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intergenic spacer region

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https://www.readbyqxmd.com/read/29310897/vicia-faba-l-in-the-bejaia-region-of-algeria-is-nodulated-by-rhizobium-leguminosarum-sv-viciae-rhizobium-laguerreae-and-two-new-genospecies
#1
Djellali Belhadi, Philippe de Lajudie, Nacer Ramdani, Christine Le Roux, Farida Boulila, Pierre Tisseyre, Abdelghani Boulila, Amar Benguedouar, Yahia Kaci, Gisèle Laguerre
Fifty-eight rhizobial strains were isolated from root nodules of Vicia faba cv. Equina and Vicia faba cv. Minor by the host-trapping method in soils collected from eleven sites in Bejaia, Eastern Algeria. Eleven genotypic groups were distinguished based on the combined PCR/RFLP of 16S rRNA, 16S-23S rRNA intergenic spacer and symbiotic (nodC and nodD-F) genes and further confirmed by multilocus sequence analysis (MLSA) of three housekeeping genes (recA, atpD and rpoB), the 16S rRNA gene and the nodulation genes nodC and nodD...
December 27, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29297348/comparative-analysis-of-inverted-repeats-of-polypod-fern-polypodiales-plastomes-reveals-two-hypervariable-regions
#2
Maria D Logacheva, Anastasiya A Krinitsina, Maxim S Belenikin, Kamil Khafizov, Evgenii A Konorov, Sergey V Kuptsov, Anna S Speranskaya
BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29250139/comprehensive-analysis-of-long-non-coding-rna-and-mrna-expression-profiles-in-rheumatoid-arthritis
#3
Qing Luo, Chuxin Xu, Xue Li, Lulu Zeng, Jianqing Ye, Yang Guo, Zikun Huang, Junming Li
Abnormal expression of long non-coding RNA (lncRNA) has been demonstrated to be involved in a variety of human diseases. However, the role of lncRNA remains largely unknown in rheumatoid arthritis (RA). The present study aimed to investigate whether lncRNA are differentially expressed in RA. Differentially expressed lncRNA and mRNA in peripheral blood mononuclear cells from individuals with RA and healthy controls were detected using a human lncRNA microarray containing 30,586 lncRNA and 26,109 coding transcripts...
December 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/29236144/technological-properties-assessment-and-two-component-systems-distribution-of-streptococcus-thermophilus-strains-isolated-from-fermented-milk
#4
Tong Hu, Yishuang Zhang, Yanhua Cui, Chunyu Zhao, Xu Jiang, Xirong Zhu, Yu Wang, Xiaojun Qu
Streptococcus thermophilus is one of the economically most representatives of lactic acid bacteria, which is widely used as a starter to produce fermented milk products. In this study, 22 S. thermophilus strains were isolated from 26 fermented milk samples. Most isolates showed the ability to ferment a broad range of carbohydrates. Interestingly, eight strains are galactose positive, which is a desirable property in various industrial dairy fermentations. Four different nucleotide sequences were found in the galR-galK intergenic regions...
December 13, 2017: Archives of Microbiology
https://www.readbyqxmd.com/read/29228389/high-resolution-melting-analysis-a-novel-approach-for-clade-differentiation-in-pythium-insidiosum-and-pythiosis
#5
Navaporn Worasilchai, Nitipong Permpalung, Ariya Chindamporn
Pythium insidiosum causes life-threatening human pythiosis. Based on phylogenetic analysis using internal transcribed spacer (ITS) region, mitochondrial cytochrome C oxidase II (COX2) gene, intergenic spacer (IGS) region and exo-1,3-β-glucanase gene (exo1), P. insidiosum is classified into clade ATH, BTH, and CTH related to geographic distribution. At present, polymerase chain reaction in any of these specific regions with DNA sequencing is the only technique to provide clade diagnosis. In this study, P. insidiosum-specific primers targeting COX2 gene were designed and used in real-time quantitative polymerase chain reaction (qPCR) with subsequent high-resolution melting (HRM) to provide rapid identification as well as clade classification for P...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29222065/testing-the-monophyly-of-simaba-simaroubaceae-evidence-from-five-molecular-regions-and-morphology
#6
Marcelo Fernando Devecchi, William Wayt Thomas, Gregory M Plunkett, José Rubens Pirani
Generic circumscriptions in the mostly pantropical family Simaroubaceae are somewhat controversial. Simaba is the largest genus, currently defined as exclusively neotropical, with around 25 species of trees and shrubs, but both its limits and infrageneric classification have been a matter of discussion and divergence. Traditionally, species of the genus have been treated in three sections: Simaba sect. Tenuiflorae, S. sect. Floribundae and S. sect. Grandiflorae, but a phylogenetic analysis suggested that the latter two may not be monophyletic...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29203807/mitochondrial-genomic-variation-and-phylogenetic-relationships-of-three-groups-in-the-genus-scaphoideus-hemiptera-cicadellidae-deltocephalinae
#7
Yimin Du, Wu Dai, Christopher H Dietrich
The widespread leafhopper genus Scaphoideus Uhler is the most diverse genus in Scaphoideini and includes some species that are serious pests and vectors of plant pathogens. Here the first Scaphoideus mitogenome sequences are provided for three species, S. maai, S. nigrivalveus and S. varius, representing three main species groups in the Oriental region based on color pattern. The lengths of these three mitogenomes were 15,188, 15,235 and 15,207 bp, respectively. Gene order of three mitogenomes is highly conserved and identical to that of the putative ancestral insect...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29181905/complete-mitochondrial-genome-of-the-leaf-muntjac-muntiacus-putaoensis-and-phylogenetics-of-the-genus-muntiacus
#8
Guo-Gang Li, Ming-Xia Zhang, Kyaw Swa, Kyaw-Win Maung, Rui-Chang Quan
The leaf muntjac (Muntiacus putaoensis) is an endemic deer species found in the east trans-Himalayan region. In recent years, population numbers have decreased due to heavy hunting and habitat loss, and little genetic data exists for this species, thus our knowledge of distribution rangs and population sizes likewise remain limited. We obtained mtDNA genes and the complete mitochondrial genome sequence of M. putaoensis using PCR, followed by direct sequencing. The complete mitogenome sequence was determined as a circular 16 349 bp mitochondrial genome, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region, the gene composition and order of which were similar to most other vertebrates so far reported...
September 18, 2017: Zoological Research
https://www.readbyqxmd.com/read/29158966/mitochondrial-genomes-of-three-tetrigoidea-species-and-phylogeny-of-tetrigoidea
#9
Li-Liang Lin, Xue-Juan Li, Hong-Li Zhang, Zhe-Min Zheng
The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region...
2017: PeerJ
https://www.readbyqxmd.com/read/29140770/specificity-and-genetic-diversity-of-xylose-fermenting-scheffersomyces-yeasts-associated-with-small-blue-stag-beetles-of-the-genus-platycerus-in-east-asia
#10
Masahiko Tanahashi, Jong-Kuk Kim, Kana Watanabe, Takema Fukatsu, Kôhei Kubota
Among insect-fungus relationships, xylose-fermenting Scheffersomyces yeasts are well known for their potential in utilizing wood hemicelluloses and their association with various wood-feeding insects. However, their specificity to host insects or strain-level diversity within host species has not been clearly elucidated. In the insect family Lucanidae, larvae usually feed on decaying wood, and adult females consistently possess a fungus-storage organ, called the mycangium, near the abdominal tip. Here the authors investigated host-symbiont relationships between Scheffersomyces yeast symbionts and small blue stag beetles of the genus Platycerus (Coleoptera: Lucanidae) in East Asia by using intergenic spacer (IGS) region as a genetic marker...
November 9, 2017: Mycologia
https://www.readbyqxmd.com/read/29104233/the-complete-amomum-kravanh-chloroplast-genome-sequence-and-phylogenetic-analysis-of-the-commelinids
#11
Mingli Wu, Qing Li, Zhigang Hu, Xiwen Li, Shilin Chen
Amomum kravanh is an important edible and medicinal herb, the dried fruits of which are widely used in traditional herbal medicine as cardamom. We sequenced and analyzed the complete chloroplast (cp) genome of A. kravanh with herbgenomics technologies. The size of the A. kravanh cp genome was 162,766 bp, which consisted of long (LSC; 87,728 bp) and short (SSC; 15,390 bp) single-copy regions, separated by a pair of inverted repeats (IRs; 29,824 bp). The genome encoded 114 unique genes, including 80 protein-coding genes, 30 tRNAs and four rRNAs...
November 1, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29057217/characterization-and-distribution-of-the-autb-gene-in-neisseria-meningitidis
#12
Aiyu Zhang, Pan Zhao, Bingqing Zhu, Fenglin Shi, Li Xu, Yuan Gao, Na Xie, Zhujun Shao
We aimed to investigate and understand the characterization and distribution of the autB gene in Neisseria meningitidis in China. autB is flanked by two conservative genes, smpB and glcD, and it can be present in the majority of meningococcal isolates, but not in 053442 of clonal complex 4821 (CC4821) which contains a 968 bp sequence. In this study, we sequenced the intervenient region between smpB and glcD in 178 Chinese N. meningitidis strains isolated from both patients and carriers. There were 110 serogroupable strains, other 68 were non-groupable (NG)...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29047380/population-genetics-of-enterocytozoon-bieneusi-in-captive-giant-pandas-of-china
#13
Wei Li, Yuan Song, Zhijun Zhong, Xiangming Huang, Chengdong Wang, Caiwu Li, Haidi Yang, Haifeng Liu, Zhihua Ren, Jingchao Lan, Kongju Wu, Guangneng Peng
BACKGROUND: Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. RESULTS: We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E...
October 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28986641/first-detection-of-rickettsia-conorii-ssp-caspia-in-rhipicephalus-sanguineus-in-zambia
#14
Lidia Chitimia-Dobler, Gerhard Dobler, Sabine Schaper, Thomas Küpper, Simone Kattner, Silke Wölfel
Ticks are important vectors for Rickettsia spp. of the spotted fever group all around the world. Rickettsia conorii is the etiological agent of boutonneuse fever in the Mediterranean region and Africa. Tick identification was based on morphological features and further characterized using the 16S rRNA gene. The ticks were individually tested using pan-Rickettsia real-time-PCR for screening, and 23S-5S intergenic spacer region, 16S rDNA, gltA, sca4, ompB, and ompA genes were used to analyze the Rickettsia positive samples...
November 2017: Parasitology Research
https://www.readbyqxmd.com/read/28975409/diversity-and-prevalence-of-bartonella-species-in-small-mammals-from-slovakia-central-europe
#15
Eva Špitalská, Lenka Minichová, Elena Kocianová, Ľudovít Škultéty, Lenka Mahríková, Zuzana Hamšíková, Mirko Slovák, Mária Kazimírová
Wild-living rodents are important hosts for zoonotic pathogens. Bartonella infections are widespread in rodents; however, in Slovakia, knowledge on the prevalence of these bacteria in small mammals is limited. We investigated the prevalence and diversity of Bartonella species in the spleens of 640 rodents of six species (Apodemus flavicollis, Apodemus sylvaticus, Myodes glareolus, Microtus arvalis, Microtus subterraneus, and Micromys minutus) and in the European mole (Talpa europaea) from three different habitat types in south-western and central Slovakia...
November 2017: Parasitology Research
https://www.readbyqxmd.com/read/28966259/phylogenic-analysis-and-evaluation-of-ephedra-plants-and-aconites-for-medicinal-use
#16
Nobuko Kakiuchi
Although Kampo medicine is now fully integrated into the modern Japanese healthcare system, most Kampo formulations depend on imported crude drugs from limited foreign areas. To prepare for possible shortages of crude drugs in the future, a wider scope for the supply of medicinal plants is necessary. We conducted field research and collaborated with international laboratories for phylogenic analysis and evaluation of medicinal plant resources. Our research on ephedra plants from a wide region of Eurasia has, for example, confirmed their phylogenic structure: based on DNA sequencing analysis of nuclear ribosomal internal transcribed spacer region 1 (ITS1) as well as the chloroplast intergenic spacer between trnL and trnF (trnL-F), the 8 major Chinese species and related plants grown on the continent could be divided into 3 groups...
2017: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/28964561/-identification-of-species-of-mycoplasma-and-ureaplasma-diversum-from-argentinian-dairy-herds
#17
Camila Sosa, Liliana Tirante, Javier Chaves, Martín Pol, Arnaldo Ambrogi, José Angel Giraudo, Pablo Tamiozzo
Several species of Mycoplasma and Ureaplasma diversum can cause diseases in dairy cattle, which can be associated or not with clinical manifestations. In our country, the presence of Mycoplasma bovis, Mycoplasma californicum and Mycoplasma canadense has been detected, being the only mycoplasma species identified so far. The objective of this study was to identify other species of the Mycoplasmataceae family. Thirty-five Mycoplasma spp.-like isolates obtained from different samples from cattle, with or without clinical symptoms, from eight herds located in the provinces of Santa Fe, Cordoba, Buenos Aires and San Luis were utilized in the present study...
September 27, 2017: Revista Argentina de Microbiología
https://www.readbyqxmd.com/read/28962847/complete-sequence-and-characterization-of-the-ectropis-oblique-mitochondrial-genome-and-its-phylogenetic-implications
#18
Li-Shang Dai, Saima Kausar, Muhammad Nadeem Abbas, Tian-Tian Wang
In the present study, we sequenced the entire mitochondrial genome (mitogenome) of Ectropis oblique using PCR amplification and sequencing methods The entire mitogenome is 15,356bp long, including 13 protein coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and A+T rich element. The base composition and gene arrangement are identical to those of other lepidopterans. Of these 37 genes, twenty three are resided on heavy strand, while fourteen located on light strand. The newly sequenced mitogenome displayed a biased Adenine/thymine 84...
September 26, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28927427/first-molecular-detection-and-characterization-of-zoonotic-bartonella-species-in-fleas-infesting-domestic-animals-in-tunisia
#19
Saba Zouari, Fatma Khrouf, Youmna M'ghirbi, Ali Bouattour
BACKGROUND: Bartonellosis is an emerging vector-borne disease caused by different intracellular bacteria of the genus Bartonella (Rhizobiales: Bartonellaceae) that is transmitted primarily by blood-sucking arthropods such as sandflies, ticks and fleas. In Tunisia, there are no data available identifying the vectors of Bartonella spp. In our research, we used molecular methods to detect and characterize Bartonella species circulating in fleas collected from domestic animals in several of the country's bioclimatic areas...
September 19, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28912548/phylogenetic-implications-of-nuclear-rrna-igs-variation-in-stipa-l-poaceae
#20
Katarzyna Krawczyk, Marcin Nobis, Arkadiusz Nowak, Monika Szczecińska, Jakub Sawicki
The article takes up the problem of deficiency of molecular marker, which could illustrate molecular variability as well as phylogenetic relation within the genus of Stipa L. (Poaceae). Researches made so far hadn't delivered sufficient information about relationships between particular taxa from the genus of Stipa. In the present study, we analyzed variability and phylogenetic informativeness of nuclear ribosomal DNA in six species from the genus against five other species from Poaceae including a division of this region into functional elements and domains...
September 14, 2017: Scientific Reports
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