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https://www.readbyqxmd.com/read/28444606/species-evolution-and-quality-evaluation-of-four-coptis-herbal-medicinal-materials-in-southwest-china
#1
Hanting Chen, Gang Fan, Yang He
Coptis herbs, which are important herbal medicinal materials, are the dried rhizomes of various plants. In China's herbal market, drying herbs can severely influence morphological markers such as shape, color, and odor, which make consumers difficult to precisely identify the herbs and effectively evaluate the quality. Here, we present the phylogenetic analysis of four Coptis herbal medicinal materials based on internal transcribed spacer sequences. C. chinensis, C. omeiensis, C. deltoidea and C. teeta constituted a monophyletic group...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28441395/molecular-phylogeny-of-oncaeidae-copepoda-using-nuclear-ribosomal-internal-transcribed-spacer-its-rdna
#2
Iole Di Capua, Fulvio Maffucci, Raimondo Pannone, Maria Grazia Mazzocchi, Elio Biffali, Alberto Amato
Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI)...
2017: PloS One
https://www.readbyqxmd.com/read/28439758/molecular-phylogeny-of-21-tropical-bamboo-species-reconstructed-by-integrating-non-coding-internal-transcribed-spacer-its1-and-2-sequences-and-their-consensus-secondary-structure
#3
Jayadri Sekhar Ghosh, Samik Bhattacharya, Amita Pal
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses...
April 24, 2017: Genetica
https://www.readbyqxmd.com/read/28438522/detection-of-leishmania-infantum-dna-in-conjunctival-swabs-of-cats-by-quantitative-real-time-pcr
#4
Julia Cristina Benassi, Graziella U Benvenga, Helena Lage Ferreira, Vanessa F Pereira, Lara B Keid, Rodrigo Soares, Tricia Maria Ferreira de Sousa Oliveira
Although some studies have investigated the potential role of cats as a reservoir for Leishmania, their role in the epidemiology of visceral leishmaniasis (VL) is still poorly understood. Molecular diagnostic techniques are an important tool in VL diagnosis, and PCR shows high sensitivity and specificity for Leishmania spp. detection. Quantitative real-time PCR (qPCR) is a method that permits quantitative analysis of a large number of samples, resulting in more sensitive, accurate, and reproducible measurements of specific DNA present in the sample...
April 21, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28438013/characterization-of-newly-bred-cordyceps-militaris-strains-for-higher-production-of-cordycepin-through-hplc-and-urp-pcr-analysis
#5
Hyun-Hee Lee, Naru Kang, Inmyoung Park, Jungwook Park, Inyoung Kim, Jieun Kim, Namgyu Kim, Jae-Yun Lee, Young-Su Seo
Cordyceps militaris, a member of Ascomycota, a mushroom referred to as caterpillar Dong-chung-ha-cho, is commercially valuable because of its high content of bioactive substances including cordycepin and its potential for artificial cultivation. Cordycepin (3'-deoxyadenosine) is highly associated with the pharmacological effects of C. militaris. C. militaris is heterothallic in that two mating type loci, idiomorph MAT1-1 and MAT1-2, exist discretely in two different spores. In this study, nine C. militaris strains were mated with each other to prepare new strains that produced a larger amount of cordycepin than the parent strains...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28436324/identification-of-a-new-fungal-pathogen-causing-white-villous-disease-on-the-fruiting-body-of-the-culinary-medicinal-mushroom-auricularia-auricula-judae-agaricomycetes-in-china
#6
Jie-Chi Zhang, Xiang-Hui Kong, Pi-Qi Zhang, Jia-Ning Liu, Yin-Peng Ma, Xiao-Dong Dai, Zeng-Hua Han, Qing-Fang Ma, Xiao-Yong Wang, Li-Ping Yu
Auricularia auricula-judae is an edible and medicinal fungus ranking fourth in production among the edible fungi cultivated worldwide. White villous disease is rampant in Northeast China; it infects the fruiting bodies of A. auricula-judae by forming a white mycelial layer on its ventral side. The disease not only causes an unacceptable morphological appearance and a poor-quality product, but it also significantly reduces the yield. In this study, based on fungal morphology, ribosomal DNA internal transcribed spacer sequences, identification of species-specific primers, and the pathogenicity of the mycelia and spores, 2 fungal pathogens were isolated and identified as Fusarium equiseti and F...
2017: International Journal of Medicinal Mushrooms
https://www.readbyqxmd.com/read/28435353/identification-and-characterization-of-pseudocercospora-pyricola-causing-leaf-spots-on-aronia-melanocarpa
#7
Sung-Hee Park, In-Young Choi, Kyoung-Won Seo, Jin-Ho Kim, Victor Galea, Hyeon-Dong Shin
Leaf spot disease on black chokeberry (Aronia melanocarpa) was observed at several locations in Korea during 2014-2015. Leaf spots were distinct, scattered over the leaf surface and along the leaf border, subcircular to irregular and brown surrounded by a distinct dark color, and were expanded and coalesced into irregularly shaped lesions. Severely infected leaves became dry and fell off eventually. The causative agent was identified as Pseudocercospora pyricola. Morphological observations and phylogenetic analyses of multiple genes, including internal transcribed spacer, translation elongation factor 1-alpha, actin, and the large subunit ribosomal DNA were conducted...
March 2017: Mycobiology
https://www.readbyqxmd.com/read/28435348/three-new-recorded-species-of-the-physalacriaceae-on-ulleung-island-korea
#8
Ki Hyeong Park, Changmu Kim, Minkyeong Kim, Nam Kyu Kim, Jae Young Park, John A Eimes, Hae Jin Cho, Sang-Kuk Han, Young Woon Lim
Most known species in the Physalacriaceae are saprotrophs that grow on decaying leaves and wood, and approximately 21 genera in the Physalacriaceae have been reported worldwide. During an ongoing survey of indigenous fungi in Korea, four specimens belonging to the Physalacriaceae were collected on Ulleung Island. These specimens were identified as three species based on morphological characteristics and molecular analysis of rDNA-internal transcribed spacer sequences. Three species in three genera were shown to be new records in Korea: Hymenopellis orientalis, Paraxerula hongoi, and Ponticulomyces orientalis...
March 2017: Mycobiology
https://www.readbyqxmd.com/read/28429818/piscirickettsia-salmonis-infection-in-cultured-lumpfish-cyclopterus-lumpus-l
#9
M Marcos-López, N M Ruane, F Scholz, M Bolton-Warberg, S O Mitchell, S Murphy O'Sullivan, A Irwin Moore, H D Rodger
A Piscirickettsia salmonis infection was diagnosed in lumpfish (Cyclopterus lumpus L.) juveniles held in a marine research facility on the west coast of Ireland. The main clinical signs and pathology included marked ascites, severe multifocal liver necrosis and severe diffuse inflammation and necrosis of the exocrine pancreas and peri-pancreatic adipose tissue. Numerous Piscirickettsia-like organisms were observed by histopathology in the affected organs, and the bacterial species was characterized by molecular analysis...
April 21, 2017: Journal of Fish Diseases
https://www.readbyqxmd.com/read/28427478/morphological-and-molecular-characteristics-of-malayfilaria-sofiani-uni-mat-udin-takaoka-n-g-n-sp-nematoda-filarioidea-from-the-common-treeshrew-tupaia-glis-diard-duvaucel-mammalia-scandentia-in-peninsular-malaysia
#10
Shigehiko Uni, Ahmad Syihan Mat Udin, Takeshi Agatsuma, Weerachai Saijuntha, Kerstin Junker, Rosli Ramli, Hasmahzaiti Omar, Yvonne Ai-Lian Lim, Sinnadurai Sivanandam, Emilie Lefoulon, Coralie Martin, Daicus Martin Belabut, Saharul Kasim, Muhammad Rasul Abdullah Halim, Nur Afiqah Zainuri, Subha Bhassu, Masako Fukuda, Makoto Matsubayashi, Masashi Harada, Van Lun Low, Chee Dhang Chen, Narifumi Suganuma, Rosli Hashim, Hiroyuki Takaoka, Mohd Sofian Azirun
BACKGROUND: The filarial nematodes Wuchereria bancrofti (Cobbold, 1877), Brugia malayi (Brug, 1927) and B. timori Partono, Purnomo, Dennis, Atmosoedjono, Oemijati & Cross, 1977 cause lymphatic diseases in humans in the tropics, while B. pahangi (Buckley & Edeson, 1956) infects carnivores and causes zoonotic diseases in humans in Malaysia. Wuchereria bancrofti, W. kalimantani Palmieri, Pulnomo, Dennis & Marwoto, 1980 and six out of ten Brugia spp. have been described from Australia, Southeast Asia, Sri Lanka and India...
April 20, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28426418/first-report-on-molecular-evidence-of-tylodelphys-cerebralis-diplostomulum-cerebralis-chakrabarti-1968-digenea-diplostomidae-from-snakehead-fish-channa-punctata
#11
Anshu Chaudhary, Richa Tripathi, Shivi Gupta, Hridaya Shanker Singh
Freshwater snakehead fish, Channa punctata (Perciformes: Channidae) from Meerut (U.P.), India were screened for infection with metacercaria from the eye (vitreous humor) and brain (cranial cavity) and were analyzed by molecular methods using PCR and sequencing of the complete internal transcribed spacers (ITS1-5.8S-ITS2) of the ribosomal RNA gene. Recovered metacercariae from sites, vitreous humor and cranial cavity were previously diagnosed as Diplostomulum cerebralis Chakrabarti, 1968 on the basis of morphological characteristics...
June 1, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/28424048/phylogeny-divergence-time-and-historical-biogeography-of-laetiporus-basidiomycota-polyporales
#12
Jie Song, Bao-Kai Cui
BACKGROUND: The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU)...
April 20, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28422071/comparative-analysis-of-the-complete-chloroplast-genome-of-four-endangered-herbals-of-notopterygium
#13
Jiao Yang, Ming Yue, Chuan Niu, Xiong-Feng Ma, Zhong-Hu Li
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28418812/phellinopsis-lonicericola-and-p-tibetica-spp-nov-hymenochaetales-basidiomycota-from-tibet-with-a-key-to-worldwide-species
#14
Li-Wei Zhou, Jie Song
Phellinopsis (Hymenochaetaceae) was recently segregated from Phellinus. Phellinopsis differs from other genera segregated from Phellinus in a combination of hymenial setae, if present, mostly originating from tramal hyphae and hyaline basidiospores becoming pale yellowish with age. In this study, two new species of Phellinopsis, P. lonicericola and P. tibetica, from Tibet in southwestern China were described and illustrated. Morphological data and sequences of the nuc rDNA ITS1-5.8S-ITS2 region (internal transcribed spacer [ITS] barcode) support the recognition of these taxa as distinct...
March 3, 2017: Mycologia
https://www.readbyqxmd.com/read/28418787/lulworthia-atlantica-a-new-species-supported-by-molecular-phylogeny-and-morphological-analysis
#15
Egídia Azevedo, Margarida Barata, Maria Isabel Marques, Maria Filomena Caeiro
This study presents morphological and molecular evidence for the establishment of a new species of Lulworthia based on the evaluation of 11 isolates of Lulworthiales collected in two marinas on the west coast of Portugal initially classified as Lulworthia sp. Maximum likelihood and Bayesian methods were applied to obtain phylogenetic trees for 18S-28S and internal transcribed spacer (ITS1-5.8S-ITS2 = internal transcribed spacer [ITS]) nuc rDNA. The isolates consistently grouped together in a distinct and highly supported clade; all other Lulworthiales analyzed, including the available sequences of Lulworthia spp...
March 9, 2017: Mycologia
https://www.readbyqxmd.com/read/28418780/unique-phylogenetic-position-of-the-african-truffle-like-fungus-octaviania-ivoryana-boletaceae-boletales-and-the-proposal-of-a-new-genus-afrocastellanoa
#16
Takamichi Orihara, Matthew E Smith
The sequestrate (truffle-like) basidiomycete Octaviania ivoryana was originally described based on collections from Zimbabwe, Kenya, Guinea, and Senegal. This species has basidiomes that stain blue-green and basidiospores with crowded spines that are characteristic of the genus Octaviania. However, O. ivoryana is the only Octaviania species described from sub-Saharan Africa, and the phylogenetic relationship of the species to other species of Octaviania sensu stricto has not been previously investigated. We examined the phylogenetic position of the isotype and paratype specimens of O...
March 7, 2017: Mycologia
https://www.readbyqxmd.com/read/28414823/comparing-in-vitro-and-in-vivo-virulence-phenotypes-of-burkholderia-pseudomallei-type-g-strains
#17
Eric R G Lewis, Paul B Kilgore, Tiffany M Mott, Gonzalo A Pradenas, Alfredo G Torres
Burkholderia pseudomallei (Bpm) is a saprophytic rod-shaped gram-negative bacterium and the causative agent of melioidosis. This disease has previously been described as endemic in areas such as northern Australia and Southeast Asia, but, more recently, a better understanding of the epidemiology of melioidosis indicated that the disease is distributed worldwide, including regions of the Americas and Africa. A 16S-23S rDNA internal transcribed spacer (ITS) typing system has been developed for Bpm and has revealed that ITS types C, E, and hybrid CE are mainly associated with Australia and Southeast Asia while type G strains are more associated with cases of melioidosis in the Western Hemisphere...
2017: PloS One
https://www.readbyqxmd.com/read/28413236/scopulariopsis-and-scopulariopsis-like-species-from-indoor-environments
#18
J H C Woudenberg, M Meijer, J Houbraken, R A Samson
Scopulariopsis-like species are often reported from the indoor environment, as well as from clinical samples. The lack of type isolates and thorough phylogenetic studies in the Microascaceae hampered the correct identification of these isolates. Based on recent phylogenetic studies, which resulted in multiple name changes, the aim is to molecularly identify the Scopulariopsis and scopulariopsis-like species which occur in the indoor environment and give an overview of the current species in these genera and their habitats...
September 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28410010/phylogeny-and-diversity-of-fomitiporella-hymenochaetales-basidiomycota
#19
Xiao-Hong Ji, Josef Vlasák, Li-Wei Zhou, Fang Wu, Yu-Cheng Dai
Fomitiporella accommodates polypores producing annual to perennial basidiocarps with an indistinct subiculum (very thin to almost lacking), mostly a dimitic hyphal structure, lacking any kind of setae, with brownish, thick-walled basidiospores, and causing a white rot. Previously, only a few samples of Fomitiporella were studied on the basis of morphological and nuc 28S rDNA (28S)-based phylogenetic analyses. In this study, we made a comprehensive study on Fomitiporella on the basis of collections from Central America, USA, Europe, and China...
March 15, 2017: Mycologia
https://www.readbyqxmd.com/read/28409116/prepare_taxa_charts-py-a-python-program-to-automate-generation-of-publication-ready-taxonomic-pie-chart-images-from-qiime
#20
Vijay Lakhujani, Chandan Badapanda
QIIME (Quantitative Insights Into Microbial Ecology) is one of the most popular open-source bioinformatics suite for performing metagenome, 16S rRNA amplicon and Internal Transcribed Spacer (ITS) data analysis. Although, it is very comprehensive and powerful tool, it lacks a method to provide publication ready taxonomic pie charts. The script plot_taxa_summary.py bundled with QIIME generate a html file and a folder containing taxonomic pie chart and legend as separate images. The images have randomly generated alphanumeric names...
June 2017: Genomics Data
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