Documents about Bacillus Subtilis

  • 1 Pages

    Trp attenuation Du 2000 discussion questions

    Cal Poly Pomona, BIO 560

    Excerpt: ... Bio560 Literature Discussion Questions 5/3/01 Du et al., 2000. trp RNA-binding attenuation protein-5 stem-loop RNA interaction is required for proper transcription attenuation control fo the Bacillus subtilis trpEDCFBA operon. J Bacteriol. 182:1819. 1. What are the differences between the trp operons of Bacillus subtilis and E. coli? Please including the discussion on the regulatory RNA leader region and how Trp level regulates each operon. 2. How did the authors quantify the binding of TRAP to the RNA leader region? 3. In order to map the 5 stem-loop structure, the authors did primer extension experiments using RNA treated with RNAse T1, RNase V1, DMS or CMCT. What is the function of each enzyme/chemical? How can they help solving RNA secondary structure? 4. From this study, does TRAP bind to the 5 stem-loop? What is the role of (G/U)AG repeats in the binding of TRAP to the 5 stem-loop? Lin, Spring 2001 ...

  • 13 Pages

    1. intro handout

    Yale, MCDB 120

    Excerpt: ... taokaetal.,Cell40,19(1985) Key Concept: Evolutionary conservation Nature keeps reusing the same building blocks while constructing an enormous diversity of organisms Researchers exploit these similarities; information gained by studying one organism can lead to better understanding of a similar process in another organism. Key concept: Evolution provides the foundation for modern biology Millions of years Populations evolve to display new biological properties Three Domains of Life (based on DNA comparisons) Over billions of years, gradual changes in the DNA sequence of organisms have resulted in an enormous variety of different species Using DNA sequence comparison these are more closely related than these. Bacillus subtilis E. coli 3 Domain view of life Plants, animals and fungi have only recently diverged from one another. Archaea form a separate grouping. They group more closely to eukaryotes than bacteria do. Key concept: All life is constructed ...

  • 3 Pages

    Assign_10

    University of Illinois, Urbana Champaign, MCB 432

    Excerpt: ... for the sequence? 2b. What is the GenInfo (gi) number of the entry? Exploring the tRNA Charging Enzymes in Bacillus subtilis 168 We will use the above proteins as a starting point for exploring the enzymes in B. subtilis. Go to the NCBI blast home page (http:/www.ncbi.nlm.nih.gov/blast/Blast.cgi). Follow the link to protein blast. In the query box put NP_461354, the RefSeq protein identifier from problem 1. Be sure that the Database is nr, and the Algorithm is blastp. Under Algorithm Parameters, set Max target sequences to 1000. Leave the rest of the settings at their defaults. Click the BLAST button. 3a. What is the search Request ID (RID)? 3b. Use the Find function on your WWW browser to locate the alignment for Bacillus subtilis . I only find one matching B. subtilis entry (sequence) in the nr database, but it is in multiple source databases.1 What are the following identifiers for the matching sequence? RefSeq accession number Swiss-Prot accession number Swiss-Prot ID2 1 2 I am calling an "entry" or "s ...

  • 1 Pages

    dicotmous key

    CofC, BIO 310

    Excerpt: ... Dichotomous Key for Identifying Unknown Bacterium #68 Bacillus subtilis Staphyloccus aureus Escherichia coli Unknown#68 Clostridium sporogenes Citrobacter freundii Proteus vulgaris Enterococcus faecalis Enterobacter aerogenes Pseudomonas aeruginosa Gram-Positive Bacillus subtilis Clostridium sporogenes Enterococcus faecalis Staphyloccus aureus Gram-Negative Citrobacter freundii Enterobacter aerogenes Escherichia coli Proteus vulgaris Pseudomonas aeruginosa Unknown#68 Sulfur Reduction Proteus vulgaris Citrobacter freundii Unknown#68 Non-Sulfur Reduction Escherichia coli Enterobacter aerogenes Pseudomonas aeruginosa Lactose Fermentation Citrobacter freundii Unknown#68 Non-Lactose Fermentation Proteus vulgaris ...

  • 3 Pages

    Bio560 final 2001

    Cal Poly Pomona, BIO 560

    Excerpt: ... Bio560 Microbial Physiology Final Exam June 4, 2001 June 4, 2001 Answers are due by Thursday 1 pm (6/7/01); you may turn in a hard copy to my office or e-mail your answer to me. Final grades will be posted by Tuesday, June 12; you may pick up your report paper at the same time. Good luck and have a great summer! Please answer the following questions using the space provided; Please focus the answers covered by the lecture note; 100 points total. 1. The initiation of DNA replication starts the _ period of bacterial cell cycle. (5 points). What is the positive and negative regulator in initiating DNA replication at OriC? Explain briefly how they work together to control the initiation of DNA replication. (15 points) 2. Sporulation in Bacillus subtilis involves temporal and compartmental control at different stages of development. Please list the key molecules/factors that are responsible for the temporal regulation and list their sequence of occurrence and their compartmentalization during the developm ...

  • 2 Pages

    practical1-251-review-ques

    UNLV, FACULTY 251

    Excerpt: ... Jensara sp07 Microbiology 251 Practicum 1 study guide This study guide is to aid you in your studies. This guide may not cover all of the information you will need to know for the exam. Be sure to read all of the labs and understand the importance of the procedures described. Week 1 1. Know all parts of the microscope. Understand the function of each part of the microscope. 2. Know how to calculate the magnification of an object viewed in a microscope. 3. Know the definition of the limit of resolution and a parfocal lens system. 4. What is the purpose of an oil immersion lens and its importance for viewing bacterial cultures. 5. Know the difference between bright-field light microscopes and phase-contrast microscopes. 6. Know the 3 domain classification system. 7. know the bacterial shapes and arrangements 8. In week 1 you viewed Bacillus subtilis , Staphylococcus epidermidis, Nostoc, Saccharomyces cerevisiae, Spirillum volutans, Amoeba proteus, Euglena and Paramecium. Know the description of these organisms ...

  • 10 Pages

    Cell 2003 Daniel

    Harvard, FEB 200

    Excerpt: ... e with which to study the topology of wall synthesis in a range of bacteria. In combination with other rapidly developing cytological methods (Shapiro and Losick, 2000; Errington, 2003) and the information from comparative genomics, the next few years should see considerable progress in understanding the molecular basis of bacterial morphogenesis and its evolution. Experimental Procedures Bacterial Strains B. subtilis strains are described in Table 3. Streptococcus pneumoniae R6, Streptomyces coelicolor M145, and Corynebacterium glutamicum NCIMB 10025 were obtained from B.G. Spratt, K. Flardh, and NCIMB, respectively. Growth Conditions Strains of Bacillus subtilis and Streptomyces coelicolor were grown in S medium (Sharpe et al., 1998) at 30 C, except in the case of the MreB-depletion experiment, in which CH medium (Partridge and Errington, 1993) was used. Generally, overnight cultures were diluted 1/20 in fresh medium and incubated for 23 hr to reestablish exponential growth in the cultures prior to ma ...

  • 2 Pages

    Quiz 3 questions

    Fairfield, SON Bi151

    Excerpt: ... Lab 3 1. How are microscope slides handled if you do not keep them to review? Microscope slides that you do not wish to keep should be placed in the red, sharps biohaxard container located at the front of the laboratory. 2. For each of the following, list the shape of the bacteria and the grouping of cells that you would expect to see in a stained slide from a broth culture of: Bacillus subtilis , Streptococcus mutans. In a stained slide from a broth culture, the shape of Bacillus subtilis is rod and Streptococcus mutans is a long, fragile chain. 3. What is the difference in one of the first steps in the preparation of a slide of organisms made from a culture growing on nutrient agar as compared to a culture growing in nutrient broth? The difference in one of the first steps in the preparation of a slide of organisms made from a culture growing in nutrient agar as compared to a culture growing in nutrient broth is the use of water on the slide with organisms made from a culture growing on nutrient agar. When u ...

  • 1 Pages

    microbes_rxns_summer06

    Fayetteville State University, MCB 4403

    Excerpt: ... MICROBES and RXN'S MCB4403L SUMMER 2005 SUMMER 2006 H2S prod. TSA deep growth fac. anaer. fac. anaer. fac. anaer. aerob. fac. anaer. aerob. fac. anaer. aerob. fac. anaer. fac. anaer. fac. anaer. fac. anaer. - or wkA / - or wkA / - or wkA / - or wkA / - or wkA / - or wkA / - or wkA / A/A/A/A/+/+/-/+ + +/+/+ -/+/Lactose ferm./gas EMB MR / Indole Citrate Mannitol/ VP High Salt (gr / ferm) POSSIBLE MICROBES & ALLOWED TESTS -MICROBE Gram rxn/ Catalase Shape Activity Enterobacter aerogenes Escherichia coli Proteus vulgaris Salmonella typhimurium Pseudomonas fluorescens Bacillus cereus Bacillus subtilis Lactobacillus plantarum Micrococcus luteus Staphylococcus aureus Staphylococcus epidermidis Streptococcus faecalis Streptococcus lactis + + + +/+ -/sl= slow + rxn Interpretation notes: + = positive rxn; A= acid production; G=gas production; wk=weak + rxn; Incubation times are 24 hours if positive, 48 hours if negative at 24. Test results obtained using small inoculum except gelatin Always check for signs o ...

  • 1 Pages

    lab2bioabstract

    Brandeis, BIOL 18a

    Excerpt: ... Genetic mapping of critical proteins in tryptophan, tyrosine, and histodine pathways for Bacillus Subtilis , the SB100 strain Bacterial transformation is a well documented phenomenon which allows for exchange of genetic material between cells and their environment, this relationship can be used to determine the recombination frequency for genes and thus a chromosomal position. B. Subtilius undergoes these transformations, and contains critical metabolic pathways that are prone to knockout in prepared strains. Here I studied the uptake of genetic material and frequency of recombination to establish a genetic map for 3 genes, encoding critical proteins in the pathways for tryptophan, histidine or tyrosine. Wild type DNA was isolated, extracted and purified from wild type B. Subtilius and added to SB100 auxotroph (a trp- tyr- his- strain) allowing for transformation. The transformed B. Subtilius were then plated on selective media, lacking between 0 and all 3 of the required amino acids; colonies that grew were t ...

  • 1 Pages

    13_questions_TxTsSec

    UCSC, BIO 119

    Excerpt: ... Study Questions for Transcription/Translation/Protein Secretion 1) What does the core part of RNA polymerase do? What about the sigma subunit? 2) Why does sigma 70 recognize different promoters than the heat shock sigma factor does? What is the purpose of having these different promoters? What does it mean that some promoters are poor matches to consensus? What is the implication of this match for gene expression? 3) Unlike actively growing cultures of Bacillus subtilis old cultures (not growing) have lots of spores. It is known that special sigma factors are expressed during sporulation. Consider a Bacillus strain that is always expression gfp (SigA promoter) vs. a mutant where that promoter was changed to a SigF promoter. What would the two Bacillus gfp strains look like under a fluorescence microscope during exponential phase of growth? How about in late stationary phase? Note: the green fluorescence protein is very stable. 4) Draw a genetic map of a typical gene. Including the essential genetic elements e ...

  • 3 Pages

    13_questions_TxTsSec

    UCSC, BIO 119

    Excerpt: ... Study Questions for Transcription/Translation/Protein Secretion 1) What does the core part of RNA polymerase do? What about the sigma subunit? 2) Why does sigma 70 recognize different promoters than the heat shock sigma factor does? What is the purpose of having these different promoters? What does it mean that some promoters are poor matches to consensus? What is the implication of this match for gene expression? 3) Unlike actively growing cultures of Bacillus subtilis old cultures (not growing) have lots of spores. It is known that special sigma factors are expressed during sporulation. Consider a Bacillus strain that is always expression gfp (SigA promoter) vs. a mutant where that promoter was changed to a SigF promoter. What would the two Bacillus gfp strains look like under a fluorescence microscope during exponential phase of growth? How about in late stationary phase? Note: the green fluorescence protein is very stable. 4) Draw a genetic map of a typical gene. Including the essential genetic elements e ...

  • 10 Pages

    Lecture #24

    Cornell, BIO 2900

    Excerpt: ... as a REPRESSOR Spo0AP as an ACTIVATOR 8 10/25/2007 Alternative Sigma Factors in Bacillus subtilis . About half are required for sporulation. Others have diverse or unknown functions. K Alternative Sigma Factors involved in sporulation H sigF F early forespore genes early mother cell genes A sigE sigG E sigK K late mother cell genes A F sigE sigG G late forespore genes Stage II E F Stage IV K G 9 10/25/2007 Summary Protein synthesis and activity can be constitutive or can be regulated. Regulation of protein synthesis is often carried out at the level of transcription initiation. Transcriptional regulatory proteins can act as repressors or as activators of transcription initiation. Both classes can be made active or made inactive by small molecules. Examples to understand: Lac Repressor, CAP, ArgR, MalT. Variations: LexA a repressor that is inactivated by protein cleavage. p p y g LuxR/LuxI induction in response to pheromones made by sibling ba ...

  • 3 Pages

    Topic17-3

    Purdue, HORT 301

    Excerpt: ... do with phytochrome? Although they lack the specific histidine residue that becomes autophosphorylated, the C termini of phytochromes have some sequence similarity to the transmitter domains of bacterial sensor proteins (Web Figure 17.11.A) (Schneider-Poetsch 1992). This sharing of sequences raises the interesting possibility that phytochrome evolved from the sensor protein of a bacterial two-component system. Web Figure 17.11.A Homologous regions of phytochrome E, cyanobacterial photoreceptor, and sensor protein from Bacillus subtilis . The percentages indicate the proportion of identical amino acids between pairs of sequences. (After Yeh et al. 1997.) Provocative new evidence for the idea that phytochrome evolved from the histidine kinase of a bacterial two-component system has recently emerged from studies of cyanobacteria. The cyanobacterium Fremyella uses light to regulate the composition of its photosynthetic pigments contained within the light-harvesting phycobilisomes (see textbook Figure 7.5(C), a ...

  • 5 Pages

    lecture04

    UNC, MATH 215

    Excerpt: ... . Note that in this (C) (M ) computation the microscopic level itself is a continuum computation from the point of view of the surrounding uid. The microscopic level does bring out the discrete nature of the bacteria. 1.3. BIOLOGICAL PATTERNS 15 Figure 1.8: Pattern formation in bioconvection (http:/galahad.elte.hu/bioconvection.html). The shadows correspond to dierent concentrations of a bacterium species ( Bacillus subtilis ) that has a agellum and can swim. It swims towards the top of the water layer where a higher concentration of oxygen favors its growth. That region subsequently becomes heavier and falls down - a pattern similar to a well known thermal convection problem (the Rayleigh-Benard problem). 16 CHAPTER 1. SIMPLE EXAMPLES Figure 1.9: Bacillus subtilis as seen with an electron microscope. The bar in the lower left corner is 1 m long. The bacterium body is 1.5-2 m long, has a diameter of ~0:4 m with a agelum roughly 5 m long. Figure 1.10: Groups of cilia on lung epithelial ce ...

  • 1 Pages

    Microbiology-list of bacteria

    Palmer Chiropractic, MICRO 101

    Excerpt: ... ive anaerobe Bacillus subtilis gram +; makes spores Bacillus mycoides coiled-shaped "to be like fungi" Corynebacterium diphtheriae found in throats; diphtheroid toxin Corynebacterium xerosis on dry skin Propionibacterium acnes Helicobacter pylori rigid cell walls; one-several coils; spirillum Treponema pallidum spirochete; syphillis Borrelia burgdorferi spirochete; lyme disease Leptospira interogans spirochete; UTI Streptococcus mutans normal flora in mouth; capsule if sucrose present; gram +, dental caries Clostridium botulinum drumstick spores Clostridium tetani tennis racket spores Mycobacterium tuberculosis obligate anaerobe; 18 hour generation time Campylobacter jejuni microaerophile; thermophile; capnophile Listeria monocytogenes psychotroph, mesophile Neisseria gonorrhoeae gram -; "velcro" with fimbriae Brucella abortus - capnophile Streptococcus lactis acid-loving; ferments lactose to curdle milk Lactobacillus acidophilus - acid-loving; ferments lactose to curdle mil ...

  • 8 Pages

    Case Study

    JMU, BIO 430

    Excerpt: ... lates with a strain of bacillus subtilis that requires phenylalanine for growth. The presence of growth is indicated by a halo surrounding the filter paper. If positive, blood phenylalanine and tyrosine levels are determined, and if elevated, a confirmatory assay for phenylalanine hydroxylase is done. PKU Inheritance: Inherited as autosomal recessive disorder. Variation to classical symptoms is result of compound heterogeneity. 65 allelic variants make compound heterogeneity more common then homogeneity for the same allele. Treatment of PKU: Phenylketonuria is treatable with a low phenylalanine diet. phenylalanine levels should be kept below 15 mg per deciliter Nutra sweet is especially high in phenylalanines Genetic Counseling: Tell the parents that the baby will be normal if they follow the prescribed dietary guidelines The child is normally out of danger of the disease after puberty Phenylalanine should be avoided Stay away from nutra sweet, meats, dairy products ...