Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and... more Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with “omics” data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various b...
The Journal of Mental Health Training, Education and Practice, 2013
Purpose – In April 2011, Nottinghamshire NHS trust created ten substantive peer support worker (P... more Purpose – In April 2011, Nottinghamshire NHS trust created ten substantive peer support worker (PSW) posts following from a pilot project the previous year. Having learnt some valuable lessons from the pilot project, taking on new roles in in-patient settings involved development and learning from everybody involved. The aim of this paper is to provide an insight into this experience from the perspective of the PSW themselves. Design/methodology/approach – A personal narrative of the next stage of peer support is provided by a PSW employed by Nottingham NHS Trust. The learning journey, originally given as a presentation at Nottingham NHR Recovery demonstration day, is described in terms of the truths of peer support (PS). Findings – The role of PSW requires constant questioning, facing dilemmas and challenging situations. The second year of PS was a time in which the PSWs met these dilemmas and found their own solutions. The process has not been entirely easy for PSWs, all of whom h...
Diet greatly impacts metabolism in health and disease. In response to the presence or absence of ... more Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by microRNAs, and feedback between metabolic genes and their regulators.
Amide proton NMR signals from the N-terminal domain of monomeric a-synuclein (aS) are lost when t... more Amide proton NMR signals from the N-terminal domain of monomeric a-synuclein (aS) are lost when the sample temperature is raised from 10°C to 35°C at pH 7.4. Although the temperature-induced effects have been attributed to conformational exchange caused by an increase in a-helix structure, we show that the loss of signals is due to fast amide proton exchange. At low ionic strength, hydrogen exchange rates are faster for the N-terminal segment of aS than for the acidic C-terminal domain. When the salt concentration is raised to 300 mM, exchange rates increase throughout the protein and become similar for the N-and C-terminal domains. This indicates that the enhanced protection of amide protons from the C-terminal domain at low salt is electrostatic in nature. Ca chemical shift data point to <10% residual a-helix structure at 10°C and 35°C. Conformational exchange contributions to R2 are negligible at both temperatures. In contrast to the situation in vitro, the majority of amide protons are observed at 37°C in 1 H-15 N HSQC spectra of aS encapsulated within living Escherichia coli cells. Our finding that temperature effects on aS NMR spectra can be explained by hydrogen exchange obviates the need to invoke special cellular factors. The retention of signals is likely due to slowed hydrogen exchange caused by the lowered intracellular pH of high-density E. coli cultures. Taken together, our results emphasize that aS remains predominantly unfolded at physiological temperature and pH-an important conclusion for mechanistic models of the association of aS with membranes and fibrils.
Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and m... more Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology.
Dietary composition has major effects on physiology. Here, we show that developmental rate, repro... more Dietary composition has major effects on physiology. Here, we show that developmental rate, reproduction, and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.
We have been interested in whether three proteins that share a five-stranded β-barrel "OB-fold" s... more We have been interested in whether three proteins that share a five-stranded β-barrel "OB-fold" structural motif but no detectable sequence homology fold by similar mechanisms. Here we describe native-state hydrogen exchange experiments as a function of urea for SN (staphylococcal nuclease), a protein with an OB-fold motif and additional nonconserved elements of structure. The regions of structure with the largest stability and unfolding cooperativity are contained within the conserved OB-fold portion of SN, consistent with previous results for CspA (cold shock protein A) and LysN (anticodon binding domain of lysyl tRNA synthetase). The OB-fold also has the subset of residues with the slowest unfolding rates in the three proteins, as determined by hydrogen exchange experiments in the EX1 limit. Although the protein folding hierarchy is maintained at the level of supersecondary structure, it is not evident for individual residues as might be expected if folding depended on obligatory nucleation sites. Rather, the site-specific stability profiles appear to be linked to sequence hydrophobicity and to the density of long-range contacts at each site in the threedimensional structures of the proteins. We discuss the implications of the correlation between stability to unfolding and conservation of structure for mechanisms of protein structure evolution. The concept of a protein fold as a recurrent unit of structure is central to modern structural biology. One of the goals of The Protein Structure Initiative is to determine representative examples of all folds (1), estimated to number between 1000 (2) and 10 000 (1,3,4). The difficulty of protein structure prediction targets and the approaches for modeling unknown structures are often predicated on whether the protein is likely to have a novel fold (5). Inferences about evolutionary relationships are often made on the basis of protein folds, because structure can be conserved even when sequences have diverged to levels where sequence homology is no longer detectable (6). While the concept of a protein fold is generally accepted, the classification of folds in practice remains somewhat subjective and ambiguous. The OB-fold 1 (Figure 1) was originally described as an oligonucleotide/oligosaccharidebinding fold (7) and consists of a five-stranded β-barrel structure. It is represented well in both sequence and structure databases (3,8-10). The October 2006 release of the SCOP database (11) classifies some 95 protein domains as OB-fold structures. These are grouped into 27 function families with activities ranging from molybdate-binding proteins to RNA chaperones.
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and... more Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with “omics” data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various b...
The Journal of Mental Health Training, Education and Practice, 2013
Purpose – In April 2011, Nottinghamshire NHS trust created ten substantive peer support worker (P... more Purpose – In April 2011, Nottinghamshire NHS trust created ten substantive peer support worker (PSW) posts following from a pilot project the previous year. Having learnt some valuable lessons from the pilot project, taking on new roles in in-patient settings involved development and learning from everybody involved. The aim of this paper is to provide an insight into this experience from the perspective of the PSW themselves. Design/methodology/approach – A personal narrative of the next stage of peer support is provided by a PSW employed by Nottingham NHS Trust. The learning journey, originally given as a presentation at Nottingham NHR Recovery demonstration day, is described in terms of the truths of peer support (PS). Findings – The role of PSW requires constant questioning, facing dilemmas and challenging situations. The second year of PS was a time in which the PSWs met these dilemmas and found their own solutions. The process has not been entirely easy for PSWs, all of whom h...
Diet greatly impacts metabolism in health and disease. In response to the presence or absence of ... more Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by microRNAs, and feedback between metabolic genes and their regulators.
Amide proton NMR signals from the N-terminal domain of monomeric a-synuclein (aS) are lost when t... more Amide proton NMR signals from the N-terminal domain of monomeric a-synuclein (aS) are lost when the sample temperature is raised from 10°C to 35°C at pH 7.4. Although the temperature-induced effects have been attributed to conformational exchange caused by an increase in a-helix structure, we show that the loss of signals is due to fast amide proton exchange. At low ionic strength, hydrogen exchange rates are faster for the N-terminal segment of aS than for the acidic C-terminal domain. When the salt concentration is raised to 300 mM, exchange rates increase throughout the protein and become similar for the N-and C-terminal domains. This indicates that the enhanced protection of amide protons from the C-terminal domain at low salt is electrostatic in nature. Ca chemical shift data point to <10% residual a-helix structure at 10°C and 35°C. Conformational exchange contributions to R2 are negligible at both temperatures. In contrast to the situation in vitro, the majority of amide protons are observed at 37°C in 1 H-15 N HSQC spectra of aS encapsulated within living Escherichia coli cells. Our finding that temperature effects on aS NMR spectra can be explained by hydrogen exchange obviates the need to invoke special cellular factors. The retention of signals is likely due to slowed hydrogen exchange caused by the lowered intracellular pH of high-density E. coli cultures. Taken together, our results emphasize that aS remains predominantly unfolded at physiological temperature and pH-an important conclusion for mechanistic models of the association of aS with membranes and fibrils.
Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and m... more Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology.
Dietary composition has major effects on physiology. Here, we show that developmental rate, repro... more Dietary composition has major effects on physiology. Here, we show that developmental rate, reproduction, and lifespan are altered in C. elegans fed Comamonas DA1877 relative to those fed a standard E. coli OP50 diet. We identify a set of genes that change in expression in response to this diet and use the promoter of one of these (acdh-1) as a dietary sensor. Remarkably, the effects on transcription and development occur even when Comamonas DA1877 is diluted with another diet, suggesting that Comamonas DA1877 generates a signal that is sensed by the nematode. Surprisingly, the developmental effect is independent from TOR and insulin signaling. Rather, Comamonas DA1877 affects cyclic gene expression during molting, likely through the nuclear hormone receptor NHR-23. Altogether, our findings indicate that different bacteria elicit various responses via distinct mechanisms, which has implications for diseases such as obesity and the interactions between the human microbiome and intestinal cells.
We have been interested in whether three proteins that share a five-stranded β-barrel "OB-fold" s... more We have been interested in whether three proteins that share a five-stranded β-barrel "OB-fold" structural motif but no detectable sequence homology fold by similar mechanisms. Here we describe native-state hydrogen exchange experiments as a function of urea for SN (staphylococcal nuclease), a protein with an OB-fold motif and additional nonconserved elements of structure. The regions of structure with the largest stability and unfolding cooperativity are contained within the conserved OB-fold portion of SN, consistent with previous results for CspA (cold shock protein A) and LysN (anticodon binding domain of lysyl tRNA synthetase). The OB-fold also has the subset of residues with the slowest unfolding rates in the three proteins, as determined by hydrogen exchange experiments in the EX1 limit. Although the protein folding hierarchy is maintained at the level of supersecondary structure, it is not evident for individual residues as might be expected if folding depended on obligatory nucleation sites. Rather, the site-specific stability profiles appear to be linked to sequence hydrophobicity and to the density of long-range contacts at each site in the threedimensional structures of the proteins. We discuss the implications of the correlation between stability to unfolding and conservation of structure for mechanisms of protein structure evolution. The concept of a protein fold as a recurrent unit of structure is central to modern structural biology. One of the goals of The Protein Structure Initiative is to determine representative examples of all folds (1), estimated to number between 1000 (2) and 10 000 (1,3,4). The difficulty of protein structure prediction targets and the approaches for modeling unknown structures are often predicated on whether the protein is likely to have a novel fold (5). Inferences about evolutionary relationships are often made on the basis of protein folds, because structure can be conserved even when sequences have diverged to levels where sequence homology is no longer detectable (6). While the concept of a protein fold is generally accepted, the classification of folds in practice remains somewhat subjective and ambiguous. The OB-fold 1 (Figure 1) was originally described as an oligonucleotide/oligosaccharidebinding fold (7) and consists of a five-stranded β-barrel structure. It is represented well in both sequence and structure databases (3,8-10). The October 2006 release of the SCOP database (11) classifies some 95 protein domains as OB-fold structures. These are grouped into 27 function families with activities ranging from molybdate-binding proteins to RNA chaperones.
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Papers by Emma Watson