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intergenic spacer region

Yvonne Ukamaka Ajamma, Enock Mararo, David Omondi, Thomas Onchuru, Anne W T Muigai, Daniel Masiga, Jandouwe Villinger
Mosquitoes are a diverse group of invertebrates, with members that are among the most important vectors of diseases. The correct identification of mosquitoes is paramount to the control of the diseases that they transmit. However, morphological techniques depend on the quality of the specimen and often unavailable taxonomic expertise, which may still not be able to distinguish mosquitoes among species complexes (sibling and cryptic species). High resolution melting (HRM) analyses, a closed-tube, post-polymerase chain reaction (PCR) method used to identify variations in nucleic acid sequences, has been used to differentiate species within the Anopheles gambiae and Culex pipiens complexes...
2016: F1000Research
P Maza-Márquez, R Vilchez-Vargas, F M Kerckhof, E Aranda, J González-López, B Rodelas
Community structure, population dynamics and diversity of fungi were monitored in a full-scale membrane bioreactor (MBR) operated throughout four experimental phases (Summer 2009, Autumn 2009, Summer 2010 and Winter, 2012) under different conditions, using the 18S-rRNA gene and the intergenic transcribed spacer (ITS2-region) as molecular markers, and a combination of temperature-gradient gel electrophoresis and 454-pyrosequencing. Both total and metabolically-active fungal populations were fingerprinted, by amplification of molecular markers from community DNA and retrotranscribed RNA, respectively...
November 15, 2016: Water Research
Ying Zheng, Jian Liu, Xun Gong
Dramatic crustal deformation and river incision in Southwest China induced by the Indo-Asian collision have long been argued to contribute to the complicated landscapes, heterogeneous environment and abundant biodiversity in this region. However, biological impacts in promoting intraspecific phylogeographical subdivision and divergence along the Red River Fault zone (RRF) remain poorly understood. To investigate the possible biological effects of tectonic movements and environment variations within the RRF, the phylogeography of Cycas dolichophylla-an endemic but widely distributed Cycas in Southwest China and North Vietnam along the RRF were carried out based on four chloroplast DNA intergenic spacers (cpDNA), three nuclear DNA sequences (nDNA) and 16 simple sequence repeat variations (SSR)...
2016: Scientific Reports
Rafael José Vivero, Natalia Gil Jaramillo, Gloria Cadavid-Restrepo, Sandra I Uribe Soto, Claudia Ximena Moreno Herrera
BACKGROUND: Lutzomyia evansi, a phlebotomine insect endemic to Colombia's Caribbean coast, is considered to be the main vector of visceral and cutaneous leishmaniasis in the region. Although insects of this species can harbor pathogenic and non-pathogenic microorganisms in their intestinal microbiota, there is little information available about the diversity of gut bacteria present in Lutzomyia evansi. In this study, conventional microbiological methods and molecular tools were used to assess the composition of bacterial communities associated with Lutzomyia evansi guts in immature and adult stages of natural populations from the department of Sucre (Caribbean coast of Colombia)...
2016: Parasites & Vectors
Saumya Agrawal, Austen R D Ganley
The ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena...
2016: Methods in Molecular Biology
Yasmine H Tartor, Hend M El Damaty, Yasser S Mahmmod
BACKGROUND: Rapid and accurate identification of dermatophytes is crucial for the effective control of disease outbreaks. Current methods based on culture and microscopic characteristics may require weeks before positive identification is made. OBJECTIVES: To (i) identify the most common pathogenic dermatophytes affecting Arabian horses; (ii) compare the performance of direct microscopy (DM), culture, PCR using hair samples (PCRhair ) and PCR based on culture isolates (PCRculture ) for the diagnosis of dermatophytosis...
October 2016: Veterinary Dermatology
Riikka Peltomaa, Silvia Vaghini, Belén Patiño, Elena Benito-Peña, María C Moreno-Bondi
Plant-pathogenic Fusarium species, Fusarium verticillioides and Fusarium proliferatum, are the major producers of fumonisins which are one of the most common mycotoxins found in maize. Herein, we report the development of specific and sensitive genosensors for detecting these two closely related Fusarium species in food samples. The sensors are based on species-specific capture and detection probes, which bind to the intergenic spacer region of rDNA (IGS). Oligonucleotide functionalized magnetic microbeads are used to capture the target DNA which is then detected using biotinylated detection probes and a streptavidin-coupled label...
September 7, 2016: Analytica Chimica Acta
Philip S Bird, Darren J Trott, Deirdre Mikkelsen, Gabriel J Milinovich, Kristine M Hillman, Paul C Burrell, Linda L Blackall
An obligatory anaerobic, Gram-negative cocco-bacillus with black-pigmented colonies was isolated from the oral cavity of selected Australian marsupial species. Phenotypic andmolecular criteria showed that this bacterium was a distinct species within the genus of Porphyromonas, and closely related to Porphyromonas gingivalis and Porphyromonas gulae. This putative novel species and P. gulae could be differentiated from P. gingivalis by catalase activity. Further characterisation by multi-locus enzyme electrophoresis of glutamate dehydrogenase and malate dehydrogenase enzyme mobility and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis showed that this putative new species could be differentiated phenotypically from P...
August 10, 2016: International Journal of Systematic and Evolutionary Microbiology
Antonio Zurita, Sara García Gutiérrez, Cristina Cutillas
In the present study, a molecular detection of Bartonella sp. and Wolbachia sp. in Ctenocephalides felis (Siphonaptera: Pulicidae) isolated from Canis lupus familiaris from different geographical areas of Spain, Iran and South Africa, and in Stenoponia tripectinata tripectinata isolated from Mus musculus from the Canary Islands has been carried out by amplification of the 16S ribosomal RNA partial gene of Wolbachia sp. and intergenic spacer region (its region) of Bartonella sp. A total of 70 % of C. felis analysed were infected by W...
November 2016: Current Microbiology
Karol Krak, Petr Vít, Alexander Belyayev, Jan Douda, Lucia Hreusová, Bohumil Mandák
Reticulate evolution is characterized by occasional hybridization between two species, creating a network of closely related taxa below and at the species level. In the present research, we aimed to verify the hypothesis of the allopolyploid origin of hexaploid C. album s. str., identify its putative parents and estimate the frequency of allopolyploidization events. We sampled 122 individuals of the C. album aggregate, covering most of its distribution range in Eurasia. Our samples included putative progenitors of C...
2016: PloS One
Kaiwen Zhuang, Xin Ran, Yaling Dai, Jiaoqing Tang, Qin Yang, Sushmita Pradhan, Yuping Ran
White piedra is a superficial mycosis characterized by soft, white-to-tan, irregular nodules attached to the hair shafts. A 36-year-old man presented with small lumps in his pubic hair, without any other symptoms. The clinical features were suggestive of trichobacteriosis. Pathology analysis of the infected hair revealed that the concretions surrounding the hair shaft were full of fungal elements, parts of which had invaded into the cuticle. Culture on Sabouraud dextrose agar grew creamy, yellow-white colonies identified as Trichosporon inkin by the sequence of the nuclear ribosomal intergenic spacer region...
August 10, 2016: Mycopathologia
Sandra Janezic
PCR-ribotyping, a method based on heterogeneity of ribosomal intergenic spacer region, is the preferred method for genotyping of Clostridium difficile. Standardly used procedure for PCR-ribotyping is culturing of C. difficile from fecal samples and subsequent typing. In this chapter, we describe a modified PCR-ribotyping method for direct detection of PCR-ribotypes directly in total stool DNA extract, without prior need to isolate C. difficile.
2016: Methods in Molecular Biology
Jun-Hong Lin, Wei-Chuan Zhou, Hong-Li Ding, Pei Wang, Hong-Mu Ai
The land snail Cernuella virgata (da Costa, 1778) is widely considered as a pest to be quarantined in most countries. In this study, the complete mitochondrial genome of Cernuella virgata is published. The mitochondrial genome has a length of 14,147 bp a DNA base composition of 29.07% A, 36.88% T, 15.59% C and 18.46% G, encoding 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The complete nucleotide composition was biased toward adenine and thymine, A+T accounting for 69...
2016: ZooKeys
Maya Ofek-Lalzar, Yonatan Gur, Sapir Ben-Moshe, Or Sharon, Evsey Kosman, Elad Mochli, Amir Sharon
Endophytes have profound impacts on plants, including beneficial effects on agriculturally important traits. We hypothesized that endophytes in wild plants include beneficial endophytes that are absent or underrepresented in domesticated crops. In this work, we studied the structure of endophyte communities in wheat-related grasses, Triticum dicoccoides and Aegilops sharonensis, and compared it to an endophyte community from wheat (T. aeastivum). Endophytes were isolated by cultivation and by cultivation-independent methods...
October 2016: FEMS Microbiology Ecology
Lianghong Ni, Zhili Zhao, Gaawe Dorje, Mi Ma
Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes...
2016: PloS One
Yu-Peng Wu, Jin-Liang Zhao, Tian-Juan Su, A-Rong Luo, Chao-Dong Zhu
To better understand the diversity and phylogeny of Lepidoptera, the complete mitochondrial genome of Choristoneura longicellana (=Hoshinoa longicellana) was determined. It is a typical circular duplex molecule with 15,759bp in length, containing the standard metazoan set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an A+T-rich region. All of the inferred tRNA secondary structures show the common cloverleaf pattern, with the exception of trnS1(AGN), which lacks the DHU arm. The rrnL of C...
October 10, 2016: Gene
Patrick S Sebastian, Maria Noelia Saracho Bottero, Luis Carvalho, Ute Mackenstedt, Marcela Lareschi, José M Venzal, Santiago Nava
This study was conducted to detect Borrelia burgdorferi sensu lato infection in ixodid ticks from the Patagonia region in the south of Argentina. Therefore, ticks were collected on rodents in the provinces of Chubut, Río Negro and Santa Cruz. These ticks were identified as nymphs of Ixodes cf. neuquenensis and Ixodes sigelos. The B. burgdorferi s.l. infection was tested by a battery of PCR methods targeting the gene flagellin (fla) and the rrfA-rrlB intergenic spacer region (IGS). Three pools of I. sigelos nymphs from Chubut and Santa Cruz provinces as well as one pool of I...
October 2016: Acta Tropica
Otomi Cho, Takashi Sugita
As DNA sequences of the intergenic spacer (IGS) region in the rRNA gene show remarkable intraspecies diversity compared with the small subunit, large subunit, and internal transcribed spacer region, the IGS region has been used as an epidemiological tool in studies on Malassezia globosa and M. restricta, which are responsible for the exacerbation of atopic dermatitis (AD) and seborrheic dermatitis (SD). However, the IGS regions of M. sympodialis and M. dermatis obtained from the skin of patients with AD and SD, as well as healthy subjects, lacked sequence diversity...
July 1, 2016: Mycopathologia
Aracelis Miranda, Franklyn Samudio, Kadir González, Azael Saldaña, Adeilton Brandão, Jose E Calzada
A precise identification of Leishmania species involved in human infections has epidemiological and clinical importance. Herein, we describe a preliminary validation of a restriction fragment length polymorphism assay, based on the calmodulin intergenic spacer region, as a tool for detecting and typing Leishmania species. After calmodulin amplification, the enzyme HaeIII yielded a clear distinction between reference strains of Leishmania mexicana, Leishmania amazonensis, Leishmania infantum, Leishmania lainsoni, and the rest of the Viannia reference species analyzed...
August 3, 2016: American Journal of Tropical Medicine and Hygiene
S Samah, E Valadez-Moctezuma, K S Peláez-Luna, S Morales-Manzano, P Meza-Carrera, R C Cid-Contreras
Molecular methods are powerful tools in characterizing and determining relationships between plants. The aim of this study was to study genetic divergence between 103 accessions of Mexican Opuntia. To accomplish this, polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of three chloroplast intergenic spacers (atpB-rbcL, trnL-trnF, and psbA-trnH), one chloroplast gene (ycf1), two nuclear genes (ppc and PhyC), and one mitochondrial gene (cox3) was conducted. The amplified products from all the samples had very similar molecular sizes, and there were only very small differences between the undigested PCR amplicons for all regions, with the exception of ppc...
2016: Genetics and Molecular Research: GMR
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