User:Etienne Robillard/Notebook/Cat eye syndrome

From OpenWetWare

< User:Etienne Robillard | Notebook(Difference between revisions)
Jump to: navigation, search
(Glossary)
Current revision (21:02, 2 June 2013) (view source)
(Role and implications of orthogonal rRNA (16S) transcription and translation promoters in the Down Syndrome mutant phenotype acquisition)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
__TOC__
__TOC__
-
=== Introduction to CES ===
+
=== Primer on ADA, CAP, CES, and CAMK2G (KCC2G) : An advanced AHL (light/energy) activated riboswitch and psychochemical agent using orthogonal (synthetic) recombinase promoters ===
* EC 3.5.4.4 [http://brenda-enzymes.org/php/result_flat.php4?ecno=3.5.4.4&Suchword=&organism%5B%5D=Homo+sapiens&show_tm=0 ref]
* EC 3.5.4.4 [http://brenda-enzymes.org/php/result_flat.php4?ecno=3.5.4.4&Suchword=&organism%5B%5D=Homo+sapiens&show_tm=0 ref]
* also named '''Adenosine deaminase CECR1'''
* also named '''Adenosine deaminase CECR1'''
-
* Uniprot accession number Q9NZK5
+
* Uniprot accession number '''Q9NZK5''' - Check this! Also you may want to verify [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=2231495 rs2231495] for hints about the relevance of auxotrophic genes (alternative splicing) in the phylogenetical evolution of CES.
 +
** See also the [http://www.ncbi.nlm.nih.gov/nuccore/224183182?report=fasta primary reference] (FASTA) for the [http://www.ncbi.nlm.nih.gov/nuccore/NT_011519.10 GRCh37.p10] assembly (genome).
 +
** The latest <font color="red">genome reference</font> for the GRCh37.p11 assembly is available [http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.23/ here].
* reaction type -> deamination
* reaction type -> deamination
* tissues: brain, liver, thymus...
* tissues: brain, liver, thymus...
Line 11: Line 13:
* related to chromosome 22q11
* related to chromosome 22q11
* for PD (Score 8.991) and [[BPA|BPA (bis-phenol-A)]], see also gene [http://www.uniprot.org/uniprot/Q13555 CAMK2G (KCC2G)] - also known as chromosome 22q10. [1] [2]
* for PD (Score 8.991) and [[BPA|BPA (bis-phenol-A)]], see also gene [http://www.uniprot.org/uniprot/Q13555 CAMK2G (KCC2G)] - also known as chromosome 22q10. [1] [2]
 +
 +
=== Positively matching SNPs (clinical data) ===
 +
 +
* Oracle: You seem lost.
 +
* Chuck: Keep going... I've seen worst than this.
 +
* Oracle: Fair enough...
 +
* Chuck: Look, I have tons of fb cuties waiting for some action.
 +
* Oracle: Sure. Do you want a little blue cheese with that, sir?
=== Parkinson disease/CES tristable riboswitch device abstraction ===
=== Parkinson disease/CES tristable riboswitch device abstraction ===
-
* A Parkinson/CES disease "riboswitch" is a AHL-activated (acyl-homoserine-lactone) xenobiotic compound (recombinase system) modulating Ca2+/Mg2+ (CAM2KG) specific ions channel to activate RNA polymerase transcription and controlled DNA release of the  V. Fischeri specific "LuxR" protein: a functional beta-amyloid ligand (NMDA receptor antagonist) regulated by the EnvZ (OmpR) gene. See also [http://partsregistry.org/Featured_Parts:Light_Sensor Featured_Parts:Light_Sensor].
+
* <font color="red">A Parkinson/CES disease "riboswitch" is a AHL-activated (Acyl-Homoserine-Lactone) xenobiotic compound (recombinase system) '''modulating Ca2+/Mg2+ (CAM2KG) specific ions channel to activate RNA polymerase transcription and controlled DNA release of the  V. Fischeri specific "LuxR" protein: a functional beta-amyloid ligand regulated by the EnvZ (OmpR) gene.</font>
 +
* See also [http://partsregistry.org/Featured_Parts:Light_Sensor Featured_Parts:Light_Sensor]. [ENVZ, CAMK2G, RIBOSWITCH]
* See also [http://www.youtube.com/watch?v=V6ycmQJOaBQ&feature=endscreen&NR=1 Mind control: An introduction movie to optogenetics from the BBC.]
* See also [http://www.youtube.com/watch?v=V6ycmQJOaBQ&feature=endscreen&NR=1 Mind control: An introduction movie to optogenetics from the BBC.]
* See also the relevant Ecocyc.org entry for EnvZ [http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10269 here].
* See also the relevant Ecocyc.org entry for EnvZ [http://ecocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG10269 here].
Line 21: Line 32:
* See also the histidine kinase entry (EC 2.7.13.3) [http://brenda-enzymes.org/php/result_flat.php4?ecno=2.7.13.3 here].
* See also the histidine kinase entry (EC 2.7.13.3) [http://brenda-enzymes.org/php/result_flat.php4?ecno=2.7.13.3 here].
* Get the latest BLAST results for EG10269 [http://www.ecogene.org/prerun/EG10269.html here].
* Get the latest BLAST results for EG10269 [http://www.ecogene.org/prerun/EG10269.html here].
 +
 +
=== DS ===
 +
 +
==== References ====
 +
# '''Down syndrome phenotype''' http://omim.org/entry/190685
 +
# http://omim.org/entry/147150
 +
 +
==== Role and implications of orthogonal rRNA (16S) transcription and translation promoters in the Down Syndrome mutant phenotype acquisition ====
 +
 +
* chromosome 21q22.3
 +
* APP: <font color=magenta>''Patients with Down syndrome develop the neuropathologic hallmarks of Alzheimer disease at a much earlier age than individuals with Alzheimer disease without trisomy 21 (Wisniewski et al., 1985). Characteristic senile plaques and neurofibrillary tangles are present in the brain of all individuals with Down syndrome over the age of 40 years (Wisniewski et al., 1985). The triplication of the amyloid precursor protein gene (APP; 104760) may be the cause of this phenomenon. Several mutations in the APP gene have been described in families with early-onset Alzheimer disease without trisomy 21 (e.g., Goate et al., 1991).''</font> [1] http://omim.org/entry/104760
 +
* (Interferon-inducible) p78 protein : ''Mapping of the chromosomal region that, if triplicated, results in the phenotypic characteristics of Down syndrome has been facilitated by the use of DNA samples from individuals who have partial trisomy 21 with or without features of the Down syndrome phenotype (Rahmani et al., 1989; McCormick et al., 1989; Korenberg et al., 1990; Delabar et al., 1993; Korenberg, 1993). Although detailed analysis of these DNAs is still under way, an area of approximately 5 Mb between loci D21S58 and D21S42 has been identified that is associated with mental retardation and most of the facial features of the syndrome. <font color="red">In particular, a subregion that includes D21S55 and MX1 (interferon-induced protein p78; 147150), the latter being located in band 21q22.3</font>, has been associated with mental retardation and several morphologic features, including oblique eye fissure, epicanthus, flat nasal bridge, protruding tongue, short broad hands, clinodactyly of the fifth finger, gap between first and second toes, hypotonia, short stature, Brushfield spots, and characteristic dermatoglyphics (Delabar et al., 1993). Additional phenotypic characteristics may map outside the minimum critical region (symbolized DCR). Material from other rare patients who have features of Down syndrome but no visible chromosomal abnormality may help to narrow down the critical region. In several such studies, however, no triplicated region has been identified (McCormick et al., 1989; Delabar et al., 1993). It is possible that these patients do not have any chromosome 21 abnormality and their phenotype is a phenocopy of Down syndrome.''  [1] http://omim.org/entry/190685
 +
* 16S RNA inducible transcriptions/translations in E.coli K12:  http://www.ncbi.nlm.nih.gov/pubmed/12732305
 +
* p78 + RNA : http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=all&keywords=p78+RNA
 +
* http://www.uniprot.org/uniprot/P20591
 +
* http://www.ncbi.nlm.nih.gov/pmc/articles/PMC43917/
 +
* '' "Look (2002) reviewed the mechanism by which GATA1 mutations might interact with trisomy 21 to result in AMKL. He pointed out that several lines of evidence indicated that at least 2 classes of mutations are needed to transform a normal hematopoietic stem cell into a clonal acute myeloid leukemia. One class imparts a myeloproliferative or survival advantage, as illustrated by activating mutations in FLT3 (136351), encoding a receptor tyrosine kinase, or the increased dosage of genes in chromosome 21 in persons with Down syndrome. To generate overt leukemia, a second class of genetic alterations must produce lineage-specific blocks in differentiation. <font color="red">The mutations responsible for this step have been demonstrated mainly in genes encoding chimeric transcription factors produced by chromosomal translocation. GATA1 is a transcription factor that plays a pivotal role in myeloid lineage commitment.</font>" ''  [1]
=== Glossary ===  
=== Glossary ===  

Current revision

Contents


Primer on ADA, CAP, CES, and CAMK2G (KCC2G) : An advanced AHL (light/energy) activated riboswitch and psychochemical agent using orthogonal (synthetic) recombinase promoters

  • EC 3.5.4.4 ref
  • also named Adenosine deaminase CECR1
  • Uniprot accession number Q9NZK5 - Check this! Also you may want to verify rs2231495 for hints about the relevance of auxotrophic genes (alternative splicing) in the phylogenetical evolution of CES.
  • reaction type -> deamination
  • tissues: brain, liver, thymus...
  • Litterature review: http://www.omim.org/entry/115470
  • related to chromosome 22q11
  • for PD (Score 8.991) and BPA (bis-phenol-A), see also gene CAMK2G (KCC2G) - also known as chromosome 22q10. [1] [2]

Positively matching SNPs (clinical data)

  • Oracle: You seem lost.
  • Chuck: Keep going... I've seen worst than this.
  • Oracle: Fair enough...
  • Chuck: Look, I have tons of fb cuties waiting for some action.
  • Oracle: Sure. Do you want a little blue cheese with that, sir?

Parkinson disease/CES tristable riboswitch device abstraction

  • A Parkinson/CES disease "riboswitch" is a AHL-activated (Acyl-Homoserine-Lactone) xenobiotic compound (recombinase system) modulating Ca2+/Mg2+ (CAM2KG) specific ions channel to activate RNA polymerase transcription and controlled DNA release of the V. Fischeri specific "LuxR" protein: a functional beta-amyloid ligand regulated by the EnvZ (OmpR) gene.
  • See also Featured_Parts:Light_Sensor. [ENVZ, CAMK2G, RIBOSWITCH]
  • See also Mind control: An introduction movie to optogenetics from the BBC.
  • See also the relevant Ecocyc.org entry for EnvZ here.
  • Accession number (E.coli K-12 MG1655 substr): "EG10269".
  • Full data available here.
  • See also the histidine kinase entry (EC 2.7.13.3) here.
  • Get the latest BLAST results for EG10269 here.

DS

References

  1. Down syndrome phenotype http://omim.org/entry/190685
  2. http://omim.org/entry/147150

Role and implications of orthogonal rRNA (16S) transcription and translation promoters in the Down Syndrome mutant phenotype acquisition

  • chromosome 21q22.3
  • APP: Patients with Down syndrome develop the neuropathologic hallmarks of Alzheimer disease at a much earlier age than individuals with Alzheimer disease without trisomy 21 (Wisniewski et al., 1985). Characteristic senile plaques and neurofibrillary tangles are present in the brain of all individuals with Down syndrome over the age of 40 years (Wisniewski et al., 1985). The triplication of the amyloid precursor protein gene (APP; 104760) may be the cause of this phenomenon. Several mutations in the APP gene have been described in families with early-onset Alzheimer disease without trisomy 21 (e.g., Goate et al., 1991). [1] http://omim.org/entry/104760
  • (Interferon-inducible) p78 protein : Mapping of the chromosomal region that, if triplicated, results in the phenotypic characteristics of Down syndrome has been facilitated by the use of DNA samples from individuals who have partial trisomy 21 with or without features of the Down syndrome phenotype (Rahmani et al., 1989; McCormick et al., 1989; Korenberg et al., 1990; Delabar et al., 1993; Korenberg, 1993). Although detailed analysis of these DNAs is still under way, an area of approximately 5 Mb between loci D21S58 and D21S42 has been identified that is associated with mental retardation and most of the facial features of the syndrome. In particular, a subregion that includes D21S55 and MX1 (interferon-induced protein p78; 147150), the latter being located in band 21q22.3, has been associated with mental retardation and several morphologic features, including oblique eye fissure, epicanthus, flat nasal bridge, protruding tongue, short broad hands, clinodactyly of the fifth finger, gap between first and second toes, hypotonia, short stature, Brushfield spots, and characteristic dermatoglyphics (Delabar et al., 1993). Additional phenotypic characteristics may map outside the minimum critical region (symbolized DCR). Material from other rare patients who have features of Down syndrome but no visible chromosomal abnormality may help to narrow down the critical region. In several such studies, however, no triplicated region has been identified (McCormick et al., 1989; Delabar et al., 1993). It is possible that these patients do not have any chromosome 21 abnormality and their phenotype is a phenocopy of Down syndrome. [1] http://omim.org/entry/190685
  • 16S RNA inducible transcriptions/translations in E.coli K12: http://www.ncbi.nlm.nih.gov/pubmed/12732305
  • p78 + RNA : http://www.genome.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1000&dbkey=all&keywords=p78+RNA
  • http://www.uniprot.org/uniprot/P20591
  • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC43917/
  • "Look (2002) reviewed the mechanism by which GATA1 mutations might interact with trisomy 21 to result in AMKL. He pointed out that several lines of evidence indicated that at least 2 classes of mutations are needed to transform a normal hematopoietic stem cell into a clonal acute myeloid leukemia. One class imparts a myeloproliferative or survival advantage, as illustrated by activating mutations in FLT3 (136351), encoding a receptor tyrosine kinase, or the increased dosage of genes in chromosome 21 in persons with Down syndrome. To generate overt leukemia, a second class of genetic alterations must produce lineage-specific blocks in differentiation. The mutations responsible for this step have been demonstrated mainly in genes encoding chimeric transcription factors produced by chromosomal translocation. GATA1 is a transcription factor that plays a pivotal role in myeloid lineage commitment." [1]

Glossary

  • ADA
  • AHL
  • BPA
  • CES
  • recombinase
  • CAMK2G
  • Calmodulin
  • LuxR
  • EnvZ
  • PC
  • ATP
  • LacZ
  • PD - Parkinson disease
  • cAMP
  • riboswitch
  • polymerase,
  • RNA
  • NMDA
  • trans-splicing

References

  1. http://www.genecards.org/cgi-bin/carddisp.pl?gene=CAMK2G
  2. http://www.sciencedaily.com/releases/2013/02/130225153122.htm?utm_source=dlvr.it&utm_medium=twitter
Personal tools