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PubMed2000

Analytical ultracentrifugation in a Gibbsian perspective.

The analytical ultracentrifuge has come into new intensive use following complete instrumental redesign and the use of advanced computer technologies for the analysis and interpretation of experimental results. Major attention is now devoted to the evaluation of interactions between similar and dissimilar biological macromolecules in dilute and concentrated systems. Electrostatically charged biological solute systems additionally comprise low molecular weight charged and non-charged cosolvents. Solvent/cosolvent interactions, insufficiently considered in most current analytical ultracentrifugation analyses, may quantitatively affect solute/solute interactions. For comprehensive analysis the Svedberg derivation considering a buoyant molar mass (1 - rho0 partial specific volume)M2 and valid at vanishing solute concentration for strictly two component systems only, should be replaced, following classical thermodynamic analysis, by the ratio (delta rho/delta c2)(mu)/d pi/dc2 of the density increment at constant chemical potential of diffusible cosolvents, to the derivative of the osmotic pressure with solute concentration. Disregard of the solvent/cosolvent and solute/cosolvent interactions should be avoided.

Centrifugation, Density Gradient↗

PubMed2006

Assessment of genetic effects of polymorphisms in the MCP-1 gene on serum MCP-1 levels and myocardial infarction in Japanese.

BACKGROUND: Recently, the Framingham Heart Study reported that genetic variations in CCL2 influence serum levels of monocyte chemoattractant protein-1 (MCP-1) and the incidence of myocardial infarction (MI). The purpose of the present study was to investigate the possible involvement of CCL2 in the pathogenesis of atherosclerosis and MI in Japanese. METHODS AND RESULTS: Multiple regression analysis indicated that the MCP-1 levels were significantly influenced by various factors including age, body mass index, smoking, alcohol intake, high density lipoprotein-cholesterol, and systolic blood pressure. Moreover, the serum MCP-1 level was significantly correlated with intima - media thickness (p < 0.0001). However, this association disappeared when other clinical confounding factors were included in the analyses. Comprehensive analysis of common polymorphisms of CCL2 in a large community-based population and in subjects with MI found that the A(-2138)T polymorphism affected the serum MCP-1 level in a subgroup of subjects 65 years and older. However, no significant differences in the frequencies of any of the polymorphisms or haplotypes were found between subjects with and without MI. None of the polymorphisms in CCL2 affected carotid atherosclerosis. CONCLUSIONS: The serum MCP-1 level was a good surrogate marker of atherosclerosis in the present study population. Although genetic variations in CCL2 may have some influence on MCP-1 production, their influence does not seem to contribute appreciably to atherosclerosis in Japanese. The present results did not support the recently published findings from the Framingham Heart Study. The discrepancy between the 2 studies may be related to differences in confounding factors that contribute to MCP-1 levels and in the haplotype structure of the 2 populations.

Aged↗

PubMed2026

Circle-seq analysis reveals the involvement of eccDNAs in salt stress response of bermudagrass (Cynodon dactylon).

Extrachromosomal circular DNAs (eccDNAs) have been identified in a wide variety of plant species and play a pivotal role in genomic plasticity, emerging as key drivers of stress adaptation. However, the putative roles of eccDNAs under environmental stress remain largely unexplored in plants. As a high-quality turfgrass, bermudagrass (Cynodon dactylon L.) is a pivotal species for the reclamation and improvement of saline-alkali soils. Therefore, we performed a comprehensive analysis of the eccDNA profiles in bermudagrass under salt stress. A total of 1,068 eccDNAs were identified across all chromosomes. These eccDNAs were characterized by short lengths (ranging from 100 bp to 1 kb) and low GC content. Their genomic distribution was not entirely random but rather exhibited a certain preference for intergenic regions and coding sequences (CDS). Crucially, null model analysis of A/T-rich junction sites revealed that these eccDNAs primarily originate from physically unstable scaffold/matrix attachment regions (S/MARs) via stochastic fragmentation, followed by opportunistic circularization predominantly mediated by the non-homologous end joining (NHEJ) pathway. Notably, salt stress specifically enriched eccDNAs derived from DNA transposons, including the Tc1/Mariner, CACTA and MITE superfamilies. Overall, our findings reveal complex extrachromosomal structural dynamics in bermudagrass, offering novel insights into its genomic adaptation under environmental stress.

Cynodon↗

PubMed1985

The value of chronic animal toxicology studies of pharmaceutical compounds: A retrospective analysis.

Extensive animal studies are carried out during the development of new medicines to assess toxicity and predict their safety for use in man. There are, however, differences of opinion concerning the nature of safety evaluation studies required prior to marketing. Any prospect of rationalizing the number and design of animal studies must stem from a reappraisal of conventional animal testing procedures and better use of available data on the toxicity of compounds previously investigated. The Centre for Medicines Research has therefore established a toxicology databank containing comprehensive data from repeated-dose animal safety evaluation studies provided by pharmaceutical companies. Thirteen companies within the United Kingdom have provided toxicological data for 32 pharmaceutical compounds studied in the rat, dog, or primate, resulting in 45 case studies for which both short-term (less than or equal to 6 months) and long-term (greater than 6 months) tests had been completed. A comprehensive analysis of these studies has been carried out to determine what new findings, if any, become apparent in studies after 6 months. The results do not support the need for animal toxicity studies of longer than 6 months duration, apart from those designed to investigate carcinogenicity.

Animals↗

PubMed2005

Fluorescence in situ hybridization and spectral imaging analysis of human oocytes and first polar bodies.

We investigated the frequencies of abnormalities involving either chromosome 1, 16, 18, or 21 in failed-fertilized human oocytes. Although abnormalities involving chromosome 16 showed an age-dependent increase, results for the other chromosomes did not show statistically significant differences among the three age groups, <35 years, 35-39 years, and >39 years. The scoring of four chromosomes is likely to underestimate the true rate of aneuploid cells. Therefore, for a pilot study investigating a more-comprehensive analysis of oocytes and their corresponding first polar bodies, we developed a novel eight-probe chromosome enumeration scheme using fluorescence in situ hybridization and spectral imaging analysis.

Adult↗

PubMed1982

Spontaneous abortion incidence in the treatment of infertility.

Analysis of published series indicates that, irrespective of the method of data collection, close agreement exists on empirically derived incidences of spontaneous abortion in North American populations, provided that age, previous abortion history, and gravidity are controlled. The normal incidence of clinically apparent abortion among first pregnancies in women under age 30 years is in the range 8.3% to 11.0%. A comprehensive analysis of published series on pregnancies after infertility treatment indicates that only three therapeutic methods are attended by an abortion incidence that approaches this asymptote: ovulation induction with bromocriptine in hyperprolactinemic anovulation (11.8%; n = 1,233 pregnancies); artificial insemination with donor semen for azoospermia (11.4%; n = 326 first pregnancies); and operation for endometriosis (9.3%; n = 768 pregnancies). Abortion incidences accompanying other modes of therapy are higher. Because increased abortion incidence is not generally recognized as a specific reproductive difficulty in infertile couples, as are the other two: i.e., refractory infertility despite technically adequate therapy and ectopic pregnancy, plausible physiologic mechanisms for abortions in specific categories of disease or treatment type are described and discussed in detail. Moreover, abortion incidence is proposed to be a sensitive and objective parameter with which to assess distortions in human reproductive physiology, especially when competing methods of infertility treatment have overall pregnancy outcomes that are thought to be similar.

Abortion, Spontaneous↗

PubMed2006

CRZ1, a target of the calcineurin pathway in Candida albicans.

Calcineurin is a major player in calcium-dependent signal transduction pathways of eukaryotes. Calcineurin acts on transcription factors (e.g. CRZ1 in Saccharomyces cerevisiae) and governs the expression of genes in a species-dependent fashion. In Candida albicans, the calcineurin pathway is involved in tolerance to antifungal agents, cation homeostasis and virulence. However, the components of the calcineurin pathway are still poorly investigated in this yeast species. Taking S. cerevisiae as a model to reconstitute this pathway, two CRZ1-like genes, CRZ1 and CRZ2 (for calcineurin-responsive zinc finger 1 and 2 genes), were found with C(2)H(2) zinc finger domains. Only CRZ1 was able to restore the calcium hypersusceptibility of a S. cerevisiae crz1Delta mutant and to mediate calcium-dependent gene expression in this yeast species. Several experiments showed that CRZ1 was dependent on calcineurin in C. albicans: (i) phenotypic analysis of a crz1Delta/Delta mutant showed impaired growth as compared with the wild type in the presence of cations (Ca(2+), Mn(2+)) as does a mutant lacking calcineurin subunit A (cnaDelta/Delta) and (ii) a green fluorescent protein (GFP)-Crz1p fusion protein showed a calcium- and calcineurin-dependent nuclear localization. To further analyse the relationship between calcineurin and CRZ1, a comprehensive analysis of calcineurin/Crz1p-dependent gene expression following addition of Ca(2+) (200 mM) was performed. Among the expression of 264 genes altered by at least twofold, the upregulation of 60 genes was dependent on both calcineurin and CRZ1. Interestingly, a motif [5'-G(C/T)GGT-3'] with similarity to the target sequence of Crz1p (GNGGCG/TCA) from S. cerevisiae was identified as a putative regulatory sequence in the upstream regions of these calcineurin/Crz1p-dependent genes. However, additional experiments showed that calcineurin may have other targets in addition to CRZ1. First, CRZ1 was not involved in tolerance to antifungal agents (fluconazole, terbinafine) on the opposite to calcineurin. Second, CRZ1 was only moderately influencing virulence in a mice model of infection which is in sharp contrast to the strong avirulence of cnaDelta/Delta mutant in the same animal model. Even though this work establishes CRZ1 as a calcineurin target, further studies are needed to identify other calcineurin-dependent elements in C. albicans.

Animals↗

PubMed2000

Active site interactions in oligomeric structures of inorganic pyrophosphatases.

Recent progress in studies of the mode of action of cytoplasmic inorganic pyrophosphatases is mainly due to the analysis of a dozen and a half structures of the apoenzyme, its complexes, and mutants. However, despite considerable research on the mechanism of action of these enzymes, many important problems remain unclear. Among them is the problem of active site interactions in oligomeric structures and their role in catalysis; this review focuses on this problem. The abundant experimental data requires generalization and comprehensive analysis. A characteristic feature of the spatial structure of inorganic pyrophosphatases is a flexible system of noncovalent interactions between protein groups penetrating the whole molecule of the oligomeric enzyme. Binding of metal ions, sulfate (an analog of the product of the enzymatic reaction), and affinity phosphorus-containing inhibitors at the active site or site-directed mutagenesis induce rearrangements in the set of hydrogen and ionic interactions, which change active site properties and in some instances, cause molecule asymmetry. In the trimeric form of Escherichia coli pyrophosphatase obtained by dissociation of a hexamer, active sites also interact with each other, which is manifested by negative cooperativity upon substrate binding. The association of trimers into the hexamer leads to perfect organization of active sites and to their coordinated functioning, probably due to the restoration of communication channels between the trimers.

Binding Sites↗

PubMed2006

Large-scale analysis of ion channel gene expression in the mouse heart during perinatal development.

The immature and mature heart differ from each other in terms of excitability, action potential properties, contractility, and relaxation. This includes upregulation of repolarizing K(+) currents, an enhanced inward rectifier K(+) (Kir) current, and changes in Ca(2+), Na(+), and Cl(-) currents. At the molecular level, the developmental regulation of ion channels is scantily described. Using a large-scale real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assay, we performed a comprehensive analysis of ion channel transcript expression during perinatal development in the embryonic (embryonic day 17.5), neonatal (postnatal days 1-2), and adult Swiss-Webster mouse hearts. These data are compared with publicly available microarray data sets (Cardiogenomics project). Developmental mRNA expression for several transcripts was consistent with the published literature. For example, transcripts such as Kir2.1, Kir3.1, Nav1.5, Cav1.2, etc. were upregulated after birth, whereas others [e.g., Ca(2+)-activated K(+) (KCa)2.3 and minK] were downregulated. Cl(-) channel transcripts were expressed at higher levels in immature heart, particularly those that are activated by intracellular Ca(2+). Defining alterations in the ion channel transcriptome during perinatal development will lead to a much improved understanding of the electrophysiological alterations occurring in the heart after birth. Our study may have important repercussions in understanding the mechanisms and consequences of electrophysiological alterations in infants and may pave the way for better understanding of clinically relevant events such as congenital abnormalities, cardiomyopathies, heart failure, arrhythmias, cardiac drug therapy, and the sudden infant death syndrome.

Animals↗

PubMed2004

Smoking-cessation interventions by type of provider: a meta-analysis.

OBJECTIVE: To synthesize the evidence on the effectiveness of smoking-cessation interventions by type of provider. METHODS: A random effects meta-regression was estimated to examine the effect of provider and whether the intervention contained nicotine replacement therapy (NRT), on the intervention's relative risk of quitting as compared to placebo or usual care from studies published in databases from inception to 2000. Thirty additional studies not included in the previous 1996 and 2000 U.S. Public Health Service clinical practice guidelines were used to provide the most comprehensive analysis to date of the comparative effectiveness of different types of providers in interventions for smoking cessation that have been published. RESULTS: The effectiveness without NRT follows: psychologist (1.94, 95% confidence interval [CI]: 1.04-3.62); physician (1.87, CI=1.42-2.45); counselor (1.82, CI=0.84-3.96); nurse (1.76, CI=1.21-2.57); unknown (1.27, CI=0.57-2.82); other (1.18, CI=0.67-2.10); and self-help (1.28, CI=0.89-1.82). Effectiveness of most providers increased by almost twofold with the use of NRT. CONCLUSIONS: Smoking-cessation interventions without NRT delivered by psychologists, physicians, or nurses are all effective. NRT increases the effectiveness of most providers.

Counseling↗

PubMed2003

Dioxouranium-carboxylate complexes. Formation and stability of acetate species at different ionic strengths in NaCl(aq).

The formation and stability of UO2(2+)-acetate complexes was studied potentiometrically, at T = 25 degrees C, at different ionic strength, 0 < I < or = 1 mol dm(-3), in aqueous NaCl solutions. Computer analysis allowed us to find the species UO2(ac)+, UO2(ac)2(0), UO2(ac)3- and UO2(ac)3(OH)2-. The dependence on ionic strength of formation constants was taken into account by using both a simple Debye-Hückel type equation and the SIT (Specific ion Interaction Theory) approach. A critical examination of the present results is given together with a comprehensive analysis of literature data.

Acetates↗

PubMed2005

Combined global localization analysis and transcriptome data identify genes that are directly coregulated by Adr1 and Cat8.

In Saccharomyces cerevisiae, glucose depletion causes a profound alteration in metabolism, mediated in part by global transcriptional changes. Many of the transcription factors that regulate these changes act combinatorially. We have analyzed combinatorial regulation by Adr1 and Cat8, two transcription factors that act during glucose depletion, by combining genome-wide expression and genome-wide binding data. We identified 32 genes that are directly activated by Adr1, 28 genes that are directly activated by Cat8, and 14 genes that are directly regulated by both. Our analysis also uncovered promoters that Adr1 binds but does not regulate and promoters that are indirectly regulated by Cat8, stressing the advantage of combining global expression and global localization analysis to find directly regulated targets. At most of the coregulated promoters, the in vivo binding of one factor is independent of the other, but Adr1 is required for optimal Cat8 binding at two promoters with a poor match to the Cat8 binding consensus. In addition, Cat8 is required for Adr1 binding at promoters where Adr1 is not required for transcription. These data provide a comprehensive analysis of the direct, indirect, and combinatorial requirements for these two global transcription factors.

Chromatin Immunoprecipitation↗

PubMed2004

Expression profile of genes regulated by activity of the Na-H exchanger NHE1.

BACKGROUND: In mammalian cells changes in intracellular pH (pHi), which are predominantly controlled by activity of plasma membrane ion exchangers, regulate a diverse range of normal and pathological cellular processes. How changes in pHi affect distinct cellular processes has primarily been determined by evaluating protein activities and we know little about how pHi regulates gene expression. RESULTS: A global profile of genes regulated in mammalian fibroblasts by decreased pHi induced by impaired activity of the plasma membrane Na-H exchanger NHE1 was characterized by using cDNA microarrays. Analysis of selected genes by quantitative RT-PCR, TaqMan, and immunoblot analyses confirmed results obtained from cDNA arrays. Consistent with established roles of pHi and NHE1 activity in cell proliferation and oncogenic transformation, grouping regulated genes into functional categories and biological pathways indicated a predominant number of genes with altered expression were associated with growth factor signaling, oncogenesis, and cell cycle progression. CONCLUSION: A comprehensive analysis of genes selectively regulated by pHi provides insight on candidate targets that might mediate established effects of pHi on a number of normal and pathological cell functions.

Amino Acid Substitution↗

PubMed2006

Defining the origins and evolution of the chemokine/chemokine receptor system.

The chemokine system has a critical role in mammalian immunity, but the evolutionary history of chemokines and chemokine receptors are ill-defined. We used comparative whole genome analysis of fruit fly, sea urchin, sea squirt, pufferfish, zebrafish, frog, and chicken to identify chemokines and chemokine receptors in each species. We report 127 chemokine and 70 chemokine receptor genes in the 7 species, with zebrafish having the most chemokines, 63, and chemokine receptors, 24. Fruit fly, sea urchin, and sea squirt have no identifiable chemokines or chemokine receptors. This study represents the most comprehensive analysis of the chemokine system to date and the only complete characterization of chemokine systems outside of mouse and human. We establish a clear evolutionary model of the chemokine system and trace the origin of the chemokine system to approximately 650 million years ago, identifying critical steps in their evolution and demonstrating a more extensive chemokine system in fish than previously thought.

Animals↗

PubMed1989

Analysis of consecutive pseudo-first-order reactions. II: Calculation of the rate constants from the co-product or co-reactant data.

The co-product or co-reactant data for a two-step pseudo-first-order consecutive reaction gives unique shape profiles for the natural logarithm of the concentration versus time plots, based on the ratio of two rate constants (k2/k1), for theoretical data without error. But, in the presence of a +/- 2.0% random error in the simulated data, the ability to distinguish between different shapes disappears. A comprehensive analysis shows that accurate rate constants can be obtained only in a limited range of k2/k1 ratios. Reliable rate constants can be obtained when k2/k1 less than 0.5. Two special cases, k1 approximately 2k2 and k2 much greater than k1, cannot be distinguished from each other and could lead to erroneous conclusions if additional information is not used to identify the correct ratio. When k2/k1 greater than 0.5, the calculated parameters are extremely sensitive to experimental errors, and other techniques involving the concentrations of starting material and intermediate should be used to obtain the rate constants.

Chemistry, Pharmaceutical↗

PubMed1996

Subunit complementation of Escherichia coli adenylosuccinate synthetase.

Data are presented, based upon subunit complementation experiments, that suggest that Escherichia coli adenylosuccinate synthetase contains two shared active sites between its dimeric interface. This conclusion was alluded to by use of mutant forms of adenylosuccinate synthetase previously prepared by site-directed mutagenesis. The experiments indicate that, although the R143L and D13A mutants have low or no activity independently, when they are mixed, a significant amount of activity was obtained. These results indicate that the subunits exchange with each other to form heterodimers with a single viable wild-type active site. The kcat value for the active hybrid active site in the R143L-D13A heterodimer is virtually identical to that observed with the wild-type enzyme, and the other kinetic parameters are very similar to those found for the wild-type enzyme. An analysis of the restoration of the activity in the presence of substrates suggests that GTP and IMP stabilize the dimeric structure of the protein. A comparison of the restoration of the activity using different combinations of mutants provides evidence indicating that some of the GTP binding elements, including the P-loop, in the protein are important for subunit integrity. Also, for the first time, a comprehensive analysis of subunit complementation is performed for the two inactive mutants (R143L and D13A) where the dissociation constants for the R143L-D13A heterodimer and the D13A homodimer were determined to be 21 and 2.9 microM, respectively. A concentration dependence of the specific activity of the wild-type protein in this study shows that the Kd for dimer dissociation is approximately 1 microM.

Adenylosuccinate Synthase↗

PubMed2002

Spatial and temporal distribution of solute leaching in heterogeneous soils: analysis and application to multisampler lysimeter data.

Accurate assessment of the fate of salts, nutrients, and pollutants in natural, heterogeneous soils requires a proper quantification of both spatial and temporal solute spreading during solute movement. The number of experiments with multisampler devices that measure solute leaching as a function of space and time is increasing. The breakthrough curve (BTC) can characterize the temporal aspect of solute leaching, and recently the spatial solute distribution curve (SSDC) was introduced to describe the spatial solute distribution. We combined and extended both concepts to develop a tool for the comprehensive analysis of the full spatio-temporal behavior of solute leaching. The sampling locations are ranked in order of descending amount of total leaching (defined as the cumulative leaching from an individual compartment at the end of the experiment), thus collapsing both spatial axes of the sampling plane into one. The leaching process can then be described by a curved surface that is a function of the single spatial coordinate and time. This leaching surface is scaled to integrate to unity, and termed S can efficiently represent data from multisampler solute transport experiments or simulation results from multidimensional solute transport models. The mathematical relationships between the scaled leaching surface S, the BTC, and the SSDC are established. Any desired characteristic of the leaching process can be derived from S. The analysis was applied to a chloride leaching experiment on a lysimeter with 300 drainage compartments of 25 cm2 each. The sandy soil monolith in the lysimeter exhibited fingered flow in the water-repellent top layer. The observed S demonstrated the absence of a sharp separation between fingers and dry areas, owing to diverging flow in the wettable soil below the fingers. Times-to-peak, maximum solute fluxes, and total leaching varied more in high-leaching than in low-leaching compartments. This suggests a stochastic-convective transport process in the high-flow streamtubes, while convection dispersion is predominant in the low-flow areas. S can be viewed as a bivariate probability density function. Its marginal distributions are the BTC of all sampling locations combined, and the SSDC of cumulative solute leaching at the end of the experiment. The observed S cannot be represented by assuming complete independence between its marginal distributions, indicating that S contains information about the leaching process that cannot be derived from the combination of the BTC and the SSDC.

Environmental Monitoring↗

PubMed2026

Proteomic analysis of ammonia-induced stress in Chinese hamster ovary (CHO) cell cultures.

Ammonia (NH₃) and its ionic form ammonium (NH₄+) are both metabolic waste products and essential nitrogen sources within Chinese hamster ovary (CHO) cell cultures. Although necessary for amino acid synthesis, excessive accumulation in the extracellular environment can exert stress, reducing cell proliferation and impairing the efficiency of recombinant protein production. Proper endoplasmic reticulum (ER) function is critical for CHO cells as biotherapeutic producers. Previous work has linked elevated ammonia concentrations to reduced productivity via altered N-glycosylation pathways, but its broader effects on ER biology remain unclear. In this study, we applied high-resolution mass spectrometry to perform a comprehensive analysis of changes in the ER proteome in CHO cells exposed to two ammonia concentrations, 10 mM and 30 mM, 48 and 120 h after supplementation. Both conditions suppressed cell growth and reduced product titre; however, the 10 mM supplementation resulted in a minor increase in specific cell productivity. Gene Ontology analysis revealed that ammonia strongly affected the tricarboxylic acid cycle, as well as key metabolic, catabolic and biogenetic processes. Several ER membrane proteins, including HMGCR and PREB, were consistently downregulated. In extended cultures, transmembrane proteins linked to Golgi-transport were upregulated, while vesicle transport associated proteins were downregulated, indicating altered intracellular trafficking. SIGNIFICANCE: This study provides a novel perspective on CHO cell biology under environmental stress by investigating the impact of ammonia accumulation in culture. Despite its presence in CHO culture, ammonia has been relatively under-investigated, compared to other culture conditions. Using high-throughput mass spectrometry for comprehensive proteomic profiling, we characterise the cellular response to ammonia build-up with a level of depth not previously applied to the study of this biological stressor. By specifically analysing proteins localised to the ER, we identify candidate pathways and molecular mechanisms that contribute to reduced CHO cell growth and productivity, offering insights directly relevant to industrial bioprocessing conditions. The link between ammonia concentration and a decrease in productivity has previously been linked to genes involved in N-glycosylation of the recombinant biotherapeutic, but the full extent of ammonia stress on ER function has not yet been investigated. These methods were applied to two IgG producing CHO cell lines to allow for comparison of cell line specific stress adaptations, as well as comparing the short- and long-term effects of excess ammonia.

Proteomics↗