User:ProteinBoxBot/PBB Log Wiki 10-21-07 debug run A

Log file for Protein Box Bot
Log page index: User:ProteinBoxBot/PBB_Log_Index

ADIPOQ

 * INFO: Beginning work on ADIPOQ... {October 21, 2007 11:45:32 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: Adiponectin {October 21, 2007 11:46:43 AM PDT} 
 * UPLOAD: Added new Image to wikiCreated new protein page: Adiponectin {October 21, 2007 11:46:58 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:47:05 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:47:05 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:47:05 AM PDT} 
 * UPDATED: Updated protein page: Adiponectin {October 21, 2007 11:47:12 AM PDT} 

ARNTL
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on ARNTL... {October 21, 2007 11:33:30 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: ARNTL {October 21, 2007 11:34:30 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:34:36 AM PDT} 
 * SKIP SUMMARY: Skipping Summary, No Errors. {October 21, 2007 11:34:36 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:34:36 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:35:01 AM PDT} 
 * UPDATED: Updated protein page (with warnings): ARNTL {October 21, 2007 11:35:01 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Aryl hydrocarbon receptor nuclear translocator-like, also known as ARNTL, Bmal1, or Mop3, is a gene.

The protein encoded by this gene is a basic-helix-loop-helix PAS (bHLH-PAS) domain containing protein that forms a heterodimer with a second bHLH-PAS protein, CLOCK, or its ortholog, Npas2. This complex binds to E-box response elements&lt;ref name=&quot;pmid9576906&quot;&gt;&lt;/ref&gt; in promoter regions of many genes including two families of repressor proteins, the Per genes&lt;ref name=&quot;pmid9616112&quot;&gt;&lt;/ref&gt; (Per1, Per2, Per3) and the Cryptochromes&lt;ref name=&quot;pmid10428031&quot;&gt;&lt;/ref&gt;&lt;ref name=&quot;pmid10531061&quot;&gt;&lt;/ref&gt; (Cry1 and Cry2). These repressor proteins are translated, and bind in a complex with casein kinase one epsilon&lt;ref name=&quot;pmid10775102&quot;&gt;&lt;/ref&gt; (Csnk1e) and delta (Csnk1d). Next, the entire complex translocates to the nucleus, where it interacts with the Arntl/Clock heterodimer to inhibit its transactivation. This hypothesis is supported by the observation that point mutants in the Arntl or Clock render them resistant to interaction and repression by Cryptochromes&lt;ref name=&quot;pmid16474406&quot;&gt;&lt;/ref&gt;. Transcription of Period and Cryptochrome genes, therefore, is inhibited, the protein levels of Period and Cryptochrome genes drop, and eventually repression is relieved to allow their transcription to build up again. This process occurs with a period length of approximately 24 hours.

Three transcript variants encoding two different isoforms have been found for this gene.&lt;ref name=&quot;pmid9144434&quot;&gt;&lt;/ref&gt; The importance of these transcript variants is unknown.

Arntl (or Bmal1 or Mop3) is the only component of the mammalian circadian clock whose sole deletion in a mouse model generates arrhythmicity.&lt;ref name=&quot;pmid11163178&quot;&gt;&lt;/ref&gt;  In addition to defects in the clock, these Arntl null-mice also have reproductive problems&lt;ref name=&quot;pmid16940279&quot;&gt;&lt;/ref&gt;, are small in stature, age quickly&lt;ref name=&quot;pmid17369106&quot;&gt;&lt;/ref&gt;, and have progressive arthropathy&lt;ref name=&quot;pmid15739187&quot;&gt;&lt;/ref&gt; that results in having less overall locomotor activity than wild type mice. Recent phenotyping data suggests that this gene&lt;ref name=&quot;pmid15523558&quot;&gt;&lt;/ref&gt; and its partner Clock&lt;ref name=&quot;pmid15845877&quot;&gt;&lt;/ref&gt; also play a role in regulation of glucose homeostasis and metabolism. Finally, Arntl, Npas2, and Per2 have been associated with seasonal affective disorder in humans&lt;ref name=&quot;pmid17457720&quot;&gt;&lt;/ref&gt;.

Arntl transcription is circadian and reciprocally regulated by NR1D1&lt;ref name=&quot;pmid12150932&quot;&gt;&lt;/ref&gt; (Rev-erb-alpha) and RORA&lt;ref name=&quot;pmid15312651&quot;&gt;&lt;/ref&gt;, which establishes a second interlocking loop&lt;ref name=&quot;pmid10807566&quot;&gt;&lt;/ref&gt; in the mammalian circadian clock.

CRY1
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 * INFO: Beginning work on CRY1... {October 21, 2007 11:35:01 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: CRY1 {October 21, 2007 11:35:31 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:35:34 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:35:34 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:35:34 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:35:46 AM PDT} 
 * UPDATED: Updated protein page (with warnings): CRY1 {October 21, 2007 11:35:46 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Cryptochrome 1 (photolyase-like), also known as CRY1, is a human gene.

&lt;!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

CRY2
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on CRY2... {October 21, 2007 11:35:46 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: CRY2 {October 21, 2007 11:36:15 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:36:18 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:36:18 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:36:18 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:36:28 AM PDT} 
 * UPDATED: Updated protein page (with warnings): CRY2 {October 21, 2007 11:36:28 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Cryptochrome 2 (photolyase-like), also known as CRY2, is a human gene.

&lt;!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

CSNK1E
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on CSNK1E... {October 21, 2007 11:36:28 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: CSNK1E {October 21, 2007 11:37:13 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:37:27 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:37:27 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:37:27 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:37:33 AM PDT} 
 * UPDATED: Updated protein page (with warnings): CSNK1E {October 21, 2007 11:37:33 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Casein kinase 1, epsilon, also known as CSNK1E, is a human gene.

&lt;!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

FAS

 * INFO: Beginning work on FAS... {October 21, 2007 11:31:51 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: Fas receptor {October 21, 2007 11:33:18 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:33:20 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:33:20 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:33:20 AM PDT} 
 * UPDATED: Updated protein page: Fas receptor {October 21, 2007 11:33:30 AM PDT} 

HBA1

 * INFO: Beginning work on HBA1... {October 21, 2007 11:37:33 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: HBA1 {October 21, 2007 11:38:17 AM PDT} 
 * UPLOAD: Added new Image to wikiCreated new protein page: HBA1 {October 21, 2007 11:38:32 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:38:39 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:38:39 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:38:39 AM PDT} 
 * UPDATED: Updated protein page: HBA1 {October 21, 2007 11:38:52 AM PDT} 

MTHFR

 * INFO: Beginning work on MTHFR... {October 21, 2007 11:38:52 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: Methylenetetrahydrofolate reductase {October 21, 2007 11:40:51 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:40:52 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:40:52 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:40:52 AM PDT} 
 * UPDATED: Updated protein page: Methylenetetrahydrofolate reductase {October 21, 2007 11:41:03 AM PDT} 

NR1D2
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on NR1D2... {October 21, 2007 11:47:12 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: NR1D2 {October 21, 2007 11:47:51 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:47:55 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:47:55 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:47:55 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:48:02 AM PDT} 
 * UPDATED: Updated protein page (with warnings): NR1D2 {October 21, 2007 11:48:02 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Nuclear receptor subfamily 1, group D, member 2, also known as NR1D2, is a human gene.

&lt;!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

PER1
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on PER1... {October 21, 2007 11:41:03 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: PER1 {October 21, 2007 11:41:20 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:41:22 AM PDT} 
 * UPDATE SUMMARY: Updating Summary, No Errors. {October 21, 2007 11:41:22 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:41:22 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:41:36 AM PDT} 
 * UPDATED: Updated protein page (with warnings): PER1 {October 21, 2007 11:41:36 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Period homolog 1 (Drosophila), also known as PER1, is a human gene.

&lt;!-- The PBB_Summary template is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

PTEN
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on PTEN... {October 21, 2007 11:41:36 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: PTEN (gene) {October 21, 2007 11:41:59 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:42:00 AM PDT} 
 * SKIP SUMMARY: Skipping Summary, No Errors. {October 21, 2007 11:42:00 AM PDT} 
 * SKIP CITATIONS: Skipping Citations, No Errors. {October 21, 2007 11:42:00 AM PDT} 
 * UPDATED: Warning while updating page: Could not find citation box.  {October 21, 2007 11:42:06 AM PDT} 
 * UPDATED: Updated protein page (with warnings): PTEN (gene) {October 21, 2007 11:42:06 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

PTEN (Phosphatase and Tensin homolog) gene is a human gene that acts as a tumor suppressor gene, which means that the protein encoded by this gene helps regulate the cycle of cell division by keeping cells from growing and dividing too rapidly or in an uncontrolled way. Mutations of this gene cause multiple advanced cancers.

The corresponding PTEN protein is found in almost all tissues in the body. The PTEN protein modifies lipids (fats) in cells by removing phosphate groups (clusters of one phosphorous and three oxygen atoms), making the PTEN protein a type of enzyme called a phosphatase. More specifically it is a phosphodiesterase and an inhibitor of the phospho-AKT pathway by removing the 3' phosphate group of phosphatidylinositol (3,4,5)-trisphosphate (PtdIns (3,4,5)P&lt;sub&gt;3&lt;/sub&gt;).

The structure of PTEN (solved by X-ray crystallography) reveals that it consists of a phosphatase domain, and a C2 domain: the phosphatase domain contains the active site which carries out the enzymatic function of the protein, whilst the C2 domain allows PTEN to bind to the phospholipid membrane so it is able to de-phosphorylate (PtdIns (3,4,5)P&lt;sub&gt;3&lt;/sub&gt;) When the PTEN enzyme is functioning properly, it acts as part of a chemical pathway that signals cells to stop dividing and causes cells to undergo programmed cell death (apoptosis) when necessary. These functions prevent uncontrolled cell growth that can lead to the formation of tumors. There is also evidence that the protein made by the PTEN gene may play a role in cell movement (migration) and sticking (adhesion) of cells to surrounding tissues.

PTEN is one of the most commonly lost tumour suppressors in human cancer. During tumor development, mutations and deletions of PTEN occur that inactivate its enzymatic activity leading to increased cell proliferation and reduced cell death. Frequent genetic inactivation of PTEN occurs in glioblastoma, endometrial cancer, prostate cancer, and reduced expression is found in many other tumor types such as lung and breast cancer.

Related conditions
PTEN mutation also causes a variety of inherited predispositions to cancer.

Cowden syndrome: Researchers have found more than 70 mutations in the PTEN gene in people with Cowden syndrome. These mutations can be changes in a small number of base pairs or, in some cases, deletions of a large number of base pairs. Most of these mutations cause the PTEN gene to make a protein that does not function properly or does not work at all. The defective protein is unable to stop cell division or signal abnormal cells to die, which can lead to tumor growth, particularly in the breast, thyroid or uterus.

Other disorders: Mutations in the PTEN gene cause several other disorders that, like Cowden syndrome, are characterized by the development of noncancerous tumors called hamartomas. These disorders include Bannayan-Riley-Ruvalcaba syndrome, Proteus syndrome, and Proteus-like syndrome. Together, the disorders caused by PTEN mutations are called PTEN hamartoma tumor syndromes, or PHTS. Mutations responsible for these syndromes cause the resulting protein to be nonfunctional or absent. The defective protein allows the cell to divide in an uncontrolled way and prevents damaged cells from dying, which can lead to the growth of tumors.

SNCA
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on SNCA... {October 21, 2007 11:42:06 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: Alpha-synuclein {October 21, 2007 11:43:07 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:43:09 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:43:09 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:43:09 AM PDT} 
 * UPDATED: Warning while updating page: Could not find summary box.  {October 21, 2007 11:43:19 AM PDT} 
 * UPDATED: Updated protein page (with warnings): Alpha-synuclein {October 21, 2007 11:43:19 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

Alpha-synuclein is a synuclein protein of unknown function primarily found in neural tissue, where it is seen mainly in presynaptic terminals. It is predominantly expressed in the neocortex, hippocampus, striatum, thalamus, and cerebellum. It is predominantly neuronal protein, but can also be found in glial cells.

Recent evidence suggests that alpha-synuclein functions as a molecular chaperone in the formation of SNARE complexes.

Alpha-synuclein is specifically upregulated in a discrete population of presynaptic terminals of the songbird brain during a period of song-acquisition-related synaptic rearrangement.&lt;ref&gt;George JM, Jin H, Woods WS, Clayton DF. (1995) Chracterization of a novel protein regulated during the critical period for song learning in the zebra finch. Neuron 15:361-372. PMID 7646890&lt;/ref&gt;

Normally an unstructured soluble protein, alpha-synuclein can aggregate to form insoluble fibrils in pathological conditions characterized by Lewy bodies, such as Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. Alpha-synuclein is the primary structural component of Lewy body fibrils. In addition, an alpha-synuclein fragment, known as the non-Abeta component (NAC), is found in amyloid plaques in Alzheimer's disease.

In rare cases of familial forms of Parkinson's disease there is a mutation in the gene coding for alpha-synuclein. Three point mutations have been identified thus far: A53T, A30P and E46K. In addition, triplication of the gene appears to be the cause of Parkinson's disease in another lineage.

Antibodies against alpha-synuclein have replaced antibodies against ubiquitin as the gold standard for immunostaining of Lewy bodies.

SP1

 * INFO: Beginning work on SP1... {October 21, 2007 11:43:19 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: Sp1 {October 21, 2007 11:44:18 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:44:21 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:44:21 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:44:21 AM PDT} 
 * UPDATED: Updated protein page: Sp1 {October 21, 2007 11:44:30 AM PDT} 

STAT3
&lt;!-- The PBB_Controls template provides controls for Protein Box Bot, please see Template:PBB_Controls for details. --&gt;
 * INFO: Beginning work on STAT3... {October 21, 2007 11:44:30 AM PDT} 
 * SEARCH REDIRECT: Control Box Found: STAT3 {October 21, 2007 11:45:17 AM PDT} 
 * UPDATE PROTEIN BOX: Updating Protein Box, No errors. {October 21, 2007 11:45:17 AM PDT} 
 * SKIP SUMMARY: SKIPPING Summary, No Errors. {October 21, 2007 11:45:17 AM PDT} 
 * UPDATE CITATIONS: Updating Citations, No Errors. {October 21, 2007 11:45:17 AM PDT} 
 * UPDATED: Warning while updating page: Could not find summary box.  {October 21, 2007 11:45:32 AM PDT} 
 * UPDATED: Updated protein page (with warnings): STAT3 {October 21, 2007 11:45:32 AM PDT} 

&lt;!-- The GNF_Protein_box is automatically maintained by Protein Box Bot. See Template:PBB_Controls to Stop updates. --&gt;

STAT3 is tyrosine-phosphorylated and activated by a number of kinases. The binding of IL-6 family cytokines (including IL-6, oncostatin M and leukemia inhibitory factor) to the gp130 receptor triggers STAT3 phosphorylation by JAK2. EGF-R and certain other receptor tyrosine kinases, such as c-MET phosphorylate STAT3 in response to their ligands.&lt;ref&gt;&lt;/ref&gt; STAT3 is also a target of the c-src non-receptor tyrosine kinase.&lt;ref&gt;&lt;/ref&gt;

STAT3-deficient mouse embryos can not develop beyond embryonic day 7 (E7.0), when gastrulation initiates.&lt;ref&gt;&lt;/ref&gt; It appears that at these early stages of development, STAT3 activation is required for self-renewal of embryonic stem cells (ESCs). Indeed, LIF, which is supplied to ESC cultures to maintain their undifferentiated state, can be omitted if STAT3 is activated through some other means.&lt;ref&gt;&lt;/ref&gt;

Constitutive STAT3 activation is associated with various human cancers and commonly suggests poor prognosis.&lt;ref name=&quot;Klampfer&quot;&gt;&lt;/ref&gt;&lt;ref&gt;&lt;/ref&gt;&lt;ref&gt;&lt;/ref&gt;&lt;ref&gt;&lt;/ref&gt; It has anti-apoptotic as well as proliferative effects.&lt;ref name=&quot;Klampfer&quot; /&gt;