Microbiology

Urinalysis Report  (50  points) Report  Due  Date:  October  18  at  11:59  PM   Submit the report on Blackboard at  Testing and Submission Center folder   Urine Analysis of urine composition and properties is often used to evaluate the function of the kidneys and other organs.  This procedure is called a urinalysis.  A  urinalysis involves three aspects:  physical characteristics,  chemical analysis, and microscopic examination.  Physical characteristics of urine include volume,  color, transparency,  and odor.  The chemical analysis of urine addresses the concentration of solutes such as glucose,  protein,  ketones,  bilirubin,  urobilinogen, nitrite,  leukocyte esterase, and hemoglobin.  The specific gravity and pH of urine are greatly influenced by the components and amounts of solutes.  An examination of microscopic solids including cells,  casts and crystals assist in the diagnosis of injury,  various diseases,  and urinary infection. This report should be considered a professional laboratory report, so avoid using idioms or layperson language in your report. Be creative and tell what you want to say in a clear and precise manner. You may start with a short introduction, but do not spend too much on the introduction, and try to focus on the actual assays in your report. If your statements are inaccurate or unclear, you will lose points. How many points you may ask? The answer depends on the inaccuracy of the statement. I will evaluate each case separately when I am grading your report. There is NO specific format for the laboratory report; however, the report must include the description of every chemical assay in the routine urinalysis including the confirmatory assays. Provide a BRIEF description of each test and its limitations. Indicate what abnormal 1 results may suggest and whether there are any interfering substances that may mislead the investigators. Discuss how each assay may reflect a patient’s health conditions. You will lose points for weak diction and grammar, so make sure to review and edit your final report before submission. Once submitted, you cannot retract the report and will be graded accordingly. The report should not exceed a maximum of 5 pages (not including the title page and references). For your report, the reference list should appear immediately following the report text (beginning on a new page; not included in 5-page maximum). References should contain complete titles and inclusive page numbers and should be numbered in chronological order as they appear in the manuscript. I do not have any preferences for the format of the references (e.g. APA or MLA, …) as long as I can quickly find the exact original reference. If your references are inaccurate or unclear, you will lose major points. If you plagiarize, the report will receive zero points, but I will also dismiss you from the course. You are an adult and responsible for your own actions, so think about your action before you do it. Maximum of 5 pages (single space). 10 points for the quality of written report (e.g. diction, grammar, fluidity). 40 points for accuracy and comprehensive response to the assignment. Urinalysis Procedure Physical Characteristics The color and appearance of the urine specimen are recorded. Usual colors are colorless, straw, yellow, amber; less commonly pink, red, brown. Usual appearances (opacity) are clear or hazy; less commonly turbid, cloudy, and opaque, unless the specimen has remained at room or refrigerated temperatures. Chemical Analysis: 1. The common chemical testing of urine utilizes commercial disposable test strips. The test strips test for Glucose, Bilirubin, Ketone, Specific Gravity, Blood, pH, Protein, Urobilinogen, Nitrite, and Leukocyte Esterase. The result of this testing is regarded as qualitatively (semi-quantitative). 2. A fresh urine specimen is collected in a clean, dry container. A Multistix strip is briefly immersed in the urine specimen, covering all reagent areas. 3. The edge of the Multistix strip is run against the rim of the urine container to remove excess urine. The strip is held in a horizontal position. 4. Time for 30 seconds and then compare the reaction colors of the test areas with those on the strip container, starting with glucose. Make sure that the test strip is properly aligned so that the test area is opposite the correct part of the color chart. The white holding strip should be held towards the top of the strip container. 5. The reactions are read visually. The strip test areas are compared to those on the Multistix color chart at the specified times. The results are recorded, and the strip is discarded.   Confirmatory Assays 1. We can perform confirmatory assays for protein, ketones, and reducing substances. Why do we perform these assays? What information is provided by these assays? Make sure to address this question in your report. 2. We can measure specific gravity for the urine specimen using a refractometer. Does the refractometer result always match the multistix strip? What may be the reason for discrepancies? Make sure to address this issue in the final report. 3. View images of cells, crystals, and casts in the presentations that are provided for you in module 2.  3 Caution: Reducing sugar confirmatory test (Clinitest) is an exothermic chemical reaction that will generate heat. Never hold the tube in your hands while performing the assay. Summary Your final report (50 points) needs to include the description of every chemical assay in the routine urinalysis which includes the confirmatory assays. Provide a BRIEF description of each test and its limitations including the interfering substances. Indicate what any abnormal results may suggest and discuss how each assay may reflect a patient’s health conditions.

The two bacteria I have are (B.cereus) (E.aerogenes). Goals:1.To isolate and identify your bacteria.2.To use the scientific method to reason through a series of questions (tests) and answers (results) to arrive at your conclusions.3.To write your dichotomous chart for your unknowns. 4. Write a short summary of the variety of known pathogen activity for both of these organisms. Please, seek two references for the current outbreak(within 10 years), beyond your book to support your finding. How bad are your bugs? Set up: 1. Write Unknowns on the first line. Section One: Your steps to identifying your unknown. This section needs to include step, what was done? Why done (purpose)? And observations, descriptions, and results of test, conclusion-or what were the results that lead to the next step? Why? Then write up the next step, etc…Section Two: Summarize the entire contents of section one in paragraph form for both bacteria.Section Three: Summarize the results in a dichotomous chart similar to the ones in your lab book appendix.Section Four: Write several paragraphs introducing your bacteria as a pathogen as observed elsewhere.EXAMPLE: (using factious organisms)Unknown report name: Tatiana JonesBacteria: Staphylococcus too harder and Klebsiella nowayoutaMy steps:One: Gram stain my unknown both purpose: to observe fresh culture at 24 hr growth, hoping to see both organize observations/results: Gram + cocci seem to be in chains, Gram –cocci or rods?Two: Made a streak isolation platePurpose: to start isolation, hoping to get separate distinct coloniesObservations/results: Where growing, no separate colony formation, but some halo around and beyond streaks and dots within streaks.Thought/conclusions: that one is nonmotile and the other is motile. Three: Did a Gram stain on the halo and where dots were found? Purpose: to see if the growth was-different organism.Observation/result: More Gram –in halo area way from inoculation site and more mixed Gram + and –from dot area on inoculum. Thoughts/conclusion: Gram –must be motile and Gram+ must be nonmotile. Four (+): Followed up with Gram +, by inoculating an MSA plate.Purpose: Mannitol Salt Agar has a high salt and mannitol sugar-more selective forGram + bacteria. Observations/results: Increased growth was seen on MSA, media turned yellow.Thoughts/conclusion: probably Gram +, can tolerate high salt and use mannitol as a carbohydrate source. Fifth (+): Gram stain a couple of growth spots from MSA. Purpose: to confirm or disprove the isolation of Gram +.Observation: mainly Gram + cocci, now in staph groups.Thought: mostly isolated organisms, probably in the Staph family.Sixth(+): Inoculated a PEA-blood agar plate or another MSA. Purpose: to isolate Staph completely, PEA-blood agar inhibits Gram –growth. Observation: Growth on PEA-blood, did not hemolyze blood (gamma hemolytic).Thought: Definitely not Strep, most likely Staph.-Gram stain.Seventh(+): Ran a catalase test on culture in MSA. Purpose: to see if this Staph? Can detoxify hydrogen peroxide to water and oxygen?Observation: yes –positive.Thought: yes this Staph has the catalase enzyme.Most likely: Due to MSA results and catalase, did not hemolyze blood, Gram + staph may have either Gram + Staphylococcus aureus Staphylococcus too harder.Eighth(+): Ran an oxidase test on the organism on the MSA plate. Purpose: to see if this organism has cytochrome oxidase to distinguish between aureus or too harder. (found test results on internet at [email protected]: negative for oxidase, no black on Q tipConclusion: The organism lacks cytochrome c, so does fermentation or oxidative phosphorylation without cytochrome c. I must have staphylococcus too harder.STEPFour Gr-: etc…-repeat steps relevant to Gr-bacteria if your Gram staining showed negative results. Summary: I was given culture with both a Gram + cocci and a Gram –rod. After several tests and attempts at isolating these into two separate cultures, I believe that I did isolate them both. The Gram + species (strain) atPEA-Blood selection media step, all could see is Gram-positive cocci. I believe that the Gram-positive cocci are Staphylococci too harder because it is definitely staph, by the morphology of gram stains and gram + coccidia gram staining. This staphylococcus can tolerate high salts, utilize mannitol as a carbohydrate source, does not hemolyze RBC, has the catalase enzyme but not the oxidase enzyme. For the Gram -…. That is all gram –rods. Unknown Project Requirements:1.You are given names of two bacteria: one Gram+, and one Gram-microorganism. You have to describe for each microorganism what steps must be taken for identification. First, you need to describe Gram staining for each. 2. Starting with the first Gram staining (see above) you need to describe the possible results of every test and every staining that you would perform during the identification of this particular microorganism. The description can be in a form of drawing, photographic pictures, tables, or simply a description of your expected results. 3. Every test that you describe must have a logical explanation as to WHY you need to do it, WHAT you would see as a result of the test.4.After outlining the results of your tests, you need to conduct Flow Chat (dichotomous chart)for your unknown bacteria clearly showing what tests you performed and why narrowing down the list of possible microorganisms in each group.5.After completing Flow Chat for yourGram+ and Gram-microorganisms, you need to write a report based on the proposed tests for both, Gram+ and Gram-bacteria, confirming your conclusions by literature references (textbook and lab manual are included). 6. You need to conclude Unknown Project Report by brief Summary describing specific characteristics of both, Gram+ and Gram-, microorganisms that you identified, highlighting potential pathogenic activity for both of these organisms, unique characteristics, and other specific features. 7. As you write your Unknown Report, you need to use at least three appropriate sources of references from the scientific literature database. Do not use your textbook to support your findings. You can use the list of Journals that are posted for Photo Quiz, or other relevant peer-reviewed Journals. Copying and pasting Journal’s URL is not an appropriate reference format. You need to arrange your references using EXACTLY the same format as you find in one of the Journals listed, or in the Journal that you choose to use. Unknown ProjectEvaluation Criteria (100% total Project’s grade):1.Ability to follow logical steps proposing tests for bacterial identification –20%2.Logical and conclusive Flow Chat –20%3.Supporting data presentation –20%4.Ability to follow the rubrics –15%5.Logical and science-based explanations of every step and tests performed–15%6.Support of the statements and conclusions by cited literature –5%7.Literature references made inappropriate format –5%_________________________________________TOTAL 100%. Guidelines for Students’ PapersThe goal of analyzing research papers and writing your own paper based on that analysis, is:?To attain the ability to comprehend and analyze research literature;?To use literature search tools to generate a pool of reliable references to support your point of view;?To conduct research papers and to appreciate differences between the structure of research papers that are based on authors’ own experimental results and review papers that are based on up-to-date literature analysis. Sections of Students’ Paper.1.Abstract.Write no more than 4 –5 sentences:?highlight the importance of the topic of your paper;?very briefly describe what type of study or experimental approaches have been used to test a proposed hypothesis (include a very limited description of hypothesis or authors points of view on the topic);?make a brief statement about the results that authors acquired and whether or not you agree with author’s conclusions.2.Introduction.Write 3 –5 sentences for each paragraph listed below:?what so far is known about the microorganism of your paper’s topic;?why authors decided to find new approaches in diagnosis or treatment of given microorganism;?what was authors’ hypothesis (detailed explanation of proposed hypothesis and its possible outcome as to the improvement of treatment, understanding of the disease pathway, or development new diagnostic techniques); ?why authors chose the methods that they used for experiments;?what have authors shown by their experiments (has been hypothesis proven? were results of experiments applicable to practical needs of biomedical science?).3. Materials and Methods. Describe study subjects or objects (patients, animal models, cells), list all groups of the subjects or objects used in experiments. Describe experimental design (treatment, challenges, techniques that have been used to assess the changes during experimental procedures). Practically you will be copying this part from the original paper, however, it is important to describe everything in your own words applying your own understanding of the methods used.4.Results.Describe what results in authors derived from performed experiments. This part you will also copy from the original paper, however, describe the results in your own words and make your comments (1-2 sentences) at the end of the result for every performed experiment. 5.Discussion.Write 3 –5 sentences for each paragraph below:?did the authors prove their hypothesis??what other experts in the field think/write about the subject of study??state your opinion about the subject of the study, proposed hypothesis, methods of testing the hypothesis, and interpretation of the results.?make realistic suggestions about experimental settings and methods. Support every statement that you make in Introduction, Results or Discussionsectionsby cited literature. Use 5 to 10 reliable references (scientific journals, NIH and CDC websites, and textbooks). The references MUST be arranged in the format that was used in the original paper, which you are using to write your paper (the list of references you can find at the end of the paper). To site reference in your text, use the number corresponding to the number of references in your references list. DO NOT “re-use” references! These means do not use the references that authors of the original paper used! Find your own.

For experiment 1: Culture A was red on MacConkey agar, white on nutrient agar and red and rod-shaped after Gram stain Culture B was orange on MacConkey agar, white on nutrient agar and red and rod-shaped after Gram stain For experiment 2 you should just analyse the class data which is on BREO. For experiment 3: The API codes you should analyse are (these results are also available on BREO: A:0776000 B:5307521 C:5214773 D:3305553 E:0207066 F:5044552

Bio 260 – Microbiology – Pathogen  Goal – Become adept at gathering and presenting information in the field of microbiology Project – Profile your assigned microbial pathogens or family of pathogens. Create an informative written report. The report will be submitted over Canvas. The profile should include   ·         Microbe identity –Genus and species, gram (+) or (-), growth patterns, etc. ·         Microbe location – Geographical specifics (ex. Malaria is found in warm, wet regions near the equator), common places in environments (ex. Helicobacter pylori is found in the stomach) ·         Pathogen mechanisms – Is this a pathogen? How? ·         Medical treatment – How do we fight this pathogen? ·         Anything else interesting? History? How can we study it? Does it grow on certain differential media? How would you stain it? Report ·         2000 words (single space size 12 times new roman font) report profiling your microbe. Word count does not include a bibliography. No quotations allowed. ·         Report should contain all the info the talk does and more detail on what makes your microbe special. ·         Report should be informative and in the style of Wikipedia articles. There should be no personal reflections. ·         References must be incorporated into the text so that it is clear what each reference refers to. ·         References must be present for every sentence which is not common knowledge. This means most sentences. Content Requirements and Grading Rubric Report Content Below are suggestions regarding the content of your report. ·         History of microbe ·         Description of microbe ·         Description of pathogen mode of action and medical treatments available ·         Impact of the pathogen in the environment/world ·         Other things you find interesting (this will depend heavily on your microbe)       References References should be done in MLA  or APA style with a complete bibliography on a separate slide. In-text references should be a superscript number (1) with references numbered in the order in which they appear (2). Some statements may be referenced in more than one source (1,2). Anything not ‘common knowledge’ should be cited. For this course, you may consider anything we have discussed in class to be common knowledge. Scientific sources can be found on PubMed or Google Scholar. Look for the lesson on scientific literacy later this quarter! 1 – First reference 2 – Second reference A handy website for creating a bibliography – http://www.easybib.com/   Advanced (5 points) Developing (3 points) Emerging (1 point) Report Content (60%)   Score weight: 3x Complete coverage of topics relevant to your microbe. Partial coverage with at least some sections very light on detail or missing. Large gaps or extremely light detail with respect to the microbes. Formatting (20%)   Score weight: 1x The report is free of spelling and grammatical mistakes. The report is size 12 times new roman font. Minor grammar or spelling mistakes may be present. Major grammatical or spelling errors that obscure the meaning of key portions of the report which are exceedingly difficult for the audience to comprehend. Citations (20%)   Score weight: 1x A minimum of 5 scientific citations are included for the report. Citations are included but maybe too few or from non-scientific sources. Citations are absent or from non-scientific sources.   Example – Kim showed Advanced skills in her report but received developing scores for her formatting. She, unfortunately, forgot to include her references and received an emerging score. Report Content                            5 x 3 = 15 Formatting                                 3 x 1 = 3 Citations                                    1 x 1 = 1 Total – 15+3+1 = 19/25 = 76%