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077487b57636f6b8c13462903f9d5794ac961cd2 | UXT | WikiDoc | mechanisms of suppression, ART-27 likely plays multiple roles that inhibit AR-mediated transcription. In the absence of androgens, ART-27 may bind the AR N terminus and thereby prevent AR-dependent activation of genes involved in cell proliferation. Other mechanisms may include recruitment of ART-27 to AREs or inhibition of histone methylation which otherwise allows for increased transcription of target genes. | 4 |
077487b57636f6b8c13462903f9d5794ac961cd2 | UXT | WikiDoc | # Interactions
UXT has been shown to interact with Androgen receptor. | 5 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | WT1
Wilms tumor protein is a protein that in humans is encoded by the WT1 gene on chromosome 11p.
# Function
This gene encodes a transcription factor that contains four zinc finger motifs at the C-terminus and a proline / glutamine-rich DNA-binding domain at the N-terminus. It has an essential role in the normal development of the urogenital system, and it is mutated in a subset of patients with Wilms' tumor, the gene's namesake. Multiple transcript variants, resulting from alternative splicing at two coding exons, have been well characterized. There is also evidence for the use of non-AUG (CUG) translation initiation site upstream of, and in-frame with the first AUG, leading to additional isoforms.
# Structure
The WT1 gene product shows similarity to the zinc fingers of the mammalian growth regulated early growth response protein 1 (EGR1) and (EGR2) proteins. | 0 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | # Clinical significance
Wilms tumour tumor suppressor gene1 (WT1) causes an embryonic malignancy of the kidney, affecting around 1 in 10,000 infants. It occurs in both sporadic and hereditary forms. Inactivation of WT1 causes Wilms tumour, and Denys-Drash syndrome (DDS), leading to nephropathy and genital abnormalities. The WT1 protein has been found to bind a host of cellular factors, e.g. p53, a known tumor suppressor.
WT1 is mutated in a mutually exclusive manner with TET2, IDH1, and IDH2 in acute myeloid leukemia. TET2 can be recruited by WT1 to its target genes and activates WT1-target genes by converting 5mC into 5hmC residues at the genes’ promoters, representing an important feature of a new regulatory WIT pathway linked to the development of AML.
The serine protease HtrA2 binds to WT1 and it cleaves WT1 at multiple sites following the treatment with cytotoxic drugs. | 1 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | The serine protease HtrA2 binds to WT1 and it cleaves WT1 at multiple sites following the treatment with cytotoxic drugs.
Using immunohistochemistry, WT1 protein can be demonstrated in the cell nuclei of 75% of mesotheliomas and in 93% of ovarian serous carcinomas, as well as in benign mesothelium and fallopian tube epithelium. This allows these tumours to be distinguished from other, similar, cancers, such as adenocarcinoma. Antibodies to the WT1 protein, however, also frequently cross-react with cytoplasmic proteins in a variety of benign and malignant cells, so that only nuclear staining can be considered diagnostic. | 2 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | ## As a drug target
WT1 has been ranked by the National Cancer Institute (NCI) as the Number 1 target for cancer immunotherapy.
A vaccine that induces an acquired immune response against WT1 is in clinical trials for various cancers.
# Interactions
WT1 has been shown to interact with TET2, U2AF2, PAWR, UBE2I and WTAP. In combination with Cited2 activates WT1 the Steroidogenic factor 1
# RNA editing
There is some evidence for RNA editing of human WT1 mRNA. As with alternative splicing of the gene RNA editing increases the number of isoforms of this protein.
Editing is tissue specific and developmentally regulated. Editing shown to be restricted in testis and kidney in the rat. Editing of this gene product has been found to occur in mice and rats as well as humans. | 3 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | ## Editing type
The editing site is found at nucleotide position 839 found in exon 6 of the gene.It causes a codon change from a Proline codon (CCC) to a Leucine codon (CUC)
The type of editing is a Uridine to Cytidine( U to C) base change .The editing reaction is thought to be an amidation of uridine which converts it to a Cytidine.The relevance of this editing is unknown as is the enzyme responsible for this editing.The region where editing occurs like that of other editing sites e.g. ApoB mRNA editing is conserved.Mice, rat and humans have conserved sequences flanking the editing site consisting of 10 nucleotides before the editing site and four after the site. | 4 |
4c3dbd1bf28e2a2c036c2690b628f18ef0d33a27 | WT1 | WikiDoc | ## Effects of editing
RNA editing results in an alternative amino acid being translated. The changes in amino acid occur in a region identified as a domain involved in transcription activation function.
Editing has been shown to decrease repressive regulation of transcription of growth promoting genes in vitro compared to the non edited protein. Although the physiological role of editing has yet to be determined, suggestions have been made that editing may play a role in the pathogenesis of Wilms tumour. | 5 |
36e7a1634042ef511d947710385cbc8ae61138b8 | YY1 | WikiDoc | YY1
YY1 (Yin Yang 1) is a transcriptional repressor protein in humans that is encoded by the YY1 gene.
# Function
YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins. The protein is involved in repressing and activating a diverse number of promoters. Hence, the YY in the name stands for "yin-yang." YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus implicating histone modification in the function of YY1. YY1 promotes enhancer-promoter chromatin loops by forming dimers and promoting DNA interactions. Its disregulation disrupts enhancer-promoter loops and gene expression. | 0 |
36e7a1634042ef511d947710385cbc8ae61138b8 | YY1 | WikiDoc | # Clinical significance
YY1 heterozygous deletions, missense, and nonsense mutations cause Gabriele-DeVries syndrome (GADEVS) , an autosomal dominant neurodevelopmental disorder characterized by intellectual disability, dysmorphic facial features, feeding problems, intrauterine growth restriction, variable cognitive impairment, behavioral problems and other congenital malformations. It is available a website to share and collect clinical information between clinical doctors and families of mutated indididuals.
# Interactions
YY1 has been shown to interact with:
- ATF6,
- EP300,
- FKBP3,
- HDAC3,
- Histone deacetylase 2,
- Myc,
- NOTCH1,
- RYBP, and
- SAP30.
- Seryl-tRNA Synthetase. | 1 |
1cede65e58751f0ccf26ecef575063596bff4181 | ZP2 | WikiDoc | ZP2
Zona pellucida sperm-binding protein 2 is a protein that in humans is encoded by the ZP2 gene. | 0 |
1cede65e58751f0ccf26ecef575063596bff4181 | ZP2 | WikiDoc | # Function
The zona pellucida is an extracellular matrix that surrounds the oocyte and early embryo. It is composed primarily of three (mouse) or four (human) glycoproteins (ZP1-4) with various functions during fertilization and preimplantation development. The protein encoded by this gene is a structural component of the zona pellucida and functions in secondary binding and penetration of acrosome-reacted spermatozoa. The nascent protein contains a N-terminal signal peptide sequence, a conserved ZP domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. It is hypothesized that furin cleavage results in release of the mature protein from the plasma membrane for subsequent incorporation into the zona pellucida matrix. However, the requirement for furin cleavage in this process remains controversial based on mouse studies. | 1 |
1cede65e58751f0ccf26ecef575063596bff4181 | ZP2 | WikiDoc | The sperm-binding domain on the ZP2 protein is necessary in both humans and mice for oocyte-sperm recognition and penetration of the zona pellucida. It is also responsible for the primary block to polyspermy in mammals. The oocyte has cortical granules peripherally located under the cortex that contain a proteolytic protein called ovastacin. After the sperm binds to ZP2, the cortical granules are exocytosed releasing ovastacin into the perivitelline space. Ovastacin cleaves ZP2 at the N terminus, preventing more sperm from binding and penetrating the oocyte, thus hardening the zona pellucida. Ovastacin is only found in oocytes, and is part of the astacin family of metalloendoproteases. Female mice engineered without ovastacin showed that ZP2 was not cleaved after fertilization. | 2 |
1cede65e58751f0ccf26ecef575063596bff4181 | ZP2 | WikiDoc | # 3D structure
The crystal structure of the sperm-binding domain of ZP2 at 0.95 Å resolution (PDB: 5II6) showed that is shares the same ZP-N fold first identified in structures of ZP3 (PDB: 3D4C, 3D4G, 3EF7, 3NK3, 3NK4). This provided experimental evidence for the suggestion that the N-terminal region of ZP2 consists of three ZP-N repeats and revealed that - despite insignificant sequence identity - ZP2 is structurally similar to VERL, the vitelline envelope receptor for egg lysin of the mollusk abalone (PDB: 5II4, 5II5, 5MR2, 5IIC, 5IIA, 5IIB, 5MR3). This established a link between invertebrate and vertebrate fertilization by suggesting that, despite being separated by 600 million years of evolution, mollusk and human use a common protein fold to interact with sperm. | 3 |
1c5af24e66c4a6b4f0a1e6910460a5a740249d42 | ZP3 | WikiDoc | ZP3
Zona pellucida sperm-binding protein 3, also known as zona pellucida glycoprotein 3 (Zp-3) or the sperm receptor, is a ZP module-containing protein that in humans is encoded by the ZP3 gene. ZP3 is the receptor in the zona pellucida which binds sperm at the beginning of fertilization. | 0 |
1c5af24e66c4a6b4f0a1e6910460a5a740249d42 | ZP3 | WikiDoc | # Function | 1 |
1c5af24e66c4a6b4f0a1e6910460a5a740249d42 | ZP3 | WikiDoc | The zona pellucida (ZP) is a specialized extracellular matrix that surrounds the oocyte and early embryo. It is composed of three or four glycoproteins (ZP1-4) with various functions during oogenesis, fertilization and preimplantation development. The protein encoded by this gene is a major structural component of the ZP and functions in primary binding and stimulation of the sperm acrosome reaction. The nascent protein contains a N-terminal signal peptide sequence, a conserved "ZP domain" module, a consensus furin cleavage site (CFCS), a polymerization-blocking external hydrophobic patch (EHP), and a C-terminal transmembrane domain. Cleavage at the CFCS separates the mature protein from the EHP, allowing it to incorporate into nascent ZP filaments. A variation in the last exon of this gene has previously served as the basis for an additional ZP3 locus; however, sequence and literature review reveals that there is only one full-length ZP3 locus in the human genome. Another locus | 2 |
1c5af24e66c4a6b4f0a1e6910460a5a740249d42 | ZP3 | WikiDoc | gene has previously served as the basis for an additional ZP3 locus; however, sequence and literature review reveals that there is only one full-length ZP3 locus in the human genome. Another locus encoding a bipartite transcript designated POMZP3 contains a duplication of the last four exons of ZP3, including the above described variation, and maps closely to this gene. | 3 |
1c5af24e66c4a6b4f0a1e6910460a5a740249d42 | ZP3 | WikiDoc | # 3D Structure
X-ray crystallographic studies of the N-terminal half of mammalian ZP3 (PDB: 3D4C, 3D4G, 3EF7) as well as its full-length avian homolog (PDB: 3NK3, 3NK4) revealed that the protein's ZP module consists of two immunoglobulin-like domains, ZP-N and ZP-C. The latter, which contains EHP as well as a ZP3-specific subdomain, interacts with the ZP-N domain of a second molecule to generate an antiparallel homodimeric arrangement required for protein secretion. | 4 |
7f51748f30eb0ffa2b5396fff8c7be045115ea7c | ZP4 | WikiDoc | ZP4
Zona pellucida sperm-binding protein 4, ZP-4 or avilesine, named after its discoverer Manuel Avilés Sánchezis a protein that in humans is encoded by the ZP4 gene. | 0 |
7f51748f30eb0ffa2b5396fff8c7be045115ea7c | ZP4 | WikiDoc | # Function
The zona pellucida is an extracellular matrix that surrounds the oocyte and early embryo. It is composed primarily of three or four glycoproteins with various functions during fertilization and preimplantation development. The nascent protein contains a N-terminal signal peptide sequence, a conserved zona pellucida-like domain, a consensus furin cleavage site, and a C-terminal transmembrane domain. It is hypothesized that furin cleavage results in release of the mature protein from the plasma membrane for subsequent incorporation into the zona pellucida matrix. However, the requirement for furin cleavage in this process remains controversial based on mouse studies.
Previously, this gene has been referred to as ZP1 or ZPB and thought to have similar functions as mouse Zp1. However, a human gene with higher similarity and chromosomal synteny to mouse Zp1 has been assigned the symbol ZP1 and this gene has been assigned the symbol ZP4. | 1 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | pH
- Acid-base extraction
- Acid-base reaction
- Acid-base physiology
- Acid-base homeostasis
- Dissociation constant
- Acidity function
- Buffer solutions
- pH
- Proton affinity
- Self-ionization of water
- Acids:
Lewis acids
Mineral acids
Organic acids
Strong acids
Superacids
Weak acids
- Lewis acids
- Mineral acids
- Organic acids
- Strong acids
- Superacids
- Weak acids
- Bases:
Lewis bases
Organic bases
Strong bases
Superbases
Non-nucleophilic bases
Weak bases
- Lewis bases
- Organic bases
- Strong bases
- Superbases
- Non-nucleophilic bases
- Weak bases | 0 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Overview
pH is a measure of the acidity or alkalinity of a solution. Aqueous solutions at 25°C with a pH less than seven are considered acidic, while those with a pH greater than seven are considered basic (alkaline). When a pH level is 7.0, it is defined as 'neutral' at 25°C because at this pH the concentration of H3O+ equals the concentration of OH− in pure water. pH is formally dependent upon the activity of hydronium ions (H3O+), but for very dilute solutions, the molarity of H3O+ may be used as a substitute with little loss of accuracy. (H+ is often used as a synonym for H3O+.) Because pH is dependent on ionic activity, a property which cannot be measured easily or fully predicted theoretically, it is difficult to determine an accurate value for the pH of a solution. The pH reading of a solution is usually obtained by comparing unknown solutions to those of known pH, and there are several ways to do so. | 1 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | The concept of pH was first introduced by Danish chemist S. P. L. Sørensen at the Carlsberg Laboratory in 1909. The name, pH, has claimed to have come from any of several sources including: pondus hydrogenii, potentia hydrogenii (Latin), potentiel hydrogène (French), and potential of hydrogen (English). | 2 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Definition
pH (potential of hydrogen) is defined operationally as follows. For a solution X, first measure the electromotive force EX of the galvanic cell
where
Defined this way, pH is a dimensionless quantity. Values pH(S) for a range of standard solutions S, along with further details, are given in the relevant IUPAC recommendation.
pH has no fundamental meaning as a unit; its official definition is a practical one. However in the restricted range of dilute aqueous solutions having an amount-of-dissolved-substance concentrations less than 0.1 mol/L, and being neither strongly alkaline nor strongly acidic (2 < pH < 12), the definition is such that
where denotes the amount-of-substance concentration of hydrogen ion H+ and γ1 denotes the activity coefficient of a typical univalent electrolyte in the solution. | 3 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Explanation
In simpler terms, the number arises from a measure of the activity of hydrogen ions (or their equivalent) in the solution. The pH scale is an inverse logarithmic representation of hydrogen proton (H+) concentration. Unlike linear scales which have a constant relations between the item being measured (H+ concentration in this case) and the value reported, each individual pH unit is a factor of 10 different than the next higher or lower unit. For example, a change in pH from 2 to 3 represents a 10-fold decrease in H+ concentration, and a shift from 2 to 4 represents a one-hundred (10 × 10)-fold decrease in H+ concentration. The formula for calculating pH is: | 4 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | Where αH+ denotes the activity of H+ ions, and is dimensionless. In solutions containing other ions, activity and concentration will not generally be the same. Activity is a measure of the effective concentration of hydrogen ions, rather than the actual concentration; it includes the fact that other ions surrounding hydrogen ions will shield them and affect their ability to participate in chemical reactions. These other ions change the effective amount of hydrogen ion concentration in any process that involves H+.
In dilute solutions (such as tap water), activity is approximately equal to the numeric value of the concentration of the H+ ion, denoted as (or more accurately written, ), measured in moles per litre (also known as molarity). Therefore, it is often convenient to define pH as: | 5 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | For both definitions, log10 denotes the base-10 logarithm, therefore pH defines a logarithmic scale of acidity. For example, if one makes a lemonade with a H+ concentration of 0.0050 moles per litre, its pH would be:
A solution of pH = 8.2 will have an concentration of 10−8.2 mol/L, or about 6.31 × 10−9 mol/L. Thus, its hydrogen activity αH+ is around 6.31 × 10−9. A solution with an concentration of 4.5 × 10−4 mol/L will have a pH value of 3.35.
In solution at 25 °C, a pH of 7 indicates neutrality (i.e. the pH of pure water) because water naturally dissociates into H+ and OH− ions with equal concentrations of 1×10−7 mol/L. A lower pH value (for example pH 3) indicates increasing strength of acidity, and a higher pH value (for example pH 11) indicates increasing strength of basicity. Note, however, that pure water, when exposed to the atmosphere, will take in carbon dioxide, some of which reacts with water to form carbonic acid and H+, thereby lowering the pH to about 5.7. | 6 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | Neutral pH at 25 °C is not exactly 7. pH is an experimental value, so it has an associated error. Since the dissociation constant of water is (1.011 ± 0.005) × 10−14, pH of water at 25 °C would be 6.998 ± 0.001. The value is consistent, however, with neutral pH being 7.00 to two significant figures, which is near enough for most people to assume that it is exactly 7. The pH of water gets smaller with higher temperatures. For example, at 50 °C, pH of water is 6.55 ± 0.01. This means that a diluted solution is neutral at 50 °C when its pH is around 6.55 and that a pH of 7.00 is basic. | 7 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | Most substances have a pH in the range 0 to 14, although extremely acidic or extremely basic substances may have pH less than 0 or greater than 14. An example is acid mine runoff, with a pH = –3.6. Note that this does not translate to a molar concentration of 3981 M; such high activity values are the result of the extremely high value of the activity coefficient while concentrations are within a "reasonable" range . E.g. a 7.622 molal H2SO4 solution has a pH = -3.13, hydrogen activity αH+ around 1350 and activity coefficient γH+ = 165.4 when using the MacInnes convention for scaling Pitzer single ion activity coefficient .
Arbitrarily, the pH is -\log_{10}{()}. Therefore,
-r, by substitution, | 8 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | Arbitrarily, the pH is -\log_{10}{()}. Therefore,
-r, by substitution,
The "pH" of any other substance may also be found (e.g. the potential of silver ions, or pAg+) by deriving a similar equation using the same process. These other equations for potentials will not be the same, however, as the number of moles of electrons transferred (n) will differ for the different reactions. | 9 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Calculation of pH for weak and strong acids
Values of pH for weak and strong acids can be approximated using certain assumptions.
Under the Brønsted-Lowry theory, stronger or weaker acids are a relative concept. But here we define a strong acid as a species which is a much stronger acid than the hydronium (H3O+) ion. In that case the dissociation reaction (strictly HX+H2O↔H3O++X− but simplified as HX↔H++X−) goes to completion, i.e. no unreacted acid remains in solution. Dissolving the strong acid HCl in water can therefore be expressed:
This means that in a 0.01 mol/L solution of HCl it is approximated that there is a concentration of 0.01 mol/L dissolved hydrogen ions. From above, the pH is: pH = −log10 :
which equals 2.
For weak acids, the dissociation reaction does not go to completion. An equilibrium is reached between the hydrogen ions and the conjugate base. The following shows the equilibrium reaction between methanoic acid and its ions: | 10 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | It is necessary to know the value of the equilibrium constant of the reaction for each acid in order to calculate its pH. In the context of pH, this is termed the acidity constant of the acid but is worked out in the same way (see chemical equilibrium):
For HCOOH, Ka = 1.6 × 10−4
When calculating the pH of a weak acid, it is usually assumed that the water does not provide any hydrogen ions. This simplifies the calculation, and the concentration provided by water, 1×10−7 mol/L, is usually insignificant.
With a 0.1 mol/L solution of methanoic acid (HCOOH), the acidity constant is equal to:
Given that an unknown amount of the acid has dissociated, will be reduced by this amount, while and will each be increased by this amount. Therefore, may be replaced by 0.1 − x, and and may each be replaced by x, giving us the following equation:
Solving this for x yields 3.9×10−3, which is the concentration of hydrogen ions after dissociation. Therefore the pH is −log(3.9×10−3), or about 2.4. | 11 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Measurement
pH can be measured:
- by addition of a pH indicator into the solution under study. The indicator color varies depending on the pH of the solution. Using indicators, qualitative determinations can be made with universal indicators that have broad color variability over a wide pH range and quantitative determinations can be made using indicators that have strong color variability over a small pH range. Precise measurements can be made over a wide pH range using indicators that have multiple equilibriums in conjunction with spectrophotometric methods to determine the relative abundance of each pH-dependent component that make up the color of solution, or
- by using a pH meter together with pH-selective electrodes (pH glass electrode, hydrogen electrode, quinhydrone electrode, ion sensitive field effect transistor and others). | 12 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | - by using a pH meter together with pH-selective electrodes (pH glass electrode, hydrogen electrode, quinhydrone electrode, ion sensitive field effect transistor and others).
- by using pH paper, indicator paper that turns color corresponding to a pH on a color key. pH paper is usually small strips of paper (or a continuous tape that can be torn) that has been soaked in an indicator solution, and is used for approximations.
The lowest and highest ends of the pH scale do not oxidize. The middle of the scale is what oxidizes, such as water and blood.
As the pH scale is logarithmic, it does not start at zero. Thus the most acidic of liquids encountered can have a pH as low as −5. The most alkaline typically has pH of 14. Measurement of extremely low pH values has various complications. Calibration of the electrode in such cases can be done with standard solutions of concentrated sulphuric acid whose pH values can be calculated with the Pitzer model. | 13 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | As an example of home application, the measurement of pH value can be used to quantify the amount of acid in a swimming pool. | 14 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # pOH
There is also pOH, in a sense the opposite of pH, which measures the concentration of OH− ions, or the basicity. Since water self ionizes, and notating as the concentration of hydroxide ions, we have
where Kw is the ionization constant of water.
Now, since
by logarithmic identities, we then have the relationship:
and thus
This formula is valid exactly for temperature = 298.15 K (25 °C) only, but is acceptable for most lab calculations.
# Indicators
An indicator is used to measure the pH of a substance. Common indicators are litmus paper, phenolphthalein, methyl orange, phenol red, bromothymol blue, bromocresol green and bromocresol purple. To demonstrate the principle with common household materials, red cabbage, which contains the dye anthocyanin, is used. | 15 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | # Seawater
In chemical oceanography pH measurement is complicated by the chemical properties of seawater, and several distinct pH scales exist.
As part of its operational definition of the pH scale, the IUPAC define a series of buffer solutions across a range of pH values (often denoted with NBS or NIST designation). These solutions have a relatively low ionic strength (~0.1) compared to that of seawater (~0.7), and consequently are not recommended for use in characterising the pH of seawater (since the ionic strength differences cause changes in electrode potential). To resolve this problem, an alternative series of buffers based on artificial seawater was developed. This new series resolves the problem of ionic strength differences between samples and the buffers, and the new pH scale is referred to as the total scale, often denoted as pHT. | 16 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | The total scale was defined using a medium containing sulphate ions. These ions experience protonation, H+ + SO42− Template:Unicode HSO4−, such that the total scale includes the effect of both protons ("free" hydrogen ions) and hydrogen sulphate ions:
An alternative scale, the free scale, often denoted pHF, omits this consideration and focuses solely on F, in principle making it a simpler representation of hydrogen ion concentration. Analytically, only T can be determined, so F must be estimated using the and the stability constant of HSO4−, KS*:
However, it is difficult to estimate KS- in seawater, limiting the utility of the otherwise more straightforward free scale.
Another scale, known as the seawater scale, often denoted pHSWS, takes account of a further protonation relationship between hydrogen ions and fluoride ions, H+ + F− Template:Unicode HF. Resulting in the following expression for SWS: | 17 |
5665a91c59b87d6aa18fa41206d073b9e1f9c579 | pH | WikiDoc | However, the advantage of considering this additional complexity is dependent upon the abundance of fluoride in the medium. In seawater, for instance, sulphate ions occur at much greater concentrations (> 400 times) than those of fluoride. Consequently, for most practical purposes, the difference between the total and seawater scales is very small.
The following three equations summarise the three scales of pH:
In practical terms, the three seawater pH scales differ in their values by up to 0.12 pH units, differences that are much larger than the accuracy of pH measurements typically required (particularly in relation to the ocean's carbonate system). Since it omits consideration of sulphate and fluoride ions, the free scale is significantly different from both the total and seawater scales. Because of the relative unimportance of the fluoride ion, the total and seawater scales differ only very slightly. | 18 |
ec7ac906f71e719093b1a2a1a3e870e88bd62597 | Rb | WikiDoc | Rb
RB or Rb may stand for:
- the chemical element Rubidium
- The Nissan RB engine
- the IATA code for Syrian Arab Airlines
- the Retinoblastoma protein, found mutated in many cancers, including retinoblastoma cancer
- an abbreviation for retinoblastoma, a cancer of the eye
- RB, the name used for a series of buses manufactured by Hyundai Motor Company
- an abbreviation for right back, a defensive position in football (soccer)
- an abbreviation for running back, an offensive position in football (American)
- Radio Bremen, a German broadcasting station in Bremen
- re-entry body (US Navy term for re-entry vehicle, rv)
- Rehoboth Beach, Delaware
- Road bike
- The Ruby programming language's typical filename extension, .rb
- .rb is also the extension associated with Rocket Ebook files.
- Rolls-Barnoldswick, one of the design and production sites for Rolls-Royce jet engines
- Rafael Benitez Liverpool manager
- Rancho Bernardo, a community in northern San Diego
de:RB
ko:RB
it:RB
no:RB | 0 |
ec7ac906f71e719093b1a2a1a3e870e88bd62597 | Rb | WikiDoc | - Rafael Benitez Liverpool manager
- Rancho Bernardo, a community in northern San Diego
de:RB
ko:RB
it:RB
no:RB
ksh:RB (Watt ėßß datt?)
sl:RB
fi:Rb
sv:RB | 1 |
8cb08964e634c890efda8edc14c9ed4a0f99d395 | SB | WikiDoc | SB
# Curators
Anyone should feel free to add themselves as a curator for this consensus protocol. You do not need to be a curator in order to contribute. The OpenWetWare community is currently discussing the idea of protocol curators. Please contribute.
# Abstract
SB (Sodium Borate or Sodium Boric Acid) buffer is a agarose gel electropheresis buffer for DNA gels. It has low conductivity and allows for less heat buildup and thus higher voltage and faster runs.
## Reagents
- Sodium Borate decahydrate (Borax)
- Boric Acid
- dH2O
# Procedure
A simple version of this buffer can be easily made as a 20X (100 mM) concentrate.
- 38.17 g Sodium Borate decahydrate
- 33 g Boric Acid
- Bring to 1L with dH2O
- Dilute to 1X and use to make gel and running buffer. | 0 |
8cb08964e634c890efda8edc14c9ed4a0f99d395 | SB | WikiDoc | # Troubleshooting
There are some caveats here. Loading DNA that is in a high-salt solution (some DNA ladders, loading dyes, or restriction enzyme buffers) can increase the local conductivity around the sample and change its running characteristics - meaning that samples in different buffers won't always run at the same speed. The quickest solution here is actually to dilute the sample to the largest volume that you can load in the well.
In addition, one should minimize the amount of indicator dye in the loading dye, as this is a salt and contributes significantly to this problem. Using a fainter dye helps to increase the resolution of these gels.
# Notes
It should be noted that there are several other "next-gen" electropheresis buffers, notably LA - Lithium acetate, which is touted as being superior in many respects to SB. | 1 |
d28cf78717cb4bad6e0dacdcf6ce4671a1ce39c6 | WD | WikiDoc | WD
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