Selective media

are used for the growth of only select microorganisms. For example, if a microorganism is resistant to a certain antibiotic, such as ampicillin or tetracycline, then that antibiotic can be added to the medium in order to prevent other cells, which do not possess the resistance, from growing. Media lacking an amino acid such as proline in conjunction with E. coli unable to synthesize it were commonly used by geneticists before the emergence of genomics to map bacterial chromosomes.
Selective growth media are also used in cell culture to ensure the survival or proliferation of cells with certain properties, such as antibiotic resistance or the ability to synthesize a certain metabolite. Normally, the presence of a specific gene or an allele of a gene confers upon the cell the ability to grow in the selective medium. In such cases, the gene is termed a marker.
Selective growth media for eukaryotic cells commonly contain neomycin to select cells that have been successfully transfected with a plasmid carrying the neomycin resistance gene as a marker. Gancyclovir is an exception to the rule as it is used to specifically kill cells that carry its respective marker, the Herpes simplex virus thymidine kinase (HSV TK).

Some examples of selective media include:
eosin-methylen blue agar (EMB) that contains methylene blue – toxic to Gram-positive bacteria, allowing only the growth of Gram negative bacteria
YM (yeast and mold) which has a low pH, deterring bacterial growth
blood agar (used in strep tests), which contains beef heart blood that becomes transparent in the presence of hemolytic Streptococcus
MacConkey agar for Gram-negative bacteria
Hektoen Enteric (HE) which is selective for Gram-negative bacteria
Mannitol Salt Agar (MSA) which is selective for Gram-positive bacteria and differential for mannitol
xylose lysine desoxyscholate (XLD), which is selective for Gram-negative bacteria
Buffered charcoal yeast extract agar, which is selective for certain gram-negative bacteria, especially Legionella pneumophila

From http://en.wikipedia.org/wiki/Selective_medium

Bromophenol blue

Tetrabromophenolsulfonephthalein, is an acid-base indicator whose useful range as an indicator lies between pH 3.0 and 4.6. It changes from yellow at pH 3.0 to purple at pH 4.6; this reaction is reversible.
Bromophenol blue is also used as a color marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. Since bromophenol blue carries a slight negative charge at moderate pH, it will migrate in the same direction as DNA or protein in a gel; the rate at which it migrates varies according to gel density and buffer composition, but in a typical 1% agarose gel in TAE buffer or TBE buffer, bromophenol blue migrates at the same rate as a DNA fragment of approximately 500 base pairs. Xylene cyanol and Orange G may also be used for this purpose.
The molecular weight of bromophenol blue is around 670 Daltons or grams per mole.
The bromophenol blue is also used as a dye. At neutral pH, the dye absorbs red light most strongly and transmits blue light. Solutions of the dye therefore are blue. At low pH, the dye absorbs ultraviolet and blue light most strongly and appears yellow in solution. In solution at pH 3.6 (in the middle of the transition range of this pH indicator) obtained by dissolution in water without any pH adjustment, bormophenol blue has a characteristic green red colour. This phenomenon is called dicromatic colour.
Bromophenol blue is commonly used in entry-level lab courses to stain proteins in wet-mount slides.
From http://en.wikipedia.org/wiki/Bromophenol_blue

Minimal media

Protocol for preparation of minimal media

1. Preparation of stock solutions
A. Vitamin Solution (1000 ml)
1.1 mg biotin Store in the refrigerator
1.1 mg folic acid* Store at room temperature
110 mg PABA (para-aminobenzoic acid) Store in the refrigerator
110 mg riboflavin* Store at room temperature
220 mg pantothenic acid Store in the refrigerator
220 mg pyridoxine HCl* Store at room temperature in dessicator
220 mg thiamine HCl* Store at room temperature
220 mg niacinamide Store at room temperature
* Note that these vitamins are light sensitive.
Add 500 ml H2O and 500 ml high-purity ethanol to the vitamins and then filter sterilize.
The solution will be bright yellow. Store the vitamin solution in the refrigerator in a dark
bottle (we wrap our solution with aluminum foil).
Proper storage for each of the individual vitamins is shown to their right.
B. Metal Stock Solution (100 ml)
8 ml concentrated HCl
5 g FeCl2·4H2O
184 mg CaCl2·2H2O
64 mg H3BO3
40 mg MnCl2·4H2O
18 mg CoCl2·6H2O
4 mg CuCl2·2H2O
340 mg ZnCl2
605 mg Na2MoO4·2H2O
Bring to a volume of 100 ml with H2O. Initially the solution will be green and you will
need to stir for several hours before everything dissolves. Store the metal stock solution
at room temperature.
C. "O" Solution (500 ml)
Add 10 ml Metal Stock Solution (above) to 26.8 g MgCl2·6H2O then add H2O to 500 ml.
Filter sterilize and store at room temperature.
Note that the Metal Stock Solution is only used to prepare the "O" solution and is not
added to the minimal media.
D. "SBMX" Solution (500 ml)
To 16.5 g KH2PO4, 87.5 g K2HPO4, and 18.25 g NaCl add H2O to 500 ml. Autoclave and
store the "SBMX" solution at room temperature. The pH of this solution should be 7.5,
however if done correctly no pH adjustment should be necessary.
E. "S" Solution (100 ml)
To 4.8 g K2SO4 add H2O to 100 ml. Autoclave and store the "S" solution at room
temperature.
F. Thiamine Solution (Small volume)
Make up a 1 mg/ml solution of thiamine in H2O. Store the thiamine solution in the
refrigerator. We generally make smaller stock solutions of the thiamine solution to avoid
letting the solution get to old.

2. Preparation of 1 liter of minimal media
To create the growth media add together
940 ml H2O
40 ml "SBMX" solution
1 ml "S" solution
Autoclave and cool
Mix together
2 ml "O" solution
1 ml vitamin solution
1 ml thiamine solution
Filter sterilize the mixture and add to cool growth media
Add together
1 g 15NH4Cl or (15NH4)2SO4
5 ml H2O
Filter sterilize and add to cool growth media
Add together
4 g glucose
10 ml H2O
Filter sterilize and add to cool growth media
Add antibiotic of choice
Note: We have found the most cost effective amount of glucose to add is between 3 and 4 grams.

3. Cell Growth
• A 5 ml culture of LB (10 g Bacto tryptone, 5 g Bacto yeast extract and 5 g NaCl per liter)
is inoculated using a single colony from a fresh LB plate and grown for ~ 6 hours at 37º
C with shaking; they should reach on OD600 of 0.5 - 1.0.
• Use 0.2 ml of the LB culture to inoculate a 25 ml minimal media culture and grow
overnight at 30 - 37º C with shaking; they should grow to an OD600 of 2-3.
o Note: Use 25 ml starter culture per liter. Therefore, if more than 1 liter of minimal
media will be induced the starter culture size will need to be increased.
• Spin down the cells (~2000g) to remove supernatant and resuspend cells in 10 ml of
minimal media.
o Note: We often skip this spin down step and simply inoculate the 1 liter of
minimal media culture with the 25 ml overnight starter culture.
• Use the 10 ml of the resuspended cells from the overnight starter culture to spike 1 liter
of minimal media culture. Grow and induce cells as normal.
Reference: Weber DJ, Gittis AG, Mullen GP, Abeygunawardana C, Lattman EE and Mildvan
AS. "NMR docking of a substrate into the X-ray structure of staphylococcal nuclease."
Proteins (1992) 4, 275-287.
Special Notes:
• The original Weber paper used two additional solutions. One is a T-U solution of
thymine and uracil and the other is the "M" solution which contains MOPS buffer and
tricine. These both have been dropped in the protocol we now use. I am not positive but
the removal of the "M" buffer was likely done to remove a possible carbon source for the
bacteria to use.
• Glucose can cause some repression of IPTG inducible transcription. Therefore, if you are
inducing at low cell densities OD600 < 0.8 where significant glucose may be present a
higher IPTG concentration may be needed.
• In general it is a good idea to try growing cultures to different OD600 values, inducing for
various times and with various amounts of IPTG and to try expression at lower
temperatures such as 30º C. All of these parameters can be adjusted to maximize protein
expression and solubility.

from http://structuralbiology.uchc.edu/Minimal_media.pdf

Nutrient agar

is used throughout the world as a medium for the growth of bacteria and fungi. Though less than 1% of all existing bacteria can be grown successfully, the basic agar formula can be used to grow most of the microbes whose needs are known. More specific nutrient agars are available, because microbes can be picky. For example, blood agar, which is generally combined with horse blood, can be used to detect the presence of haemorrhagic micro-organisms such as E.coli O:157 H:7. The bacteria digest the blood, turning the plate clear.

OATMEAL AGAR

Oatmeal (Quaker White Oats) 20.0g
Agar (Difco) 18.0g
Distilled water 1000.0ml
Adjust pH to 7.2. Cook or steam 20.0 g in 1000.0 ml distilled water for 20 min. Filter through cheese cloth. Add 18.0 g agar and make up to 1000.0 ml. Add 1 ml of trace salts solution (see below).
Trace salt solution:
FeSO4 x 7 H2O 0.1g
MnCl2 x 4 H2O 0.1g
ZnSO4 x 7 H2O 0.1g
Distilled water 100.0ml

From http://www.dsmz.de/microorganisms/html/media/medium000609.html

Cornmeal Agar.

Cornmeal agar (BD) 8.5 g
Distilled water 500 ml
Method:
1. Mix dry ingredients into 100 ml H2O, boil remaining water
2. Add boiling water to mixture and bring to boil.
3. Dispense for slopes.
4. Autoclave for 10 minutes at 120C, then slope on racks.
From http://www.mycology.adelaide.edu.au/Laboratory_Methods/Culture_Techniques_and_Media/cma.html

Glucose medium for Streptomyces

Glucose 10.0 g
Yeast extract 1.0 g
Meat extract 4.0 g
Peptone 4.0 g
NaCl 2.5 g
Agar 20.0 g
Distilled water 1.0 L
pH 7.2

Czapek`s agar

Sucrose 30.0 g
NaNO 33.0 g
MgSO4 x 7 H2O 0.5 g
KCl 0.5 g
FeSO4 x 7 H2O 0.01 g
K2HPO4 1.0 g
Agar 15.0 g
Distilled water 1.0 L
Add sucrose prior to dispensing

Competitiveness

is a comparative concept of the ability and performance of a firm, sub-sector or country to sell and supply goods and/or services in a given market. The usefulness of the concept, particularly in the context of national competitiveness, is vigorously disputed by economists, such as Paul Krugman.
The term may also be applied to markets, where it is used to refer to the extent to which the market structure may be regarded as perfectly competitive. This usage has nothing to do with the extent to which individual firms are "competitive'.

Chitin

(C8H13O5N)n is a long-chain polymeric polysaccharide of beta-glucose that forms a hard, semitransparent material found throughout the natural world. It is the main component of the cell walls of fungi, the exoskeletons of arthropods, such as crustaceans (e.g. crab, lobster and shrimp) and insects (e.g. ants, beetles and butterflies), the radula of molluscs and the beaks of cephalopods (e.g. squid, and octopuses). Chitin has also proven useful for several medical and industrial purposes.

Septum

(Latin: something that encloses; plural Septa) is a partition separating two cavities or spaces. Examples include:
Nasal Septum: the cartilage wall separating the nostrils of the human nose.Often deviated or perforated through physical injury or cocaine abuse.
Cephalopod Septa: walls between each chamber, or siphuncle, in shells of nautiloids, ammonites, and belemnites; i.e. cephalopods that retain an external shell.
The wall dividing the right side of the heart from the left side.
Fungi produce septa to partition filamentous hyphae into discrete cells.

Depsipeptide

is a peptide in which one or more of the amide (-CONHR-) bonds are replaced by ester (COOR) bonds.
Depsipeptides have often been used in research to probe the importance of hydrogen bond networks in protein folding kinetics and thermodynamics. They are also found in nature as natural products. An infamous example is the L-Lys-D-Ala-D-Lac motif found in vancomycin resistant bacteria's cell wall building blocks. The amide to ester mutation disrupts its hydrogen bonding network with vancomycin, which is key to the antibiotic's activity.

Ceramides

are a family of lipid molecules. A ceramide is composed of sphingosine and a fatty acid. Ceramides are found in high concentrations within the cell membrane of cells. They are one of the component lipids that make up sphingomyelin, one of the major lipids in the lipid bilayer. For years, it was assumed that ceramides and other sphingolipids found in the cell membrane were purely structural elements. This is now known to be not completely true. Perhaps one of the most fascinating aspects of ceramide is the fact that it can be released from the cell membrane by enzymes and then act as a signaling molecule. The most well-known functions of ceramides as cellular signals include regulating the differentiation, proliferation, programmed cell death (PCD), and apoptosis (Type I PCD) of cells. Due to this function, ceramides are sometimes called "messengers of cell death"

Inositol phosphates

are a group of mono- to polyphosphorylated inositols. They have important messaging functions in the cells.
See also
· inositol monophosphate
· inositol trisphosphate
· inositol pentakisphosphate
· inositol hexaphosphate
· inositol triphosphate receptor

Anidulafungin

or Eraxis is an anti-fungal drug manufactured by Pfizer that gained approval by the Food and Drug Administration (FDA) in February 21, 2006; it was previously known as LY303366. There is preliminary evidence that it has a similar safety profile to caspofungin. It has proven efficacy against oesophageal candidiasis, but its main utility will probably be in invasive Candida infection; it will probably also have application in treating invasive Aspergillus infection. It is a member of the class of anti-fungal drugs known as the echinocandins: its mechanism of action is by inhibition of (1→3)β-D-glucan synthase, which is an important component of the fungal cell wall.

Caspofungin

is an antifungal drug, the first of a new class termed the echinocandins. It shows activity against infections with Aspergillus and Candida, and works by inhibiting β(1,3)-D-Glucan of the fungal cell wall. Note that mammalian cell walls are not affected making this drug remarkably non-toxic. Caspofungin is administered intravenously.

Echinocandins

are antifungal drugs that inhibit the synthesis of glucan in the cell wall, probably via the enzyme 1,3-β glucan synthase. They are fungicidal against yeast and fungistatic against mold.
· Anidulafungin
· Caspofungin
· Micafungin

Host

In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. In botany, a host plant is one that supplies food resources and substrate for certain insects or other fauna. Examples of such interactions include a cell being host to a virus, a legume plant hosting helpful nitrogen-fixing bacteria, and animals as hosts to parasitic worms, e.g. nematodes.
Classification
A primary host or definitive host is a host in which the parasite reaches maturity and, if applicable, reproduces sexually. A secondary host or intermediate host is a host that harbors the parasite only for a short transition period, during which (usually) some developmental stage is completed. For trypanosomes, the cause of sleeping sickness, humans are the primary host, while the tsetse fly is the secondary host. Cestodes (tapeworms) and other parasitic flatworms have complex life-cycles, in which specific developmental stages are completed in a sequence of several different hosts.
A paratenic host is similar to an intermediate host, only that it is not needed for the parasite's development cycle to progress. There are also reservoir hosts. These are animals that host a human pathogen while it isn't infecting humans, and are used by the disease as a source of maintenance. A single reservoir host may be reinfected several times. The difference between a paratenic and reservoir host is that the latter is a primary host, whereas paratenic hosts serve as "dumps" for non-mature stages of a parasite which they can accumulate in high numbers.
A dead-end host is an intermediate host that does generally not allow transmission to the definite host, thereby preventing the parasite from completing its development. For example, humans are dead-end hosts for Echinococcus canine tapeworms. As infected humans are not usually eaten by dogs, foxes etc., the immature Echinococcus - although it causes serious disease in the dead-end host - is unable to infect the primary host and mature.
Host range
The host range or host specificity of a parasite is the collection of hosts that an organism can utilize as a partner. In the case of human parasites, the host range influences the epidemiology of the parasitism or disease. For instance, the production of antigenic shifts in Influenza A virus can result from pigs being infected with the virus from several different hosts (such as human and bird). This co-infection provides an opportunity for mixing of the viral genes between existing strains, thereby producing a new viral strain. An influenza vaccine produced against an existing viral strain might not be effective against this new strain, which then requires a new influenza vaccine to be prepared for the protection of the human population.

Epithelium

In biology and medicine, epithelium is a tissue composed of a layer of cells. Epithelium lines both the outside (skin) and the inside cavities and lumen of bodies. The outermost layer of our skin is composed of dead stratified squamous, keratinized epithelial cells. Mucous membranes lining the inside of the mouth, the esophagus, and part of the rectum are lined by nonkeratinized stratified squamous epithelium. Other, open to outside body cavities are lined by simple squamous or columnar epithelial cells. Other epithelial cells line the insides of the lungs, the gastrointestinal tract, the reproductive and urinary tracts, and make up the exocrine and endocrine glands.
Functions of epithelial cells include secretion, absorption, protection, transcellular transport, sensation detection, and selective permeability. Endothelium (the inner lining of blood vessels) is a specialized form of epithelium.
In humans, epithelium is classified as a primary body tissue, the other ones being connective tissue, muscle tissue and nerve tissue.

Phase III

studies are randomized controlled trials on large patient groups (300–3,000 or more depending upon the condition) and are aimed at being the definitive assessment of the efficacy of the new therapy, in comparison with current 'Gold Standard' treatment. Phase III trials are the most expensive, time-consuming and difficult trials to design and run, especially in therapies for chronic conditions. Once a drug has proven satisfactory over Phase III trials, the trial results are usually combined into a large document containing a comprehensive description of the methods and results of human and animal studies, manufacturing procedures, formulation details, and shelf life. This collection of information makes up the "regulatory submission" that is provided for review to various regulatory authorities in different countries for marketing approval.
It is also common practice with many drugs whose approval is pending, that certain phase III trials will continue. This typically serves to provide lifesaving products after involvement in a clinical trial until the marketed product can be obtained. Other reasons for performing trials at this stage include attempts at "label expansion” to prove additional efficacy for uses beyond the original use for which the drug was designed, to obtain additional safety data, or to support marketing claims. Studies in this phase are by some companies categorised as "Phase IIIB studies."
While not required in all studies, it is typically expected that there be at least two successful phase III trials, proving a drug's safety and efficacy, for approval from the standard regulatory agencies (FDA, TGA, EMEA, etc.). Though the current trend in recent months seems to be a move toward adaptive (live, changing) studies to expedite the process, there are no formal regulations for these trials in the pharmaceutical industry as of yet.