Methods in Microbiology最新文献

{"title":"Use of epifluorescence widefield deconvolution microscopy for imaging and three-dimensional rendering of <i>Pseudomonas aeruginosa</i> biofilms and extracellular matrix materials.","authors":"Heidi J Smith, Michael J Franklin","doi":"10.1016/bs.mim.2023.05.005","DOIUrl":"10.1016/bs.mim.2023.05.005","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225936/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions.","authors":"Ankita Bhattacharyya, Olga Mavrodi, Niladri Bhowmik, David Weller, Linda Thomashow, Dmitri Mavrodi","doi":"10.1016/bs.mim.2023.05.006","DOIUrl":"10.1016/bs.mim.2023.05.006","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10898258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139984368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Preface","authors":"C. Pavia, V. Gűrtler","doi":"10.1016/S0580-9517(22)00017-4","DOIUrl":"https://doi.org/10.1016/S0580-9517(22)00017-4","url":null,"abstract":"","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49604083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike.","authors":"Kelsey Caetano-Anollés, Nicolas Hernandez, Fizza Mughal, Tre Tomaszewski, Gustavo Caetano-Anollés","doi":"10.1016/bs.mim.2021.10.002","DOIUrl":"10.1016/bs.mim.2021.10.002","url":null,"abstract":"<p><p>Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8590929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46833463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A review of hypersensitivity methods to detect immune responses to SARS-CoV-2.","authors":"Fernando Díaz-Espada, Victor Matheu, Yvelise Barrios","doi":"10.1016/bs.mim.2021.12.001","DOIUrl":"10.1016/bs.mim.2021.12.001","url":null,"abstract":"<p><p>The investigation of the immune response after SARS-CoV-2 infection has been the goal of many researchers worldwide. The study of humoral immune responses and <i>in vitro</i> T cell production after infection requires the obtaining of individualized blood samples to test the presence of antibodies or activated T cells specific for the virus. <i>In vitro</i> T cell studies are especially troublesome due to the need for more specialized resources often outside the daily routine of clinical laboratories. For this reason the development of a simple and objective method to achieve these T cell studies is needed. In this manuscript we reviewed the hypersensitivity reactions, the theoretical basis and the historical background of delayed type hypersensitivity (DTH) which uses the principles of use of this test in the clinical setting for the past century. In the second part of the review, we focus on COVID adaptive immune responses, to understand the differences and challenges offered by this new application of DTH to investigate immune responses elicited after infection. In the last part of the review a vision provided for the use of this test to investigate the immunogenicity elicited by the vaccines. In our opinion, the clinical guidelines of immune assessment of SARS-CoV-2-infected or vaccinated individuals should include this simple and low-cost test to measure T-cell immunity. Rationale and improved vaccination schemes could be obtained after its implementation in the routine assessment of immunity in this pandemic situation.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8919898/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48943988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sensitive methods for detection of SARS-CoV-2 RNA.","authors":"Xi Chen, Simin Xia","doi":"10.1016/bs.mim.2021.06.001","DOIUrl":"10.1016/bs.mim.2021.06.001","url":null,"abstract":"<p><p>The occurrence of the COVID-19 pandemic caused by the SARS-CoV-2 virus since the end of 2019 has significantly affected the entire world. Now SARS-CoV-2 diagnostic tests are not only required for screening of suspected infected people for their medical treatment, but have also become a routine diagnosis for all people at a place where new cases have emerged in order to control spread of the disease from that region. For these reasons, sensitive methods for detection of SARS-CoV-2 are highly needed in order to avoid undetected infections. In addition, sample pooling that uses pooled specimens has been routinely employed as a time- and cost-effective strategy for community monitoring of SARS-CoV-2. In this regard, the content of each viral RNA sample of an individual will be further diluted in detection; therefore, higher detection sensitivity would be rather preferred. Among nucleic acid-based detection methods, isothermal nucleic acid amplifications are considered quite promising because they typically take less time to complete the test (even less than 20 min) without the need of thermal cycles. Hence, it does not necessitate the use of highly costly real-time PCR machines. According to recently published isothermal nucleic acid amplification methods, the reverse transcription recombinase polymerase amplification (RT-RPA) approach shows outstanding sensitivity with up to single-copy sensitivity in a test reaction. This chapter will mainly focus on how to employ RT-RPA technology to sensitively detect SARS-CoV-2 RNA. Besides, recently published RT-RPA based detection methods will be summarized and compared regarding their detection parameters and the primers and probes being used. In addition, we will also highlight the key considerations on how to design an ultrasensitive RT-RPA assay and the precautions needed to conduct the assay. Moreover, based on our recent report, we will also detail the methods we developed to detect SARS-CoV-2 RNA using modified RT-RPA, or RT-ERA, with single-copy sensitivity and the possible extensions beyond this method.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8283572/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47886704","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hesitancy to get vaccinated against COVID-19 and how it might be overcome.","authors":"Charles S Pavia","doi":"10.1016/bs.mim.2021.10.001","DOIUrl":"10.1016/bs.mim.2021.10.001","url":null,"abstract":"<p><p>The hesitancy and resistance to get vaccinated against COVID-19, by a relatively small but significant part of the general population, has become a serious worldwide problem, and particularly in the United States, despite a vigorous and highly organized governmental advertising campaign promoting vaccination. The unwillingness to get vaccinated has its roots in mostly the spreading of non-scientific, unproven or misleading information. This chapter explains many of the reasons, including an historical connection, behind this anti-vaccine movement, and proposes several possible and feasible remedies to counter this sentiment.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8610375/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47132800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR use in diagnosis and therapy for COVID-19.","authors":"Pallavi Deol, Aashwina Madhwal, Gaurav Sharma, Rahul Kaushik, Yashpal Singh Malik","doi":"10.1016/bs.mim.2022.03.002","DOIUrl":"10.1016/bs.mim.2022.03.002","url":null,"abstract":"<p><p>Since the beginning of the COVID-19 pandemic, many diagnostic approaches (RT-qPCR, RAPID, LFA) have been adopted, with RT-qPCR being the most popular/gold standard. But, one of the major problems of COVID-19 diagnostics is the presentation of a wide range of symptoms which varies among different patients and needs early diagnosis for better management. Even though RT-qPCR is a precise molecular technique false negative results may be obtained. On the other hand, CRISPR-based SARS-CoV-2 detection approaches are cost and time efficient, highly sensitive and specific, and do not require sophisticated instruments. Moreover, they also show promise for increased scalability and diagnostic tests can be carried out at the point-of-care (POC). The CRISPR can be customized to the target of any genomic region of interest within the desired genome possessing a broad range of other applications and has been efficiently implemented for diagnosis of SARS-CoV-2. The CRISPR/Cas systems provide the specific gene targeting with immense potential to develop new generation diagnostics and therapeutics. Moreover, with the CRISPR/Cas based therapeutics, multiplexing is possible, where different sgRNAs or crRNAs can be guided to more than one target within the same gene thus decreasing the possibility of viral escape mutants. As an exceptionally efficient tool CRISPR/Cas13 and CARVER (Cas13-assisted restriction of viral expression and readout) systems can be implemented to target a broad range of ssRNA viruses that can be used for both, diagnosis and treatment for a variety of viral diseases including SARS-CoV-2. However, the efficacy and safety of the CRISPR-based therapeutics needs to be assessed in pre-clinical and clinical settings. Although the CRISPR biotechnologies are not very helpful to control the present pandemic of COVID-19 it is hopeful that the limitations of the CRISPR/Cas system can be overcome in the near future. The CRISPR based strategies may lead to a new era in the field of disease diagnosis and therapeutic development that would make us better prepared for future viral threats.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073596/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48185218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent and advanced nano-technological strategies for COVID-19 vaccine development.","authors":"Chinekwu Sherridan Nwagwu, Chinenye Nnenna Ugwu, John Dike Nwabueze Ogbonna, Adaeze Linda Onugwu, Chinazom Precious Agbo, Adaeze Chidiebere Echezona, Ezinwanne Nneoma Ezeibe, Samuel Uzondu, Frankline Chimaobi Kenechukwu, Paul Achile Akpa, Mumuni Audu Momoh, Petra Obioma Nnamani, Clemence Tarirai, Kenneth Chibuzor Ofokansi, Anthony Amaechi Attama","doi":"10.1016/bs.mim.2022.03.001","DOIUrl":"10.1016/bs.mim.2022.03.001","url":null,"abstract":"<p><p>The outbreak of the COVID-19 pandemic in 2019 has been one of the greatest challenges modern medicine and science has ever faced. It has affected millions of people around the world and altered human life and activities as we once knew. The high prevalence as well as an extended period of incubations which usually does not present with symptoms have played a formidable role in the transmission and infection of millions. A lot of research has been carried out on developing suitable treatment and effective preventive measures for the control of the pandemic. Preventive strategies which include social distancing, use of masks, washing of hands, and contact tracing have been effective in slowing the spread of the virus; however, the infectious nature of the SARS-COV-2 has made these strategies unable to eradicate its spread. In addition, the continuous increase in the number of cases and death, as well as the appearance of several variants of the virus, has necessitated the development of effective and safe vaccines in a bid to ensure that human activities can return to normalcy. Nanotechnology has been of great benefit in the design of vaccines as nano-sized materials have been known to aid the safe and effective delivery of antigens as well as serve as suitable adjuvants to potentiate responses to vaccines. There are only four vaccine candidates currently approved for use in humans while many other candidates are at various levels of development. This review seeks to provide updated information on the current nano-technological strategies employed in the development of COVID-19 vaccines.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9015106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42885904","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Current molecular diagnostics assays for SARS-CoV-2 and emerging variants.","authors":"Jonathan M Banks, Kristelle Capistrano, Pari Thakkar, Hemangi Ranade, Vaidik Soni, Manali Datta, Afsar R Naqvi","doi":"10.1016/bs.mim.2021.10.003","DOIUrl":"10.1016/bs.mim.2021.10.003","url":null,"abstract":"<p><p>Since the SARS-CoV-2 virus triggered the beginning of the COVID-19 pandemic, scientists, government officials, and healthcare professionals around the world recognized the need for accessible, affordable, and accurate testing to predict and contain the spread of COVID-19. In the months that followed, research teams designed, tested, and rolled out hundreds of diagnostic assays, each with different sampling methods, diagnostic technologies, and sensitivity levels. However, the contagious virus continued to spread; SARS-CoV-2 travelled through airborne particles and spread rapidly, despite the widening use of diagnostic assays. As the pandemic continued, hundreds of millions of people contracted COVID-19 and millions died worldwide. With so many infections, SARS-CoV-2 received many opportunities to replicate and mutate, and from these mutations emerged more contagious, deadly, and difficult-to-diagnose viral mutants. Each change to the viral genome presented potential added challenges to containing the virus, and as such, researchers have continued developing and improving testing methods to keep up with COVID-19. In this chapter, we examine several SARS-CoV-2 variants that have emerged during the pandemic. Additionally, we discuss a few major COVID-19 diagnostic technique categories, including those involving real-time PCR, serology, CRISPR, and electronic biosensors. Finally, we address SARS-CoV-2 variants and diagnostic assays in the age of COVID-19 vaccines.</p>","PeriodicalId":49823,"journal":{"name":"Methods in Microbiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8655725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49018278","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}