Mg2+-dependent unwinding of DNA by nonhistone chromosomal protein HMG(1 + 2) from pig thymus as determined by DNA melting temperature analysis

In the previous studies with endonucleases specific for single-stranded DNA, we have indicated that the nonhistone chromosomal protein HMG(1 + 2) prepared from pig thymus has an activity to unwind DNA partially at low protein-to-DNA weight ratios (Yoshida, M. & Shimura, K. (1984) J. Biochem. 95, 117-124). In the present work, we have pursued the unwinding reaction by HMG(1 + 2) by thermal melting temperature analysis of DNA, and by investigating the effect of Mg2+ on the reaction. The melting temperature of DNA in the presence of HMG(1 + 2) at low protein weight ratios decreased in 2 mM Tris-HCl, pH 7.8, whereas it increased at higher ratios. The depressions of melting temperature by HMG(1 + 2) at low ratios were not observed either in the system of 2 mM Tris-HCl, pH 7.8, containing EDTA or in the system containing samples treated in advance with EDTA. An addition of Mg2+ to the system reproduced the depression of melting temperature at low protein-to-DNA ratios as well as the increase at higher ratios. Analysis by Mg2+-equilibrated gel filtration revealed that HMG(1 + 2) is a Mg2+-binding protein. However, the depression of melting temperature at low protein-to-DNA ratios was not due to removal of Mg2+ from DNA by HMG(1 + 2). From these results, it is concluded that HMG(1 + 2) causes a partial DNA unwinding detectable by thermal melting temperature analysis of DNA, and that Mg2+ is necessary for the unwinding reaction.     

2D:4D ratios predict hand grip strength (but not hand grip endurance) in men (but not in women)

In humans, the ratio of the second digit to the fourth digit — the 2D:4D ratio — is a sexually dimorphic trait (men, on average, exhibit lower 2D:4D ratios than do women) that is influenced by prenatal testosterone exposure, but not by circulating testosterone levels in adulthood. Consequently, 2D:4D ratios are commonly used as indirect measures of prenatal testosterone exposure. Many studies have examined the associations of 2D:4D ratios with sexually dimorphic adaptations that are thought to be influenced by such exposure, including physical prowess. The existing literature, however, remains unclear as to (1) whether 2D:4D ratios are more closely linked to strength or to endurance; and (2) whether 2D:4D ratios are linked with physical prowess for both men and women. In 100 men and 122 women, the relationship of 2D:4D ratios with maximum voluntary contraction (MVC) scores (hand grip strength) and maximum endurance time (MET) scores (local muscular endurance) using a hand dynamometer was examined. Controlling for age, height, weight, and average digit length, we found that 2D:4D ratios significantly predicted MVC scores in men, but not in women. 2D:4D ratios did not significantly predict MET scores for either sex. These results suggest that prenatal testosterone exposure in this sample is significantly related to hand grip strength in men, but not in women (and to local muscular endurance in neither sex), and, therefore, that strength, rather than local muscular endurance, potentially drives the relationship between 2D:4D ratios and physical prowess.     

The stimulation of tricarboxylic acid-cycle flux by alpha-adrenergic agonists in perfused rat liver.

Output of 14CO2 from 1-14C-labelled glutamate, 2-oxoglutarate or octanoate and from 4-methyl-2-oxo[2-14C]pentanoate was increased by more than 100% after infusion of phenylephrine into perfused livers of fed rats. Infusion of ethanol or sorbitol raised 3-hydroxybutyrate/acetoacetate ratios and decreased the output of 14CO2. Increases in 14CO2 output induced by phenylephrine were observed in the presence or absence of ethanol or sorbitol and were accompanied by elevated 3-hydroxybutyrate/acetoacetate ratios under all conditions examined. Phenylephrine had no effect on total tissue ATP/ADP ratios in livers from fed or starved rats. The data suggest that phenylephrine-induced increases in tricarboxylic acid-cycle flux do not arise from lowered matrix NADH/NAD+ or ATP/ADP ratios.     

Effect of lipid composition on the calcium/adenosine 5'-triphosphate coupling ratio of the Ca2+-ATPase of sarcoplasmic reticulum

The Ca2+-ATPase of sarcoplasmic reticulum was purified and depleted of proteolipids by solubilization in Triton X-100 and by fractionation on a DE-52 column. The protein reconstituted by deoxycholate-cholate dialysis at low lipid to protein ratios (2-5 mg of lipid/mg of protein), with either dioleoylphosphatidylethanolamine or monogalactosyldiglyceride, exhibited high initial rates of ATP-dependent Ca2+ uptake [300-900 nmol min-1 (mg of protein)-1] and coupling ratios (Ca2+ transported/ATP hydrolyzed) up to 1.2. Ca2+-ATPase reconstituted with lipids of increasing degrees of methylation (dioleoylphosphatidylethanolamine, dioleoylmonomethylphosphatidylethanolamine, dioleoyldimethylphosphatidylethanolamine and dioleoylphosphatidylcholine) or increasing degrees of glycosylation (monogalactosyldiglyceride and digalactosyldiglyceride) revealed a progressive decrease in both ATP-dependent Ca2+-uptake and coupling ratios. The rate and extent of Ca2+ uptake decreased as the dioleoylphosphatidylethanolamine/dioleoylphosphatidylcholine or monogalactosyldiglyceride/dioleoylphosphatidylcholine molar ratios in the reconstituted vesicles were reduced. Vesicles reconstituted with high molar ratios of dioleoylphosphatidylethanolamine/dioleoylphosphatidylcholine or monogalactosyldiglyceride/dioleoylphosphatidylcholine and at a high lipid to protein ratio became leaky and released the Ca2+ accumulated inside the vesicles when the temperature of the incubation mixture was increased (e.g., from 20 to 37 degrees C).(ABSTRACT TRUNCATED AT 250 WORDS)     

The effects of pyruvate concentration, dichloroacetate and alpha-cyano-4-hydroxycinnamate on gluconeogenesis, ketogenesis and [3-hydroxybutyrate]/[3-oxobutyrate] ratios in isolated rat hepatocytes.

1. In isolated rat hepatocytes incubated with pyruvate, ketogenesis increased with increasing pyruvate concentrations and decreased under the influence of 1 mM-alpha-cyano-4-hydroxycinnamate, a known inhibitor of pyruvate transport. Ketogenesis from pyruvate was higher by 30% in hepatocytes prepared from starved than from fed rats. 2. With pyruvate as substrate, 2 mM-dichloroacetate had no effect on ketogenesis of starved-rat hepatocytes, but increased ketogenesis of fed-rat hepatocytes to the 'starved' value. Gluconeogenesis from pyruvate, lactate and alanine, but not from glycerol, was inhibited by dichloroacetate. Both increased ketogenesis and decreased gluconeogenesis may result from an inhibition of pyruvate carboxylase by dichloroacetate. 3. Mitochondria were rapidly isolated from incubated hepatocytes, and [3-hydroxybutyrate]/[3-oxobutyrate] ratios were measured in the mitochondrial pellet ('mitochondrial' ratios) and in whole-cell suspensions ('total' ratios). Increasing pyruvate concentrations increased mitochondrial and decreased total ratios. In the presence of pyruvate (2 to 10 mM), dichloroacetate decreased mitochondrial and increased total ratios.     

Chelator-induced enhancement of 67Ga tumour imaging: Comparison of desferrioxamine with N,N′-ethylene-bis[2-hydroxy-5-carboxyphenylglycine]

Intravenous injection of the gallium chelating agents, N,N′-ethylene bis[2-hydroxy-5-carboxyphenylglycine], (COOH-EHPG), or desferrioxamine (DFO) after gallium-67 (⁶⁷Ga) injection, improved tumour/non-tumour tissue uptake ratios in mice bearing the EMT-6 sarcoma. Six hours post injection of gallium and 2 h post chelator, COOH-EHPG enhanced the tumour/blood ratios by an order of magnitude compared to untreated controls, whereas DFO increased the ratios three-fold. Twenty two hours post gallium and 2 h post chelator, the increases in ratios compared to controls were seven-fold for COOH-EHPG and two-fold for DFO. The study thus demonstrated the superior ability of COOH-EHPG for the enhancement of ⁶⁷Ga tumour/blood ratios compared with DFO.     

Serum Protein Electrophoresis in Tuberculosis

Serial serum protein electrophoretic determinations at two-month intervals were carried out on 84 tuberculous patients undergoing treatment in a sanatorium. An attempt was made to correlate changes in the albumin/alpha-2 globulin ratios and gamma globulin levels with clinical and roentgenographic status. It was observed that before treatment of the tuberculous process the albumin/alpha-2 globulin ratios were low and the gamma globulin levels were increased. As improvement occurred, albumin/alpha-2 globulin ratios increased and gamma globulin values decreased. A poor prognosis was indicated by decreasing albumin/alpha-2 globulin ratios. Electrophoretograms are of particular value in assessing the effect of surgery, especially when roentgenographic studies are not informative. They are also a valuable guide in deciding upon the duration of therapy necessary for individual cases.     

Effects of medium carbon-to-nitrogen ratio on biofilm formation and plasmid stability

Biofilm formation and plasmid segregational instability in biofilm cultures of Escherichia coli DH5alpha (pMJR1750) were investigated under different medium-carbon-to-nitrogen (C/N) ratios. At C/N ratios of 0.07 and 1, net accumulation of both biofilm plasmid-bearing and plasmid-free cells continued through the entire experiment without attaining any apparent steady state. At C/N ratios of 5 and 10, net biofilm cell accumulation for the two populations reached apparent steady states after 84 and 72 h, respectively. At C/N ratios of 0.07 and 1, polysaccharide production increased slowly and reached about 2g alginate equivalent/cm(2) by the end of both experiments. At a C/N ratio of 5, polysaccharide increase significantly after 84 h, reaching about 7mug alginate equivalent/cm(2) prior to termination. At a C/N ratio of 10, polysaccharide increased significantly after 72 h and reached 21 mug alginate equivalent/cm(2) at 108 h. At C/N ratios of 0.07 and 1, protein production reached 6.5 and 4 mug/cm(2), respectively. At C/N ratios of 5 and 10, protein production increased slightly for the first 84 h and reached a maximum at 108 h, at 3 and 2 mug/cm(2), respectively, then decreased over the last 12 h of the experiment. Ratios of polysaccharide to protein increased with increasing C/N ratios. At C/N ratios of 0.07 and 1, the ratios between extracellular polysaccharide (EP) and protein were no more than 205 mug polysaccharide/mug protein, whereas those at C/N ratios of 5 and 10 increased to about 7 and 12 mug polysaccharide/mug protein, respectively.Probabilities of plasmid loss in the biofilm cultures increased with increasing C/N ratios. At C/N ratios of 0.07, 1, and 5, the probabilities of plasmid loss were 0.0013 +/- 0.011, 0.020 +/- 0.006 and 0.122 +/- 0.021, respectively. At a C/N ratio of 10, the probability of plasmid loss was significantly higher, reaching 0.38 +/- 0.125. The increase of probability of plasmid loss at higher C/N ratios results from competition between cell replication and extracellular polysaccharide production. (c) 1994 John Wiley & Sons, Inc.     

Experimental manipulation of yolk testosterone affects digit length ratios in the ring-necked pheasant (Phasianus colchicus)

In humans, most of the mammals and one bird species studied so far, the relative length of individual digits is sexually dimorphic. Most studies of humans have been concerned with the ratio between second (2D) and fourth digits (4D), whereas some studies of humans and other mammals have also investigated other digit ratios. Inter- and intra-sexual variation in 2D:4D may depend on differential exposure to androgens during embryonic life, and the genetic mechanisms linking 2D:4D to androgens may be mediated by Hox genes. Because Hox genes are conserved in vertebrates, similar patterns of variation in digit ratios might be expected across vertebrate classes. The observation of correlations between digit ratios and physiological, psychological and performance traits in humans has generated interest in exploring the possibility that digit ratios are a marker of embryonic exposure to androgens, which have diverse consequences on several phenotypic traits. However, the hypothesis that digit ratios depend on androgen effects during development has never been tested experimentally. In this study, we increased testosterone concentration in ring-necked pheasant eggs and measured length ratios between the second, third and fourth digits of both feet in fully grown offspring. Females from testosterone-injected eggs had larger 2D:3D in the left foot, whereas this was not the case in males. The other digit ratios were unaffected by hormone treatment in both sexes. However, digit ratios showed no sexual dimorphism among controls. Thus, present results are consistent with the hypothesis that variation in testosterone levels during development affects digit ratios.     

Effect of different acetate:propionate ratios on the methanogenic community during thermophilic anaerobic digestion in batch experiments

The present study investigated the metabolism of different acetate:propionate ratios (0.25, 0.33, 0.5, 1.0, 2.0, 3.0, 4.0) in equimolar carbon concentration during an anaerobic decomposition process under defined laboratory conditions and evaluated the engaged methanogenic community. Significant differences on a metabolic level (gas production, gas composition, volatile fatty acid (VFA) concentration) were observed between acetate:propionate ratios ≤1 and ≥2. Generally ratios ≥2 resulted in a faster methane production and VFA decomposition compared to ratios ≤1. Regarding the composition of the methanogenic community as well as the abundance of Methanosarcinales these differences were not reflected in an appropriate manner when DNA based methods (dHPLC and qPCR) were applied. However, by a culture based approach these differences could be documented showing a significant difference in the number of cultivable methanogens between initial acetate:propionate ratios ≤1 and ≥2.     

Regulation of proteins in the VLA cell substrate adhesion family: influence of cell growth conditions on VLA-1, VLA-2, and VLA-3 expression

Cell quiescence resulting from culture of normal human fibroblasts in low serum (0.5%) was associated with a subsequent gradual increase in the expression of the cell-surface glycoprotein VLA-1, and a corresponding decrease in the expression of extracellular matrix adhesion receptors VLA-2 and VLA-3. Quantitation using either flow cytometry or immunoprecipitation showed that both the VLA-1/VLA-2 and VLA-1/VLA-3 ratios increased 10- to 28-fold and were still rising when cells remained quiescent for 20-30 days. Although induced by cell quiescence, changes in the levels of VLA-1, VLA-2, and VLA-3 continued to occur well after cell proliferation had stopped and thus do not directly correlate with cell cycle transition events. Despite prolonged serum deprivation resulting in elevated VLA-1/VLA-2 and VLA-1/VLA-3 ratios, growth-arrested cells remained viable and were fully capable of proliferating when restimulated. The increases in VLA-1/VLA-2 and VLA-1/VLA-3 ratios observed on quiescent cells were readily reversible, since after restimulation with 10% serum, these ratios quickly returned within 1-2 days to a level near that found on normal exponentially grown cells. Elevation of VLA-1/VLA-2 and VLA-1/VLA-3 ratios is generally associated with quiescence and is not due just to serum deprivation since density arrest of cells at confluence had similar effects on these ratios.     

Copper(II) complexes of carnosine, glycylglycine, and glycylglycine-imidazole mixtures

Carnosine complexes with copper(II) ions were studied with magnetic resonance techniques over a wide range of ligand to metal ratios at various pH values. Water proton relaxation rates increased with decreasing carnosine to copper ratios until a molar ratio of 48 was reached. Over the ratio range of 48–2 carnosine molecules per copper ion, the relaxation rate decreased so that in the 2:1 carnosine-copper(II) complex, the water-copper(II) distance was estimated to be 1.92 Å. Proton NMR studies revealed the broadening of imidazole proton lines at high mole ratios followed by other histidyl protons as the ratio decreased. The β-alanyl methylene protons were the last to be broadened by the addition of copper(II) ions. Carbon to copper(II) distances were determined for the carnosine to copper mole ratios of 500:1 and 5000:1. EPR spectra obtained at 93°K revealed the probable existence of four carnosine imidazoles as the sole coordinated ligands to copper(II) at high dipeptide-to-metal ratios (>10). At mole ratios below four, nuclear hyperfine lines characteristic of both monomeric and dimeric carnosine-copper(II) forms were observed. These results reveal that imidazole from carnosine is the sole ligand contributed to copper(II) for coordination over the pH range 5 to 7 at high carnosine to copper(II) ratios     

Biodegradation and adsorption of C1- and C2-phenanthrenes and C1- and C2-dibenzothiophenes in the presence of clay minerals: effect on forensic diagnostic ratios

The impact of modified montmorillonites on adsorption and biodegradation of crude oil C1-phenanthrenes, C1-dibenzothiophenes, C2-phenanthrenes and C2-dibenzothiophenes was investigated in aqueous clay/oil microcosm experiments with a hydrocarbon degrading microorganism community. Consequently, the effect on C1-dibenzothiophenes/C1-phenanthrenes, C2-dibenzothiophenes/C2-phenanthrenes, 2+3-methyldibenzothiophene/4-methyldibenzothiophene and 1-methyldibenzothiophene/4-methyldibenzothiophene ratios commonly used as diagnostic ratios for oil forensic studies was evaluated. The clay mineral samples were treated to produce acid activated montmorillonite, organomontmorillonite and homoionic montmorillonite which were used in this study. The different clay minerals (modified and unmodified) showed varied degrees of biodegradation and adsorption of the C1-phenanthrenes, C1-dibenzothiophenes, C2-phenanthrenes and C2-dibenzothiophenes. The study indicated that as opposed to biodegradation, adsorption has no effect on the diagnostic ratios. Among the diagnostic ratios reviewed, only C2-dibenzothiophenes/C2-phenanthrenes ratio was neither affected by adsorption nor biodegradation making this ratio very useful in forensic studies of oil spills and oil–oil correlation.     

人类指长比的研究进展

个体指长比形成于胚胎发育早期,男性低于女性,具有性别差异;食指与环指的指长比(2D∶4D)与雄性激素和精子数量成负相关,与雌性激素成正相关。指长比的形成和性腺的分化由HOXA和HOXD两组基因决定。研究表明:指长比与孤僻症、难语症、周期性偏头痛、免疫功能缺陷、口吃、心肌梗塞、乳腺癌等疾病具有相关性,提示:指长比可以作为提示某些疾病,如:指长比是心肌梗塞和乳腺癌等早期易感性的重要指标之一,对于疾病的早期预防与干预可能具有重要的价值。     

Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.     

Improved methods of AAV-mediated gene targeting for human cell lines using ribosome-skipping 2A peptide

The adeno-associated virus (AAV)-based targeting vector has been one of the tools commonly used for genome modification in human cell lines. It allows for relatively efficient gene targeting associated with 1–4-log higher ratios of homologous-to-random integration of targeting vectors (H/R ratios) than plasmid-based targeting vectors, without actively introducing DNA double-strand breaks. In this study, we sought to improve the efficiency of AAV-mediated gene targeting by introducing a 2A-based promoter-trap system into targeting constructs. We generated three distinct AAV-based targeting vectors carrying 2A for promoter trapping, each targeting a GFP-based reporter module incorporated into the genome, PIGA exon 6 or PIGA intron 5. The absolute gene targeting efficiencies and H/R ratios attained using these vectors were assessed in multiple human cell lines and compared with those attained using targeting vectors carrying internal ribosome entry site (IRES) for promoter trapping. We found that the use of 2A for promoter trapping increased absolute gene targeting efficiencies by 3.4–28-fold and H/R ratios by 2–5-fold compared to values obtained with IRES. In CRISPR-Cas9-assisted gene targeting using plasmid-based targeting vectors, the use of 2A did not enhance the H/R ratios but did upregulate the absolute gene targeting efficiencies compared to the use of IRES.     

The effect of S-100a and S-100b proteins and Zn2+ on the assembly of brain microtubule proteins in vitro

The homologous proteins S-100a and S-100b affect the microtubule system in a distinctly different way in the presence of low molar ratios of Zn2+. Assembly of brain microtubule proteins can be almost completely inhibited and rapid disassembly can be induced by low molar amounts of S-100b in the presence of low molar ratios [2-4] of Zn2+. Higher molar ratios per S-100b (greater than 4) potentiate the general Zn2+ effect, promoting the formation of sheets of microtubules. However, the effect of S-100a is quite different, no inhibition of assembly can be observed and the presence of S-100a seems to protect the microtubule proteins against the effect of Zn2+ by chelating the Zn2+ and decreasing the free metal-ion concentration. S-100a or S-100b cannot bind to the microtubule polymer-form, either in the absence or in the presence of Zn2+.     

Statistics of sexual size dimorphism

In comparative studies of sexual size dimorphism (SSD), the methods used to quantify dimorphism are controversial. SSD is commonly expressed as a ratio between species mean values of males and females, such as M/F or (M-F)/([M+F]/2), but a number of investigators have suggested that ratios should not be used, mainly because their distributions usually violate the assumptions of parametric statistical tests, or because they lead to spurious relationships that invalidate the interpretation and statistical significance of regressions and correlations. As an alternative to ratios, the comparative study of SSD can be conducted by a combination of regression with sex-specific data and residuals from this regression. Twenty-five data sets were selected from the literature and used to duplicate a variety of statistical procedures commonly employed in studies of SSD. All analyses were repeated with five different ratios and with methods that avoid the calculation of any ratios. These data and a review of the statistical properties of ratios and residuals indicate that: (1) most of the ratios used in the SSD literature are unnecessary, and several commonly used ratios are statistically inferior to others. Only two ratios are needed, one on a logarithmic scale and one on a linear scale; (2) there is no problem with spurious correlation or non-normality when ratios are used in several types of statistical procedures commonly employed in studies of SSD; (3) residuals cannot replace ratios for the evaluation of many questions regarding the pattern of SSD among species; and (4) residuals usually are used incorrectly, leading to misspecified regression equations. Most of the questions for which residuals are used should be addressed by multiple regression. These results apply to studies using comparative methods with or without adjustments for phylogenetic effects.     

Activity ratios of ribulose-1,5-bisphosphate carboxylase accurately reflect carbamylation ratios

Activity ratios and carbamylation ratios of ribulose-1,5-bisphosphate carboxylase (RuBPCase) were determined for leaves of Phaseolus vulgaris and Spinacia oleracea exposed to a variety of partial pressures of CO₂ and O₂ and photon flux densities (PFD). It was found that activity ratios accurately predicted carbamylation ratios except in extracts from leaves held in low PFD. In particular, it was confirmed that the loss of RuBPCase activity in low partial pressure of O₂ and high PFD results from reduced carbamylation. Activity ratios of RuBPCase were lower than carbamylation ratios for Phaseolus leaves sampled in low PFD, presumably because of the presence of 2-carboxyarabinitol 1-phosphate. Spinacia leaves sampled in darkness also exhibited lower activity ratios than carbamylation ratios indicating that this species may also have an RuBPCase inhibitor even though carboxyarabinitol 1-phosphate has not been detected in this species in the past.     

Leaf-twig carbon isotope ratio differences in photosynthetic-twig desert shrubs

Summary Carbon isotope ratios were determined for bulk tissues of both leaves and current season twigs of 29 species of Mohave Desert shrubs. Leaf and twig tissues were found to differ in their carbon isotope ratios, only in those species which had photosynthetic twigs. These data suggest that the twigs of these species operate at lower intercellular CO₂ values than leaves, an interpretation which is consistent with available gas-exchange data. An effect of microhabitat was also evident between the mean isotope ratios of leaves from wash versus slope habitats.This research has been supported by NSF Grant BSR-8410943 and by DOE Grant DE-FGO2-86ER60399.