Hypergraph and protein function prediction with gene expression data
... with equal weights and the high time complexity of optimization methods. The un-normalized, symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods are developed based on the assumption that the labels of two adjacent proteins or genes in the network are likely t ...
... with equal weights and the high time complexity of optimization methods. The un-normalized, symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods are developed based on the assumption that the labels of two adjacent proteins or genes in the network are likely t ...
Bioinformatics
... supplement to SWISS PROT. • The database helps the SWISS PROT format and contains translations of all coding sequences (CDS) in EMBL. It has two main sections: • SP-TrEMBL: (SWISS PROT -TrEMBL): It contains the entries that eventually be incorporated into SWISS PROT; that have not yet been manually ...
... supplement to SWISS PROT. • The database helps the SWISS PROT format and contains translations of all coding sequences (CDS) in EMBL. It has two main sections: • SP-TrEMBL: (SWISS PROT -TrEMBL): It contains the entries that eventually be incorporated into SWISS PROT; that have not yet been manually ...
Inhibition of signal transduction pathways involved in inflammation G. Haegeman
... even in conditions of repression by GR. Moreover, this hypothesis proposes a general way of gene repression and does not explain the specificity of glucocorticoids towards inflammation [9, 10]. No effect of glucocorticoids on chromatin modification, nor any interference with the abovementioned phosp ...
... even in conditions of repression by GR. Moreover, this hypothesis proposes a general way of gene repression and does not explain the specificity of glucocorticoids towards inflammation [9, 10]. No effect of glucocorticoids on chromatin modification, nor any interference with the abovementioned phosp ...
Response to Nelson-Sathi et al. (Nature 517, 77-80
... The 6 phyla for which Nelson-Sathi et al. (2015) [NS] claim a strong signal for HGTs from bacteria at their origins are shown. NS estimates are represented in purple. Maximum Likelihood expectations of gains at the origin for the same datasets are represented by red crosses. Expectations of gains we ...
... The 6 phyla for which Nelson-Sathi et al. (2015) [NS] claim a strong signal for HGTs from bacteria at their origins are shown. NS estimates are represented in purple. Maximum Likelihood expectations of gains at the origin for the same datasets are represented by red crosses. Expectations of gains we ...
Judge, P.J. and Watts, A.
... Peter J Judge and Anthony Watts The plasma membrane functions as a semi-permeable barrier, defining the interior (or cytoplasm) of an individual cell. This highly dynamic and complex macromolecular assembly comprises predominantly lipids and proteins held together by entropic forces and provide the ...
... Peter J Judge and Anthony Watts The plasma membrane functions as a semi-permeable barrier, defining the interior (or cytoplasm) of an individual cell. This highly dynamic and complex macromolecular assembly comprises predominantly lipids and proteins held together by entropic forces and provide the ...
PLoS Pathogens
... proteasome-dependent degradation. Using a mutant approach, we demonstrate that enzymatically active NopM promotes establishment of symbiosis with Lablab purpureus, the host plant from which NGR234 was originally isolated. We further examine effects of NopM when directly expressed in eukaryotic cells ...
... proteasome-dependent degradation. Using a mutant approach, we demonstrate that enzymatically active NopM promotes establishment of symbiosis with Lablab purpureus, the host plant from which NGR234 was originally isolated. We further examine effects of NopM when directly expressed in eukaryotic cells ...
Annotations
... 1. All GO terms for the BLAST hit sequences are collected For the first step, BLAST results are parsed and the identifiers of the BLAST hits are found and used to query the Gene Ontology database to recover associated functional terms. Also the evidence code of each particular annotation is recovere ...
... 1. All GO terms for the BLAST hit sequences are collected For the first step, BLAST results are parsed and the identifiers of the BLAST hits are found and used to query the Gene Ontology database to recover associated functional terms. Also the evidence code of each particular annotation is recovere ...
CP p53 Fahraeus, Jan 20, 2012
... Three is the magic number: a chain reaction required to prevent tumour formation Protein p53 is known for controlling the life and death of a cell and has a key role in cancer research. P53 is known to be inactive in 50% of cancer patients. If researchers succeed in re-establishing the presence of p ...
... Three is the magic number: a chain reaction required to prevent tumour formation Protein p53 is known for controlling the life and death of a cell and has a key role in cancer research. P53 is known to be inactive in 50% of cancer patients. If researchers succeed in re-establishing the presence of p ...
Table of Contents - Milan Area Schools
... • Polymers are formed by covalent linkages of smaller units called monomers. • Molecules with molecular weights greater than 1,000 daltons (atomic mass units) are usually classified as macromolecules. ...
... • Polymers are formed by covalent linkages of smaller units called monomers. • Molecules with molecular weights greater than 1,000 daltons (atomic mass units) are usually classified as macromolecules. ...
2006
... show a series of insertions and deletions of entire motifs. The aligned nucleotide sequences are presented in Appendix A and a schematic is presented in Fig. 1. Comparison of multiple sequences of the same clone showed only three nucleotide substitutions apparently due to the sequencing reaction (N ...
... show a series of insertions and deletions of entire motifs. The aligned nucleotide sequences are presented in Appendix A and a schematic is presented in Fig. 1. Comparison of multiple sequences of the same clone showed only three nucleotide substitutions apparently due to the sequencing reaction (N ...
Protein translation - San Diego Mesa College
... - binds also to the small sub-unit of the ribosome - its correct alignment with the A- and P-sites is enabled with the help of the ribosomal RNA (= rRNA) - the 2 anti-codon sequences of two closely neighbored and ‘loaded’ tRNA molecules base-pair with the corresponding codon on the bound mRNA strand ...
... - binds also to the small sub-unit of the ribosome - its correct alignment with the A- and P-sites is enabled with the help of the ribosomal RNA (= rRNA) - the 2 anti-codon sequences of two closely neighbored and ‘loaded’ tRNA molecules base-pair with the corresponding codon on the bound mRNA strand ...
Transmembrane domains control exclusion of membrane proteins
... what the determinants for this sorting could be. Here, we show that in the absence of cytosolic sorting signals, transmembrane domains control the access of surface proteins to endosomal compartments. They act in particular by determining the degree of exclusion of membrane proteins from endocytic c ...
... what the determinants for this sorting could be. Here, we show that in the absence of cytosolic sorting signals, transmembrane domains control the access of surface proteins to endosomal compartments. They act in particular by determining the degree of exclusion of membrane proteins from endocytic c ...
Analysis of protein carbonylation
... In the case when there are no reference materials, manufacturers of in vitro diagnostic tests prepare their ...
... In the case when there are no reference materials, manufacturers of in vitro diagnostic tests prepare their ...
Protein A CIP Resin
... selectivity and suitability for platform separations. There are a few factors of concern when using protein A resins for process scale antibody purification, with the major issue being the high cost of resin followed by protein A ligand leakage, resin lifetime and performance, especially resin stabi ...
... selectivity and suitability for platform separations. There are a few factors of concern when using protein A resins for process scale antibody purification, with the major issue being the high cost of resin followed by protein A ligand leakage, resin lifetime and performance, especially resin stabi ...
Phosphoproteomics reveals extensive in vivo phosphorylation of
... phosphorylation sites into conserved motifs, which may be targeted by identical or similar kinases. Thus, large-scale phosphoproteomics can increase our knowledge of posttranslational regulation of plant proteins because of its unbiased, global approach. We have set up the IMAC-based mass spectromet ...
... phosphorylation sites into conserved motifs, which may be targeted by identical or similar kinases. Thus, large-scale phosphoproteomics can increase our knowledge of posttranslational regulation of plant proteins because of its unbiased, global approach. We have set up the IMAC-based mass spectromet ...
Folding quality control in the export of proteins by the
... Robinson and Bolhuis, Nature, May 2001 ...
... Robinson and Bolhuis, Nature, May 2001 ...
Gene converter - Bioinformatics Platform
... SUMMARY CBS is a very helpful tool when characterizing the binding sites for certain TFs in a regulatory sequence. However, it is not uncommon that other applications deal with a different nomenclature for the genes involved in the study. Thus, it is interesting to use this CBS tool to convert gene ...
... SUMMARY CBS is a very helpful tool when characterizing the binding sites for certain TFs in a regulatory sequence. However, it is not uncommon that other applications deal with a different nomenclature for the genes involved in the study. Thus, it is interesting to use this CBS tool to convert gene ...
Gene Section VAV1 (vav 1 oncogene) Atlas of Genetics and Cytogenetics
... a dbl homology (DH) region, which exhibits a guanine nucleotide exchange factor (GEF) activity towards the Rho family GTPases; a pleckstrin homology (PH) domain which interacts with polyphosphoinositides; a Src Homology 2 (SH2) and two Src Homology 3 (SH3) domains that mediate protein-protein intera ...
... a dbl homology (DH) region, which exhibits a guanine nucleotide exchange factor (GEF) activity towards the Rho family GTPases; a pleckstrin homology (PH) domain which interacts with polyphosphoinositides; a Src Homology 2 (SH2) and two Src Homology 3 (SH3) domains that mediate protein-protein intera ...
IMPROVING ENANTIOSELECTIVITY OF ENZYMES THROUGH
... not feasible, even with today’s high-throughput methods.4 METHODS OF DIRECTED EVOLUTION Many practical methods to accomplish directed evolution have been reported, including error prone polymerase ...
... not feasible, even with today’s high-throughput methods.4 METHODS OF DIRECTED EVOLUTION Many practical methods to accomplish directed evolution have been reported, including error prone polymerase ...
Operon
... Control of how often and how rapidly mRNA transcripts are translated into proteins Posttranslational gene regulation Modifications made to the polypeptide chain ...
... Control of how often and how rapidly mRNA transcripts are translated into proteins Posttranslational gene regulation Modifications made to the polypeptide chain ...
Spring 2013
... functions of each. Describe the basic structure and function of the endocrine system. Describe the basic structure and function of the musculoskeletal system Name the functions of the major axial muscles of the body. Name the functions of the major appendicular muscles of the upper limbs. Name the f ...
... functions of each. Describe the basic structure and function of the endocrine system. Describe the basic structure and function of the musculoskeletal system Name the functions of the major axial muscles of the body. Name the functions of the major appendicular muscles of the upper limbs. Name the f ...
Intracellular signalling: The chloroplast talks!
... defects in developmental responses to light — photomorphogenesis — they isolated a novel mutant with a Ds transposon inserted into the nuclear gene for a chloroplast protein. The mutant is called long after far-red 6 (laf6) and, as the name suggests, its main phenotype is impaired hypocotyl growth i ...
... defects in developmental responses to light — photomorphogenesis — they isolated a novel mutant with a Ds transposon inserted into the nuclear gene for a chloroplast protein. The mutant is called long after far-red 6 (laf6) and, as the name suggests, its main phenotype is impaired hypocotyl growth i ...
Protein moonlighting
Protein moonlighting (or gene sharing) is a phenomenon by which a protein can perform more than one function. Ancestral moonlighting proteins originally possessed a single function but through evolution, acquired additional functions. Many proteins that moonlight are enzymes; others are receptors, ion channels or chaperones. The most common primary function of moonlighting proteins is enzymatic catalysis, but these enzymes have acquired secondary non-enzymatic roles. Some examples of functions of moonlighting proteins secondary to catalysis include signal transduction, transcriptional regulation, apoptosis, motility, and structural.Protein moonlighting may occur widely in nature. Protein moonlighting through gene sharing differs from the use of a single gene to generate different proteins by alternative RNA splicing, DNA rearrangement, or post-translational processing. It is also different from multifunctionality of the protein, in which the protein has multiple domains, each serving a different function. Protein moonlighting by gene sharing means that a gene may acquire and maintain a second function without gene duplication and without loss of the primary function. Such genes are under two or more entirely different selective constraints.Various techniques have been used to reveal moonlighting functions in proteins. The detection of a protein in unexpected locations within cells, cell types, or tissues may suggest that a protein has a moonlighting function. Furthermore, sequence or structure homology of a protein may be used to infer both primary function as well as secondary moonlighting functions of a protein.The most well-studied examples of gene sharing are crystallins. These proteins, when expressed at low levels in many tissues function as enzymes, but when expressed at high levels in eye tissue, become densely packed and thus form lenses. While the recognition of gene sharing is relatively recent—the term was coined in 1988, after crystallins in chickens and ducks were found to be identical to separately identified enzymes—recent studies have found many examples throughout the living world. Joram Piatigorsky has suggested that many or all proteins exhibit gene sharing to some extent, and that gene sharing is a key aspect of molecular evolution. The genes encoding crystallins must maintain sequences for catalytic function and transparency maintenance function.Inappropriate moonlighting is a contributing factor in some genetic diseases, and moonlighting provides a possible mechanism by which bacteria may become resistant to antibiotics.