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Plant Taxonomy

Mikhail A Moldovan, Svetlana A Petrova, Mikhail S Gelfand
Riboswitches are conserved RNA structures located in non-coding regions of mRNA and able to bind small molecules (e.g. metabolites) changing conformation upon binding. This feature enables them to function as regulators of gene expression. The thiamin pyrophosphate (TPP) riboswitch is the only type of riboswitches found not only in bacteria, but also in eukaryotes - in plants, green algae, protists, and fungi. Two main mechanisms of fungal TPP riboswitch action, involving alternative splicing, have been established so far...
March 13, 2018: Fungal Genetics and Biology: FG & B
Jinbo Chen, Uwe Scholz, Ruonan Zhou, Matthias Lange
In order to access and filter content of life-science databases, full text search is a widely applied query interface. But its high flexibility and intuitiveness is paid for with potentially imprecise and incomplete query results. To reduce this drawback, query assistance systems suggest those combinations of keywords with the highest potential to match most of the relevant data records. Widespread approaches are syntactic query corrections that avoid misspelling and support expansion of words by suffixes and prefixes...
March 12, 2018: PLoS Computational Biology
Shi-Jun Liu, Zhi-Shu Tang, Zhi-Xin Liao, Chun-Li Cui, Hong-Bo Liu, Yan-Ni Liang, Yu Zhang, Hong-Bo Xu, Dong-Bo Zhang, Ya-Ting Zheng, Huan-Xian Shi, Shi-Ying Li
ETHNOPHARMACOLOGICAL RELEVANCE: Ligularia przewalskii (Maxim.) Diels (LP) (called zhangyetuowu in Chinese), is generally found in moist forest areas in the western regions of China. The root, leaves and flower of LP are utilized as a common traditional medicine in China. It has been utilized conventionally in herbal remedies for the remedy of haemoptysis, asthma, pulmonary phthisis, jaundice hepatitis, food poisoning, bronchitis, cough, fever, wound healing, measles, carbuncle, swelling and phlegm diseases...
March 8, 2018: Journal of Ethnopharmacology
Jonathan W Leff, Richard D Bardgett, Anna Wilkinson, Benjamin G Jackson, William J Pritchard, Jonathan R De Long, Simon Oakley, Kelly E Mason, Nicholas J Ostle, David Johnson, Elizabeth M Baggs, Noah Fierer
There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa)...
March 9, 2018: ISME Journal
Vera Thiel, Marcus Tank, Donald A Bryant
Because of recent advances in omics methodologies, knowledge of chlorophototrophy (i.e., chlorophyll-based phototrophy) in bacteria has rapidly increased. Chlorophototrophs currently are known to occur in seven bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, Acidobacteria, and Gemmatimonadetes. Other organisms that can produce chlorophylls and photochemical reaction centers may still be undiscovered. Here we summarize the current status of the taxonomy and phylogeny of chlorophototrophic bacteria as revealed by genomic methods...
March 5, 2018: Annual Review of Plant Biology
Shi-Man Gao, Jiu-Shi Liu, Min Wang, Ting-Ting Cao, Yao-Dong Qi, Ben-Gang Zhang, Xiao-Bo Sun, Hai-Tao Liu, Pei-Gen Xiao
ETHNOPHARMACOLOGICAL RELEVANCE: Species of the genus Codonopsis are perennial herbs mainly distributed throughout East, Southeast and Central Asia. As recorded, they have been used as traditional Chinese medicines since the Qing Dynasty, where they were claimed for strengthening the spleen and tonifying the lung, as well as nourishing blood and engendering liquid. Some species are also used as food materials in southern China and Southeast Asia, such as tea, wine, soup, plaster, and porridge...
February 28, 2018: Journal of Ethnopharmacology
Han Ming Gan, Michael A Savka
This chapter presents a historical overview of the development and changes in scientific approaches to classifying members of the Agrobacterium genus. We also describe the changes in the inference of evolutionary relationships among Agrobacterium biovars and Agrobacterium strains from using the 16S rRNA marker to recA genes and to the use of multilocus sequence analysis (MLSA). Further, the impacts of the genomic era enabling low cost and rapid whole genome sequencing on Agrobacterium phylogeny are reviewed with a focus on the use of new and sophisticated bioinformatics approaches to refine phylogenetic inferences...
March 3, 2018: Current Topics in Microbiology and Immunology
Marike Palmer, Emma T Steenkamp, Martin P A Coetzee, Juanita R Avontuur, Wai-Yin Chan, Elritha van Zyl, Jochen Blom, Stephanus N Venter
The Erwiniaceae contain many species of agricultural and clinical importance. Although relationships among most of the genera in this family are relatively well resolved, the phylogenetic placement of several taxa remains ambiguous. In this study, we aimed to address these uncertainties by using a combination of phylogenetic and genomic approaches. Our multilocus sequence analysis and genome-based maximum-likelihood phylogenies revealed that the arsenate-reducing strain IMH and plant-associated strain ATCC 700886, both previously presumptively identified as members of Pantoea, represent novel species of Erwinia...
February 27, 2018: International Journal of Systematic and Evolutionary Microbiology
Daniel Mason, Honor Hsin
Psychiatric classification remains a complex endeavour; since the Enlightenment, nosologists have made use of various models and metaphors to describe their systems. Here we present the most common model, botanical taxonomy, and trace its history from the nosologies of Sydenham, Sauvages and Linnaeus; to evolutionary models; to the later contributions of Hughlings-Jackson, Kraepelin and Jaspers. Over time, there has been a shift from explicit attempts to pattern disease classification on botanical systems, to a more metaphorical use...
February 1, 2018: History of Psychiatry
Catherine Reeb, Jaap Kaandorp, Fredrik Jansson, Nicolas Puillandre, Jean-Yves Dubuisson, Raphaël Cornette, Florian Jabbour, Yoan Coudert, Jairo Patiño, Jean-François Flot, Alain Vanderpoorten
Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles...
February 22, 2018: New Phytologist
Peter J Walker, Kim R Blasdell, Charles H Calisher, Ralf G Dietzgen, Hideki Kondo, Gael Kurath, Ben Longdon, David M Stone, Robert B Tesh, Noël Tordo, Nikos Vasilakis, Anna E Whitfield, Ictv Report Consortium
The family Rhabdoviridae comprises viruses with negative-sense (-) single-stranded RNA genomes of 10.8-16.1 kb. Virions are typically enveloped with bullet-shaped or bacilliform morphology but can also be non-enveloped filaments. Rhabdoviruses infect plants and animals including mammals, birds, reptiles and fish, as well as arthropods which serve as single hosts or act as biological vectors for transmission to animals or plants. Rhabdoviruses include important pathogens of humans, livestock, fish and agricultural crops...
February 19, 2018: Journal of General Virology
Kenji Suetsugu, Chie Shimaoka, Hirokazu Fukunaga, Shinichiro Sawa
To elucidate the taxonomy of the Lecanorchis nigricans Honda, 1931 species complex, the present study investigated the detailed morphology of three L. nigricans varieties in Japan. While L. nigricans var. patipetala Y.Sawa, 1980 and L. nigricans var. yakusimensis T.Hashim., 1990 have often been treated as synonyms of L. nigricans var. nigricans, the present study demonstrates that the three varieties are morphologically distinct. More specifically, L. nigricans var. nigricans only produces complete cleistogamous flowers and is distinct from the plants currently called "L...
2018: PhytoKeys
Dong-Hui Yan, Qian Gao, Xiaoming Sun, Xiaoyu Song, Hongchang Li
For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s...
February 3, 2018: Genetica
Jae Sung Lee, Hyeon-Dong Shin, Hyang Burm Lee, Young-Joon Choi
The genus Peronospora, an obligate biotrophic group belonging to Oomycota, causes serious damage to a variety of wild and ornamental plants, as well as cultivated crops, such as beet, rose, spinach, and tobacco. To investigate the diversity of Peronospora species parasitic to Stellaria and Pseudostellaria (Caryophyllaceae) plants in Korea, we performed a morphological analysis on dried herbarium specimens and molecular phylogenetic inferences based on internal transcribed spacer rDNA and cox2 mitochondrial DNA sequences...
December 2017: Mycobiology
Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
Qingping Liu, Jiahao Wang, Yan Zhu, Yongqun He
BACKGROUND: Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive information source for these drugs is still missing, and their anti-rheumatism mechanisms remain unclear. An ontology for anti-rheumatism traditional Chinese drugs would strongly support the representation, analysis, and understanding of these drugs...
December 21, 2017: BMC Systems Biology
An-Dong Li, Jacob W Metch, Yulin Wang, Emily Garner, An Ni Zhang, Maria V Riquelme, Peter J Vikesland, Amy Pruden, Tong Zhang
With the growing application of high-throughput sequencing-based metagenomics for profiling antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), comparison of sample pretreatment and DNA extraction methods are needed to move towards standardized comparisons among laboratories. Three widely employed DNA extraction methods (FastDNA® Spin Kit for Soil, PowerSoil® DNA Isolation Kit, and ZR Fecal DNA MiniPrep™), with and without preservation in 50% ethanol and freezing, were applied to the influent, activated sludge and effluent of two WWTPs, in Hong Kong and in the USA...
December 27, 2017: FEMS Microbiology Ecology
Ramona Marasco, Eleonora Rolli, Marco Fusi, Grégoire Michoud, Daniele Daffonchio
BACKGROUND: The plant compartments of Vitis vinifera, including the rhizosphere, rhizoplane, root endosphere, phyllosphere and carposphere, provide unique niches that drive specific bacterial microbiome associations. The majority of phyllosphere endophytes originate from the soil and migrate up to the aerial compartments through the root endosphere. Thus, the soil and root endosphere partially define the aerial endosphere in the leaves and berries, contributing to the terroir of the fruit...
January 3, 2018: Microbiome
Saule Abugalieva, Lyubov Volkova, Yuliya Genievskaya, Anna Ivaschenko, Yuri Kotukhov, Gulzhahan Sakauova, Yerlan Turuspekov
BACKGROUND: As part of nation-wide project to infer the genetic variation of the native flora in Kazakhstan, a study was attempted to assess phylogenetic relationships of endemic and rare Allium species. In total, 20 Allium species were collected in field trips in five different regions of Kazakhstan during 2015-2016. Most species (9) were collected in the southern part of the country along of Karatau mountains, followed by Altai mountains (5) in eastern Kazakhstan. The ITS and matK DNA regions were applied in order to assess the taxonomic relationships among species...
December 28, 2017: BMC Plant Biology
Jian-Yu Jiao, Nimaichand Salam, Lan Liu, Manik Prabhu Narsing Rao, Xiao-Tong Zhang, Bao-Zhu Fang, Ming-Xian Han, Zi-Tong Zhang, Jing Chen, Jiao Zhao, Yu Zhou, Dalal Hussien M Alkhalifah, Qing Liu, Min Xiao, Hans-Peter Klenk, Wen-Jun Li
A draft genome sequence of Jiangella alba YIM 61503T revealed a genome size of 7,664,864 bp arranged in 33 scaffolds. The genome was predicted to contain 7196 predicted genes, including 51 coding for RNA. Phylogenetic and comparative analyses of the draft genome of J. alba YIM 61503T with the available genomes of other Jiangella species suggested a proximal similarity between strains J. alba YIM 61503T and J. muralis DSM 45357T, while indicating a high divergence between J. gansuensis YIM 002T and other Jiangella species...
December 29, 2017: Antonie Van Leeuwenhoek
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