
evolution of protein function by domain swapping
... of sequence, structure, and function, strategies that seem most applicable are combinatorial methods. Sequence and structural space are enormously large yet likely to be sparse in function. Nature must explore these spaces in a manner that preferentially examines areas relatively high in function. T ...
... of sequence, structure, and function, strategies that seem most applicable are combinatorial methods. Sequence and structural space are enormously large yet likely to be sparse in function. Nature must explore these spaces in a manner that preferentially examines areas relatively high in function. T ...
Nutrition acquisition strategies during fungal infection of plants
... Fig. 2. Examples of the entrainment of plant metabolism by phytopathogenic fungi. Sensing of nitrogen or carbon availability (NS, CS; flash arrow), or the absence of preferable nutrient sources, triggers signal transduction pathways that initiate transcription of transporters and pathway-specific me ...
... Fig. 2. Examples of the entrainment of plant metabolism by phytopathogenic fungi. Sensing of nitrogen or carbon availability (NS, CS; flash arrow), or the absence of preferable nutrient sources, triggers signal transduction pathways that initiate transcription of transporters and pathway-specific me ...
GEFs: master regulators of G
... pleckstrin homology (PH) domains1. GEFs that act upon Ras, Ral and Rap contain domains homologous to that in the cdc25 protein of Saccharomyces cerevisiae2. A separate class of sec7-type GEFs couple with the ARF-family of G proteins that are involved in vesicular transport3. GEFs with similar guanin ...
... pleckstrin homology (PH) domains1. GEFs that act upon Ras, Ral and Rap contain domains homologous to that in the cdc25 protein of Saccharomyces cerevisiae2. A separate class of sec7-type GEFs couple with the ARF-family of G proteins that are involved in vesicular transport3. GEFs with similar guanin ...
Sporopollenin Biosynthetic Enzymes Interact and
... large array of sporophytic genes are involved in tapetum development and exine formation (Aarts et al., 1997; Paxson-Sowders et al., 2001; Morant et al., 2007; Suzuki et al., 2008; de Azevedo Souza et al., 2009; Dobritsa et al., 2009a, 2009b, 2010, 2011; Tang et al., 2009; Grienenberger et al., 2010 ...
... large array of sporophytic genes are involved in tapetum development and exine formation (Aarts et al., 1997; Paxson-Sowders et al., 2001; Morant et al., 2007; Suzuki et al., 2008; de Azevedo Souza et al., 2009; Dobritsa et al., 2009a, 2009b, 2010, 2011; Tang et al., 2009; Grienenberger et al., 2010 ...
Possibilities and Limitations of Genetic Engineering
... step in lignin biosynthesis, was downregulated with an antisense construct. The quantity of lignin was not changed, however the composition of the lignin was altered (Baucher et al., 1999). Down regulation of either caffeic acid 3-O-methyltransferase (COMT) or caffeoyl coenzyme A 3-O-methyltransfera ...
... step in lignin biosynthesis, was downregulated with an antisense construct. The quantity of lignin was not changed, however the composition of the lignin was altered (Baucher et al., 1999). Down regulation of either caffeic acid 3-O-methyltransferase (COMT) or caffeoyl coenzyme A 3-O-methyltransfera ...
Study of the distribution of autotrophic CO2 fixation
... Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarb ...
... Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarb ...
METABOLIC ADAPTATION OF CANDIDA
... 1.2 Study Objective High resistance exhibition is a peculiar trait of biofilms. C. albicans like bacterial biofilms is 1000X tolerant to treatment therapy unlike their free floating cells (Ballie & Douglas, 2000). Metabolic flexibility is an attribute extensively explored for survival, allowing for ...
... 1.2 Study Objective High resistance exhibition is a peculiar trait of biofilms. C. albicans like bacterial biofilms is 1000X tolerant to treatment therapy unlike their free floating cells (Ballie & Douglas, 2000). Metabolic flexibility is an attribute extensively explored for survival, allowing for ...
A GENOMIC ANALYSIS OF Paenibacillus macerans
... been known to anaerobically ferment glycerol (Gupta et al. 2009). It is also able to ferment hexoses, deoxyhexoses, pentoses, cellulose, and hemicelluloses. Since it has been reported to be associated with several pseudo bacteriamia cases, P. macerans has been described as having features of opportu ...
... been known to anaerobically ferment glycerol (Gupta et al. 2009). It is also able to ferment hexoses, deoxyhexoses, pentoses, cellulose, and hemicelluloses. Since it has been reported to be associated with several pseudo bacteriamia cases, P. macerans has been described as having features of opportu ...
BIO 106 Principles of Cell Biology Fall 2012 Tentative Lecture
... Concept 2.3 The formation and function of molecules depend on chemical bonding between atoms Concept 2.4 Chemical reactions make and break chemical bonds Chapter 3: Water and the Fitness of the Environment Overview: The Molecule That Supports All of Life Concept 3.1 Polar covalent bonds in water mol ...
... Concept 2.3 The formation and function of molecules depend on chemical bonding between atoms Concept 2.4 Chemical reactions make and break chemical bonds Chapter 3: Water and the Fitness of the Environment Overview: The Molecule That Supports All of Life Concept 3.1 Polar covalent bonds in water mol ...
Role of glucokinase and glucose-6 phosphatase glucose production
... endoplasmic reticulum (Shelly et al, 1993). It has been suggested, but not proven, that a regulatory subunit is associated with the Glc6Pase-catalytic subunit within the membrane (Mithieux et al, 1995). These two enzymes constitute a futile cycle, also called the Glc-Glc6P cycle. Regulatory mechanis ...
... endoplasmic reticulum (Shelly et al, 1993). It has been suggested, but not proven, that a regulatory subunit is associated with the Glc6Pase-catalytic subunit within the membrane (Mithieux et al, 1995). These two enzymes constitute a futile cycle, also called the Glc-Glc6P cycle. Regulatory mechanis ...
Bio2 Gene prediction DNA structure Codons and ORFs Predicting
... What is the function? Where is the protein localised? What is the structure? What might it interact with? These are not fully solved problems. The latest issue of Bioinformatics (today) contains many new studies and tools addressing these problems. ...
... What is the function? Where is the protein localised? What is the structure? What might it interact with? These are not fully solved problems. The latest issue of Bioinformatics (today) contains many new studies and tools addressing these problems. ...
Analysis - The Journal of Cell Biology
... strategy used by eukaryotic organisms to regulate a host of biological functions, including DNA replication, cell cycle progression, energy metabolism, and cell growth and differentiation. Levels of cellular protein phosphorylation are modulated both by protein kinases and phosphatases. Although the ...
... strategy used by eukaryotic organisms to regulate a host of biological functions, including DNA replication, cell cycle progression, energy metabolism, and cell growth and differentiation. Levels of cellular protein phosphorylation are modulated both by protein kinases and phosphatases. Although the ...
Kinetic models of metabolism: model construction, model
... are inadequate and instead a kinetic modelling approach is necessary. Given the large number of reactions included in the network, a pipeline has been built to automatically generate kinetic laws from reaction stoichiometries. In this context a precise description of the reactional mechanism is impo ...
... are inadequate and instead a kinetic modelling approach is necessary. Given the large number of reactions included in the network, a pipeline has been built to automatically generate kinetic laws from reaction stoichiometries. In this context a precise description of the reactional mechanism is impo ...
Evolution of Metabolisms - Theoretical and Computational
... Ferredoxins, besides thioredoxin, avodoxin, and rubredoxin, are important coenzymes in metabolic pathways. They serve as electron acceptors and donors in many anabolic, catabolic, and electron transfer reactions. For example, ferredoxin is a redox partner in more than 50 known pathways. An example ...
... Ferredoxins, besides thioredoxin, avodoxin, and rubredoxin, are important coenzymes in metabolic pathways. They serve as electron acceptors and donors in many anabolic, catabolic, and electron transfer reactions. For example, ferredoxin is a redox partner in more than 50 known pathways. An example ...
Monocyte chemoattrac- tant protein
... A, B) and interstitium, and then isolated their mRNA. In the glomeruli, IL-12 transcripts were greatly reduced in the 7ND-treated mice, although no significant difference in IFN-γ mRNA was observed (Fig. 1C). However, the signal for the production of cells infiltrating the interstitium revealed redu ...
... A, B) and interstitium, and then isolated their mRNA. In the glomeruli, IL-12 transcripts were greatly reduced in the 7ND-treated mice, although no significant difference in IFN-γ mRNA was observed (Fig. 1C). However, the signal for the production of cells infiltrating the interstitium revealed redu ...
Cloning and functional characterization of temperature responsive
... Background: Ricinus communis L. (Castor bean) is an oilseed crop widely grown for vegetable oil and renewable bio‐products for pharmaceutical and industrial purposes. However, castor oil production does not meet the increase of its world consumption due to the use of cultivars with ...
... Background: Ricinus communis L. (Castor bean) is an oilseed crop widely grown for vegetable oil and renewable bio‐products for pharmaceutical and industrial purposes. However, castor oil production does not meet the increase of its world consumption due to the use of cultivars with ...
Neema Bhukhan
... Of the 14 conserved non-coding sequences found, 2 were determined to be gene regulatory elements. The results they obtained suggest that a large fraction of non-coding elements identified are conserved because of functional constraints. Cawley et al (Cawley et al, 2004) have discovered data that sug ...
... Of the 14 conserved non-coding sequences found, 2 were determined to be gene regulatory elements. The results they obtained suggest that a large fraction of non-coding elements identified are conserved because of functional constraints. Cawley et al (Cawley et al, 2004) have discovered data that sug ...
Figure 1000G Allele Frequencies
... S1. [11] had another rule for transcripts containing more than two 3’UTRs in the transcript. However, we observed that the stop codons in Ensembl gene annotation did not follow this particular rule, so we eliminated this rule and simply followed rule 2 if there was more than one 3’ UTR. c. Eukaryoti ...
... S1. [11] had another rule for transcripts containing more than two 3’UTRs in the transcript. However, we observed that the stop codons in Ensembl gene annotation did not follow this particular rule, so we eliminated this rule and simply followed rule 2 if there was more than one 3’ UTR. c. Eukaryoti ...
PowerPoint Presentation - Foundations of Biology
... The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or ...
... The transfer of information from nucleic acid to nucleic acid, or from nucleic acid to protein, may be possible, but transfer from protein to protein, or from protein to nucleic acid, is impossible. Information means here the precise determination of sequence, either of bases in the nucleic acid or ...
Use of the Polymerase Chain Reaction to Detect B
... rigorous testing of different vitrectomy solutions to determine how these would affect viability of the cells, and we could not test how long a specimen would survive before degradation of the DNA; this would also depend on how viable the cells were when removed from the patient. We did not think th ...
... rigorous testing of different vitrectomy solutions to determine how these would affect viability of the cells, and we could not test how long a specimen would survive before degradation of the DNA; this would also depend on how viable the cells were when removed from the patient. We did not think th ...
Histones - scientia.global
... database and contains a novel 73-aminoacid RNA-binding domain. Professor Marzluff and his group developed antibodies specific for the cloned SLBP, which allowed them to study the function of SLBP. These advances by Professor Marzluff and his team have paved the way for much of the research performed ...
... database and contains a novel 73-aminoacid RNA-binding domain. Professor Marzluff and his group developed antibodies specific for the cloned SLBP, which allowed them to study the function of SLBP. These advances by Professor Marzluff and his team have paved the way for much of the research performed ...
The families of pathogenesis-related proteins, their activities, and
... letters in the order in which they are described. In the literature, besides proteins, newly defined mRNAs (cDNAs) are often considered as additional members of the existing families when shown to be induced by pathogens or specific elicitors. However, because PRs are generally defined by their occu ...
... letters in the order in which they are described. In the literature, besides proteins, newly defined mRNAs (cDNAs) are often considered as additional members of the existing families when shown to be induced by pathogens or specific elicitors. However, because PRs are generally defined by their occu ...
Cloning and characterization of the Xenopus laevis p8 gene
... developing embryos (Figs 5,6). Xp8 expression was detected in the middle body of the prospective neural region at stage 14 (Fig. 5a,b), where it was maintained to stage 18 (Fig. 5c,d). Expression in the prospective neural region extended to the anteroposterior area and branched in the brain area at ...
... developing embryos (Figs 5,6). Xp8 expression was detected in the middle body of the prospective neural region at stage 14 (Fig. 5a,b), where it was maintained to stage 18 (Fig. 5c,d). Expression in the prospective neural region extended to the anteroposterior area and branched in the brain area at ...
DOC-file of additional text
... allows us not only to ignore unknown genetic interactions among non-metabolic genes, but (more importantly) it overestimates the possible sizes of deleted blocks. 3) If growth rate is nearly unaffected (in this case less than 1% effect), the deletion is assumed to be viable, and the genes are consid ...
... allows us not only to ignore unknown genetic interactions among non-metabolic genes, but (more importantly) it overestimates the possible sizes of deleted blocks. 3) If growth rate is nearly unaffected (in this case less than 1% effect), the deletion is assumed to be viable, and the genes are consid ...
Transcriptome profiling identifies candidate genes associated with
... seed weight of 50 mg, at 15 days after flowering (DAF) (Figure 1) (Walbot et al., 1972) was selected for transcript profiling of developing P. vulgaris seeds because it corresponds to the beginning of the active phase of γ-Glu-S-methyl-Cys accumulation, before free S-methyl-Cys levels start to decli ...
... seed weight of 50 mg, at 15 days after flowering (DAF) (Figure 1) (Walbot et al., 1972) was selected for transcript profiling of developing P. vulgaris seeds because it corresponds to the beginning of the active phase of γ-Glu-S-methyl-Cys accumulation, before free S-methyl-Cys levels start to decli ...
Gene regulatory network

A gene regulatory network or genetic regulatory network (GRN) is a collection of regulators thatinteract with each other and with other substances in the cell to govern the gene expression levels of mRNA and proteins.The regulator can be DNA, RNA, protein and their complex. The interaction can be direct or indirect (through their transcribed RNA or translated protein).In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases this protein will be structural, and will accumulate at the cell membrane or within the cell to give it particular structural properties. In other cases the protein will be an enzyme, i.e., a micro-machine that catalyses a certain reaction, such as the breakdown of a food source or toxin. Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some transcription factors are inhibitory.In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for survival in this environment. Thus a yeast cell, finding itself in a sugar solution, will turn on genes to make enzymes that process the sugar to alcohol. This process, which we associate with wine-making, is how the yeast cell makes its living, gaining energy to multiply, which under normal circumstances would enhance its survival prospects.In multicellular animals the same principle has been put in the service of gene cascades that control body-shape. Each time a cell divides, two cells result which, although they contain the same genome in full, can differ in which genes are turned on and making proteins. Sometimes a 'self-sustaining feedback loop' ensures that a cell maintains its identity and passes it on. Less understood is the mechanism of epigenetics by which chromatin modification may provide cellular memory by blocking or allowing transcription. A major feature of multicellular animals is the use of morphogen gradients, which in effect provide a positioning system that tells a cell where in the body it is, and hence what sort of cell to become. A gene that is turned on in one cell may make a product that leaves the cell and diffuses through adjacent cells, entering them and turning on genes only when it is present above a certain threshold level. These cells are thus induced into a new fate, and may even generate other morphogens that signal back to the original cell. Over longer distances morphogens may use the active process of signal transduction. Such signalling controls embryogenesis, the building of a body plan from scratch through a series of sequential steps. They also control and maintain adult bodies through feedback processes, and the loss of such feedback because of a mutation can be responsible for the cell proliferation that is seen in cancer. In parallel with this process of building structure, the gene cascade turns on genes that make structural proteins that give each cell the physical properties it needs.It has been suggested that, because biological molecular interactions are intrinsically stochastic, gene networks are the result of cellular processes and not their cause (i.e. cellular Darwinism). However, recent experimental evidence has favored the attractor view of cell fates.