Freshwater Beach Microbial Ecology, Community Dynamics and Adaptive Responses to Environmental Changes Using Metabarcoding and Transcriptomics

The Laurentian Great Lakes (LGLs) represent the single most valuable natural resource on the North American continent and are a critical source of drinking water, important aquatic species habitat, water for the industrial sector and tourism/recreational activities as well as many other ecological services. LGLs ecosystems are changing rapidly due to climate change effects and are thus highly susceptible and responsive to any added anthropogenic stressors. The aquatic bacterial community affects critical ecosystem functions, such as nutrient cycling, water quality, recreational activities, etc., in ecosystems such as the LGLs, but perturbations can alter both the composition and functionality of the bacterial community. These changes can result in negative effects on whole ecosystem health with an associated loss in economic and social values. Understanding the temporal and spatial variation in the composition, diversity and ultimately activity of the bacterial community is paramount in understanding overall ecosystem services providing by the bacterial community. Characterizing spatial and temporal variation (and the factors that contribute to it) can provide deeper insight into the processes and mechanisms operating in LGLs ecosystems, and ultimately improve our basic knowledge and ability to predict bacterial community composition, dynamics and function. Enumeration of Escherichia coli as a bioindicator of human fecal contamination is widely used to quantify recreational water quality and safety. The inclusion of microbial source tracking (MST) as part of water quality monitoring along with E. coli and waterborne pathogens in a novel monitoring tool could help to determine the specific fecal source (e.g. human, dog, cattle, wildlife, etc.) and has great potential for accurate estimation of water-related health risks. On the other hand, we still have an incomplete understanding of freshwater microbial ecology and community dynamics and their response to disturbance, particularly to human-related environmental stressors. We must be able to predict and track the sources of harmful bacterial outbreaks; this will require a clear understanding of the impact of environmental and anthropogenic stressors on microbial community diversity and function. The research comprising this dissertation was designed to characterize broad to fine-scale temporal and spatial variation in freshwater bacterial community composition and gene transcription. Temporal variation in freshwater bacterial community composition (bi-hourly, monthly and seasonal variation) and gene transcription profile (seasonally) was significant while spatial variation was significant but limited in magnitude. A novel monitoring approach (nanofluidic TaqMan qRT-PCR) was designed and optimized for rapid and reliable monitoring of freshwater quality for waterborne pathogens, MST markers and E. coli as a bioindicator of fecal contamination. Finally, an experimental bacterial microcosm study was used to study the response of adapted (pre-exposure to different levels of nutrient stress) bacteria communities to very high nutrient stress. This experiment revealed that pre-exposure to a higher level of nutrient stress provides greater protection against community change than low levels when the bacterial community is challenged with a very high level of a stressor. These cumulative insights into the temporal and spatial variation of the freshwater bacteria community composition and transcriptome, the development of a novel nanofluidic TaqMan qRT-PCR tool for detecting and quantifying harmful bacteria and our microcosm study outcomes provide baseline knowledge and tools which will be valuable for improving best management practices, monitoring and accurate prediction of changes in freshwater ecosystem function

Antidepressant- like effect of essential oil of Lavandula angustifolia Mill and Citrus bigaradia Duh in mice.

زمینه و هدف: اسطوخدوس و بهارنارنج دارای ترکیبات فلاونوئیدی بوده ودر طب سنتی ایران به عنوان آرام بخش استفاده می‌شوند. این مطالعه به منظور تعیین و مقایسه اثرات ضد افسردگی اسانس اسطوخدوس و بهارنارنج بر موش‌های سوری بود. روش بررسی: در این مطالعه تجربی 54 سر موش سوری به 9 گروه 6‌تایی تقسیم شدند. گروه یک: گروه کنترل دریافت کننده نرمال سالین، گروه دوم ،سوم، چهارم و پنجم بترتیب اسانس اسطوخودوس با دوزهای 25، 50، 75 و 100 میلی‌گرم به ازای هر کیلوگرم وزن بدن و گروه های ششم، هفتم و هشتم اسانس بهارنارنج با دوزهای 25، 50 و 100 میلی‌گرم به ازای هر کیلوگرم وزن بدن و گروه نهم ایمی پرامین با دوز 15 میلی گرم بازای هر کیلوگرم بصورت داخل صفاقی دریافت کردند. در همه گروه‌ها آزمون شنای اجباری انجام وزمان بی حرکتی توسط نرم افزار SPSS و آزمون آماری ANOVA و دانکن آنالیز شدند. یافته ها: اسطوخودوس با دوز 25 میلی‌گرم بازای هر کیلوگرم وزن بدن مدت زمان بی‌حرکتی را نسبت به گروه کنترل کاهش داد (05/P <) اما با دوز 100 میلی‌گرم بازای هر کیلوگرم وزن بدن مدت زمان بی‌حرکتی را نسبت به گروه کنترل افزایش داد(01/P <) . همچنین بهارنارنج با دوز 25، 50 و 100 میلی‌گرم بازای هر کیلوگرم وزن بدن مدت زمان بی‌حرکتی را نسبت به گروه کنترل تغییر نداد (05/P >). نتیجه‌گیری: گیاه اسطوخدوس و بهارنارنج دارای اثرات ضد افسردگی هستند و ممکن است با خاصیت آنتی اکسیدانی در ارتباط باشد

Ranking and Level of Development According to the Agricultural Indices, Case Study: Sistan Region

Sistan region is one of the most important agricultural areas in the province of Sistan and Baluchistan. Therefore, given the heterogeneity in agriculture and recognizing these differences, the aim of this study was to obtain the level of development of agriculture in the Sistan region. To obtain this purpose Fuzzy Analytical Hierarchy Process (FAHP) and the numerical taxonomy were used in a view of 20 indicators in the agricultural sector in the region. The required data were achieved by filling out the questionnaire certified experts and statistical yearbooks in the agricultural sector. Data analysis was used by Matlab and SPSS softwares. Results of numerical taxonomy showed that Markazi, Shibab and Poshteab sectors component parts were less developed. Also, Jazinak and Miyankangi are in the category sections were undeveloped. The results of Fuzzy Analytical Hierarchy Process(FAHP) model indicated that Markazi, Shibab and Poshteab sectors are in the first rank of development, in terms of agricultural indices in the region. Jazinak and Miyankangi are in the fourth and fifth ranking. Therefore, in general, it is clear that the level of development of agricultural in Sistan region isn’t in good condition. In this regard it is suggested that appropriate planning to promote agricultural development is on the agenda should be applied

Differentiation of Mycobacterium tuberculosis clinical strains using restrikction fragment length polymorphism technique based on hsp65 gene

زمینه و هدف: در سالهای اخیر، به کارگیری تکنیک PCR (Polymerase Chain Reaction) و به دنبال آن آنالیز محصولPCR توسط آنزیمهای محدودالاثر (Restriction Fragment Length Polymorphism=RFLP) برای افتراق مایکوباکتریومها تا سطح گونه، استفاده شده است. در حالی که جزئیات افتراقی گونههای غیرتوبرکلوزی مایکوباکتریومها توسط این تکنیک مشخص شده و حتی در تعدادی از آنها این روش برای پیگیری مولکولار اپیدمیولوژی اثبات شده است، تنها تعداد کمی از سویههای مایکوباکتریوم توبرکلوزیس مورد بررسی قرار گرفتهاند. مطالعه حاضر این متد افتراقی را برای سویههای جدا شده در مقیاس وسیعتر با هدف تعیین پلی مورفیسم احتمالی مورد ارزیابی قرار داد. روش بررسی: یکصد و پنجاه سویه کلینیکی از بیماران مراجعهکننده به مرکز سل اهواز جمعآوری شد. رنگآمیزی اسیدفست برای سویهها انجام گرفت، سپس سویهها به عنوان مایکوباکتریوم توبرکلوزیس توسط خصوصیات کشت و تستهای بیوشیمیایی دستهبندی شدند. تکنیک PCR-RFLP با استفاده از DNA ژنومی استخراج شده به دنبال PCR بر مبنای تکثیر قطعه bp439 از ژن hsp65 توسط پرایمرهای اختصاصی جنس مورد استفاده قرار گرفت. بعد از هضم محصولات PCR توسط آنزیمهای BstEII و HaeIII آنالیز آنزیمی انجام گرفت. یافته ها: بر اساس نتایج بدست آمده، 145 سویه کلینیکی (6/96) الگوهای یکسان شبیه به سویههای استاندارد مایکوباکتریوم توبرکلوزیس، برای HaeIII فراگمنتهایی به طول 72/140/165 و برای BstEII به طول 82/120/250، نشان دادند. سه الگوی متفاوت در پنج سویه کلینیکی در الگوهای بدست آمده از هضم HaeIII با فراگمنتهایی به طول 145/165 (سه سویه)، 80/100/180 (یک سویه) و 72/194 (یک سویه) مشاهده شد در حالی که الگوی بدست آمده از هضم BstEII این سویهها تنوع نداشت و شبیه به دیگر سویهها بود. نتیجهگیری: نتایج به دست آمده در این مطالعه نشان داد که در موارد نادر، پلیمورفیسمهایی در توالی ژن hsp65 سویه های کلینیکی مایکوباکتریوم توبرکلوزیس ممکن است وجود داشته باشد

An Experimental and Theoretical Analysis of Foam Formation in the Sour Gas Sweetening Process

Use of amine solutions for the removal of acid gases such as carbon dioxide (CO2) and hydrogen sulfide (H2S) from natural gas is the most common method, and, in this process, operational problems because of foaming are reported. Foaming can lead to the entrainment of liquid into downstream process equipment and might result in a situation in which the process specifications cannot be met for acid gases. Alkanolamines in general have a negative effect on downstream process equipment, and the loss of amines has a negative effect on the health, safety, and environment (HSE). The foam reducing agents are often used to reduce the risk of heavy foaming in amine plants. This study concerns with foaming in amine-based CO2 plants. To investigate foaming related to CO2 removal from natural gas by amine solutions, the fundamental theory of foaming in gas-liquid contactors was first reviewed. Then, experimental techniques related to this phenomenon in diethanolamine (DEA)/CO2 absorbers were considered. After that, foaming of diethanolamine solution polluted with different impurities was noticed, and the tendency of foam was measured by considering their foaming indices. To analyze the experimental measurements and experimental observations, a mathematical model was developed too. The model could justify the experimental measurement reasonably

Study of the effect of bacterial lipopolysaccharide on the structure and dynamics on mouse tubulin polymerization

Background and aims: In recent decades, there has been much research on the microtubule dynamics as well as on factors affecting it. According to different studies, lipopolysaccharide (LPS) is thought to play an indirect role in neurodegenerative diseases through enzymatic pathways which hyperphosphorylate Tau protein and dissociate it from microtubules. In the present study, it was aimed to assess the direct effect of LPS on the structure and dynamics of tubulin polymerization in vitro. Methods: In this study, mouse tubulins were purified through two cycles of temperature-dependent polymerization-depolymerization. Cellulose-phosphate chromatography was used to further purify tubulins. SDS-PAGE was used to analyze the purity of the tubulins. Circular dichroism (CD), intrinsic fluorescence and turbidity assays were used to assess the changes in secondary and tertiary structures, and the dynamics of tubulin polymerization in the presence of different concentrations of LPS (5pM, 5nM, 50nM, 0.5µM and 5µM), respectively. Results: SDS-PAGE analysis confirmed the purity of tubulins. The intrinsic fluorescence analysis and CD assay revealed the changes in the secondary and tertiary structures of tubulins in the presence of LPS. The results of turbidity assay indicated that LPS could reduce the polymerization of tubulins. Conclusion: Our results indicate that LPS is able to change the secondary and tertiary structures of tubulin and decreases tubulin polymerization. According to our results, lipopolysaccharide in addition to an indirect effect on the microtubules stability, as well as by decreases in tubulin polymerization could result in neurodegenerative diseases specially Alzheimer's diseases

Identification of clinical isolates of Acinetobacter baumannii from Iran and study of their heterogeneity

AbstractBackgroundAcinetobacter baumannii has become one of the most serious causative agents of nosocomial infections due to its significant ability to survive on hospital surfaces. It is mainly an emerging opportunistic pathogen infecting patients in intensive care units. This study was aimed to identify the clinical isolates of A. baumannii and to investigate their heterogeneity using polymerase chain reaction (PCR)-based typing methods.MethodsA total of 197 nonduplicate isolates recovered from a wide range of clinical samples were subjected to conventional cultural and biochemical tests. For those isolates that were preliminary identified as A. baumannii, rpoB-based PCR with subsequent restriction fragment length polymorphism (RFLP) using two restriction enzymes (TagI and HaeIII) was performed to investigate the genetic diversity of the strains and their presumptive relationships with different clinical presentation of the disease caused by this pathogen.ResultsIn total, 50 isolates (25.4%) were identified as A. baumannii using conventional phenotypic methods with subsequent confirmation by rpoB sequencing. RFLP analysis demonstrated five different restriction enzyme patterns, designated as A–E clusters. Most A. baumannii isolates were categorized under Cluster A (32%). We found no significant relationship between clinical presentation and the clustering of the isolates.ConclusionThis study showed that the rpoB region possesses high discriminatory power to identify the isolates to the species level. This marker showed high interspecies variability that might be useful for strain typing. The results also suggest the possibility of the existence of a predominant clone of A. baumannii among infected patients in Iran

Molecular Methods for Identification of Acinetobacter Species by Partial Sequencing of the rpoB and 16S rRNA Genes.

BACKGROUND Acinetobacter spp. is a diverse group of Gram-negative bacteria which are ubiquitous in soil and water, and an important cause of nosocomial infections. The purpose of this study was to identify a collection of Acinetobacter spp. clinical isolates accurately and to investigate their antibiotic susceptibility patterns. MATERIALS AND METHODS A total of 197 non-duplicate clinical isolates of Acinetobacter spp. isolates identified using conventional biochemical tests. The molecular technique of PCR-RFLP and sequence analysis of rpoB and 16S rRNA genes was applied for species identification. Antimicrobial susceptibility test was performed with a disk diffusion assay. RESULTS Based on 16S rRNA and rpoB genes analysis separately, most of clinical isolates can be identified with high bootstrap values. However, the identity of the isolate 555T was uncertain due to high similarity of A. grimontii and A. junii. Identification by concatenation of 16S rRNA and rpoB confirmed the identity of clinical isolates of Acenitobacer to species level confidently. Accordingly, the isolate 555T assigned as A. grimontii due to 100% similarity to A. grimontii. Moreover, this isolate showed 98.64% to A. junii. Besides, the identity of the isolates 218T and 364T was confirmed as Genomic species 3 and A. calcoaceticus respectively. So, the majority of Acinetobacter spp. isolates, were identified as: A. baumannii (131 isolates, 66%), A. calcoaceticus (9 isolates, 4.5%), and A. genomosp 16 (8 isolates, 4%). The rest of identified species showed the lower frequencies. In susceptibility test, 105 isolates (53%), presented high antibiotic resistance of 90% to ceftriaxone, piperacillin, piperacillin tazobactam, amikacin, and 81% to ciprofloxacin. CONCLUSION Sequence analysis of the 16S rRNA and rpoB spacer simultaneously was able to do identification of Acinetobacter spp. to species level. A.baumannii was identified as the most prevalent species with high antibiotic resistance. Other species showed lower frequencies ranged from 4 to 9 strains

Antimicrobial activity of endophytic bacterial populations isolated from medical plants of Iran

Endophytic actinobacteria colonize inside the plant tissues without causing damages to the host plant. Since these microorganisms colonize in the different parts of plants and can stop plant disease, they have been applied as biological agents for controlling human diseases. The aim of this study was molecular identification and measuring the antimicrobial activity of endophytic Actinomycetes isolated from medicinal plants of Iran. Materials and Methods: The total of 23 medicinal plant samples were collected, sterilized, and crushed. Small pieces of the crushed samples were then cultured directly on three selective media. Grown colonies were identified by 16S rRNA gene sequencing method. Each isolate was cultured in TSB medium and then antimicrobial compound was extracted using ethyl acetate and tested against the target bacteria. Results: Sixteen out of 23 bacterial isolates (69%) exhibited antimicrobial activity against the selected pathogenic bacteria, such as Bacillus cereus, Staphylococcus aureus, Bacillus subtilis, Klebsiella pneumoniae, Citrobacter freundii, Proteus mi-rabilis, Shigella flexneri and Escherichia coli. Conclusion: Our Study showed a high phylogenetic diversity and the potent antibiotic activity of endophytic bacteria in medicinal plants of Iran. © 2017, Tehran University of Medical Science. All rights reserved

Antidepressant-like effect of essential oil of Lavandula angustifolia Mill and Citrus bigaradia Duh with forced swimming test in reserpinized mice Balb/C.

Background: Levandula angustifolia and Citrus aurantium essential oils possess phenolic compounds and in Iranian traditional medicine are commonly used as sedative. The aim of this study was to evaluate the antidepressant activities of Levandula angustifolia and Citrus bigaradia in adult reserpinized mice. Methods: In this experimental study, mice were divided into 10 groups of 8 mice each, including: Group 1, control group received normal saline. Group 2, was treated reserpine (5 mg/kg, IP). Group 3, 4, 5 and 6 were treated with reserpine (5 mg/kg, IP) and four Citrus aurantium different doses (25, 50, 100, 200 mg/kg). Group 7, 8 and 9 were treated with reserpine (5 mg/kg, IP) and three Levandula angustifolia doses (25, 50, 100 mg/kg). Group 10 was treated with reserpine (5 mg/kg, IP) and imipramine (15 mg/kg). In all groups the forced swimming test was done and the level of malondialdehyde (MDA) in brain tissue was measured to estimate the oxidative stress status. Data were analyzed by one-way ANOVA and Tukey post hoc test. Results: Levandula angustifolia, Citrus aurantium and imipramine in reserpinized mice caused the mice to spend less time in the forced swimming test, compared to the control group (p<0.01). Also Citrus aurantium with dose of 50 and 100 mg/kg and Lavandula angustifolia with dose of 25 and 50 mg/kg in reserpinized mice reduced immobility time and levels of MDA compared the control group (p<0.01). Conclusion: Lavander and Citrus aurantium essential oils have considerable antidepressant activity which might be attributed to their antioxidant effects