Dev Cell , IF:10.092 , 2019 Mar , V48 (6) : P840-852.e5 doi: 10.1016/j.devcel.2019.02.022
Spatiotemporal Developmental Trajectories in the Arabidopsis Root Revealed Using High-Throughput Single-Cell RNA Sequencing.
Center for Plant Molecular Biology, University of Tubingen, Auf der Morgenstelle 32, Tubingen 72076, Germany.; Center for Bioinformatics, University of Tubingen, Sand 14, Tubingen 72076, Germany.; Center for Plant Molecular Biology, University of Tubingen, Auf der Morgenstelle 32, Tubingen 72076, Germany. Electronic address: marja.timmermans@zmbp.uni-tuebingen.de.
High-throughput single-cell RNA sequencing (scRNA-seq) is becoming a cornerstone of developmental research, providing unprecedented power in understanding dynamic processes. Here, we present a high-resolution scRNA-seq expression atlas of the Arabidopsis root composed of thousands of independently profiled cells. This atlas provides detailed spatiotemporal information, identifying defining expression features for all major cell types, including the scarce cells of the quiescent center. These reveal key developmental regulators and downstream genes that translate cell fate into distinctive cell shapes and functions. Developmental trajectories derived from pseudotime analysis depict a finely resolved cascade of cell progressions from the niche through differentiation that are supported by mirroring expression waves of highly interconnected transcription factors. This study demonstrates the power of applying scRNA-seq to plants and provides an unparalleled spatiotemporal perspective of root cell differentiation.
PMID: 30913408
Crit Rev Biotechnol , IF:8.108 , 2019 Mar , V39 (2) : P235-248 doi: 10.1080/07388551.2018.1530634
Current status and perspectives of 2-phenylethanol production through biological processes.
a State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering , Nanjing Tech University , Nanjing , China.; b Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing Tech University , Nanjing , China.; c Institute of Process Engineering in Life Sciences , Section II: Technical Biology, Karlsruhe Institute of Technology , Karlsruhe , Germany.
2-Phenylethanol (2-PE), an important flavor and fragrance compound with a rose-like smell has been widely used in the cosmetics, perfume, and food industries. Traditional production of 2-PE was mainly through the extraction from plant materials or by chemical synthesis. However, the increasing demand of consumers for natural flavors cannot be met by these methods. Biological production of 2-PE has emerged to be an appealing solution due to an environmental friendly process and the definition of a "natural" product. In this review, we have comprehensively summarized the current status and perspectives for biological 2-PE production in terms of its advantages over classical chemical synthesis and extraction from natural plants. A comprehensive description of 2-PE synthetic pathways and global regulation mechanisms, strategies to increase 2-PE production, and the utilization of agro-industrial wastes as feedstocks has been systematically discussed. Furthermore, the application of in situ product removal techniques have also been highlighted.
PMID: 30570367
Environ Int , IF:7.577 , 2019 Mar , V124 : P121-129 doi: 10.1016/j.envint.2018.12.039
The presence of in situ sulphamethoxazole degraders and their interactions with other microbes in activated sludge as revealed by DNA stable isotope probing and molecular ecological network analysis.
College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China.; Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; Joint Institute for Environmental Research and Education, South China Agricultural University, Guangzhou 510642, China. Electronic address: clluo@gig.ac.cn.; Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China.; College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.; School of Environment, Tsinghua University, Beijing 100084, China.; School of Marine Sciences, Guangxi University, Nanning 530004, China.
Wastewater treatment plants (WWTPs) are the main hotspots for the release of antibiotics, including the widely used sulphonamides. Microbes play important roles in eliminating sulphonamides in WWTPs, and knowledge about these degraders and their interactions within the microbial community is crucial for operating and optimising WWTPs. In the present study, stable isotope probing (SIP) coupled with high-throughput sequencing as culture-independent approach revealed four operational taxonomic units (OTUs) involved in sulphamethoxazole (SMX) degradation in activated sludge. Except for the OTU affiliated with Gammaproteobacteria, the others have not been previously reported to possess the ability to metabolise SMX. The isolated SMX degrader by culture-dependent method did not participate in SMX biodegradation in situ according to the SIP analysis, and showed weak correlations with other members in the activated sludge. The complex interactions between in situ active SMX degraders and non-degrading microbes might explain our failure to isolate these degraders. In addition, sul1 genes associated with SMX resistance were also labelled with (13)C, suggesting that they might benefit from SMX degradation and/or originate from the active SMX degraders. These findings broaden our understanding of the diversity of SMX-degrading microbes and their associated characteristics in WWTPs.
PMID: 30641255
Sci Total Environ , IF:6.551 , 2019 Mar , V658 : P723-731 doi: 10.1016/j.scitotenv.2018.12.144
Soil available phosphorus content drives the spatial distribution of archaeal communities along elevation in acidic terrace paddy soils.
Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China.; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.; Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China. Electronic address: jmxu@zju.edu.cn.
Archaea play crucial roles in geochemical cycles and influence the emission of greenhouse gases in acidic soils. However, little is known about the distribution pattern of total archaeal diversity and community composition with increasing elevation, especially in acidic agricultural ecosystems. Terraces, characterized by vertical climate changes and unique hydrological properties, are "natural experiments" to explore the spatial distribution of microorganisms along elevation in paddy soils. Here we investigated the diversity and structure of soil archaeal communities in nine increasingly elevated acidic paddy soils of the Yunhe terrace, China. Archaeal communities were dominated by Methanomicrobia of Euryarchaeota (38.5%), Group 1.1a-associated cluster (SAGSCG-1) of Thaumarchaeota (22.0%) and Subgroup-6 (previously described as crenarchaeotal group 1.3b) of Bathyarchaeota (17.8%). The archaeal phylotype richness decreased with increasing elevation. Both the species richness and phylogenetic diversity of the archaeal communities were significantly negatively correlated with soil available phosphorus (AP) content according to linear regression analyses. The archaeal communities differed greatly between soils of increasing elevation, and were roughly clustered into three groups, mostly in relation to AP contents. A variation partitioning analysis further confirmed that edaphic factors including the content of AP (17.1%), nitrate (7.83%), soil organic carbon (4.69%), dissolved organic carbon (4.22%) and soil pH (4.07%) shaped the archaeal community. The variation of soil properties were probably induced by elevation. The co-occurrence network indicated a modular structure of the archaeal community. Overall, our results emphasized that soil AP content was the best predictor of archaeal diversity and community structure, and the impacts of elevation on soil archaeal communities were not diminished by long-term rice cultivation, although minor compared with the effects of soil properties.
PMID: 30583167
Sci Total Environ , IF:6.551 , 2019 Mar , V656 : P625-633 doi: 10.1016/j.scitotenv.2018.11.359
Responses of paddy soil bacterial community assembly to different long-term fertilizations in southeast China.
College of Applied Meteorology, Nanjing University of Information Science and Technology, Nanjing 210044, PR China; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China; School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.; School of Civil Engineering and Geosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.; Soil and Fertilizer Institute of Hunan Province, Changsha 410125, PR China; Key Field Monitoring Experimental Station for Reddish Paddy Soil Eco-Environment in Wangcheng, Ministry of Agriculture of China, Changsha 410125, PR China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China. Electronic address: xglin@issas.ac.cn.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China. Electronic address: yzfeng@issas.ac.cn.
Recent works have shown that long-term fertilization has a critical influence on soil microbial communities; however, the underlying ecological assemblage of microbial community as well as its linkage with soil fertility and crop yield are still poorly understood. In this study, using analysis of high-throughput sequencing of 16S rRNA gene amplicons, we investigate mean pairwise phylogenetic distance (MPD), nearest relative index (NRI), taxonomic compositions and network topological properties to evaluate the assembly of the soil microbial community developed in 30-year fertilized soils. The phylogenetic signal indicates that environmental filtering was a more important assembly process that structure the microbial community than the stochastic process. Increase of soil fertility indexes, such as cation exchange capacity (CEC), soil organic matter (SOM) and available P (AP), driven by balanced fertilizations and straw returning amendment, result in the decrease of environmental filtering on the bacterial community assembly. Network parameters show that the amendment of straw returning provides with more niches, which lead to more complex phylotype co-occurrence. Increase of crop yield under balanced fertilizations might due to the increase of soil microbial function traits, which is associated with decreasing influence of environmental filtering. The significantly increased bacterial genera, Candidatus Koribacter, Candidatus Solibacter, and Fimbriimonas, in straw returning treatments, might be the key species in the competition caused by long-term environmental filtering. These results are helpful for a unified understanding of the ecological processes for microbial communities in different fertilized agroecosystem and the development of sustainable agriculture.
PMID: 30529966
Int J Mol Sci , IF:4.556 , 2019 Mar , V20 (7) doi: 10.3390/ijms20071587
Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum.
Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. szywangrui@126.com.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. szywangrui@126.com.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. sjxu@rcees.ac.cn.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. sjxu@rcees.ac.cn.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. yesiamcan@163.com.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. yesiamcan@163.com.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. sunhaishu0525@163.com.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. sunhaishu0525@163.com.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. fengshugeng@163.com.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. fengshugeng@163.com.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. zsining@hotmail.com.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. zsining@hotmail.com.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. gqzhuang@rcees.ac.cn.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. gqzhuang@rcees.ac.cn.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. zhbai@rcees.ac.cn.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. zhbai@rcees.ac.cn.; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. xlzhuang@rcees.ac.cn.; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China. xlzhuang@rcees.ac.cn.
Massively input and accumulated ammonium is one of the main causes of eutrophication in aquatic ecosystems, which severely deteriorates water quality. Previous studies showed that one of the commonly used macrophytes, Myriophyllum aquaticum, was capable of not only withstanding ammonium of high concentration, but also efficiently assimilating extracellular ammonium to constitutive amino acids and proteins. However, the genetic mechanism regulating such efficient nitrogen metabolism in M. aquaticum is still poorly understood. Therefore, RNA-based analysis was performed in this study to understand the ammonium regulatory mechanism in M. aquaticum in response to various concentrations of ammonium. A total of 7721 genes were differentially expressed, of which those related to nitrogen-transport, assimilation, and remobilization were highly-regulated in response to various concentrations of ammonium. We have also identified transcription factors and protein kinases that were rapidly induced in response to ammonium, which suggests their involvement in ammonium-mediated signalling. Meanwhile, secondary metabolism including phenolics and anthocyanins biosynthesis was also activated in response to various concentrations of ammonium, especially at high ammonium concentrations. These results proposed a complex physiological and genetic regulation network related to nitrogen, carbohydrate, transcription factors, and secondary metabolism for nitrogen use efficiency in M. aquaticum.
PMID: 30934901
iScience , IF:4.447 , 2019 Mar , V13 : P154-162 doi: 10.1016/j.isci.2019.02.017
The Hidden Control Architecture of Complex Brain Networks.
Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.; Laboratory for Systems Biology and Bio-inspired Engineering, Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. Electronic address: ckh@kaist.ac.kr.
The brain controls various cognitive functions in a robust and efficient way. What is the control architecture of brain networks that enables such robust and optimal control? Is this brain control architecture distinct from that of other complex networks? Here, we developed a framework to delineate a control architecture of a complex network that is compatible with the behavior of the network and applied the framework to structural brain networks and other complex networks. As a result, we revealed that the brain networks have a distributed and overlapping control architecture governed by a small number of control nodes, which may be responsible for the robust and efficient brain functions. Moreover, our artificial network evolution analysis showed that the distributed and overlapping control architecture of the brain network emerges when it evolves toward increasing both robustness and efficiency.
PMID: 30844695
Plant Cell Physiol , IF:4.062 , 2019 Mar , V60 (3) : P702-712 doi: 10.1093/pcp/pcy240
Cold Acclimation of the Thermoacidophilic Red Alga Galdieria sulphuraria: Changes in Gene Expression and Involvement of Horizontally Acquired Genes.
Institute of Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, Di inverted question mark(1/2)sseldorf, Germany.; Department of Plant Biology, Ecology & Evolution, Oklahoma State University, Stillwater, OK, USA.; Graduate School of Semiconductor and Chemical Engineering, Chonbuk National University, Jeonju, South Korea.; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbors up to 5% of genes that were most likely acquired through horizontal gene transfer. These genes probably contributed to G.sulphuraria's adaptation to its extreme habitats, resulting in today's polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42i inverted question mark(1/2)C/46i inverted question mark(1/2)C to 28i inverted question mark(1/2)C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon return to optimal growth temperature. Numerous genes acquired by horizontal gene transfer displayed temperature-dependent expression changes, indicating that these genes contributed to adaptive evolution in G.sulphuraria.
PMID: 30590832
Rice (N Y) , IF:3.912 , 2019 Mar , V12 (1) : P15 doi: 10.1186/s12284-019-0276-z
Infrastructures of systems biology that facilitate functional genomic study in rice.
Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.; Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea. khjung2010@khu.ac.kr.
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
PMID: 30874968
Int J Parasitol , IF:3.53 , 2019 Mar , V49 (3-4) : P277-286 doi: 10.1016/j.ijpara.2018.11.005
Identifying 'firebreaks' to fragment dispersal networks of a marine parasite.
School of BioSciences, University of Melbourne, 3010 Victoria, Australia; CSIRO, Castray Esplanade, Hobart 7004 TAS, Australia. Electronic address: francisca.samsingpedrals@csiro.au.; Institute of Marine Research, P.O. Box 1870 Nordnes, N-5817 Bergen, Norway.; School of BioSciences, University of Melbourne, 3010 Victoria, Australia; School of Life and Environmental Sciences, Deakin University, Victoria 3220, Australia.; School of BioSciences, University of Melbourne, 3010 Victoria, Australia.
Marine ecosystems are beset by disease outbreaks, and efficient strategies to control dispersal of pathogens are scarce. We tested whether introducing no-farming areas or 'firebreaks' could disconnect dispersal networks of a parasitic disease affecting the world's largest marine fish farming industry ( approximately 1000 farms). Larval salmon lice (Lepeophtheirus salmonis) are released from and transported among salmon farms by ocean currents, creating inter-farm networks of louse dispersal. We used a state-of-the-art biophysical model to predict louse movement along the Norwegian coastline and network analysis to identify firebreaks to dispersal. At least one firebreak that fragmented the network into two large unconnected groups of farms was identified for all seasons. During spring, when wild salmon migrate out into the ocean, and louse levels per fish at farms must be minimised, two effective firebreaks were created by removing 13 and 21 farms (1.3% and 2.2% of all farms in the system) at approximately 61 degrees N and 67 degrees N, respectively. We have demonstrated that dispersal models coupled with network analysis can identify no-farming zones that fragment dispersal networks. Reduced dispersal pathways should lower infection pressure at farms, slow the evolution of resistance to parasite control measures, and alleviate infection pressure on wild salmon populations.
PMID: 30660636
J Plant Res , IF:2.185 , 2019 Mar , V132 (2) : P197-209 doi: 10.1007/s10265-019-01095-w
Genome-wide analysis of MpBHLH12, a IIIf basic helix-loop-helix transcription factor of Marchantia polymorpha.
Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan.; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan. morohashi.1@rs.noda.tus.ac.jp.
The evolution of plants on land required adaptation to UV radiation and dry environments, and involved the appearance and/or rewiring of genetic connections, known as gene regulatory networks (GRNs), which consist of one or more transcription factors (TFs). The liverwort, Marchantia polymorpha, is a basal land plant, with a recently sequenced genome. The number of genes encoding basic helix-loop-helix (bHLH) family members is considerably higher in M. polymorpha than in charophyte green algae, suggesting the contribution of bHLH proteins to the evolution of GRNs associated with the adaptation of plants to land. Although an understanding of the evolutionary aspects of GRNs is fundamental for elucidating the mechanisms of environmental adaptation, the evolution of GRNs that led to land adaptation in plants remains poorly understood. In this study, we isolated a single gene encoding a IIIf bHLH TF from M. polymorpha, MpBHLH12. Transgenic M. polymorpha constitutively overexpressing MpBHLH12 showed smaller and fewer gemma cups than wild type, suggesting that MpBHLH12 is involved in the regulation of morphological development. Transcriptomic analysis of MpBHLH12 overexpressor (MpBHLH12ox) lines revealed an overlap with the GRN of MpMYB14, which regulates the biosynthesis of anthocyanins and phenolic compounds. However, MpBHLH12ox did not show anthocyanin accumulation. Results of the transient reporter assay suggest that MpBHLH12 could function in repression rather than activation. Our findings suggest that although the IIIf bHLH MpBHLH12 shows highest amino acid similarity with IIIf bHLH clade and is involved in developmental process and partly biosynthesis of phenolic compounds in M. polymorpha like Arabidopsis IIIf bHLH, the GRN involving MpBHLH12 would be distinct one from those of the IIIf bHLH TFs of seed plants.
PMID: 30840209
Plant Direct , IF:1.725 , 2019 Mar , V3 (3) : Pe00123 doi: 10.1002/pld3.123
Identification of gene expression logical invariants in Arabidopsis.
University of California San Diego San Diego California.
Numerous gene expression datasets from diverse tissue samples from the plant variety Arabidopsis thaliana have been already deposited in the public domain. There have been several attempts to do large scale meta-analyses of all of these datasets. Most of these analyses summarize pairwise gene expression relationships using correlation, or identify differentially expressed genes in two conditions. We propose here a new large scale meta-analysis of the publicly available Arabidopsis datasets to identify Boolean logical relationships between genes. Boolean logic is a branch of mathematics that deals with two possible values. In the context of gene expression datasets we use qualitative high and low expression values. A strong logical relationship between genes emerges if at least one of the quadrants is sparsely populated. We pointed out serious issues in the data normalization steps widely accepted and published recently in this context. We put together a web resource where gene expression relationships can be explored online which helps visualize the logical relationships between genes. We believe that this website will be useful in identifying important genes in different biological context. The web link is http://hegemon.ucsd.edu/plant/.
PMID: 31245766
Heliyon , 2019 Mar , V5 (3) : Pe01373 doi: 10.1016/j.heliyon.2019.e01373
In vivo antihyperglycemic, antihyperlipidemic, antioxidative stress and antioxidant potential activities of Syzygium paniculatum Gaertn. in Streptozotocin-induced diabetic rats.
Biochemistry Division, National Institute of Nutrition, Hyderabad 500007, India.; Department of Biochemistry, Sri Venkateswara University, Tirupati 517502, India.; Department of Biotechnology, Sri Krishnadevaraya University, Anantapur 515003, India.; Department of Microbiology, Trichy SRM Medical College Hospital and Research Centre, Tiruchirapalli 621 105, India.
Abnormal glucose metabolism causes various complications in many metabolic diseases such as obesity, hypertension, cardiovascular diseases and mainly diabetes. But commonly used oral hypoglycemic drugs cause severe side effects. Hence, there is a need to find the medicine without side effects. Compounds of medicinal plants were nontoxic, inexpensive and less or no side effects. Syzygium paniculatum Gaertn. (Magenta Cherry) is one of the important medicinal plants in the genus Syzygium. The fruit of S. paniculatum is sour apple-like flavor which tribes using for diabetes without scientific evidence. The purpose of study was to investigate the phytochemical analysis, antihyperglycemic, antihyperlipidemic, antioxidative stress and antioxidant activities of the daily oral administration of the fruit aqueous extract of S. paniculatum at a dose of 100 mg/kg bw over a period of 120 days in Streptozotocin-induced diabetic rats. The plant material collected, shade dried and the extracts prepared in increasing order of polarity and screened for different phytoconstituents by Harborne method. The extract with significant antihyperglycemic activity evaluated for antihyperlipidemic, antioxidative stress, antioxidant activity and also for insulin resistance by OGTT. The levels of insulin, HbA1c, lipid profile, glycogen, total proteins, liver and kidney functional markers were measured. The changes in antioxidant defense system were evaluated by TBARS assay. Histopathological examination of pancreas sections carried by hematoxylin and eosin stain. The findings confirm that S. paniculatum possesses potential antihyperglycemic, antihyperlipidemic, antioxidative stress and antioxidant activity. The histological changes also coincide with its potential on insulin secretion, glycemic control, lipid metabolisms, oxidative stress and antioxidant enzyme activities. This investigation confirms the traditional use of this plant in the folk medicine.
PMID: 30976672
Heliyon , 2019 Mar , V5 (3) : Pe01365 doi: 10.1016/j.heliyon.2019.e01365
Antioxidant and nephroprotection activities of Combretum micranthum: A phytochemical, in-vitro and ex-vivo studies.
Faculty of Sciences, University of Lome, Togo.; University of Agricultural Science and Veterinary Medicine, Manastur Street. 3-5, 400372, Cluj-Napoca, Romania.; Sree Siddaganga College of Pharmacy, B.H. Road, Tumkur 572 102, Karnataka, India.; Anthem Biosciences Pvt. Ltd., Industrial Area Phase I, Bommasandra, Hosur Road, Bangalore, 560099, India.
Management of chronic renal failure is exceedingly expensive. Despite of encouraging experimental outcomes, there is a lack of potent nephroprotective drugable molecules in a clinics or market. To develop a nephroprotective phytomedicine, the present study was designed to do a literature survey on reported phytochemical and biological analysis of Combretum micranthum and to carry out chemoprofiling, in-vitro antioxidant and ex-vivo nephroprotective capacity of the title plant. The phytochemical and biological activity survey of C. micranthum has reveals the presence of many bioactive compounds such as flavonoids, terpenoids, steroids and alkaloids with many biological activities. Phytochemical investigation re-confirmed the presence of these compounds. Hydroalcoholic extract of C. micranthum (CM extract) showed a strong antioxidant activity by scavenging AAPH, DPPH, nitric oxide, hydrogen peroxide and chelating metal ions. CM extract exhibited significant (P < 0.001) dose dependent inhibition of ferric chloride-ascorbic acid induced lipid peroxidation. Diabetic nephropathy is a serious and common complication leading to end stage renal disease. Therefore, in the present study, glucose-induced toxicity was also studied in human embryonic kidney cells (HEK-293) as an in vitro model for diabetic nephropathy. The results showed that exposure of cells to high glucose (100 mM) for 72 h significantly reduced the cell viability resulting in morphological changes such as cell shrinkage, rounded cell shape and cytoplasmic vacuolation. Treatment with CM extract at 10 and 25 mug/mL resulted in significant improvement in cell viability from 10 to 23% compared to the high glucose control. This study demonstrated the potential antioxidant and nephroprotective properties of C. micranthum, justifying its traditional use in the treatment of various diseases.
PMID: 30976670
Microbes Environ , 2019 Mar , V34 (1) : P23-32 doi: 10.1264/jsme2.ME18109
Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields.
Graduate School of Life Sciences, Tohoku University.; Central Region Agricultural Research Center, National Agriculture and Food Research Organization (NARO).; Kazusa DNA Research Institute.; Graduate School of Agriculture, Hokkaido University.; Faculty of Agriculture, Yamagata University.; Field Science Center, Graduate School of Agriculture, Tohoku University.; Western Region Agricultural Research Center, NARO.; Faculty of Bioresource Sciences, Akita Prefectural University.; Department of Innovation Research, Japan Science and Technology Agency.
Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.
PMID: 30584188