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Real-Time PCR in Clinical Microbiology: Applications for Routine Laboratory Testing

Espy, M. J.; Uhl, J. R.; Sloan, L. M.; Buckwalter, S. P.; Jones, M. F.; Vetter, E. A.; Yao, J. D. C.; Wengenack, N. L.; Rosenblatt, J. E.; Cockerill, F. R.; Smith, T. F.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /01/2006 EN
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35.97%
Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Microarray and Real-Time PCR Analyses of the Responses of High-Arctic Soil Bacteria to Hydrocarbon Pollution and Bioremediation Treatments▿

Yergeau, Etienne; Arbour, Mélanie; Brousseau, Roland; Juck, David; Lawrence, John R.; Masson, Luke; Whyte, Lyle G.; Greer, Charles W.
Fonte: American Society for Microbiology (ASM) Publicador: American Society for Microbiology (ASM)
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
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High-Arctic soils have low nutrient availability, low moisture content, and very low temperatures and, as such, they pose a particular problem in terms of hydrocarbon bioremediation. An in-depth knowledge of the microbiology involved in this process is likely to be crucial to understand and optimize the factors most influencing bioremediation. Here, we compared two distinct large-scale field bioremediation experiments, located at the Canadian high-Arctic stations of Alert (ex situ approach) and Eureka (in situ approach). Bacterial community structure and function were assessed using microarrays targeting the 16S rRNA genes of bacteria found in cold environments and hydrocarbon degradation genes as well as quantitative reverse transcriptase PCR targeting key functional genes. The results indicated a large difference between sampling sites in terms of both soil microbiology and decontamination rates. A rapid reorganization of the bacterial community structure and functional potential as well as rapid increases in the expression of alkane monooxygenases and polyaromatic hydrocarbon-ring-hydroxylating dioxygenases were observed 1 month after the bioremediation treatment commenced in the Alert soils. In contrast, no clear changes in community structure were observed in Eureka soils...

A Critical Appraisal of the Role of the Clinical Microbiology Laboratory in the Diagnosis of Bloodstream Infections

Weinstein, Melvin P.; Doern, Gary V.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2011 EN
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The detection of bloodstream infections is one of the most important functions of clinical microbiology laboratories. Despite advances in blood culture technology and clinical studies that have focused on the detection of bacteremia and fungemia, perfection has not been achieved and uncertainties persist. This review provides perspectives on a number of areas, including the recommended number of blood cultures, duration of incubation of blood cultures, use of anaerobic, in addition to aerobic, blood culture media, value of the lysis-centrifugation method, processing and reporting of probable blood culture contaminants, and limitations of current blood culture methods and systems. We also address the handling of blood cultures in point-of-care locations that lack full microbiology capabilities.

New Technologies in Clinical Microbiology

Wolk, Donna M.; Dunne, W. Michael
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /09/2011 EN
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Rapid identification of microorganisms in the clinical microbiology laboratory can be of great value for selection of optimal patient management strategies for infections caused by bacteria, viruses, fungi, mycobacteria, and parasites. Rapid identification of microorganisms in clinical samples enables expedient de-escalation from broad-spectrum agents to targeted antimicrobial therapy. The switch to tailored therapy minimizes risks of antibiotics, namely, disruption of normal flora, toxic side effects, and selective pressure. There is a critical need for new technologies in clinical microbiology, particularly for bloodstream infections, in which associated mortality is among the highest of all infections. Just as importantly, there is a need for the clinical laboratory community to embrace the practices of evidence-based interventional laboratory medicine and collaborate in translational research projects to establish the clinical utility, cost benefit, and impact of new technologies.

PCR Identification of Bacteria in Blood Culture Does Not Fit the Daily Workflow of a Routine Microbiology Laboratory

Karumaa, Santra; Kärpänoja, Pauliina; Sarkkinen, Hannu
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /03/2012 EN
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We have evaluated the GenoType blood culture assay (Hain Lifescience, Nehren, Germany) for the identification of bacteria in 233 positive blood cultures and assessed its suitability in the workflow of a routine microbiology laboratory. In 68/233 (29.2%) samples, the culture result could not be confirmed by the GenoType assay due to a lack of primers in the test, multiple organisms in the sample, or inconsistency with respect to the identification by culture. Although the GenoType blood culture assay gives satisfactory results for bacteria for which primers are available, there are difficulties in applying the test in the routine microbiology laboratory.

The Influence of Rickettsiologists on Post-Modern Microbiology

Georgiades, Kalliopi; Merhej, Vicky; Raoult, Didier
Fonte: Frontiers Research Foundation Publicador: Frontiers Research Foundation
Tipo: Artigo de Revista Científica
Publicado em 31/10/2011 EN
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Many of the definitions in microbiology are currently false. We have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. The presence of compartmentation and a nucleoid in Planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. Archaea are viewed as prokaryotes resembling bacteria. However, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent with the lifestyle of this family. Viruses are defined as small, filterable infectious agents, but giant viruses challenge the size criteria used for the definition of a virus. Pathogenicity does not require the acquisition of virulence factors (except for toxins), and in many cases, gene loss is significantly inked to the emergence of virulence. Species classification based on 16S rRNA is useless for taxonomic purposes of human pathogens, as a 2% divergence would classify all Rickettsiae within the same species and would not identify bacteria specialized for mammal infection. The use of metagenomics helps us to understand evolution and physiology by elucidating the structure, function, and interactions of the major microbial communities, but it neglects the minority populations. Finally...

Implementation of a Service-learning Module in Medical Microbiology and Cell Biology Classes at an Undergraduate Liberal Arts University †

Larios-Sanz, Maia; Simmons, Alexandra D.; Bagnall, Ruth Ann; Rosell, Rosemarie C.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em 19/05/2011 EN
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Here we discuss the implementation of a service-learning module in two upper-division biology classes, Medical Microbiology and Cell Biology. This exciting hands-on learning experience provided our students with an opportunity to extend their learning of in-class topics to a real-life scenario. Students were required to volunteer their time (a minimum of 10 hours in a semester) at an under-served clinic in Houston, Texas. As they interacted with the personnel at the clinic, they were asked to identify the most prevalent disease (infectious for Medical Microbiology, and cellular-based for Cell) seen at the clinic and, working in groups, come up with educational material in the form of a display or brochure to be distributed to patients. The material was meant to educate patients about the disease in general terms, as well as how to recognize (symptoms), prevent and treat it. Students were required to keep a reflective journal in the form of a blog throughout the semester, and present their final materials to the class orally. Students were surveyed about their opinion of the experience at the end of the semester. The vast majority of student participants felt that the project was a positive experience and that it helped them develop additional skills beyond what they learn in the classroom and understand how lecture topics relate to every day life.

Using Small Group Debates to Actively Engage Students in an Introductory Microbiology Course†

Shaw, Joyce A.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em 03/12/2012 EN
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Debates stimulate critical thinking and can be a highly effective way to actively engage students in the classroom. This paper describes a small group debate format in which groups of four to six students debated preassigned topics in microbiology in front of the rest of the class. Rapid advancements in science, especially in microbiology, provide the scaffolding for students to locate and share evidence-based information from a plethora of complex and often conflicting sources. Student-generated debate presentations can be a welcome respite from the lecture format. Debates were scheduled throughout the course to coincide with topics being covered. Questionnaires distributed immediately after each debate revealed that the debates were well received by students and were effective in changing student attitudes and misconceptions. Debate preparation provided students the opportunity to gain proficiency in accessing information from electronic databases, to use resources from professional organizations, and to synthesize and analyze information. In addition, the debate process gave students experience in developing oral communication skills.

An Activity-Based Format Increased Student Retention in a Community College Microbiology Course

LUX, MARY F.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2002 EN
Relevância na Pesquisa
35.97%
Microbiology is offered each semester at the Allied Health Campus of Pearl River Community College. The evening course meets weekly for 16 sessions from 5 p.m. to 10 p.m. Most students enrolled in the course are in one of the seven associate degree allied health programs on the allied health campus. Among the challenges of teaching a course in this situation is retention of enrolled students. Although the course is required for most of the allied health programs on the campus, many students enrolled, attended class for a few weeks, and withdrew from the course. During the 1998–1999 school year the retention rates for students enrolled in the night microbiology classes for Fall and Spring semesters were 52% and 47%, respectively. The format for the 1998–1999 academic year was a conventional course with 2½ hours of lecture material followed by 2 hours of laboratory. Little or no effort was made to correlate laboratory and lecture topics. The course format for Fall 1999 was modified to (i) provide the laboratory component at the beginning of the time slot, (ii) tailor the lecture topics to relate to the laboratory component each night, and (iii) add an outside reading component. The laboratory served as an introduction to the lecture topic...

Learning Microbiology Through Cooperation: Designing Cooperative Learning Activities that Promote Interdependence, Interaction, and Accountability

TREMPY, JANINE E.; SKINNER, MONICA M.; SIEBOLD, WILLIAM A.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2002 EN
Relevância na Pesquisa
35.97%
A microbiology course and its corresponding learning activities have been structured according to the Cooperative Learning Model. This course, The World According to Microbes, integrates science, math, engineering, and technology (SMET) majors and non-SMET majors into teams of students charged with problem solving activities that are microbial in origin. In this study we describe development of learning activities that utilize key components of Cooperative Learning—positive interdependence, promotive interaction, individual accountability, teamwork skills, and group processing. Assessments and evaluations over an 8-year period demonstrate high retention of key concepts in microbiology and high student satisfaction with the course.

Development of a Microbiology Course for Diverse Majors; Longitudinal Survey of the Use of Various Active, Problem-Based Learning Assignments

CUNDELL, DIANA R.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2002 EN
Relevância na Pesquisa
35.97%
Educators are increasingly being encouraged to use more active- and problem-based-learning techniques and assignments in the classroom to improve critical and analytical thinking skills. Active learning-based courses have been purported to be more time consuming than traditional lecture methods and for many instructors have therefore proven difficult to include in many one-semester science courses. To address this problem, a series of assignments was developed for use in a basic microbiology course involving sophomore-, junior-, and senior-level students from five different biology majors (environmental science, biology, biochemistry, premedicine, and physician assistant). Writing assignments included global, historical, and social themes for which a standardized grading format was established. Students also participated in a class debate in which the merits of the living microbial kingdoms were discussed, with only one kingdom being saved from an imaginary global catastrophe. Traditional lectures were facilitated by the use of a dedicated note packet developed by the instructor and specific for course content. Laboratories involved group analysis of mini-case history studies involving pathogenic microbes. Students’ perceptions of the subject were assessed using an exit questionnaire sent to 100 of the 174 students who had taken the course during the 5-year time period. The majority of the 64 students who responded were sophomores (78%)...

Promoting Student Involvement with Environmental Laboratory Experiments in a General Microbiology Course

TARAS, LORETTA BRANCACCIO
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2003 EN
Relevância na Pesquisa
35.97%
This is a descriptive study of a series of laboratory exercises on environmental microbiology carried out by students in a general microbiology course during eight of the twelve weeks of the semester. The revised laboratory component is predicated upon seawater and sediment samples collected by student pairs using marine sampling equipment on a field trip aboard a research vessel. Two longitudinal studies were performed: assay for antibiotic production from isolated actinomycetes and construction and observation of Winogradsky columns. Two additional experiments: culturing microalgae and water testing for coliforms also used the samples collected by the students. The advantages of long-term, challenging laboratory experiences actively involving the students in group process, self-direction, and scientific practices are discussed. Also considered are development of laboratory skills, scientific competencies, and students’ self-confidence in carrying out such environmental investigations. Plans for future assessment of student learning are presented.

Efficacy of MedMyst: an Internet Teaching Tool for Middle School Microbiology

MILLER, LESLIE M.; MORENO, JANETTE; ESTRERA, VICKY; LANE, DAVID
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2004 EN
Relevância na Pesquisa
35.97%
Can web-based technology be used to effectively introduce or reinforce aspects of microbiology to middle school students? This central hypothesis examines whether brief exposure to a web adventure format containing virtual lab experiments and computer games within an engaging story line can impact student learning. An episodic adventure series, MedMyst (http://medmyst.rice.edu), focuses on infectious diseases and the microbes that cause them. The website is not intended to replace classroom instruction, but rather to engage students in problem-solving activities not likely to be encountered elsewhere. It also provides scientists with a resource to introduce microbiology to adolescent audiences through outreach activities. In the online adventure, the player (student) enters a futuristic world in which he or she becomes a “Reconstructor,” a member of an elite team charged with preventing the spread of infectious disease. The series consists of three “missions,” each lasting approximately 30 to 40 minutes and designed to address a limited set of learning objectives. Middle school students participated in the creation of the characters and the stylized design through focus groups. Classroom teachers oversaw the alignment of the web adventure objectives with the National Science Content Standards. Scientists and clinicians reviewed the web adventure for content and accuracy. A field test involving over 700 students from nine different schools assessed the knowledge gains attributable to playing MedMyst. Gain scores from pretest to posttest indicated that middle school students retained important information by interacting with the online material for as little as 30 minutes per adventure; however...

The Delta Cooperative Model: a Dynamic and Innovative Team-Work Activity to Develop Research Skills in Microbiology

RIOS-VELAZQUEZ, CARLOS; ROBLES-SUAREZ, REYNALDO; GONZALEZ-NEGRON, ALBERTO J.; BAEZ-SANTOS, IVAN
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em /05/2006 EN
Relevância na Pesquisa
35.97%
The Delta Cooperative Model (DCM) is a dynamic and innovative teamwork design created to develop fundamentals in research skills. High school students in the DCM belong to the Upward Bound Science and Math (UBSM) program at the Inter American University, Ponce Campus. After workshops on using the scientific method, students were organized into groups of three students with similar research interests. Each student had to take on a role within the group as either a researcher, data analyst, or research editor. Initially, each research team developed hypothesis-driven ideas on their proposed project. In intrateam research meetings, they emphasized team-specific tasks. Next, interteam meetings were held to present ideas and receive critical input. Finally, oral and poster research presentations were conducted at the UBSM science fair. Several team research projects covered topics in medical, environmental, and general microbiology. The three major assessment areas for the workshop and DCM included: (i) student’s perception of the workshops’ effectiveness in developing skills, content, and values; (ii) research team self- and group participation evaluation, and (iii) oral and poster presentation during the science fair. More than 91% of the students considered the workshops effective in the presentation of scientific method fundamentals. The combination of the workshop and the DCM increased student’s knowledge by 55% from pre- to posttests. Two rubrics were designed to assess the oral presentation and poster set-up. The poster and oral presentation scores averaged 83% and 75% respectively. Finally...

A Genomic Day in the Life of a Clinical Microbiology Laboratory

Long, S. Wesley; Williams, Dawn; Valson, Chandni; Cantu, Concepcion C.; Cernoch, Patricia; Musser, James M.; Olsen, Randall J.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /04/2013 EN
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Next-generation sequencing technology is available to many clinical laboratories; however, it is not yet widely used in routine microbiology practice. To demonstrate the feasibility of using whole-genome sequencing in a routine clinical microbiology workflow, we sequenced the genome of every organism isolated in our laboratory for 1 day.

Oxford-Style Debates in a Microbiology Course for Majors: A Method for Delivering Content and Engaging Critical Thinking Skills †

Boucaud, Dwayne W.; Nabel, Michael; Eggers, Christian H.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em 06/05/2013 EN
Relevância na Pesquisa
35.97%
Developing scientific expertise in the classroom involves promoting higher-order cognitive skills as well as content mastery. Effective use of constructivism can facilitate these outcomes. However this is often difficult to accomplish when delivery of content is paramount. Utilizing many of the tenets of constructivist pedagogy, we have designed an Oxford-style debate assignment to be used in an introductory microbiology course. Two teams of students were assigned a debatable topic within microbiology. Over a five-week period students completed an informative web page consisting of three parts: background on the topic, data-based positions for each side of the argument, and a data-based persuasive argument to support their assigned position. This was followed by an in-class presentation and debate. Analysis of student performance on knowledge-based questions shows that students retain debate-derived content acquired primarily outside of lectures significantly better than content delivered during a normal lecture. Importantly, students who performed poorly on the lecture-derived questions did as well on debate-derived questions as other students. Students also performed well on questions requiring higher-order cognitive skills and in synthesizing data-driven arguments in support of a position during the debate. Student perceptions of their knowledge-base in areas covered by the debate and their skills in using scientific databases and analyzing primary literature showed a significant increase in pre- and postassignment comparisons. Our data demonstrate that an Oxford-style debate can be used effectively to deliver relevant content...

The Role of the Clinical Laboratory in the Future of Health Care: Lean Microbiology

Samuel, Linoj; Novak-Weekley, Susan
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Publicado em /06/2014 EN
Relevância na Pesquisa
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This commentary will introduce lean concepts into the clinical microbiology laboratory. The practice of lean in the clinical microbiology laboratory can remove waste, increase efficiency, and reduce costs. Lean, Six Sigma, and other such management initiatives are useful tools and can provide dividends but must be accompanied by organizational leadership commitment to sustaining the lean culture in the laboratory setting and providing resources and time to work through the process.

Atomic Force Microscopy in Microbiology: New Structural and Functional Insights into the Microbial Cell Surface

Dufrêne, Yves F.
Fonte: American Society of Microbiology Publicador: American Society of Microbiology
Tipo: Artigo de Revista Científica
Publicado em 22/07/2014 EN
Relevância na Pesquisa
35.97%
Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights.

Efficacy of MedMyst: an Internet Teaching Tool for Middle School Microbiology

Miller, Leslie M.; Moreno, Janette; Estrera, Vicky; Lane, David
Fonte: Universidade Rice Publicador: Universidade Rice
Tipo: Artigo de Revista Científica
ENG
Relevância na Pesquisa
35.97%
Can web-based technology be used to effectively introduce or reinforce aspects of microbiology to middle school students? This central hypothesis examines whether brief exposure to a web adventure format containing virtual lab experiments and computer games within an engaging story line can impact student learning. An episodic adventure series, MedMyst (http://medmyst.rice.edu), focuses on infectious diseases and the microbes that cause them. The website is not intended to replace classroom instruction, but rather to engage students in problem-solving activities not likely to be encountered elsewhere. It also provides scientists with a resource to introduce microbiology to adolescent audiences through outreach activities. In the online adventure, the player (student) enters a futuristic world in which he or she becomes a “Reconstructor,” a member of an elite team charged with preventing the spread of infectious disease. The series consists of three “missions,” each lasting approximately 30 to 40 minutes and designed to address a limited set of learning objectives. Middle school students participated in the creation of the characters and the stylized design through focus groups. Classroom teachers oversaw the alignment of the web adventure objectives with the National Science Content Standards. Scientists and clinicians reviewed the web adventure for content and accuracy. A field test involving over 700 students from nine different schools assessed the knowledge gains attributable to playing MedMyst. Gain scores from pretest to posttest indicated that middle school students retained important information by interacting with the online material for as little as 30 minutes per adventure; however...

Historical Adventures in Scientific Discovery: Microbiology/Biochemistry

Gest, Howard
Fonte: Universidade de Indiana Publicador: Universidade de Indiana
Tipo: Artigo de Revista Científica Formato: 1222055 bytes; application/pdf
EN_US
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ERRATUM: on p.87 bottom, delete [see Figure 1].; Recent textbooks are generally deficient in respect to the history of major discoveries in microbiology/biochemistry. These "Historical Adventures" focus on the backgrounds and contributions of a number of relatively unknown pioneering investigators, as well as some of the familiar "giants." This publication is part of "An Experiment in Scientific Biography". A companion part, "Associations with distinguished scientists ..." can be accessed at https://scholarworks.iu.edu/dspace/bitstream/2022/1083/1/Gestfinal.pdf.