabolomics, together with 12 SD bioactives, onto the network platform termed the context-oriented directed associations. The resulting vascular subnetwork demonstrates that ellagic acid, caffeic acid, protocatechuic acid, cryptotanshinone, tanshinone I, and tanshinone IIA are linked to NOS3, ARG2, and EDN1 for vascular dilation, implicated with arginine/proline metabolism. They are also linked to SUCLG1, CYP1A1, and succinate related to the mitochondrial metabolism and detoxification, implicated with various metabolic pathways. These results could explain the synergistic action mechanisms of SD bioactives in the regulation of vascular endothelial dilation and metabolism, confirming the potential of SD in improving vascular stiffness and blood pressure in healthy smokers.
PMID: 30621047
Plant Cell Rep , IF:3.825 , 2019 Jan , V38 (1) : P1-13 doi: 10.1007/s00299-018-2344-z
Comparative transcriptome analysis shows the defense response networks regulated by miR482b.
School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China.; School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China.; School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China. ysluan@dlut.edu.cn.
KEY MESSAGE: The transcriptomic profile in the leaves of miR482b-overexpressing tomato plants revealed that miR482b may suppress alpha-linolenic acid metabolism, cysteine and methionine metabolism, plant-pathogen interaction, and the MAPK pathway to reduce resistance to Phytophthora infestans. Our previous study showed that tomato miR482b acted as a negative regulator during tomato resistance to Phytophthora infestans by silencing NBS-LRR genes. To investigate pathways related to miR482b, the transcriptomic profile of tomato plants that overexpressed miR482b was constructed. A total of 47,124,670 raw sequence reads from the leaves of miR482b-overexpressing tomato plants were generated by Illumina sequencing. A total of 746 genes in miR482b-overexpressing tomato plants were found to show significantly differential expression relative to those in wild-type tomato plants, including 132 up-regulated genes and 614 down-regulated genes. GO and KEGG enrichment analyses showed that plant-pathogen interaction, the MAPK pathway, and the pathways related to JA and ET biosynthesis were affected by miR482b in tomato. qRT-PCR results showed that all the enriched genes in these pathways were down-regulated in tomato plants that overexpressed miR482b and up-regulated in tomato plants that overexpressed an NBS-LRR gene (Soly02g036270.2, the target gene of miR482b). After P. infestans infection, the expression of the enriched genes showed a time-dependent response, and the genes played different roles between resistant tomato (Solanum pimpinellifolium L3708) and tomato susceptible to P. infestans (S. lycopersicum Zaofen No. 2). Our results have, therefore, demonstrated that miR482b is an important component of defense response network. This will also help to identify candidate genes involved in plant-pathogen interaction.
PMID: 30191311
J Ethnopharmacol , IF:3.69 , 2019 Jan , V229 : P127-136 doi: 10.1016/j.jep.2018.09.029
In vitro antiplasmodial, antitrypanosomal and antileishmanial activities of selected medicinal plants from Ugandan flora: Refocusing into multi-component potentials.
Department of Biological Sciences, Egerton University, P.O. Box 536-20115, Egerton, Njoro, Kenya; Department of Biological Sciences, Kyambogo University, Post Box 1, Kyambogo, Kampala, Uganda. Electronic address: obbochristopher995@gmail.com.; Department of Biological Sciences, Egerton University, P.O. Box 536-20115, Egerton, Njoro, Kenya.; Kenya Medical Research Institute (KEMRI), P.O. Box 54840, Nairobi 00200, Kenya.; African Union-Interafrican Bureau for Animal Resources, P.O. Box 30786, Nairobi, Kenya.; Department of Chemistry, Egerton University, P.O. Box 536-20115, Egerton, Njoro, Kenya. Electronic address: pcheplogoi@egerton.ac.ke.; Department of Chemistry, Egerton University, P.O. Box 536-20115, Egerton, Njoro, Kenya.
ETHNOPHARMACOLOGICAL RELEVANCE: Seven medicinal plants from Ugandan flora, namely Entada abyssinica, Khaya anthotheca, Vernonia amygdalina, Baccharoides adoensis, Schkuhria pinnata, Entandropragma utile and Momordica foetida, were selected in this study. They are used to treat conditions and infections ranging from inflammations, pains and fevers to viruses, bacteria, protozoans and parasites. Two of the plants, V. amygdalina and M. foetida, are also used as human food or relish, while others are important in ethnoveterinary practices and in zoopharmacognosy in the wild. The aim of this study was to evaluate the in vitro antiplasmodial, antitrypanosomal and antileishmanial activities, along with cytotoxicity of the multi-component extracts of these plants. MATERIALS AND METHODS: Different parts of the plants were prepared and serially extracted with hexane, petroleum ether, dichloromethane, ethyl acetate, methanol and double distilled water. Solvent free extracts were assayed for in vitro inhibition against four reference parasite strains, Plasmodium falciparum (K1), Trypanosoma brucei rhodesiense (STIB 900), Trypanosoma cruzi (Talahuen C2C4) and Leishmania donovani (MHOM-ET-67/L82) using standard methods. Toxicity was assessed against L6 skeletal fibroblast and mouse peritoneal macrophage (J774) cells and selectivity indices (SIs) calculated for the most active extracts. RESULTS: The strongest activities, demonstrating median inhibitory concentration (IC50) values 90mug/ml. Out of 22 extracts demonstrating IC50s <20mug/ml, seven were against T. b. rhodesiense (IC50: 1.6-16.2mug/ml), six against T. cruzi (IC50: 2.1-18.57mug/ml), none against L. donovani (IC50: falling >3.3 and >10mug/ml), and nine against P. falciparum (IC50: 0.96mug/ml to 4.69mug/ml). Selectivity indices (SI) calculated for the most active extracts ranged from <1.00 to 94.24. However, the B. adoensis leaf dichloromethane extract (a) was equipotent (IC50 =3.3mug/ml) against L. donovani and L6 cells respectively, indicating non-specific selection. Trypanosome and Plasmodium parasites were comparatively more sensitive to the test extracts. CONCLUSIONS: The benefits achieved from the seven tested plant species as traditional ethnomedicinal and ethnoveterinary therapies or in zoopharmacognosy against infections and conditions of animals in the wild are strongly supported by results of this study. The synergy of plant extracts, so achieved by concerted actions of the ligands, produces adequate perturbation of targets in the four parasite genera, resulting in the strong potencies exhibited by low IC50 values. The total inhibitory effect, achieved as a sum of perturbations contributed by each participating compound in the extract, minimises toxic effects of the compounds as seen in the high SI's obtained with some extracts. Those extracts demonstrating SI >/= 4 form promising candidates for further cell-based and system pharmacology studies.
PMID: 30273736
J Ethnopharmacol , IF:3.69 , 2019 Jan , V229 : P1-14 doi: 10.1016/j.jep.2018.09.033
Hepatoprotection of Herpetospermum caudigerum Wall. against CCl4-induced liver fibrosis on rats.
Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing 210094, People's Republic of China; School of Life Sciences, Anhui Normal University, No. 1 Beijing East Road, Wuhu 241000, People's Republic of China. Electronic address: cpu_lmh@126.com.; Tibetan Medicine Institute, China Tibetology Research Center, Beijing 100101, People's Republic of China. Electronic address: fengxin0303@163.com.; Tibetan Medicine Institute, China Tibetology Research Center, Beijing 100101, People's Republic of China. Electronic address: 525184660@qq.com.; Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing 210094, People's Republic of China. Electronic address: 917051703@qq.com.; Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing 210094, People's Republic of China. Electronic address: 2601584016@qq.com.; Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing 210094, People's Republic of China. Electronic address: 571929365@qq.com.; School of Pharmacy, South-Central University for Nationalities, 182 National Road, Wuhan 430074, People's Republic of China. Electronic address: clyhappy05@163.com.; Tibetan Medicine Institute, China Tibetology Research Center, Beijing 100101, People's Republic of China. Electronic address: zhonggejia@sina.com.; Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing 210094, People's Republic of China. Electronic address: wang.junsong@gmail.com.
ETHNOPHARMACOLOGICAL RELEVANCE: Herpetospermum caudigerum Wall. (HCW) is a traditional Tibetan medicine, which has been used to ameliorate liver injuries in the folk. AIM OF THE STUDY: Liver fibrosis has been recognized as a major lesion of the liver that leads to liver cirrhosis/hepatocarcinoma and even to death in the end. This study aims to demonstrate the protective effect of HCW against CCl4-induced liver injury in rats and to explore the underlying mechanisms. MATERIALS AND METHODS: Hepatic fibrosis was induced by intraperitoneal injection of CCl4. Liver function markers, fibrosis markers, serum anti-oxidation enzymes as well as elements levels were determined. Serum and liver tissues were subjected to NMR-based metabolomics and multivariate statistical analysis. RESULTS: HCW could significantly reduce the elevated levels of fibrosis markers such as hyaluronidase, laminin, Type III procollagen and Type IV collagen in the serum, improve the activities of the antioxidant enzymes, and effectively reverse the abnormal levels of elements in liver fibrosis rats. Correlation network analysis revealed that HCW could treat liver fibrosis by ameliorating oxidative stress, repairing the impaired energy metabolisms and reversing the disturbed amino acids and nucleic acids metabolisms. CONCLUSION: This integrated metabolomics approach confirmed the validity of the traditional use of HCW in the treatment of liber fibrosis, providing new insights into the underlying mechanisms.
PMID: 30268654
BMC Plant Biol , IF:3.497 , 2019 Jan , V19 (1) : P11 doi: 10.1186/s12870-018-1589-6
Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis.
Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.; University of Chinese Academy of Sciences, Beijing, 10049, China.; Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.; Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. lnchen@sibs.ac.cn.; Key Laboratory of Plant Germplasm Enhancement and Specially Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. zhangxj@wbgcas.cn.
BACKGROUND: The flowering transition which is controlled by a complex and intricate gene regulatory network plays an important role in the reproduction for offspring of plants. It is a challenge to identify the critical transition state as well as the genes that control the transition of flower development. With the emergence of massively parallel sequencing, a great number of time-course transcriptome data greatly facilitate the exploration of the developmental phase transition in plants. Although some network-based bioinformatics analyses attempted to identify the genes that control the phase transition, they generally overlooked the dynamics of regulation and resulted in unreliable results. In addition, the results of these methods cannot be self-explained. RESULTS: In this work, to reveal a critical transition state and identify the transition-specific genes of flower development, we implemented a genome-wide dynamic network analysis on temporal gene expression data in Arabidopsis by dynamic network biomarker (DNB) method. In the analysis, DNB model which can exploit collective fluctuations and correlations of different metabolites at a network level was used to detect the imminent critical transition state or the tipping point. The genes that control the phase transition can be identified by the difference of weighted correlations between the genes interested and the other genes in the global network. To construct the gene regulatory network controlling the flowering transition, we applied NARROMI algorithm which can reduce the noisy, redundant and indirect regulations on the expression data of the transition-specific genes. In the results, the critical transition state detected during the formation of flowers corresponded to the development of flowering on the 7th to 9th day in Arabidopsis. Among of 233 genes identified to be highly fluctuated at the transition state, a high percentage of genes with maximum expression in pollen was detected, and 24 genes were validated to participate in stress reaction process, as well as other floral-related pathways. Composed of three major subnetworks, a gene regulatory network with 150 nodes and 225 edges was found to be highly correlated with flowering transition. The gene ontology (GO) annotation of pathway enrichment analysis revealed that the identified genes are enriched in the catalytic activity, metabolic process and cellular process. CONCLUSIONS: This study provides a novel insight to identify the real causality of the phase transition with genome-wide dynamic network analysis.
PMID: 30616516
BMC Plant Biol , IF:3.497 , 2019 Jan , V19 (1) : P6 doi: 10.1186/s12870-018-1591-z
Gene regulatory network and abundant genetic variation play critical roles in heading stage of polyploidy wheat.
National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China.; National Key Laboratory of Wheat and Maize Crop Science/Agronomy College, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, China. chf0088@163.com.
BACKGROUND: The extensive adaptability of polyploidy wheat is attributed to its complex genome, and accurately controlling heading stage is a prime target in wheat breeding process. Wheat heading stage is an essential growth and development processes since it starts at a crucial point in the transition from vegetative phase to reproductive phase. MAIN BODY: Heading stage is mainly decided by vernalization, photoperiod, hormone (like gibberellic acid, GA), and earliness per se (Eps). As a polyploidy species, common wheat possesses the abundant genetic variation, such as allelic variation, copy number variation etc., which have a strong effect on regulation of wheat growth and development. Therefore, understanding genetic manipulation of heading stage is pivotal for controlling the heading stage in wheat. In this review, we summarized the recent advances in the genetic regulatory mechanisms and abundant variation in genetic diversity controlling heading stage in wheat, as well as the interaction mechanism of different signals and the contribution of different genetic variation. We first summarized the genes involved in vernalization, photoperoid and other signals cross-talk with each other to control wheat heading stage, then the abundant genetic variation related to signal components associated with wheat heading stage was also elaborated in detail. CONCLUSION: Our knowledge of the regulatory network of wheat heading can be used to adjust the duration of the growth phase for the purpose of acclimatizing to different geographical environments.
PMID: 30606101
Planta , IF:3.39 , 2019 Jan , V249 (1) : P257-270 doi: 10.1007/s00425-018-2970-2
Transcriptomic changes triggered by carotenoid biosynthesis inhibitors and role of Citrus sinensis phosphate transporter 4;2 (CsPHT4;2) in enhancing carotenoid accumulation.
Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China.; Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, LE12 5RD, UK.; Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China. chjxu@zju.edu.cn.
MAIN CONCLUSION: Carotenoid accumulation and chromoplast development in orange were perturbed by carotenoid inhibitors, and candidate genes were identified via transcriptomic analysis. The role of CsPHT4;2 in enhancing carotenoid accumulation was revealed. Carotenoids are important plant pigments and their accumulation can be affected by biosynthesis inhibitors, but the genes involved were largely unknown. Here, application of norflurazon (NFZ), 2-(4-chlorophenylthio)-triethylamine hydrochloride (CPTA) and clomazone for 30 days to in vitro cultured sweet orange juice vesicles caused over-accumulation of phytoene (over 1000-fold), lycopene (2.92 mug g(-1) FW, none in control), and deficiency in total carotenoids (reduced to 22%), respectively. Increased carotenoids were associated with bigger chromoplasts with enlarged plastoglobules or a differently crystalline structure in NFZ, and CPTA-treated juice vesicles, respectively. Global transcriptomic changes following inhibitor treatments were profiled. Induced expression of 1-deoxy-D-xylulose 5-phosphate synthase 1 by CPTA, hydroxymethylbutenyl 4-diphosphate reductase by both NFZ and CPTA, and reduced expression of chromoplast-specific lycopene beta-cyclase by CPTA, as well as several downstream genes by at least one of the three inhibitors were observed. Expression of fibrillin 11 (CsFBN11) was induced following both NFZ and CPTA treatments. Using weighted correlation network analysis, a plastid-type phosphate transporter 4;2 (CsPHT4;2) was identified as closely correlated with high-lycopene accumulation induced by CPTA. Transient over-expression of CsPHT4;2 significantly enhanced carotenoid accumulation over tenfold in 'Cara Cara' sweet orange juice vesicle-derived callus. The study provides a valuable overview of the underlying mechanisms for altered carotenoid accumulation and chromoplast development following carotenoid inhibitor treatments and sheds light on the relationship between carotenoid accumulation and chromoplast development.
PMID: 30083809
Bull Math Biol , IF:1.812 , 2019 Jan , V81 (1) : P277-311 doi: 10.1007/s11538-018-0528-x
Deterministic and Stochastic Models of Arabidopsis thaliana Flowering.
Department of Mathematics and Information Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK.; School of Information Technology, Deakin University, Melbourne Burwood Campus, Burwood, VIC, 3125, Australia. maia.a@deakin.edu.au.
Experimental studies of the flowering of Arabidopsis thaliana have shown that a large complex gene regulatory network (GRN) is responsible for its regulation. This process has been mathematically modelled with deterministic differential equations by considering the interactions between gene activators and inhibitors (Valentim et al. in PLoS ONE 10(2):e0116973, 2015; van Mourik et al. in BMC Syst Biol 4(1):1, 2010). However, due to complexity of the model, the properties of the network and the roles of the individual genes cannot be deducted from the numerical solution the published work offers. Here, we propose simplifications of the model, based on decoupling of the original GRN to motifs, described with three and two differential equations. A stable solution of the original model is sought by linearisation of the original model which contributes to further investigation of the role of the individual genes to the flowering. Furthermore, we study the role of noise by introducing and investigating two types of stochastic elements into the model. The deterministic and stochastic nonlinear dynamic models of Arabidopsis flowering time are considered by following the deterministic delayed model introduced in Valentim et al. (2015). Steady-state regimes and stability of the deterministic original model are investigated analytically and numerically. By decoupling some concentrations, the system was reduced to emphasise the role played by the transcription factor Suppressor of Overexpression of Constants1 ([Formula: see text]) and the important floral meristem identity genes, Leafy ([Formula: see text]) and Apetala1 ([Formula: see text]). Two-dimensional motifs, based on the dynamics of [Formula: see text] and [Formula: see text], are obtained from the reduced network and parameter ranges ensuring flowering are determined. Their stability analysis shows that [Formula: see text] and [Formula: see text] are regulating each other for flowering, matching experimental findings. New sufficient conditions of mean square stability in the stochastic model are obtained using a stochastic Lyapunov approach. Our numerical simulations demonstrate that the reduced models of Arabidopsis flowering time, describing specific motifs of the GRN, can capture the essential behaviour of the full system and also introduce the conditions of flowering initiation. Additionally, they show that stochastic effects can change the behaviour of the stability region through a stability switch. This study thus contributes to a better understanding of the role of [Formula: see text] and [Formula: see text] in Arabidopsis flowering.
PMID: 30411251
Can J Microbiol , IF:1.793 , 2019 Jan , V65 (1) : P1-33 doi: 10.1139/cjm-2018-0377
Multidisciplinary approaches for studying rhizobium-legume symbioses.
a Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy.; b Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.; c Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA.
The rhizobium-legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
PMID: 30205015