= EQUIPMENT = * Incubator (37°C) * Refrigerator (4°C) * Freezer (20°C) * Freezer (70°C) * Autoclave * Thermocycler * Water baths * Microcentrifuge (preferably three, one for each color-coded area; at least two are necessary, one for the Grey Area and one for the White Area) * Adjustable pipettors (at least three sets of 1000 µL, 200 µL, and 20 µL, one set for each color-coded area; if possible a 0.5–10-µL pipettor for manipulating enzymes in the White Area) * Vor tex mixers * Magnetic stirrer * Rocker or rotator * Hot plates * pH meter * Vacuum pump (optional) * Microwave (preferable for melting agarose solutions; however, a hot plate or Bunsen burner can substitute for this function) * Power supplies * UV transilluminator * Polaroid camera with orange filter * Hood or camera stand and darkroom * Bunsen burner * Analytical balance = MATERIALS = * Erlenmeyer flasks (100 mL, 250 mL, 1000 mL) * Graduated cylinders (100 mL, 250 mL, 500 mL, 1000 mL) * Beakers (250 mL, 500 mL, 1000 mL) * Bottles (100 mL, 500 mL) * Glass pipets (25 mL, 10 mL, 5 mL, 2 mL) and rubber bulbs or Pipette Pumps® * Sterile Pasteur pipets and rubber bulbs * Plastic racks for microcentrifuge tubes * Floating racks for microcentrifuge tubes * Thermometers * Squir t bottles for ddH2O, 95% ethanol, 1.5% sodium hypochlorite (bleach) * 15-mL screw-cap polypropylene tubes tubes and racks * 50-mL screw-cap polypropylene tubes and racks * Sterile yellow polypropylene pipet tips (1–200 µL) * Sterile blue polypropylene pipet tips (200–1000 µL) * Sterile 1.5-mL microcentrifuge tubes * Sterile 0.5-mL microcentrifuge tubes * Sterile 0.2-mL PCR reaction tubes * 1.5-mL screw-cap microcentrifuge tubes with O-rings * Parafilm® * Gloves (disposable latex or vinyl) * Colored laboratory tape * Paper towels or Kimwipes® * Magnetic stir-bars * Weigh boats * Spatulas * Scissors or razor blade * Permanent markers * Ice buckets * Sterile lancets * Vacuum-sealed blood collection tubes, e.g., Vacutainer® tubes * Collection vials * Cotton * Talc powder (for re-using gloves) * Sterile toothpicks * Inoculating loop * Petri plates * Gel trays * Gel boxes * Combs * UV protective eyewear (goggles or face shield) * Polaroid 667 film * Plexiglass shield (high-grade UV-transmitting Plexiglass) = GENERAL REAGENTS = * Boric acid * EDTA * Tris base * Sodium chloride * Sodium hydroxide * Sodium acetate * Potassium chloride * Potassium acetate * Bleach (diluted to a final concentration of 1.5% sodium hypochlorite) * Hydrochloric acid * Glacial acetic acid * Triton® X-100 * Glycogen * Glycerol * Gelatin * Sodium sulfate * Sodium iodide * Silica particles * Nitric acid * Chelex® 100 (Bio-Rad Laboratories, Richmond, CA, No. 143-2832) * Proteinase K * Potassium phosphate * Disodium phosphate * Sodium dodecyl sulfate (SDS) * Guanidine isothiocyanate * Sodium citrate *β-mercaptoethanol * Sarkosyl * Saponin * tRNA (yeast or E. coli) * Phenol (equilibrated with water for RNA and equilibrated with Tris pH 8.0 for DNA) * Isoamyl alcohol * Chloroform * Isopropanol * 100% ethanol * Peptone * Tryptone * Yeast extract * Agar * Agarose * Ethidium bromide * Bromophenol blue * Xylene cyanol * DNA markers (“PCR markers”): = SPECIALTY REAGENTS = * Tryptic Soy Agar (V. cholerae) * Barium chloride dihydrate for MacFarland’s Standard (V. cholerae) * Sulfuric acid for MacFarland’s Standard (V. cholerae) * Saponin (P. falciparum/P. vivax) * N-acetyl cysteine (M. tuberculosis) * Sterile phosphate buffered saline (PBS) * Sodium thioglycolate for Cary-Blair transport medium (E. coli) * Calcium chloride for Cary-Blair transport medium (E. coli) * MacConkey agar (E. coli) * Acetone (Leptospira) * Sterile Dacron®-tipped applicators (Fisherbrand #14-959-90) (C. trachomatis/N. gonorrhoeae) = PCR REAGENTS = * Primers (Operon Technologies, Alameda, CA; New England Biolabs, Inc., Beverly, MA; Gibco BRL, Grand Island, NY; Applied Biosystems Perkin-Elmer, Foster City, CA) * Nucleotides (dNTPs: dATP, dCTP, dGTP, dTTP) * 10X Buffers * MgCl2 * Taq polymerase (see section 5.1.2) * Reverse transcriptase RAV-2 (Amersham Corp., Arlington Heights, IL) * rTth reverse transcriptase-polymerase (Perkin-Elmer Corp.) * Dithiothreitol (DTT) * Dimethyl sulfoxide (DMSO) * Tetramethylammonium chloride (TMAC) * Betaine (Sigma Chemical Co., St. Louis, MO, B-2629) * Bovine serum albumin (BSA) * Manganese acetate * Bicine * Nuclease-free sterile ddH20 * Mineral oil * Wax beads = ADDITIONAL MATERIALS AND REAGENTS FOR NONRADIOACTIVE PROBES = * Dot blot microfiltration apparatus * Rocker/orbital shaker * “Seal-a-meal”® for sealing hybridization bags * Plastic bags for hybridization * Plastic dishes with covers * Filter forceps * Digoxigenin-11-dUTP, alkali-labile (Boehringer Mannheim, Indianapolis, IN, No. 1573152) * Anti-digoxigenin alkaline phosphatase conjugate (Boehringer Mannheim, No. 1093274) * Nonfat milk powder * Blocking Reagent (e.g., Boehringer Mannheim, No. 1096176) * Nylon membranes (e.g., Boehringer Mannheim) * Whatman 3MM paper * Nitrotetrazolium blue (NBT) * 5-bromo-4-cloro-3-indolyl-phosphate, toluidine salt (BCIP) * For chemiluminescent detection: * Darkroom setup (trays, wooden forceps, etc.) or automatic developer for X-ray film * Lumi-phos 530® (chemiluminescent substrate; Lumigen, Inc., Southfield, MI) * Plastic sheets * X-ray film * film cassettes * GBX developer and fixer = ADDITIONAL MATERIALS AND REAGENTS FOR CLONING = * Metal block for microcentrifuge tubes (precooled to 20°C) * Centrifuge with 3500-rpm capability * Spectrophotometer measuring optical density at 600-nm wavelength * Plate spinner, if available * Air shaker (37°C) * Plate spreader (i.e., made from a glass rod) * Sterile wooden sticks * Ampicillin * Potassium acetate * Glucose * Polyethylene glycol (MW 8000) * Polyethylene glycol (MW 3350) * Magnesium sulfate * 5-Bromo-4-chloro-3-indolyl-D-galactopyranoside (X-Gal) * Isopropyl β-D-thiogalactopyranoside (IPTG) * Dimethyl formamide (DMF) * Cloning vector (e.g., Bluescript, Stratagene Cloning Systems) * Restiction enzymes * Restriction enzyme buffers * T4 DNA Ligase * 10X T4 DNA Ligase Buffer * RNase * Transparent tape