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At least 1,045 records · Page 58Linked to original sources
PubMed1992

Molecular characterization of the Entner-Doudoroff pathway in Escherichia coli: sequence analysis and localization of promoters for the edd-eda operon.

The nucleotide sequence of the entire Escherichia coli edd-eda region that encodes the enzymes of the Entner-Doudoroff pathway was determined. The edd structural gene begins 236 bases downstream of zwf. The eda structural gene begins 34 bases downstream of edd. The edd reading frame is 1,809 bases long and encodes the 602-amino-acid, 64,446-Da protein 6-phosphogluconate dehydratase. The deduced primary amino acid sequences of the E. coli and Zymomonas mobilis dehydratase enzymes are highly conserved. The eda reading frame is 642 bases long and encodes the 213-amino-acid, 22,283-Da protein 2-keto-3-deoxy-6-phosphogluconate aldolase. This enzyme had been previously purified and sequenced by others on the basis of its related enzyme activity, 2-keto-4-hydroxyglutarate aldolase. The data presented here provide proof that the two enzymes are identical. The primary amino acid sequences of the E. coli, Z. mobilis, and Pseudomonas putida aldolase enzymes are highly conserved. When E. coli is grown on gluconate, the edd and eda genes are cotranscribed. Four putative promoters within the edd-eda region were identified by transcript mapping and computer analysis. P1, located upstream of edd, appears to be the primary gluconate-responsive promoter of the edd-eda operon, responsible for induction of the Entner-Doudoroff pathway, as mediated by the gntR product. High basal expression of eda is explained by constitutive transcription from P2, P3, and/or P4 but not P1.

Aldehyde-Lyases↗
PubMed2005

Retinal G-substrate, potential downstream component of NO/cGMP/PKG pathway, is located in subtype of retinal ganglion cells and amacrine cells with protein phosphatases.

The aim of this study was to determine the distribution and function of G-substrate, a specific substrate of the nitric oxide (NO)-cyclic guanosine monophosphate (cGMP)-cGMP-dependent protein kinase (PKG) signaling pathway, in normal rat retina and in G-substrate knockout mice. The retinas of adult wild-type rats and mice and G-substrate knockout mice were studied immunohistologically to characterize the upstream and downstream components of the NO-cGMP-PKG pathway. Immunoblot analysis showed that the molecular weight of retinal G-substrate was similar to that of cerebellar G-substrate. In adult rats and mice, retinal G-substrate was located in a subpopulation of amacrine cells and in C38-positive retinal ganglion cells (RGCs) but not in alpha RGCs. In addition, retinal G-substrate was co-expressed with other upstream and downstream signaling components of the NO-cGMP-PKG-G-substrate-phosphatase pathway in the adult retina. Electroretinographic (ERG) analysis demonstrated that there was no significant difference between the ERGs of wild-type and G-substrate knockout mice. These results suggest that retinal G-substrate plays a role as a downstream component of the NO-cGMP-PKG pathway. The co-localization of retinal G-substrate with protein Ser/Thr phosphatases suggests that it acts as an endogenous protein phosphatase inhibitor as in the cerebellum.

Amacrine Cells↗
PubMed1984

Effect of atrial pacing on phase analysis in patients with the Wolff-Parkinson-White syndrome.

Phase analysis of ECG-gated radionuclide ventriculography was performed during sinus rhythm and atrial pacing for 11 patients with the Wolff-Parkinson-White (WPW) syndrome. During sinus rhythm, phase analysis demonstrated abnormal early-emptying segments reflecting preexcitation in six of the 11 patients. In the remaining five patients, the precise site of abnormal early-emptying could not be detected. Atrial pacing increased the degree of pre-excitation, and abnormal early-emptying segments became clear in all patients. Our study demonstrated the utility of atrial pacing in performing phase analysis for patients with the WPW syndrome. Seven patients had abnormal early-emptying segments; four of them with ECG type A, in the left ventricle, and three of them with ECG type B, in the right ventricle. These results were consistent with results of the body surface and electrophysiologic mapping. In patients with posterior septal accessory pathways, phase analysis suggested probable laterality of the accessory pathway.

Adolescent↗
PubMed2026

ZNF695 Promotes Colorectal Cancer Progression Through Transcriptional Activation of CBX8 and Subsequent Wnt/β-Catenin Signaling Activation.

In this investigation, we examined the functional mechanism of the transcription factor zinc finger protein 695 (ZNF695) and its target gene chromobox protein homolog 8 (CBX8) in colorectal cancer (CRC) migration and invasion. HCT-116 and LOVO cell lines were used to establish cell models with knocked-down ZNF695 and knocked-down or over-expressed CBX8. To comprehensively evaluate the functional contributions of ZNF695 and CBX8 to cellular phenotypes, we employed CCK-8, wound-healing, and Transwell assays to evaluate cell proliferation, migration, and invasion, respectively. To assess the impact of ZNF695 on tumor progression, we generated a xenograft model utilizing nude mice. A FLAG-ZNF695 expression plasmid was constructed, and ChIP-seq experiments were performed. By integrating mRNA sequencing data following ZNF695 knockdown with highly expressed genes in CRC from the TCGA database, CBX8 was identified as a putative downstream target of ZNF695. We employed a dual-luciferase reporter assay to validate the specific binding affinity of ZNF695 toward the CBX8 promoter region. To elucidate the specific biological cascades modulated by ZNF695 and CBX8, we conducted a comprehensive pathway enrichment analysis. Rescue experiments were conducted to determine whether the ZNF695/CBX8 regulatory axis upregulates the expression of the Wnt signaling pathway downstream targets, AXIN2 and CCND1. Both in vitro assays and in vivo models confirmed that silencing ZNF695 dramatically suppresses CRC cell proliferation, migration, and invasion, while concurrently impeding tumor progression. ChIP-seq coupled with dual-luciferase reporter assays substantiated the direct binding of ZNF695 to the CBX8 promoter. Furthermore, CBX8 depletion significantly attenuated the migratory and invasive phenotypes of CRC cells. Restoring CBX8 expression effectively rescued the migratory and invasive deficits in CRC cells induced by ZNF695 silencing. Re-expression of CBX8 in ZNF695-silenced cells restored Wnt/β-catenin signaling activity, accompanied by increased expression of AXIN2 and CCND1. ZNF695 promotes CRC progression by transcriptionally activating CBX8 and subsequently enhancing Wnt/β-catenin signaling, thereby promoting tumor cell proliferation, migration, and invasion.

Humans↗
PubMed2005

Overlapping and distinct functions for a Caenorhabditis elegans SIR2 and DAF-16/FOXO.

The conserved SIR2 protein regulates life span in both yeast and worms: in both organisms overexpression of SIR2 can extend life span and in Caenorhabditis elegans this life span extension is dependent on the forkhead transcription factor, DAF-16. Here, we have done extensive genetic analysis with sir-2.1(ok434), a null mutant of C. elegans sir-2.1, the closest homolog to yeast Sir2p and human SIRT1 to further elucidate its function in life span regulation. sir-2.1(ok434) mutants show a slight decrease in life span as well as sensitivity to various stresses. Our genetic analysis suggests that sir-2.1 is required for life span extension by caloric restriction, independent of the insulin/IGF-1 signaling pathway. Importantly, analysis with unc-13 mutants indicates that sir-2.1 and daf-16 have overlapping and distinct roles in life span regulation. Our expression analysis shows that sir-2.1 has overlapping and distinct expression pattern compared with daf-16, consistent with the results from our genetic data. Our data defines a central role for C. elegans SIR2 in regulation of life span by caloric restriction and demonstrates that sir-2.1 and daf-16 have both overlapping and distinct functions in regulation of C. elegans life span.

Aging↗
PubMed1996

Plant clathrin heavy chain: sequence analysis and restricted localisation in growing pollen tubes.

Clathrin-coated vesicles were isolated from soybean (Glycine max L.) cells in suspension culture and their purity was assessed using SDS-PAGE, peptide sequencing and electron microscopy. Antibodies raised to these coated vesicles were used to immunoscreen a soybean cDNA library in lambda gt11 and isolate a partial clone of the clathrin heavy chain (HC) gene. Full-length cDNA for soybean clathrin HC was deduced by 5' and 3' cDNA amplification. The cDNA encodes an amino acid sequence of 1,700 residues, which is slightly larger than rat clathrin HC and may account for the reduced mobility of plant clathrin on SDS-PAGE. Insertion of these extra residues is largely confined to the amino and carboxy termini. Other domains within the heavy chain arms, including those implicated in light chain binding and trimerisation, are relatively well conserved between eukaryotes. A computer algorithm to determine alpha-helical coiled-coil structures reveals that only one domain, aligning to residues 1,460-1,489 in rat clathrin HC, has a high probability for coiled-coil structure in all five eukaryotic clathrin HC sequences. This provides further evidence that the interaction between clathrin heavy and light chains is mediated by three bundles of coiled-coils near to the carboxy terminus. In analysing the role of plant clathrin in endocytotic trafficking, as against trafficking from the Golgi apparatus to the vacuole, our attention was focused on membrane recycling in tip-growing pollen tubes. These rapidly growing cells are highly secretory and require a high level of plasma membrane recycling to maintain the tube tip architecture. Monoclonal antibodies to plant clathrin HC confirmed that coated vesicles are relatively abundant in tip-growing pollen tubes of Lilium longiflorum. This analysis also demonstrated that a high proportion of the clathrin present is in an assembled state, suggesting a highly dynamic trafficking pathway. Immunofluorescence analysis of pollen tubes revealed that clathrin localises to the plasma membrane at the apex of the pollen tube tip, which is consistent with high levels of clathrin-mediated membrane recycling. The use of these reagents in conjunction with tip-growing pollen tubes has created a unique opportunity to examine the basis for constitutive endocytosis, so that the more complex question of receptor-mediated pathways in plants can also be assessed.

Amino Acid Sequence↗
PubMed2005

Spectral integration in primary auditory cortex: laminar processing of afferent input, in vivo and in vitro.

Auditory cortex neurons integrate information over a broad range of sound frequencies, yet it is not known how such integration is accomplished at the cellular or systems levels. Whereas information about frequencies near a neuron's characteristic frequency is likely to be relayed to the neuron by lemniscal thalamocortical inputs from the ventral division of the medial geniculate nucleus, we recently proposed that information about frequencies spectrally distant from characteristic frequency is mainly relayed to the neuron via "horizontal" intracortical projections from neurons with spectrally-distant characteristic frequencies [J Neurophysiol 91 (2004) 2551]. Here we test this hypothesis by using current source density analysis to determine if characteristic frequency and spectrally-distant non-characteristic frequency stimuli preferentially activate thalamocortical and horizontal pathways, respectively, in rat auditory cortex. Characteristic frequency stimuli produced current source density profiles with prominent initial current sinks in layers 3 and 4--the termination zone of lemniscal inputs from medial geniculate nucleus. In contrast, stimuli three octaves below characteristic frequency produced initial current sinks mainly in the infragranular layers. Differences between current source density profiles were only apparent for initial current sinks; profiles for longer-latency current sinks evoked by characteristic frequency and non-characteristic frequency stimuli overlapped to a greater degree, likely due to shared mechanisms of intracortical processing or to longer-latency thalamocortical contributions (lemniscal and nonlemniscal). To identify current source density profiles produced by activation of lemniscal thalamocortical inputs alone, we utilized the mouse auditory thalamocortical slice preparation. Electrical stimulation of the medial geniculate nucleus in vitro produced major current sinks in cortical layers 3/4, and excitation spread horizontally from this point throughout primary auditory cortex to produce current sinks in multiple cortical layers. These data support the hypothesis that relay of thalamocortical information throughout auditory cortex via horizontal intracortical projections may be the basis of broad spectral integration in vivo.

Acoustic Stimulation↗
PubMed1997

Mutational analysis of the BPTI folding pathway: II. Effects of aromatic-->leucine substitutions on folding kinetics and thermodynamics.

The rates of the individual steps in the disulfide-coupled folding and unfolding of eight BPTI variants, each containing a single aromatic to leucine amino acid replacement, were measured. From this analysis, the contributions of the four phenylalanine and four tyrosine residues to the stabilities of the native protein and the disulfide-bonded folding intermediates were determined. While the substitutions were found to destabilize the native protein by 2 to 7 kcal/mol, they had significantly smaller effects on the intermediates that represent the earlier stages of folding, even when the site of the substitution was located within the ordered regions of the intermediates. These results suggest that stabilizing interactions contribute less to conformational stability in the context of a partially folded intermediate than in a fully folded native protein, perhaps because of decreased cooperativity among the individual interactions. The kinetic analysis also provides new information about the transition states associated with the slowest steps in folding and unfolding, supporting previous suggestions that these transition states are extensively unfolded. Although the substitutions caused large changes in the distribution of folding intermediates and in the rates of some steps in the folding pathway, the kinetically-preferred pathway for all of the variants involved intramolecular disulfide rearrangements, as observed previously for the wild-type protein. These results suggest that the predominance of the rearrangement mechanism reflects conformational constraints present relatively early in the folding pathway.

Alkylation↗
PubMed1994

Genetic analysis of the acetan biosynthetic pathway in Acetobacter xylinum.

We have identified, cloned and sequenced an 8422 base pair fragment of Acetobacter xylinum genomic DNA containing part of the acetan biosynthetic gene cluster. Computer analysis of the nucleotide sequence data generated revealed the presence of six open reading frames. Comparison of the translated sequences of putative genes to the amino acid sequences of genes from other organisms was used to assign functions to the aceA, aceC and manB genes. These genes were predicted to encode a UDP-glycosyl transferase, a GDP-mannosyl transferase and a phosphomannose isomerase/GDP-mannose pyrophosphorylase, respectively.

Bacterial Proteins↗
PubMed1999

Analysis of cytokine dynamics in corneal allograft rejection.

Motivated by the discovery of oscillations in tumour necrosis factor-alpha (TNF-alpha) concentration in the aqueous humour of rabbits undergoing corneal allograft rejection, a simple mathematical model is developed for the regulation of TNF-alpha, which incorporates both negative feedback and amplification pathways. Mathematical analysis reveals a surprisingly rich behavioural repertoire for this simple cytokine pathway, including excitability, threshold behaviour, hysteresis, oscillations and bistability. This suggests new possibilities for experimental demonstration, and reveals the potential contributions of nonlinear dynamics to understanding cytokine regulation.

Animals↗
PubMed1988

Characterization of doxylamine and pyrilamine metabolites via thermospray/mass spectrometry and tandem mass spectrometry.

Analysis of doxylamine N-oxide and pyrilamine N-oxide as synthetic standards and biologically derived metabolites by thermospray mass spectrometry (TSP/MS) provided [M + H]+ ions for each metabolite. TSP/tandem mass spectrometry (TSP/MS/MS) of the [M + H]+ ions provided fragment ions characteristic of these metabolites. In addition, TSP mass spectrometry and TSP/MS/MS analysis of ring-hydroxylated N-desmethyldoxylamine, N-desmethylpyrilamine and O-dealkylated pyrilamine is also reported. A fragmentation pathway for analysis by MS/MS of pyrilamine and its metabolites is also proposed. The results demonstrate the utility of TSP/MS for biologically derived metabolites of pyrilamine and doxylamine.

Aminopyridines↗
PubMed1984

Computational analysis of models for cotransport.

The order of substrate interaction with a cotransport carrier is studied by numerically fitting theoretical models to empirical data for a Na+-D-glucose pathway. Our analysis is based on a least-squares minimization routine developed at CERN, and uses data derived from tracer flux of substrate under equilibrium exchange conditions. Random, Ordered mirror, and Ordered glide models are considered and the applicability of both Random and Glide systems to the experimental observations is demonstrated. A more detailed study of the Glide model provides an estimation of the relative values of the individual rate constants describing each kinetic step in the mechanism. We argue that parameterization of competing models can result in tests which will distinguish between them, even when these contain many unknowns in the proposed structure of the kinetic mechanism. The essence of this means of model discrimination is the ability to find a single set of parameter values that fits a variety of experimental observations. The ability to obtain numerical estimates of obtain numerical estimates of individual rate constants is also a useful tool in investigation of the kinetic fine structure of the carrier. For the data at hand we conclude that a complete parameterization of the Glide model cannot be attained, possibly due to a heterogeneity in the temperature at which the experiments have been performed. Three solutions to the Glide model are presented, each of which corresponds to a fit of the Glide model to a subset of the experimental data.

Biological Transport↗
PubMed1992

Purine biosynthetic genes are required for cadmium tolerance in Schizosaccharomyces pombe.

Phytochelatins (PCs) are metal-chelating peptides produced in plants and some fungi in response to heavy metal exposure. A Cd-sensitive mutant of the fission yeast Schizosaccharomyces pombe, defective in production of a PC-Cd-sulfide complex essential for metal tolerance, was found to harbor mutations in specific genes of the purine biosynthetic pathway. Genetic analysis of the link between metal complex accumulation and purine biosynthesis enzymes revealed that genetic lesions blocking two segments of the pathway, before and after the IMP branchpoint, are required to produce the Cd-sensitive phenotype. The biochemical functions of these two segments of the pathway are similar, and a model based on the alternate use of a sulfur analog substrate is presented. The novel participation of purine biosynthesis enzymes in the conversion of the PC-Cd complex to the PC-Cd-sulfide complex in the fission yeast raises an intriguing possibility that these same enzymes might have a role in sulfur metabolism in the fission yeast S. pombe, and perhaps in other biological systems.

Adenylosuccinate Synthase↗
PubMed1993

Petri net representations in metabolic pathways.

The present methods for representing metabolic pathways are limited in their ability to handle complex systems, incorporate new information, and to provide for drawing qualitative conclusions from the structure of pathways. The theory of Petri nets is introduced as a tool for computer-implementable representation of pathways. Petri nets have the potential to overcome the present limitations, and through a multitude of properties, enable the preliminary qualitative analysis of pathways.

Computer Simulation↗
PubMed1996

Signaling through chemoattractant receptors in Dictyostelium.

Dictyostelium discoideum displays chemoattractant-directed cell migration typical of many higher cell types. Signaling through chemoattractant receptors involves a standard G-protein-linked pathway. Genetic analysis has distinguished essential and dispensable components and demonstrated that some signaling events are independent of G proteins. Genetic analysis has also led to the identification of additional genes involved in chemosensory transduction. Further studies on the newly discovered components and pathways should help in elucidating the molecular mechanisms of eukaryotic chemotaxis.

Animals↗
PubMed1995

A fast and reliable algorithm to localize accessory pathways based on the polarity of the QRS complex on the surface ECG during sinus rhythm.

BACKGROUND: Many criteria have been published to localize accessory pathways from the 12-lead ECG during sinus rhythm. This study analyzed whether the localization of an accessory pathway could be predicted by using the polarity of the QRS complex during sinus rhythm on the surface ECG, instead of the delta wave polarity as used in many reports. METHODS: The ECGs of 140 patients with an overt and single accessory pathway were evaluated. Eight localizations were taken into account. The precise location was previously known from successful radiofrequency ablation sites. RESULTS: In 128 patients (92%), the new algorithm allowed an accurate diagnosis of the site of implantation of the accessory pathway. CONCLUSION: Analysis of the polarity of the QRS complex on five electrocardiographic leads provides an easy, fast and reliable way to localize accessory pathways during sinus rhythm.

Algorithms↗
PubMed1995

An integrated kinetic analysis of intermediates and transition states in protein folding reactions.

Relaxation rates for folding and unfolding of two proteins have been measured over a range of denaturant concentrations to examine the reaction pathways leading to the late transition state. The proteins were chosen for their marked differences in both kinetic and structural properties. Results for the N-terminal domain of phosophoglycerate kinase (N-PGK), from Bacillus stearothermophilus, reveal the existence of a single intermediate (pathway = U-I-F), and obey the general relationship: kobs = k(U-I) + k(I-U)/[1 + 1/KU/I]. Hen egg white lysozyme folds through two intermediates (pathway = U-I-I.-F) and the relaxation kinetics for formation and decay of the fully folded state are described by: kobs = k(F-I.)+KI.-F)/[1+ 1/KI./I+ 1/(KI/U.KI./I)]. Rate constants apply to the first step in unfolding and the last step in folding, respectively, these being rate-limiting in the stated directions. Equilibrium constants describe the stability of transient intermediates, as indicated by the subscripts. Rate constants alter with denaturant according to the generalized equation k = kw.exp((mg-mt).D), where kw is the rate constant in water, mg and mt are parameters describing the relative solvent exposures of the ground and transition state conformations respectively, and D is the calculated denaturant activity. The same principle applies to equilibrium constants for rapid steps, i.e. for a process A = B; KA/B = KA/B(w).exp((mB-mA).D). The combined application of these relationships allows measurement of the relative free energy and degree of solvation or compactness of intermediates and transition states in folding pathways from a single set of kinetic data. In the case of lysozyme, the fast but measurable rates of interconversion of intermediate states (I and I.) have been examined by use of a sequential mixing technique, so providing additional information on a transition state which is not rate-limiting in the overall pathway. The analysis of rate profiles for folding and unfolding of these proteins yields parameters which are in precise agreement with those derived from equilibrium data.

Animals↗
PubMed2004

Proteomic analysis of rutin-induced secreted proteins from Aspergillus flavus.

Few studies have been conducted to identify the extracellular proteins and enzymes secreted by filamentous fungi, particularly with respect to dispensable metabolic pathways. Proteomic analysis has proven to be the most powerful method for identification of proteins in complex mixtures and is suitable for the study of the alteration of protein expression under different environmental conditions. The filamentous fungus Aspergillus flavus can degrade the flavonoid rutin as the only source of carbon via an extracellular enzyme system. In this study, a proteomic analysis was used to differentiate and identify the extracellular rutin-induced and non-induced proteins secreted by A. flavus. The secreted proteins were analyzed by two-dimensional electrophoresis and MALDI-TOF mass spectrometry. While 15 rutin-induced proteins and 7 non-induced proteins were identified, more than 90 protein spots remain unidentified, indicating that these proteins are either novel proteins or proteins that have not yet been sequenced.

Aspergillus flavus↗