keyword
MENU ▼
Read by QxMD icon Read
search

Oryza genus

keyword
https://www.readbyqxmd.com/read/27902309/flexivirga-oryzae-sp-nov-isolated-from-soil-of-a-rice-paddy-and-emended-description-of-the-genus-flexivirga-anzai-et-al-2012
#1
Jong Woo Hyeon, Hye Rim Kim, Hyo Jung Lee, Sang Eun Jeong, Sang Ho Choi, Che Ok Jeon
A Gram-staining-positive, strictly aerobic bacterium, designated R1T, was isolated from a rice paddy in South Korea. Cells were non-motile cocci showing oxidase-negative and catalase-positive activities. Growth of strain R1T was observed at 10-37 °C (optimum, 30 C) and pH 5.0-9.0 (optimum, pH 7.0). Strain R1T contained iso-C16 : 0, summed feature 9 (comprising iso-C17 : 1 ω9c/C16 : 0 10-methyl) , anteiso-C17 : 0, iso-C17 : 0 and anteiso-C17 : 1 ω9c as the major fatty acids and MK-8 (H4) and MK-8 (H6) as the isoprenoid quinones...
November 11, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902265/oharaeibacter-diazotrophicus-gen-nov-sp-nov-a-diazotrophic-and-facultatively-methylotrophic-bacterium-isolated-from-rice-rhizosphere
#2
Haoxin Lv, Sachiko Masuda, Yoshiko Fujitani, Nurettin Sahin, Akio Tani
A new facultative methanol-utilizing bacterial strain SM30T was isolated from rice rhizosphere. Strain SM30T was Gram-stain negative, aerobic, motile, short rod, and grows optimally at pH 7 and at 28°C. It can tolerate 0 to 2% concentration of NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with low similarity of 94.17%. As one of the lanthanide metals, lanthanum could enhance its growth on methanol slightly. Phylogenetic trees based on mxaF, xoxF, and cpn60 genes of SM30T showed its distinct phylogenetic positions with known species...
November 14, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27889940/sequencing-of-australian-wild-rice-genomes-reveals-ancestral-relationships-with-domesticated-rice
#3
Marta Brozynska, Dario Copetti, Agnelo Furtado, Rod A Wing, Darren Crayn, Glen Fox, Ryuji Ishikawa, Robert J Henry
The related A genome species of the Oryza genus are the effective gene pool for rice. Here we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short and long read next generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A, has a sequence that is much closer to that of domesticated rice (O...
November 27, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27858291/molecular-characterization-of-a-novel-ssrna-ourmia-like-virus-from-the-rice-blast-fungus-magnaporthe-oryzae
#4
Adriana Illana, Marco Marconi, Julio Rodríguez-Romero, Ping Xu, Tamas Dalmay, Mark D Wilkinson, Maria Ángeles Ayllón, Ane Sesma
In this study we characterize a novel positive and single stranded RNA (ssRNA) mycovirus isolated from the rice field isolate of Magnaporthe oryzae Guy11. The ssRNA contains a single open reading frame (ORF) of 2,373 nucleotides in length and encodes an RNA-dependent RNA polymerase (RdRp) closely related to ourmiaviruses (plant viruses) and ourmia-like mycoviruses. Accordingly, we name this virus Magnaporthe oryzae ourmia-like virus 1 (MOLV1). Although phylogenetic analysis suggests that MOLV1 is closely related to ourmia and ourmia-like viruses, it has some features never reported before within the Ourmiavirus genus...
November 17, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27811915/interfering-tal-effectors-of-xanthomonas-oryzae-neutralize-r-gene-mediated-plant-disease-resistance
#5
Zhiyuan Ji, Chonghui Ji, Bo Liu, Lifang Zou, Gongyou Chen, Bing Yang
Plant pathogenic bacteria of the genus Xanthomonas possess transcription activator-like effectors (TALEs) that activate transcription of disease susceptibility genes in the host, inducing a state of disease. Here we report that some isolates of the rice pathogen Xanthomonas oryzae use truncated versions of TALEs (which we term interfering TALEs, or iTALEs) to overcome disease resistance. In comparison with typical TALEs, iTALEs lack a transcription activation domain but retain nuclear localization motifs and are expressed from genes that were previously considered pseudogenes...
November 4, 2016: Nature Communications
https://www.readbyqxmd.com/read/27688210/microbacterium-rhizosphaerae-sp-nov-isolated-from-a-ginseng-field-south-korea
#6
Sung-Jin Cho, Sang-Seob Lee
A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1(T), was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1(T) was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1(T) was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids...
September 29, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27605714/discrimination-of-aspergillosis-mucormycosis-fusariosis-and-scedosporiosis-in-formalin-fixed-paraffin-embedded-tissue-specimens-using-multiple-real-time-quantitative-pcr-assays
#7
Elham Salehi, Mohammad T Hedayati, Jan Zoll, Haleh Rafati, Maryam Ghasemi, Atosa Doroudinia, Mahdi Abastabar, Ali Tolooe, Eveline Snelders, Henrich A van der Lee, Antonius J M M Rijs, Paul E Verweij, Seyedmojtaba Seyedmousavi, Willem J G Melchers
In a retrospective multicenter study, 102 formalin-fixed paraffin-embedded (FFPE) tissue specimens with histopathology results were tested. Two 4-5 μm FFPE tissue sections from each specimen was digested with proteinase K followed by automated nucleic acid extraction.A specific quantitative real-time quantitative PCR (qPCR) assay targeting the internal transcribed spacer (ITS2) region of ribosomal DNA, using fluorescently labeled primers, was performed to identify clinically important genus and species of Aspergillus, Fusarium, Scedosporium and the Mucormycetes...
September 7, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27565704/paenibacillus-oryzae-sp-nov-isolated-from-rice-root
#8
Jun Zhang, Xiao-Tong Ma, Jun-Sheng Gao, Juan-Juan Zhao, Hua-Qun Yin, Cai-Wen Zhang, Rui-Jie Zhang, Xiao-Xia Zhang
A novel endophytic bacterium, strain 1DrF-4T, isolated from rice root, was characterized on the basis of its phenotypic characteristics and genotypic information. The novel strain was Gram-positive staining, endospore-forming, facultatively anaerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1DrF-4T formed a monophyletic clade within the genus Paenibacillus. The most phylogenetically related species was Paenibacillus pinisoli KACC 17472T, with which strain 1DrF-4T showed 16S rRNA gene sequence similarity of 95...
August 26, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27558124/complete-nucleotide-sequence-of-magnaporthe-oryzae-partitivirus-1
#9
Yanan Du, Xiang He, Xuan Zhou, Shouguo Fang, Qingchao Deng
A novel double-stranded RNA (dsRNA) mycovirus, designated Magnaporthe oryzae partitivirus 1 (MoPV1), was isolated from a strain of the plant pathogenic fungus Magnaporthe oryzae. The MoPV1 genome has two dsRNA genome segments. The larger segment (1763 bp) has a single open reading frame (ORF) with a conserved RNA-dependent RNA polymerase (RdRp) domain. The smaller segment (1491 bp) contains a single ORF encoding a putative coat protein (CP). Homology searches and phylogenetic analysis indicated that MoPV1 is a new member of the genus Gammapartitivirus...
November 2016: Archives of Virology
https://www.readbyqxmd.com/read/27557607/effect-of-wild-and-cultivated-rice-genotypes-on-rhizosphere-bacterial-community-composition
#10
Matthew Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
BACKGROUND: Deposition and secretion from roots influences the composition of the microbial communities surrounding them in the rhizosphere, and microbial activities influence the growth and health of the plant. Different host plant genotypes result in differences in those microbial communities. Crop genomes may have a narrow genetic base because of bottlenecks that occurred when domesticated crops were derived from small populations within the progenitor species. Desirable traits influencing root-associated microbial communities might therefore have been lost in the transition from wild species to modern cultivars...
December 2016: Rice
https://www.readbyqxmd.com/read/27521144/lysobacter-rhizophilus-sp-nov-isolated-from-rhizosphere-soil-of-national-flower-mugunghwa-from-south-korea
#11
Zheng-Fei Yan, Huan Trinh, Gabriela Moya, Pei Lin, Chang-Tian Li, Moo-Chang Kook, Tae-Hoo Yi
A Gram-negative, aerobic, motile, rod with one polar flagellum, catalase and oxidase-negative strain, designated THG-YS3.6T, was isolated from rhizosphere soil of flower Mugunghwa collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10-37 oC (optimum 25-30 oC), at pH 6-8 (optimum 7.0) and at 0-2.0% NaCl (optimum 1%). The isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were iso-C11:0, iso-C11:0 3OH, iso-C15:0, iso-C16:0, C16:1 7c alcohol, C16:0, iso-C17:0, summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl)...
August 12, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27499106/mycobacterium-oryzae-sp-nov-a-scotochromogenic-rapidly-growing-species-is-able-to-infect-human-macrophage-cell-line
#12
Ramaprasad E V V, Rizvi A, Benerjee S, Sasikala Ch, Ramana Ch V
Gram-stain-positive, acid-fast positive, rapidly growing, rod shaped bacteria (designated as strains JC290T, JC430 and JC431) were isolated from paddy cultivated soils on the Western Ghats of India. The phylogenetic analysis placed the three strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium tokaiense 47503T (98.8%), Mycobacterium murale MA112/96T (98.8%) and a few other Mycobacterium spp. The level of DNA-DNA reassociation of the three strains with M. tokaiense DSM44635T was 23...
August 5, 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27443638/the-first-non-clostridial-botulinum-like-toxin-cleaves-vamp-within-the-juxtamembrane-domain
#13
Irene Zornetta, Domenico Azarnia Tehran, Giorgio Arrigoni, Fabrizio Anniballi, Luca Bano, Oneda Leka, Giuseppe Zanotti, Thomas Binz, Cesare Montecucco
The genome of Weissella oryzae SG25T was recently sequenced and a botulinum neurotoxin (BoNT) like gene was identified by bioinformatics methods. The typical three-domains organization of BoNTs with a N-terminal metalloprotease domain, a translocation and a cell binding domains could be identified. The BoNT family of neurotoxins is rapidly growing, but this was the first indication of the possible expression of a BoNT toxin outside the Clostridium genus. We performed molecular modeling and dynamics simulations showing that the 50 kDa N-terminal domain folds very similarly to the metalloprotease domain of BoNT/B, whilst the binding part is different...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27393690/chromobacterium-rhizoryzae-sp-nov-isolated-from-rice-roots
#14
Shan Zhou, Xiang Guo, Huimin Wang, Delong Kong, Yanwei Wang, Jie Zhu, Weiwei Dong, Mingxiong He, Guoquan Hu, Bingqiang Zhao, Bin Zhao, Zhiyong Ruan
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryzasativa) in Hubei Province. Cells of LAM1188T were Gram-stain-negative and motile. The temperature and pH ranges for growth were 15-40 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium, and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98...
October 2016: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27377971/lysobacter-humi-sp-nov-a-bacterium-isolated-from-rice-field
#15
Shahina Akter, Md Amdadul Huq, Tae-Hoo Yi
A novel bacterial strain THG-PC4(T) was isolated from soil sample of rice field and was characterized by using a polyphasic approach. Cells were Gram-negative, bright yellow colored, nonmotile and rod shaped. The strain was aerobic and catalase positive, optimum growth temperature, and pH were 28 °C and 7, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-PC4(T) belongs to the genus Lysobacter and is most closely related to Lysobacter fragariae KCTC 42236(T), followed by Lysobacter oryzae KCTC 22249(T), Lysobacter tyrosinelyticus KCTC 42235(T), Lysobacter terrae KACC 17646(T), Lysobacter yangpyeongensis KACC 11407(T), Lysobacter rhizosphaerae KCTC 42237(T) and Lysobacter niabensis KACC 11587(T)...
December 2016: Archives of Microbiology
https://www.readbyqxmd.com/read/27260265/microbacterium-gilvum-sp-nov-isolated-from-civet-faeces
#16
Xiu Chen, Qin-Yuan Li, Gui-Ding Li, Fang-Ji Xu, Yi Jiang, Li Han, Cheng-Lin Jiang, Xue-Shi Huang
A novel aerobic, non-motile, Gram-positive, rod-shaped actinobacterium, designated YIM 100951(T), was isolated from the faeces of civets (Viverra zibetha) living in the National Nature Protect Region in Selangor, Malaysia. Strain YIM 100951(T) shows high similarities with Microbacterium barkeri DSM 20145(T) (97.6 %), Microbacterium oryzae MB10(T) (97.3 %), Microbacterium lemovicicum ViU22(T) (97.1 %) and Microbacterium indicum BBH6(T) (97.0 %) based on their 16S rRNA genes. However, phylogenetic analysis showed that strain YIM 100951(T) formed a clade with Microbacterium halotolerans YIM 70130(T) (96...
September 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/26950515/meloidogyne-graminicola-a-major-threat-to-rice-agriculture
#17
Sophie Mantelin, Stéphane Bellafiore, Tina Kyndt
: Taxonomy: The rice root-knot nematode Meloidogyne graminicola (Golden and Birchfield 1965). Superkingdom Eukaryota; Kingdom Metazoa; Phylum Nematoda; Class Chromadorea; Order Tylenchida; Suborder Tylenchina; Infraorder Tylenchomorpha; Superfamily Tylenchoidea; Family Meloidogynidae; Subfamily Meloidogyninae; Genus Meloidogyne. Biology: Microscopic non-segmented roundworm. Plant pathogen; obligate sedentary endoparasitic root-knot nematode. Reproduction: facultative meiotic parthenogenetic species in which amphimixis can occur at a low frequency (ca...
March 7, 2016: Molecular Plant Pathology
https://www.readbyqxmd.com/read/26852191/in-vitro-antifungal-susceptibility-of-clinical-species-belonging-to-aspergillus-genus-and-rhizopus-oryzae
#18
R Kachuei, S Khodavaisy, S Rezaie, S Sharifynia
OBJECTIVE: Among filamentous fungal pathogens, Aspergillus spp. and zygomycetes account for highest rates of morbidity and mortality among immunocompromised patients. Recently developed antifungal drugs offer the potential to improve management and therapeutic outcomes of fungal infections. The aim of this study was to analyse the in vitro activities of voriconazole, itraconazole, amphotericin B and caspofungin against clinical isolates of Aspergillus spp. and Rhizopus oryzae. MATERIAL AND METHODS: The in vitro antifungal susceptibility of 54 isolates belonging to different clinical isolates of Aspergillus spp...
March 2016: Journal de Mycologie Médicale
https://www.readbyqxmd.com/read/26819544/structural-diversity-of-a-novel-ltr-retrotransposon-rtposon-in-the-genus-oryza
#19
Yu-Chia Hsu, Chang-Sheng Wang, Yann-Rong Lin, Yong-Pei Wu
Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups...
2016: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/26818982/exploring-the-bacterial-diversity-of-belgian-steak-tartare-using-metagenetics-and-quantitative-real-time-pcr-analysis
#20
L Delhalle, N Korsak, B Taminiau, C Nezer, S Burteau, V Delcenserie, J B Poullet, G Daube
Steak tartare is a popular meat dish in Belgium. It is prepared with raw minced beef and is eaten with sauce, vegetables, and spices. Because it contains raw meat, steak tartare is highly prone to bacterial spoilage. The objective of this study was to explore the diversity of bacterial flora in steak tartare in Belgium according to the source and to determine which bacteria are able to grow during shelf life. A total of 58 samples from butchers' shops, restaurants, sandwich shops, and supermarkets were collected...
February 2016: Journal of Food Protection
keyword
keyword
98995
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"