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61.
Hug LA Salehi M Nuin P Tillier ER Edwards EA 《Applied and environmental microbiology》2011,77(15):5361-5369
Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This "pangenome" probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined. 相似文献
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Leishmaniasis is a geographically widespread severe disease which includes visceral leishmaniasis, cutaneous leishmaniasis (CL). There are 350 million people at risk in over 80 countries. In the Old World, CL is usually caused by Leishmania major, Leishmania tropica, and Leishmania aethiopica complex which 90 % of cases occurring in Afghanistan, Algeria, Iran, Iraq, Saudi Arabia, Syria, Brazil, and Peru. Recently, some reports showed that some strains of L. major have internal transcribed space (ITS-1) with differential size exhibiting homology with the related gene in a divergent genus of kinetoplastida, the Crithidia. This prompted us to analyze the mentioned gene in 100 isolates obtained from patients with suspected CL. After obtaining samples from 100 patients, DNA extraction was performed and ITS-1 was analyzed using PCR–RFLP. These samples were sequenced for verifying their homology. Then, RPOIILS gene was analyzed in the samples that their ITS-1 gene exhibiting homology with the related gene in Crithidia. Results showed that 10 % of the isolates have ITS-1 exhibiting different size with the routine ones. Sequencing of them showed their similarity to the one from Crithidia fasciculata. RPOIILS gene encoding RNA polymerase II largest subunit analysis showed genetic diversity. This study might also help in solving the problems concerning Leishmaniasis outbreak currently facing in Iran and some other endemic regions of the world. 相似文献
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Mariëlle Alders Lihadh Al-Gazali Isabelle Cordeiro Bruno Dallapiccola Livia Garavelli Beyhan Tuysuz Faranak Salehi Martin A. Haagmans Olaf R. Mook Charles B. Majoie Marcel M. Mannens Raoul C. Hennekam 《Human genetics》2014,133(9):1161-1167
The Hennekam lymphangiectasia–lymphedema syndrome is a genetically heterogeneous disorder. It can be caused by mutations in CCBE1 which are found in approximately 25 % of cases. We used homozygosity mapping and whole-exome sequencing in the original HS family with multiple affected individuals in whom no CCBE1 mutation had been detected, and identified a homozygous mutation in the FAT4 gene. Subsequent targeted mutation analysis of FAT4 in a cohort of 24 CCBE1 mutation-negative Hennekam syndrome patients identified homozygous or compound heterozygous mutations in four additional families. Mutations in FAT4 have been previously associated with Van Maldergem syndrome. Detailed clinical comparison between van Maldergem syndrome and Hennekam syndrome patients shows that there is a substantial overlap in phenotype, especially in facial appearance. We conclude that Hennekam syndrome can be caused by mutations in FAT4 and be allelic to Van Maldergem syndrome. 相似文献
65.
Specific protein detection by means of antibody-nanoparticle conjugates is a new field in medical nanobiotechnology. Among many nanoparticles used, gold nanoparticles show strong light-absorption properties which have been exploited in designing nanobiosensors. Fibronectin (FN) plays an important role in extracellular matrix (ECM) structure and function of normal cells; however, in conditions like lung carcinoma, its expression increases, especially in non small cell lung carcinoma (NSCLC). In this study, we conjugated gold nanoparticles to human fibronectin antibody (anti-hFN) to design a colorimetric nanobiosensor for detection of FN present in ECM of cultured cells. Three different cell lines, namely A549 (target cells), AGO-1522 (control cells), and Nalm-6 (negative control cells), were used to compare changes in color resulting from aggregation of gold nanoparticles due to higher amount of FN. Our construct was able to detect increased level of FN which was distinguishable visually by change in color and could be confirmed by spectrophotometer as well. 相似文献
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Structure,composition and regeneration of riparian forest along an altitudinal gradient in northern Iran 总被引:1,自引:0,他引:1
Mohammad Naghi Adel Hassan Pourbabaei Ali Salehi Seyed Jalil Alavi Daniel C. Dey 《Folia Geobotanica》2018,53(1):63-75
In order to protect and understand the regeneration of riparian forests, it is important to understand the environmental conditions that lead to their vegetation differentiation. We evaluated the structure, composition, density and regeneration of woody species in forests along the river Safaroud in Ramsar forest in northern Iran in relation to elevation, soil properties and distance from the river. Using 60 transects located perpendicularly to river and 300 quadrats, we examined forests 0, 50, 100, 150 and 200 m from the stream along an elevation gradient spanning from 350 to 2,400 m a.s.l. We found that total density, regeneration, diameter and basal area of trees were significantly higher in the interior of the forest whereas shrub density was higher close to the river. The uneven-aged forest structure showed no significant differences among gradient from the river to the forest interior. Hydro-geomorphic processes, flooding, the elevation gradient, distance from the river and soil properties were the most important factors that influenced plant community distribution in relation to the river. 相似文献
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