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https://www.readbyqxmd.com/read/28231512/the-impact-of-third-generation-genomic-technologies-on-plant-genome-assembly
#1
REVIEW
Wen-Biao Jiao, Korbinian Schneeberger
Since the introduction of next generation sequencing, plant genome assembly projects do not need to rely on dedicated research facilities or community-wide consortia anymore, even individual research groups can sequence and assemble the genomes they are interested in. However, such assemblies are typically not based on the entire breadth of genomic technologies including genetic and physical maps and their contiguities tend to be low compared to the full-length gold standard reference sequences. Recently emerging third generation genomic technologies like long-read sequencing or optical mapping promise to bridge this quality gap and enable simple and cost-effective solutions for chromosomal-level assemblies...
February 20, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28230182/suppression-of-fusarium-wilt-of-cucumber-by-ammonia-gas-fumigation-via-reduction-of-fusarium-population-in-the-field
#2
Jun Zhao, Zhong Mei, Xu Zhang, Chao Xue, Chenzhi Zhang, Tengfei Ma, Shusheng Zhang
Cucumber plants subjected to consecutive monoculture for 9 years were found to suffer from severe Fusarium wilt disease, caused by the soil-borne fungus Fusarium oxysporum f. sp. Cucumerinum J. H. Owen. In the present study, greenhouse experiments were performed to evaluate the influence of ammonia gas fumigation on Fusarium wilt suppression, fungal abundance and fungal community composition. Results showed that ammonia gas fumigation remarkably reduced disease incidence from 80% to 27%, resulting in a four-fold increase in yield, compared to the control...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28219787/a-novel-archaeal-species-belonging-to-methanoculleus-genus-identified-via-de-novo-assembly-and-metagenomic-binning-process-in-biogas-reactors
#3
Panagiotis G Kougias, Stefano Campanaro, Laura Treu, Xinyu Zhu, Irini Angelidaki
Recently, a first comprehensive catalogue of microbial genomes populating biogas reactors treating manure and agro-industrial residues was determined by sequencing samples collected from 22 biogas reactors including laboratory and full scale. Among the archaeal community, one of the most abundant methanogens belongs to Methanoculleus genus and for this reason it was provisionally named Methanoculleus sp. DTU006. Its full length 16S rRNA sequence is 97% similar to Methanoculleus marisnigri JR1 and to Methanoculleus palmolei DSM 4273...
February 17, 2017: Anaerobe
https://www.readbyqxmd.com/read/28217111/integration-of-metagenomic-and-stable-carbon-isotope-evidence-reveals-the-extent-and-mechanisms-of-carbon-dioxide-fixation-in-high-temperature-microbial-communities
#4
Ryan de Montmollin Jennings, James J Moran, Zackary J Jay, Jacob P Beam, Laura M Whitmore, Mark A Kozubal, Helen W Kreuzer, William P Inskeep
Although the biological fixation of CO2 by chemolithoautotrophs provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs as a carbon and energy source, the relative amounts of autotrophic C in chemotrophic microbial communities are not well-established. The extent and mechanisms of CO2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable (13)C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous "streamer" communities) were investigated...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28214038/maximising-synergy-among-tropical-plant-systematists-ecologists-and-evolutionary-biologists
#5
REVIEW
Timothy R Baker, R Toby Pennington, Kyle G Dexter, Paul V A Fine, Helen Fortune-Hopkins, Euridice N Honorio, Isau Huamantupa-Chuquimaco, Bente B Klitgård, Gwilym P Lewis, Haroldo C de Lima, Peter Ashton, Christopher Baraloto, Stuart Davies, Michael J Donoghue, Maria Kaye, W John Kress, Caroline E R Lehmann, Abel Monteagudo, Oliver L Phillips, Rodolfo Vasquez
Closer collaboration among ecologists, systematists, and evolutionary biologists working in tropical forests, centred on studies within long-term permanent plots, would be highly beneficial for their respective fields. With a key unifying theme of the importance of vouchered collection and precise identification of species, especially rare ones, we identify four priority areas where improving links between these communities could achieve significant progress in biodiversity and conservation science: (i) increasing the pace of species discovery; (ii) documenting species turnover across space and time; (iii) improving models of ecosystem change; and (iv) understanding the evolutionary assembly of communities and biomes...
February 14, 2017: Trends in Ecology & Evolution
https://www.readbyqxmd.com/read/28213498/dispersal-assembly-of-rain-forest-tree-communities-across-the-amazon-basin
#6
Kyle G Dexter, Mathew Lavin, Benjamin M Torke, Alex D Twyford, Thomas A Kursar, Phyllis D Coley, Camila Drake, Ruth Hollands, R Toby Pennington
We investigate patterns of historical assembly of tree communities across Amazonia using a newly developed phylogeny for the species-rich neotropical tree genus Inga We compare our results with those for three other ecologically important, diverse, and abundant Amazonian tree lineages, Swartzia, Protieae, and Guatteria Our analyses using phylogenetic diversity metrics demonstrate a clear lack of geographic phylogenetic structure, and show that local communities of Inga and regional communities of all four lineages are assembled by dispersal across Amazonia...
February 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28209362/relative-influence-of-sediment-variables-on-mangrove-community-assembly-in-leizhou-peninsula-china
#7
Jing Liu, Keming Ma, Laiye Qu
Effective conservation of mangroves requires a complete understanding of vegetation structure and identification of the variables most important to their assembly. Using canonical correspondence analysis (CCA) combined with variation partition, we determined the independent and joint effects of sediment variables, including physicochemical characteristics and heavy metals, on mangrove community assemblies in the overstory and understory in Leizhou Peninsula, China. The results indicated that the contributions of sediment physicochemical variables to community assembly were greater than were those of heavy metals, particularly in overstory vegetation...
February 13, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28208793/chitosan-recombinamer-layer-by-layer-coatings-for-multifunctional-implants
#8
Jeevan Prasaad Govindharajulu, Xi Chen, Yuping Li, Jose Carlos Rodriguez-Cabello, Mrinal Battacharya, Conrado Aparicio
The main clinical problems for dental implants are (1) formation of biofilm around the implant-a condition known as peri-implantitis and (2) inadequate bone formation around the implant-lack of osseointegration. Therefore, developing an implant to overcome these problems is of significant interest to the dental community. Chitosan has been reported to have good biocompatibility and anti-bacterial activity. An osseo-inductive recombinant elastin-like biopolymer (P-HAP), that contains a peptide derived from the protein statherin, has been reported to induce biomineralization and osteoblast differentiation...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207957/phylogenetic-relatedness-explains-highly-interconnected-and-nested-symbiotic-networks-of-woody-plants-and-arbuscular-mycorrhizal-fungi-in-a-chinese-subtropical-forest
#9
Liang Chen, Yong Zheng, Cheng Gao, Xiang-Cheng Mi, Ke-Ping Ma, Tesfaye Wubet, Liang-Dong Guo
Elucidating symbiotic relationships between arbuscular mycorrhizal fungi (AMF) and plants contributes to a better understanding of their reciprocally dependent co-existence and community assembly. However, the main drivers of plant and AMF community assembly remain unclear. In this study, we examined AMF communities from 166 root samples of 17 woody plant species from 10 quadrats in a Chinese subtropical forest using 454 pyrosequencing of 18S rRNA gene to describe symbiotic AMF-plant association. Our results show the woody plant-AMF networks to be highly interconnected and nested, but in anti-modular and anti-specialized manners...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28207255/supramolecular-complexation-of-carbon-nanostructures-by-crown-ethers
#10
Luis Moreira, Beatriz M Illescas, Nazario Martín
Since its discovery, crown ethers as well as the most recent carbon nanostructures, namely fullerenes, carbon nanotubes and graphene, have received a lot of attention from the chemical community. As a proof, these innovative chemical structures have gathered three Nobel Prizes in 1987, 1996 and 2010 corresponding to crown ethers, fullerenes and graphene, respectively. Merging these singular chemical structures has provided a wealth number of unprecedented supramolecular assemblies with new geometrical and electronic properties whose more representative examples have been presented in this synopsis organized according to the different nature of the carbon nanostructures...
February 16, 2017: Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28205371/integrating-gut-microbiota-immaturity-and-disease-discriminatory-taxa-to-diagnose-the-initiation-and-severity-of-shrimp-disease
#11
Jinbo Xiong, Jinyong Zhu, Wenfang Dai, Chunming Dong, Qiongfen Qiu, Chenghua Li
Increasing evidence has emerged a tight link among the gut microbiota, host age and health status. This osculating interplay impedes the definition of gut microbiome features associated with host health from that in developmental stages. Consequently, gut microbiota-based prediction of health status is promising yet not well established. Here we firstly tracked shrimp gut microbiota (N = 118) over an entire cycle of culture; shrimp either stayed healthy, or progressively transitioned into severe disease. The results showed that the gut microbiota were significantly distinct over shrimp developmental stages, and disease progression...
February 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28195390/self-assembly%C3%A2-of%C3%A2-renewable%C3%A2-nano-sized-triterpenoids
#12
REVIEW
Braja Gopal Bag, Rakhi Majumdar
Studies on plant metabolites have gained renewed interest in recent years because these can serve as renewable chemicals for the development of a sustainable society.Among various plant secondary metabolites, terpenoids constitute the major component and triterpenoids are the 30C subset of it.In recent years, triterpenoids have drawn the attention of scientific community due to many of its potential and realized applications in medicine, drug delivery, thermochromic materials, pollutant capture, catalysis, liquid crystals, etc...
February 14, 2017: Chemical Record: An Official Publication of the Chemical Society of Japan ... [et Al.]
https://www.readbyqxmd.com/read/28191629/functional-and-phylogenetic-structure-of-island-bird-communities
#13
Xingfeng Si, Marc W Cadotte, Di Zeng, Andrés Baselga, Yuhao Zhao, Jiaqi Li, Yiru Wu, Siyu Wang, Ping Ding
1. Biodiversity change in anthropogenically transformed habitats is often nonrandom, yet the nature and importance of the different mechanisms shaping community structure are unclear. Here, we extend the classic Theory of Island Biogeography (TIB) to account for nonrandom processes by incorporating species traits and phylogenetic relationships into a study of faunal relaxation following habitat loss and fragmentation. 2. Two possible mechanisms can create nonrandom community patterns on fragment islands. First, small and isolated islands might consist of similar or closely related species because they are environmentally homogeneous or select for certain shared traits, such as dispersal ability...
February 13, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28191504/distinct-biogeographic-patterns-for-archaea-bacteria-and-fungi-along-the-vegetation-gradient-at-the-continental-scale-in-eastern-china
#14
Bin Ma, Zhongmin Dai, Haizhen Wang, Melissa Dsouza, Xingmei Liu, Yan He, Jianjun Wu, Jorge L M Rodrigues, Jack A Gilbert, Philip C Brookes, Jianming Xu
The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China...
January 2017: MSystems
https://www.readbyqxmd.com/read/28191038/physiological-and-molecular-characterizations-of-the-interactions-in-two-cellulose-to-methane-cocultures
#15
Hongyuan Lu, Siu-Kin Ng, Yangyang Jia, Mingwei Cai, Patrick K H Lee
BACKGROUND: The interspecies interactions in a biomethanation community play a vital role in substrate degradation and methane (CH4) formation. However, the physiological and molecular mechanisms of interaction among the microbial members of this community remain poorly understood due to the lack of an experimentally tractable model system. In this study, we successfully established two coculture models combining the cellulose-degrading bacterium Clostridium cellulovorans 743B with Methanosarcina barkeri Fusaro or Methanosarcina mazei Gö1 for the direct conversion of cellulose to CH4...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28183172/dynamic-changes-of-yak-bos-grunniens-gut-microbiota-during-growth-revealed-by-pcr-dgge-and-metagenomics
#16
Yuanyang Nie, Zhiwei Zhou, Jiuqiang Guan, Baixue Xia, Xiaolin Luo, Yang Yang, Yu Fu, Qun Sun
Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Method: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon content of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analize the DGGE fingerprint...
January 26, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28181524/lack-of-phylogenetic-signals-within-environmental-niches-of-tropical-tree-species-across-life-stages
#17
Caicai Zhang, Jie Yang, Liqing Sha, Xiuqin Ci, Jie Li, Min Cao, Calum Brown, Nathan G Swenson, Luxiang Lin
The lasting imprint of phylogenetic history on current day ecological patterns has long intrigued biologists. Over the past decade ecologists have increasingly sought to quantify phylogenetic signals in environmental niche preferences and, especially, traits to help uncover the mechanisms driving plant community assembly. However, relatively little is known about how phylogenetic patterns in environmental niches and traits compare, leaving significant uncertainty about the ecological implications of trait-based analyses...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28174556/plants-assemble-species-specific-bacterial-communities-from-common-core-taxa-in-three-arcto-alpine-climate-zones
#18
Manoj Kumar, Günter Brader, Angela Sessitsch, Anita Mäki, Jan D van Elsas, Riitta Nissinen
Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28166176/applying-instructional-design-strategies-and-behavior-theory-to-household-disaster-preparedness-training
#19
Tracy N Thomas, Robyn K Sobelson, Corinne J Wigington, Alyson L Davis, Victoria H Harp, Michelle Leander-Griffith, Joan P Cioffi
CONTEXT: Interventions and media campaigns promoting household disaster preparedness have produced mixed results in affecting behaviors. In large part, this is due to the limited application of instructional design strategies and behavior theory, such as the Transtheoretical Model (TTM). This study describes the development and evaluation of Ready CDC, an intervention designed to increase household disaster preparedness among the Centers for Disease Control and Prevention (CDC) workforce...
February 3, 2017: Journal of Public Health Management and Practice: JPHMP
https://www.readbyqxmd.com/read/28158947/ambiguous-bodies-uncertain-diseases-knowledge-of-cervical-cancer-in-papua-new-guinea
#20
A Kelly-Hanku, S Ase, V Fiya, P Toliman, H Aeno, G M Mola, J M Kaldor, L M Vallely, A J Vallely
OBJECTIVES: Within their local realities, people experience and interpret disease in diverse ways that do not necessarily correlate or converge with Western biomedical interventions. In the high cervical cancer burden setting of Papua New Guinea, understanding how people experience and interpret cervical cancer is necessary for effective intervention. Drawing on work by Street on the production of unstable biomedical knowledge, we explored how ambiguity and uncertainty, coupled with cultural taboos and linguistic limitations, affect what and how people 'know' about women's reproductive organs and their associated disease...
February 3, 2017: Ethnicity & Health
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