DNA barcoding of Aphanius vladykovi from different habitats in Chaharmahal va Bakhtiari Province, Iran

This study was aimed to reveal the possible cryptic diversity of the Aphanius vladykovi populations in the Chaharmahal va Bakhtiari Province, Iran using mitochondrial cytochrome-c oxidase subunit I (COI). A total of 30 specimens from the Beheshtabad River, Choghakhor and Gandoman Wetlands, and Brovi, Shalamzar, and Balagholi springs from the Chaharmahal va Bakhtiari Province were collected. The maximum within-population genetic distance based on K2P was 0.28% and this distance was 0.22% between populations of Gandoman and Brovi with Shalmazar, whereas the least genetic distance was observed between Choghakhor and Beheshtabad (0.09%). A total of six haplotypes were observed between the studied specimens. Maximum Likelihood (ML) and Neighbor-Joining (NJ) trees reconstructed and all haplotypes from A. vladykovi specimens collected from non-type localities nested in one group with A. vladykovi from Choghakhor wetland i.e. type locality. The results of this study detected no cryptic diversity in A. vladykovi inhabiting different habitats in the studied region. Hence, it is proposed to consider all the studied populations in conservation measures related to A. vladycovi

FISH Analysis for del6q21 and del17p13 in B-cell Chronic Lymphocytic Leukemia in Iranians

Background: B-cell chronic lymphocytic leukemia (B-CLL) is the most common leukemia in the Western world. Major progress has been made in assessing typical chromosomal abnormalities and recognition of the correlation of these chromosomal abnormalities with laboratory features and clinical course of the disease. The most frequent genomic changes are deletions at 13q14, 11q22-23 and 17p13 and trisomy of chromosome 12. Objectives: The aim of this study was to investigate the frequency of chromosomal aberrations in B-CLL patients' peripheral blood and/or bone marrow using a molecular cytogenetic method, interphase fluorescence in situ hybridization (I-FISH) and to evaluate the correlation between these genomic changes and clinical findings. Patients and Methods: I-FISH analyses were performed on bone marrow and blood samples of 66 B-CLL patients. Results: Deletion of 17p13 was found in 11 (16.6%) and deletion 6q21 was present in 5 (7.5%). Statistical analyses were performed to investigate the correlation of these molecular-cytogenetic findings with family history, Rai staging and CD38 marker. No clear differences in distribution was noted for del17p13 and del6q21 among patients with and without family history, and no direct correlation was noted between these genomic changes and CD38 marker, but the correlation of del17p13 and Rai stage was significant. There was a high frequency of Rai stage II within del17p13 patients. Conclusions: It was demonstrated that the presence of del6q21 in B-CLL patients indicates poor prognosis and on the contrary, presence of del17p13 points at the good prognostic value of the disease

Content Analysis of Articles on Reading Culture and Habits: A Case of LIS Journals Indexed in Science Direct And ISC

This study aims to analyze the content of reading culture, reading development strategies, and the application of technology to expand reading habits published in LIS journals indexed in ScienceDirect and ISC. This study is an applied-descriptive study in terms of its objectives. This study is also a part of Scientometrics and employs content analysis. A total of 363 articles from the ScienceDirect database and 82 articles from the ISC database were selected using purposive sampling, in which "word" was taken as the registration unit and "article" as the unit of analysis. The data were collected using a researcher-made checklist whose validity was reviewed and confirmed by experts, and its reliability was measured using the kappa coefficient (κ) with an interrater agreement of 0.7. The findings of this study showed that out of 445 articles reviewed, about 120 articles addressed the reading culture, 273 articles focused on reading development strategies, and 52 articles assessed the application of technology to expand reading skills. The research method most frequently used in the reviewed articles was the descriptive method. Besides, students constituted the most extensive research population. Encouraging students to engage in reading, teaching, and promoting effective reading methods and access to free digital books and publications wherever possible had the highest rankings among the extracted categories related to the reading culture, reading development strategies, and the application of technology to promote reading habits. Besides, the reviewed articles addressed practical methods of promoting reading habits. Our data highlighted the importance of reading and belief in its value in societies. Thus, there is no way to achieve scientific, cultural, and economic growth and prosperity other than expanding the community's constant and goal-directed reading habits. To this end, establishing school libraries and developing reading habits in children and adolescents need to receive more attention. In recent years, due to fundamental changes in social institutions, improving the quality of education has also received special attention

Burden of potentially novel species of non tuberculosis mycobacteria in Iranian tuberculosis laboratories

AbstractAims and objectivesNontuberculous mycobacterium (NTM) infections are caused by mycobacteria that are found in water and soil. The chances of missing NTM species are higher in tuberculosis endemic countries like Iran, which are poorly equipped and overburdened with other diseases. The aim of this study is to access the diversity of rare, unusual and frequent species in Iranian tuberculosis laboratories.MethodsFrom 2012–2014 a total of 243 different clinical isolates of NTM were recovered from Mycobacteriology Reference Laboratories across Iran (Ahvaz, Esfahan, Tehran, Gorgan, Kermanshah). The isolates identified by rpoB gene sequencing are useful markers in mycobacterium identification.ResultsBased on rpoB gene sequencing, 20 groups do not belong to any of the officially recognized mycobacteria. A total of 210 isolates of NTM were identified to species level, including M. fortuitum (66), M. kansasii (20), M. simiae (20), M. conceptionense (10), M. peregrinum (9), M. thermoresistibile (9), M gordonae (8), M. lentiflavum (8), M. phlei (6), M. intracellulare (6), M. abscessus subsp. abscessus (5), M. chelonae (5), M. abscessus subsp. bolletii (4), M. avium (4), M. flavescents (4), M. nonchromogenicum (4), M. terrae (4), M. branderi (3), M. iranicum (3), M. mucogenicum (3), M. scrofulaceum (3), M. smegmatis (3) and M. triplex (2).Among all isolates, M. fortuitum was identified as the most frequent encounter (27%) of NTM, and M. kansasii and M. simiae were the second most dominant species (8.2%) among the isolates. A total of 33 isolates (13%) were unidentifiable to species level. M. fortutium was the most frequent species in Ahvaz, Esfahan, Tehran and Gorgan, but M. simiae was the most frequent species in Kermanshah. Thirty-three isolates (20 groups) presented unique genetic features. Further molecular tests should be carried out to reliable identification of these isolates to species level.ConclusionsThe present study provides evidence for the importance of NTM identification in the clinical setting and the presence of diverse species in clinical samples as a causative agent of disease.The presence of diverse species of NTM and unidentifiable strains in a clinical setting in Iran emphasizes the use of sequence analysis of genes for reliable identification

In Vitro Antimicrobial Susceptibility of Nontuberculous Mycobacteria in Iran

Many species of nontuberculous mycobacteria (NTM) have long been identified as important causes of human disease, the incidence of which is rising. Several reports have suggested increasing trend of both in vitro and in vivo resistance to available treatment regimes. The aim of this study was to evaluate antibiotic susceptibility of clinically relevant NTM isolates using standard microbroth dilution test. Antimicrobial susceptibility testing was performed following National Committee for Clinical Laboratory Standards methods for NTM isolates, including 85 Mycobacterium fortuitum , 39 Mycobacterium chelonae , and 30 Mycobacterium abscessus subsp. abscessus as rapidly growing mycobacteria and 48 Mycobacterium simiae and 40 Mycobacterium kansasii as slowly growing mycobacteria. All isolates were recovered from various types of clinical samples and identified by multilocus sequence analysis. Trimethoprim–sulfamethoxazole (TMP-SMZ), amikacin, tobramycin, clarithromycin, moxifloxacin, linezolid, and imipenem showed better activity against M. fortuitum rather than meropenem, ciprofloxacin, cefoxitin, and doxycycline. Amikacin was active against 93% of M. abscessus subsp. abscessus. Linezolid, clarithromycin, cefoxitin, ciprofloxacin, imipenem, moxifloxacin, tobramycin, TMP-SMZ, doxycycline, and meropenem showed some activities on M. abscessus subsp. abscessus as well. The majority of M. abscessus subsp. abscessus and M. chelonae strains were multidrug resistant. Among the 40 isolates of M. kansasii , all were susceptible to ethambutol, isoniazid, clarithromycin, moxifloxacin, and linezolid. These isolates were also resistant to doxycycline and 50% were resistant to rifampicin and ciprofloxacin. M. simiae was resistant to clarithromycin, doxycycline, isoniazid, and TMP-SMZ, and the majority of isolates showed high levels of resistance to linezolid, ethambutol, ciprofloxacin, streptomycin, and rifampicin. The majority of M. simiae isolates were multidrug resistant. Our data confirm the need for performing of standard susceptibility testing of any clinically important NTM isolate

Mycobacterium persicum sp. nov., a novel species closely related to Mycobacterium kansasii and Mycobacterium gastri

Four strains isolated in Iran from pulmonary specimens of unrelated patients are proposed as representative of a novel Mycobacterium species. Similarity, at the phenotypic level, with Mycobacterium kansasii is remarkable with the photochromogenic yellow pigmentation of the colonies being the salient feature. They differ, however, genotypically from this species and present unique sequences in 16S rRNA, hsp65 and rpoB genes. The average nucleotide identity and the genome-to-genome distance fully support the status of an independent species. The name proposed for this species is Mycobacterium persicum sp. nov. with AFPC-000227T (=DSM 104278T=CIP 111197T) as the type strain

Mycobacterium ahvazicum sp. nov., the nineteenth species of the Mycobacterium simiae complex

Abstract Four slowly growing mycobacteria isolates were isolated from the respiratory tract and soft tissue biopsies collected in four unrelated patients in Iran. Conventional phenotypic tests indicated that these four isolates were identical to Mycobacterium lentiflavum while 16S rRNA gene sequencing yielded a unique sequence separated from that of M. lentiflavum. One representative strain AFP-003T was characterized as comprising a 6,121,237-bp chromosome (66.24% guanosine-cytosine content) encoding for 5,758 protein-coding genes, 50 tRNA and one complete rRNA operon. A total of 2,876 proteins were found to be associated with the mobilome, including 195 phage proteins. A total of 1,235 proteins were found to be associated with virulence and 96 with toxin/antitoxin systems. The genome of AFP-003T has the genetic potential to produce secondary metabolites, with 39 genes found to be associated with polyketide synthases and non-ribosomal peptide syntases and 11 genes encoding for bacteriocins. Two regions encoding putative prophages and three OriC regions separated by the dnaA gene were predicted. Strain AFP-003T genome exhibits 86% average nucleotide identity with Mycobacterium genavense genome. Genetic and genomic data indicate that strain AFP-003T is representative of a novel Mycobacterium species that we named Mycobacterium ahvazicum, the nineteenth species of the expanding Mycobacterium simiae complex

Mycobacterium aquaticum sp. nov., a rapidly growing species isolated from haemodialysis water.

The characterization of five Iranian isolates, four from hospital haemodialysis water and one from the sputum of a patient, led to the detection of a novel mycobacterium species. The strains were characterized by mucoid colonies developing in 3-5 days at temperatures ranging from 25 to 37 °C. The biochemical test pattern was unremarkable while the HPLC profile of mycolic acids resembled that of Mycobacterium fortuitum. The sequences of three major housekeeping genes (16S rRNA, hsp65 and rpoB) were unique and differed from those of any other mycobacterium. Mycobacterium brisbanense, which is the species that shared the highest 16S rRNA gene sequence similarity (99.03 %), was distinct, as shown by the average nucleotide identity and by the genome to genome distance values (91.05 and 43.10 %, respectively). The strains are thus considered to represent a novel species of the genus Mycobacterium, for which the name Mycobacterium aquaticum sp. nov. is proposed. The type strain is RW6T (=DSM 104277T=CIP111198T)

Mycobacterium celeriflavum sp nov., a rapidly growing scotochromogenic bacterium isolated from clinical specimens

Six strains of a rapidly growing scotochromogenic mycobacterium were isolated from pulmonary specimens of independent patients. Biochemical and cultural tests were not suitable for their identification. The mycolic acid pattern analysed by HPLC was different from that of any other mycobacterium. Genotypic characterization, targeting seven housekeeping genes, revealed the presence of microheterogeneity in all of them. Different species were more closely related to the test strains in various regions: the type strain of Mycobacterium moriokaense showed 99.0% 16S rRNA gene sequence similarity, and 91.5-96.5% similarity for the remaining six regions. The whole genome sequences of the proposed type strain and that of M. moriokaense presented an average nucleotide identity (ANI) of 82.9%. Phylogenetic analysis produced poorly robust trees in most genes with the exception of rpoB and sodA where Mycobacterium flavescens and Mycobacterium novocastrense were the closest species. This phylogenetic relatedness was confirmed by the tree inferred from five concatenated genes, which was very robust. The polyphasic characterization of the test strains, supported by the ANI value, demonstrates that they belong to a previously unreported species, for which the name Mycobacterium celeriflavum sp. nov. is proposed. The type strain is AFPC-000207(T) (=DSM 46765(T)=JCM 18439(T))