Genotypic characterization of Iranian camel (Camelus dromedarius) isolates of Echinoccocus granulosus

In the present study, Echinoccocus granulosus isolates collected from camels (Camelus dromedarius) in eastern Iran were characterized based on the nucleotide sequences of mitochondrial CO1 and NDI genes. The molecular results for camel isolates demonstrated that at least 2 different genotypes are present, i.e., a buffalo genotype (G3) and the camel genotype (G6). Although the sequences of the Iranian camel genotype (G6) are completely homologous to the reference sequence of G6 (M84666) of E. granulosus , a nucleotide mutation (C to T at position 168) was detected in the CO1 sequences of the Iranian G3 isolates (HM626405) when compared with the reference G3 genotype (M84663). The findings of the present study represent the demonstration of the buffalo strain in camels. As previously reported, humans can be infected by this genotype; accordingly, the epidemiological importance of this genotype in the camel population should be considered in further studies.     

Bacteriological follow-up of pulmonary tuberculosis treatment: a study with a simple colorimetric assay

The viability of Mycobacterium tuberculosis (MTB) in serial sputum specimens from persistently smear positive patients was evaluated. The assay was based on oxidation-reduction of Alamar Blue and Malachite Green dyes that change their color in response to MTB growth. A total of 280 sputum specimens from 40 persistently smear positive TB patients and 40 sputa from non-tuberculosis patients were digested, decontaminated and examined microscopically. To check the MTB viability, the sediments from decontaminated samples were inoculated into three culture media: Lowenstein-Jensen (LJ) slants, Alamar Blue and Malachite Green culture tubes. We found that out of 280 smear positive specimens, the LJ culture was positive in 124 (44%). The numbers of correctly identified S+/C+ cases by Alamar Blue and Malachite Green were 118 (95%) and 116 (93%), respectively. The mean time required for reporting the positive signal in Alamar Blue culture tubes was 9 versus 11 days by Malachite Green culture tubes. In the standard LJ culture media the average detection time was 27 days (P < 0.05). The sensitivity of LJ was 99%, Alamar Blue 95% and Malachite Green 93%. The specificity was 100%, 92% and 93%, respectively. The oxidation-reduction method is rapid, sensitive and inexpensive in monitoring the treatment response of patients with pulmonary TB. Thus, using this method can be of paramount importance, particularly in resource-constrained areas.     

Bacterial community analysis in chlorpyrifos enrichment cultures via DGGE and use of bacterial consortium for CP biodegradation

The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6–7.4 mg L^?1 day^?1 of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L^?1 day^?1 of CP (100 mg L^?1). Addition of glucose as an additional C source increased the degradation capacity by 8–14 %. After inoculation of contaminated soil with CP (200 mg kg^?1) disappearance rates were 3.83–4.30 mg kg^?1 day^?1 for individual strains and 4.76 mg kg^?1 day^?1 for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.     

Occurrence of Staphylococcus aureus and evaluation of anti-staphylococcal activity of Lactococcus lactis subsp. lactis in ready-to-eat poultry meat

A total of 181 ready-to-eat poultry meat samples were examined for the presence of Staphylococcus aureus, and 11 (6 %) were found to have S. aureus contamination. Of 11 S. aureus isolates, 10 (91 %) were resistant to at least one antibiotic used in this study, and 2 were resistant to oxacillin. Lactococcus lactis subsp. lactis was tested as a bio-control agent. All the S. aureus isolates were found to be sensitive to antimicrobial products in L. lactis subsp. lactis supernatants; the zones of inhibition were in the range of 5.0 mm?±?0.70 mm to 19.8 mm?±?0.83 mm with the majority of isolates. As a competitive flora in mixed culture (LAPTg broth) and protective culture in poultry meat, L. lactis subsp. lactis was effective against S. aureus isolates; the growth of S. aureus isolates was almost negative after 32 h incubation in mixed culture. The population of S. aureus was reduced substantially to almost log 1 CFU/g after 25 days of incubation in protective culture. The pH of the test cultures also decreased sharply with time.     

Molecular Epidemiology of Nontuberculous Mycobacteria Isolates from Clinical and Environmental Sources of a Metropolitan City

Introduction

While NTM infection is mainly acquired from environmental exposure, monitoring of environmental niches for NTM is not a routine practice. This study aimed to find the prevalence of environmental NTM in soil and water in four highly populated suburbs of Tehran, Iran.

Material and Methods

A total of 4014 samples from soil and water resources were collected and studied. Sediments of each treated sample were cultured in Lowenstein-Jensen medium and observed twice per week for growth rate, colony morphology, and pigmentation. Colonies were studied with phenotypic tests. Molecular analysis was performed on single colonies derived from subculture of original isolates. Environmental samples were compared with 34 NTM isolates from patients who were residents of the study locations.

Results

Out of 4014 samples, mycobacteria were isolated from 862 (21.4%) specimens; 536 (62.1%) belonged to slow growing mycobacteria (SGM) and 326 (37.8%) were rapid growing mycobacteria (RGM). The five most frequent NTM were M. farcinogens (105/862; 12.1%), M. fortuitum (72/862; 8.3%), M. senegalense (58/862; 6.7%), M. kansasii (54/862; 6.2%), and M. simiae (46/862; 5.3%). In total, 62.5% (539/862) of mycobacterial positive samples were isolated from water and only 37.4% (323/862) of them were isolated from soil samples (P<0.05). Out of 5314 positive clinical samples for mycobacteria, 175 (3.2%) isolates were NTM. The trend of NTM isolates increased from 1.2% (13 out of 1078) in 2004 to 3.8% (39 out of 1005) in 2014 (P = 0.0001). The major clinical isolates were M. simiae (51; 29.1%), M. kansasii (26; 14.8%), M. chelonae (28; 16%), and M. fortuitum (13; 7.4%).

Conclusions

Comparing the distribution pattern of environmental NTM isolates with clinical isolates suggests a possible transmission link, but this does not apply to all environmental NTM species. Our study confirms an increasing trend of NTM isolation from clinical samples that needs further investigation.     

High cell density provides potent survival signals for resting T-cells.

Activated T-cells are susceptible to apoptosis through two particularly important pathways: ligation of CD95 (Fas/Apo-1) or cytokine deprivation. Resting T-cells have until recently been considered to be relatively resistant to apoptosis. In this report we show that resting T-cells die rapidly by apoptosis when deprived of serum or cell contact. Primed CD45RO+ cells were more susceptible than naive CD45RA+ cells, consistent with their relative expression of Bcl-2. CD4+, CD8+ and gammadelta T-cells were equally prone to apoptosis under all studied conditions. A linear relationship between cell survival and serum concentration was observed for cells cultured between 0.5-2x10(6)/ml. T-cells cultured at low density died even in high concentrations of serum. However, resting T-cells cultured at high cell density (4x10(6)/ml) survived for extended periods in the absence of serum or other survival factors. This effect was mediated by the production of soluble factors and independent of integrin mediated signals. These results suggest that T-cells at sites of high density such as the lymph node paracortex are independent of external survival factors, while those trafficking through the peripheral circulation are highly dependent on serum derived factors for survival.     

Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus‐Iranian Isolate

The full‐length nucleotide sequence of the Iranian isolate of Eggplant mottled dwarf virus (EMDV), a phytorhabdovirus, was determined using the random polymerase chain reaction method (rPCR) followed by PCR with specific primers to fill in the gaps. The negative‐sense RNA genome of the Iranian isolate of EMDV contains 13154 nucleotides and seven open‐reading frames (ORFs) in the order 3′‐leader‐N‐X‐P‐Y‐M‐G‐L‐trailer‐5′. These ORFs encode the nucleocapsid, X protein (of unknown function), phosphoprotein, Y protein (putative movement protein), matrix protein, glycoprotein and RNA‐dependent RNA polymerase, respectively. EMDV has a 199 nt 3′ leader RNA and a 151 nt 5′ trailer, and the ORFs are separated by conserved intergenic sequences. Phylogenetic analyses indicate that EMDV is most closely related to Potato yellow dwarf virus, which has a distinctly different geographical distribution.     

基于生态位模型的艾比湖国家级自然保护区马鹿生境评价

生境评价和预测是对濒危物种进行有效保护的基础。通过2013年9月和2014年10月对新疆艾比湖国家级自然保护区开展2次秋季野外调查共收集了92处马鹿(Cervuselaphus)出现数据,利用马鹿出现数据作为分布点数据,选取地形、植被类型和气候因子3类23种因子作为生境变量,利用MAXENT生态位模型分析了新疆艾比湖国家级自然保护区马鹿秋季生境适宜性分布特征和主要生境因子对马鹿分布的影响。结果表明:模型预测结果较高,平均AUC(area under the curve,受试工作者曲线下面值)值为0.976;Jackknife检验结果显示:最热月最高温度对马鹿生境分布的影响较大。植被类型和坡度对马鹿生境分布的影响不大。海拔、年降雨量、气温日较差和最热季平均温度是影响马鹿生境分布的主要生境因子。马鹿秋季生境划分为高适宜、次适宜、低适宜和不适宜4个等级,马鹿的高适宜生境区主要分布在研究区域的北部,次适宜及低适宜生境区则分布于高适宜生境区的边缘,而不适宜生境区主要集中在西部和东部地区。研究不仅提供了马鹿在艾比湖的实际分布状况,也为马鹿生境和生境因子的关系方面提供了一个重要的科学依据。