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نتیجه جستجو - میکروبیولوژی

تعداد مقالات یافته شده: 20
ردیف عنوان نوع
1 Use of standardized bioinformatics for the analysis of fungal DNA signatures applied to sample provenance
استفاده از بیوانفورماتیک استاندارد برای تجزیه و تحلیل امضاهای DNA قارچی اعمال شده برای پیشروی نمونه-2020
The use of environmental trace material to aid criminal investigations is an ongoing field of research within forensic science. The application of environmental material thus far has focused upon a variety of different objectives relevant to forensic biology, including sample provenance (also referred to as sample attribution). The capability to predict the provenance or origin of an environmental DNA sample would be an advantageous addition to the suite of investigative tools currently available. A metabarcoding approach is often used to predict sample provenance, through the extraction and comparison of the DNA signatures found within different environmental materials, such as the bacteria within soil or fungi within dust. Such approaches are combined with bioinformatics workflows and statistical modelling, often as part of large-scale study, with less emphasis on the investigation of the adaptation of these methods to a smaller scale method for forensic use. The present work was investigating a small-scale approach as an adaptation of a larger metabarcoding study to develop a model for global sample provenance using fungal DNA signatures collected from dust swabs. This adaptation was to facilitate a standardized method for consistent, reproducible sample treatment, including bioinformatics processing and final application of resulting data to the available prediction model. To investigate this small-scale method, 76 DNA samples were treated as anonymous test samples and analyzed using the standardized process to demonstrate and evaluate processing and customized sequence data analysis. This testing included samples originating from countries previously used to train the model, samples artificially mixed to represent multiple or mixed countries, as well as outgroup samples. Positive controls were also developed to monitor laboratory processing and bioinformatics analysis. Through this evaluation we were able to demonstrate that the samples could be processed and analyzed in a consistent manner, facilitated by a relatively user-friendly bioinformatic pipeline for sequence data analysis. Such investigation into standardized analyses and application of metabarcoding data is of key importance for the future use of applied microbiology in forensic science.
Keywords: Forensic microbiology | Bioinformatics | Metabarcoding | Sample provenance
مقاله انگلیسی
2 Detecting personal microbiota signatures at artificial crime scenes
تشخیص امضاهای میکروبیوت شخصی در صحنه های جرم ساختگی -2020
When mapped to the environments we interact with on a daily basis, the 36 million microbial cells per hour that humans emit leave a trail of evidence that can be leveraged for forensic analysis. We employed 16S rRNA amplicon sequencing to map unique microbial sequence variants between human skin and building surfaces in three experimental conditions: over time during controlled and uncontrolled incidental interactions with a door handle, and during multiple mock burglaries in ten real residences. We demonstrate that humans (n = 30) leave behind microbial signatures that can be used to track interaction with various surfaces within a building, but the likelihood of accurately detecting the specific burglar for a given home was between 20–25%. Also, the human microbiome contains rare microbial taxa that can be combined to create a unique microbial profile, which when compared to 600 other individuals can improve our ability to link an individual ‘burglar’ to a residence. In total, 5512 discriminating, nonsingleton unique exact sequence variants (uESVs) were identified as unique to an individual, with a minimum of 1 and a maximum of 568, suggesting some people maintain a greater degree of unique taxa compared to our population of 600. Approximate 60–77% of the unique exact sequence variants originated from the hands of participants, and these microbial discriminators spanned 36 phyla but were dominated by the Proteobacteria (34%). A fitted regression generated to determine whether an intruder’s uESVs found on door handles in an office decayed over time in the presence or absence of office workers, found no significant shift in proportion of uESVs over time irrespective of the presence of office workers. While it was possible to detect the correct burglars’ microbiota as having contributed to the invaded space, the predictions were very weak in comparison to accepted forensic standards. This suggests that at this time 16S rRNA amplicon sequencing of the built environment microbiota cannot be used as a reliable trace evidence standard for criminal investigations.
Keywords: Forensic microbiology | Built-environment | Host-microbe | Trace evidence | Human microbiome
مقاله انگلیسی
3 یک مطالعه بیومکانیکی و فیزیولوژیکی روی صندلی اداری و تعامل با تبلت
سال انتشار: 2017 - تعداد صفحات فایل pdf انگلیسی: 11 - تعداد صفحات فایل doc فارسی: 36
بیست سابجکت چند وظیفه تایپ کردن با کامپیوتر روی میز و تبلتِ دارای صفحه نمایش لمسی را، روی دو صندلی، هریک به مدت یک ساعت، انجام دادند و آثارِ صندلی، دستگاه، و تعاملات آنها برروی هر یک از معیارهای وابسته ثبت شد. معیارهای بیومکانیکی شاملِ نیروی عضله، بارِ وارد بر نخاع، و وضعِ نشستن بررسی شدند، درحالیکه ناراحتی ازطریقِ تغییرپذیریِ نرخ ضربان قلب (HRV) و گزارشات سابجکتیو اندازه¬گیری شد. HRV به اندازه¬ی کافی حساس بود که بین تعاملات دستگاه و صندلی تمایز بگذارد. از نظر بیومکانیکی، فقدان حرکت¬پذیریِ پشتیِ صندلی، افراد را مجبور کرد که یک وضعِ نشسته¬ی قائم را همراه¬با افزایش نیروهایِ عضله¬ی اکستنسور و افزایش فشردگیِ نخاعی حفظ کنند. فلکشن به¬سمت جلو هنگام تعامل با تبلت یا به¬دلیل دولا شدن ، آثار را بدتر کرد. صندلی¬های اداری باید هم با در نظر گرفتن انسان و هم وظیفه¬ی کاری طراحی شوند و به وضع¬های نشستنِ خمیده اجازه دهند که بار نخاع را کنار بگذارند. با این حال، درجه¬ی خمیدگی باید محدود باشد تا از کاهش لوردوسیسِ لومبار درنتیجه¬ی چرخشِ خلفی مفصل ران در وضع¬های نشستنِ شدیداً خمیده، اجتناب شود.
مقاله ترجمه شده
4 An efficient strategy using k-mers to analyse 16S rRNA sequences
یک راهبرد کارآمد با استفاده از k-mer ها برای تحلیل ترتیب های 16S rRNA-2017
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k- mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.http://dx.doi.org/10.1016/j.heliyon.2017.e003702405-8440/ © 2017 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
مقاله انگلیسی
5 The Human Microbiota in Health and Disease
میکروبیولوژیک انسان در سلامت و بیماری-2017
Trillions of microbes have evolved with and continue to live on and within human beings. A variety of environmental factors can affect intestinal microbial imbalance, which has a close relationship with human health and disease. Here, we focus on the interactions between the human microbiota and the host in order to provide an overview of the microbial role in basic biological processes and in the development and progression of major human diseases such as infectious diseases, liver diseases, gastrointestinal cancers, metabolic diseases, respiratory diseases, mental or psychological diseases, and autoimmune diseases. We also review important advances in techniques associated with microbial research, such as DNA sequencing, metabonomics, and proteomics combined with computation-based bioinformatics. Current research on the human microbiota has become much more sophisticated and more comprehensive. Therefore, we propose that research should focus on the host-microbe interaction and on causeeffect mechanisms, which could pave the way to an understanding of the role of gut microbiota in health and disease, and provide new therapeutic targets and treatment approaches in clinical practice.
Keywords: Microbiome | Health | Infectious disease | Liver diseases | Gastrointestinal malignancy | Metabolic disorder | Microbiota technology | Probiotics
مقاله انگلیسی
6 An efficient strategy using k-mers to analyse 16S rRNA sequences
استراتژی کارآمد با استفاده از k-mers برای تحلیل توالی rRNA 16S-2017
The use of k-mers has been a successful strategy for improving metagenomics studies, including taxonomic classifications, or de novo assemblies, and can be used to obtain sequences of interest from the available databases. The aim of this manuscript was to propose a simple but efficient strategy to generate k-mers and to use them to obtain and analyse in silico 16S rRNA sequence fragments. A total of 513,309 bacterial sequences contained in the SILVA database were considered for the study, and homemade PHP scripts were used to search for specific nucleotide chains, recover fragments of bacterial sequences, make calculations and organize information. Consensus sequences matching conserved regions were constructed by aligning most of the primers used in the literature. Sequences of k nucleotides (9- to 15-mers) were extracted from the generated primer contigs. Frequency analysis revealed that k-mer size was inversely proportional to the occurrence of k mers in the different conserved regions, suggesting a stringency relationship; high numbers of duplicate reactions were observed with short k-mers, and a lower proportion of sequences were obtained with large ones, with the best results obtained using 12-mers. Using 12-mers with the proposed method to obtain and study sequences was found to be a reliable approach for the analysis of 16S rRNA sequences and this strategy may probably be extended to other biomarkers. Furthermore, additional applications such as evaluating the degree of conservation and designing primers and other calculations are proposed as examples.
Keywords: Bioinformatics | Microbiology | Biological sciences
مقاله انگلیسی
7 مناسب بودن آزمایش میکروبی محصول نهایی در مدیریت امنیت مواد غذایی
سال انتشار: 2016 - تعداد صفحات فایل pdf انگلیسی: 13 - تعداد صفحات فایل doc فارسی: 41
مدیریت میکروبیولوژیکی امنیت مواد غذایی تاحد زیادی بر پایه طراحی مناسب فرآیندها، محصولات و شیوه ها، استوار است. آزمایش محصولِ آماده به فروش، می تواند به عنوان یک سنجش کیفیت در انتهای فرآیند تولید تلقی شود. با این حال، آزمایش کردن، تنها اطلاعات بسیار محدودی از وضعیت ایمنی یک ماده غذایی می دهد. اگر یک موجود زنده خطرناک در داخل غذا یافت شود، به معنای عدم ایمنی است اما عدم وجود حتی مقدار کمی از این موجودات زنده، تضمینی برای امنیت کل محصولات تولید شده نیست. آزمایش محصول آماده فروش اغلب بسیار مختصر و بسیار دیرهنگام است. بنابراین توجه بیشتری باید روی مدیریت و کنترل خطرات از طریق روشهای پیشگیرانه و اجرای یک سیستم مدیریت موثر امنیت مواد غذایی متمرکز شود. برای وارسی فعالیتهای یک سیستم مدیریت امنیت مواد غذایی، آزمایش محصول آماده فروش می تواند مفید باشد. برای سه مورد از مطالعات انجام شده روی مواد غذایی کنسروی، شکلاتی و ژامبون پخته شده، مناسب بودن آزمایش این مواد هم برای محصولات آماده و هم برای محیط تولید، مورد بحث قرار می گیرد. از آنجایی که سطح کنترل فرآیندهای مختلف می تواند تاحد زیادی متفاوت باشد و اگر تعداد نمونه های محصولات آماده و محیط تولید وابسته به خطر سلامتی انسانی باشد، آزمایش مواد غذایی می تواند سودمند باشد و می تواند بر پایه بررسی خطر و داده های مربوط به همه گیری انجام شود.
کلیدواژه ها: نمونه گیری | وارسی | امنیت میکروبیولوژیکی مواد غذایی
مقاله ترجمه شده
8 Relevance of microbial finished product testing in food safety management
ارتباط تست محصول به پایان رسیده میکروبی در مدیریت ایمنی مواد غذایی-2016
Management of microbiological food safety is largely based on good design of processes, products and procedures. Finished product testing may be considered as a control measure at the end of the pro- duction process. However, testing gives only very limited information on the safety status of a food. If a hazardous organism is found it means something, but absence in a limited number of samples is no guarantee of safety of a whole production batch. Finished product testing is often too little and too late. Therefore most attention should be focussed on management and control of the hazards in a more pro- active way by implementing an effective food safety management system. For verification activities in a food safety management system, finished product testing may however be useful. For three cases studies; canned food, chocolate and cooked ham, the relevance of testing both of finished products and the production environment is discussed. Since the level of control of different processes can be largely different it is beneficial if the frequency of sampling of finished products and production environments would be related to the associated human health risk, which can be assessed on the basis of risk assessment and epidemiological data.© 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-NDlicense (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Sampling | Verification | Microbiological food safety
مقاله انگلیسی
9 Relevance of microbial finished product testing in food safety management
ارتباط تست محصول به پایان رسیده میکروبی در مدیریت ایمنی مواد غذایی-2016
Management of microbiological food safety is largely based on good design of processes, products and procedures. Finished product testing may be considered as a control measure at the end of the pro- duction process. However, testing gives only very limited information on the safety status of a food. If a hazardous organism is found it means something, but absence in a limited number of samples is no guarantee of safety of a whole production batch. Finished product testing is often too little and too late. Therefore most attention should be focussed on management and control of the hazards in a more pro- active way by implementing an effective food safety management system. For verification activities in a food safety management system, finished product testing may however be useful. For three cases studies; canned food, chocolate and cooked ham, the relevance of testing both of finished products and the production environment is discussed. Since the level of control of different processes can be largely different it is beneficial if the frequency of sampling of finished products and production environments would be related to the associated human health risk, which can be assessed on the basis of risk assessment and epidemiological data.© 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-NDlicense (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Sampling | Verification | Microbiological food safety
مقاله انگلیسی
10 تصویر برداری نانومقیاس برای رشد و تقسیم سلولهای باکتری روی زیر لایه مسطح با میکروسکوپ نیروی اتمی
سال انتشار: 2015 - تعداد صفحات فایل pdf انگلیسی: 8 - تعداد صفحات فایل doc فارسی: 25
با استفاده از میکروسکوپ نیروی اتمی(AFM), محدوده نانومیکروبیولوژی به شدت پیشرفت نمود. به دلیل پیچیدگی تصویر برداری فرایندهای باکتری زنده در محیطهای رشد طبیعی، باید بهبودهایی در این زمینه صورت گیرد. ما تصویر برداری در موقعیت نانومقیاس برای رشد و تقسیم سلولهای تک باکتری را روی زیر لایه مسطح با میکروسکوپ نیروی اتمی بررسی نمودیم. برای انجام اینکار، ما نیروی جانبی برشی مسئول جداسازی باکترهایی که به صورت ضعیفی روی زیر لایه مسطح جذب شده بودند را با استفاده از مد پرش از پیش ذکر شده با ردیابهای پایه خیلی نرم کاهش دادیم . با اینکار، شرایط تصویر برداری خیلی خوبی برای تصویر برداری پیوسته رشد سلولهای باکتری و تقسیم انها حتی در زیر لایه های نرم، فراهم شد. نتایج حاصله امکان مشاهده فرایند زنده باکتریهای غیر تله اندازی شده که به صورت ضعیف به زیر لایه مسطح چسبیده بودند، فراهم شد.
کلمات کلیدی: میکروسکوپ نیروی اتمی (AFM) | تصویربرداری زندگی سلول | بخش باکتریایی | بیحرکتی ژلاتین | حالت پرش پویا
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