Factors related to the formation of buccal mucosa ridging in university students

PubMed Central

Mizutani, Shinsuke; Tomofuji, Takaaki; Azuma, Tetsuji; Irie, Koichiro; Machida, Tatsuya; Yoneda, Toshiki; Iwasaki, Yoshiaki; Morita, Manabu

2014-01-01

Objective Buccal mucosa ridging (BMR) is known as a clinical sign of clenching, which is one of the major manifestations of bruxism. However, there are few reports about the formation of BMR and no data regarding the association between BMR and factors such as malocclusion. The purpose of the current study was to investigate the relationship between BMR and factors such as the number of teeth present, gender, body mass index (BMI), occlusion and clenching habit in university students. Materials and methods A total of 2101 students (1164 males, 937 females), aged 18–29 years old, were included in the study. BMR and the number of teeth present were recorded and malocclusion was defined using a modified version of the Index of Orthodontic Treatment Need. Additional information regarding gender, clenching habit and BMI was collected via a questionnaire. Results Forty-six per cent of the subjects had BMR and the prevalence of BMR in females was significantly higher than that of males (chi square test, p < 0.001). According to logistic regression analysis, the probability of BMR was significantly associated with female gender (OR = 1.501, 95% CI = 1.259–1.790, p < 0.001), crowding (OR = 2.102, 95% CI = 1.706–2.590, p < 0.001) and overjet (OR = 0.585, 95% CI = 0.418–0.818, p = 0.002). On the other hand, BMR was not associated with awareness of clenching habit and BMI. Conclusions Gender, crowding and overjet were related to the formation of BMR in university students. When evaluating BMR as a clinical sign of clenching, one might have to take factors such as gender and crowding into consideration. PMID:23692316

Basal metabolic rate studies in humans: measurement and development of new equations.

PubMed

Henry, C J K

2005-10-01

To facilitate the Food and Agriculture Organization/World Health Organization/United Nations University Joint (FAO/WHO/UNU) Expert Consultation on Energy and Protein Requirements which met in Rome in 1981, Schofield et al. reviewed the literature and produced predictive equations for both sexes for the following ages: 0-3, 3-10, 10-18, 18-30, 30-60 and >60 years. These formed the basis for the equations used in 1985 FAO/WHO/UNU document, Energy and Protein Requirements. While Schofield's analysis has served a significant role in re-establishing the importance of using basal metabolic rate (BMR) to predict human energy requirements, recent workers have subsequently queried the universal validity and application of these equations. A survey of the most recent studies (1980-2000) in BMR suggests that in most cases the current FAO/WHO/UNU predictive equations overestimate BMR in many communities. The FAO/WHO/UNU equations to predict BMR were developed using a database that contained a disproportionate number--3388 out of 7173 (47%)--of Italian subjects. The Schofield database contained relatively few subjects from the tropical region. The objective here is to review the historical development in the measurement and application of BMR and to critically review the Schofield et al. BMR database presenting a series of new equations to predict BMR. This division, while arbitrary, will enable readers who wish to omit the historical review of BMR to concentrate on the evolution of the new BMR equations. BMR data collected from published and measured values. A series of new equations (Oxford equations) have been developed using a data set of 10,552 BMR values that (1) excluded all the Italian subjects and (2) included a much larger number (4018) of people from the tropics. In general, the Oxford equations tend to produce lower BMR values than the current FAO/WHO/UNU equations in 18-30 and 30-60 year old males and in all females over 18 years of age. This is an opportune moment to re-examine the role and place of BMR measurements in estimating total energy requirements today. The Oxford equations' future use and application will surely depend on their ability to predict more accurately the BMR in contemporary populations.

Predicting basal metabolic rates in Malaysian adult elite athletes.

PubMed

Wong, Jyh Eiin; Poh, Bee Koon; Nik Shanita, Safii; Izham, Mohd Mohamad; Chan, Kai Quin; Tai, Meng De; Ng, Wei Wei; Ismail, Mohd Noor

2012-11-01

This study aimed to measure the basal metabolic rate (BMR) of elite athletes and develop a gender specific predictive equation to estimate their energy requirements. 92 men and 33 women (aged 18-31 years) from 15 sports, who had been training six hours daily for at least one year, were included in the study. Body composition was measured using the bioimpedance technique, and BMR by indirect calorimetry. The differences between measured and estimated BMR using various predictive equations were calculated. The novel equation derived from stepwise multiple regression was evaluated using Bland and Altman analysis. The predictive equations of Cunningham and the Food and Agriculture Organization/World Health Organization/United Nations University either over- or underestimated the measured BMR by up to ± 6%, while the equations of Ismail et al, developed from the local non-athletic population, underestimated the measured BMR by 14%. The novel predictive equation for the BMR of athletes was BMR (kcal/day) = 669 + 13 (weight in kg) + 192 (gender: 1 for men and 0 for women) (R2 0.548; standard error of estimates 163 kcal). Predicted BMRs of elite athletes by this equation were within 1.2% ± 9.5% of the measured BMR values. The novel predictive equation presented in this study can be used to calculate BMR for adult Malaysian elite athletes. Further studies may be required to validate its predictive capabilities for other sports, nationalities and age groups.

Best Fitting Prediction Equations for Basal Metabolic Rate: Informing Obesity Interventions in Diverse Populations

PubMed Central

Sabounchi, Nasim S.; Rahmandad, Hazhir; Ammerman, Alice

2014-01-01

Basal Metabolic Rate (BMR) represents the largest component of total energy expenditure and is a major contributor to energy balance. Therefore, accurately estimating BMR is critical for developing rigorous obesity prevention and control strategies. Over the past several decades, numerous BMR formulas have been developed targeted to different population groups. A comprehensive literature search revealed 248 BMR estimation equations developed using diverse ranges of age, gender, race, fat free mass, fat mass, height, waist-to-hip ratio, body mass index, and weight. A subset of 47 studies included enough detail to allow for development of meta-regression equations. Utilizing these studies, meta-equations were developed targeted to twenty specific population groups. This review provides a comprehensive summary of available BMR equations and an estimate of their accuracy. An accompanying online BMR prediction tool (available at http://www.sdl.ise.vt.edu/tutorials.html) was developed to automatically estimate BMR based on the most appropriate equation after user-entry of individual age, race, gender, and weight. PMID:23318720

Adaptation of metabolism and evaporative water loss along an aridity gradient.

PubMed

Tieleman, B Irene; Williams, Joseph B; Bloomer, Paulette

2003-01-22

Broad-scale comparisons of birds indicate the possibility of adaptive modification of basal metabolic rate (BMR) and total evaporative water loss (TEWL) in species from desert environments, but these might be confounded by phylogeny or phenotypic plasticity. This study relates variation in avian BMR and TEWL to a continuously varying measure of environment, aridity. We test the hypotheses that BMR and TEWL are reduced along an aridity gradient within the lark family (Alaudidae), and investigate the role of phylogenetic inertia. For 12 species of lark, BMR and TEWL decreased along a gradient of increasing aridity, a finding consistent with our proposals. We constructed a phylogeny for 22 species of lark based on sequences of two mitochondrial genes, and investigated whether phylogenetic affinity played a part in the correlation of phenotype and environment. A test for serial independence of the data for mass-corrected TEWL and aridity showed no influence of phylogeny on our findings. However, we did discover a significant phylogenetic effect in mass-corrected data for BMR, a result attributable to common phylogenetic history or to common ecological factors. A test of the relationship between BMR and aridity using phylogenetic independent constrasts was consistent with our previous analysis: BMR decreased with increasing aridity.

Metabolic risk factors in mice divergently selected for BMR fed high fat and high carb diets.

PubMed

Sadowska, Julita; Gębczyński, Andrzej K; Konarzewski, Marek

2017-01-01

Factors affecting contribution of spontaneous physical activity (SPA; activity associated with everyday tasks) to energy balance of humans are not well understood, as it is not clear whether low activity is related to dietary habits, precedes obesity or is a result of thereof. In particular, human studies on SPA and basal metabolic rates (BMR, accounting for >50% of human energy budget) and their associations with diet composition, metabolic thrift and obesity are equivocal. To clarify these ambiguities we used a unique animal model-mice selected for divergent BMR rates (the H-BMR and L-BMR line type) presenting a 50% between-line type difference in the primary selected trait. Males of each line type were divided into three groups and fed either a high fat, high carb or a control diet. They then spent 4 months in individual cages under conditions emulating human "sedentary lifestyle", with SPA followed every month and measurements of metabolic risk indicators (body fat mass %, blood lipid profile, fasting blood glucose levels and oxidative damage in the livers, kidneys and hearts) taken at the end of study. Mice with genetically determined high BMR assimilated more energy and had higher SPA irrespective of type of diet. H-BMR individuals were characterized by lower dry body fat mass %, better lipid profile and lower fasting blood glucose levels, but higher oxidative damage in the livers and hearts. Genetically determined high BMR may be a protective factor against diet-induced obesity and most of the metabolic syndrome indicators. Elevated spontaneous activity is correlated with high BMR, and constitutes an important factor affecting individual capability to sustain energy balance even under energy dense diets.

Basal metabolic rate is decreased in women with polycystic ovary syndrome and biochemical hyperandrogenemia and is associated with insulin resistance.

PubMed

Georgopoulos, Neoklis A; Saltamavros, Alexandros D; Vervita, Vasiliki; Karkoulias, Kyriakos; Adonakis, George; Decavalas, George; Kourounis, George; Markou, Kostas B; Kyriazopoulou, Venetsana

2009-07-01

To evaluate basal metabolic rate (BMR) in women with PCOS and to determine its association with insulin resistance (IR). Prospective assessment of BMR in women with PCOS. Outpatient clinic of the Division of Reproductive Endocrinology. The study included 91 Greek women with PCOS and biochemical hyperandrogenemia, with mean age 24.03 +/- 0.55 years and mean body mass index (BMI) 26.67 +/- 0.69 kg/m(2), and 48 matched regularly menstruating women, with mean age 26.33 +/- 0.93 years and mean BMI 23.35 +/- 0.85 kg/m(2), as control subjects. Assessment of BMR by indirect calorimetry, IR by HOMA and QUICKI indices, fasting insulin, and fasting glucose/insulin ratio. Reduced BMR in PCOS with or without IR. Adjusted BMR was 1,868 +/- 41 kcal/day in the control group, 1,445.57 +/- 76 in all PCOS women, 1,590 +/- 130 in PCOS women without IR and 1,116 +/- 106 in PCOS women with IR. Adjusted BMR showed a statistically significant difference between women with PCOS and control subjects, with lowest values in the group of PCOS women with IR, even after adjusting all groups for age and BMI. Women with PCOS, particularly those with IR, present a significantly decreased BMR.

Adaptation of metabolism and evaporative water loss along an aridity gradient.

PubMed Central

Tieleman, B Irene; Williams, Joseph B; Bloomer, Paulette

2003-01-01

Broad-scale comparisons of birds indicate the possibility of adaptive modification of basal metabolic rate (BMR) and total evaporative water loss (TEWL) in species from desert environments, but these might be confounded by phylogeny or phenotypic plasticity. This study relates variation in avian BMR and TEWL to a continuously varying measure of environment, aridity. We test the hypotheses that BMR and TEWL are reduced along an aridity gradient within the lark family (Alaudidae), and investigate the role of phylogenetic inertia. For 12 species of lark, BMR and TEWL decreased along a gradient of increasing aridity, a finding consistent with our proposals. We constructed a phylogeny for 22 species of lark based on sequences of two mitochondrial genes, and investigated whether phylogenetic affinity played a part in the correlation of phenotype and environment. A test for serial independence of the data for mass-corrected TEWL and aridity showed no influence of phylogeny on our findings. However, we did discover a significant phylogenetic effect in mass-corrected data for BMR, a result attributable to common phylogenetic history or to common ecological factors. A test of the relationship between BMR and aridity using phylogenetic independent constrasts was consistent with our previous analysis: BMR decreased with increasing aridity. PMID:12590762

Phenotypic plasticity in the scaling of avian basal metabolic rate

PubMed Central

McKechnie, Andrew E; Freckleton, Robert P; Jetz, Walter

2006-01-01

Many birds exhibit short-term, reversible adjustments in basal metabolic rate (BMR), but the overall contribution of phenotypic plasticity to avian metabolic diversity remains unclear. The available BMR data include estimates from birds living in natural environments and captive-raised birds in more homogenous, artificial environments. All previous analyses of interspecific variation in BMR have pooled these data. We hypothesized that phenotypic plasticity is an important contributor to interspecific variation in avian BMR, and that captive-raised populations exhibit general differences in BMR compared to wild-caught populations. We tested this hypothesis by fitting general linear models to BMR data for 231 bird species, using the generalized least-squares approach to correct for phylogenetic relatedness when necessary. The scaling exponent relating BMR to body mass in captive-raised birds (0.670) was significantly shallower than in wild-caught birds (0.744). The differences in metabolic scaling between captive-raised and wild-caught birds persisted when migratory tendency and habitat aridity were controlled for. Our results reveal that phenotypic plasticity is a major contributor to avian interspecific metabolic variation. The finding that metabolic scaling in birds is partly determined by environmental factors provides further support for models that predict variation in scaling exponents, such as the allometric cascade model. PMID:16627278

Effects of behavioural exercise therapy on the effectiveness of a multidisciplinary rehabilitation for chronic non-specific low back pain: study protocol for a randomised controlled trial.

PubMed

Hofmann, Jana; Peters, Stefan; Geidl, Wolfgang; Hentschke, Christian; Pfeifer, Klaus

2013-03-11

In Germany, a multidisciplinary rehabilitation named "behavioural medical rehabilitation" (BMR) is available for treatment of chronic low back pain (clbp). A central component of BMR is standard exercise therapy (SET), which is directed mainly to improve physical fitness. There is a need to address psychosocial factors within SET and therefore to improve behavior change with a focus on the development of self-management skills in dealing with clbp. Furthermore, short-term effectiveness of BMR with a SET has been proven, but the impact of a behavioural exercise therapy (BET) for improvement of the long-term effectiveness of BMR is unclear. To compare the effectiveness of two exercise programs with different approaches within BMR on the effects of BMR a prospective randomized controlled trial (RCT) in two rehabilitation centres will be performed. 214 patients aged 18-65 with clbp will be, based on an "urn randomisation"-algorithm, randomly assigned to a BMR with SET (function-oriented, n=107) and BMR with BET (behaviour-oriented, n=107). Both exercise programs have a mean duration of 26 hours in three weeks and are delivered by a limited number of not-blinded study therapists in closed groups with six to twelve patients who will be masked regarding study group. The main differences of BET lie in its detailed manualised program with a theory-based, goal-orientated combination of exercise, education and behavioural elements, active participation of patients and consideration of their individual preferences and previous experiences with exercise. The primary outcome is functional ability assessed with the Hannover Functional Ability Questionnaire directly before and after the rehabilitation program, as well as a six and twelve-month follow-up. This RCT is designed to explore the effects of BET on the effectiveness of a BMR compared to a BMR with SET in the management of patients with clbp. Methodological challenges arise from conducting a RCT within routine health care as well as from ensuring high treatment integrity. Findings of this study might contribute to a better understanding of the mechanism of action of BMR and the special effects of BET and may be used to improve the quality of these interventions in routine care, therefore reducing the burden to patients with disabling clbp. Current controlled trials NCT01666639.

Genome-wide association study for the interaction between BMR and BMI in obese Korean women including overweight.

PubMed

Lee, Myoungsook; Kwon, Dae Young; Kim, Myung-Sunny; Choi, Chong Ran; Park, Mi-Young; Kim, Ae-Jung

2016-02-01

This is the first study to identify common genetic factors associated with the basal metabolic rate (BMR) and body mass index (BMI) in obese Korean women including overweight. This will be a basic study for future research of obese gene-BMR interaction. The experimental design was 2 by 2 with variables of BMR and BMI. A genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) was conducted in the overweight and obesity (BMI > 23 kg/m(2)) compared to the normality, and in women with low BMR (< 1426.3 kcal/day) compared to high BMR. A total of 140 SNPs reached formal genome-wide statistical significance in this study (P < 1 × 10(-4)). Surveys to estimate energy intake using 24-h recall method for three days and questionnaires for family history, a medical examination, and physical activities were conducted. We found that two NRG3 gene SNPs in the 10q23.1 chromosomal region were highly associated with BMR (rs10786764; P = 8.0 × 10(-7), rs1040675; 2.3 × 10(-6)) and BMI (rs10786764; P = 2.5 × 10(-5), rs10786764; 6.57 × 10(-5)). The other genes related to BMI (HSD52, TMA16, MARCH1, NRG1, NRXN3, and STK4) yielded P <10 × 10(-4). Five new loci associated with BMR and BMI, including NRG3, OR8U8, BCL2L2-PABPN1, PABPN1, and SLC22A17 were identified in obese Korean women (P < 1 × 10(-4)). In the questionnaire investigation, significant differences were found in the number of starvation periods per week, family history of stomach cancer, coffee intake, and trial of weight control in each group. We discovered several common BMR- and BMI-related genes using GWAS. Although most of these newly established loci were not previously associated with obesity, they may provide new insights into body weight regulation. Our findings of five common genes associated with BMR and BMI in Koreans will serve as a reference for replication and validation of future studies on the metabolic rate.

Yield and forage value of a dual-purpose bmr-12 sorghum hybrid

USDA-ARS?s Scientific Manuscript database

Grain sorghum [Sorghum bicolor (L.) Moench] is an important crop for rainfed production systems with 2.7 million ha grown in the USA in 2013. The brown-midrib (bmr) mutations, especially bmr-12, have resulted in low stover lignin and high fiber digestibility without reducing grain yield in some sor...

Avian BMR in Marine and Non-Marine Habitats: A Test Using Shorebirds

PubMed Central

Gutiérrez, Jorge S.; Abad-Gómez, José M.; Sánchez-Guzmán, Juan M.; Navedo, Juan G.; Masero, José A.

2012-01-01

Basal metabolic rate (BMR) is closely linked to different habitats and way of life. In birds, some studies have noted that BMR is higher in marine species compared to those inhabiting terrestrial habitats. However, the extent of such metabolic dichotomy and its underlying mechanisms are largely unknown. Migratory shorebirds (Charadriiformes) offer a particularly interesting opportunity for testing this marine–non-marine difference as they are typically divided into two broad categories in terms of their habitat occupancy outside the breeding season: ‘coastal’ and ‘inland’ shorebirds. Here, we measured BMR for 12 species of migratory shorebirds wintering in temperate inland habitats and collected additional BMR values from the literature for coastal and inland shorebirds along their migratory route to make inter- and intraspecific comparisons. We also measured the BMR of inland and coastal dunlins Calidris alpina wintering at a similar latitude to facilitate a more direct intraspecific comparison. Our interspecific analyses showed that BMR was significantly lower in inland shorebirds than in coastal shorebirds after the effects of potentially confounding climatic (latitude, temperature, solar radiation, wind conditions) and organismal (body mass, migratory status, phylogeny) factors were accounted for. This indicates that part of the variation in basal metabolism might be attributed to genotypic divergence. Intraspecific comparisons showed that the mass-specific BMR of dunlins wintering in inland freshwater habitats was 15% lower than in coastal saline habitats, suggesting that phenotypic plasticity also plays an important role in generating these metabolic differences. We propose that the absence of tidally-induced food restrictions, low salinity, and less windy microclimates associated with inland freshwater habitats may reduce the levels of energy expenditure, and hence BMR. Further research including common-garden experiments that eliminate phenotypic plasticity as a source of phenotypic variation is needed to determine to what extent these general patterns are attributable to genotypic adaptation. PMID:22860084

Comparative analyses of basal rate of metabolism in mammals: data selection does matter.

PubMed

Genoud, Michel; Isler, Karin; Martin, Robert D

2018-02-01

Basal rate of metabolism (BMR) is a physiological parameter that should be measured under strictly defined experimental conditions. In comparative analyses among mammals BMR is widely used as an index of the intensity of the metabolic machinery or as a proxy for energy expenditure. Many databases with BMR values for mammals are available, but the criteria used to select metabolic data as BMR estimates have often varied and the potential effect of this variability has rarely been questioned. We provide a new, expanded BMR database reflecting compliance with standard criteria (resting, postabsorptive state; thermal neutrality; adult, non-reproductive status for females) and examine potential effects of differential selectivity on the results of comparative analyses. The database includes 1739 different entries for 817 species of mammals, compiled from the original sources. It provides information permitting assessment of the validity of each estimate and presents the value closest to a proper BMR for each entry. Using different selection criteria, several alternative data sets were extracted and used in comparative analyses of (i) the scaling of BMR to body mass and (ii) the relationship between brain mass and BMR. It was expected that results would be especially dependent on selection criteria with small sample sizes and with relatively weak relationships. Phylogenetically informed regression (phylogenetic generalized least squares, PGLS) was applied to the alternative data sets for several different clades (Mammalia, Eutheria, Metatheria, or individual orders). For Mammalia, a 'subsampling procedure' was also applied, in which random subsamples of different sample sizes were taken from each original data set and successively analysed. In each case, two data sets with identical sample size and species, but comprising BMR data with different degrees of reliability, were compared. Selection criteria had minor effects on scaling equations computed for large clades (Mammalia, Eutheria, Metatheria), although less-reliable estimates of BMR were generally about 12-20% larger than more-reliable ones. Larger effects were found with more-limited clades, such as sciuromorph rodents. For the relationship between BMR and brain mass the results of comparative analyses were found to depend strongly on the data set used, especially with more-limited, order-level clades. In fact, with small sample sizes (e.g. <100) results often appeared erratic. Subsampling revealed that sample size has a non-linear effect on the probability of a zero slope for a given relationship. Depending on the species included, results could differ dramatically, especially with small sample sizes. Overall, our findings indicate a need for due diligence when selecting BMR estimates and caution regarding results (even if seemingly significant) with small sample sizes. © 2017 Cambridge Philosophical Society.

An explanation of the relationship between mass, metabolic rate and characteristic length for placental mammals

PubMed Central

2015-01-01

The Mass, Metabolism and Length Explanation (MMLE) was advanced in 1984 to explain the relationship between metabolic rate and body mass for birds and mammals. This paper reports on a modernized version of MMLE. MMLE deterministically computes the absolute value of Basal Metabolic Rate (BMR) and body mass for individual animals. MMLE is thus distinct from other examinations of these topics that use species-averaged data to estimate the parameters in a statistically best fit power law relationship such as BMR = a(bodymass)b. Beginning with the proposition that BMR is proportional to the number of mitochondria in an animal, two primary equations are derived that compute BMR and body mass as functions of an individual animal’s characteristic length and sturdiness factor. The characteristic length is a measureable skeletal length associated with an animal’s means of propulsion. The sturdiness factor expresses how sturdy or gracile an animal is. Eight other parameters occur in the equations that vary little among animals in the same phylogenetic group. The present paper modernizes MMLE by explicitly treating Froude and Strouhal dynamic similarity of mammals’ skeletal musculature, revising the treatment of BMR and using new data to estimate numerical values for the parameters that occur in the equations. A mass and length data set with 575 entries from the orders Rodentia, Chiroptera, Artiodactyla, Carnivora, Perissodactyla and Proboscidea is used. A BMR and mass data set with 436 entries from the orders Rodentia, Chiroptera, Artiodactyla and Carnivora is also used. With the estimated parameter values MMLE can calculate characteristic length and sturdiness factor values so that every BMR and mass datum from the BMR and mass data set can be computed exactly. Furthermore MMLE can calculate characteristic length and sturdiness factor values so that every body mass and length datum from the mass and length data set can be computed exactly. Whether or not MMLE can calculate a sturdiness factor value so that an individual animal’s BMR and body mass can be simultaneously computed given its characteristic length awaits analysis of a data set that simultaneously reports all three of these items for individual animals. However for many of the addressed MMLE homogeneous groups, MMLE can predict the exponent obtained by regression analysis of the BMR and mass data using the exponent obtained by regression analysis of the mass and length data. This argues that MMLE may be able to accurately simultaneously compute BMR and mass for an individual animal. PMID:26355655

Basal metabolic rate in free-living tropical birds: the influence of phylogenetic, behavioral, and ecological factors

PubMed Central

Tolstenkov, Oleg; Zubkova, Ekaterina; Solovyeva, Eugenia; Kerimov, Anvar

2018-01-01

Abstract The majority of our knowledge of avian energetics is based on studies of birds from temperate and high latitudes. Using the largest existing sample of wild-caught Old World tropical species, we showed that birds from Southern Vietnam had lower basal metabolic rate (BMR) than temperate species. The strongest dissimilarity between tropical and temperate species was the low scaling exponent in the allometric relation between BMR and body mass in tropical birds (the regression slope was 0.573). The passerine migrants to temperate and high latitudes had higher BMR than tropical sedentary passerines. Body mass alone accounted for 93% of the variation in BMR (body mass ranged from 5 to 252 g). Contrary to some other studies, we did not find evidence besides the above mentioned that phylogeny, taxonomy, behavior, or ecology have a significant influence on BMR variation among tropical birds. PMID:29492036

The effect of long term combined yoga practice on the basal metabolic rate of healthy adults.

PubMed

Chaya, M S; Kurpad, A V; Nagendra, H R; Nagarathna, R

2006-08-31

Different procedures practiced in yoga have stimulatory or inhibitory effects on the basal metabolic rate when studied acutely. In daily life however, these procedures are usually practiced in combination. The purpose of the present study was to investigate the net change in the basal metabolic rate (BMR) of individuals actively engaging in a combination of yoga practices (asana or yogic postures, meditation and pranayama or breathing exercises) for a minimum period of six months, at a residential yoga education and research center at Bangalore. The measured BMR of individuals practicing yoga through a combination of practices was compared with that of control subjects who did not practice yoga but led similar lifestyles. The BMR of the yoga practitioners was significantly lower than that of the non-yoga group, and was lower by about 13 % when adjusted for body weight (P < 0.001). This difference persisted when the groups were stratified by gender; however, the difference in BMR adjusted for body weight was greater in women than men (about 8 and 18% respectively). In addition, the mean BMR of the yoga group was significantly lower than their predicted values, while the mean BMR of non-yoga group was comparable with their predicted values derived from 1985 WHO/FAO/UNU predictive equations. This study shows that there is a significantly reduced BMR, probably linked to reduced arousal, with the long term practice of yoga using a combination of stimulatory and inhibitory yogic practices.

The effect of long term combined yoga practice on the basal metabolic rate of healthy adults

PubMed Central

Chaya, MS; Kurpad, AV; Nagendra, HR; Nagarathna, R

2006-01-01

Background Different procedures practiced in yoga have stimulatory or inhibitory effects on the basal metabolic rate when studied acutely. In daily life however, these procedures are usually practiced in combination. The purpose of the present study was to investigate the net change in the basal metabolic rate (BMR) of individuals actively engaging in a combination of yoga practices (asana or yogic postures, meditation and pranayama or breathing exercises) for a minimum period of six months, at a residential yoga education and research center at Bangalore. Methods The measured BMR of individuals practicing yoga through a combination of practices was compared with that of control subjects who did not practice yoga but led similar lifestyles. Results The BMR of the yoga practitioners was significantly lower than that of the non-yoga group, and was lower by about 13 % when adjusted for body weight (P < 0.001). This difference persisted when the groups were stratified by gender; however, the difference in BMR adjusted for body weight was greater in women than men (about 8 and 18% respectively). In addition, the mean BMR of the yoga group was significantly lower than their predicted values, while the mean BMR of non-yoga group was comparable with their predicted values derived from 1985 WHO/FAO/UNU predictive equations. Conclusion This study shows that there is a significantly reduced BMR, probably linked to reduced arousal, with the long term practice of yoga using a combination of stimulatory and inhibitory yogic practices. PMID:16945127

Effect of corn silage hybrids differing in starch and neutral detergent fiber digestibility on lactation performance and total-tract nutrient digestibility by dairy cows.

PubMed

Ferraretto, L F; Fonseca, A C; Sniffen, C J; Formigoni, A; Shaver, R D

2015-01-01

Selection for hybrids with greater starch and NDF digestibility may be beneficial for dairy producers. The objective of this study was to determine the effect of feeding a TMR containing a floury-leafy corn silage hybrid (LFY) compared with a brown midrib corn silage hybrid (BMR) for intake, lactation performance, and total-tract nutrient digestibility in dairy cows. Ninety-six multiparous Holstein cows, 105±31d in milk at trial initiation, were stratified by DIM and randomly assigned to 12 pens of 8 cows each. Pens were randomly assigned to 1 of 2 treatments, BMR or LFY, in a completely randomized design; a 2-wk covariate period with cows fed a common diet followed by a 14-wk treatment period with cows fed their assigned treatment diet. Starch digestibilities, in situ, in vitro, and in vivo, were greater for LFY compared with BMR; the opposite was observed for NDF digestibility. Cows fed BMR consumed 1.7kg/d more dry matter than LFY. Although, actual-, energy-, and solids-corrected milk yields were greater for BMR than LFY, feed conversions (kg of milk or component-corrected milk per kg of DMI) did not differ. Fat-corrected milk and milk fat yield were similar, as milk fat content was greater for cows fed LFY (4.05%) than BMR (3.83%). Cows fed BMR had lower milk urea nitrogen concentration, but greater milk protein and lactose yields compared with LFY. Body weight change and condition score were unaffected by treatment. Total-tract starch digestibility was greater for cows fed the LFY corn silage; however, dry matter intake and milk and protein yields were greater for cows fed the BMR corn silage. Although total-tract starch digestibility was greater for cows fed the LFY corn silage, feed efficiency was not affected by hybrid type due to greater dry matter intake and milk and protein yields by cows fed the BMR corn silage. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Total Body Capacitance for Estimating Human Basal Metabolic Rate in an Egyptian Population

PubMed Central

M. Abdel-Mageed, Samir; I. Mohamed, Ehab

2016-01-01

Determining basal metabolic rate (BMR) is important for estimating total energy needs in the human being yet, concerns have been raised regarding the suitability of sex-specific equations based on age and weight for its calculation on an individual or population basis. It has been shown that body cell mass (BCM) is the body compartment responsible for BMR. The objectives of this study were to investigate the relationship between total body capacitance (TBC), which is considered as an expression for BCM, and BMR and to develop a formula for calculating BMR in comparison with widely used equations. Fifty healthy nonsmoking male volunteers [mean age (± SD): 24.93 ± 4.15 year and body mass index (BMI): 25.63 ± 3.59 kg/m2] and an equal number of healthy nonsmoking females matched for age and BMI were recruited for the study. TBC and BMR were measured for all participants using octopolar bioelectric impedance analysis and indirect calorimetry techniques, respectively. A significant regressing equation based on the covariates: sex, weight, and TBC for estimating BMR was derived (R=0.96, SEE=48.59 kcal, and P<0.0001), which will be useful for nutritional and health status assessment for both individuals and populations. PMID:27127453

Exploring individual quality: Basal metabolic rate and reproductive performance in storm-petrels

USGS Publications Warehouse

Blackmer, A.L.; Mauck, R.A.; Ackerman, Joshua T.; Huntington, C.E.; Nevitt, G.A.; Williams, J.B.

2005-01-01

Despite evidence that some individuals achieve both superior reproductive performance and high survivorship, the factors underlying variation in individual quality are not well understood. The compensation and increased-intake hypotheses predict that basal metabolic rate (BMR) influences reproductive performance; if so, variation in BMR may be related to differences in individual quality. We evaluated whether BMR measured during the incubation period provides a proximate explanation for variation in individual quality by measuring the BMRs and reproductive performance of Leach's storm-petrels (Oceanodroma leucorhoa) breeding on Kent Island, New Brunswick, Canada, during 2000 and 2001. We statistically controlled for internal (body mass, breeding age, sex) and external (year, date, time of day) effects on BMR. We found that males with relatively low BMRs hatched their eggs earlier in the season and that their chicks' wing growth rates were faster compared to males with relatively high BMRs. Conversely, BMR was not related to egg volume, hatching date, or chick growth rate for females or to lifetime (???23 years) hatching success for either sex. Thus, for males but not for females, our results support the compensation hypothesis. This hypothesis predicts that animals with low BMRs will achieve better reproductive performance than animals with high BMRs because they have lower self-maintenance costs and therefore can apportion more energy to reproduction. These results provide evidence that intraspecific variation in reproductive performance is related to BMR and suggest that BMR may influence individual quality in males. ?? The Author 2005. Published by Oxford University Press on behalf of the International Society for Behavioral Ecology. All rights reserved.

Estimation of basal metabolic rate in Chinese: are the current prediction equations applicable?

PubMed

Camps, Stefan G; Wang, Nan Xin; Tan, Wei Shuan Kimberly; Henry, C Jeyakumar

2016-08-31

Measurement of basal metabolic rate (BMR) is suggested as a tool to estimate energy requirements. Therefore, BMR prediction equations have been developed in multiple populations because indirect calorimetry is not always feasible. However, there is a paucity of data on BMR measured in overweight and obese adults living in Asia and equations developed for this group of interest. The aim of this study was to develop a new BMR prediction equation for Chinese adults applicable for a large BMI range and compare it with commonly used prediction equations. Subjects were 121 men and 111 women (age: 21-67 years, BMI: 16-41 kg/m(2)). Height, weight, and BMR were measured. Continuous open-circuit indirect calorimetry using a ventilated hood system for 30 min was used to measure BMR. A regression equation was derived using stepwise regression and accuracy was compared to 6 existing equations (Harris-Benedict, Henry, Liu, Yang, Owen and Mifflin). Additionally, the newly derived equation was cross-validated in a separate group of 70 Chinese subjects (26 men and 44 women, age: 21-69 years, BMI: 17-39 kg/m(2)). The equation developed from our data was: BMR (kJ/d) = 52.6 x weight (kg) + 828 x gender + 1960 (women = 0, men = 1; R(2) = 0.81). The accuracy rate (within 10 % accurate) was 78 % which compared well to Owen (70 %), Henry (67 %), Mifflin (67 %), Liu (58 %), Harris-Benedict (45 %) and Yang (37 %) for the whole range of BMI. For a BMI greater than 23, the Singapore equation reached an accuracy rate of 76 %. Cross-validation proved an accuracy rate of 80 %. To date, the newly developed Singapore equation is the most accurate BMR prediction equation in Chinese and is applicable for use in a large BMI range including those overweight and obese.

[Study of Basal metabolic rate of 81 young adults aged 20-29 years old in Changsha].

PubMed

Zhou, X; Mao, D Q; Luo, J Y; Wu, J H; Zhuo, Q; Li, Y M

2017-07-06

Objective: To determine the basal metabolic rate (BMR) of young adults aged between 20-29 years old in Changsha. Methods: We recruited volunteers to join in our research project from April to May, 2015. All recruited volunteers must meet the inclusion criteria: aged 20-29 years old, height between 164-180 centimeters in males and 154-167 centimeters in females, in good health condition, and with no habit of regular physical exercise in last year. Finally, 81 qualified volunteers were selected as research objects, including 43 males and 38 females. The BMR, resting lying metabolism rate and resting sitting metabolism rate of the subjects were detected, and the determined BMR was compared with the calculated results: from the adjusted Schofield equation. Results The BMR, resting lying metabolism rate and resting sitting metabolism rate among males were (166.10±22.09), (174.22±24.56), and (179.54±23.35) kJ·m(-2)·h(-1), respectively, which were all higher than those among females were (137.70±20.04), (149.79±19.25), and (167.78±26.02) kJ·m(-2)·h(-1), respectively, ( P< 0.001). The BMR of males and females calculated from the adjusted Schofield equation were (160.83±3.93), and (140.29±4.18) kJ·m(-2)·h(-1), respectively, and there was no significantly statistical difference found between the determined BMR and the calculated results from Schofield equation (adjusted) classified by sex, all P values >0.05. Conclusion: The BMR of young adults aged 20-29 years old in Changsha was in the national average level, and the adjusted Schofield equation displayed fine accuracy in predicting BMR of young adults aged 20-29 years old in Changsha.

Basal metabolic rate in women with PCOS compared to eumenorrheic controls.

PubMed

Churchill, Sara J; Wang, Erica T; Bhasin, Gaisu; Alexander, Carolyn; Bresee, Catherine; Pall, Marita; Azziz, Ricardo; Mathur, Ruchi; Pisarska, Margareta D

2015-09-01

PCOS is associated with obesity and insulin resistance. Efforts have focused on whether an abnormal energy homeostasis contributes to the development of obesity in these patients. There are conflicting results in the literature regarding whether women with PCOS have an altered basal metabolic rate (BMR), thereby leading to difficulties in weight loss. The objective of this study is to compare basal metabolic rate (BMR) in women with PCOS and controls. Cross-sectional study. One hundred and twenty-eight PCOS patients diagnosed by original NIH consensus criteria and 72 eumenorrheic, non-hirsute controls were recruited from an academic medical centre. Assessment of BMR using the InBody portable bioelectrical impedance analysis (BIA) device and insulin resistance by HOMA-IR indices. PCOS women were younger than controls. As expected, PCOS subjects had higher body mass index (BMI), serum androgens and estimated insulin resistance. After adjusting for age and BMI, there was no significant difference in BMR between PCOS subjects (adjusted mean 5807 kJ/day, 95% CI 5715-5899) and controls (adjusted mean 5916 kJ/day, 95% CI 5786-6046) (P = 0·193). BMR was also comparable in a secondary analysis comparing PCOS women with and without insulin resistance. After adjusting for age and BMI, there was no difference in BMR between PCOS women and controls. © 2015 John Wiley & Sons Ltd.

Detergent-mediated incorporation of transmembrane proteins in giant unilamellar vesicles with controlled physiological contents

PubMed Central

Dezi, Manuela; Di Cicco, Aurelie; Bassereau, Patricia; Lévy, Daniel

2013-01-01

Giant unilamellar vesicles (GUVs) are convenient biomimetic systems of the same size as cells that are increasingly used to quantitatively address biophysical and biochemical processes related to cell functions. However, current approaches to incorporate transmembrane proteins in the membrane of GUVs are limited by the amphiphilic nature or proteins. Here, we report a method to incorporate transmembrane proteins in GUVs, based on concepts developed for detergent-mediated reconstitution in large unilamellar vesicles. Reconstitution is performed either by direct incorporation from proteins purified in detergent micelles or by fusion of purified native vesicles or proteoliposomes in preformed GUVs. Lipid compositions of the membrane and the ionic, protein, or DNA compositions in the internal and external volumes of GUVs can be controlled. Using confocal microscopy and functional assays, we show that proteins are unidirectionally incorporated in the GUVs and keep their functionality. We have successfully tested our method with three types of transmembrane proteins. GUVs containing bacteriorhodopsin, a photoactivable proton pump, can generate large transmembrane pH and potential gradients that are light-switchable and stable for hours. GUVs with FhuA, a bacterial porin, were used to follow the DNA injection by T5 phage upon binding to its transmembrane receptor. GUVs incorporating BmrC/BmrD, a bacterial heterodimeric ATP-binding cassette efflux transporter, were used to demonstrate the protein-dependent translocation of drugs and their interactions with encapsulated DNA. Our method should thus apply to a wide variety of membrane or peripheral proteins for producing more complex biomimetic GUVs. PMID:23589883

Surface flux transport simulations: Effect of inflows toward active regions and random velocities on the evolution of the Sun's large-scale magnetic field

NASA Astrophysics Data System (ADS)

Martin-Belda, D.; Cameron, R. H.

2016-02-01

Aims: We aim to determine the effect of converging flows on the evolution of a bipolar magnetic region (BMR), and to investigate the role of these inflows in the generation of poloidal flux. We also discuss whether the flux dispersal due to turbulent flows can be described as a diffusion process. Methods: We developed a simple surface flux transport model based on point-like magnetic concentrations. We tracked the tilt angle, the magnetic flux and the axial dipole moment of a BMR in simulations with and without inflows and compared the results. To test the diffusion approximation, simulations of random walk dispersal of magnetic features were compared against the predictions of the diffusion treatment. Results: We confirm the validity of the diffusion approximation to describe flux dispersal on large scales. We find that the inflows enhance flux cancellation, but at the same time affect the latitudinal separation of the polarities of the bipolar region. In most cases the latitudinal separation is limited by the inflows, resulting in a reduction of the axial dipole moment of the BMR. However, when the initial tilt angle of the BMR is small, the inflows produce an increase in latitudinal separation that leads to an increase in the axial dipole moment in spite of the enhanced flux destruction. This can give rise to a tilt of the BMR even when the BMR was originally aligned parallel to the equator.

A 'slow pace of life' in Australian old-endemic passerine birds is not accompanied by low basal metabolic rates.

PubMed

Bech, Claus; Chappell, Mark A; Astheimer, Lee B; Londoño, Gustavo A; Buttemer, William A

2016-05-01

Life history theory suggests that species experiencing high extrinsic mortality rates allocate more resources toward reproduction relative to self-maintenance and reach maturity earlier ('fast pace of life') than those having greater life expectancy and reproducing at a lower rate ('slow pace of life'). Among birds, many studies have shown that tropical species have a slower pace of life than temperate-breeding species. The pace of life has been hypothesized to affect metabolism and, as predicted, tropical birds have lower basal metabolic rates (BMR) than temperate-breeding birds. However, many temperate-breeding Australian passerines belong to lineages that evolved in Australia and share 'slow' life-history traits that are typical of tropical birds. We obtained BMR from 30 of these 'old-endemics' and ten sympatric species of more recently arrived passerine lineages (derived from Afro-Asian origins or introduced by Europeans) with 'faster' life histories. The BMR of 'slow' temperate-breeding old-endemics was indistinguishable from that of new-arrivals and was not lower than the BMR of 'fast' temperate-breeding non-Australian passerines. Old-endemics had substantially smaller clutches and longer maximal life spans in the wild than new arrivals, but neither clutch size nor maximum life span was correlated with BMR. Our results suggest that low BMR in tropical birds is not functionally linked to their 'slow pace of life' and instead may be a consequence of differences in annual thermal conditions experienced by tropical versus temperate species.

The Effect of "Rogue" Active Regions on the Solar Cycle

NASA Astrophysics Data System (ADS)

Nagy, Melinda; Lemerle, Alexandre; Labonville, François; Petrovay, Kristóf; Charbonneau, Paul

2017-11-01

The origin of cycle-to-cycle variations in solar activity is currently the focus of much interest. It has recently been pointed out that large individual active regions with atypical properties can have a significant impact on the long-term behavior of solar activity. We investigate this possibility in more detail using a recently developed 2×2D dynamo model of the solar magnetic cycle. We find that even a single "rogue" bipolar magnetic region (BMR) in the simulations can have a major effect on the further development of solar activity cycles, boosting or suppressing the amplitude of subsequent cycles. In extreme cases, an individual BMR can completely halt the dynamo, triggering a grand minimum. Rogue BMRs also have the potential to induce significant hemispheric asymmetries in the solar cycle. To study the effect of rogue BMRs in a more systematic manner, a series of dynamo simulations were conducted, in which a large test BMR was manually introduced in the model at various phases of cycles of different amplitudes. BMRs emerging in the rising phase of a cycle can modify the amplitude of the ongoing cycle, while BMRs emerging in later phases will only affect subsequent cycles. In this model, the strongest effect on the subsequent cycle occurs when the rogue BMR emerges around cycle maximum at low latitudes, but the BMR does not need to be strictly cross-equatorial. Active regions emerging as far as 20° from the equator can still have a significant effect. We demonstrate that the combined effect of the magnetic flux, tilt angle, and polarity separation of the BMR on the dynamo is via their contribution to the dipole moment, δ D_{BMR}. Our results indicate that prediction of the amplitude, starting epoch, and duration of a cycle requires an accurate accounting of a broad range of active regions emerging in the previous cycle.

Genetic dissection of bioenerrgy traits in sorghum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vermerris, Wilfred; Kresovich, Stephen; Murray, Seth

Specific Objectives: 1. To identify the gene(s) underlying a major QTL for stem sugar concentration located on chromosome 3. 2. To identify QTL for stem juice volume and stalk sugar concentration and to identify the underlying genes. 3. To classify 60 novel sorghum bmr mutants from the USDA TILLING population in allelic groups based on cell wall chemistry and allelism tests. 4. To select representative bmr mutants from each allelic group and selected NIR spectral mutants for their potential value as feedstock for ethanol production. 5. To clone and characterize those Bmr genes that represent loci other than Bmr12 andmore » Bmr6 using a mapping and a candidate gene approach. Objective 1 The experiments for this objective are largely complete and the data have been analyzed. Data interpretation and follow-up experiments are still in progress. A manuscript is in preparation (Vermerris et al.; see publication list for full details). The main results are: 1) 16 cDNA libraries were prepared and sequenced at Cornell University. The libraries represent internode tissue and flag leaf tissue at booting, internode tissue and peduncle at soft-dough stage, from two plants per sampling time with the Rio allele for the QTL on chromosome 3, and two plants with the BTx623 allele on chromosome 3 (4 tissues x 2 genotypes x 2 replicates) 2) 480 million 86-nucleotide reads were generated from four lanes of Illuminia HiSeqII 3) 74% of the reads could be mapped to the sorghum transcriptome, indicative of good sequence quality 4) Of the 216 genes within the QTL, 17 genes were differentially expressed among plants with and without the Rio QTL. None of these 17 genes had obvious roles in sucrose metabolism 5) Clustering algorithms identified a group of 721 co-expressed genes. One of these genes is a sucrose synthase gene. This cluster also contains 10 genes from the QTL. 6) Among these co-expressed genes are regulatory genes for which knock-out lines in Arabidopsis have been obtained. Analysis of these lines is in progress. Objective 2 The experiments from this objective have been completed and the data were published in the journal Crop Science by Felderhoff et al. (2012). A second publication by Felderhoff et al. is in progress (see publication list for full details). The experiments were based on a mapping population derived from the sweet sorghum 'Rio' and the dry-stalk grain sorghum BTx3197. The main findings were: 1) The apparent juiciness of the sorghum stalk, based on the appearance of a cut stem surface (moist vs. pithy), is not representative of the moisture content of the stalk. This was surprising, as pithy stalks have been associated with low moisture content. This means that in order to assess 'juiciness', a different evaluation needs to be used, for example by removing juice with a roller press or by measuring the difference in mass between a fresh and dried stalk segment. 2) A total of five QTLs associated with juice volume (corrected for height) or moisture content were identified, but not all QTLs were detected in all environments, providing evidence for genotype x environment interactions. This finding complicates breeding for juice volume using marker-assisted selection. 3) The QTL for sugar concentration identified on chromosome 3, and the subject of Objective 1, was confirmed in this mapping population, but unlike in previous studies (Murray et al., 2008), the presence of this QTL was associated with negative impacts on agronomic performance (fresh and dry biomass yield, juice yield). Consequently, introgression of the Brix QTL from Rio as part of a commercial breeding program will require monitoring of the precise impacts of this QTL on agronomic performance. 4) The absence of dominance effects for the Brix trait (= sugar concentration) indicated that Brix must be high in both parents to produce high Brix in hybrids. This means an extra constraint on the development of hybrid parents. With the results from Objective 1, the selection of progeny containing favorable alleles for sugar concentration is expected to be more efficient. Objectives 3 and 4 The experiments from these objectives have been completed. Some of the data have been published in the journal BioEnergy Research (Sattler et al. 2012) and in a book chapter on the utilization of sorghum biomass by Vermerris and Saballos (2012) (see publication list for full details). One manuscript is in progress and is expected to be submitted in 2013. The experiments for these objectives were based on the characterization of a set of novel sorghum mutants identified in a TILLING population generated by Dr. Zhanguo Xin (USDA-RS, Lubbock, TX). The main findings were: 1) Based on allelism tests of bmr mutants from the USDA TILLING population, there are three novel sorghum bmr loci, currently referred to as bmr-20, bmr-100 and bmr-1107. This brings the total number of bmr loci to a maximum of seven (manuscript in preparation). 2) The biomass conversion properties of the novel bmr mutants are not significantly better than the wildtype control, limiting their utility for bioenergy production (manuscript in preparation). This also means that all three bmr loci that positively influence biomass conversion (bmr2, bmr6 and bmr12) have been cloned. Two of these genes (Bmr6 and Bmr2) were cloned with funding from this project. 3) Four novel mutant alleles of bmr12 were identified and characterized. These mutants alleles are bmr12-30, bmr12-34, bmr12-35and bmr12-820, and they all contain missense mutations, leading to amino acid substitutions with varying effects on lignin content and lignin subunit composition (syringyl/guaiacyl ratio). One of the mutants, bmr-35, represents a phenotype that is intermediate between the wild type and the bmr12-reference mutant, which is a null mutant. This intermediate phenotype may offer a balance between enhanced biomass conversion properties and good agronomic performance (Sattler et al., 2012). 4) It is possible to identify sorghum mutants with altered biomass conversion properties using analysis of leaf segments by near infrared reflectance spectroscopy (NIRS). Approximately 10% of 200 M3 families contained spectral outliers suggestive of cell wall changes, and half of those showed variation in biomass conversion efficiency (Vermerris and Saballos, 2012). Objective 5 The experiments from this objective were completed and the data were published by Saballos et al. (2012) in The Plant Journal. The main findings were: 1) The Bmr2 gene encodes the main 4-coumarate CoA ligase in sorghum; the genetic proof consisted of showing how two independent mutations in this gene both resulted in the same phenotype, and by showing that these mutations were allelic. Reduced Bmr2 activity leads to reduced lignin content and brown vascular tissue. 2) Allele-specific molecular markers were developed so that the inheritance of these recessive alleles can be tracked in sorghum breeding programs aimed at improving biomass conversion. 3) Together with four other bona fide 4CL genes, the Bmr2 gene is a member of a multigene family in sorghum. Based on phylogentic analysis, one of those genes is involved in flavonoid metabolism, the others in monolignol biosynthesis. Enzymatic activities for the enzymes encoded by Bmr2 and itsparalogs were determined. 4) Both bmr2 mutations are missense mutations that result in the substitution of apolar amino acids with polar amino acids. In both cases, these substitutions are in hydrophobic domains, which destabilize the protein, leading to degradation. This is apparent from western blots and activity assays with heterologously expressed enzymes. 5) The plant tries to compensate for the reduced 4CL activity by increasing the expression of Bmr2 and its paralogs. As a result of the higher expression levels of the paralogs, there is enough 4CL activity to minimize negative impacts on growth and development. List of all publications to date in which the funding of this project is acknowledged 1) Vermerris W, Saballos A (2012) Genetic enhancement of sorghum for biomass utilization. In Paterson, A. (Ed.) Genetics and Genomics of the Saccharinae, Springer, New York, NY. pp. 391-428. 2) Felderhoff T, Murray SC, Klein PE, Sharma A, Hamblin MT, Kresovich S, Vermerris W, Rooney, WL (2012) QTLs for energy-related traits in a sweet x grain sorghum [Sorghum bicolor (L.) Moench] mapping population. Crop Science 52: 2040-2049. 3) Sattler SE, Palmer NA, Saballos A, Greene AM, Xin Z, Sarath G, Vermerris W, Pedersen JF (2012) Identification and characterization of four missense mutations in Brown midrib12 (Bmr12), the caffeic acid O-methyltranferase (COMT) of sorghum. BioEnergy Research (in press) DOI 10.1007/s12155-012-9197-z 4) Saballos A, Sattler S, Sanchez E, Foster TP, Xin Z, Kang CH, Pedersen J, Vermerris W (2012). Brown midrib2 encodes the major 4-coumarate:CoA ligase involved in lignin biosynthesis in sorghum (Sorghum bicolor (L.) Moench). The Plant Journal 70: 818-830. doi: 10.1111/j.1365-313X.2012.04933. 5) Vermerris, W (2011) Survey of genomics approaches to improve bioenergy traits in maize, sorghum and sugarcane. Journal of Integrative Plant Biology 53: 105-119 6) Saballos A, Ejeta G, Sanchez E, Kang CH, Vermerris W (2009) A genome-wide analysis of the cinnamyl alcohol dehydrogenase family in sorghum [Sorghum bicolor (L.) Moench] identifies SbCAD2 as the Brown midrib6 gene. Genetics 181: 783-795. 7) Saballos A, Vermerris W, Rivera L, Ejeta G (2008) Allelic association, chemical characterization and saccharification properties of brown midrib mutants of sorghum (Sorghum bicolor (L.) Moench). BioEnergy Research 2: 193-204 8) Felderhoff TJ. (2012) QTLs for energy related traits in a sweet x grain RIL sorghum [Sorghum bicolor (L.) Moench] population. M.S. Thesis, Texas A&M University. Publications in preparation (tentative titles) 9) Felderhoff T, Murray SC, Klein PE, Sharma A, Hamblin MT, Kresovich S, Vermerris W, Rooney, WL (2013) QTLs for biomass and juice composition in a sweet x grain sorghum [Sorghum bicolor (L.) Moench] mapping population. 10) Vermerris W, Fear J, Saballos A, Murray SC, Rooney WL, Kresovich S. Identification of candidate genes for sucrose accumulation in sweet sorghum using RNA-seq. 11) Sattler SE, Palmer NA, Saballos A, Xin Z, Vermerris W, Pedersen JF. Characterization of novel sorghum brown midrib mutants. Presentations since last progress report truncated due to space limitations.« less

Scaling of basal metabolic rate with body mass and temperature in mammals.

PubMed

Clarke, Andrew; Rothery, Peter; Isaac, Nick J B

2010-05-01

1. We present a statistical analysis of the scaling of resting (basal) metabolic rate, BMR, with body mass, B(m) and body temperature, T(b), in mammals. 2. Whilst the majority of the variance in ln BMR is explained by ln B(m), the T(b) term is statistically significant. The best fit model was quadratic, indicating that the scaling of ln BMR with ln B(m) varies with body size; the value of any scaling exponent estimated for a sample of mammals will therefore depend on the size distribution of species in the study. This effect can account for much of the variation in scaling exponents reported in the literature for mammals. 3. In all models, inclusion of T(b) reduced the strength of scaling with ln B(m). The model including T(b) suggests that birds and mammals have a similar underlying thermal dependence of BMR, equivalent to a Q(10) of 2.9 across the range of T(b) values 32-42 degrees C. 4. There was significant heterogeneity in both the mass scaling exponent and mean BMR across mammalian orders, with a tendency for orders dominated by larger taxa to have steeper scaling exponents. This heterogeneity was particularly marked across orders with smaller mean B(m) and the taxonomic composition of the sample will thus also affect the observed scaling exponent. After correcting for the effects of ln B(m) and T(b), Soricomorpha, Didelphimorphia and Artiodactyla had the highest BMR of those orders represented by more than 10 species in the data set. 5. Inclusion of T(b) in the model removed the effect of diet category evident from a model in ln B(m) alone and widely reported in the literature; this was caused by a strong interaction between diet category and T(b) in mammals. 6. Inclusion of mean ambient temperature, T(a), in the model indicated a significant inverse relationship between ln BMR and T(a), complicated by an interaction between T(a) and T(b). All other things being equal, a polar mammal living at -10 degrees C has a body temperature approximately 2.7 degrees C warmer and a BMR higher by approximately 40% than a tropical mammal of similar size living at 25 degrees C.

Helicoverpa zea (Lepidoptera: Noctuidae) and Spodoptera frugiperda (Lepidoptera: Noctuidae) Responses to Sorghum bicolor (Poales: Poaceae) Tissues From Lowered Lignin Lines

PubMed Central

Dowd, Patrick F.; Sattler, Scott E.

2015-01-01

The presence of lignin within biomass impedes the production of liquid fuels. Plants with altered lignin content and composition are more amenable to lignocellulosic conversion to ethanol and other biofuels but may be more susceptible to insect damage where lignin is an important resistance factor. However, reduced lignin lines of switchgrasses still retained insect resistance in prior studies. Therefore, we hypothesized that sorghum lines with lowered lignin content will also retain insect resistance. Sorghum excised leaves and stalk pith Sorghum bicolor (L.) Moench (Poales: Poaceae) from near isogenic brown midrib (bmr) 6 and 12 mutants lines, which have lowered lignin content and increased lignocellulosic ethanol conversion efficiency, were examined for insect resistance relative to wild-type (normal BTx623). Greenhouse and growth chamber grown plant tissues were fed to first-instar larvae of corn earworms, Helicoverpa zea (Boddie) and fall armyworms Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), two sorghum major pests. Younger bmr leaves had significantly greater feeding damage in some assays than wild-type leaves, but older bmr6 leaves generally had significantly less damage than wild-type leaves. Caterpillars feeding on the bmr6 leaves often weighed significantly less than those feeding on wild-type leaves, especially in the S. frugiperda assays. Larvae fed the pith from bmr stalks had significantly higher mortality compared with those larvae fed on wild-type pith, which suggested that bmr pith was more toxic. Thus, reducing lignin content or changing subunit composition of bioenergy grasses does not necessarily increase their susceptibility to insects and may result in increased resistance, which would contribute to sustainable production. PMID:25601946

Mammalian basal metabolic rate is proportional to body mass2/3

PubMed Central

White, Craig R.; Seymour, Roger S.

2003-01-01

The relationship between mammalian basal metabolic rate (BMR, ml of O2 per h) and body mass (M, g) has been the subject of regular investigation for over a century. Typically, the relationship is expressed as an allometric equation of the form BMR = aMb. The scaling exponent (b) is a point of contention throughout this body of literature, within which arguments for and against geometric (b = 2/3) and quarter-power (b = 3/4) scaling are made and rebutted. Recently, interest in the topic has been revived by published explanations for quarter-power scaling based on fractal nutrient supply networks and four-dimensional biology. Here, a new analysis of the allometry of mammalian BMR that accounts for variation associated with body temperature, digestive state, and phylogeny finds no support for a metabolic scaling exponent of 3/4. Data encompassing five orders of magnitude variation in M and featuring 619 species from 19 mammalian orders show that BMR ∝ M2/3. PMID:12637681

The influence of foraging mode and arid adaptation on the basal metabolic rates of burrowing mammals.

PubMed

White, Craig R

2003-01-01

Two competing but nonexclusive hypotheses to explain the reduced basal metabolic rate (BMR) of mammals that live and forage underground (fossorial species) are examined by comparing this group with burrowing mammals that forage on the surface (semifossorial species). These hypotheses suggest that the low BMR of fossorial species either compensates for the enormous energetic demands of subterranean foraging (the cost-of-burrowing hypothesis) or prevents overheating in closed burrow systems (the thermal-stress hypothesis). Because phylogentically informed allometric analysis showed that arid burrowing mammals have a significantly lower BMR than mesic ones, fossorial and semifossorial species were compared within these groups. The BMRs of mesic fossorial and semifossorial mammals could not be reliably distinguished, nor could the BMRs of large (>77 g) arid fossorial and semifossorial mammals. This finding favours the thermal-stress hypothesis, because the groups appear to have similar BMRs despite differences in foraging costs. However, in support of the cost-of-burrowing hypothesis, small (<77 g) arid fossorial mammals were found to have a significantly lower BMR than semifossorial mammals of the similar size. Given the high mass-specific metabolic rates of small animals, they are expected to be under severe energy and water stress in arid environments. Under such conditions, the greatly reduced BMR of small fossorial species may compensate for the enormous energetic demands of subterranean foraging.

Evolution of basal metabolic rate in bank voles from a multidirectional selection experiment.

PubMed

Sadowska, Edyta T; Stawski, Clare; Rudolf, Agata; Dheyongera, Geoffrey; Chrząścik, Katarzyna M; Baliga-Klimczyk, Katarzyna; Koteja, Paweł

2015-05-07

A major theme in evolutionary and ecological physiology of terrestrial vertebrates encompasses the factors underlying the evolution of endothermy in birds and mammals and interspecific variation of basal metabolic rate (BMR). Here, we applied the experimental evolution approach and compared BMR in lines of a wild rodent, the bank vole (Myodes glareolus), selected for 11 generations for: high swim-induced aerobic metabolism (A), ability to maintain body mass on a low-quality herbivorous diet (H) and intensity of predatory behaviour towards crickets (P). Four replicate lines were maintained for each of the selection directions and an unselected control (C). In comparison to C lines, A lines achieved a 49% higher maximum rate of oxygen consumption during swimming, H lines lost 1.3 g less mass in the test with low-quality diet and P lines attacked crickets five times more frequently. BMR was significantly higher in A lines than in C or H lines (60.8, 56.6 and 54.4 ml O2 h(-1), respectively), and the values were intermediate in P lines (59.0 ml O2 h(-1)). Results of the selection experiment provide support for the hypothesis of a positive association between BMR and aerobic exercise performance, but not for the association of adaptation to herbivorous diet with either a high or low BMR. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

An Investigation of the Relative Effectiveness of the Basic Mathematics Review Program at Essex Community College.

ERIC Educational Resources Information Center

Bloomberg, Jerome

Basic Mathematics Review (BMR) is a remedial non-credit course at Essex Community College (Maryland) being taught on an individualized basis. Following diagnostic testing and placement, instruction utilizes programmed materials, tutors, and self-tests. Evaluation of the new individualized BMR and comparison with the traditional remedial course…

Response of Fusarium thapsinum to sorghum brown midrib lines and to phenolic metabolites

USDA-ARS?s Scientific Manuscript database

Presentation type: poster Presentation title: Response of Fusarium thapsinum to sorghum brown midrib lines and to phenolic metabolites Sorghum lines were bred for reduced lignin for cellulosic bioenergy uses, through the incorporation of brown midrib (bmr) bmr6 and/or 12 into two gen...

Response of fusarium thapsinum to sorghum brown midrib lines and to phenolic metabolites

USDA-ARS?s Scientific Manuscript database

Sorghum lines were bred for reduced lignin for cellulosic bioenergy uses, through the incorporation of brown midrib (bmr) bmr6 and/or 12 into two genetic backgrounds, either as single or double mutant lines. When these lines were assessed for resistance to F. thapsinum stalk rot, a cause of lodging,...

Response of fusarium thapsinum to sorghum brown midrib lines and to phenolic metabolites

USDA-ARS?s Scientific Manuscript database

Sorghum lines were bred for reduced lignin for cellulosic bioenergy uses, through the incorporation of brown midrib (bmr) bmr6 and/or 12 into two genetic backgrounds, either as single or double mutant lines. These lines were assessed for resistance to Fusarium thapsinum stalk rot, a cause of lodging...

A general theory of effect size, and its consequences for defining the benchmark response (BMR) for continuous endpoints.

PubMed

Slob, Wout

2017-04-01

A general theory on effect size for continuous data predicts a relationship between maximum response and within-group variation of biological parameters, which is empirically confirmed by results from dose-response analyses of 27 different biological parameters. The theory shows how effect sizes observed in distinct biological parameters can be compared and provides a basis for a generic definition of small, intermediate and large effects. While the theory is useful for experimental science in general, it has specific consequences for risk assessment: it solves the current debate on the appropriate metric for the Benchmark response in continuous data. The theory shows that scaling the BMR expressed as a percent change in means to the maximum response (in the way specified) automatically takes "natural variability" into account. Thus, the theory supports the underlying rationale of the BMR 1 SD. For various reasons, it is, however, recommended to use a BMR in terms of a percent change that is scaled to maximum response and/or within group variation (averaged over studies), as a single harmonized approach.

Variation in energy expenditure among black-legged kittiwakes: Effects of activity-specific metabolic rates and activity budgets

USGS Publications Warehouse

Jodice, P.G.R.; Roby, D.D.; Suryan, R.M.; Irons, D.B.; Kaufman, A.M.; Turco, K.R.; Visser, G. Henk

2003-01-01

We sought to determine the effect of variation in time-activity budgets (TABs) and foraging behavior on energy expenditure rates of parent black-legged kittiwakes (Rissa tridactyla). We quantified TABs using direct observations of radio-tagged adults and simultaneously measured field metabolic rates (FMR) of these same individuals (n = 20) using the doubly labeled water technique. Estimated metabolic rates of kittiwakes attending their brood at the nest or loafing near the colony were similar (ca. 1.3 x basal metabolic rate [BMR]), although loafing during foraging trips was more costly (2.9 x BMR). Metabolic rates during commuting flight (7.3 x BMR) and prey-searching flight (6.2 x BMR) were similar, while metabolic rates during plunge diving were much higher (ca. 47 x BMR). The proportion of the measurement interval spent foraging had a positive effect on FMR (R2 = 0.68), while the combined proportion of time engaged in nest attendance and loafing near the colony had a negative effect on FMR (R2 = 0.72). Thus, more than two-thirds of the variation in kittiwake FMR could be explained by the allocation of time among various activities. The high energetic cost of plunge diving relative to straight flight and searching flight suggests that kittiwakes can optimize their foraging strategy under conditions of low food availability by commuting long distances to feed in areas where gross foraging efficiency is high.

Helicoverpa zea (Lepidoptera: Noctuidae) and Spodoptera frugiperda (Lepidoptera: Noctuidae) Responses to Sorghum bicolor (Poales: Poaceae) Tissues From Lowered Lignin Lines.

PubMed

Dowd, Patrick F; Sattler, Scott E

2015-01-01

The presence of lignin within biomass impedes the production of liquid fuels. Plants with altered lignin content and composition are more amenable to lignocellulosic conversion to ethanol and other biofuels but may be more susceptible to insect damage where lignin is an important resistance factor. However, reduced lignin lines of switchgrasses still retained insect resistance in prior studies. Therefore, we hypothesized that sorghum lines with lowered lignin content will also retain insect resistance. Sorghum excised leaves and stalk pith Sorghum bicolor (L.) Moench (Poales: Poaceae) from near isogenic brown midrib (bmr) 6 and 12 mutants lines, which have lowered lignin content and increased lignocellulosic ethanol conversion efficiency, were examined for insect resistance relative to wild-type (normal BTx623). Greenhouse and growth chamber grown plant tissues were fed to first-instar larvae of corn earworms, Helicoverpa zea (Boddie) and fall armyworms Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), two sorghum major pests. Younger bmr leaves had significantly greater feeding damage in some assays than wild-type leaves, but older bmr6 leaves generally had significantly less damage than wild-type leaves. Caterpillars feeding on the bmr6 leaves often weighed significantly less than those feeding on wild-type leaves, especially in the S. frugiperda assays. Larvae fed the pith from bmr stalks had significantly higher mortality compared with those larvae fed on wild-type pith, which suggested that bmr pith was more toxic. Thus, reducing lignin content or changing subunit composition of bioenergy grasses does not necessarily increase their susceptibility to insects and may result in increased resistance, which would contribute to sustainable production. Published by Oxford University Press on behalf of the Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

Hypertension prevalence and influence of basal metabolic rate on blood pressure among adult students in Bangladesh.

PubMed

Ali, Nurshad; Mahmood, Shakil; Manirujjaman, M; Perveen, Rasheda; Al Nahid, Abdullah; Ahmed, Shamim; Khanum, Farida Adib; Rahman, Mustafizur

2017-07-25

Hypertension is a global health issue and is currently increasing at rapid pace in South Asian countries including Bangladesh. Although, some studies on hypertension have been conducted in Bangladesh, there is a lack of scientific evidence in the adult student population that was missing from the previous and recent national cross-sectional studies. Moreover, the specific risk factors of hypertension in the Bangladeshi adults still need to be investigated. This study was conducted to estimate hypertension prevalence among adult students in Bangladesh and to test the hypothesis of Luke et al. (Hypertension 43:555-560, 2004) that basal metabolic rate (BMR) and blood pressure are positively associated independent of body size. The data was collected on 184 adult university students (118 female and 66 male) in Dhaka, Bangladesh. Anthropometric, BMR details and an average of at least two blood pressure measurements were obtained. Hypertension was defined by a systolic blood pressure (SBP) ≥ 140 mmHg and/or, diastolic blood pressure (DBP) ≥ 90 mmHg. Overall, 6.5% of participants had hypertension with significantly (p < 0.001) higher prevalence in male (12.1%) than in the female (3.4%) students. Age and BMI showed positive and significant correlation with hypertension among the students. When adjusted for body mass index (BMI), as well as other potentially confounding variables such as age, sex, smoking status and degree of urbanization, BMR was positively correlated with SBP and DBP (p < 0.001). Thus, higher BMR is associated with SBP and DBP; this is opposite the well documented inverse relationship between physical activity and blood pressure. If the influence of BMR on blood pressure is confirmed, the systematically elevated BMR might be an important predictor that can explain relatively high blood pressure and hypertension in humans. This study reports the prevalence and associated risk factors of hypertension in the Bangladeshi adult students. The study also showed a positive association between BMR and blood pressure among the participants. A large scale longitudinal study across the country is needed to find out the underlying causes of hypertension in the Bangladeshi adults. In addition, comprehensive and integrated intervention programs focusing on modifiable risk factors are recommended to make awareness and prevent hypertension.

Identification and characterization of 4 missense mutations in brown midrib 12 (Bmr12); the caffeic O-methyltranferase (COMT) of sorghum

USDA-ARS?s Scientific Manuscript database

Modifying lignin content and composition are targets to improve bioenergy crops for cellulosic conversion to biofuels. In sorghum and other C4 grasses, the brown midrib mutants have been shown to reduce lignin content and alter its composition. Bmr12 encodes the sorghum caffeic O-methyltransferase...

Differences in fusarium species in brown midrib sorghum and in air populations in production fields

USDA-ARS?s Scientific Manuscript database

Several Fusarium spp. cause sorghum (Sorghum bicolor) grain mold, resulting in deterioration and mycotoxin production in the field and during storage. Fungal isolates from the air (2005 to 2006) and from leaves and grain from wild-type and brown midrib (bmr)-6 and bmr12 plants (2002 to 2003) were co...

Wrestlers' minimal weight: anthropometry, bioimpedance, and hydrostatic weighing compared.

PubMed

Oppliger, R A; Nielsen, D H; Vance, C G

1991-02-01

The need for accurate assessment of minimal wrestling weight among interscholastic wrestlers has been well documented. Previous research has demonstrated the validity of anthropometric methods for this purpose, but little research has examined the validity of bioelectrical impedance (BIA) measurements. Comparisons between BIA systems has received limited attention. With these two objectives, we compared the prediction of minimal weight (MW) among 57 interscholastic wrestlers using three anthropometric methods (skinfolds (SF) and two skeletal dimensions equations) and three BIA systems (Berkeley Medical Research (BMR), RJL, and Valhalla (VAL]. All methods showed high correlations (r values greater than 0.92) with hydrostatic weighting (HW) and between methods (r values greater than 0.90). The standard errors of estimate (SEE) were relatively small for all methods, especially for SF and the three BIA systems (SEE less than 0.70 kg). The total errors of prediction (E) for RJL and VAL (E = 4.4 and 3.9 kg) were significantly larger than observed nonsignificant BMR and SF values (E = 2.3 and 1.8 kg, respectively). Significant mean differences were observed between HW, RJL, VAL, and the two skeletal dimensions equations, but nonsignificant differences were observed between HW, BMR, and SF. BMR differed significantly from the RJL and VAL systems. The results suggest that RJL and VAL have potential application for this subpopulation. Prediction equation refinement with the addition of selected anthropometric measurement or moderating variables may enhance their utility. However, within the scope of our study, SF and BMR BIA appear to be the most valid methods for determining MW in interscholastic wrestlers.

Body weight and basal metabolic rate in childhood narcolepsy: a longitudinal study.

PubMed

Wang, Zongwen; Wu, Huijuan; Stone, William S; Zhuang, Jianhua; Qiu, Linli; Xu, Xing; Wang, Yan; Zhao, Zhengqing; Han, Fang; Zhao, Zhongxin

2016-09-01

The aims of this study were to document the trajectory of weight gain and body mass index (BMI) in children with type 1 narcolepsy, and to analyze basal metabolic rate (BMR). A total of 65 Chinese children with type 1 narcolepsy with a disease duration ≤12 months were included. In addition, 79 healthy age-matched students were enrolled as controls. Height and body weight were measured every six months for up to 36 months to calculate BMI growth. BMR was measured using COSMED K4b2 indirect calorimetry in 34 patients and 30 healthy controls at six months. At the end of 36 months, the BMR was compared among 18 patients and 16 healthy controls. The children with type 1 narcolepsy showed higher BMIs at follow-up assessments. At the end of the study, 38.46% of the patients were obese and an additional 26.15% were overweight. The patients' BMI growth at six, 12, 18, 24 and 30 months of follow-up was significantly higher, but not at month 36. The patients' basal energy expenditure was significantly lower than that of the controls at six months but not at 36 months. BMI increased rapidly in children with type 1 narcolepsy after disease onset, but BMI growth decreased gradually with prolonged disease. Decreased BMR is an important cause underlying rapid weight gain. The gradual restoration of BMI growth and BMR in narcolepsy emphasizes the importance of compensatory metabolic mechanisms in this disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Constitutive innate immunity is a component of the pace-of-life syndrome in tropical birds.

PubMed

Irene Tieleman, B; Williams, Joseph B; Ricklefs, Robert E; Klasing, Kirk C

2005-08-22

We studied the relationship between one component of immune function and basal metabolic rate (BMR), an indicator of the 'pace-of-life syndrome', among 12 tropical bird species and among individuals of the tropical house wren (Troglodytes aedon), to gain insights into functional connections between life history and physiology. To assess constitutive innate immunity we introduced a new technique in the field of ecological and evolutionary immunology that quantifies the bactericidal activity of whole blood. This in vitro assay utilises a single blood sample to provide a functional, integrated measure of constitutive innate immunity. We found that the bactericidal activity of whole blood varied considerably among species and among individuals within a species. This variation was not correlated with body mass or whole-organism BMR. However, among species, bacteria killing activity was negatively correlated with mass-adjusted BMR, suggesting that species with a slower pace-of-life have evolved a more robust constitutive innate immune capability. Among individuals of a single species, the house wren, bacteria killing activity was positively correlated with mass-adjusted BMR, pointing to physiological differences in individual quality on which natural selection potentially could act.

Energetic cost of standard activities in Gurkha and British soldiers.

PubMed

Strickland, S S; Ulijaszek, S J

1990-01-01

Measurements of basal metabolic rate and energy expenditure at lying, sitting, standing, and performing a step test at four levels of exercise, were made on Gurkha soldiers stationed in Britain and on British controls matched by body weight and occupational background. There was no significant difference in basal metabolic rate (BMR), nor in the energy cost of lying, sitting and standing between the two groups. Gurhas showed significantly lower gross and net energy expenditure, and so significantly greater net mechanical efficiency, at the lower levels of step exercise. The ratio of gross energy expenditure to BMR was lower in Gurkhas at the lowest rates of stepping compared with the British controls. These results suggest that the energy cost of some physical activities expressed as multiples of BMR may not be constant across populations.

A phylogenetic analysis of basal metabolism, total evaporative water loss, and life-history among foxes from desert and mesic regions.

PubMed

Williams, J B; Muñoz-Garcia, A; Ostrowski, S; Tieleman, B I

2004-01-01

We measured basal metabolic rate (BMR) and total evaporative water loss (TEWL) of species of foxes that exist on the Arabian Peninsula, Blanford's fox (Vulpes cana) and two subspecies of Red fox (Vulpes vulpes). Combining these data with that on other canids from the literature, we searched for specialization of physiological traits among desert foxes using both conventional least squares regression and regressions based on phylogenetic independent contrasts. Further, we explored the consequences of reduced body size of foxes on life history parameters such as litter size and neonate mass. For Blanford's foxes, Red foxes from the central desert of Arabia, and Red foxes from the more mesic Asir mountains, body mass averaged 1,285 +/- 52 g, 1,967 +/- 289 g, and 3,060 +/- 482 g, respectively, whereas mean BMR, during summer, was 304.5 +/- 32.3 kJ/day, 418.0 +/- 32.4 kJ/day, and 724.1 +/- 120.2 kJ/day (+/- SD). An analysis of covariance with body mass as a covariate showed no statistical differences in BMR among foxes. Analysis of covariance indicated that Red fox from the Asir mountains had a higher TEWL than Red foxes from central Arabia or than Blanford's foxes also from the mountains. Comparisons of all species of desert and mesic foxes showed no significant differences in BMR, nor did desert foxes have a significantly lower BMR than other carnivores. TEWL of desert foxes was lower than other more mesic carnivores; deviations in TEWL ranged from -17.7% for the Fennec fox (Fennecus zerda) to -57.4% for the Kit fox (Vulpes velox). Although desert foxes have a BMR comparable to other more mesic species, it appears that desert foxes do have a smaller body mass, lowering overall energy requirements. We attribute this reduction in body size to the "resource limitation hypothesis" whereby natural selection favors smaller individuals in a resource-limited environment, especially during periods of severe food shortage. However, until common garden experiments are performed, developmental plasticity and acclimation cannot be ruled out as contributors to this pattern.

Compilation of basal metabolic and blood perfusion rates in various multi-compartment, whole-body thermoregulation models

NASA Astrophysics Data System (ADS)

Shitzer, Avraham; Arens, Edward; Zhang, Hui

2016-07-01

The assignments of basal metabolic rates (BMR), basal cardiac output (BCO), and basal blood perfusion rates (BBPR) were compared in nine multi-compartment, whole-body thermoregulation models. The data are presented at three levels of detail: total body, specific body regions, and regional body tissue layers. Differences in the assignment of these quantities among the compared models increased with the level of detail, in the above order. The ranges of variability in the total body BMR was 6.5 % relative to the lowest value, with a mean of 84.3 ± 2 W, and in the BCO, it was 8 % with a mean of 4.70 ± 0.13 l/min. The least variability among the body regions is seen in the combined torso (shoulders, thorax, and abdomen: ±7.8 % BMR and ±5.9 % BBPR) and in the combined head (head, face, and neck ±9.9 % BMR and ±10.9 % BBPR), determined by the ratio of the standard deviation to the mean. Much more variability is apparent in the extremities with the most showing in the BMR of the feet (±117 %), followed by the BBPR in the arms (±61.3 %). In the tissue layers, most of the bone layers were assigned zero BMR and BBPR, except in the shoulders and in the extremities that were assigned non-zero values in a number of models. The next lowest values were assigned to the fat layers, with occasional zero values. Skin basal values were invariably non-zero but involved very low values in certain models, e.g., BBPR in the feet and the hands. Muscle layers were invariably assigned high values with the highest found in the thorax, abdomen, and legs. The brain, lung, and viscera layers were assigned the highest of all values of both basal quantities with those of the brain layers showing rather tight ranges of variability in both basal quantities. Average basal values of the "time-seasoned" models presented in this study could be useful as a first step in future modeling efforts subject to appropriate adjustment of values to conform to most recently available and reliable data.

Association of the Pro12Ala polymorphism in peroxisome proliferator-activated receptor gamma2 with decreased basic metabolic rate in women with polycystic ovary syndrome.

PubMed

Koika, Vasiliki; Marioli, Dimitra J; Saltamavros, Alexandros D; Vervita, Vasiliki; Koufogiannis, Kleanthis D; Adonakis, George; Decavalas, George; Georgopoulos, Neoklis A

2009-08-01

The peroxisome proliferator-activated receptor (PPAR)gamma is a transcription factor involved in glucose homeostasis and energy metabolism. A missense mutation at codon 12 in the PPARgamma2 has been associated with increased body mass index (BMI) and attenuated insulin resistance (IR) in polycystic ovary syndrome (PCOS). We have recently shown a decreased basic metabolic rate (BMR) in PCOS. The aim of the present study is to determine the prevalence of the Pro12Ala polymorphism of the PPARgamma2 gene and its associations with indices of IR and BMR in lean and slightly overweight PCOS women. Case-control association study involving 156 PCOS women with biochemical hyperandrogenism, chronic anovulation and polycystic ovarian morphology in ultrasound and 56 unrelated healthy controls. Hormonal determinations were performed by electrochemiluminescence quantitation or RIA. BMR was measured by indirect calorimetry. All subjects were genotyped by a PCR-restriction fragment length polymorphism assay. Genotype frequencies of the Pro12Ala polymorphism in PPARgamma2 did not differ among PCOS women and control subjects. The presence of Pro12Ala polymorphism of PPARgamma2 was associated with lower BMR (P=0.04). This finding was valid in our subgroup of lean PCOS (BMI<25 kg/m(2)), in which the Ala variant was also associated with higher total testosterone values. The Pro12Ala polymorphism in the PPARgamma2 gene is associated with decreased BMR in women with PCOS and biochemical hyperandrogenemia. These young women are therefore at risk to increase their body weight and should restrict their energy intake by diet and enhance their energy expenditure by exercise.

[Effect of two hypocaloric diets and their combination with physical exercise on basal metabolic rate and body composition].

PubMed

Bonfanti, Noelia; Fernández, Juan Marcelo; Gomez-Delgado, Francisco; Pérez-Jiménez, Francisco

2014-03-01

Metabolic syndrome (MetS) is diagnosed by the detection of at least three criteria (hypertriglyceridemia, low HDL-C, hypertension, obesity and altered fasting glucose). Visceral fat excess would be the starting point for its development. Scientific evidence supports hypocaloric diets -mediterranean or low fat diet and rich in complex carbohydrates diet included- as the best treatment to reduce fat mass (FM), maximizing its impact by combining them with physical exercise (PE). However, the effects of these treatments on basal metabolic rate (BMR) of patients with MetS, are unknown. To study the effect of the hypocaloric diet - mediterranean or low fat diet- with or without PE on the BMR and body composition (BC) of adults with MetS. 36 volunteers, MetS, both sexes, > 50 years, meeting the inclusion criteria. They were randomly assigned to a group of intervention (3 months) of hypocaloric diet: mediterranean diet (MED), low fat and rich in complex carbohydrates diet (CHO) and both combined with PE (MEDE and CHOE respectively). Anthropometric data was taken (weight, muscle mass (MM) and FM) and BMR was determined by indirect calorimetry, before and after intervention. The addition of PE to both hypocaloric treatments produced greater FM loss and weight loss than dieting alone, being this loss in CHOE > MEDE (p < 0.05). These groups decreased the BMR after treatment being MEDE > CHOE (p < 0.05). Mediterranean diet with or without PE lost MM (p < 0.05) being MEDE > MED CONCLUSIONS: CHOE induces less reduction of BMR while supporting a better profile of BC than MEDE. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

Effects of helium/oxygen and temperature on aerobic metabolism in the marsupial sugar glider, Petaurus breviceps.

PubMed

Holloway, J C; Geiser, F

2001-01-01

Helox (79% helium and 21% oxygen) has often been used for thermobiological studies, primarily because helium is thought to be metabolically inert and to produce no adverse effects other than increasing heat loss. However, these assumptions have been questioned. As basal metabolic rate (BMR) represents maintenance energy requirements for vital body functions, potential physiological effects of helox should be reflected in changes of BMR. In this study, sugar gliders were subjected to both air and helox atmospheres over a wide range of T(a)'s, including the thermoneutral zone (TNZ), to determine (1) whether helox has any influence other than on heat loss and (2) the maximum heat production (HP(max)) and thermal limits of this species. Although thermal conductance in the TNZ increased in helox, BMR was similar in air and helox (0.55+/-0.07 and 0.57+/-0.06 mL g(-1) h(-1), respectively). The TNZ in helox, however, was shifted upwards by about 3 degrees C. Below the TNZ, sugar gliders were able to withstand an effective temperature of -24.7+/-7.3 degrees C with an HP(max) of 3.14+/-0.36 mL g(-1) h(-1). The low effective temperature tolerated by sugar gliders shows that they are competent thermoregulators despite their apparent lack of functional brown fat. Similarities of BMRs in air and helox suggest that the effect of helox is restricted to an increase of heat loss, and, consequently, helox represents a useful tool for thermal physiologists. Moreover, the lack of increase of BMR in helox despite an increase in thermal conductance of sugar gliders suggests that BMR is not a function of body surface.

A comparison of theory and flight test of the BO 105/BMR in hover and forward flight

NASA Technical Reports Server (NTRS)

Mirick, Paul H.

1988-01-01

Four cases were selected for comparison with theoretical predictions using stability data obtained during the flight test of the Bearingless Main Rotor (BMR) on a Messerschmidt-Boelkow-Blohm BO 105 helicopter. The four cases selected form the flight test included two ground resonance cases and two air resonance cases. The BMR used four modified BO 105 blades attached to a bearingless hub. The hub consisted of dual fiberglass C-channel beams attached to the hub center at 0.0238R and attached to the blade root at 0.25R with blade pitch control provided by a torque tube. Analyses from Bell Helicopter Textron, Boeing Vertol, and Sikorsky Aircraft were compared with the data and the correlation ranged from very poor-to-poor to poor-to-fair.

Intra-Seasonal Flexibility in Avian Metabolic Performance Highlights the Uncoupling of Basal Metabolic Rate and Thermogenic Capacity

PubMed Central

Petit, Magali; Lewden, Agnès; Vézina, François

2013-01-01

Stochastic winter weather events are predicted to increase in occurrence and amplitude at northern latitudes and organisms are expected to cope through phenotypic flexibility. Small avian species wintering in these environments show acclimatization where basal metabolic rate (BMR) and maximal thermogenic capacity (MSUM) are typically elevated. However, little is known on intra-seasonal variation in metabolic performance and on how population trends truly reflect individual flexibility. Here we report intra-seasonal variation in metabolic parameters measured at the population and individual levels in black-capped chickadees ( Poecile atricapillus ). Results confirmed that population patterns indeed reflect flexibility at the individual level. They showed the expected increase in BMR (6%) and MSUM (34%) in winter relative to summer but also, and most importantly, that these parameters changed differently through time. BMR began its seasonal increase in November, while MSUM had already achieved more than 20% of its inter-seasonal increase by October, and declined to its starting level by March, while MSUM remained high. Although both parameters co-vary on a yearly scale, this mismatch in the timing of variation in winter BMR and MSUM likely reflects different constraints acting on different physiological components and therefore suggests a lack of functional link between these parameters. PMID:23840843

Open-wheel race car driving: energy cost for pilots.

PubMed

Beaune, Bruno; Durand, Sylvain; Mariot, Jean-Pierre

2010-11-01

The aim of this study was to evaluate the energy cost of speedway open-wheel race car driving using actimetry. Eight pilot students participated in a training session consisting of 5 successive bouts of around 30 minutes driving at steady speed on the Bugatti speedway of Le Mans (France). Energy expenditure (EE, kcal) was determined continuously by the actimetric method using the standard equation. Energy cost was estimated through physical activity ratio (PAR = EE/BMR ratio, Mets) calculation after basal metabolism rate (BMR, kcal·min-1) estimation. A 1-met PAR value was attributed to the individual BMR of each volunteer. Bout durations and EE were not significantly different between driving bouts. Mean speed was 139.94 ± 2.96 km·h-1. Physical activity ratio values ranged 4.92 ± 0.50 to 5.43 ± 0.47 Mets, corresponding to a 5.27 ± 0.47-Mets mean PAR values and a 1.21 ± 0.41 kcal·min-1 mean BMR value. These results suggest that actimetry is a simple and efficient method for EE and PAR measurements in motor sports. However, further studies are needed in the future to accurately evaluate relationships between PAR and driving intensity or between PAR and race car type.

Polymorphisms of the FTO gene are associated with variation in energy intake, but not energy expenditure.

PubMed

Speakman, John R; Rance, Kellie A; Johnstone, Alexandra M

2008-08-01

The FTO gene has significant polymorphic variation associated with obesity, but its function is unknown. We screened a population of 150 whites (103F/47M) resident in NE Scotland, United Kingdom, for variants of the FTO gene and linked these to phenotypic variation in their energy expenditure (basal metabolic rate (BMR) and maximal oxygen consumption VO(2)max) and energy intake. There was no significant association between the FTO genotype and BMR or VO(2)max. The FTO genotype was significantly associated (P = 0.024) with variation in energy intake, with average daily intake being 9.0 MJ for the wild-type TT genotype and 10.2 and 9.5 MJ for the "at risk" AT and AA genotypes, respectively. Adjusting intake for BMR did not remove the significance (P = 0.043). FTO genotype probably affects obesity via effects on food intake rather than energy expenditure.

Solar Cycle Variability and Grand Minima Induced by Joy's Law Scatter

NASA Astrophysics Data System (ADS)

Karak, Bidya Binay; Miesch, Mark S.

2017-08-01

The strength of the solar cycle varies from one cycle to another in an irregular manner and the extreme example of this irregularity is the Maunder minimum when Sun produced only a few spots for several years. We explore the cause of these variabilities using a 3D Babcock--Leighton dynamo. In this model, based on the toroidal flux at the base of the convection zone, bipolar magnetic regions (BMRs) are produced with flux, tilt angle, and time of emergence all obtain from their observed distributions. The dynamo growth is limited by a tilt quenching.The randomnesses in the BMR emergences make the poloidal field unequal and eventually cause an unequal solar cycle. When observed fluctuations of BMR tilts around Joy's law, i.e., a standard deviation of 15 degrees, are considered, our model produces a variation in the solar cycle comparable to the observed solar cycle variability. Tilt scatter also causes occasional Maunder-like grand minima, although the observed scatter does not reproduce correct statistics of grand minima. However, when we double the tilt scatter, we find grand minima consistent with observations. Importantly, our dynamo model can operate even during grand minima with only a few BMRs, without requiring any additional alpha effect.

The effect of hybrid type and dietary proportions of corn silage on the lactation performance of high-producing dairy cows.

PubMed

Lim, J M; Nestor, K E; Kung, L

2015-02-01

We evaluated the effects of corn silage hybrids [control vs. brown midrib (BMR)] and the proportion of corn silage in rations on the performance of high-producing dairy cows. The chemical composition of the corn silages was similar except for lignin, which was higher in the control hybrid [3.09%, dry matter (DM) basis] compared with the BMR hybrid (2.19%). The 30-h in vitro neutral detergent fiber (NDF) digestibility was also higher (62.8% of NDF) in the BMR hybrid than in the control hybrid (52.2%). Twenty-seven Holstein cows were fed 1 of 3 diets comprising 62% forage and 38% concentrate (DM basis) containing 35% (DM basis) corn silage from the control hybrid (NLO), 35% of the BMR hybrid (BLO), or 50% of the BMR (BHI). Cows were fed the diets in a replicated 3×3 Latin square design with 28-d periods. Intake of DM was similar among treatments but milk production was greater for cows fed BLO (50.1kg/d) and BHI (51.1kg/d) than for NLO (47.9kg/d). Milk fat percentage was lower for cows fed BHI (3.37%) than for those fed BLO (3.55%) and NLO (3.56%) but yield of milk fat was similar among treatments. Yield and percentage of milk protein was higher for cows in BHI compared with NLO. The concentration of milk urea N was lower in cows fed BHI (14.0mg/dL) than in those fed NLO (14.7mg/dL) and intermediate for BLO (14.5mg/dL). The yield of 3.5% fat-corrected milk was higher in cows fed BLO (50.2kg/d) than in NLO (48.2kg/d) and was intermediate for BHI (49.8kg/d). The total-tract digestibility of dietary DM, organic matter, starch, and crude protein was lower for cows in NLO compared with the other treatments. The total-tract digestibility of NDF was highest for BHI (54.4%), intermediate for BLO (50.9%), and lowest for NLO (43.2%). We conclude that BMR corn silage can be included in rations at moderate and high proportions of a total ration, resulting in high levels of milk production. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Production response to corn silage produced from normal, brown midrib, or waxy corn hybrids.

PubMed

Barlow, J S; Bernard, J K; Mullis, N A

2012-08-01

The objective was to evaluate the nutrient intake and digestibility and milk production response of lactating dairy cows fed diets based on corn silage produced from 3 different types of corn hybrids. Experimental diets contained 36.4% of the dietary dry matter (DM) from corn silage produced from normal (Agratech 1021, AgraTech Seeds Inc., Atlanta, GA), brown midrib (BMR; Mycogen F2F797, Mycogen Seeds, Indianapolis, IN), or waxy (Master's Choice 590, Master's Choice Hybrids, Ullin, IL) hybrids. Thirty-six multiparous and primiparous Holstein cows (66 ± 22 d in milk, 41 ± 8 kg/d of milk) were used in an 11-wk completely randomized design trial during the fall of 2009. All cows were fed a diet containing normal corn silage during the first 2wk of the trial before being assigned to 1 of 3 treatments for the following 9 wk. Data collected during the first 2 wk were used as a covariate in the statistical analysis. No difference was observed in dry matter intake (DMI) among treatments, which averaged 22.6 kg/d. Milk yield was higher for cows fed BMR (37.6 kg/d) compared with waxy (35.2 kg/d) but was similar to that of cows fed control (36.2 kg/d). Milk fat percentage tended to be lower for cows fed control (3.28%) compared with those fed BMR (3.60%) or waxy (3.55%) corn silage. Milk protein percentage tended to be lower for cows fed control (2.79%) compared with waxy (2.89%) but similar to that of those fed BMR (2.85%). No differences were observed in yield of milk components. Energy-corrected milk (ECM) yield and dairy efficiency (ECM:DMI) did not differ among treatments. Cows fed BMR tended to gain more body weight compared with those fed control and waxy. Results of this trial are consistent with previous reports in which cows fed diets based on corn silage produced from BMR hybrids have higher milk yield compared with those fed other hybrids. Corn silage produced from the waxy hybrid supported a similar yield of ECM because of higher milk components, but milk yield was not improved compared with the control. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan

2012-02-15

The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, suchmore » as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.« less

Basal metabolic rate of endotherms can be modeled using heat-transfer principles and physiological concepts: reply to "can the basal metabolic rate of endotherms be explained by biophysical modeling?".

PubMed

Roberts, Michael F; Lightfoot, Edwin N; Porter, Warren P

2011-01-01

Our recent article (Roberts et al. 2010 ) proposes a mechanistic model for the relation between basal metabolic rate (BMR) and body mass (M) in mammals. The model is based on heat-transfer principles in the form of an equation for distributed heat generation within the body. The model can also be written in the form of the allometric equation BMR = aM(b), in which a is the coefficient of the mass term and b is the allometric exponent. The model generates two interesting results: it predicts that b takes the value 2/3, indicating that BMR is proportional to surface area in endotherms. It also provides an explanation of the physiological components that make up a, that is, respiratory heat loss, core-skin thermal conductance, and core-skin thermal gradient. Some of the ideas in our article have been questioned (Seymour and White 2011 ), and this is our response to those questions. We specifically address the following points: whether a heat-transfer model can explain the level of BMR in mammals, whether our test of the model is inadequate because it uses the same literature data that generated the values of the physiological variables, and whether geometry and empirical values combine to make a "coincidence" that makes the model only appear to conform to real processes.

Energy expenditure and intake during puberty in healthy nonobese adolescents: a systematic review.

PubMed

Cheng, Hoi Lun; Amatoury, Mazen; Steinbeck, Katharine

2016-10-01

Puberty is a time of rapid growth and changing energy requirements and is a risk period for obesity. There is little high-quality evidence on the pubertal alterations of energy expenditure and intake, and this has limited our understanding of energy balance during this important life stage. The purpose of this study was to summarize existing evidence on pubertal energy expenditure and intake in healthy nonobese adolescents. Studies were identified through CINAHL, the Cochrane Library, Embase, MEDLINE, and Web of Science databases up to August 2015. Articles presenting objectively measured data for basal or resting metabolic rate (BMR/RMR), total daily energy expenditure (TDEE), and/or energy intake (EI) for ≥2 categories of puberty were included. Relevant data adjusted for fat-free mass (FFM) also were extracted. Data were dichotomized into prepubertal and pubertal groups and compared through the use of standardized mean differences (SMDs). Heterogeneous study methodologies precluded meta-analysis. The search netted 6770 articles, with 12 included for review. From these, 6 of 9 studies supported significantly higher absolute BMR/RMR during puberty (SMD: 1.10-5.93), and all of the studies favored significantly higher absolute TDEE during puberty (SMD: 0.46-9.55). These corresponded to a 12% difference and an 18% difference in absolute BMR/RMR and TDEE, respectively. Results adjusted for FFM were equivocal, with 3 studies favoring higher (1 significantly) and 3 favoring significantly lower adjusted BMR/RMR during puberty. Only 1 study reported EI, showing 41% and 25% greater absolute intakes in pubertal males and females, respectively. These differences were not significant after adjustment for FFM. Reasonably consistent evidence exists to support higher absolute BMR/RMR and TDEE in pubertal than in prepubertal adolescents. Differences are largely accounted for by FFM, among other potential factors such as growth- and puberty-related hormones. This review argues for further research into hormonal influences on pubertal energy balance and subsequent effects on obesity risk. © 2016 American Society for Nutrition.

Energy requirements of lactating women derived from doubly labeled water and milk energy output.

PubMed

Butte, N F; Wong, W W; Hopkinson, J M

2001-01-01

Instead of using an incremental approach to assess the energy requirements of lactation, a more comprehensive approach may be taken by measuring total energy expenditure (TEE), milk energy output and energy mobilization from tissue stores. The latter approach avoids assumptions regarding energetic efficiency and changes in physical activity and adiposity. The purpose of this study was threefold: to assess the energy requirements of lactation; to compare these estimates with energy requirements in the nonpregnant, nonlactating state and to test for energetic adaptations in basal metabolic rate (BMR) and physical activity during the energy-demanding process of lactation. Milk production and composition, body weight and composition, TEE, BMR and physical activity levels were measured in 24 well-nourished women during exclusive breastfeeding at 3 mo postpartum and after the cessation of breastfeeding at 18 or 24 mo postpartum. TEE was measured by the doubly labeled water method, milk production by 3-d test-weighing, milk energy by bomb calorimetry on a 24-h milk sample, body composition by dual-energy x-ray absorptiometry and BMR by room respiration calorimetry. TEE, BMR and physical activity level (physical activity level = TEE/BMR) did not differ between the lactating and nonlactating state (TEE 10.0 +/- 1.5 versus 10.6 +/- 2.1 MJ/d). Mean milk energy output was equivalent to 2.02 +/- 0.33 MJ/d. Total energy requirements were greater during lactation than afterward (12.0 +/- 1.4 versus 10.6 +/- 2.1 MJ/d, P: = 0.002). Energy mobilization from tissue stores (-0.65 +/- 0.97 MJ/d) resulted in net energy requirements during lactation of 11.4 +/- 1.8 MJ/d. Because adaptations in basal metabolism and physical activity were not evident in these well-nourished women, energy requirements during lactation were met primarily from the diet and only partially by mobilization of tissue stores.

Cross-validation of bioelectrical impedance analysis of body composition in children and adolescents.

PubMed

Wu, Y T; Nielsen, D H; Cassady, S L; Cook, J S; Janz, K F; Hansen, J R

1993-05-01

The reliability and validity of measurements obtained with two bioelectrical impedance analyzers (BIAs), an RJL Systems model BIA-103 and a Berkeley Medical Research BMR-2000, were investigated using the manufacturers' prediction equations for the assessment of fat-free mass (FFM) (in kilograms) in children and adolescents. Forty-seven healthy children and adolescents (23 male, 24 female), ranging in age from 8 to 20 years (mean = 12.1, SD = 2.3), participated. In the context of a repeated-measures design, the data were analyzed according to gender and maturation (Tanner staging). Hydrostatic weighing (HYDRO) and Lohman's Siri age-adjusted body density prediction equation served as the criteria for validating the BIA-obtained measurements. High intraclass correlation coefficients (ICC > or = .987) demonstrated good test-retest (between-week) measurement reliability for HYDRO and both BIA methods. Between-method (HYDRO versus BIA) correlation coefficients were high for both boys and girls (r > or = .97). The standard errors of estimate (SEEs) for FFM were slightly larger for boys than for girls and were consistently smaller for the RJL system than for the BMR system (RJL SEE = 1.8 kg for boys, 1.3 kg for girls; BMR SEE = 2.4 kg for boys, 1.9 kg for girls). The coefficients of determination were high for both BIA methods (r2 > or = .929). Total prediction errors (TEs) for FFM showed similar between-method trends (RJL TE = 2.1 kg for boys, 1.5 kg for girls; BMR TE = 4.4 kg for boys, 1.9 kg for girls). This study demonstrated that the RJL BIA with the manufacturer's prediction equations can be used to reliably and accurately assess FFM in 8- to 20-year-old children and adolescents. The prediction of FFM by the BMR system was acceptable for girls, but significant overprediction of FFM for boys was noted.

Thyroid function and cold acclimation in the hamster, Mesocricetus auratus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tomasi, T.E.; Horwitz, B.A.

1987-02-01

Basal metabolic rate (BMR), thyroxine utilization rate (T4U), and triiodothyronine utilization rate (T3U) were measured in cold-acclimated (CA) and room temperature-acclimated (RA) male golden hamsters, Mesocricetus auratus. Hormone utilization rates were calculated via the plasma disappearance technique using SVI-labeled hormones and measuring serum hormone levels via radioimmunoassay. BMR showed a significant 28% increase with cold acclimation. The same cold exposure also produced a 32% increase in T4U, and a 204% increase in T3U. The much greater increase in T3U implies that previous assessments of the relationship between cold acclimation and thyroid function may have been underestimated and that cold exposuremore » induces both quantitative and qualitative changes in thyroid function. It is concluded that in the cold-acclimated state, T3U more accurately reflects thyroid function than does T4U. A mechanism for the cold-induced change in BMR is proposed.« less

Energy balance in lactating undernourished Indian women.

PubMed

Madhavapeddi, R; Rao, B S

1992-05-01

An energy balance study was conducted in eight lactating poor-income Indian women from delivery to 6 months. Energy intake and expenditure were assessed for 7 days every month (30-37 days). Every month, basal metabolic rate (BMR) and milk ingested by infants was measured. An energy balance was computed. As a group these women were in energy balance, indicated by small body weight changes with respect to time. However, only two of these women were in a positive energy balance. Women with higher body weight lost more weight. Estimated mean energy intake was higher than energy expenditure. BMR showed a slight but not significant fall during the second month of lactation and was not different from the BMR seen in 13 non-pregnant, non-lactating women matched for body weight from the staff of the Institute. The energy cost of lactation was 2.3 MJ (549 kcal), a figure that justifies the Recommended Dietary Allowance for energy recommended by FAO/WHO/UNU (1985) and ICMR (1989).

Thermal conductance and basal metabolic rate are part of a coordinated system for heat transfer regulation

PubMed Central

Naya, Daniel E.; Spangenberg, Lucía; Naya, Hugo; Bozinovic, Francisco

2013-01-01

Thermal conductance measures the ease with which heat leaves or enters  an organism's body. Although the analysis of this physiological variable in relation to climatic and ecological factors can be traced to studies by Scholander and colleagues, only small advances have occurred ever since. Here, we analyse the relationship between minimal thermal conductance estimated during summer (Cmin) and several ecological, climatic and geographical factors for 127 rodent species, in order to identify the exogenous factors that have potentially affected the evolution of thermal conductance. In addition, we evaluate whether there is compensation between Cmin and basal metabolic rate (BMR)—in such a way that a scale-invariant ratio between both variables is equal to one—as could be expected from the Scholander–Irving model of heat transfer. Our major findings are (i) annual mean temperature is the best single predictor of mass-independent Cmin. (ii) After controlling for the effect of body mass, there is a strong positive correlation between log10 (Cmin) and log10 (BMR). Further, the slope of this correlation is close to one, indicating an almost perfect compensation between both physiological variables. (iii) Structural equation modelling indicated that Cmin values are adjusted to BMR values and not the other way around. Thus, our results strongly suggest that BMR and thermal conductance integrate a coordinated system for heat regulation in endothermic animals and that summer conductance values are adjusted (in an evolutionary sense) to track changes in BMRs. PMID:23902915

Expensive Brains: "Brainy" Rodents have Higher Metabolic Rate.

PubMed

Sobrero, Raúl; May-Collado, Laura J; Agnarsson, Ingi; Hernández, Cristián E

2011-01-01

Brains are the centers of the nervous system of animals, controlling the organ systems of the body and coordinating responses to changes in the ecological and social environment. The evolution of traits that correlate with cognitive ability, such as relative brain size is thus of broad interest. Brain mass relative to body mass (BM) varies among mammals, and diverse factors have been proposed to explain this variation. A recent study provided evidence that energetics play an important role in brain evolution (Isler and van Schaik, 2006). Using composite phylogenies and data drawn from multiple sources, these authors showed that basal metabolic rate (BMR) correlates with brain mass across mammals. However, no such relationship was found within rodents. Here we re-examined the relationship between BMR and brain mass within Rodentia using a novel species-level phylogeny. Our results are sensitive to parameter evaluation; in particular how species mass is estimated. We detect no pattern when applying an approach used by previous studies, where each species BM is represented by two different numbers, one being the individual that happened to be used for BMR estimates of that species. However, this approach may compromise the analysis. When using a single value of BM for each species, whether representing a single individual, or available species mean, our findings provide evidence that brain mass (independent of BM) and BMR are correlated. These findings are thus consistent with the hypothesis that large brains evolve when the payoff for increased brain mass is greater than the energetic cost they incur.

The centrifugal and centripetal force influence on spatial competition of agricultural land in Bandung Metropolitan Region

NASA Astrophysics Data System (ADS)

Sadewo, E.

2017-06-01

Agricultural activity has suffered a massive land functional shift caused by market mechanism in Bandung metropolitan region (BMR). We argue that the existence of agricultural land in urban spatial structure is the result of interaction between centrifugal and centripetal force on spatial competition. This research aims to explore how several recognized centrifugal and centripetal force influence to the existence of agricultural land in BMR land development. The analysis using multivariate regression indicates that there exists spatial competition between population density and degree of urbanization with agricultural land areas. Its extended spatial regression model suggested that neighboring situation plays an important role to preserve agricultural land areas existences in BMR. Meanwhile, the influence of distance between the location of the city center and employment opportunities is found to be insignificant in the spatial competition. It is opposed to the theory of von Thünen and monocentric model in general. One of the possible explanation of such condition is that the assumption of centrality does not met. In addition, the agricultural land density decay in the southern parts of the area was related to its geographical conditions as protected areas or unfavorable for farming activity. It is suggested that BMR was in the early phase of polycentric development. Hence, better policies that lead redirected development to the southern part of the region is needed as well as population control and regulation of land use.

Thermal conductance and basal metabolic rate are part of a coordinated system for heat transfer regulation.

PubMed

Naya, Daniel E; Spangenberg, Lucía; Naya, Hugo; Bozinovic, Francisco

2013-09-22

Thermal conductance measures the ease with which heat leaves or enters an organism's body. Although the analysis of this physiological variable in relation to climatic and ecological factors can be traced to studies by Scholander and colleagues, only small advances have occurred ever since. Here, we analyse the relationship between minimal thermal conductance estimated during summer (Cmin) and several ecological, climatic and geographical factors for 127 rodent species, in order to identify the exogenous factors that have potentially affected the evolution of thermal conductance. In addition, we evaluate whether there is compensation between Cmin and basal metabolic rate (BMR)-in such a way that a scale-invariant ratio between both variables is equal to one-as could be expected from the Scholander-Irving model of heat transfer. Our major findings are (i) annual mean temperature is the best single predictor of mass-independent Cmin. (ii) After controlling for the effect of body mass, there is a strong positive correlation between log10 (Cmin) and log10 (BMR). Further, the slope of this correlation is close to one, indicating an almost perfect compensation between both physiological variables. (iii) Structural equation modelling indicated that Cmin values are adjusted to BMR values and not the other way around. Thus, our results strongly suggest that BMR and thermal conductance integrate a coordinated system for heat regulation in endothermic animals and that summer conductance values are adjusted (in an evolutionary sense) to track changes in BMRs.

Etude du comportement sous charges laterales des ossatures de beton arme avec murs de remplissage de maconnerie, construites avant les annees 1960

NASA Astrophysics Data System (ADS)

Lefebvre, Karine

Reinforced concrete structures with unreinforced masonry infills (BMR) are considered vulnerable to earthquakes. Under seismic actions, infills could fail (causing injuries or death) and cause damages to columns. In Quebec and Canada, most of BMR structures have been constructed prior to the introduction of modern seismic design codes raising question on the contribution of the infill to the structure lateral resistance. The aim of this thesis is to improve modelling technique of BMR structures built in Quebec between 1915 and 1960. This type of structures is found in hospitals or schools buildings, which must comply with some post-earthquake functionality requirements. They could also be residential or office buildings. Actually, practicing engineers usually calculate seismic capacity of BMR structures without considering the infill's structural contribution to the lateral resistance. Yet, this contribution should not be omitted. The first part of the thesis investigates the construction techniques and material properties of the old BMR structures in the Province. The results are the material properties (concrete, reinforcing steel, brick, terra cotta tile, and mortar) and the characteristics of the assemblies (wall section, reinforcement details…). The second part of the thesis presents the results of series of parametric analyses to identify among modelling and geometric parameters, which ones are the most influent on the lateral load response (rigidity, fundamental period, normal modes). Linear and modal analyses were performed. The most influent parameters identified are: number of storeys, number of bays, bay's width, soft storey, openings, upper storeys modelized (instead of being replaced by punctual loads) and the modelization technique of infills panels (strut or shell). Nonlinear static analyses have been performed to identify the most influent parameters to be considered for evaluating the lateral resistance, the capacity (load / displacement) and the yielding sequence (beam versus columns versus infills). The identified parameters are the presence of the infills, the openings and the geometric characteristics of the models (number of storeys and number of bays). One important contribution of this work is the development of an equivalent strut model to represent the action of the infill. The model could be easily implemented in standard analysis software. A central axial hinge reproducing the nonlinear behaviour of the masonry is added to the strut element. This model is a hybridization of existing proposals (FEMA and others) with added innovations by the author. It has been validated with experimental and numerical analyses results from literature. An important conclusion of this thesis is that the contribution of infills to lateral load resisting capacities of BMR structures should be considered for structure of more than one storey. Infills can add up to 51 % to bare frame capacity. The National building code requires that the lateral resistance of existing buildings must be at least 60 % of the equivalent static seismic force (V2005). It is concluded that one storey BMR buildings have a sufficient resistance, while three-storeys structures exhibit plastic deformations for loads under 0,6* V2005.

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries.

PubMed

Godin, Bruno; Nagle, Nick; Sattler, Scott; Agneessens, Richard; Delcarte, Jérôme; Wolfrum, Edward

2016-01-01

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In this work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib ( bmr ) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

DOE PAGES

Godin, Bruno; Nagle, Nick; Sattler, Scott; ...

2016-11-21

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

Improved sugar yields from biomass sorghum feedstocks: comparing low-lignin mutants and pretreatment chemistries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godin, Bruno; Nagle, Nick; Sattler, Scott

For biofuel production processes to be economically efficient, it is essential to maximize the production of monomeric carbohydrates from the structural carbohydrates of feedstocks. One strategy for maximizing carbohydrate production is to identify less recalcitrant feedstock cultivars by performing some type of experimental screening on a large and diverse set of candidate materials, or by identifying genetic modifications (random or directed mutations or transgenic plants) that provide decreased recalcitrance. Economic efficiency can also be increased using additional pretreatment processes such as deacetylation, which uses dilute NaOH to remove the acetyl groups of hemicellulose prior to dilute acid pretreatment. In thismore » work, we used a laboratory-scale screening tool that mimics relevant thermochemical pretreatment conditions to compare the total sugar yield of three near-isogenic brown midrib (bmr) mutant lines and the wild-type (WT) sorghum cultivar. We then compared results obtained from the laboratory-scale screening pretreatment assay to a large-scale pretreatment system. After pretreatment and enzymatic hydrolysis, the bmr mutants had higher total sugar yields than the WT sorghum cultivar. Increased pretreatment temperatures increased reactivity for all sorghum samples reducing the differences observed at lower reaction temperatures. Deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples, and reduced the differences in total sugar yields among them, but solubilized a sizable fraction of the non-structural carbohydrates. The general trends of increased total sugar yield in the bmr mutant compared to the WT seen at the laboratory scale were observed at the large-scale system. However, in the larger reactor system, the measured total sugar yields were lower and the difference in total sugar yield between the WT and bmr sorghum was larger. Sorghum bmr mutants, which have a reduced lignin content showed higher total sugar yields than the WT cultivar after dilute acid pretreatment and enzymatic hydrolysis. In conclusion, deacetylation prior to dilute acid pretreatment increased the total sugar yield for all four sorghum samples. However, since deacetylation also solubilizes a large fraction of the non-structural carbohydrates, the ability to derive value from these solubilized sugars will depend greatly on the proposed conversion process.« less

Is Maximum Food Intake in Endotherms Constrained by Net or Factorial Aerobic Scope? Lessons from the Leaf-Eared Mouse.

PubMed

Maldonado, Karin; Sabat, Pablo; Piriz, Gabriela; Bogdanovich, José M; Nespolo, Roberto F; Bozinovic, Francisco

2016-01-01

Food availability varies substantially throughout animals' lifespans, thus the ability to profit from high food levels may directly influence animal fitness. Studies exploring the link between basal metabolic rate (BMR), growth, reproduction, and other fitness traits have shown varying relationships in terms of both magnitude and direction. The diversity of results has led to the hypothesis that these relationships are modulated by environmental conditions (e.g., food availability), suggesting that the fitness consequences of a given BMR may be context-dependent. In turn, there is indirect evidence that individuals with an increased capacity for aerobic work also have a high capacity for acquiring energy from food. Surprisingly, very few studies have explored the correlation between maximum rates of energy acquisition and BMR in endotherms, and to the best of our knowledge, none have attempted to elucidate relationships between the former and aerobic capacity [e.g., maximum metabolic rate (MMR), aerobic scope (Factorial aerobic scope, FAS; Net aerobic scope, NAS)]. In this study, we measured BMR, MMR, maximum food intake (recorded under low ambient temperature and ad libitum food conditions; MFI), and estimated aerobic scope in the leaf-eared mouse ( Phyllotis darwini ). We, then, examined correlations among these variables to determine whether metabolic rates and aerobic scope are functionally correlated, and whether an increased aerobic capacity is related to a higher MFI. We found that aerobic capacity measured as NAS is positively correlated with MFI in endotherms, but with neither FAS nor BMR. Therefore, it appears plausible that the capacity for assimilating energy under conditions of abundant resources is determined adaptively by NAS, as animals with higher NAS would be promoted by selection. In theory, FAS is an invariant measurement of the extreme capacity for energy turnover in relation to resting expenditure, whereas NAS represents the maximum capacity for simultaneous aerobic processes above maintenance levels. Accordingly, in our study, FAS and NAS represent different biological variables; FAS, in contrast to NAS, may not constrain food intake. The explanations for these differences are discussed in biological and mathematical terms; further, we encourage the use of NAS rather than FAS when analyzing the aerobic capacity of animals.

Polymorphism of the beta3-adrenergic receptor gene affects basal metabolic rate in obese Finns.

PubMed

Sipiläinen, R; Uusitupa, M; Heikkinen, S; Rissanen, A; Laakso, M

1997-01-01

Low basal metabolic rate (BMR) is a risk factor for weight gain and obesity. The polymorphism at codon 64 of the beta3-adrenergic receptor gene has been suggested to be associated with BMR. We investigated the frequency of the Trp64Arg of the beta3-adrenergic receptor gene and the effects of this polymorphism on BMR in obese Finns. Altogether, 170 obese subjects (29 men, 141 women, BMI 34.7 +/- 3.8 kg/m2, mean +/- SD) participated in the study. The frequency of the Trp64Arg polymorphism was 19%. None of the obese subjects were homozygous for the Arg-encoding allele. The frequency of the Trp64Arg polymorphism in obese Finns did not differ from nonobese and normoglycemic control subjects. BMR adjusted for lean body mass and age was lower in subjects with the Trp64Arg polymorphism (n = 20) than in normal homozygotes Trp64Trp (n = 99) (1,569 +/- 73 vs. 1,635 +/- 142 kcal/day, P = 0.004). For the female group (n = 98), the respective values were 1,501 +/- 66 kcal/day vs. 1,568 +/- 127 kcal/day (P = 0.004). There were no significant differences in weight, BMI, waist-to-hip ratio, lean body mass, percentage of fat, and respiratory quotient between the groups with or without the Trp64Arg polymorphism. Neither serum glucose nor insulin levels differed between the two groups. We conclude that the Trp64Arg polymorphism of the beta3-adrenergic receptor gene affects basal metabolic rate in obese Finns but does not have significant effect on glucose metabolism.

Brown midrib corn silage and Tifton 85 bermudagrass in rations for early-lactation cows.

PubMed

Castro, J J; Bernard, J K; Mullis, N A; Eggleston, R B

2010-05-01

Forty Holstein cows were used in an 8-wk randomized trial to evaluate the effects of feeding combinations of forages with improved fiber digestibility on performance during early lactation. Treatments were arranged as a 2 x 2 factorial to include silage from normal (NCS) or brown midrib (BMR) corn silage with or without 10% Tifton 85 bermudagrass hay (T85). In a simultaneous digestion trial, degradation and passage kinetics and ruminal fermentation parameters were evaluated in a 4 x 4 Latin square design trial using late-lactation Holstein cows fitted with ruminal cannulas. Dry matter intake (DMI) and neutral detergent fiber (NDF) intake were greater with BMR than with NCS; however, milk yield and composition were similar among corn silage types. Inclusion of T85 reduced milk yield but supported higher milk fat percentage, resulting in similar yields of energy-corrected milk. Blood glucose concentrations were higher for BMR compared with NCS, and inclusion of T85 increased blood urea N concentrations. Treatments did not alter liquid or solid phase passage rates or rumen turnover. Corn silage type did not affect ruminal pH or volatile fatty acid concentrations, but inclusion of T85 increased pH and molar proportion of acetate but decreased butyrate. Molar proportions of propionate were greater for NCS and T85 compared with BMR and T85, resulting in an interaction. Results of this trial indicate that combinations of forages with improved fiber digestibility can be used to support intake and performance of cows during early lactation. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

A Coupled 2 × 2D Babcock-Leighton Solar Dynamo Model. II. Reference Dynamo Solutions

NASA Astrophysics Data System (ADS)

Lemerle, Alexandre; Charbonneau, Paul

2017-01-01

In this paper we complete the presentation of a new hybrid 2 × 2D flux transport dynamo (FTD) model of the solar cycle based on the Babcock-Leighton mechanism of poloidal magnetic field regeneration via the surface decay of bipolar magnetic regions (BMRs). This hybrid model is constructed by allowing the surface flux transport (SFT) simulation described in Lemerle et al. to provide the poloidal source term to an axisymmetric FTD simulation defined in a meridional plane, which in turn generates the BMRs required by the SFT. A key aspect of this coupling is the definition of an emergence function describing the probability of BMR emergence as a function of the spatial distribution of the internal axisymmetric magnetic field. We use a genetic algorithm to calibrate this function, together with other model parameters, against observed cycle 21 emergence data. We present a reference dynamo solution reproducing many solar cycle characteristics, including good hemispheric coupling, phase relationship between the surface dipole and the BMR-generating internal field, and correlation between dipole strength at cycle maximum and peak amplitude of the next cycle. The saturation of the cycle amplitude takes place through the quenching of the BMR tilt as a function of the internal field. The observed statistical scatter about the mean BMR tilt, built into the model, acts as a source of stochasticity which dominates amplitude fluctuations. The model thus can produce Dalton-like epochs of strongly suppressed cycle amplitude lasting a few cycles and can even shut off entirely following an unfavorable sequence of emergence events.

Seasonal Metabolic Acclimatization Varies in Direction and Magnitude among Populations of an Afrotropical Passerine Bird.

PubMed

Noakes, Matthew J; Wolf, Blair O; McKechnie, Andrew E

Avian metabolic responses demonstrate considerable diversity under fluctuating environmental conditions, a well-studied example being the seasonal upregulation of basal metabolic rate (BMR) and summit metabolism (M sum ) in temperate species experiencing harsh winters. Fewer studies have examined seasonal metabolic acclimatization in subtropical or tropical species. We investigated seasonal metabolic variation in an Afrotropical ploceid passerine, the white-browed sparrow-weaver (Plocepasser mahali; ∼47 g), at three sites along a climatic gradient of approximately 7°C in winter minimum air temperature (T a ). We measured M sum (n ≥ 10 per site per season) in a helox atmosphere, BMR of the same birds at thermoneutrality (T a ≈ 30°C), and resting metabolic rates at 5°C ≤ T a ≤ 20°C. Patterns of seasonal adjustments in BMR varied among populations in a manner not solely related to variation in seasonal T a extremes, ranging from BMR ∼52% higher in winter than in summer to no seasonal difference. Greater cold tolerance was found in a population at a colder desert site, manifested as higher M sum (∼25% higher) and lower helox temperature at cold limit values compared with a milder, mesic site. Our results lend support to the idea that greater variance in the pattern of seasonal metabolic responses occurs in subtropical and tropical species compared with their temperate-zone counterparts and that factors other than T a extremes (e.g., food availability) may be important in determining the magnitude and direction of seasonal metabolic adjustments in subtropical birds.

Effects of dietary quality on basal metabolic rate and internal morphology of European starlings (Sturnus vulgaris)

USGS Publications Warehouse

Geluso, Keith; Hayes, J.P.

1999-01-01

European starlings (Sturnus vulgaris) were fed either a low- or high-quality diet to test the effects of dietary quality on basal metabolic rate (BMR) and internal morphology. Basal metabolic rate did not differ significantly between the two dietary groups, but internal morphology differed greatly. Starlings fed the low-quality diet had heavier gastrointestinal tracts, gizzards, and livers. Starlings fed the high-quality diet had heavier breast muscles. Starlings on the low-quality diet maintained mass, while starlings on the high-quality diet gained mass. Dry matter digestibility and energy digestibility were lower for starlings fed the low-quality diet, and their food and water intake were greater than starlings on the high-quality diet. The lack of dietary effect on BMR may be the result of increased energy expenditure of digestive organs paralleling a reduction of energy expenditure of organs and tissues not related to digestion (i.e., skeletal muscle). This trade-off in energy allocation among organs suggests a mechanism by which organisms may alter BMR in response to a change in seasonal variation in food availability.

Metabolic rate and evaporative water loss in the silky starling (Sturnus sericeus)

PubMed Central

Huan-Huan, BAO; Qing-Jian, LIANG; Hong-Lei, ZHU; Xiao-Qiu, ZHOU; Wei-Hong, ZHENG; Jin-Song, LIU

2014-01-01

To better understand the physiological characteristics of the silky starling (Sturnus sericeus), its body temperature (Tb), basal metabolic rate (BMR), evaporative water loss (EWL) and thermal conductance (C) elicited by different ambient temperatures (Ta) (5−30 ℃) were determined in the present study. Our results showed that they have a high Tb (41.6±0.1 ℃), a wide thermal neutral zone (TNZ) (20−27.5 ℃) and a relatively low BMR within the TNZ (3.37±0.17 mL O2/g·h). The EWL was nearly stable below the TNZ (0.91±0.07 mg H2O/g·h) but increased remarkably within and above the TNZ. The C was constant below the TNZ, with a minimum value of 0.14±0.01 mL O2/g·h·℃. These findings indicate that the BMR, Tb and EWL of the silky starling were all affected by Ta, especially when Ta was below 20 ℃ and the EWL plays an important role in thermal regulation. PMID:25017746

Relationship between delayed embryonic development and metabolic factors and fat deposition in fruit bat Cynopterus sphinx.

PubMed

Banerjee, Arnab; Meenakumari, K J; Krishna, Amitabh

2007-01-01

The present study was undertaken in the fruit bat Cynopterus sphinx, which breeds twice in quick succession at Varanasi, India. Its gestation period varies significantly in the two successive pregnancies of the year owing to delayed embryonic development during the first (winter) pregnancy. The primary aim of the present study was to determine the role of metabolic factors in delayed embryonic development in the fruit bat C. sphinx. Variation in bodyweight, fat deposition, oxygen (O(2)) consumption rate, basal metabolic rate (BMR), body temperature (Tb) and hepatic succinate dehydrogenase (SDH) activity, along with circulating levels of thyroid hormones (tri-iodothyronine and thyroxine), were examined as metabolic factors during the two successive pregnancies in C. sphinx. The increase in bodyweight observed in November was due to accumulation of white adipose tissue in the posterior abdominal region. A significant decline in O(2) consumption rate, BMR, Tb and SDH activity was found in early winter in November-December, which coincides closely with the period of fat accumulation and with the period of delayed embryonic development in C. sphinx. A significantly higher O(2) consumption rate, BMR, Tb and SDH activity was noted during the second pregnancy in, when embryonic development was relatively faster. Thyroid hormone levels were high during the period of embryonic delay compared with levels during the remaining months. The results of the present study suggest that the delayed embryonic development in C. sphinx during early winter may be due to a low O(2) consumption rate, BMR, Tb and SDH activity in November-December. The energy saved by suppressing embryonic development in this species may be advantageous for fat accumulation. Increased thyroid hormone levels during the early winter period might facilitate fat accumulation in C. sphinx.

Changes in Energy Metabolism after Continuous Positive Airway Pressure for Obstructive Sleep Apnea.

PubMed

Tachikawa, Ryo; Ikeda, Kaori; Minami, Takuma; Matsumoto, Takeshi; Hamada, Satoshi; Murase, Kimihiko; Tanizawa, Kiminobu; Inouchi, Morito; Oga, Toru; Akamizu, Takashi; Mishima, Michiaki; Chin, Kazuo

2016-09-15

Disrupted energy homeostasis in obstructive sleep apnea (OSA) may lead to weight gain. Paradoxically, treating OSA with continuous positive airway pressure (CPAP) may also promote weight gain, although the underlying mechanism remains unclear. To explore the underlying mechanism by which patients with OSA gain weight after CPAP. A comprehensive assessment of energy metabolism was performed in 63 newly diagnosed OSA study participants (51 men; 60.8 ± 10.1 yr; apnea-hypopnea index >20 h(-1)) at baseline, CPAP initiation, and at a 3-month follow-up. Measurements included polysomnography, body weight, body composition, basal metabolic rate (BMR), hormones (norepinephrine, cortisol, leptin, ghrelin, insulin-like growth factor-1), dietary intake, eating behavior, and physical activity. BMR significantly decreased after CPAP (1,584 kcal/d at baseline, 1,561 kcal/d at CPAP initiation, and 1,508 kcal/d at follow-up; P < 0.001), whereas physical activity and total caloric intake did not significantly change. In multivariate regression, baseline apnea-hypopnea index, Δurine norepinephrine, and CPAP adherence were significant predictors of ΔBMR. The weight gainers had higher leptin levels, lower ghrelin levels, and higher eating behavior scores than the non-weight gainers, indicating a positive energy balance and disordered eating behavior among the weight gainers. Among the parameters related to energy metabolism, increased caloric intake was a particularly significant predictor of weight gain. Although a reduction in BMR after CPAP predisposes to a positive energy balance, dietary intake and eating behavior had greater impacts on weight change. These findings highlight the importance of lifestyle modifications combined with CPAP. Clinical trial registered with http://www.umin.ac.jp/english/ (UMIN000012639).

Functional characterisation of an engineered multidomain human P450 2E1 by molecular Lego.

PubMed

Fairhead, Michael; Giannini, Silva; Gillam, Elizabeth M J; Gilardi, Gianfranco

2005-12-01

The human cytochrome P450s constitute an important family of monooxygenase enzymes that carry out essential roles in the metabolism of endogenous compounds and foreign chemicals. We present here results of a fusion between a human P450 enzyme and a bacterial reductase that for the first time is shown does not require the addition of lipids or detergents to achieve wild-type-like activities. The fusion enzyme, P450 2E1-BMR, contains the N-terminally modified residues 22-493 of the human P450 2E1 fused at the C-terminus to residues 473-1049 of the P450 BM3 reductase (BMR). The P450 2E1-BMR enzyme is active, self-sufficient and presents the typical marker activities of the native human P450 2E1: the hydroxylation of p-nitrophenol (KM=1.84+/-0.09 mM and kcat of 2.98+/-0.04 nmol of p-nitrocatechol formed per minute per nanomole of P450) and chlorzoxazone (KM=0.65+/-0.08 mM and kcat of 0.95+/-0.10 nmol of 6-hydroxychlorzoxazone formed per minute per nanomole of P450). A 3D model of human P450 2E1 was generated to rationalise the functional data and to allow an analysis of the surface potentials. The distribution of charges on the model of P450 2E1 compared with that of the FMN domain of BMR provides the ground for the understanding of the interaction between the fused domains. The results point the way to successfully engineer a variety of catalytically self-sufficient human P450 enzymes for drug metabolism studies in solution.

A COUPLED 2 × 2D BABCOCK–LEIGHTON SOLAR DYNAMO MODEL. II. REFERENCE DYNAMO SOLUTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemerle, Alexandre; Charbonneau, Paul, E-mail: lemerle@astro.umontreal.ca, E-mail: paulchar@astro.umontreal.ca

In this paper we complete the presentation of a new hybrid 2 × 2D flux transport dynamo (FTD) model of the solar cycle based on the Babcock–Leighton mechanism of poloidal magnetic field regeneration via the surface decay of bipolar magnetic regions (BMRs). This hybrid model is constructed by allowing the surface flux transport (SFT) simulation described in Lemerle et al. to provide the poloidal source term to an axisymmetric FTD simulation defined in a meridional plane, which in turn generates the BMRs required by the SFT. A key aspect of this coupling is the definition of an emergence function describing the probabilitymore » of BMR emergence as a function of the spatial distribution of the internal axisymmetric magnetic field. We use a genetic algorithm to calibrate this function, together with other model parameters, against observed cycle 21 emergence data. We present a reference dynamo solution reproducing many solar cycle characteristics, including good hemispheric coupling, phase relationship between the surface dipole and the BMR-generating internal field, and correlation between dipole strength at cycle maximum and peak amplitude of the next cycle. The saturation of the cycle amplitude takes place through the quenching of the BMR tilt as a function of the internal field. The observed statistical scatter about the mean BMR tilt, built into the model, acts as a source of stochasticity which dominates amplitude fluctuations. The model thus can produce Dalton-like epochs of strongly suppressed cycle amplitude lasting a few cycles and can even shut off entirely following an unfavorable sequence of emergence events.« less

Contaminants and energy expenditure in an Arctic seabird: Organochlorine pesticides and perfluoroalkyl substances are associated with metabolic rate in a contrasted manner.

PubMed

Blévin, Pierre; Tartu, Sabrina; Ellis, Hugh I; Chastel, Olivier; Bustamante, Paco; Parenteau, Charline; Herzke, Dorte; Angelier, Frédéric; Gabrielsen, Geir W

2017-08-01

Basal metabolic rate (BMR), the minimal energetic cost of living in endotherms, is known to be influenced by thyroid hormones (THs) which are known to stimulate in vitro oxygen consumption of tissues in birds and mammals. Several environmental contaminants may act on energy expenditure through their thyroid hormone-disrupting properties. However, the effect of contaminants on BMR is still poorly documented for wildlife. Here, we investigated the relationships between three groups of contaminants (organochlorines (OCs), perfluoroalkyl substances (PFASs), and mercury) with metabolic rate (MR), considered here as a proxy of BMR and also with circulating total THs (thyroxine (TT4) and triiodothyronine (TT3)) in Arctic breeding adult black-legged kittiwakes (Rissa tridactyla) from Svalbard, during the chick rearing period. Our results indicate a negative relationship between the sum of all detected chlordanes (∑CHLs) and MR in both sexes whereas perfluorotridecanoate (PFTrA) and MR were positively related in females only. MR was not associated with mercury. Additionally, levels of TT3 were negatively related to ∑CHLs but not to PFTrA. The findings from the present study indicate that some OCs (in both sexes) and some PFASs (only in females) could disrupt fine adjustment of BMR during reproduction in adult kittiwakes. Importantly, highly lipophilic OCs and highly proteinophilic PFASs appear, at least in females, to have the ability to disrupt the metabolic rate in an opposite way. Therefore, our study highlights the need for ecotoxicological studies to include a large variety of contaminants which can act in an antagonistic manner. Copyright © 2017 Elsevier Inc. All rights reserved.

Somatotype and body composition analysis of Korean youth soccer players according to playing position for sports physiotherapy research

PubMed Central

Noh, Ji-Woong; Kim, Mee-Young; Lee, Lim-Kyu; Park, Byoung-Sun; Yang, Seung-Min; Jeon, Hye-Joo; Lee, Won-Deok; Kim, Ju-Hyun; Lee, Jeong-Uk; Kwak, Taek-Yong; Lee, Tae-Hyun; Kim, Ju-Young; Kim, Junghwan

2015-01-01

[Purpose] The purpose of this study was to investigate the somatotype and physical characteristic differences among elite youth soccer players. [Subjects and Methods] In the present study, we evaluated twenty-two Korean youth soccer players in different playing positions. The playing positions were divided into forward (FW), midfielder (MF), defender (DF), and goalkeeper (GK). The participants’ lean body mass (LBM), fat free mass (FFM), fat mass (FM), and basal metabolic rate (BMR) were measured and their somatotype determined according to the Heath-Carter method. [Results] The youth soccer players had twelve ectomorphic, eight mesomorphic, and two central predominant types. The DFs were taller than, but otherwise similar in physical characteristics to the FWs and MFs. The GKs were taller and heavier than the other players; however, their somatotype components were not significantly different. LBM, FFM, and BMR were significantly higher in GKs than in FWs and MFs. Although LBM, FFM, and BMR values between GKs and DFs showed large differences, they were not statistically significant. [Conclusion] The present study may contribute to our understanding of the differences in somatotype and body composition of Korean youth soccer players involved in sports physiotherapy research. PMID:25995545

Somatotype and body composition analysis of Korean youth soccer players according to playing position for sports physiotherapy research.

PubMed

Noh, Ji-Woong; Kim, Mee-Young; Lee, Lim-Kyu; Park, Byoung-Sun; Yang, Seung-Min; Jeon, Hye-Joo; Lee, Won-Deok; Kim, Ju-Hyun; Lee, Jeong-Uk; Kwak, Taek-Yong; Lee, Tae-Hyun; Kim, Ju-Young; Kim, Junghwan

2015-04-01

[Purpose] The purpose of this study was to investigate the somatotype and physical characteristic differences among elite youth soccer players. [Subjects and Methods] In the present study, we evaluated twenty-two Korean youth soccer players in different playing positions. The playing positions were divided into forward (FW), midfielder (MF), defender (DF), and goalkeeper (GK). The participants' lean body mass (LBM), fat free mass (FFM), fat mass (FM), and basal metabolic rate (BMR) were measured and their somatotype determined according to the Heath-Carter method. [Results] The youth soccer players had twelve ectomorphic, eight mesomorphic, and two central predominant types. The DFs were taller than, but otherwise similar in physical characteristics to the FWs and MFs. The GKs were taller and heavier than the other players; however, their somatotype components were not significantly different. LBM, FFM, and BMR were significantly higher in GKs than in FWs and MFs. Although LBM, FFM, and BMR values between GKs and DFs showed large differences, they were not statistically significant. [Conclusion] The present study may contribute to our understanding of the differences in somatotype and body composition of Korean youth soccer players involved in sports physiotherapy research.

Short photoperiod increases energy intake, metabolic thermogenesis and organ mass in silky starlings Sturnus sericeus

PubMed Central

WANG, Jia-Qi; WANG, Jia-Jia; WU, Xu-Jian; ZHENG, Wei-Hong; LIU, Jin-Song

2016-01-01

Environmental cues play important roles in the regulation of an animal’s physiology and behavior. One such cue, photoperiod, plays an important role in the seasonal acclimatization of birds. It has been demonstrated that an animal’s body mass, basal metabolic rate (BMR), and energy intake, are all affected by photoperiod. The present study was designed to examine photoperiod induced changes in the body mass, metabolism and metabolic organs of the silky starling, Sturnus sericeus. Captive silky starlings increased their body mass and BMR during four weeks of acclimation to a short photoperiod. Birds acclimated to a short photoperiod also increased the mass of certain organs (liver, gizzard and small intestine), and both gross energy intake (GEI) and digestible energy intake (DEI), relative to those acclimated to a long photoperiod. Furthermore, BMR was positively correlated with body mass, liver mass, GEI and DEI. These results suggest that silky starlings increase metabolic thermogenesis when exposed to a short photoperiod by increasing their body and metabolic organ mass, and their GEI and DEI. These findings support the hypothesis that bird species from temperate climates typically display high phenotypic flexibility in thermogenic capacity. PMID:27029864

Basal metabolic rate and work energy expenditure of mature, pregnant women.

PubMed

Blackburn, M W; Calloway, D H

1976-07-01

Resting and working metabolic rates and physical fitness of twenty-one mature women were studied at various intervals during the last half of pregnance and in sixteen of them again eight to twelve weeks postpartum. Basal rate (BMR) was increased more than body weight during pregnancy, and there was a small drop in BMR per unit body mass near term. Data on lean body mass (40K) suggest that the small terminal fall in BMR is not explained by a shift in body composition toward increased fat or water. The increase in energy cost of work paralleled the gain in body weight during preganacy. Net energetic efficiency thus appeared to be higher for work performed during pregnancy, if recovery rates are assumed to be uniform. However, according to their heart rate reponses to fixed hard work, the women were less fit during pregnancy than they were postpartum, with the level of fitness decreasing as pregnancy advanced. The prolonged rate of recovery suggests that oxygen uptake may be increased for a longer period after work in the pregnant woman. If this is true, energy expenditure will be seriously underestimated by the application of energy cost figures obtained in the conventional manner.

Reaction Norms in Natural Conditions: How Does Metabolic Performance Respond to Weather Variations in a Small Endotherm Facing Cold Environments?

PubMed Central

Petit, Magali; Vézina, François

2014-01-01

Reaction norms reflect an organisms' capacity to adjust its phenotype to the environment and allows for identifying trait values associated with physiological limits. However, reaction norms of physiological parameters are mostly unknown for endotherms living in natural conditions. Black-capped chickadees (Poecile atricapillus) increase their metabolic performance during winter acclimatization and are thus good model to measure reaction norms in the wild. We repeatedly measured basal (BMR) and summit (Msum) metabolism in chickadees to characterize, for the first time in a free-living endotherm, reaction norms of these parameters across the natural range of weather variation. BMR varied between individuals and was weakly and negatively related to minimal temperature. Msum varied with minimal temperature following a Z-shape curve, increasing linearly between 24°C and −10°C, and changed with absolute humidity following a U-shape relationship. These results suggest that thermal exchanges with the environment have minimal effects on maintenance costs, which may be individual-dependent, while thermogenic capacity is responding to body heat loss. Our results suggest also that BMR and Msum respond to different and likely independent constraints. PMID:25426860

Characterization and cross calibration of Agfa D4, D7, and D8 and Kodak SR45 x-ray films against direct exposure film at 4.0-5.5 keV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lanier, N.E.; Cowan, J.S.; Workman, J.

2006-04-15

Kodak direct exposure film (DEF) [B. L. Henke et al., J. Opt. Soc. Am. B 3, 1540 (1986)] has been the standard for moderate energy (1-10 keV) x-ray diagnostic applications among the high-energy-density and inertial confinement fusion research communities. However, market forces have prompted Kodak to discontinue production of DEF, leaving these specialized communities searching for a replacement. We have conducted cross-calibration experiments and film characterizations on five possible substitutes for Kodak DEF. The film types studied were Kodak's Biomax MR (BMR) and SR45 along with Agfa's D8, D7, and D4sc. None of the films tested matched the speed ofmore » DEF. BMR and D8 were closest but D8 exhibited lower noise, with superior resolution and dynamic range. Agfa D7, Agfa D4sc, and Kodak SR45 were significantly less sensitive than BMR and D8, however, the improvements they yielded in resolution and dynamic range warrant their use if experimental constraints allow.« less

A Macrophysiological Analysis of Energetic Constraints on Geographic Range Size in Mammals

PubMed Central

Ceballos, Gerardo; Steele, Michael A.

2013-01-01

Physiological processes are essential for understanding the distribution and abundance of organisms, and recently, with widespread attention to climate change, physiology has been ushered back to the forefront of ecological thinking. We present a macrophysiological analysis of the energetics of geographic range size using combined data on body size, basal metabolic rate (BMR), phylogeny and range properties for 574 species of mammals. We propose three mechanisms by which interspecific variation in BMR should relate positively to geographic range size: (i) Thermal Plasticity Hypothesis, (ii) Activity Levels/Dispersal Hypothesis, and (iii) Energy Constraint Hypothesis. Although each mechanism predicts a positive correlation between BMR and range size, they can be further distinguished based on the shape of the relationship they predict. We found evidence for the predicted positive relationship in two dimensions of energetics: (i) the absolute, mass-dependent dimension (BMR) and (ii) the relative, mass-independent dimension (MIBMR). The shapes of both relationships were similar and most consistent with that expected from the Energy Constraint Hypothesis, which was proposed previously to explain the classic macroecological relationship between range size and body size in mammals and birds. The fact that this pattern holds in the MIBMR dimension indicates that species with supra-allometric metabolic rates require among the largest ranges, above and beyond the increasing energy demands that accrue as an allometric consequence of large body size. The relationship is most evident at high latitudes north of the Tropics, where large ranges and elevated MIBMR are most common. Our results suggest that species that are most vulnerable to extinction from range size reductions are both large-bodied and have elevated MIBMR, but also, that smaller species with elevated MIBMR are at heightened risk. We also provide insights into the global latitudinal trends in range size and MIBMR and more general issues of phylogenetic and geographic scale. PMID:24058444

The quantitative genetics of maximal and basal rates of oxygen consumption in mice.

PubMed Central

Dohm, M R; Hayes, J P; Garland, T

2001-01-01

A positive genetic correlation between basal metabolic rate (BMR) and maximal (VO(2)max) rate of oxygen consumption is a key assumption of the aerobic capacity model for the evolution of endothermy. We estimated the genetic (V(A), additive, and V(D), dominance), prenatal (V(N)), and postnatal common environmental (V(C)) contributions to individual differences in metabolic rates and body mass for a genetically heterogeneous laboratory strain of house mice (Mus domesticus). Our breeding design did not allow the simultaneous estimation of V(D) and V(N). Regardless of whether V(D) or V(N) was assumed, estimates of V(A) were negative under the full models. Hence, we fitted reduced models (e.g., V(A) + V(N) + V(E) or V(A) + V(E)) and obtained new variance estimates. For reduced models, narrow-sense heritability (h(2)(N)) for BMR was <0.1, but estimates of h(2)(N) for VO(2)max were higher. When estimated with the V(A) + V(E) model, the additive genetic covariance between VO(2)max and BMR was positive and statistically different from zero. This result offers tentative support for the aerobic capacity model for the evolution of vertebrate energetics. However, constraints imposed on the genetic model may cause our estimates of additive variance and covariance to be biased, so our results should be interpreted with caution and tested via selection experiments. PMID:11560903

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eudes, Aymerick; Dutta, Tanmoy; Deng, Kai

Lignin in plant biomass represents a target for engineering strategies towards the development of a sustainable bioeconomy. In addition to the conventional lignin monomers, namely p-coumaryl, coniferyl and sinapyl alcohols, tricin has been shown to be part of the native lignin polymer in certain monocot species. Because tricin is considered to initiate the polymerization of lignin chains, elucidating its biosynthesis and mechanism of export to the cell wall constitute novel challenges for the engineering of bioenergy crops. Late steps of tricin biosynthesis require two methylation reactions involving the pathway intermediate selgin. It has recently been demonstrated in rice and maizemore » that caffeate O-methyltransferase (COMT) involved in the synthesis syringyl (S) lignin units derived from sinapyl alcohol also participates in the synthesis of tricin in planta. In this work, we validate in sorghum (Sorghum bicolor L.) that the O-methyltransferase responsible for the production of S lignin units (SbCOMT / Bmr12) is also involved in the synthesis of lignin-linked tricin. In particular, we show that biomass from the sorghum bmr12 mutant contains lower level of tricin incorporated into lignin, and that SbCOMT can methylate the tricin precursors luteolin and selgin. Our genetic and biochemical data point toward a general mechanism whereby COMT is involved in the synthesis of both tricin and S lignin units.« less

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum

PubMed Central

Eudes, Aymerick; Dutta, Tanmoy; Deng, Kai; Jacquet, Nicolas; Sinha, Anagh; Benites, Veronica T.; Baidoo, Edward E. K.; Richel, Aurore; Sattler, Scott E.; Northen, Trent R.; Singh, Seema; Simmons, Blake A.

2017-01-01

Lignin in plant biomass represents a target for engineering strategies towards the development of a sustainable bioeconomy. In addition to the conventional lignin monomers, namely p-coumaryl, coniferyl and sinapyl alcohols, tricin has been shown to be part of the native lignin polymer in certain monocot species. Because tricin is considered to initiate the polymerization of lignin chains, elucidating its biosynthesis and mechanism of export to the cell wall constitute novel challenges for the engineering of bioenergy crops. Late steps of tricin biosynthesis require two methylation reactions involving the pathway intermediate selgin. It has recently been demonstrated in rice and maize that caffeate O-methyltransferase (COMT) involved in the synthesis syringyl (S) lignin units derived from sinapyl alcohol also participates in the synthesis of tricin in planta. In this work, we validate in sorghum (Sorghum bicolor L.) that the O-methyltransferase responsible for the production of S lignin units (SbCOMT / Bmr12) is also involved in the synthesis of lignin-linked tricin. In particular, we show that biomass from the sorghum bmr12 mutant contains lower level of tricin incorporated into lignin, and that SbCOMT can methylate the tricin precursors luteolin and selgin. Our genetic and biochemical data point toward a general mechanism whereby COMT is involved in the synthesis of both tricin and S lignin units. PMID:28594846

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum

DOE PAGES

Eudes, Aymerick; Dutta, Tanmoy; Deng, Kai; ...

2017-06-08

Lignin in plant biomass represents a target for engineering strategies towards the development of a sustainable bioeconomy. In addition to the conventional lignin monomers, namely p-coumaryl, coniferyl and sinapyl alcohols, tricin has been shown to be part of the native lignin polymer in certain monocot species. Because tricin is considered to initiate the polymerization of lignin chains, elucidating its biosynthesis and mechanism of export to the cell wall constitute novel challenges for the engineering of bioenergy crops. Late steps of tricin biosynthesis require two methylation reactions involving the pathway intermediate selgin. It has recently been demonstrated in rice and maizemore » that caffeate O-methyltransferase (COMT) involved in the synthesis syringyl (S) lignin units derived from sinapyl alcohol also participates in the synthesis of tricin in planta. In this work, we validate in sorghum (Sorghum bicolor L.) that the O-methyltransferase responsible for the production of S lignin units (SbCOMT / Bmr12) is also involved in the synthesis of lignin-linked tricin. In particular, we show that biomass from the sorghum bmr12 mutant contains lower level of tricin incorporated into lignin, and that SbCOMT can methylate the tricin precursors luteolin and selgin. Our genetic and biochemical data point toward a general mechanism whereby COMT is involved in the synthesis of both tricin and S lignin units.« less

Effects of whole-plant corn silage hybrid type on intake, digestion, ruminal fermentation, and lactation performance by dairy cows through a meta-analysis.

PubMed

Ferraretto, L F; Shaver, R D

2015-04-01

Understanding the effect of whole-plant corn silage (WPCS) hybrids in dairy cattle diets may allow for better decisions on hybrid selection by dairy producers, as well as indicate potential strategies for the seed corn industry with regard to WPCS hybrids. Therefore, the objective of this study was to perform a meta-analysis using literature data on the effects of WPCS hybrid type on intake, digestibility, rumen fermentation, and lactation performance by dairy cows. The meta-analysis was performed using a data set of 162 treatment means from 48 peer-reviewed articles published between 1995 and 2014. Hybrids were divided into 3 categories before analysis. Comparative analysis of WPCS hybrid types differing in stalk characteristics were in 4 categories: conventional, dual-purpose, isogenic, or low-normal fiber digestibility (CONS), brown midrib (BMR), hybrids with greater NDF but lower lignin (%NDF) contents or high in vitro NDF digestibility (HFD), and leafy (LFY). Hybrid types differing in kernel characteristics were in 4 categories: conventional or yellow dent (CONG), NutriDense (ND), high oil (HO), and waxy. Genetically modified (GM) hybrids were compared with their genetically similar non-biotech counterpart (ISO). Except for lower lignin content for BMR and lower starch content for HFD than CONS and LFY, silage nutrient composition was similar among hybrids of different stalk types. A 1.1 kg/d greater intake of DM and 1.5 and 0.05 kg/d greater milk and protein yields, respectively, were observed for BMR compared with CONS and LFY. Likewise, DMI and milk yield were greater for HFD than CONS, but the magnitude of the difference was smaller. Total-tract NDF digestibility was greater, but starch digestibility was reduced, for BMR and HFD compared with CONS or LFY. Silage nutrient composition was similar for hybrids of varied kernel characteristics, except for lower CP and EE content for CONG than ND and HO. Feeding HO WPCS to dairy cows decreased milk fat content and yield and protein content compared with the other kernel-type hybrids. Hybrids varying in kernel characteristics did not affect intake, milk production, or total-tract nutrient digestibilities by lactating dairy cows. Nutrient composition and lactation performance were similar between GM and ISO. Positive effects of BMR and HFD on intake and milk yield were observed for lactating dairy cows, but the reduced total-tract starch digestibility for these hybrids merits further study. Except for negative effects of HO on milk components, differences were minimal among corn silage hybrids differing in kernel type. Feeding GM WPCS did not affect lactation performance by dairy cows. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Physiological adjustments to arid and mesic environments in larks (Alaudidae).

PubMed

Tieleman, B Irene; Williams, Joseph B; Buschur, Michael E

2002-01-01

Because deserts are characterized by low food availability, high ambient temperature extremes, and absence of drinking water, one might expect that birds that live in these conditions exhibit a lower basal metabolic rate (BMR), reduced total evaporative water loss (TEWL), and greater ability to cope with high air temperatures than their mesic counterparts. To minimize confounding effects of phylogeny, we compared the physiological performance of four species of larks at ambient temperatures (T(a)'s) ranging from 0 degrees to 50 degrees C: hoopoe larks (Alaemon alaudipes) and Dunn's larks (Eremalauda dunni) live in hot and dry deserts, whereas skylarks (Alauda arvensis) and woodlarks (Lullula arborea) occur in temperate mesic areas. Mass-adjusted BMR and TEWL were indistinguishable between hoopoe lark and Dunn's lark and between skylark and woodlark. When grouping the data of the two desert larks in one set and the data of the two mesic larks in another, desert larks are shown to have 43% lower BMR levels and 27% lower TEWL values than the mesic species. Their body temperatures (T(b)'s) were 1.1 degrees C lower, and the minimal dry heat transfer coefficients (h) were 26% below values for the mesic larks. When T(a) exceeded T(b), the h of hoopoe larks and Dunn's larks was high and indistinguishable from h at 40 degrees C, in contrast to the prediction that h should be decreased to minimize heat gain through conductance, convection, or radiation from the environment when T(a) exceeds T(b).

Engineering human cytochrome P450 enzymes into catalytically self-sufficient chimeras using molecular Lego.

PubMed

Dodhia, Vikash Rajnikant; Fantuzzi, Andrea; Gilardi, Gianfranco

2006-10-01

The membrane-bound human cytochrome P450s have essential roles in the metabolism of endogenous compounds and drugs. Presented here are the results on the construction and characterization of three fusion proteins containing the N-terminally modified human cytochrome P450s CYP2C9, CY2C19 and CYP3A4 fused to the soluble NADPH-dependent oxidoreductase domain of CYP102A1 from Bacillus megaterium. The constructs, CYP2C9/BMR, CYP2C19/BMR and CYP3A4/BMR are well expressed in Escherichia coli as holo proteins. The chimeras can be purified in the absence of detergent and the purified enzymes are both active and correctly folded in the absence of detergent, as demonstrated by circular dichroism and functional studies. Additionally, in comparison with the parent P450 enzyme, these chimeras have greatly improved solubility properties. The chimeras are catalytically self-sufficient and present turnover rates similar to those reported for the native enzymes in reconstituted systems, unlike previously reported mammalian cytochrome P450 fusion proteins. Furthermore the specific activities of these chimeras are not dependent on the enzyme concentration present in the reaction buffer and they do not require the addition of accessory proteins, detergents or phospholipids to be fully active. The solubility, catalytic self-sufficiency and wild-type like activities of these chimeras would greatly simplify the studies of cytochrome P450 mediated drug metabolism in solution.

Duration of detection of anti-BmR1 IgG4 antibodies after mass-drug administration (MDA) in Sarawak, Malaysia.

PubMed

Noordin, R; Muhi, J; Md Idris, Z; Arifin, N; Kiyu, A

2012-03-01

The detection rates of brugian filariasis in three regions of Sarawak namely Central, North and South after three courses of mass drug administration (MDA) from year 2004 to 2006 was investigated. A recombinant BmR1 antigen-based IgG4 detection test, named Brugia Rapid and night blood smear for microfilaria (mf) detection were used. All three regions recorded a sharp fall in mf positive rates after a year post-MDA. Meanwhile Brugia Rapid positive rates declined more gradually to 3.8% and 5.6% of the pre-MDA levels in the Central and North regions, respectively. This study showed that in filariasis endemic areas in Sarawak, anti-filarial IgG4 antibodies to BmR1, as detected by the Brugia Rapid test, were positive for one to two years after mf disappearance.

The Enzyme Activity and Substrate Specificity of Two Major Cinnamyl Alcohol Dehydrogenases in Sorghum (Sorghum bicolor), SbCAD2 and SbCAD4.

PubMed

Jun, Se-Young; Walker, Alexander M; Kim, Hoon; Ralph, John; Vermerris, Wilfred; Sattler, Scott E; Kang, ChulHee

2017-08-01

Cinnamyl alcohol dehydrogenase (CAD) catalyzes the final step in monolignol biosynthesis, reducing sinapaldehyde, coniferaldehyde, and p -coumaraldehyde to their corresponding alcohols in an NADPH-dependent manner. Because of its terminal location in monolignol biosynthesis, the variation in substrate specificity and activity of CAD can result in significant changes in overall composition and amount of lignin. Our in-depth characterization of two major CAD isoforms, SbCAD2 (Brown midrib 6 [bmr6]) and SbCAD4, in lignifying tissues of sorghum ( Sorghum bicolor ), a strategic plant for generating renewable chemicals and fuels, indicates their similarity in both structure and activity to Arabidopsis ( Arabidopsis thaliana ) CAD5 and Populus tremuloides sinapyl alcohol dehydrogenase, respectively. This first crystal structure of a monocot CAD combined with enzyme kinetic data and a catalytic model supported by site-directed mutagenesis allows full comparison with dicot CADs and elucidates the potential signature sequence for their substrate specificity and activity. The L119W/G301F-SbCAD4 double mutant displayed its substrate preference in the order coniferaldehyde > p -coumaraldehyde > sinapaldehyde, with higher catalytic efficiency than that of both wild-type SbCAD4 and SbCAD2. As SbCAD4 is the only major CAD isoform in bmr6 mutants, replacing SbCAD4 with L119W/G301F-SbCAD4 in bmr6 plants could produce a phenotype that is more amenable to biomass processing. © 2017 American Society of Plant Biologists. All Rights Reserved.

Energetic costs and implications of the intake of plant secondary metabolites on digestive and renal morphology in two austral passerines.

PubMed

Barceló, Gonzalo; Ríos, Juan Manuel; Maldonado, Karin; Sabat, Pablo

2016-07-01

Seed-eating birds have a diet of high nutritional value; however, they must cope with plant secondary metabolites (PSM). We postulated that the detoxification capacity of birds is associated with a metabolic cost, given that the organs responsible for detoxification significantly contribute to energetic metabolism. We used an experimental approach to assess the effects of phenol-enriched diets on two passerines with different feeding habits: the omnivorous rufous-collared sparrow (Zonotrichia capensis) and the granivorous common diuca-finch (Diuca diuca). The birds were fed with one of three diets: control diet, supplemented with tannic acid, or supplemented with Opuntia ficus-indica phenolic extract (a common food of the sparrow but not the finch). After 5 weeks of exposure to the diets, we measured basal metabolic rates (BMR), energy intake, glucuronic acid output and digestive and kidney structure. In both species, detoxification capacity expressed as glucuronic acid output was higher in individuals consuming phenol-enriched diets compared to the control diet. However, whereas sparrows increase energy intake and intestinal mass when feeding on phenol-enriched diets, finches had lower intestinal mass and energy intake remains stable. Furthermore, sparrows had higher BMR on phenol-enriched diets compared to the control group, whereas in the finches BMR remains unchanged. Interspecific differences in response to phenols intake may be determined by the dietary habits of these species. While both species can feed on moderate phenolic diets for 5 weeks, energy costs may differ due to different responses in food intake and organ structure to counteract the effects of PSM intake.

Lean Body Mass as a Predictive Value of Hypertension in Young Adults, in Ankara, Turkey

PubMed Central

VAZIRI, Yashar; BULDUK, Sidika; SHADMAN, Zhaleh; BULDUK, Emre Ozgur; HEDAYATI, Mehdi; KOC, Haluk; ER, Fatmanur; ERDOGAN, Ceren Suveren

2015-01-01

Background: The aim of this study was to assess the predictive capacity of body composition estimated by bioelectrical impedance analysis (BIA) to identify abnormal blood pressure in physical education and sport teaching students in the city of Ankara. Methods: Data for this cross-sectional study were obtained in the city of Ankara in 2014. A total of 133 students aged 20–35 yr participated in this study. Anthropometric measurements were measured. Body composition was assessed by BIA. Physical activity level (PAL) and usual dietary intake were assessed. Pre-hypertension and hypertension were defined, respectively, as BP ≥120 and/or 80, and ≥140 and /or 90 mmHg. Results: More overweight students showed abnormal BP especially SBP (P=0.005 and 0.002, respectively). Age adjusted regression showed significant association between arm circumference (β= 0.176, P 0.044), mid arm muscle circumference (MAMC) (β= 0.235, P 0.007), lean body mass (LBM) (β= 0.238, P 0.006), basal metabolism rate (BMR) (β= 0.219, P 0.012) and SBP and, also, MAMC (β= 0.201, P 0.022), LBM (β= 0.203, P 0.021), BMR (β= 0.189, P 0.030) and DBP. Fat intake was associated with DBP (β= 0.14, P =0.040). Multivariate regression models adjusted for age, BMI, WC and fat intake/kg body weight showed positive association of SBP with MAMC, BMR and LBM (P<0.05). Conclusion: The relationship between blood pressure and body composition in young adults may be associated to LBM and MAMC. LBM or MAMC in this population may be indirect indicators of heart muscle mass and heart pumping power. PMID:26811815

Microvascular dysfunction in the immediate aftermath of chronic total coronary occlusion recanalization.

PubMed

Ladwiniec, Andrew; Cunnington, Michael S; Rossington, Jennifer; Thackray, Simon; Alamgir, Farquad; Hoye, Angela

2016-05-01

The aim of this study was to compare microvascular resistance under both baseline and hyperemic conditions immediately after percutaneous coronary intervention (PCI) of a chronic total occlusion (CTO) with an unobstructed reference vessel in the same patient Microvascular dysfunction has been reported to be prevalent immediately after CTO PCI. However, previous studies have not made comparison with a reference vessel. Patients with a CTO may have global microvascular and/or endothelial dysfunction, making comparison with established normal values misleading. After successful CTO PCI in 21 consecutive patients, coronary pressure and flow velocity were measured at baseline and hyperemia in distal segments of the CTO/target vessel and an unobstructed reference vessel. Hemodynamics including hyperemic microvascular resistance (HMR), basal microvascular resistance (BMR), and instantaneous minimal microvascular resistance at baseline and hyperemia were calculated and compared between reference and target/CTO vessels. After CTO PCI, BMR was reduced in the target/CTO vessel compared with the reference vessel: 3.58 mm Hg/cm/s vs 4.94 mm Hg/cm/s, difference -1.36 mm Hg/cm/s (-2.33 to -0.39, p = 0.008). We did not detect a difference in HMR: 1.82 mm Hg/cm/s vs 2.01 mm Hg/cm/s, difference -0.20 (-0.78 to 0.39, p = 0.49). Instantaneous minimal microvascular resistance correlated strongly with the length of stented segment at baseline (r = 0.63, p = 0.005) and hyperemia (r = 0.68, p = 0.002). BMR is reduced in a recanalized CTO in the immediate aftermath of PCI compared to an unobstructed reference vessel; however, HMR appears to be preserved. A longer stented segment is associated with increased microvascular resistance. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Response of nematode-trapping fungi to organic substrates in a coastal grassland soil.

PubMed

Nguyen, Vi L; Bastow, Justin L; Jaffee, Bruce A; Strong, Don R

2007-07-01

To understand why Arthrobotrys oligospora and other nematode-trapping fungi are common and sometimes abundant in the coastal grassland soils of the Bodega Marine Reserve (BMR, Sonoma County, CA), we examined how resident trapping fungi responded to the addition of eight organic substrates (lupine leaves, grass leaves, dead isopods, dead moth larvae, isopod faeces, deer faeces, shrimp shells, and powdered chitin). We were especially interested in the effects of dead isopods because isopods are abundant at BMR and because previous studies had documented strong responses of A. oligospora to other arthropods (dead moth larvae). Soil from BMR was packed into vials (40 g dry mass equivalent per vial with water potential at -230 kPa and bulk density at 0.9 gcm(-3)), and one substrate or no substrate was added to the soil surface. After 30 d at 20 degrees C, trapping fungi were quantified by dilution plating and most probable number procedures. The response of A. oligospora was inversely related to substrate carbon:nitrogen (C:N) ratio: substrates with low C:N ratios (dead isopods, lupine leaves, dead moth larvae) usually caused large increases in A. oligospora whereas those with higher C:N ratios (isopod faeces, deer faeces, grass leaves) did not. An exception was chitin powder, which had a low C:N ratio, but which did not cause A. oligospora to proliferate. Responses of A. oligospora were directly related to the quantity of nitrogen added with each substrate, and those substrates that caused large increases in resident nematodes usually caused large increases in A. oligospora. Other trapping fungi did not respond as strongly as A. oligospora.

Critical evaluation of energy intake using the Goldberg cut-off for energy intake:basal metabolic rate. A practical guide to its calculation, use and limitations.

PubMed

Black, A E

2000-09-01

To re-state the principles underlying the Goldberg cut-off for identifying under-reporters of energy intake, re-examine the physiological principles and update the values to be substituted into the equation for calculating the cut-off, and to examine its use and limitations. New values are suggested for each element of the Goldberg equation. The physical activity level (PAL) for comparison with energy intake:basal metabolic rate (EI:BMR) should be selected to reflect the population under study; the PAL value of 1.55 x BMR is not necessarily the value of choice. The suggested value for average within-subject variation in energy intake is 23% (unchanged), but other sources of variation are increased in the light of new data. For within-subject variation in measured and estimated BMR, 4% and 8.5% respectively are suggested (previously 2.5% and 8%), and for total between-subject variation in PAL, the suggested value is 15% (previously 12.5%). The effect of these changes is to widen the confidence limits and reduce the sensitivity of the cut-off. The Goldberg cut-off can be used to evaluate the mean population bias in reported energy intake, but information on the activity or lifestyle of the population is needed to choose a suitable PAL energy requirement for comparison. Sensitivity for identifying under-reporters at the individual level is limited. In epidemiological studies information on home, leisure and occupational activity is essential in order to assign subjects to low, medium or high PAL levels before calculating the cut-offs. In small studies, it is desirable to measure energy expenditure, or to calculate individual energy requirements, and to compare energy intake directly with energy expenditure.

Longitudinal changes in body composition and metabolic profile between exercise clinical trials in men with chronic spinal cord injury

PubMed Central

Gorgey, Ashraf S.; Martin, Heather; Metz, Alyse; Khalil, Refka E.; Dolbow, David R.; Gater, David R.

2016-01-01

Study design Longitudinal design. Objectives The study was undertaken to determine the effects of cessation of exercise interventions on body composition and metabolic profiles in men with chronic SCI. Settings Clinical trials within a Medical Center. Methods Eleven men with motor complete SCI were followed on average over a period of 2.5 years. Six men were involved in two different exercise interventions (functional electrical stimulation cycling versus arm cycling ergometer), 5 days/week for 16 weeks (exercise group), and five men served as a control (control group). Anthropometrics and dual energy X-ray absorptiometry (DXA) were captured to measure changes in lean mass (LM), fat mass (FM), percentage FM before, immediately after exercise, and after a period of 2.5 years. Basal metabolic rate (BMR) and lipid panel were also measured. Results Thigh circumference increased by 8.5% following exercise (P = 0.042) and remained 6.4% greater than baseline measurements (P = 0.012). Leg LM increased by 9% following the exercise intervention (P = 0.03) and decreased by 16% in the follow-up visit (P = 0.02). Percentage trunk and total body FM increased by 4.5% (P = 0.008) and 3.5% (P = 0.019) in the follow-up visit, respectively, and whole body LM increased by 8.4% and decreased back by 5.4% following a 2.5 year-period. BMR significantly decreased by 15.5% following the exercise (P = 0.029) interventions. Conclusion Exercise training is accompanied with positive changes in body composition as well as compensatory decrease in BMR, that regressed back following 2.5 years of exercise cessation. Participation in an exercise trial is unlikely to confound the measurements of a follow-up trial. PMID:27077574

Torpor and thermal energetics in a tiny Australian vespertilionid, the little forest bat (Vespadelus vulturnus).

PubMed

Willis, Craig K R; Turbill, Christopher; Geiser, Fritz

2005-10-01

Data on thermal energetics for vespertilionid bats are under-represented in the literature relative to their abundance, as are data for bats of very small body mass. Therefore, we studied torpor use and thermal energetics in one of the smallest (4 g) Australian vespertilionids, Vespadelus vulturnus. We used open-flow respirometry to quantify temporal patterns of torpor use, upper and lower critical temperatures (T (uc) and T (lc)) of the thermoneutral zone (TNZ), basal metabolic rate (BMR), resting metabolic rate (RMR), torpid metabolic rate (TMR), and wet thermal conductance (C (wet)) over a range of ambient temperatures (T (a)). We also measured body temperature (T (b)) during torpor and normothermia. Bats showed a high proclivity for torpor and typically aroused only for brief periods. The TNZ ranged from 27.6 degrees C to 33.3 degrees C. Within the TNZ T (b) was 33.3+/-0.4 degrees C and BMR was 1.02+/-0.29 ml O(2) g(-1) h(-1) (5.60+/-1.65 mW g(-1)) at a mean body mass of 4.0+/-0.69 g, which is 55 % of that predicted for a 4 g bat. Minimum TMR of torpid bats was 0.014+/-0.006 ml O(2) g(-1) h(-1) (0.079+/-0.032 mW g(-1)) at T (a)=4.6+/-0.4 degrees C and T (b)=7.5+/-1.9. T (lc) and C (wet) of normothermic bats were both lower than that predicted for a 4 g bat, which indicates that V. vulturnus is adapted to minimising heat loss at low T (a). Our findings support the hypothesis that vespertilionid bats have evolved energy-conserving physiological traits, such as low BMR and proclivity for torpor.

Characterization of Hydrophobic Peptides in the Presence of Detergent by Photoionization Mass Spectrometry

PubMed Central

Bagag, Aïcha; Jault, Jean-Michel; Sidahmed-Adrar, Nazha; Réfrégiers, Matthieu; Giuliani, Alexandre; Le Naour, François

2013-01-01

The characterization of membrane proteins is still challenging. The major issue is the high hydrophobicity of membrane proteins that necessitates the use of detergents for their extraction and solubilization. The very poor compatibility of mass spectrometry with detergents remains a tremendous obstacle in studies of membrane proteins. Here, we investigated the potential of atmospheric pressure photoionization (APPI) for mass spectrometry study of membrane proteins. This work was focused on the tetraspanin CD9 and the multidrug transporter BmrA. A set of peptides from CD9, exhibiting a broad range of hydropathicity, was investigated using APPI as compared to electrospray ionization (ESI). Mass spectrometry experiments revealed that the most hydrophobic peptides were hardly ionized by ESI whereas all peptides, including the highly hydrophobic one that corresponds to the full sequence of the first transmembrane domain of CD9, were easily ionized by APPI. The native protein BmrA purified in the presence of the non-ionic detergent beta-D-dodecyl maltoside (DDM) was digested in-solution using trypsin. The resulting peptides were investigated by flow injection analysis of the mixture followed by mass spectrometry. Upon ESI, only detergent ions were detected and the ionic signals from the peptides were totally suppressed. In contrast, APPI allowed many peptides distributed along the sequence of the protein to be detected. Furthermore, the parent ion corresponding to the first transmembrane domain of the protein BmrA was detected under APPI conditions. Careful examination of the APPI mass spectrum revealed a-, b-, c- and y- fragment ions generated by in-source fragmentation. Those fragment ions allowed unambiguous structural characterization of the transmembrane domain. In conclusion, APPI–MS appears as a versatile method allowing the ionization and fragmentation of hydrophobic peptides in the presence of detergent. PMID:24236085

Dietary intakes assessed by 24-h recalls in peri-urban African adolescents: validity of energy intake compared with estimated energy expenditure.

PubMed

Rankin, D; Ellis, S M; Macintyre, U E; Hanekom, S M; Wright, H H

2011-08-01

The objective of this study is to determine the relative validity of reported energy intake (EI) derived from multiple 24-h recalls against estimated energy expenditure (EE(est)). Basal metabolic rate (BMR) equations and physical activity factors were incorporated to calculate EE(est). This analysis was nested in the multidisciplinary PhysicaL Activity in the Young study with a prospective study design. Peri-urban black South African adolescents were investigated in a subsample of 131 learners (87 girls and 44 boys) from the parent study sample of 369 (211 girls and 158 boys) who had all measurements taken. Pearson correlation coefficients and Bland-Altman plots were calculated to identify the most accurate published equations to estimate BMR (P<0.05 statistically significant). EE(est) was estimated using BMR equations and estimated physical activity factors derived from Previous Day Physical Activity Recall questionnaires. After calculation of EE(est), the relative validity of reported energy intake (EI(rep)) derived from multiple 24-h recalls was tested for three data subsets using Pearson correlation coefficients. Goldberg's formula identified cut points (CPs) for under and over reporting of EI. Pearson correlation coefficients between calculated BMRs ranged from 0.97 to 0.99. Bland-Altman analyses showed acceptable agreement (two equations for each gender). One equation for each gender was used to calculate EE(est). Pearson correlation coefficients between EI(rep) and EE(est) for three data sets were weak, indicating poor agreement. CPs for physical activity groups showed under reporting in 87% boys and 95% girls. The 24-h recalls measured at five measurements over 2 years offered poor validity between EI(rep) and EE(est).

FTO variant, energy intake, physical activity and basal metabolic rate in Caucasians. The HAPIEE study.

PubMed

Hubáček, J A; Pikhart, H; Peasey, A; Kubínová, R; Bobák, M

2011-01-01

The FTO gene variants are the most important genetic determinants of body weight and obesity known so far, but the mechanism of their effect remains unclear. We have analyzed FTO rs17817449 variant (G>T in first intron) in 6024 adults aged 45-69 years to assess the potential mediating role of diet and physical activity. Diet was assessed by a 140-item food frequency questionnaire. Physical activity was measured by hours spent during a typical week by sport, walking and other activities outside of work requiring heavy and medium physical activity. Basal metabolic rate was calculated according Schofield formula. The FTO variant was significantly associated with body mass index (means in GG, GT and TT carriers were 28.7, 28.2 and 27.8 kg/m(2), p<0.001) and basal metabolic rate (BMR) (means in GG, GT and TT were 1603, 1588 and 1576 kcal per day, respectively, p<0.008) but it was not associated with physical activity, total energy intake or with energy intakes from fat, carbohydrates, proteins or alcohol. Results were essentially similar in men and women and the adjustment for physical activity or dietary energy intake did not reduce the effect of the FTO polymorphism. Means of BMR per kg of body weight was lowest in GG carriers (20.09, 20.21 for GT and 20.30 for TT, p<0.006) and this effect was more pronounced in females. These results suggest that the effect of the FTO rs17817449 variant on BMI in Caucasian adults is not mediated by energy intake or physical activity, but some effect on BMR per kg of body weight is possible.

Components of feed efficiency in broiler breeding stock: energetics, performance, carcass composition, metabolism, and body temperature.

PubMed

Skinner-Noble, D O; Teeter, R G

2003-07-01

Two experiments were conducted to identify factors influencing feed conversion in broilers. The first experiment was conducted to develop a test for body temperature (BT) under mild handling stress. In the first experiment, BT was recorded periodically with birds briefly restrained after they had been removed from feed with either continuous lighting or 16L:8D. Body temperature was affected by photoperiod and declined following feed removal. The second experiment was conducted to investigate metabolic-physiologic differences existing between good (G) and poor (P) converting broilers, initially classified in a commercial breeding company's feed conversion (FCR) test. Basal metabolic rate (BMR) and BT were measured at the beginning and end of the FCR test following appropriate time without feed. Heat production (HP) was recorded throughout the study both for BMR calculations and to measure net energy (NE). Excreta were collected for measurement of AME, and at study termination, birds were analyzed for carcass composition. The G and P converters, however, had similar BMR and feed consumption but differed in AME (58 kcal/kg) and total NE (184 kcal/kg). Generally, G and P broilers had similar starting BW, but the G broilers gained more weight on the same amount of feed than did P broilers. The two BT measurements recorded in the present study were correlated with each other. The BT was also correlated with subsequent gain and FCR, indicating potential use as an indicator trait for feed conversion. Further, the data indicated that processes other than basal metabolism (measured as average hourly HP) may impact FCR. These might include variability in fear response during BT measurement or variations in bird activity level.

Frequency of Dietary Recalls, Nutritional Assessment, and Body Composition Assessment in Men With Chronic Spinal Cord Injury.

PubMed

Gorgey, Ashraf S; Caudill, Caleb; Sistrun, Sakita; Khalil, Refka E; Gill, Ranjodh; Castillo, Teodoro; Lavis, Timothy; Gater, David R

2015-09-01

To assess different frequencies of dietary recalls while evaluating caloric intake and the percentage of macronutrients in men with spinal cord injury (SCI) and to examine the relations between caloric intake or percentage of macronutrients and assessment of whole and regional body composition using dual-energy x-ray absorptiometry. Cross-sectional and longitudinal. Laboratory and hospital. Men with chronic (>1 y postinjury) motor complete SCI (N=16). Participants were asked to turn in a 5-day dietary recall on a weekly basis for 4 weeks. The averages of 5-, 3-, and 1-day dietary recalls for caloric intake and percentage of macronutrients (carbohydrates, fat, protein) were calculated. Body composition was evaluated using whole-body dual-energy x-ray absorptiometry. After overnight fast, basal metabolic rate (BMR) was evaluated using indirect calorimetry and total energy expenditure (TEE) was estimated. Caloric intake, percentage of macronutrients, BMR, and body composition. Caloric intake and percentage of macronutrients were not different after using 5-, 3-, and 1-day dietary recalls (P>.05). Caloric intake was significantly lower than TEE (P<.05). The percentage of fat accounted for 29% to 34% of the whole and regional body fat mass (P=.037 and P=.022). The percentage of carbohydrates was positively related to the percentage of whole-body lean mass (r=.54; P=.037) and negatively related to the percentage of fat mass. The frequency of dietary recalls does not vary while evaluating caloric intake and macronutrients. Total caloric intake was significantly lower than the measured BMR and TEE. Percentages of dietary fat and carbohydrates are related to changes in body composition after SCI. Copyright © 2015 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Lean Body Mass as a Predictive Value of Hypertension in Young Adults, in Ankara, Turkey.

PubMed

Vaziri, Yashar; Bulduk, Sidika; Shadman, Zhaleh; Bulduk, Emre Ozgur; Hedayati, Mehdi; Koc, Haluk; Er, Fatmanur; Erdogan, Ceren Suveren

2015-12-01

The aim of this study was to assess the predictive capacity of body composition estimated by bioelectrical impedance analysis (BIA) to identify abnormal blood pressure in physical education and sport teaching students in the city of Ankara. Data for this cross-sectional study were obtained in the city of Ankara in 2014. A total of 133 students aged 20-35 yr participated in this study. Anthropometric measurements were measured. Body composition was assessed by BIA. Physical activity level (PAL) and usual dietary intake were assessed. Pre-hypertension and hypertension were defined, respectively, as BP ≥120 and/or 80, and ≥140 and /or 90 mmHg. More overweight students showed abnormal BP especially SBP (P=0.005 and 0.002, respectively). Age adjusted regression showed significant association between arm circumference (β= 0.176, P 0.044), mid arm muscle circumference (MAMC) (β= 0.235, P 0.007), lean body mass (LBM) (β= 0.238, P 0.006), basal metabolism rate (BMR) (β= 0.219, P 0.012) and SBP and, also, MAMC (β= 0.201, P 0.022), LBM (β= 0.203, P 0.021), BMR (β= 0.189, P 0.030) and DBP. Fat intake was associated with DBP (β= 0.14, P =0.040). Multivariate regression models adjusted for age, BMI, WC and fat intake/kg body weight showed positive association of SBP with MAMC, BMR and LBM (P<0.05). The relationship between blood pressure and body composition in young adults may be associated to LBM and MAMC. LBM or MAMC in this population may be indirect indicators of heart muscle mass and heart pumping power.

Mathematical analysis of running performance and world running records.

PubMed

Péronnet, F; Thibault, G

1989-07-01

The objective of this study was to develop an empirical model relating human running performance to some characteristics of metabolic energy-yielding processes using A, the capacity of anaerobic metabolism (J/kg); MAP, the maximal aerobic power (W/kg); and E, the reduction in peak aerobic power with the natural logarithm of race duration T, when T greater than TMAP = 420 s. Accordingly, the model developed describes the average power output PT (W/kg) sustained over any T as PT = [S/T(1 - e-T/k2)] + 1/T integral of T O [BMR + B(1 - e-t/k1)]dt where S = A and B = MAP - BMR (basal metabolic rate) when T less than TMAP; and S = A + [Af ln(T/TMAP)] and B = (MAP - BMR) + [E ln(T/TMAP)] when T greater than TMAP; k1 = 30 s and k2 = 20 s are time constants describing the kinetics of aerobic and anaerobic metabolism, respectively, at the beginning of exercise; f is a constant describing the reduction in the amount of energy provided from anaerobic metabolism with increasing T; and t is the time from the onset of the race. This model accurately estimates actual power outputs sustained over a wide range of events, e.g., average absolute error between actual and estimated T for men's 1987 world records from 60 m to the marathon = 0.73%. In addition, satisfactory estimations of the metabolic characteristics of world-class male runners were made as follows: A = 1,658 J/kg; MAP = 83.5 ml O2.kg-1.min-1; 83.5% MAP sustained over the marathon distance. Application of the model to analysis of the evolution of A, MAP, and E, and of the progression of men's and women's world records over the years, is presented.

Gaseous Criteria Pollutants in Bangkok Metropolitan Region, Thailand: Analysis, Issues and Management

NASA Astrophysics Data System (ADS)

Uttamang, P.; Aneja, V. P.; Hanna, A. F.

2017-12-01

Analysis of gaseous criteria pollutants in Bangkok Metropolitan Region (BMR), Thailand, during 2010 to 2014 reveals that the hourly concentrations of CO, SO2 and NO2 were mostly below the National Ambient Air Quality Standards (NAAQs) of Thailand. However, the hourly concentrations of Ozone (O3) exceeded the Thailand NAAQs. The maximum concentrations of O3 were from 120 to 190 ppb. On average, the number of hourly O3 exceedances were from 1 to 60 hours a year depending on monitoring station locations. The exceedances were found during the dry season in both summer and winter. Inter-conversion between O3, NO and NO2 indicates the crossover point between species occur when the concentration of NOx ([NOx = NO + NO2]) is about 60 ppb. When [NOx] < 60 ppb, O3 is the dominant species; conversely, NO dominates when [NOx] > 60 ppb. The calculated photochemical reaction rate during photostationary state ranges from 0.12 to 1.22 min-1. Linear regression analysis between the concentrations of Ox ([Ox = O3 + NO2]) and NOx provides the role of local and regional contributions to Ox. Both the local and regional Ox contributions play an important role in the increase of [Ox] and those values were about double during O3 episodes ([O3] > 100 ppb). Ratio analysis suggests that the major contributors of primary pollutants over BMR are mobile sources (CO/NOx = 19.8). However, this region may also be influenced by point sources, but they are not dominant. An analysis of the air quality showed that the air quality index (AQI) for BMR was predominantly between good to moderate; however, during episode conditions in the region, unhealthy O3 categories were also observed. Note the manuscript is under review by a publication

Electron transfer in the complex of membrane-bound human cytochrome P450 3A4 with the flavin domain of P450BM-3: the effect of oligomerization of the heme protein and intermittent modulation of the spin equilibrium†

PubMed Central

Davydov, Dmitri R.; Sineva, Elena V.; Sistla, Srinivas; Davydova, Nadezhda Y.; Frank, Daniel J.; Sligar, Stephen G.; Halpert, James R.

2009-01-01

We studied the kinetics of NADPH-dependent reduction of human CYP3A4 incorporated into Nanodiscs (CYP3A4-ND) and proteoliposomes in order to probe the effect of P450 oligomerization on its reduction. The flavin domain of cytochrome P450-BM3 (BMR) was used as a model electron donor partner. Unlike CYP3A4 oligomers, where only 50% of the enzyme was shown to be reducible by BMR, CYP3A4-ND could be reduced almost completely. High reducibility was also observed in proteoliposomes with a high lipid-to-protein ratio (L/P=910), where the oligomerization equilibrium is displaced towards monomers. In contrast, the reducibililty in proteoliposomes with L/P=76 did not exceed 55 ± 6%. The effect of the surface density of CYP3A4 in proteoliposomes on the oligomerization equilibrium was confirmed with a FRET-based assay employing a cysteine-depleted mutant labeled on Cys-468 with BODIPY iodoacetamide. These results confirm a pivotal role of CYP3A4 oligomerization in its functional heterogeneity. Furthermore, the investigation of the initial phase of the kinetics of CYP3A4 reduction showed that the addition of NADPH causes a rapid low-to-high spin transition in the CYP3A4-BMR complex, which is followed by a partial slower reversal. This observation reveals a mechanism whereby the CYP3A4 spin equilibrium is modulated by the redox state of the bound flavoprotein. PMID:20026040

The use of metabolic balance studies in the objective discrimination between intestinal insufficiency and intestinal failure.

PubMed

Prahm, August P; Brandt, Christopher F; Askov-Hansen, Carsten; Mortensen, Per B; Jeppesen, Palle B

2017-09-01

Background : In research settings that use metabolic balance studies (MBSs) of stable adult patients with short bowel syndrome, intestinal failure (IF) and dependence on parenteral support (PS) have been defined objectively as energy absorption <84% of calculated basal metabolic rate (BMR), wet weight (WW) absorption <23 g · kg body weight -1 · d -1 , or both. Objective: This study aimed to explore and validate these borderlines in the clinical setting. Design: Intestinal absorption was measured from April 2003 to March 2015 in 175 consecutive patients with intestinal insufficiency (INS) in 96-h MBSs. They had not received PS 3 mo before referral. Results: To avoid the need for PS, the minimum absorptive requirements were energy absorption of ≥81% of BMR and WW absorption of ≥21 g · kg body weight -1 · d -1 , which were equivalent to findings in research settings (differences of 3.6% and 8.7%; P = 0.65 and 0.60, respectively). Oral failure defined as energy intake <130% of calculated BMR or WW intake <40 g · kg body weight -1 · d -1 was seen in 71% and 82% of the 10% of patients with the lowest energy absorption and WW absorption, respectively. Conclusions: In clinical settings, the borderlines between INS and IF were not significantly different from those in research settings, even in an unselected patient population in which oral failure was also a predominant cause of nutritional dyshomeostasis. MBSs may be recommended to identify the individual patient in the spectrum from INS to IF, to objectivize the cause of nutritional dyshomeostasis (oral failure, malabsorption, or both), and to quantify the effects of treatment. © 2017 American Society for Nutrition.

Biliopancreatic Diversion is associated with greater increases in energy expenditure than Roux-en-Y Gastric Bypass.

PubMed

Werling, Malin; Fändriks, Lars; Olbers, Torsten; Mala, Tom; Kristinsson, Jon; Stenlöf, Kaj; Wallenius, Ville; Docherty, Neil G; le Roux, Carel W

2018-01-01

The greater weight loss achieved following Biliopancreatic Diversion with Duodenal Switch (BPDS) versus Roux-en-Y Gastric Bypass (RYGB) has been attributed to the malabsorptive effects of BPDS. Increased weight loss after BPDS could also be underpinned by larger increases in energy expenditure. Hypothetically, the more radical reconfiguration of the small intestine in BPDS could result in an accentuated increase in meal associated thermogenesis (MAT). Female subjects (baseline mean age 40 years, mean BMI-55kg/m2) were assessed four years after randomization to BPDS (n = 6) or RYGB (n = 6). Energy expenditure (EE) and respiratory quotient (RQ) were measured by indirect calorimetry over 24 hours. A detailed protocol allowed for discrimination of basal metabolic rate (BMR), fasting EE and MAT as components of total energy expenditure (TEE) normalised for total and lean tissue by dual-energy x-ray absorptiometry. Median weight loss at follow-up was 1.5-fold higher following BPDS relative to RYGB, resulting in respective median BMIs of 29.5 kg/m2 (21.7 to 36.7) after BPDS and 37.8 kg/m2 (34.1 to 45.7) after RYGB (p = 0.015). The BPDS group had a lower fat:lean ratio compared to the RYGB group (p = 0.009). Overall 24-hour TEE adjusted for total tissue was higher in the BPDS group, as were BMR, fasting EE and MAT (all p<0.05). Differences between RYGB and BPDS in BMR and TEE were nullified when normalised for lean mass. Postprandial RQ increased significantly but to a similar extent in both groups. Enhanced and prolonged MAT and lower fat:lean mass ratios after BPDS may explain relative increases in total energy expenditure as compared to RYGB.

Biliopancreatic Diversion is associated with greater increases in energy expenditure than Roux-en-Y Gastric Bypass

PubMed Central

Werling, Malin; Fändriks, Lars; Olbers, Torsten; Mala, Tom; Kristinsson, Jon; Stenlöf, Kaj; Wallenius, Ville; le Roux, Carel W.

2018-01-01

Objective The greater weight loss achieved following Biliopancreatic Diversion with Duodenal Switch (BPDS) versus Roux-en-Y Gastric Bypass (RYGB) has been attributed to the malabsorptive effects of BPDS. Increased weight loss after BPDS could also be underpinned by larger increases in energy expenditure. Hypothetically, the more radical reconfiguration of the small intestine in BPDS could result in an accentuated increase in meal associated thermogenesis (MAT). Design Female subjects (baseline mean age 40 years, mean BMI-55kg/m2) were assessed four years after randomization to BPDS (n = 6) or RYGB (n = 6). Energy expenditure (EE) and respiratory quotient (RQ) were measured by indirect calorimetry over 24 hours. A detailed protocol allowed for discrimination of basal metabolic rate (BMR), fasting EE and MAT as components of total energy expenditure (TEE) normalised for total and lean tissue by dual-energy x-ray absorptiometry. Results Median weight loss at follow-up was 1.5-fold higher following BPDS relative to RYGB, resulting in respective median BMIs of 29.5 kg/m2 (21.7 to 36.7) after BPDS and 37.8 kg/m2 (34.1 to 45.7) after RYGB (p = 0.015). The BPDS group had a lower fat:lean ratio compared to the RYGB group (p = 0.009). Overall 24-hour TEE adjusted for total tissue was higher in the BPDS group, as were BMR, fasting EE and MAT (all p<0.05). Differences between RYGB and BPDS in BMR and TEE were nullified when normalised for lean mass. Postprandial RQ increased significantly but to a similar extent in both groups. Conclusion Enhanced and prolonged MAT and lower fat:lean mass ratios after BPDS may explain relative increases in total energy expenditure as compared to RYGB. PMID:29617391

Does encephalization correlate with life history or metabolic rate in Carnivora?

PubMed

Finarelli, John A

2010-06-23

A recent analysis of brain size evolution reconstructed the plesiomorphic brain-body size allometry for the mammalian order Carnivora, providing an important reference frame for comparative analyses of encephalization (brain volume scaled to body mass). I performed phylogenetically corrected regressions to remove the effects of body mass, calculating correlations between residual values of encephalization with basal metabolic rate (BMR) and six life-history variables (gestation time, neonatal mass, weaning time, weaning mass, litter size, litters per year). No significant correlations were recovered between encephalization and any life-history variable or BMR, arguing against hypotheses relating encephalization to maternal energetic investment. However, after correcting for clade-specific adaptations, I recovered significant correlations for several variables, and further analysis revealed a conserved carnivoran reproductive strategy, linking degree of encephalization to the well-documented mammalian life-history trade-off between neonatal mass and litter size. This strategy of fewer, larger offspring correlating with increased encephalization remains intact even after independent changes in encephalization allometries in the evolutionary history of this clade.

Simultaneous glucose production from cellulose and fouling reduction using a magnetic responsive membrane reactor with superparamagnetic nanoparticles carrying cellulolytic enzymes.

PubMed

Gebreyohannes, Abaynesh Yihdego; Dharmjeet, Madhav; Swusten, Tom; Mertens, Matthias; Verspreet, Joran; Verbiest, Thierry; Courtin, Christophe M; Vankelecom, Ivo F J

2018-05-02

This work aimed at investigating simultaneous hydrolysis of cellulose and in-situ foulant degradation in a cellulose fed superparamagnetic biocatalytic membrane reactor (BMR SP ). In this reactor, a dynamic layer of superparamagnetic bionanocomposites with immobilized cellulolytic enzymes were reversibly immobilized on superparamagnetic polymeric membrane using an external magnetic field. The formation of a dynamic layer of bionanocomposites on the membrane helped to prevent direct membrane-foulant interaction. Due to in-situ biocatalysis, there was limited filtration resistance. Simultaneous separation of the product helped to avoid enzyme product inhibition, achieve constant reaction rate over time and 50% higher enzyme efficiency than batch reactor. Stable enzyme immobilization and the ability to keep enzyme in the system for long period helped to achieve continuous productivity at very low enzyme but high solid loading, while also reducing the extent of membrane fouling. Hence, the BMR SP paves a path for sustainable production of bioethanol from the cheaply available lignocellulose. Copyright © 2018 Elsevier Ltd. All rights reserved.

Is domestication driven by reduced fear of humans? Boldness, metabolism and serotonin levels in divergently selected red junglefowl (Gallus gallus).

PubMed

Agnvall, Beatrix; Katajamaa, Rebecca; Altimiras, Jordi; Jensen, Per

2015-09-01

Domesticated animals tend to develop a coherent set of phenotypic traits. Tameness could be a central underlying factor driving this, and we therefore selected red junglefowl, ancestors of all domestic chickens, for high or low fear of humans during six generations. We measured basal metabolic rate (BMR), feed efficiency, boldness in a novel object (NO) test, corticosterone reactivity and basal serotonin levels (related to fearfulness) in birds from the fifth and sixth generation of the high- and low-fear lines, respectively (44-48 individuals). Corticosterone response to physical restraint did not differ between selection lines. However, BMR was higher in low-fear birds, as was feed efficiency. Low-fear males had higher plasma levels of serotonin and both low-fear males and females were bolder in an NO test. The results show that many aspects of the domesticated phenotype may have developed as correlated responses to reduced fear of humans, an essential trait for successful domestication. © 2015 The Author(s).

Does encephalization correlate with life history or metabolic rate in Carnivora?

PubMed Central

Finarelli, John A.

2010-01-01

A recent analysis of brain size evolution reconstructed the plesiomorphic brain–body size allometry for the mammalian order Carnivora, providing an important reference frame for comparative analyses of encephalization (brain volume scaled to body mass). I performed phylogenetically corrected regressions to remove the effects of body mass, calculating correlations between residual values of encephalization with basal metabolic rate (BMR) and six life-history variables (gestation time, neonatal mass, weaning time, weaning mass, litter size, litters per year). No significant correlations were recovered between encephalization and any life-history variable or BMR, arguing against hypotheses relating encephalization to maternal energetic investment. However, after correcting for clade-specific adaptations, I recovered significant correlations for several variables, and further analysis revealed a conserved carnivoran reproductive strategy, linking degree of encephalization to the well-documented mammalian life-history trade-off between neonatal mass and litter size. This strategy of fewer, larger offspring correlating with increased encephalization remains intact even after independent changes in encephalization allometries in the evolutionary history of this clade. PMID:20007169

BENCHMARK DOSES FOR CHEMICAL MIXTURES: EVALUATION OF A MIXTURE OF 18 PHAHS.

EPA Science Inventory

Benchmark doses (BMDs), defined as doses of a substance that are expected to result in a pre-specified level of "benchmark" response (BMR), have been used for quantifying the risk associated with exposure to environmental hazards. The lower confidence limit of the BMD is used as...

Lactobacillus plantarum effects on silage fermentation and in vitro microbial yield

USDA-ARS?s Scientific Manuscript database

Four alfalfa trials, one corn, and one bmr corn were treated with no inoculant (Control), Lactobacillus plantarum (MTD/1) and formic acid (FA), ensiled in 1-L mini-silos, and fermented for 60 d at room temperature (22 C). Mini-silos were opened and analyzed for fermentation characteristics and solub...

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum

USDA-ARS?s Scientific Manuscript database

Lignin in plant biomass represents a target for engineering strategies towards the development of a sustainable bioeconomy. In addition to the conventional lignin monomers, namely p-coumaryl, coniferyl and sinapyl alcohols, tricin has been shown to be part of the native lignin polymer in certain mon...

Dietary change, energy balance and body weight regulation among migrating students.

PubMed

Reeves, S L; Henry, C J

2000-11-01

This study was conducted to examine how subjects modulate their food intake and energy balance when they migrate from a low energy density food intake pattern to one of high energy density. It was hypothesised that an increase in the energy density of food consumed would result in increased body weight of the migrating subjects unless food intake and energy balance could be modulated. Food selection, food intake, basal metabolic rate (BMR) and anthropometric measurements were made on 53 female and 56 male newly arrived overseas students. All subjects were from Malaysia, but the data was collected at Oxford Brookes University where the subjects were studying. Food intake using 3-day food diaries and food frequency questionnaires (FFQs). BMR and anthropometric measurements including body weight were measured on arrival in the UK and after 3 and 6 months' stay. Student's t-tests and analysis of variance (ANOVA) were used to compare the data. A significant difference (P < 0.05) was found between the energy density of the foods consumed in Malaysia and after 3 and 6 months in the UK. There was also a significant decrease (P < 0.05) in protein consumed. However, there were no differences in total energy intake. From results of the FFQs, differences were found in food selection due mainly to the lack of availability of certain foods in UK supermarkets. No significant differences were found in the BMR and anthropometric measurements made at the start of the study and later assessments. It appears that Malaysian students are able to remain in energy balance and are weight stable at least during the first 6 months of residence in the UK, despite the wider choice of energy dense food available. This suggests that at least in the short term, subjects are able to modulate their food intake in response to changes in the energy densities and free choice of food.

Validity of U.S. nutritional surveillance:National Health and Nutrition Examination Survey caloric energy intake data, 1971-2010.

PubMed

Archer, Edward; Hand, Gregory A; Blair, Steven N

2013-01-01

Methodological limitations compromise the validity of U.S. nutritional surveillance data and the empirical foundation for formulating dietary guidelines and public health policies. Evaluate the validity of the National Health and Nutrition Examination Survey (NHANES) caloric intake data throughout its history, and examine trends in the validity of caloric intake estimates as the NHANES dietary measurement protocols evolved. Validity of data from 28,993 men and 34,369 women, aged 20 to 74 years from NHANES I (1971-1974) through NHANES 2009-2010 was assessed by: calculating physiologically credible energy intake values as the ratio of reported energy intake (rEI) to estimated basal metabolic rate (BMR), and subtracting estimated total energy expenditure (TEE) from NHANES rEI to create 'disparity values'. 1) Physiologically credible values expressed as the ratio rEI/BMR and 2) disparity values (rEI-TEE). The historical rEI/BMR values for men and women were 1.31 and 1.19, (95% CI: 1.30-1.32 and 1.18-1.20), respectively. The historical disparity values for men and women were -281 and -365 kilocalorie-per-day, (95% CI: -299, -264 and -378, -351), respectively. These results are indicative of significant under-reporting. The greatest mean disparity values were -716 kcal/day and -856 kcal/day for obese (i.e., ≥30 kg/m2) men and women, respectively. Across the 39-year history of the NHANES, EI data on the majority of respondents (67.3% of women and 58.7% of men) were not physiologically plausible. Improvements in measurement protocols after NHANES II led to small decreases in underreporting, artifactual increases in rEI, but only trivial increases in validity in subsequent surveys. The confluence of these results and other methodological limitations suggest that the ability to estimate population trends in caloric intake and generate empirically supported public policy relevant to diet-health relationships from U.S. nutritional surveillance is extremely limited.

Circulating Levels of Orexin-A, Nesfatin-1, Agouti-Related Peptide, and Neuropeptide Y in Patients with Hyperthyroidism.

PubMed

Tohma, Yusuf; Akturk, Mujde; Altinova, Alev; Yassibas, Emine; Cerit, Ethem Turgay; Gulbahar, Ozlem; Arslan, Metin; Sanlier, Nevin; Toruner, Fusun

2015-07-01

There is insufficient information about the appetite-related hormones orexin-A, nesfatin-1, agouti-related peptide (AgRP), and neuropeptide Y (NPY) in hyperthyroidism. The aim of the present study was to investigate the effects of hyperthyroidism on the basal metabolic rate (BMR) and energy intake, orexin-A, nesfatin-1, AgRP, NPY, and leptin levels in the circulation, and their relationship with each other and on appetite. In this prospective study, patients were evaluated in hyperthyroid and euthyroid states in comparison with healthy subjects. Twenty-one patients with overt hyperthyroidism and 33 healthy controls were included in the study. Daily energy intake in the hyperthyroid state was found to be higher than that in the euthyroid state patient group (p=0.039). BMR was higher in hyperthyroid patients than the control group (p=0.018). Orexin-A was lower and nesfatin-1 was higher in hyperthyroid patients compared to the controls (p<0.001), whereas orexin-A increased and nesfatin-1 decreased after euthyroidism (p=0.003, p<0.001). No differences were found in the AgRP, NPY, and leptin levels between the hyperthyroid and euthyroid states and controls (p>0.05). Orexin-A correlated negatively with nesfatin-1 (p=0.042), BMR (p=0.013), free triiodothyronine (fT3; p<0.001), and free thyroxine (fT4; p<0.001) and positively with thyrotropin (TSH; p<0.001). Nesfatin-1 correlated negatively with orexin-A (p=0.042) and TSH (p<0.001) and positively with fT3 (p=0.005) and fT4 (p=0.001). In the regression analysis, "diagnosis of hyperthyroidism" was the main factor affecting orexin-A (p<0.001). Although it seems that no relationship exists among orexin-A, nesfatin-1, and increased appetite in hyperthyroidism, the orexin-A and nesfatin-1 levels are markedly affected by hyperthyroidism.

Impact of demographic, genetic, and bioimpedance factors on gestational weight gain and birth weight in a Romanian population

PubMed Central

Mărginean, Claudiu; Mărginean, Cristina Oana; Bănescu, Claudia; Meliţ, Lorena; Tripon, Florin; Iancu, Mihaela

2016-01-01

Abstract The present study had 2 objectives, first, to investigate possible relationships between increased gestational weight gain and demographic, clinical, paraclinical, genetic, and bioimpedance (BIA) characteristics of Romanian mothers, and second, to identify the influence of predictors (maternal and newborns characteristics) on our outcome birth weight (BW). We performed a cross-sectional study on 309 mothers and 309 newborns from Romania, divided into 2 groups: Group I—141 mothers with high gestational weight gain (GWG) and Group II—168 mothers with normal GWG, that is, control group. The groups were evaluated regarding demographic, anthropometric (body mass index [BMI], middle upper arm circumference, tricipital skinfold thickness, weight, height [H]), clinical, paraclinical, genetic (interleukin 6 [IL-6]: IL-6 -174G>C and IL-6 -572C>G gene polymorphisms), and BIA parameters. We noticed that fat mass (FM), muscle mass (MM), bone mass (BM), total body water (TBW), basal metabolism rate (BMR) and metabolic age (P < 0.001), anthropometric parameters (middle upper arm circumference, tricipital skinfold thickness; P < 0.001/P = 0.001) and hypertension (odds ratio = 4.65, 95% confidence interval: 1.27–17.03) were higher in mothers with high GWG. BW was positively correlated with mothers’ FM (P < 0.001), TBW (P = 0.001), BMR (P = 0.02), while smoking was negatively correlated with BW (P = 0.04). Variant genotype (GG+GC) of the IL-6 -572C>G polymorphism was higher in the control group (P = 0.042). We observed that high GWG may be an important predictor factor for the afterward BW, being positively correlated with FM, TBW, BMR, metabolic age of the mothers, and negatively with the mother's smoking status. Variant genotype (GG+GC) of the IL-6 -572C>G gene polymorphism is a protector factor against obesity in mothers. All the variables considered explained 14.50% of the outcome variance. PMID:27399105

Impact of demographic, genetic, and bioimpedance factors on gestational weight gain and birth weight in a Romanian population: A cross-sectional study in mothers and their newborns: the Monebo study (STROBE-compliant article).

PubMed

Mărginean, Claudiu; Mărginean, Cristina Oana; Bănescu, Claudia; Meliţ, Lorena; Tripon, Florin; Iancu, Mihaela

2016-07-01

The present study had 2 objectives, first, to investigate possible relationships between increased gestational weight gain and demographic, clinical, paraclinical, genetic, and bioimpedance (BIA) characteristics of Romanian mothers, and second, to identify the influence of predictors (maternal and newborns characteristics) on our outcome birth weight (BW).We performed a cross-sectional study on 309 mothers and 309 newborns from Romania, divided into 2 groups: Group I-141 mothers with high gestational weight gain (GWG) and Group II-168 mothers with normal GWG, that is, control group.The groups were evaluated regarding demographic, anthropometric (body mass index [BMI], middle upper arm circumference, tricipital skinfold thickness, weight, height [H]), clinical, paraclinical, genetic (interleukin 6 [IL-6]: IL-6 -174G>C and IL-6 -572C>G gene polymorphisms), and BIA parameters.We noticed that fat mass (FM), muscle mass (MM), bone mass (BM), total body water (TBW), basal metabolism rate (BMR) and metabolic age (P < 0.001), anthropometric parameters (middle upper arm circumference, tricipital skinfold thickness; P < 0.001/P = 0.001) and hypertension (odds ratio = 4.65, 95% confidence interval: 1.27-17.03) were higher in mothers with high GWG. BW was positively correlated with mothers' FM (P < 0.001), TBW (P = 0.001), BMR (P = 0.02), while smoking was negatively correlated with BW (P = 0.04). Variant genotype (GG+GC) of the IL-6 -572C>G polymorphism was higher in the control group (P = 0.042).We observed that high GWG may be an important predictor factor for the afterward BW, being positively correlated with FM, TBW, BMR, metabolic age of the mothers, and negatively with the mother's smoking status. Variant genotype (GG+GC) of the IL-6 -572C>G gene polymorphism is a protector factor against obesity in mothers. All the variables considered explained 14.50% of the outcome variance.

Brown midrib corn shredlage in diets for high-producing dairy cows.

PubMed

Vanderwerff, L M; Ferraretto, L F; Shaver, R D

2015-08-01

A novel method of harvesting whole-plant corn silage, shredlage, may increase kernel processing and physically effective fiber. Improved fiber effectiveness may be especially advantageous when feeding brown midrib (BMR) corn hybrids, which have reduced lignin content. The objective of this study was to determine the effect of feeding TMR containing BMR corn shredlage (SHRD) compared with BMR conventionally processed corn silage (KP) or KP plus chopped alfalfa hay (KPH) on intake, lactation performance, and total-tract nutrient digestibility in dairy cows. The KP was harvested using conventional rolls (2-mm gap) and the self-propelled forage harvester set at 19mm of theoretical length of cut, whereas SHRD was harvested using novel cross-grooved rolls (2-mm gap) and the self-propelled forage harvester set at 26mm of theoretical length of cut. Holstein cows (n=120; 81±8 d in milk at trial initiation), stratified by parity, days in milk, and milk yield, were randomly assigned to 15 pens of 8 cows each. Pens were randomly assigned to 1 of 3 treatment diets, SHRD, KP, or KPH, in a completely randomized design using a 2-wk covariate period with cows fed a common diet followed by a 14-wk treatment period with cows fed their assigned treatment diet. The TMR contained (dry matter basis) KP or SHRD forages (45%), alfalfa silage (10%), and a concentrate mixture (45%). Hay replaced 10% of KP silage in the KPH treatment TMR (dry matter basis). Milk, protein, and lactose yields were 3.4, 0.08, and 0.16kg/d greater, respectively, for cows fed KP and SHRD than KPH. A week by treatment interaction was detected for milk yield, such that cows fed SHRD produced or tended to produce 1.5kg/d per cow more milk, on average, than cows fed KP during 6 of the 14 treatment weeks. Component-corrected milk yields were similar among treatments. Cows fed KPH had greater milk fat concentration than cows fed KP and SHRD (3.67 vs. 3.30% on average). Consumption of dry matter, rumination activity, and sorting behavior were similar among treatments. Ruminal in situ starch digestibility was greater for SHRD than KP forages, and total-tract dietary starch digestibility was greater for SHRD than KP. Milk yield and starch digestibility were greater for SHRD than KP. Lack of improvement in milk fat content and rumination activity for SHRD compared with KP and reduced milk fat content for SHRD compared with KPH, however, suggest no improvement in physically effective fiber from the longer theoretical length of cut used with SHRD in a BMR hybrid. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Expression of brown-midrib in a spontaneous sorghum mutant is linked to a 5'-UTR deletion in lignin biosynthesis gene SbCAD2

USDA-ARS?s Scientific Manuscript database

Brown midrib (bmr) mutants in sorghum (Sorghum bicolor (L.) Moench) and several other C4 grasses are associated with reduced lignin concentration, altered lignin composition and improved cell wall digestibility, which are desirable properties in biomass development for the emerging lignocellulosic b...

Replacing conventional or brown-mid rib corn silage with brown-mid rib sudangrass silage in the diets of lactating dairy cows

USDA-ARS?s Scientific Manuscript database

Forages that use less water, but are high in digestibility, are sought as alternatives to traditional forages such as corn silage. Brown mid-rib (BMR) sudangrass is a possible alternative that can provide high-quality forage as a replacement for corn silage. The objective of this study was to evalua...

Full scale wind tunnel investigation of a bearingless main helicopter rotor. [Ames 40 by 80 foot wind tunnel test using the BO-105 helicopter

NASA Technical Reports Server (NTRS)

1980-01-01

A stability test program was conducted to determine the effects of airspeed, collective pitch, rotor speed and shaft angle on stability and loads at speeds beyond that attained in the BMR/BO-105 flight test program. Loads and performance data were gathered at forward speeds up to 165 knots. The effect of cyclic pitch perturbations on rotor response was investigated at simulated level flight conditions. Two configuration variations were tested for their effect on stability. One variable was the control system stiffness. An axially softer pitch link was installed in place of the standard BO-105 pitch link. The second variation was the addition of elastomeric damper strips to increase the structural damping. The BMR was stable at all conditions tested. At fixed collective pitch, shaft angle and rotor speed, damping generally increased between hover and 60 knots, remained relatively constant from 60 to 90 knots, then decreased above 90 knots. Analytical predictions are in good agreement with test data up to 90 knots, but the trend of decreasing damping above 90 knots is contrary to the theory.

Geographic variation in the association between exploratory behavior and physiology in rufous-collared sparrows.

PubMed

Maldonado, Karin; van Dongen, Wouter F D; Vásquez, Rodrigo A; Sabat, Pablo

2012-01-01

Increasing research has attempted to clarify the links between animal personality and physiology. However, the mechanisms driving this association remain largely unknown, and knowledge of how ecological factors may affect its direction and strength is scant. In this study, we quantified variation in the association between exploratory behavior, basal metabolic rate (BMR), and total evaporative water loss (TEWL) in rufous-collared sparrows (Zonotrichia capensis) inhabiting desert, Mediterranean, and cold-temperate climates. We found that the exploratory behavior score was highest in birds from the cold-temperate site, which was characterized by a moderate level of ecological variability (seasonality). Moreover, the association between exploratory behavior and physiological variables differed among localities. Only birds from the Mediterranean site showed a positive correlation between exploratory behavior and BMR. We found no association between exploration and TEWL at any study site. Our findings suggest that differences in the ecological conditions experienced by each sparrow population result in a particular combination of behavioral and physiological traits. An understanding of this intraspecific variation along ecological gradients provides unique insights into how specific ecological conditions affect the coupling of behavioral and physiological traits and the mechanisms underlying that relationship.

Seasonal acclimatization of metabolism in Eurasian tree sparrows (Passer montanus).

PubMed

Zheng, Wei-Hong; Li, Ming; Liu, Jin-Song; Shao, Shu-Li

2008-12-01

Acclimatization to winter conditions is an essential prerequisite for survival of small passerines of the northern temperate zone. Changes in photoperiod, ambient temperature and food availability trigger seasonal acclimatization in physiology and behavior of many birds. In the present study, seasonal adjustments in several physiological, hormonal, and biochemical markers were examined in wild-captured Eurasian tree sparrows (Passer montanus) from the Heilongjiang Province in China. In winter sparrows had higher body mass and basal metabolic rate (BMR). Consistently, the dry mass of liver, heart, gizzard, small intestine, large intestine and total digestive tract were higher in winter than in that in summer. The contents of mitochondrial protein in liver, and state-4 respiration and cytochrome c oxidase (COX) activity in liver and muscle increased significantly in winter. Circulating level of serum triiodothyronine (T3) was significantly higher in winter than in summer. Together, these data suggest that tree sparrows mainly coped with cold by enhancing thermogenic capacities through increased organ masses and heightened activity of respiratory enzymes activities. The results support the view that prominent winter increases in BMR are manifestations of winter acclimatization in tree sparrows and that seasonal variation in metabolism in sparrows is similar to that in other small temperate-wintering birds.

Cinnamic acid 4-hydroxylase of sorghum [Sorghum biocolor (L.) Moench] gene SbC4H1 restricts lignin synthesis in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Cinnamic acid 4-hydroxylase (C4H) is the first hydroxylase enzyme of the phenylpropanoid pathway, and its content and activity affects the lignin synthesis. In this study, we isolated a C4H gene SbC4H1 from the suppression subtractive hybridization library of brown midrib (bmr) mutants of Sorghum b...

Symptomatic Overt Hypothyroidism Post Induction

DTIC Science & Technology

2017-10-21

to increased sensitivity of anesthetic agents due to decreased ca rdiac contractility, cardiac output, blood volume, 02 consumption and increased SVR...risk of increasing myocardial oxygen demand, and causing ischemia. However, delay in therapy may place the patient at risk of developing myxedema...endocrinologists recommend starting at least low dose T4 ENDO: BMR is only 55 -60% of normal -7 inability to increase core temperature Chronically

Parental expenditure of time and energy in the Abert's Towhee (Pipilo aberti)

Treesearch

Deborah M. Finch

1984-01-01

Daily activity budgets of male and female Abert's Towhees (Pipilo aberti) were measured in 1980 during the reproductive cycle and then converted into energy budgets to determine the relative demands of different nesting phases. Mean daily energy expenditures (DEEtot) in males reached a seasonal maximum of 126.7 kJ, or 2.16 times basal metabolic rate (BMR), in the...

Validity of U.S. Nutritional Surveillance: National Health and Nutrition Examination Survey Caloric Energy Intake Data, 1971–2010

PubMed Central

Archer, Edward; Hand, Gregory A.; Blair, Steven N.

2013-01-01

Importance Methodological limitations compromise the validity of U.S. nutritional surveillance data and the empirical foundation for formulating dietary guidelines and public health policies. Objectives Evaluate the validity of the National Health and Nutrition Examination Survey (NHANES) caloric intake data throughout its history, and examine trends in the validity of caloric intake estimates as the NHANES dietary measurement protocols evolved. Design Validity of data from 28,993 men and 34,369 women, aged 20 to 74 years from NHANES I (1971–1974) through NHANES 2009–2010 was assessed by: calculating physiologically credible energy intake values as the ratio of reported energy intake (rEI) to estimated basal metabolic rate (BMR), and subtracting estimated total energy expenditure (TEE) from NHANES rEI to create ‘disparity values’. Main Outcome Measures 1) Physiologically credible values expressed as the ratio rEI/BMR and 2) disparity values (rEI–TEE). Results The historical rEI/BMR values for men and women were 1.31 and 1.19, (95% CI: 1.30–1.32 and 1.18–1.20), respectively. The historical disparity values for men and women were −281 and −365 kilocalorie-per-day, (95% CI: −299, −264 and −378, −351), respectively. These results are indicative of significant under-reporting. The greatest mean disparity values were −716 kcal/day and −856 kcal/day for obese (i.e., ≥30 kg/m2) men and women, respectively. Conclusions Across the 39-year history of the NHANES, EI data on the majority of respondents (67.3% of women and 58.7% of men) were not physiologically plausible. Improvements in measurement protocols after NHANES II led to small decreases in underreporting, artifactual increases in rEI, but only trivial increases in validity in subsequent surveys. The confluence of these results and other methodological limitations suggest that the ability to estimate population trends in caloric intake and generate empirically supported public policy relevant to diet-health relationships from U.S. nutritional surveillance is extremely limited. PMID:24130784

The effects of calcium hydroxide-treated whole-plant and fractionated corn silage on intake, digestion, and lactation performance in dairy cows.

PubMed

Cook, D E; Bender, R W; Shinners, K J; Combs, D K

2016-07-01

The objective of this trial was to evaluate, in dairy cattle, the effects of calcium hydroxide treatment of whole-plant corn and a treatment applied to the bottom stalk fraction of the corn plant, achieved by harvesting corn in 2 crop streams. The treatments were calcium hydroxide-treated corn silage (TRTCS), toplage supplemented with calcium hydroxide-treated stalklage (TPL), a positive control of brown midrib corn silage (BMR), and a negative control of conventional whole-plant corn silage (WPCS). The toplage was harvested at a height of 82 cm with 2 of the 6 rows set as ear-snapping to incorporate higher tissues into the stalklage. Stalklage was harvested at 12 cm, and other corn silages were harvested at 27 cm. Sixteen pens, each with 8 Holstein cows averaging 70±25 d in milk and 46±11 kg of milk d(-1), were assigned 4 per treatment in a completely randomized design. The diet was approximately 40% corn silage, 20% alfalfa silage, and 40% concentrate on a dry matter basis. A 2-wk covariate period with conventional corn silage was followed by an 8-wk treatment period in which the 4 corn silage treatments were the only effective difference in diets. Cows fed TPL and TRTCS consumed more (1.9 and 1.4 kg of organic matter d(-1), respectively) than did cows fed WPCS. Milk yield was greater for cows fed BMR, TPL, and TRTCS. Cows fed BMR and TPL produced 2.9 and 2.7 kg d(-1), respectively, more energy-corrected milk (ECM) than cows fed WPCS, and cows fed TRTCS had the greatest ECM production (4.8 kg of ECM d(-1) greater than cows fed WPCS). No differences in body weight or body condition scored were observed. Milk fat concentration was similar among treatments and milk protein concentration was reduced for TRTCS. Starch and neutral detergent fiber digestibility were greater for cows fed TRTCS. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Quantification of trunk and android lean mass using dual energy x-ray absorptiometry compared to magnetic resonance imaging after spinal cord injury.

PubMed

Rankin, Kathleen C; O'Brien, Laura C; Gorgey, Ashraf S

2018-02-20

To determine whether dual energy x-ray absorptiometry (DXA) compared to magnetic resonance imaging (MRI) may accurately quantify trunk lean mass (LM) after chronic spinal cord injury (SCI) and to investigate the relationships between trunk LM, visceral adiposity, trunk fat mass and basal metabolic rate (BMR). Cross-sectional design and correlational analysis. Research setting in a medical center. Twenty-two men with motor complete paraplegia (n = 14; T4-T11) and tetraplegia (n = 8; C5-C7) were recruited as part of a clinical trial. Not applicable. Trunk and android LM were measured using DXA. The volume of six trunk muscle groups were then measured using MRI to quantify trunk LM-MRI. Subcutaneous and visceral adipose tissue (VAT) cross-sectional areas were also measured using MRI. After overnight fast, BMR was evaluated using indirect calorimetry. Trunk LM-DXA (24 ± 3.3 kg) and android LM-DXA (3.6 ± 0.7 kg) overestimated (P < 0.0001) trunk LM-MRI (1.7 ± 0.5 kg). Trunk LM-MRI = 0.088* log (trunk LM-DXA)-0.415; r 2 =0.29, SEE= 0.44 kg, P = 0.007. Trunk LM-MRI = 1.53* android LM-DXA + 0.126; r 2 =0.26, SEE= 0.21 kg, P = 0.018. Percentage trunk LM-MRI was inversely related to VAT (r=-0.79, P < 0.0001) and trunk fat mass (r=-0.83, P < 0.001). Only trunk LM-DXA was related to BMR (r = 0.61, P = 0.002). Persons with tetraplegia have 13% smaller trunk muscle cross-sectional areas (P = 0.036) compared to those with paraplegia. Trunk LM-DXA and android LM-DXA overestimated trunk LM-MRI. Percentage trunk LM-MRI, but not LM-DXA, was inversely related to trunk central adiposity. The findings highlight the importance of exercising trunk LM to attenuate cardio-metabolic disorders after SCI.

Life in the unthinking depths: energetic constraints on encephalization in marine fishes.

PubMed

Iglesias, T L; Dornburg, A; Brandley, M C; Alfaro, M E; Warren, D L

2015-05-01

Several hypotheses have been proposed to explain the limitation of brain size in vertebrates. Here, we test three hypotheses of brain size evolution using marine teleost fishes: the direct metabolic constraints hypothesis (DMCH), the expensive tissue hypothesis and the temperature-dependent hypothesis. Our analyses indicate that there is a robust positive correlation between encephalization and basal metabolic rate (BMR) that spans the full range of depths occupied by teleosts from the epipelagic (< 200 m), mesopelagic (200-1000 m) and bathypelagic (> 4000 m). Our results disentangle the effects of temperature and metabolic rate on teleost brain size evolution, supporting the DMCH. Our results agree with previous findings that teleost brain size decreases with depth; however, we also recover a negative correlation between trophic level and encephalization within the mesopelagic zone, a result that runs counter to the expectations of the expensive tissue hypothesis. We hypothesize that mesopelagic fishes at lower trophic levels may be investing more in neural tissue related to the detection of small prey items in a low-light environment. We recommend that comparative encephalization studies control for BMR in addition to controlling for body size and phylogeny. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

High prevalence of malnutrition and deranged relationship between energy demands and food intake in advanced non-small cell lung cancer.

PubMed

Mohan, A; Poulose, R; Kulshreshtha, I; Chautani, A M; Madan, K; Hadda, V; Guleria, R

2017-07-01

The relation between dietary intake and metabolic profile in non-small cell lung cancer (NSCLC) was evaluated. Patients with NSCLC were recruited and their caloric requirement and resting energy expenditure (REE) were calculated using the Harris-Benedict equation and Katch-McArdle formula respectively. Hypermetabolic state was defined as REE more than 10% above the basal metabolic rate (BMR). Body composition parameters were calculated by bioelectric impedance method. The 24-h dietary intake method and Malnutrition Universal Screening Tool assessed nutritional intake. One hundred and forty-eight subjects were included (87% males). Of these, 46.6% subjects were hypermetabolic and 31% cachexic, with lower calorie and protein intakes than recommended, although per cent of total energy derived from protein, fat and carbohydrates were similar. Hypermetabolic patients had lower BMI, though the per cent deficit in energy and protein consumption was similar. Cachexia was associated with lower BMR but not with deficit in energy or protein consumption. No correlation was seen between dietary intake and body composition parameters. The calorie and protein intake of NSCLC patients is lower than recommended. The discordance between elevated REE and dietary intake implies that the relationship between increased energy demands and food intake may be altered. © 2016 John Wiley & Sons Ltd.

Recombinant antigen-based antibody assays for the diagnosis and surveillance of lymphatic filariasis – a multicenter trial

PubMed Central

Lammie, Patrick J; Weil, Gary; Noordin, Rahmah; Kaliraj, Perumal; Steel, Cathy; Goodman, David; Lakshmikanthan, Vijaya B; Ottesen, Eric

2004-01-01

The development of antifilarial antibody responses is a characteristic feature of infection with filarial parasites. It should be possible to exploit this fact to develop tools to monitor the progress of the global program to eliminate lymphatic filariasis (LF); however, assays based on parasite extracts suffer from a number of limitations, including the paucity of parasite material, the difficulty of assay standardization and problems with assay specificity. In principle, assays based on recombinant filarial antigens should address these limitations and provide useful tools for diagnosis and surveillance of LF. The present multicenter study was designed to compare the performance of antibody assays for filariasis based on recombinant antigens Bm14, WbSXP, and BmR1. Coded serum specimens were distributed to five participating laboratories where assays for each antigen were conducted in parallel. Assays based on Bm14, WbSXP, or BmR1 demonstrated good sensitivity (>90%) for field use and none of the assays demonstrated reactivity with specimens from persons with non-filarial helminth infections. Limitations of the assays are discussed. Well-designed field studies are now needed to assess sampling methodology and the application of antibody testing to the monitoring and surveillance of LF elimination programs. PMID:15347425

A COUPLED 2 × 2D BABCOCK–LEIGHTON SOLAR DYNAMO MODEL. I. SURFACE MAGNETIC FLUX EVOLUTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemerle, Alexandre; Charbonneau, Paul; Carignan-Dugas, Arnaud, E-mail: lemerle@astro.umontreal.ca, E-mail: paulchar@astro.umontreal.ca

The need for reliable predictions of the solar activity cycle motivates the development of dynamo models incorporating a representation of surface processes sufficiently detailed to allow assimilation of magnetographic data. In this series of papers we present one such dynamo model, and document its behavior and properties. This first paper focuses on one of the model’s key components, namely surface magnetic flux evolution. Using a genetic algorithm, we obtain best-fit parameters of the transport model by least-squares minimization of the differences between the associated synthetic synoptic magnetogram and real magnetographic data for activity cycle 21. Our fitting procedure also returnsmore » Monte Carlo-like error estimates. We show that the range of acceptable surface meridional flow profiles is in good agreement with Doppler measurements, even though the latter are not used in the fitting process. Using a synthetic database of bipolar magnetic region (BMR) emergences reproducing the statistical properties of observed emergences, we also ascertain the sensitivity of global cycle properties, such as the strength of the dipole moment and timing of polarity reversal, to distinct realizations of BMR emergence, and on this basis argue that this stochasticity represents a primary source of uncertainty for predicting solar cycle characteristics.« less

Cross-training in birds: cold and exercise training produce similar changes in maximal metabolic output, muscle masses and myostatin expression in house sparrows (Passer domesticus)

PubMed Central

Zhang, Yufeng; Eyster, Kathleen; Liu, Jin-Song; Swanson, David L.

2015-01-01

ABSTRACT Maximal metabolic outputs for exercise and thermogenesis in birds presumably influence fitness through effects on flight and shivering performance. Because both summit (Msum, maximum thermoregulatory metabolic rate) and maximum (MMR, maximum exercise metabolic rate) metabolic rates are functions of skeletal muscle activity, correlations between these measurements and their mechanistic underpinnings might occur. To examine whether such correlations occur, we measured the effects of experimental cold and exercise training protocols for 3 weeks on body (Mb) and muscle (Mpec) masses, basal metabolic rate (BMR), Msum, MMR, pectoralis mRNA and protein expression for myostatin, and mRNA expression of TLL-1 and TLL-2 (metalloproteinase activators of myostatin) in house sparrows (Passer domesticus). Both training protocols increased Msum, MMR, Mb and Mpec, but BMR increased with cold training and decreased with exercise training. No significant differences occurred for pectoralis myostatin mRNA expression, but cold and exercise increased the expression of TLL-1 and TLL-2. Pectoralis myostatin protein levels were generally reduced for both training groups. These data clearly demonstrate cross-training effects of cold and exercise in birds, and are consistent with a role for myostatin in increasing pectoralis muscle mass and driving organismal increases in metabolic capacities. PMID:25987736

A microcomputer controlled snow ski binding system--I. Instrumentation and field evaluation.

PubMed

MacGregor, D; Hull, M L; Dorius, L K

1985-01-01

This paper presents the design and field evaluation of the first microcomputer controlled ski binding system. This system incorporates an Intel 8086 microcomputer controller and an integral binding/dynamometer. This instrumentation system not only undertakes real time control, but also it records dynamometer data via a miniature digital cassette tape recorder. The integral binding/dynamometer offers the same operational and mounting convenience of commercially available mechanical bindings. The binding may be released either manually or electrically via the controller. Comprised of four octagonal half strain rings, the strain gage dynamometer measures the three moment load components at the boot. To enable the user to conveniently operate the computer, extensive operating software was developed. The operating software is discussed in relation to both the acquisition and storage of data from the dynamometer and the control of the electro-mechanical snow ski binding. The binding system has been used successfully to both record boot moment components and control ski binding release during actual skiing maneuvers. Moment histories typical of three common recreational skiing maneuvers are presented.

Nutritional Determination of Bone Health: A Survey of Australian Defence Force (ADF) Trainees

DTIC Science & Technology

2005-07-01

aims to determine the prevalence of key risk factors, including diet, exercise, bone turn-over, bone mineral density and anthropometry , and to relate...incorporated in bone matrix during bone formation. The ratio of undercarboxylated osteocalcin (a protein with low biological activity) to total...serves returned to DSTO- Scottsdale. 2.3 Data Manipulation A ratio of energy intake (EI) to Basal Metabolic Rate (BMR) of 0.9 represents the

Nutritional Determinants of Bone Health: A Survey of Australian Defence Force (ADF) Trainees

DTIC Science & Technology

2005-07-01

aims to determine the prevalence of key risk factors, including diet, exercise, bone turn-over, bone mineral density and anthropometry , and to relate...incorporated in bone matrix during bone formation. The ratio of undercarboxylated osteocalcin (a protein with low biological activity) to total...serves returned to DSTO- Scottsdale. 2.3 Data Manipulation A ratio of energy intake (EI) to Basal Metabolic Rate (BMR) of 0.9 represents the

Novel Magnetic Devices

DTIC Science & Technology

2007-10-12

Vincent, Magnetism Magnetic Materials (LAW3MO5), Vifia del Mar, Chile, December 11-15, 2005. 5. Nanomagnetism, Ivan K. Schuller, Pan America Advanced Study Institute, PASI 2007, Zacatecas , Mexico , June 19, 2007. 6 ...project explored the design, preparation, measurement and theoretical study of these novel magnetic devices. Modem thin film techniques (sputtering and...results to motion associated with the unstable nature of mechanical contacts In order to exploit BMR from a device point of view (or to make it useful in a

Cross-training in birds: cold and exercise training produce similar changes in maximal metabolic output, muscle masses and myostatin expression in house sparrows (Passer domesticus).

PubMed

Zhang, Yufeng; Eyster, Kathleen; Liu, Jin-Song; Swanson, David L

2015-07-01

Maximal metabolic outputs for exercise and thermogenesis in birds presumably influence fitness through effects on flight and shivering performance. Because both summit (Msum, maximum thermoregulatory metabolic rate) and maximum (MMR, maximum exercise metabolic rate) metabolic rates are functions of skeletal muscle activity, correlations between these measurements and their mechanistic underpinnings might occur. To examine whether such correlations occur, we measured the effects of experimental cold and exercise training protocols for 3 weeks on body (Mb) and muscle (Mpec) masses, basal metabolic rate (BMR), Msum, MMR, pectoralis mRNA and protein expression for myostatin, and mRNA expression of TLL-1 and TLL-2 (metalloproteinase activators of myostatin) in house sparrows (Passer domesticus). Both training protocols increased Msum, MMR, Mb and Mpec, but BMR increased with cold training and decreased with exercise training. No significant differences occurred for pectoralis myostatin mRNA expression, but cold and exercise increased the expression of TLL-1 and TLL-2. Pectoralis myostatin protein levels were generally reduced for both training groups. These data clearly demonstrate cross-training effects of cold and exercise in birds, and are consistent with a role for myostatin in increasing pectoralis muscle mass and driving organismal increases in metabolic capacities. © 2015. Published by The Company of Biologists Ltd.

Intraspecific variation in the energetics of the Cabrera vole.

PubMed

Castellanos-Frías, Elena; García-Perea, Rosa; Gisbert, Julio; Bozinovic, Francisco; Virgós, Emilio

2015-12-01

Basal metabolic rate (BMR) is an intensively topic studied in ecophysiology for the purpose of understanding energy budgets of the species, variations of energy expenditure during their diary activities and physiological acclimatization to the environment. Establishing how the metabolism is assembled to the environment can provide valuable data to improve conservation strategies of endangered species. In this sense, metabolic differences associated to habitats have been widely reported in the interspecific level, however little is known about the intraspecific view of BMR under an environmental gradient. In this study, we researched the effect of the habitat on metabolic rate of an Iberian endemic species: Iberomys cabrerae. Animals were captured in different subpopulations of its altitudinal range and their MR was studied over a thermal gradient. MR was analyzed through a Linear Mixed Model (LMM) in which, in addition to thermal effects, the bioclimatic zone and sex also influenced the metabolism of the species. The beginning of thermoneutrality zone was set on 26.5°C and RMR was 2.3ml O2g(-1)h(-1), intermediate between both bioclimatic zones. Supramediterranean subpopulations started the Tlc earlier (24.9°C) and had higher RMR than the mesomediterranean ones (26.9°C). The thermal environment together with primary productivity conditions could explain this difference in the metabolic behaviour of the Cabrera voles. Copyright © 2015 Elsevier Inc. All rights reserved.

The metabolic cost of an integrated exercise program performed during 14 days of bed rest.

PubMed

Scott, Jessica M; Hackney, Kyle; Downs, Meghan; Guined, Jamie; Ploutz-Snyder, Robert; Fiedler, James; Cunningham, David; Ploutz-Snyder, Lori

2014-06-01

Exercise countermeasures designed to mitigate muscle atrophy during long-duration spaceflight may not be as effective if crewmembers are in negative energy balance (energy output > energy input). This study determined the energy cost of supine exercise (resistance, interval, aerobic) during the spaceflight analogue of bed rest. Nine subjects (eight men and one woman; 34.5 +/- 8.2 yr) completed 14 d of bed rest and concomitant exercise countermeasures. Body mass and basal metabolic rate (BMR) were assessed before and during bed rest. Exercise energy expenditure was measured during and immediately after [excess post-exercise oxygen consumption (EPOC)] each of five different exercise protocols (30-s, 2-min, and 4-min intervals, continuous aerobic, and a variety of resistance exercises) during bed rest. On days when resistance and continuous aerobic exercise were performed daily, energy expenditure was significantly greater (2879 +/- 280 kcal) than 2-min (2390 +/- 237 kcal), 30-s (2501 +/- 264 kcal), or 4-min (2546 +/- 264 kcal) exercise. There were no significant differences in BMR (pre-bed rest: 1649 +/- 216 kcal; week 1: 1632 +/- 174 kcal; week 2:1657 +/- 176 kcal) or body mass (pre-bed rest: 75.2 +/- 10.1 kg; post-bed rest: 75.2 +/- 9.6 kg). These findings highlight the importance of energy balance for long-duration crewmembers completing a high-intensity exercise program with multiple exercise sessions daily.

Advances in the simulation of toroidal gyro-Landau fluid model turbulence

NASA Astrophysics Data System (ADS)

Waltz, R. E.; Kerbel, G. D.; Milovich, J.; Hammett, G. W.

1995-06-01

The gyro-Landau fluid (GLF) model equations for toroidal geometry [R. E. Waltz, R. R. Dominguez, and G. W. Hammett, Phys. Fluids B 4, 3138 (1992)] have been recently applied to study ion temperature gradient (ITG) mode turbulence using the three-dimensional (3-D) nonlinear ballooning mode representation (BMR) outlined earlier [R. E. Waltz, G. D. Kerbel, and J. Milovich, Phys. Plasmas 1, 2229 (1994)]. The present paper extends this work by treating some unresolved issues concerning ITG turbulence with adiabatic electrons. Although eddies are highly elongated in the radial direction, long time radial correlation lengths are short and comparable to poloidal lengths. Although transport at vanishing shear is not particularly large, transport at reverse global shear, is significantly less. Electrostatic transport at moderate shear is not much affected by inclusion of local shear and average favorable curvature. Transport is suppressed when critical E×B rotational shear is comparable to the maximum linear growth rate with only a weak dependence on magnetic shear. Self-consistent turbulent transport of toroidal momentum can result in a transport bifurcation at sufficiently large r/(Rq). However, the main thrust of the new formulation in the paper deals with advances in the development of finite beta GLF models with trapped electrons and BMR numerical methods for treating the fast parallel field motion of the untrapped electrons.

Metabolic heat production and thermal conductance are mass-independent adaptations to thermal environment in birds and mammals.

PubMed

Fristoe, Trevor S; Burger, Joseph R; Balk, Meghan A; Khaliq, Imran; Hof, Christian; Brown, James H

2015-12-29

The extent to which different kinds of organisms have adapted to environmental temperature regimes is central to understanding how they respond to climate change. The Scholander-Irving (S-I) model of heat transfer lays the foundation for explaining how endothermic birds and mammals maintain their high, relatively constant body temperatures in the face of wide variation in environmental temperature. The S-I model shows how body temperature is regulated by balancing the rates of heat production and heat loss. Both rates scale with body size, suggesting that larger animals should be better adapted to cold environments than smaller animals, and vice versa. However, the global distributions of ∼9,000 species of terrestrial birds and mammals show that the entire range of body sizes occurs in nearly all climatic regimes. Using physiological and environmental temperature data for 211 bird and 178 mammal species, we test for mass-independent adaptive changes in two key parameters of the S-I model: basal metabolic rate (BMR) and thermal conductance. We derive an axis of thermal adaptation that is independent of body size, extends the S-I model, and highlights interactions among physiological and morphological traits that allow endotherms to persist in a wide range of temperatures. Our macrophysiological and macroecological analyses support our predictions that shifts in BMR and thermal conductance confer important adaptations to environmental temperature in both birds and mammals.

Conformational and thermodynamic hallmarks of DNA operator site specificity in the copper sensitive operon repressor from Streptomyces lividans

PubMed Central

Tan, Benedict G.; Vijgenboom, Erik; Worrall, Jonathan A. R.

2014-01-01

Metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. The copper sensitive operon repressor (CsoR) family is widely distributed in bacteria and controls the expression of copper efflux systems. CsoR operator sites consist of G-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. Here, we use a structurally characterized CsoR from Streptomyces lividans (CsoRSl) together with three specific operator targets to reveal the salient features pertaining to the mechanism of DNA binding. We reveal that CsoRSl binds to its operator site through a 2-fold axis of symmetry centred on a conserved 5′-TAC/GTA-3′ inverted repeat. Operator recognition is stringently dependent not only on electropositive residues but also on a conserved polar glutamine residue. Thermodynamic and circular dichroic signatures of the CsoRSl–DNA interaction suggest selectivity towards the A-DNA-like topology of the G-tracts at the operator site. Such properties are enhanced on protein binding thus enabling the symmetrical binding of two CsoRSl tetramers. Finally, differential binding modes may exist in operator sites having more than one 5′-TAC/GTA-3′ inverted repeat with implications in vivo for a mechanism of modular control. PMID:24121681

The FTO gene polymorphism (rs9939609) is associated with metabolic syndrome in morbidly obese subjects from southern Italy.

PubMed

Liguori, Rosario; Labruna, Giuseppe; Alfieri, Andreina; Martone, Domenico; Farinaro, Eduardo; Contaldo, Franco; Sacchetti, Lucia; Pasanisi, Fabrizio; Buono, Pasqualina

2014-08-01

Gene variants in MC4R, SIRT1 and FTO are associated with severe obesity and metabolic impairment in Caucasians. We investigated whether common variants in these genes are associated with metabolic syndrome (MetS) in a large group of morbidly obese young adults from southern Italy. One thousand morbidly obese subjects (62% women, mean body mass index 46.5 kg/m(2), mean age 32.6 years) whose families had lived in southern Italy for at least 2 generations were recruited. Single-nucleotide polymorphisms (SNPs) rs12970134, rs477181, rs502933 (MC4R locus), rs3818292, rs7069102, rs730821, rs2273773, rs12413112 (SIRT1 locus) and rs1421085, rs9939609, 9930506, 1121980 (FTO locus) were genotyped by Taqman assay; blood parameters were assayed by routine methods; the Fat Mass, Fat Free Mass, Respiratory Quotient, Basal Metabolic Rate (BMR) and waist circumference were also determined. Binomial logistic regression showed that the TA heterozygous genotype of SNP rs9939609 in the FTO gene was associated with the presence of MetS in our population [OR (95% CI): 2.53 (1.16-5.55)]. Furthermore, the FTO rs9939609 genotype accounted for 21.3% of the MetS phenotype together with total cholesterol, BMR and age. Our results extend the knowledge on genotype susceptibility for MetS in relation to a specific geographical area of residence. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Metabolic Cost of a High Intensity Exercise Program During Bed Rest

NASA Technical Reports Server (NTRS)

Hackney, Kyle; Everett, Meghan; Guined, Jamie; Cunningham, Daid

2012-01-01

Background: Given that disuse-related skeletal muscle atrophy may be exacerbated by an imbalance between energy intake and output, the amount of energy required to complete exercise countermeasures is an important consideration in the well being of subject health during bed rest and spaceflight. Objective: To evaluate the energy cost of a high intensity exercise program performed during short duration bed rest. Methods: 9 subjects (8 male and 1 female; 34.5 +/- 8.2 years) underwent 14 days of bed rest and exercise countermeasures. Exercise energy expenditure and excess post exercise oxygen consumption (EPOC) were collected once in each of 5 different exercise protocols (30 second, 2 minute and 4 minute intervals, continuous aerobic and a variety of resistance exercises) during bed rest. Body mass, basal metabolic rate (BMR), upper and lower leg muscle, subcutaneous, and intramuscular adipose tissue (IMAT) volumes were assessed before and at the end of bed rest. Results: There were no significant differences in body mass (pre: 75.1 +/- 10.5 kg; post: 75.2 +/- 10.1 kg), BMR (pre: 1649 +/- 216 kcal; post: 1657 +/- 177 kcal), muscle subcutaneous, or IMAT volumes (Table 2) after 14 days of bed rest and exercise. Body mass was maintained with an average daily intake of 2710 +/- 262 kcal (36.2 +/- 2.1 kcal/kg/day), while average daily energy expenditure was 2579 +/-311 kcal (34.5 +/- 3.6 kcal/kg/day). Exercise energy expenditure was significantly greater as a result of continuous aerobic exercise than all other exercise protocols.

Adaptive dimensions of health research among indigenous Siberians.

PubMed

Snodgrass, J Josh; Sorensen, Mark V; Tarskaia, Larissa A; Leonard, William R

2007-01-01

Present evidence suggests that modern humans were the first hominid species to successfully colonize high-latitude environments (> or =55 degrees N). Given evidence for a recent (<200,000 years) lower latitude naissance of modern humans, the global dispersal and successful settlement of arctic and subarctic regions represent an unprecedented adaptive shift. This adaptive shift, which included cultural, behavioral, and biological dimensions, allowed human populations to cope with the myriad environmental stressors encountered in circumpolar regions. Although unique morphological and physiological adaptations among contemporary northern residents have been recognized for decades, human biologists are only now beginning to consider whether biological adaptations to regional environmental conditions influence health changes associated with economic modernization and lifestyle change. Recent studies have documented basal metabolic rates (BMRs) among indigenous Siberian populations that are systematically elevated compared to lower latitude groups; this metabolic elevation apparently is a physiological adaptation to cold stress experienced in the circumpolar environment. Important health implications of metabolic adaptation are suggested by research with the Yakut (Sakha), Evenki, and Buriat of Siberia. BMR is significantly positively correlated with blood pressure, independently of body size, body composition, and various potentially confounding variables (e.g., age and smoking). Further, this research has documented a significant negative association between BMR and LDL cholesterol, which remains after controlling for potential confounders; this suggests that high metabolic turnover among indigenous Siberians has a protective effect with regard to plasma lipid levels. These results underscore the importance of incorporating an evolutionary approach into health research among northern populations.

Long-term effect of yogic practices on diurnal metabolic rates of healthy subjects.

PubMed

Chaya, M S; Nagendra, H R

2008-01-01

The metabolic rate is an indicator of autonomic activity. Reduced sympathetic arousal probably resulting in hypometabolic states has been reported in several yogic studies. The main objective of this study was to assess the effect of yoga training on diurnal metabolic rates in yoga practitioners at two different times of the day (at 6 a.m. and 9 p.m.). Eighty eight healthy volunteers were selected and their metabolic rates assessed at 6 a.m. and 9 p.m. using an indirect calorimeter at a yoga school in Bangalore, India. The results show that the average metabolic rate of the yoga group was 12% lower than that of the non-yoga group (P < 0.001) measured at 9 p.m. and 16% lower at 6 a.m. (P < 0.001). The 9 p.m. metabolic rates of the yoga group were almost equal to their predicted basal metabolic rates (BMRs) whereas the metabolic rate was significantly higher than the predicted BMR for the non-yoga group. The 6 a.m. metabolic rate was comparable to their predicted BMR in the non-yoga group whereas it was much lower in the yoga group (P < 0.001). The lower metabolic rates in the yoga group at 6 a.m. and 9 p.m. may be due to coping strategies for day-to-day stress, decreased sympathetic nervous system activity and probably, a stable autonomic nervous system response (to different stressors) achieved due to training in yoga.

Metabolic heat production and thermal conductance are mass-independent adaptations to thermal environment in birds and mammals

PubMed Central

Fristoe, Trevor S.; Burger, Joseph R.; Balk, Meghan A.; Khaliq, Imran; Hof, Christian; Brown, James H.

2015-01-01

The extent to which different kinds of organisms have adapted to environmental temperature regimes is central to understanding how they respond to climate change. The Scholander–Irving (S-I) model of heat transfer lays the foundation for explaining how endothermic birds and mammals maintain their high, relatively constant body temperatures in the face of wide variation in environmental temperature. The S-I model shows how body temperature is regulated by balancing the rates of heat production and heat loss. Both rates scale with body size, suggesting that larger animals should be better adapted to cold environments than smaller animals, and vice versa. However, the global distributions of ∼9,000 species of terrestrial birds and mammals show that the entire range of body sizes occurs in nearly all climatic regimes. Using physiological and environmental temperature data for 211 bird and 178 mammal species, we test for mass-independent adaptive changes in two key parameters of the S-I model: basal metabolic rate (BMR) and thermal conductance. We derive an axis of thermal adaptation that is independent of body size, extends the S-I model, and highlights interactions among physiological and morphological traits that allow endotherms to persist in a wide range of temperatures. Our macrophysiological and macroecological analyses support our predictions that shifts in BMR and thermal conductance confer important adaptations to environmental temperature in both birds and mammals. PMID:26668359

A Randomized Study of the Effects of Additional Fruit and Nuts Consumption on Hepatic Fat Content, Cardiovascular Risk Factors and Basal Metabolic Rate.

PubMed

Agebratt, Christian; Ström, Edvin; Romu, Thobias; Dahlqvist-Leinhard, Olof; Borga, Magnus; Leandersson, Per; Nystrom, Fredrik H

2016-01-01

Fruit has since long been advocated as a healthy source of many nutrients, however, the high content of sugars in fruit might be a concern. To study effects of an increased fruit intake compared with similar amount of extra calories from nuts in humans. Thirty healthy non-obese participants were randomized to either supplement the diet with fruits or nuts, each at +7 kcal/kg bodyweight/day for two months. Major endpoints were change of hepatic fat content (HFC, by magnetic resonance imaging, MRI), basal metabolic rate (BMR, with indirect calorimetry) and cardiovascular risk markers. Weight gain was numerically similar in both groups although only statistically significant in the group randomized to nuts (fruit: from 22.15 ± 1.61 kg/m(2) to 22.30 ± 1.7 kg/m(2), p = 0.24 nuts: from 22.54 ± 2.26 kg/m(2) to 22.73 ± 2.28 kg/m(2), p = 0.045). On the other hand BMR increased in the nut group only (p = 0.028). Only the nut group reported a net increase of calories (from 2519 ± 721 kcal/day to 2763 ± 595 kcal/day, p = 0.035) according to 3-day food registrations. Despite an almost three-fold reported increased fructose-intake in the fruit group (from 9.1 ± 6.0 gram/day to 25.6 ± 9.6 gram/day, p<0.0001, nuts: from 12.4 ± 5.7 gram/day to 6.5 ± 5.3 gram/day, p = 0.007) there was no change of HFC. The numerical increase in fasting insulin was statistical significant only in the fruit group (from 7.73 ± 3.1 pmol/l to 8.81 ± 2.9 pmol/l, p = 0.018, nuts: from 7.29 ± 2.9 pmol/l to 8.62 ± 3.0 pmol/l, p = 0.14). Levels of vitamin C increased in both groups while α-tocopherol/cholesterol-ratio increased only in the fruit group. Although BMR increased in the nut-group only this was not linked with differences in weight gain between groups which potentially could be explained by the lack of reported net caloric increase in the fruit group. In healthy non-obese individuals an increased fruit intake seems safe from cardiovascular risk perspective, including measurement of HFC by MRI. ClinicalTrials.gov NCT02227511.

A Randomized Study of the Effects of Additional Fruit and Nuts Consumption on Hepatic Fat Content, Cardiovascular Risk Factors and Basal Metabolic Rate

PubMed Central

Romu, Thobias; Dahlqvist-Leinhard, Olof; Borga, Magnus; Leandersson, Per; Nystrom, Fredrik H.

2016-01-01

Background Fruit has since long been advocated as a healthy source of many nutrients, however, the high content of sugars in fruit might be a concern. Objectives To study effects of an increased fruit intake compared with similar amount of extra calories from nuts in humans. Methods Thirty healthy non-obese participants were randomized to either supplement the diet with fruits or nuts, each at +7 kcal/kg bodyweight/day for two months. Major endpoints were change of hepatic fat content (HFC, by magnetic resonance imaging, MRI), basal metabolic rate (BMR, with indirect calorimetry) and cardiovascular risk markers. Results Weight gain was numerically similar in both groups although only statistically significant in the group randomized to nuts (fruit: from 22.15±1.61 kg/m2 to 22.30±1.7 kg/m2, p = 0.24 nuts: from 22.54±2.26 kg/m2 to 22.73±2.28 kg/m2, p = 0.045). On the other hand BMR increased in the nut group only (p = 0.028). Only the nut group reported a net increase of calories (from 2519±721 kcal/day to 2763±595 kcal/day, p = 0.035) according to 3-day food registrations. Despite an almost three-fold reported increased fructose-intake in the fruit group (from 9.1±6.0 gram/day to 25.6±9.6 gram/day, p<0.0001, nuts: from 12.4±5.7 gram/day to 6.5±5.3 gram/day, p = 0.007) there was no change of HFC. The numerical increase in fasting insulin was statistical significant only in the fruit group (from 7.73±3.1 pmol/l to 8.81±2.9 pmol/l, p = 0.018, nuts: from 7.29±2.9 pmol/l to 8.62±3.0 pmol/l, p = 0.14). Levels of vitamin C increased in both groups while α-tocopherol/cholesterol-ratio increased only in the fruit group. Conclusions Although BMR increased in the nut-group only this was not linked with differences in weight gain between groups which potentially could be explained by the lack of reported net caloric increase in the fruit group. In healthy non-obese individuals an increased fruit intake seems safe from cardiovascular risk perspective, including measurement of HFC by MRI. Trial Registration ClinicalTrials.gov NCT02227511 PMID:26788923

Molecular materials for high performance OPV devices (Conference Presentation)

NASA Astrophysics Data System (ADS)

Jones, David J.

2016-09-01

We recently reported the high performing molecular donor for OPV devices based on a benzodithiophene core, a terthiophene bridge and a rhodamine acceptor (BTR) [1]. In this work we optimized side-chain placement of a known chromophore by ensuring the thiophene hexyl side-chains are regioregular, which should allow the chromophore to lie flat. The unexpected outcome was a nematic liquid crystalline material with significantly improved performance (now 9.6% PCE), excellent charge transport properties, reduced geminate recombination rates and excellent performance with active layers up to 400nm. Three phase changes were indicated by DSC analysis with a melt to a crystalline domain at 175 oC, transition to a nematic liquid crystalline domain at 186 oC and an isotropic melt at 196 oC. In our desire to better understand the structure property relationships of this class of p-type organic semiconductor we have synthesized a series of analogues where the length of the chromophore has been altered through modification of the oligothiophene bridge to generate, the monothiophene (BMR), the bisthiophene (BBR), the known terthiophene (BTR), the quaterthiophene (BQR) and the pentathiophene (BPR). BMR, BBR and BPR have clean melting points while BQR, like BTR shows a complicated series of phase transitions. Device efficiencies after solvent vapour annealing are BMR (3.5%), BBR (6.0%), BTR (9.3%), BQR (9.4%), and BPR (8.7%) unoptimised. OPV devices with BTR in the active layer are not stable under thermal annealing, however the bridge extended BQR and BPR form thermally stable devices. We are currently optimising these devices, but initial results indicate PCEs >9% for thermally annealed devices containing BQR, while BPR devices have not yet been optimised and have PCEs > 8%. In order to develop the device performance we have included BQR in ternary devices with the commercially available PTB7-Th and we report device efficiencies of over 10.5%. We are currently optimising device assembly and annealing conditions and relating these back to key materials properties. I will discuss the development of these new materials, their materials properties, structural data, and optimised device performance. I will examination of chromophore length on the Nematic Liquid Crystalline properties and on materials development and performance resulting in materials with > 9% PCE in OPV. [1] Sun, K.; Xiao, Z.; Lu, S.; Zajaczkowski, W.; Pisula, W.; Hanssen, E.; White, J. M.; Williamson, R. M.; Subbiah, J.; Ouyang, J.; Holmes, A. B.; Wong, W. W.; Jones, D. J., Nat. Commun. 2015, 6, 6013. DOI: 10.1038/ncomms7013

Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation.

PubMed

Tretyachenko-Ladokhina, Vira; Cocco, Melanie J; Senear, Donald F

2006-09-15

Interactions between DNA-bound transcription factors CytR and CRP regulate the promoters of the Escherichia coli CytR regulon. A distinctive feature of the palindromic CytR operators is highly variable length central spacers (0-9 bp). Previously we demonstrated distinct modes of CytR binding to operators that differ in spacer length. These different modes are characterized by opposite enthalpic and entropic contributions at 25 degrees C. Of particular note were radically different negative DeltaCp values suggesting variable contribution from coupled protein folding and/or DNA structural transitions. We proposed that the CytR DNA binding-domain adopts either a more rigid or flexible DNA-bound conformation in response to the different spacer lengths. More recently, similar effects were shown to contribute to discrimination between operator and non-specific DNA binding by LacR, a CytR homolog. Here we have extended the thermodynamic analysis to the remaining natural CytR operators plus a set of synthetic operators designed to isolate spacing as the single variable. The thermodynamic results show a broad and monotonic range of effects that are primarily dependent on spacer length. The magnitude of effects suggests participation by more than the DNA-binding domain. 15N HSQC NMR and CD spectral analyses were employed to characterize the structural basis for these effects. The results indicate that while CytR forms a well-ordered structure in solution, it is highly dynamic. We propose a model in which a large ensemble of native state conformations narrows upon binding, to an extent governed by operator spacing. This in turn is expected to constrain intermolecular interactions in the CytR-CRP-DNA complex, thus generating operator-specific effects on repression and induction of transcription.

Regulation of nif expression in Methanococcus maripaludis: roles of the euryarchaeal repressor NrpR, 2-oxoglutarate, and two operators.

PubMed

Lie, Thomas J; Wood, Gwendolyn E; Leigh, John A

2005-02-18

The methanogenic archaean Methanococcus maripaludis can use ammonia, alanine, or dinitrogen as a nitrogen source for growth. The euryarchaeal nitrogen repressor NrpR controls the expression of the nif (nitrogen fixation) operon, resulting in full repression with ammonia, intermediate repression with alanine, and derepression with dinitrogen. NrpR binds to two tandem operators in the nif promoter region, nifOR(1) and nifOR(2). Here we have undertaken both in vivo and in vitro approaches to study the way in which NrpR, nifOR(1), nifOR(2), and the effector 2-oxoglutarate (2OG) combine to regulate nif expression, leading to a comprehensive understanding of this archaeal regulatory system. We show that NrpR binds as a dimer to nifOR(1) and cooperatively as two dimers to both operators. Cooperative binding occurs only with both operators present. nifOR(1) has stronger binding and by itself can mediate the repression of nif transcription during growth on ammonia, unlike the weakly binding nifOR(2). However, nifOR(2) in combination with nifOR(1) is critical for intermediate repression during growth on alanine. Accordingly, NrpR binds to both operators together with higher affinity than to nifOR(1) alone. NrpR responds directly to 2OG, which weakens its binding to the operators. Hence, 2OG is an intracellular indicator of nitrogen deficiency and acts as an inducer of nif transcription via NrpR. This model is upheld by the recent finding (J. A. Dodsworth and J. A. Leigh, submitted for publication) in our laboratory that 2OG levels in M. maripaludis vary with growth on different nitrogen sources.

Operator design and mechanism for CarA repressor-mediated down-regulation of the photoinducible carB operon in Myxococcus xanthus.

PubMed

López-Rubio, José Juan; Padmanabhan, S; Lázaro, Jose María; Salas, Margarita; Murillo, Francisco José; Elías-Arnanz, Montserrat

2004-07-09

The carB operon encodes all except one of the enzymes involved in light-induced carotenogenesis in Myxococcus xanthus. Expression of its promoter (P(B)) is repressed in the dark by sequence-specific DNA binding of CarA to a palindrome (pI) located between positions -47 and -64 relative to the transcription start site. This promotes subsequent binding of CarA to additional sites that remain to be defined. CarS, produced in the light, interacts physically with CarA, abrogates CarA-DNA binding, and thereby derepresses P(B). In this study, we delineate the operator design that exists for CarA by precisely mapping out the second operator element. For this, we examined how stepwise deletions and site-directed mutagenesis in the region between the palindrome and the transcription start site affect CarA binding around P(B) in vitro and expression of P(B) in vivo. These revealed the second operator element to be an imperfect interrupted palindrome (pII) spanning positions -26 to -40. In vitro assays using purified M. xanthus RNA polymerase showed that CarA abolishes P(B)-RNA polymerase binding and runoff transcription and that both were restored by CarS, thus rationalizing the observations in vivo. CarA binding to pII (after association with pI) effectively occludes RNA polymerase from P(B) and so provides the operative mechanism for the repression of the carB operon by CarA. The bipartite operator design, whereby transcription is blocked by the low affinity CarA-pII binding and is readily restored by CarS, may have evolved to match the needs for a rapid and an effective response to light.

Solar Radiation during Rewarming from Torpor in Elephant Shrews: Supplementation or Substitution of Endogenous Heat Production?

PubMed Central

Thompson, Michelle L.; Mzilikazi, Nomakwezi; Bennett, Nigel C.; McKechnie, Andrew E.

2015-01-01

Many small mammals bask in the sun during rewarming from heterothermy, but the implications of this behaviour for their energy balance remain little understood. Specifically, it remains unclear whether solar radiation supplements endogenous metabolic thermogenesis (i.e., rewarming occurs through the additive effects of internally-produced and external heat), or whether solar radiation reduces the energy required to rewarm by substituting (i.e, replacing) metabolic heat production. To address this question, we examined patterns of torpor and rewarming rates in eastern rock elephant shrews (Elephantulus myurus) housed in outdoor cages with access to either natural levels of solar radiation or levels that were experimentally reduced by means of shade cloth. We also tested whether acclimation to solar radiation availability was manifested via phenotypic flexibility in basal metabolic rate (BMR), non-shivering thermogenesis (NST) capacity and/or summit metabolism (Msum). Rewarming rates varied significantly among treatments, with elephant shrews experiencing natural solar radiation levels rewarming faster than conspecifics experiencing solar radiation levels equivalent to approximately 20% or 40% of natural levels. BMR differed significantly between individuals experiencing natural levels of solar radiation and conspecifics experiencing approximately 20% of natural levels, but no between-treatment difference was evident for NST capacity or Msum. The positive relationship between solar radiation availability and rewarming rate, together with the absence of acclimation in maximum non-shivering and total heat production capacities, suggests that under the conditions of this study solar radiation supplemented rather than substituted metabolic thermogenesis as a source of heat during rewarming from heterothermy. PMID:25853244

Evaluation of methods to assess physical activity in free-living conditions.

PubMed

Leenders, N Y; Sherman, W M; Nagaraja, H N; Kien, C L

2001-07-01

The purpose of this study was to compare different methods of measuring physical activity (PA) in women by the doubly labeled water method (DLW). Thirteen subjects participated in a 7-d protocol during which total daily energy expenditure (TDEE) was measured with DLW. Body composition, basal metabolic rate (BMR), and peak oxygen consumption were also measured. Physical activity-related energy expenditure (PAEE) was then calculated by subtracting measured BMR and the estimated thermic effect of food from TDEE. Simultaneously, over the 7 d, PA was assessed via a 7-d Physical Activity Recall questionnaire (PAR), and subjects wore secured at the waist, a Tritrac-R3D (Madison, WI), a Computer Science Application Inc. activity monitor (CSA; Shalimar, FL), and a Yamax Digi Walker-500 (Tokyo, Japan). Pearson-product moment correlations were calculated to determine the relationships among the different methods for estimating PAEE. Paired t-tests with appropriate adjustments were used to compare the different methods with DLW-PAEE. There was no significant difference between PAEE determined from PAR and DLW. The differences between the two methods ranged from -633 to 280 kcal.d(-1). Compared with DLW, PAEE determined from CSA, Tritrac, and Yamax was significantly underestimated by 59% (-495 kcal.d(-1)), 35% (-320 kcal.d(-1)) and 59% (-497 kcal.d(-1)), respectively. VO2peak explained 43% of the variation in DLW-PAEE. Although the group average for PAR-PAEE agreed with DLW-PAEE, there were differences in the methods among the subjects. PAEE determined by Tritrac, CSA, and Yamax significantly underestimate free-living PAEE in women.

Solar radiation during rewarming from torpor in elephant shrews: supplementation or substitution of endogenous heat production?

PubMed

Thompson, Michelle L; Mzilikazi, Nomakwezi; Bennett, Nigel C; McKechnie, Andrew E

2015-01-01

Many small mammals bask in the sun during rewarming from heterothermy, but the implications of this behaviour for their energy balance remain little understood. Specifically, it remains unclear whether solar radiation supplements endogenous metabolic thermogenesis (i.e., rewarming occurs through the additive effects of internally-produced and external heat), or whether solar radiation reduces the energy required to rewarm by substituting (i.e, replacing) metabolic heat production. To address this question, we examined patterns of torpor and rewarming rates in eastern rock elephant shrews (Elephantulus myurus) housed in outdoor cages with access to either natural levels of solar radiation or levels that were experimentally reduced by means of shade cloth. We also tested whether acclimation to solar radiation availability was manifested via phenotypic flexibility in basal metabolic rate (BMR), non-shivering thermogenesis (NST) capacity and/or summit metabolism (Msum). Rewarming rates varied significantly among treatments, with elephant shrews experiencing natural solar radiation levels rewarming faster than conspecifics experiencing solar radiation levels equivalent to approximately 20% or 40% of natural levels. BMR differed significantly between individuals experiencing natural levels of solar radiation and conspecifics experiencing approximately 20% of natural levels, but no between-treatment difference was evident for NST capacity or Msum. The positive relationship between solar radiation availability and rewarming rate, together with the absence of acclimation in maximum non-shivering and total heat production capacities, suggests that under the conditions of this study solar radiation supplemented rather than substituted metabolic thermogenesis as a source of heat during rewarming from heterothermy.

Metabolic rate and environmental productivity: Well-provisioned animals evolved to run and idle fast

PubMed Central

Mueller, Pamela; Diamond, Jared

2001-01-01

Even among vertebrate species of the same body mass and higher-level taxonomic group, metabolic rates exhibit substantial differences, for which diverse explanatory factors—such as dietary energy content, latitude, altitude, temperature, and rainfall—have been postulated. A unifying underlying factor could be food availability, in turn controlled by net primary productivity (NPP) of the animal's natural environment. We tested this possibility by studying five North American species of Peromyscus mice, all of them similar in diet (generalist omnivores) and in gut morphology but differing by factors of up to 13 in NPP of their habitat of origin. We maintained breeding colonies of all five species in the laboratory under identical conditions and consuming identical diets. Basal metabolic rate (BMR) and daily ad libitum food intake both increased with NPP, which explained 88% and 90% of their variances, respectively. High-metabolism mouse species from high-NPP environments were behaviorally more active than were low-metabolism species from low-NPP environments. Intestinal glucose uptake capacity also increased with NPP (and with BMR and food intake), because species of high-NPP environments had larger small intestines and higher uptake rates. For metabolic rates of our five species, the driving environmental variable is environmental productivity itself (and hence food availability), rather than temporal variability of productivity. Thus, species that have evolved in the presence of abundant food run their metabolism “fast,” both while active and while idling, as compared with species of less productive environments, even when all species are given access to unlimited food. PMID:11606744

Evaluation of nutritional status and dietary intake in patients with advanced cancer on palliative care.

PubMed

Bovio, G; Bettaglio, R; Bonetti, G; Miotti, D; Verni, P

2008-09-01

Cancer cachexia and malnutrition are very common in patients receiving palliative care. They cause a deterioration in the quality of life. We studied 144 patients (52 females, 92 males) admitted to our Palliative Care Unit. Anthropometric measurements, food and nutritional intake, and plasma levels of few serum proteins were determined. Basal metabolic rate (BMR) was calculated. A body mass index (BMI) below 18.5 kg/m2 was observed in 23% of females and in 13% of males (P = NS). Twenty females (44%) and 52 males (63%) showed a weight loss of more than 10% over the 6-month period (P = 0.073). Ten females (19%) and 58 males (63%) had an arm muscle area (AMA) below the 5th percentile (P < 0.001), while 20 females (38%) and 21 males (23%) had an arm fat area (AFA) below the 5th percentile (P = 0.071). The daily calorie intake was below the BMR in 22 females (42%) and in 53 males (58%) (P = NS). Plasma levels of prealbumin, transferrin, and albumin were found below the normal range in more than 70% in both sexes. Protein energy malnutrition can be easily detected by anthropometric and laboratory indexes. The larger percentage of males with a reduction in lean body mass compared to females could signify an advantage for females since lean body mass is preserved for longer in them. Patients with advanced cancer receiving palliative care should thus be evaluated routinely to assess their nutritional status in order to plan an adequate nutritional program when appropriate.

Long-term effect of yogic practices on diurnal metabolic rates of healthy subjects

PubMed Central

Chaya, M S; Nagendra, H R

2008-01-01

Background: The metabolic rate is an indicator of autonomic activity. Reduced sympathetic arousal probably resulting in hypometabolic states has been reported in several yogic studies. Aim: The main objective of this study was to assess the effect of yoga training on diurnal metabolic rates in yoga practitioners at two different times of the day (at 6 a.m. and 9 p.m.). Materials and Methods: Eighty eight healthy volunteers were selected and their metabolic rates assessed at 6 a.m. and 9 p.m. using an indirect calorimeter at a yoga school in Bangalore, India. Results and conclusions: The results show that the average metabolic rate of the yoga group was 12% lower than that of the non-yoga group (P < 0.001) measured at 9 p.m. and 16% lower at 6 a.m. (P < 0.001). The 9 p.m. metabolic rates of the yoga group were almost equal to their predicted basal metabolic rates (BMRs) whereas the metabolic rate was significantly higher than the predicted BMR for the non-yoga group. The 6 a.m. metabolic rate was comparable to their predicted BMR in the non-yoga group whereas it was much lower in the yoga group (P < 0.001). The lower metabolic rates in the yoga group at 6 a.m. and 9 p.m. may be due to coping strategies for day-to-day stress, decreased sympathetic nervous system activity and probably, a stable autonomic nervous system response (to different stressors) achieved due to training in yoga. PMID:21829281

Timed activity studies for assessing the energy expenditure of women from an urban slum in south India.

PubMed

Sujatha, Tetali; Shatrugna, Veena; Vidyasagar, P; Begum, Nazeema; Padmavathy, K S; Reddy, G Chenna Krishna; Rao, G V

2003-06-01

Time-disposition studies are necessary for computing energy requirements of populations. This study captures the rich information on the timed activity pattern of adult women from poor households engaged in home-based work. We studied 34 women beedimakers (cigarette makers), 21 tailors, and 34 homemakers. Data were collected by direct observation of the women's activities on a typical day. Time spent on related activities was pooled and classified as sleep, household work, child care, occupational work, and residual work. These were further categorized on the basis of our published work on the energy cost of women's activities and the World Health Organization (WHO) classification of occupational activities as sedentary, moderate, and heavy. Most of the household activities could be classified as moderate to heavy (> 2.2 times basal metabolic rate [BMR]). Childcare activities were distributed on a scale from sedentary to heavy, whereas occupational activities, such as beedimaking and tailoring, were sedentary (< 2.2 BMR). Homemakers spent significantly more time on moderate to heavy work (p < .05) than beedimakers and tailors. Women working for income spent only four to six hours on occupational work, which was possible because they reduced the time spent on heavy work (i.e., housework), and reduced the time on personal care. Still, more than 80% of women could not put in eight hours of paid work. Thus, women in the home-based sector constantly negotiate among time spent on heavy household work, child care, and occupational work in order to continue in the labor market.

Energy and macronutrient intake after gastric bypass for morbid obesity: a 3-y observational study focused on protein consumption.

PubMed

Giusti, Vittorio; Theytaz, Fanny; Di Vetta, Véronique; Clarisse, Muriel; Suter, Michel; Tappy, Luc

2016-01-01

The effect of a Roux-en-Y gastric bypass (RYGB) on body weight has been amply documented, but few studies have simultaneously assessed the evolution of energy and macronutrient intakes, energy expenditure, and changes in body composition over time after an RYGB. We evaluated energy and macronutrient intakes, body composition, and the basal metabolic rate (BMR) in obese female patients during the initial 3 y after an RYGB. Sixteen women with a mean ± SEM body mass index (in kg/m(2)) of 44.1 ± 1.6 were included in this prospective observational study. The women were studied on 6 different occasions as follows: before and 1, 3, 6, 12 (n = 16), and 36 (n = 8) mo after surgery. On each occasion, food intake was evaluated from 4- or 7-d dietary records, body composition was assessed with the use of bio-impedancemetry, and energy expenditure was measured with the use of indirect calorimetry. Body weight evolution showed the typical pattern reported after an RYGB. Total energy intake was 2072 ± 108 kcal/d at baseline and decreased to 681 ± 58 kcal/d at 1 mo after surgery (P < 0.05 compared with at baseline). Total energy intake progressively increased to reach 1240 ± 87 kcal/d at 12 mo after surgery (P < 0.05 compared with at 1 mo after surgery) and 1448 ± 57 kcal/d at 36 mo after surgery (P < 0.05 compared with at 12 mo after surgery). Protein intake was 87 ± 4 g/d at baseline and ± 2 g/d 1 mo after surgery (P < 0.05 compared with at baseline) and increased progressively thereafter to reach 57 ± 3 g/d at 36 mo after surgery (P < 0.05 compared with at 1 mo after surgery). Carbohydrate and fat intakes over time showed similar patterns. Protein intake from meat and cheese were significantly reduced early at 1 mo after surgery but increased thereafter (P < 0.05). The BMR decreased from 1.12 ± 0.04 kcal/min at baseline to 0.93 ± 0.03, 0.86 ± 0.03, and 0.85 ± 0.04 kcal/min at 3, 12, and 36 mo after surgery, respectively (all P < 0.05 compared with at baseline). Total energy, carbohydrate, fat, and protein intakes decreased markedly during the initial 1-3 mo after an RYGB, whereas the BMR moderately decreased. The reduction in protein intake was particularly severe at 1 mo after surgery, and protein intake increased gradually after 3-6 mo after surgery. This trial was registered at clinicaltrials.gov as NCT01891591. © 2016 American Society for Nutrition.

Obesity in Malaysia.

PubMed

Ismail, M N; Chee, S S; Nawawi, H; Yusoff, K; Lim, T O; James, W P T

2002-08-01

This study was undertaken to assess the recent data on Malaysian adult body weights and associations of ethnic differences in overweight and obesity with comorbid risk factors, and to examine measures of energy intake, energy expenditure, basal metabolic rate (BMR) and physical activity changes in urban and rural populations of normal weight. Three studies were included (1) a summary of a national health morbidity survey conducted in 1996 on nearly 29 000 adults > or =20 years of age; (2) a study comparing energy intake, BMR and physical activity levels (PALs) in 409 ethnically diverse, healthy adults drawn from a population of 1165 rural and urban subjects 18-60 years of age; and (3) an examination of the prevalence of obesity and comorbid risk factors that predict coronary heart disease and type 2 diabetes in 609 rural Malaysians aged 30-65 years. Overweight and obesity were calculated using body mass index (BMI) measures and World Health Organization (WHO) criteria. Energy intake was assessed using 3-d food records, BMR and PALs were assessed with Douglas bags and activity diaries, while hypertension, hyperlipidaemia and glucose intolerance were specified using standard criteria. The National Health Morbidity Survey data revealed that in adults, 20.7% were overweight and 5.8% obese (0.3% of whom had BMI values of >40.0 kg m(-2)); the prevalence of obesity was clearly greater in women than in men. In women, obesity rates were higher in Indian and Malay women than in Chinese women, while in men the Chinese recorded the highest obesity prevalences followed by the Malay and Indians. Studies on normal healthy subjects indicated that the energy intake of Indians was significantly lower than that of other ethnic groups. In women, Malays recorded a significantly higher energy intake than the other groups. Urban male subjects consumed significantly more energy than their rural counterparts, but this was not the case in women. In both men and women, fat intakes (%) were significantly higher in Chinese and urban subjects. Men were moderately active with the exception of the Dayaks. Chinese women were considerably less active than Chinese men. Chinese and Dayak women were less active than Malay and Indian women. In both men and women, Indians recorded the highest PALs. Hence, current nutrition and health surveys reveal that Malaysians are already affected by western health problems. The escalation of obesity, once thought to be an urban phenomenon, has now spread to the rural population at an alarming rate. As Malaysia proceeds rapidly towards a developed economy status, the health of its population will probably continue to deteriorate. Therefore, a national strategy needs to be developed to tackle both dietary and activity contributors to the excess weight gain of the Malaysian population.

Evidence for co-operativity in coenzyme binding to tetrameric Sulfolobus solfataricus alcohol dehydrogenase and its structural basis: fluorescence, kinetic and structural studies of the wild-type enzyme and non-co-operative N249Y mutant.

PubMed

Giordano, Antonietta; Febbraio, Ferdinando; Russo, Consiglia; Rossi, Mosè; Raia, Carlo A

2005-06-01

The interaction of coenzyme with thermostable homotetrameric NAD(H)-dependent alcohol dehydrogenase from the thermoacidophilic sulphur-dependent crenarchaeon Sulfolobus solfataricus (SsADH) and its N249Y (Asn-249-->Tyr) mutant was studied using the high fluorescence sensitivity of its tryptophan residues Trp-95 and Trp-117 to the binding of coenzyme moieties. Fluorescence quenching studies performed at 25 degrees C show that SsADH exhibits linearity in the NAD(H) binding [the Hill coefficient (h) approximately 1) at pH 9.8 and at moderate ionic strength, in addition to positive co-operativity (h=2.0-2.4) at pH 7.8 and 6.8, and at pH 9.8 in the presence of salt. Furthermore, NADH binding is positively co-operative below 20 degrees C (h approximately 3) and negatively co-operative at 40-50 degrees C (h approximately 0.7), as determined at moderate ionic strength and pH 9.8. Steady-state kinetic measurements show that SsADH displays standard Michaelis-Menten kinetics between 35 and 45 degrees C, but exhibits positive and negative co-operativity for NADH oxidation below (h=3.3 at 20 degrees C) and above (h=0.7 at 70-80 degrees C) this range of temperatures respectively. However, N249Y SsADH displays non-co-operative behaviour in coenzyme binding under the same experimental conditions used for the wild-type enzyme. In loop 270-275 of the coenzyme domain and segments at the interface of dimer A-B, analyses of the wild-type and mutant SsADH structures identified the structural elements involved in the intersubunit communication and suggested a possible structural basis for co-operativity. This is the first report of co-operativity in a tetrameric ADH and of temperature-induced co-operativity in a thermophilic enzyme.

A high-resolution structure of the DNA-binding domain of AhrC, the arginine repressor/activator protein from Bacillus subtilis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garnett, James A.; Baumberg, Simon; Stockley, Peter G.

2007-11-01

The structure of the winged helix–turn–helix DNA-binding domain of AhrC has been determined at 1.0 Å resolution. The largely hydrophobic β-wing shows high B factors and may mediate the dimer interface in operator complexes. In Bacillus subtilis the concentration of l-arginine is controlled by the transcriptional regulator AhrC, which interacts with 18 bp DNA operator sites called ARG boxes in the promoters of arginine biosynthetic and catabolic operons. AhrC is a 100 kDa homohexamer, with each subunit having two domains. The C-terminal domains form the core, mediating intersubunit interactions and binding of the co-repressor l-arginine, whilst the N-terminal domains containmore » a winged helix–turn–helix DNA-binding motif and are arranged around the periphery. The N-terminal domain of AhrC has been expressed, purified and characterized and it has been shown that the fragment still binds DNA operators as a recombinant monomer. The DNA-binding domain has also been crystallized and the crystal structure refined to 1.0 Å resolution is presented.« less

Phosphotriesterase-magnetic nanoparticles bioconjugates with improved enzyme activity in a biocatalytic membrane reactor.

PubMed

Gebreyohannes, Abaynesh Yihdego; Mazzei, Rosalinda; Yahia Marei Abdelrahim, Mohamed; Vitola, Giuseppe; Porzio, Elena; Manco, Giuseppe; Barboiu, Mihail; Giorno, Lidietta

2018-05-24

The need to find alternative bioremediation solutions for organophosphate degradation pushed the research to develop technologies based on organophosphate degrading enzymes, such as phosphotriesterase. The use of free phosphotriesterase poses limits in terms of enzyme reuse, stability and process development. The heterogenization of enzyme on a support and their use in bioreactors implemented by membrane seems a suitable strategy, thanks to the ability of membranes to compartmentalize, to govern mass transfer and provide microenvironment with tuned physico-chemical and structural properties. Usually, hydrophilic membranes are used since they easily guarantee the presence of water molecules needed for the enzyme catalytic activity. However, hydrophobic materials exhibit a larger shelf life and are preferred for the construction of filters and masks. Therefore, in this work, hydrophobic polyvinylidene fluoride (PVDF) porous membranes were used to develop biocatalytic membrane reactors (BMR). The phosphotriesterase-like lactonase (PLL) enzyme (SsoPox triple mutant from S. solfataricus) endowed with thermostable phosphotriesterase activity was used as model biocatalyst. The enzyme was covalently bound directly to the PVDF hydrophobic membrane or it was bound to magnetic nanoparticles and then positioned on the hydrophobic membrane surface by means of an external magnetic field. Investigation of kinetic properties of the two BMRs and the influence of immobilized enzyme amount revealed that the performance of the BMR was mostly dependent on the amount of enzyme and its distribution on the immobilization support. Magnetic nanocomposite mediated immobilization showed a much better performance, with an observed specific activity higher than 90% compared to grafting of the enzyme on the membrane. Even though the present work focused on phosphotriesterase, it can be easily translated to other class of enzymes and related application.

Low Energy Turnover of Physically Inactive Participants as a Determinant of Insufficient Mineral and Vitamin Intake in NHANES

PubMed Central

Heydenreich, Juliane; Melzer, Katarina; Flury, Céline

2017-01-01

Micronutrient requirements do not scale linearly with physical activity-related energy expenditure (AEE). Inactive persons may have insufficient micronutrient intake because of low energy intake (EI). We extracted data from NHANES 2003–2006 on 4015 adults (53 ± 18 years (mean ± SD), 29 ± 6 kg/m2, 48% women) with valid physical activity (accelerometry) and food intake (2 × 24 h-dietary recall) measures. Total energy expenditure (TEE) was estimated by summing the basal metabolic rate (BMR, Harris-Benedict), AEE, and 10% of TEE for the thermic effect of food, to calculate the physical activity levels (PAL = TEE/BMR). Energy intake (EI) was scaled to match TEE assuming energy balance. Adjusted food intake was then analyzed for energy and micronutrient content and compared to estimated average requirements. The NHANES population was physically insufficiently active. There were 2440 inactive (PAL < 1.4), 1469 lightly to moderately active (PAL1.4 < 1.7), 94 sufficiently active (PAL1.7 < 2.0), and 12 very active participants (PAL ≥ 2.0). The inactive vs. active had significantly lower intake for all micronutrients apart from vitamin A, B12, C, K, and copper (p < 0.05). The inactive participants had insufficient intake for 6/19 micronutrients, while the active participants had insufficient intake for 5/19 (p < 0.05) micronutrients. Multiple linear regression indicated a lower risk for insufficient micronutrient intake for participants with higher PAL and BMI (p < 0.001). Symmetrical up-scaling of PAL and EI to recommended physical activity levels reduced the frequency of micronutrient insufficiencies. It follows that prevalence of insufficient micronutrient intake from food in NHANES might be partly determined by low energy turnover from insufficient PAL. PMID:28708118

Solar Cycle Variability Induced by Tilt Angle Scatter in a Babcock-Leighton Solar Dynamo Model

NASA Astrophysics Data System (ADS)

Karak, Bidya Binay; Miesch, Mark

2017-09-01

We present results from a three-dimensional Babcock-Leighton (BL) dynamo model that is sustained by the emergence and dispersal of bipolar magnetic regions (BMRs). On average, each BMR has a systematic tilt given by Joy’s law. Randomness and nonlinearity in the BMR emergence of our model produce variable magnetic cycles. However, when we allow for a random scatter in the tilt angle to mimic the observed departures from Joy’s law, we find more variability in the magnetic cycles. We find that the observed standard deviation in Joy’s law of {σ }δ =15^\\circ produces a variability comparable to the observed solar cycle variability of ˜32%, as quantified by the sunspot number maxima between 1755 and 2008. We also find that tilt angle scatter can promote grand minima and grand maxima. The time spent in grand minima for {σ }δ =15^\\circ is somewhat less than that inferred for the Sun from cosmogenic isotopes (about 9% compared to 17%). However, when we double the tilt scatter to {σ }δ =30^\\circ , the simulation statistics are comparable to the Sun (˜18% of the time in grand minima and ˜10% in grand maxima). Though the BL mechanism is the only source of poloidal field, we find that our simulations always maintain magnetic cycles even at large fluctuations in the tilt angle. We also demonstrate that tilt quenching is a viable and efficient mechanism for dynamo saturation; a suppression of the tilt by only 1°-2° is sufficient to limit the dynamo growth. Thus, any potential observational signatures of tilt quenching in the Sun may be subtle.

Self-reported dietary energy intake of normal weight, overweight and obese adolescents.

PubMed

Vance, Vivienne A; Woodruff, Sarah J; McCargar, Linda J; Husted, Janice; Hanning, Rhona M

2009-02-01

The purpose of the present paper was to assess dietary energy reporting as a function of sex and weight status among Ontario and Alberta adolescents, using the ratio of energy intake (EI) to estimated BMR (BMRest). Data were collected using the FBQ, a validated web-based dietary assessment tool (including a 24 h dietary recall, FFQ, and food and physical activity behavioural questions). BMI was calculated from self-reported height and weight and participants were classified as normal weight, overweight or obese. BMR was calculated using the WHO equations (based on weight). Reporting status was identified using the ratio EI:BMRest. Data were collected in public, Catholic and private schools in Ontario and Alberta, Canada. A total of 1917 (n 876 male and n 1041 female) students (n 934 grade 9 and n 984 grade 10) participated. The mean EI:BMRest ratio across all participants was 1.4 (sd 0.6), providing evidence of under-reporting for the total sample. Females under-reported more than males (t = 6.27, P < 0.001), and under-reporting increased with increasing weight status for both males (F = 33.21, P < 0.001) and females (F = 14.28, P < 0.001). After removing those who reported eating less to lose weight, the EI:BMRest was 1.56 (sd 0.6) for males and 1.4 (sd 0.6) for females. The present study highlights methodological challenges associated with self-reported dietary data. Systematic differences in under-reporting of dietary intake by gender and weight status were observed using a web-based survey, similar to observations made using paper-based 24 h recalls and dietitian interviews.

Effect of Selection for High Activity-Related Metabolism on Membrane Phospholipid Fatty Acid Composition in Bank Voles.

PubMed

Stawski, Clare; Valencak, Teresa G; Ruf, Thomas; Sadowska, Edyta T; Dheyongera, Geoffrey; Rudolf, Agata; Maiti, Uttaran; Koteja, Paweł

2015-01-01

Endothermy, high basal metabolic rates (BMRs), and high locomotor-related metabolism were important steps in the evolution of mammals. It has been proposed that the composition of membrane phospholipid fatty acids plays an important role in energy metabolism and exercise muscle physiology. In particular, the membrane pacemaker theory of metabolism suggests that an increase in cell membrane fatty acid unsaturation would result in an increase in BMR. We aimed to determine whether membrane phospholipid fatty acid composition of heart, liver, and gastrocnemius muscles differed between lines of bank voles selected for high swim-induced aerobic metabolism-which also evolved an increased BMR-and unselected control lines. Proportions of fatty acids significantly differed among the organs: liver was the least unsaturated, whereas the gastrocnemius muscles were most unsaturated. However, fatty acid proportions of the heart and liver did not differ significantly between selected and control lines. In gastrocnemius muscles, significant differences between selection directions were found: compared to control lines, membranes of selected voles were richer in saturated C18:0 and unsaturated C18:2n-6 and C18:3n-3, whereas the pattern was reversed for saturated C16:0 and unsaturated C20:4n-6. Neither unsaturation index nor other combined indexes of fatty acid proportions differed between lines. Thus, our results do not support the membrane pacemaker hypothesis. However, the differences between selected and control lines in gastrocnemius muscles reflect chain lengths rather than number of double bonds and are probably related to differences in locomotor activity per se rather than to differences in the basal or routine metabolic rate.

Phytochemicals in regulating fatty acid β-oxidation: Potential underlying mechanisms and their involvement in obesity and weight loss.

PubMed

Rupasinghe, H P Vasantha; Sekhon-Loodu, Satvir; Mantso, Theodora; Panayiotidis, Mihalis I

2016-09-01

Excessive accumulation of fat as the result of more energy intake and less energy expenditure is known as obesity. Lipids are essential components in the human body and are vital for maintaining homeostasis and physiological as well as cellular metabolism. Fatty acid synthesis and catabolism (by fatty acid oxidation) are normal part of basic fuel metabolism in animals. Fatty acids are degraded in the mitochondria by a biochemical process called β-oxidation in which two-carbon fragments are produced in each cycle. The increase in fatty acid β-oxidation is negatively correlated with body mass index. Although healthy life style, avoiding Western diet, dieting and strenuous exercise are the commonly used methods to lose weight, they are not considered a permanent solution in addition to risk attenuation of basal metabolic rate (BMR). Pharmacotherapy offers benefits of weight loss by altering the satiety and lowering absorption of fat from the food; however, its side effects may outweigh the benefits of weight loss. Alternatively, dietary phytochemicals and natural health products offer great potential as an efficient weight loss strategy by modulating lipid metabolism and/or increasing BMR and thermogenesis. Specifically, polyphenols such as citrus flavonoids, green tea epigallocatechin gallate, resveratrol, capsaicin and curcumin, have been reported to increase lipolysis and induce fatty acid β-oxidation through modulation of hormone sensitive lipase, acetyl-coA carboxylase, carnitine acyl transferase and peroxisome proliferator-activated receptor gamma coactivator-1. In this review article, we discuss selected phytochemicals in relation to their integrated functionalities and specific mechanisms for weight loss. Copyright © 2016 Elsevier Inc. All rights reserved.

Seasonal variation in body mass, body temperature and thermogenesis in the Hwamei, Garrulax canorus.

PubMed

Wu, Mei-Xiu; Zhou, Li-Meng; Zhao, Li-Dan; Zhao, Zhi-Jun; Zheng, Wei-Hong; Liu, Jin-Song

2015-01-01

The basal thermogenesis of birds is beginning to be viewed as a highly flexible physiological trait influenced by environmental fluctuations, particularly changes in ambient temperature (Ta). Many birds living in regions with seasonal fluctuations in Ta typically respond to cold by increasing their insulation and adjusting their metabolic rate. To understand these metabolic adaptations, body temperature (Tb), metabolic rate (MR), thermal neutral zone (TNZ) and thermal conductance were measured within a range of temperatures from 5 to 40°C in free-living Hwamei, Garrulax canorus, in both winter and summer. Body mass was 61.2±0.3g in winter and 55.5±1.0g in summer, and mean Tb was 41.6±0.1°C in winter and 42.3±0.1°C in summer. TNZ was between 28.3 and 35.1°C in winter and between 28.7 and 33.2°C in summer. The mean basal metabolic rate (BMR) within TNZ was 203.32±11.81ml O2 h(-1) in winter and 168.99±6.45ml O2 h(-1) in summer. Minimum thermal conductance was 3.73±0.09joulesg(-1)h(-1)°C(-1) in winter and 3.26±0.06joulesg(-1)h(-1)°C(-1) in summer. Birds caught in winter had higher body mass, MR, and more variable TNZ than those in summer. The increased winter BMR indicates improved ability to cope with cold and maintenance of a high Tb. These results show that the Hwamei's metabolism is not constant, but exhibits pronounced seasonal phenotypic flexibility associated with maintenance of a high Tb. Copyright © 2014 Elsevier Inc. All rights reserved.

Hospital outpatients are satisfactory for case-control studies on cancer and diet in China: a comparison of population versus hospital controls.

PubMed

Li, Lin; Zhang, Min; Holman, C D'Arcy J

2013-01-01

To investigate the internal validity of a food-frequency questionnaire (FFQ) developed for use in Chinese women and to compare habitual dietary intakes between population and hospital controls measured by the FFQ. A quantitative FFQ and a short food habit questionnaire (SFHQ) were developed and adapted for cancer and nutritional studies. Habitual dietary intakes were assessed in 814 Chinese women aged 18-81 years (407 outpatients and 407 population controls) by face-to-face interview using the FFQ in Shenyang, Northeast China in 2009-2010. The Goldberg formula (ratio of energy intake to basal metabolic rate, EI/BMR) was used to assess the validity of the FFQ. Correlation analyses compared the SFHQ variables with those of the quantitative FFQ. Differences in dietary intakes between hospital and population controls were investigated. Odds ratios (ORs) and 95% confidence intervals (CIs) were obtained using conditional logistic regression analyses. The partial correlation coefficients were moderate to high (0.42 to 0.80; all p<0.05) for preserved food intake, fat consumption and tea drinking variables between the SFHQ and the FFQ. The average EI/BMR was 1.93 with 88.5% of subjects exceeding the Goldberg cut-off value of 1.35. Hospital controls were comparable to population controls in consumption of 17 measured food groups and mean daily intakes of energy and selected nutrients. The FFQ had reasonable validity to measure habitual dietary intakes of Chinese women. Hospital outpatients provide a satisfactory control group for food consumption and intakes of energy and nutrients measured by the FFQ in a Chinese hospital setting.

Simultaneous Validation of Seven Physical Activity Questionnaires Used in Japanese Cohorts for Estimating Energy Expenditure: A Doubly Labeled Water Study.

PubMed

Sasai, Hiroyuki; Nakata, Yoshio; Murakami, Haruka; Kawakami, Ryoko; Nakae, Satoshi; Tanaka, Shigeho; Ishikawa-Takata, Kazuko; Yamada, Yosuke; Miyachi, Motohiko

2018-04-28

Physical activity questionnaires (PAQs) used in large-scale Japanese cohorts have rarely been simultaneously validated against the gold standard doubly labeled water (DLW) method. This study examined the validity of seven PAQs used in Japan for estimating energy expenditure against the DLW method. Twenty healthy Japanese adults (9 men; mean age, 32.4 [standard deviation {SD}, 9.4] years, mainly researchers and students) participated in this study. Fifteen-day daily total energy expenditure (TEE) and basal metabolic rate (BMR) were measured using the DLW method and a metabolic chamber, respectively. Activity energy expenditure (AEE) was calculated as TEE - BMR - 0.1 × TEE. Seven PAQs were self-administered to estimate TEE and AEE. The mean measured values of TEE and AEE were 2,294 (SD, 318) kcal/day and 721 (SD, 161) kcal/day, respectively. All of the PAQs indicated moderate-to-strong correlations with the DLW method in TEE (rho = 0.57-0.84). Two PAQs (Japan Public Health Center Study [JPHC]-PAQ Short and JPHC-PAQ Long) showed significant equivalence in TEE and moderate intra-class correlation coefficients (ICC). None of the PAQs showed significantly equivalent AEE estimates, with differences ranging from -547 to 77 kcal/day. Correlations and ICCs in AEE were mostly weak or fair (rho = 0.02-0.54, and ICC = 0.00-0.44). Only JPHC-PAQ Short provided significant and fair agreement with the DLW method. TEE estimated by the PAQs showed moderate or strong correlations with the results of DLW. Two PAQs showed equivalent TEE and moderate agreement. None of the PAQs showed equivalent AEE estimation to the gold standard, with weak-to-fair correlations and agreements. Further studies with larger sample sizes are needed to confirm these findings.

Energy metabolism and evaporative water loss in the European free-tailed bat and Hemprich's long-eared bat (Microchiroptera): species sympatric in the Negev Desert.

PubMed

Marom, Sagi; Korine, Carmi; Wojciechowski, Michał S; Tracy, Christopher R; Pinshow, Berry

2006-01-01

We compared the thermoregulatory abilities of two insectivorous bat species, Tadarida teniotis (mean body mass 32 g) and Otonycteris hemprichii (mean body mass 25 g), that are of different phylogenetic origins and zoogeographic distributions but are sympatric in the Negev Desert. At night, both were normothermic. By day, both were torpid when exposed to ambient temperatures (T(a)) below 25 degrees Celsius, with concomitant adjustments in metabolic rate (MR). Otonycteris hemprichii entered torpor at higher T(a) than T. teniotis, and, when torpid, their body temperatures (T(b)) were 1 degrees -2 degrees Celsius and 5 degrees -8 degrees Celsius above T(a), respectively; MR was correspondingly reduced. At night, the lower critical temperature of T. teniotis was 31.5 degrees Celsius, and that of O. hemprichii was 33 degrees Celsius. Mean nocturnal thermoneutral MR of T. teniotis was 37% greater than that of O. hemprichii. At high T(a), evaporative water loss (EWL) increased markedly in both species, but it was significantly higher in T. teniotis above 38 degrees Celsius. In both species, the dry heat transfer coefficient (thermal conductance) followed the expected pattern for small mammals, by day and by night. Total EWL was notably low in normothermic and torpid animals of both species, much lower than values reported for other bats, indicating efficient water conservation mechanisms in the study species. Comparing thermoregulatory abilities suggests that O. hemprichii is better adapted to hot, arid environments than T. teniotis, which may explain its wider desert distribution. By both standard and phylogenetically informed ANCOVA, we found no differences in basal metabolic rate (BMR) between desert and nondesert species of insectivorous bats, substantiating previous studies suggesting that low BMR is a characteristic common to insectivorous bats in general.

Dielectric response of molecules in empirical tight-binding theory

NASA Astrophysics Data System (ADS)

Boykin, Timothy B.; Vogl, P.

2002-01-01

In this paper we generalize our previous approach to electromagnetic interactions within empirical tight-binding theory to encompass molecular solids and isolated molecules. In order to guarantee physically meaningful results, we rederive the expressions for relevant observables using commutation relations appropriate to the finite tight-binding Hilbert space. In carrying out this generalization, we examine in detail the consequences of various prescriptions for the position and momentum operators in tight binding. We show that attempting to fit parameters of the momentum matrix directly generally results in a momentum operator which is incompatible with the underlying tight-binding model, while adding extra position parameters results in numerous difficulties, including the loss of gauge invariance. We have applied our scheme, which we term the Peierls-coupling tight-binding method, to the optical dielectric function of the molecular solid PPP, showing that this approach successfully predicts its known optical properties even in the limit of isolated molecules.

Dimeric, trimeric and tetrameric complexes of immunoglobulin G fix complement.

PubMed Central

Wright, J K; Tschopp, J; Jaton, J C; Engel, J

1980-01-01

The binding of pure dimers, trimers and tetramers of randomly cross-linked non-immune rabbit immunoglobulin G to the first component and subcomponent of the complement system, C1 and C1q respectively, was studied. These oligomers possessed open linear structures. All three oligomers fixed complement with decreasing affinity in the order: tetramer, trimer, dimer. Complement fixation by dimeric immunoglobulin exhibited the strongest concentration-dependence. No clear distinction between a non-co-operative and a co-operative binding mechanism could be achieved, although the steepness of the complement-fixation curves for dimers and trimers was better reflected by the co-operative mechanism. Intrinsic binding constants were about 10(6)M-1 for dimers, 10(7)M-1 for trimers and 3 X 10(9)M-1 for tetramers, assuming non-co-operative binding. The data are consistent with a maximum valency of complement component C1 for immunoglobulin G protomers in the range 6-18. The binding of dimers to purified complement subcomponent C1q was demonstrated by sedimentation-velocity ultracentrifugation. Mild reduction of the complexes by dithioerythritol caused the immunoglobulin to revert to the monomeric state (S20,w = 6.2-6.5S) with concomitant loss of complement-fixing ability. Images Fig. 2. PMID:6985362

Promoter Engineering Reveals the Importance of Heptameric Direct Repeats for DNA Binding by Streptomyces Antibiotic Regulatory Protein-Large ATP-Binding Regulator of the LuxR Family (SARP-LAL) Regulators in Streptomyces natalensis.

PubMed

Barreales, Eva G; Vicente, Cláudia M; de Pedro, Antonio; Santos-Aberturas, Javier; Aparicio, Jesús F

2018-05-15

The biosynthesis of small-size polyene macrolides is ultimately controlled by a couple of transcriptional regulators that act in a hierarchical way. A Streptomyces antibiotic regulatory protein-large ATP-binding regulator of the LuxR family (SARP-LAL) regulator binds the promoter of a PAS-LuxR regulator-encoding gene and activates its transcription, and in turn, the gene product of the latter activates transcription from various promoters of the polyene gene cluster directly. The primary operator of PimR, the archetype of SARP-LAL regulators, contains three heptameric direct repeats separated by four-nucleotide spacers, but the regulator can also bind a secondary operator with only two direct repeats separated by a 3-nucleotide spacer, both located in the promoter region of its unique target gene, pimM A similar arrangement of operators has been identified for PimR counterparts encoded by gene clusters for different antifungal secondary metabolites, including not only polyene macrolides but peptidyl nucleosides, phoslactomycins, or cycloheximide. Here, we used promoter engineering and quantitative transcriptional analyses to determine the contributions of the different heptameric repeats to transcriptional activation and final polyene production. Optimized promoters have thus been developed. Deletion studies and electrophoretic mobility assays were used for the definition of DNA-binding boxes formed by 22-nucleotide sequences comprising two conserved heptameric direct repeats separated by four-nucleotide less conserved spacers. The cooperative binding of PimR SARP appears to be the mechanism involved in the binding of regulator monomers to operators, and at least two protein monomers are required for efficient binding. IMPORTANCE Here, we have shown that a modulation of the production of the antifungal pimaricin in Streptomyces natalensis can be accomplished via promoter engineering of the PAS-LuxR transcriptional activator pimM The expression of this gene is controlled by the Streptomyces antibiotic regulatory protein-large ATP-binding regulator of the LuxR family (SARP-LAL) regulator PimR, which binds a series of heptameric direct repeats in its promoter region. The structure and importance of such repeats in protein binding, transcriptional activation, and polyene production have been investigated. These findings should provide important clues to understand the regulatory machinery that modulates antibiotic biosynthesis in Streptomyces and open new possibilities for the manipulation of metabolite production. The presence of PimR orthologues encoded by gene clusters for different secondary metabolites and the conservation of their operators suggest that the improvements observed in the activation of pimaricin biosynthesis by Streptomyces natalensis could be extrapolated to the production of different compounds by other species. Copyright © 2018 Barreales et al.

Covalent attachment of Arc repressor subunits by a peptide linker enhances affinity for operator DNA.

PubMed

Robinson, C R; Sauer, R T

1996-01-09

By designing a recombinant gene containing tandem copies of the arc coding sequence with intervening DNA encoding the linker sequence GGGSGGGTGGGSGGG, the two subunits of the P22 Are repressor dimer have been covalently linked to form a single-chain protein called Arc-L1-Arc. The 15-residue linker joins the C-terminus of one monomer to the N-terminus of the second, a distance of approximately 45 A in the Arc-operator cocrystal structure. Arc-L1-Arc is expressed at high levels in Escherichia coli, with no evidence of degradation or proteolytic clipping of the linker, and is more active than wild-type Arc in repression assays. The purified Arc-L1-Arc protein has the molecular weight expected for the designed protein and unfolds cooperatively, reversibly, and with no concentration dependence in thermal-denaturation studies. Arc-L1-Arc protects operator DNA in a manner indistinguishable from that of wild-type Arc in DNase I and copper-phenanthroline footprinting studies, but the covalent attachment of the two monomers results in enhanced affinity for operator DNA. Arc-L1-Arc binds operator DNA half-maximally at a concentration of 1.7 pM, compared with the wild-type value of 185 pM, and also binds DNA fragments containing the left or right operator half-sites more tightly than wild type. Because wild-type Arc is monomeric at sub-nanomolar concentrations and must dimerize before binding to the operator, it was anticipated that Arc-L1-Arc would exhibit a lower half-maximal binding concentration. However, even when the change from a monomeric to a dimeric species is taken into account, the affinity of Arc-L1-Arc for operator and half-operator DNA is greater than the wild-type affinity. This tighter binding appears to result from slower dissociation, as Arc-L1-Arc DNA complexes with full or half-site operators dissociate at rates 5-10 times slower than the corresponding Arc--DNA complexes. Hence, the activity of the designed Arc-L1-Arc protein is substantially increased relative to wild-type Arc in a variety of assays.

Evidence for co-operativity in coenzyme binding to tetrameric Sulfolobus solfataricus alcohol dehydrogenase and its structural basis: fluorescence, kinetic and structural studies of the wild-type enzyme and non-co-operative N249Y mutant

PubMed Central

2005-01-01

The interaction of coenzyme with thermostable homotetrameric NAD(H)-dependent alcohol dehydrogenase from the thermoacidophilic sulphur-dependent crenarchaeon Sulfolobus solfataricus (SsADH) and its N249Y (Asn-249→Tyr) mutant was studied using the high fluorescence sensitivity of its tryptophan residues Trp-95 and Trp-117 to the binding of coenzyme moieties. Fluorescence quenching studies performed at 25 °C show that SsADH exhibits linearity in the NAD(H) binding [the Hill coefficient (h)∼1) at pH 9.8 and at moderate ionic strength, in addition to positive co-operativity (h=2.0–2.4) at pH 7.8 and 6.8, and at pH 9.8 in the presence of salt. Furthermore, NADH binding is positively co-operative below 20 °C (h∼3) and negatively co-operative at 40–50 °C (h∼0.7), as determined at moderate ionic strength and pH 9.8. Steady-state kinetic measurements show that SsADH displays standard Michaelis–Menten kinetics between 35 and 45 °C, but exhibits positive and negative co-operativity for NADH oxidation below (h=3.3 at 20 °C) and above (h=0.7 at 70–80 °C) this range of temperatures respectively. However, N249Y SsADH displays non-co-operative behaviour in coenzyme binding under the same experimental conditions used for the wild-type enzyme. In loop 270–275 of the coenzyme domain and segments at the interface of dimer A–B, analyses of the wild-type and mutant SsADH structures identified the structural elements involved in the intersubunit communication and suggested a possible structural basis for co-operativity. This is the first report of co-operativity in a tetrameric ADH and of temperature-induced co-operativity in a thermophilic enzyme. PMID:15651978

Cytochrome P450BM-3 reduces aldehydes to alcohols through a direct hydride transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaspera, Ruediger; Sahele, Tariku; Lakatos, Kyle

Highlights: Black-Right-Pointing-Pointer Cytochrome P450BM-3 reduced aldehydes to alcohols efficiently (k{sub cat} {approx} 25 min{sup -1}). Black-Right-Pointing-Pointer Reduction is a direct hydride transfer from R-NADP{sup 2}H to the carbonyl moiety. Black-Right-Pointing-Pointer P450 domain variants enhance reduction through potential allosteric/redox interactions. Black-Right-Pointing-Pointer Novel reaction will have implications for metabolism of xenobiotics. -- Abstract: Cytochrome P450BM-3 catalyzed the reduction of lipophilic aldehydes to alcohols efficiently. A k{sub cat} of {approx}25 min{sup -1} was obtained for the reduction of methoxy benzaldehyde with wild type P450BM-3 protein which was higher than in the isolated reductase domain (BMR) alone and increased in specific P450-domain variants. Themore » reduction was caused by a direct hydride transfer from preferentially R-NADP{sup 2}H to the carbonyl moiety of the substrate. Weak substrate-P450-binding of the aldehyde, turnover with the reductase domain alone, a deuterium incorporation in the product from NADP{sup 2}H but not D{sub 2}O, and no inhibition by imidazole suggests the reductase domain of P450BM-3 as the potential catalytic site. However, increased aldehyde reduction by P450 domain variants (P450BM-3 F87A T268A) may involve allosteric or redox mechanistic interactions between heme and reductase domains. This is a novel reduction of aldehydes by P450BM-3 involving a direct hydride transfer and could have implications for the metabolism of endogenous substrates or xenobiotics.« less

The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes.

PubMed

Ni, Lisheng; Jensen, Slade O; Ky Tonthat, Nam; Berg, Tracey; Kwong, Stephen M; Guan, Fiona H X; Brown, Melissa H; Skurray, Ronald A; Firth, Neville; Schumacher, Maria A

2009-11-01

Plasmids harbored by Staphylococcus aureus are a major contributor to the spread of bacterial multi-drug resistance. Plasmid conjugation and partition are critical to the dissemination and inheritance of such plasmids. Here, we demonstrate that the ArtA protein encoded by the S. aureus multi-resistance plasmid pSK41 is a global transcriptional regulator of pSK41 genes, including those involved in conjugation and segregation. ArtA shows no sequence homology to any structurally characterized DNA-binding protein. To elucidate the mechanism by which it specifically recognizes its DNA site, we obtained the structure of ArtA bound to its cognate operator, ACATGACATG. The structure reveals that ArtA is representative of a new family of ribbon-helix-helix (RHH) DNA-binding proteins that contain extended, N-terminal basic motifs. Strikingly, unlike most well-studied RHH proteins ArtA binds its cognate operators as a dimer. However, we demonstrate that it is also able to recognize an atypical operator site by binding as a dimer-of-dimers and the extended N-terminal regions of ArtA were shown to be essential for this dimer-of-dimer binding mode. Thus, these data indicate that ArtA is a master regulator of genes critical for both horizontal and vertical transmission of pSK41 and that it can recognize DNA utilizing alternate binding modes.

The Staphylococcus aureus pSK41 plasmid-encoded ArtA protein is a master regulator of plasmid transmission genes and contains a RHH motif used in alternate DNA-binding modes

PubMed Central

Ni, Lisheng; Jensen, Slade O.; Ky Tonthat, Nam; Berg, Tracey; Kwong, Stephen M.; Guan, Fiona H. X.; Brown, Melissa H.; Skurray, Ronald A.; Firth, Neville; Schumacher, Maria A.

2009-01-01

Plasmids harbored by Staphylococcus aureus are a major contributor to the spread of bacterial multi-drug resistance. Plasmid conjugation and partition are critical to the dissemination and inheritance of such plasmids. Here, we demonstrate that the ArtA protein encoded by the S. aureus multi-resistance plasmid pSK41 is a global transcriptional regulator of pSK41 genes, including those involved in conjugation and segregation. ArtA shows no sequence homology to any structurally characterized DNA-binding protein. To elucidate the mechanism by which it specifically recognizes its DNA site, we obtained the structure of ArtA bound to its cognate operator, ACATGACATG. The structure reveals that ArtA is representative of a new family of ribbon–helix–helix (RHH) DNA-binding proteins that contain extended, N-terminal basic motifs. Strikingly, unlike most well-studied RHH proteins ArtA binds its cognate operators as a dimer. However, we demonstrate that it is also able to recognize an atypical operator site by binding as a dimer-of-dimers and the extended N-terminal regions of ArtA were shown to be essential for this dimer-of-dimer binding mode. Thus, these data indicate that ArtA is a master regulator of genes critical for both horizontal and vertical transmission of pSK41 and that it can recognize DNA utilizing alternate binding modes. PMID:19759211

Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range

PubMed Central

Ventura, Alejandra C.; Bush, Alan; Vasen, Gustavo; Goldín, Matías A.; Burkinshaw, Brianne; Bhattacharjee, Nirveek; Folch, Albert; Brent, Roger; Chernomoretz, Ariel; Colman-Lerner, Alejandro

2014-01-01

Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general “systems level” mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, pre-equilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. PMID:25172920

Structure of the MecI repressor from Staphylococcus aureus in complex with the cognate DNA operator of mec

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safo, Martin K., E-mail: msafo@vcu.edu; Ko, Tzu-Ping; Musayev, Faik N.

The up-and-down binding of dimeric MecI to mecA dyad DNA may account for the cooperative effect of the repressor. The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of β-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Å resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA,more » and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtual DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI–mec complex, but unlike the MecI–bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.« less

Action of tremorgenic mycotoxins on GABA/sub A/ receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gant, D.B.; Cole, R.J.; Valdes, J.J.

1987-11-09

The effects of four tremorgenic and one nontremorgenic mycotoxins were studied on ..gamma..-aminobutyric acid (GABA/sub A/) receptor binding and function in rat brain and on binding of a voltage-operated Cl/sup -/ channel in Torpedo electric organ. None of the mycotoxins had significant effect on (/sup 3/H)muscimol or (/sup 3/H)flunitrazepam binding to the GAMA/sup A/ receptor. However, only the four tremorgenic mycotoxins inhibited GABA-induced /sup 36/Cl/sup -/ influx and (/sup 35/S)t-butylbicyclophosphorothionate ((/sup 35/S)TBPS) binding in rate brain membranes, while the nontremorgenic verruculotoxin had no effect. Inhibition of (/sup 35/S)TBPS binding by paspalinine was non-competitive. This suggests that tremorgenic mycotoxins inhibit GABA/submore » A/ receptor function by binding close to the receptor's Cl/sup -/ channel. On the voltage-operated Cl/sup -/ channel, only high concentrations of verruculogen and verruculotoxin caused significant inhibition of the channel's binding of (/sup 35/S)TBPS. The data suggest that the tremorgenic action of these mycotoxins may be due in part to their inhibition of GABA/sub A/ receptor function. 21 references, 4 figures, 2 tables.« less

FY2016 Advanced Batteries R&D Annual Progress Report - Part 4 of 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

The Advanced Batteries research and development (R&D) subprogram within the DOE Vehicle Technologies Office (VTO) provides support and guidance for projects focusing on batteries for plug-in electric vehicles. Program targets focus on overcoming technical barriers to enable market success including: (1) significantly reducing battery cost, (2) increasing battery performance (power, energy, durability), (3) reducing battery weight & volume, and (4) increasing battery tolerance to abusive conditions such as short circuit, overcharge, and crush. This report describes the progress made on the research and development projects funded by the Battery subprogram in 2016. This section covers Advanced Battery Materials Research (BMR)more » part 1.« less

Structure of the Mecl Repressor from Staphylococcus aureus in Complex with the Cognate DNA Operator of mec

DOE Office of Scientific and Technical Information (OSTI.GOV)

Safo,M.; Ko, T.; Musayev, F.

The dimeric repressor MecI regulates the mecA gene that encodes the penicillin-binding protein PBP-2a in methicillin-resistant Staphylococcus aureus (MRSA). MecI is similar to BlaI, the repressor for the blaZ gene of {beta}-lactamase. MecI and BlaI can bind to both operator DNA sequences. The crystal structure of MecI in complex with the 32 base-pair cognate DNA of mec was determined to 3.8 Angstroms resolution. MecI is a homodimer and each monomer consists of a compact N-terminal winged-helix domain, which binds to DNA, and a loosely packed C-terminal helical domain, which intertwines with its counter-monomer. The crystal contains horizontal layers of virtualmore » DNA double helices extending in three directions, which are separated by perpendicular DNA segments. Each DNA segment is bound to two MecI dimers. Similar to the BlaI-mec complex, but unlike the MecI-bla complex, the MecI repressors bind to both sides of the mec DNA dyad that contains four conserved sequences of TACA/TGTA. The results confirm the up-and-down binding to the mec operator, which may account for cooperative effect of the repressor.« less

Ada/POSIX binding: A focused Ada investigation

NASA Technical Reports Server (NTRS)

Legrand, Sue

1988-01-01

NASA is seeking an operating system interface definition (OSID) for the Space Station Program (SSP) in order to take advantage of the commercial off-the-shelf (COTS) products available today and the many that are expected in the future. NASA would also like to avoid the reliance on any one source for operating systems, information system, communication system, or instruction set architecture. The use of the Portable Operating System Interface for Computer Environments (POSIX) is examined as a possible solution to this problem. Since Ada is already the language of choice for SSP, the question of an Ada/POSIX binding is addressed. The intent of the binding is to provide access to the POSIX standard operation system (OS) interface and environment, by which application portability of Ada applications will be supported at the source code level. A guiding principle of Ada/POSIX binding development is a clear conformance of the Ada interface with the functional definition of POSIX. The interface is intended to be used by both application developers and system implementors. The objective is to provide a standard that allows a strictly conforming application source program that can be compiled to execute on any conforming implementation. Special emphasis is placed on first providing those functions and facilities that are needed in a wide variety of commercial applications

Benchmark Dose for Urinary Cadmium based on a Marker of Renal Dysfunction: A Meta-Analysis

PubMed Central

Woo, Hae Dong; Chiu, Weihsueh A.; Jo, Seongil; Kim, Jeongseon

2015-01-01

Background Low doses of cadmium can cause adverse health effects. Benchmark dose (BMD) and the one-sided 95% lower confidence limit of BMD (BMDL) to derive points of departure for urinary cadmium exposure have been estimated in several previous studies, but the methods to derive BMD and the estimated BMDs differ. Objectives We aimed to find the associated factors that affect BMD calculation in the general population, and to estimate the summary BMD for urinary cadmium using reported BMDs. Methods A meta-regression was performed and the pooled BMD/BMDL was estimated using studies reporting a BMD and BMDL, weighted by sample size, that were calculated from individual data based on markers of renal dysfunction. Results BMDs were highly heterogeneous across studies. Meta-regression analysis showed that a significant predictor of BMD was the cut-off point which denotes an abnormal level. Using the 95th percentile as a cut off, BMD5/BMDL5 estimates for 5% benchmark responses (BMR) of β2-microglobulinuria (β2-MG) estimated was 6.18/4.88 μg/g creatinine in conventional quantal analysis and 3.56/3.13 μg/g creatinine in the hybrid approach, and BMD5/BMDL5 estimates for 5% BMR of N-acetyl-β-d-glucosaminidase (NAG) was 10.31/7.61 μg/g creatinine in quantal analysis and 3.21/2.24 g/g creatinine in the hybrid approach. However, the meta-regression showed that BMD and BMDL were significantly associated with the cut-off point, but BMD calculation method did not significantly affect the results. The urinary cadmium BMDL5 of β2-MG was 1.9 μg/g creatinine in the lowest cut-off point group. Conclusion The BMD was significantly associated with the cut-off point defining the abnormal level of renal dysfunction markers. PMID:25970611

Plasticity in body composition in breeding birds: what drives the metabolic costs of egg production?

PubMed

Vézina, François; Williams, Tony D

2003-01-01

Body composition in vertebrates is known to show phenotypic plasticity, and changes in organ masses are usually rapid and reversible. One of the most rapid and reversible changes is the transformation of the female avian reproductive organs before breeding. This provides an excellent system to investigate the effects of plasticity in organ size on basal metabolic rate (BMR) through relationships between organ masses and BMR. We compared body composition of female European starlings (Sturnus vulgaris) during various reproductive stages over 3 yr and investigated the pattern of changes in reproductive and nonreproductive organ mass during follicular development and ovulation. Furthermore, we analyzed the relationship between organ mass and resting metabolic rate (RMR) in nonbreeding, laying, and chick-rearing females. Our analysis revealed marked variation in organ masses between breeding stages but no consistent pattern among years except for kidney and pectoralis muscle. Furthermore, changes in nonreproductive organs did not parallel the cycle of growth and regression of the reproductive organs. The oviduct gained 62% of its 22-fold increase in mass in only 3 d, and oviduct regression was just as rapid and began even before the final egg of the clutch was laid, with 42% of the oviduct mass lost before laying of the final egg. In laying females, 18% of variation in mass-corrected RMR was explained by the mass of the oviduct (r2=0.18, n=80, P<0.0005), while pectoralis muscle mass in nonbreeding individuals and liver and gizzard mass in chick-rearing females were the only organs significantly related to RMR (r2=0.31-0.44). We suggest that the nonreproductive organs are affected more by changes in local ecological conditions than the reproductive state itself and that the activity and maintenance cost of the oviduct is high enough that selection has led to a very tight size-function relationship for this organ.

Replication initiator protein RepE of mini-F plasmid: functional differentiation between monomers (initiator) and dimers (autogenous repressor).

PubMed Central

Ishiai, M; Wada, C; Kawasaki, Y; Yura, T

1994-01-01

Replication of mini-F plasmid requires the plasmid-encoded RepE initiator protein and several host factors including DnaJ, DnaK, and GrpE, heat shock proteins of Escherichia coli. The RepE protein plays a crucial role in replication and exhibits two major functions: initiation of replication from the origin, ori2, and autogenous repression of repE transcription. One of the mini-F plasmid mutants that can replicate in the dnaJ-defective host produces an altered RepE (RepE54) with a markedly enhanced initiator activity but little or no repressor activity. RepE54 has been purified from cell extracts primarily in monomeric form, unlike the wild-type RepE that is recovered in dimeric form. Gel-retardation assays revealed that RepE54 monomers bind to ori2 (direct repeats) with a very high efficiency but hardly bind to the repE operator (inverted repeat), in accordance with the properties of RepE54 in vivo. Furthermore, the treatment of wild-type RepE dimers with protein denaturants enhanced their binding to ori2 but reduced binding to the operator: RepE dimers were partially converted to monomers, and the ori2 binding activity was uniquely associated with monomers. These results strongly suggest that RepE monomers represent an active form by binding to ori2 to initiate replication, whereas dimers act as an autogenous repressor by binding to the operator. We propose that RepE is structurally and functionally differentiated and that monomerization of RepE dimers, presumably mediated by heat shock protein(s), activates the initiator function and participates in regulation of mini-F DNA replication. Images PMID:8170998

The electrostatic role of the Zn-Cys2His2 complex in binding of operator DNA with transcription factors: mouse EGR-1 from the Cys2His2 family.

PubMed

Chirgadze, Y N; Boshkova, E A; Polozov, R V; Sivozhelezov, V S; Dzyabchenko, A V; Kuzminsky, M B; Stepanenko, V A; Ivanov, V V

2018-01-07

The mouse factor Zif268, known also as early growth response protein EGR-1, is a classical representative for the Cys2His2 transcription factor family. It is required for binding the RNA polymerase with operator dsDNA to initialize the transcription process. We have shown that only in this family of total six Zn-finger protein families the Zn complex plays a significant role in the protein-DNA binding. Electrostatic feature of this complex in the binding of factor Zif268 from Mus musculus with operator DNA has been considered. The factor consists of three similar Zn-finger units which bind with triplets of coding DNA. Essential contacts of the factor with the DNA phosphates are formed by three conservative His residues, one in each finger. We describe here the results of calculations of the electrostatic potentials for the Zn-Cys2His2 complex, Zn-finger unit 1, and the whole transcription factor. The potential of Zif268 has a positive area on the factor surface, and it corresponds exactly to the binding sites of each of Zn-finger units. The main part of these areas is determined by conservative His residues, which form contacts with the DNA phosphate groups. Our result shows that the electrostatic positive potential of this histidine residue is enhanced due to the Zn complex. The other contacts of the Zn-finger with DNA are related to nucleotide bases, and they are responsible for the sequence-specific binding with DNA. This result may be extended to all other members of the Cys2His2 transcription factor family.

Hypophysectomy eliminates and growth hormone (GH) maintains the midpregnancy elevation in GH receptor and serum binding protein in the mouse

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Jimenez, F.; Fielder, P.J.; Martinez, R.R.

1990-02-01

({sup 125}I)Iodomouse GH (({sup 125}I)iodo-mGH) binding to samples of serum and hepatic microsomal membranes was measured in hypophysectomized pregnant, sham-operated pregnant, intact pregnant, and intact adult virgin mice. Surgeries were carried out on day 11 of pregnancy, and the animals were killed on day 14. The binding of mGH to both serum and hepatic microsomal membranes of intact virgin mice was much lower than to those of intact pregnant mice. In hypophysectomized mice, the mGH-binding capacity of both serum and hepatic microsomes decreased to values similar to those of nonpregnant mice. No significant differences were observed between intact and sham-operatedmore » pregnant animals in the maternal serum mGH concentration, the serum GH-binding protein concentration, or the hepatic GH receptor concentration. GH receptor and binding protein-encoding mRNAs were also higher in intact and sham-operated pregnant mice than in virgin and hypophysectomized mice. Hypophysectomized mice were treated with 200 micrograms/day bovine GH, administered by osmotic minipump; after 3 days of treatment, a significant elevation of hepatic GH receptor and serum GH-binding protein levels was observed. These results demonstrate an up-regulation of hepatic GH receptors and serum GH-binding protein by GH during pregnancy in the mouse.« less

Exploring the sequence-function relationship in transcriptional regulation by the lac O1 operator.

PubMed

Maity, Tuhin S; Jha, Ramesh K; Strauss, Charlie E M; Dunbar, John

2012-07-01

Understanding how binding of a transcription factor to an operator is influenced by the operator sequence is an ongoing quest. It facilitates discovery of alternative binding sites as well as tuning of transcriptional regulation. We investigated the behavior of the Escherichia coli Lac repressor (LacI) protein with a large set of lac O(1) operator variants. The 114 variants examined contained a mean of 2.9 (range 0-4) mutations at positions -4, -2, +2 and +4 in the minimally required 17 bp operator. The relative affinity of LacI for the operators was examined by quantifying expression of a GFP reporter gene and Rosetta structural modeling. The combinations of mutations in the operator sequence created a wide range of regulatory behaviors. We observed variations in the GFP fluorescent signal among the operator variants of more than an order of magnitude under both uninduced and induced conditions. We found that a single nucleotide change may result in changes of up to six- and 12-fold in uninduced and induced GFP signals, respectively. Among the four positions mutated, we found that nucleotide G at position -4 is strongly correlated with strong repression. By Rosetta modeling, we found a significant correlation between the calculated binding energy and the experimentally observed transcriptional repression strength for many operators. However, exceptions were also observed, underscoring the necessity for further improvement in biophysical models of protein-DNA interactions. © 2012 The Authors Journal compilation © 2012 FEBS.

Biology of the sauropod dinosaurs: the evolution of gigantism

PubMed Central

Sander, P Martin; Christian, Andreas; Clauss, Marcus; Fechner, Regina; Gee, Carole T; Griebeler, Eva-Maria; Gunga, Hanns-Christian; Hummel, Jürgen; Mallison, Heinrich; Perry, Steven F; Preuschoft, Holger; Rauhut, Oliver W M; Remes, Kristian; Tütken, Thomas; Wings, Oliver; Witzel, Ulrich

2011-01-01

The herbivorous sauropod dinosaurs of the Jurassic and Cretaceous periods were the largest terrestrial animals ever, surpassing the largest herbivorous mammals by an order of magnitude in body mass. Several evolutionary lineages among Sauropoda produced giants with body masses in excess of 50 metric tonnes by conservative estimates. With body mass increase driven by the selective advantages of large body size, animal lineages will increase in body size until they reach the limit determined by the interplay of bauplan, biology, and resource availability. There is no evidence, however, that resource availability and global physicochemical parameters were different enough in the Mesozoic to have led to sauropod gigantism. We review the biology of sauropod dinosaurs in detail and posit that sauropod gigantism was made possible by a specific combination of plesiomorphic characters (phylogenetic heritage) and evolutionary innovations at different levels which triggered a remarkable evolutionary cascade. Of these key innovations, the most important probably was the very long neck, the most conspicuous feature of the sauropod bauplan. Compared to other herbivores, the long neck allowed more efficient food uptake than in other large herbivores by covering a much larger feeding envelope and making food accessible that was out of the reach of other herbivores. Sauropods thus must have been able to take up more energy from their environment than other herbivores. The long neck, in turn, could only evolve because of the small head and the extensive pneumatization of the sauropod axial skeleton, lightening the neck. The small head was possible because food was ingested without mastication. Both mastication and a gastric mill would have limited food uptake rate. Scaling relationships between gastrointestinal tract size and basal metabolic rate (BMR) suggest that sauropods compensated for the lack of particle reduction with long retention times, even at high uptake rates. The extensive pneumatization of the axial skeleton resulted from the evolution of an avian-style respiratory system, presumably at the base of Saurischia. An avian-style respiratory system would also have lowered the cost of breathing, reduced specific gravity, and may have been important in removing excess body heat. Another crucial innovation inherited from basal dinosaurs was a high BMR. This is required for fueling the high growth rate necessary for a multi-tonne animal to survive to reproductive maturity. The retention of the plesiomorphic oviparous mode of reproduction appears to have been critical as well, allowing much faster population recovery than in megaherbivore mammals. Sauropods produced numerous but small offspring each season while land mammals show a negative correlation of reproductive output to body size. This permitted lower population densities in sauropods than in megaherbivore mammals but larger individuals. Our work on sauropod dinosaurs thus informs us about evolutionary limits to body size in other groups of herbivorous terrestrial tetrapods. Ectothermic reptiles are strongly limited by their low BMR, remaining small. Mammals are limited by their extensive mastication and their vivipary, while ornithsichian dinosaurs were only limited by their extensive mastication, having greater average body sizes than mammals. PMID:21251189

Biology of the sauropod dinosaurs: the evolution of gigantism.

PubMed

Sander, P Martin; Christian, Andreas; Clauss, Marcus; Fechner, Regina; Gee, Carole T; Griebeler, Eva-Maria; Gunga, Hanns-Christian; Hummel, Jürgen; Mallison, Heinrich; Perry, Steven F; Preuschoft, Holger; Rauhut, Oliver W M; Remes, Kristian; Tütken, Thomas; Wings, Oliver; Witzel, Ulrich

2011-02-01

The herbivorous sauropod dinosaurs of the Jurassic and Cretaceous periods were the largest terrestrial animals ever, surpassing the largest herbivorous mammals by an order of magnitude in body mass. Several evolutionary lineages among Sauropoda produced giants with body masses in excess of 50 metric tonnes by conservative estimates. With body mass increase driven by the selective advantages of large body size, animal lineages will increase in body size until they reach the limit determined by the interplay of bauplan, biology, and resource availability. There is no evidence, however, that resource availability and global physicochemical parameters were different enough in the Mesozoic to have led to sauropod gigantism. We review the biology of sauropod dinosaurs in detail and posit that sauropod gigantism was made possible by a specific combination of plesiomorphic characters (phylogenetic heritage) and evolutionary innovations at different levels which triggered a remarkable evolutionary cascade. Of these key innovations, the most important probably was the very long neck, the most conspicuous feature of the sauropod bauplan. Compared to other herbivores, the long neck allowed more efficient food uptake than in other large herbivores by covering a much larger feeding envelope and making food accessible that was out of the reach of other herbivores. Sauropods thus must have been able to take up more energy from their environment than other herbivores. The long neck, in turn, could only evolve because of the small head and the extensive pneumatization of the sauropod axial skeleton, lightening the neck. The small head was possible because food was ingested without mastication. Both mastication and a gastric mill would have limited food uptake rate. Scaling relationships between gastrointestinal tract size and basal metabolic rate (BMR) suggest that sauropods compensated for the lack of particle reduction with long retention times, even at high uptake rates. The extensive pneumatization of the axial skeleton resulted from the evolution of an avian-style respiratory system, presumably at the base of Saurischia. An avian-style respiratory system would also have lowered the cost of breathing, reduced specific gravity, and may have been important in removing excess body heat. Another crucial innovation inherited from basal dinosaurs was a high BMR. This is required for fueling the high growth rate necessary for a multi-tonne animal to survive to reproductive maturity. The retention of the plesiomorphic oviparous mode of reproduction appears to have been critical as well, allowing much faster population recovery than in megaherbivore mammals. Sauropods produced numerous but small offspring each season while land mammals show a negative correlation of reproductive output to body size. This permitted lower population densities in sauropods than in megaherbivore mammals but larger individuals. Our work on sauropod dinosaurs thus informs us about evolutionary limits to body size in other groups of herbivorous terrestrial tetrapods. Ectothermic reptiles are strongly limited by their low BMR, remaining small. Mammals are limited by their extensive mastication and their vivipary, while ornithsichian dinosaurs were only limited by their extensive mastication, having greater average body sizes than mammals. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

Mechanism of Sulfide Binding by Ferric Hemeproteins.

PubMed

Boubeta, Fernando M; Bieza, Silvina A; Bringas, Mauro; Estrin, Darío A; Boechi, Leonardo; Bari, Sara E

2018-06-19

The reaction of hydrogen sulfide (H 2 S) with hemeproteins is a key physiological reaction; still, its mechanism and implications are not completely understood. In this work, we propose a combination of experimental and theoretical tools to shed light on the reaction in model system microperoxidase 11 (MP11-Fe III ) and myoglobin (Mb-Fe III ), from the estimation of the intrinsic binding constants of the species H 2 S and hydrosulfide (HS - ), and the computational description of the overall binding process. Our results show that H 2 S and HS - are the main reactive species in Mb-Fe III and MP11-Fe III , respectively, and that the magnitude of their intrinsic binding constants are similar to most of the binding constants reported so far for hemeproteins systems and model compounds. However, while the binding of HS - to Mb-Fe III was negligible, the binding of H 2 S to MP11-Fe III was significant, providing a frame for a discriminated analysis of both species and revealing differential mechanistic aspects. A joint inspection of the kinetic data and the free energy profiles of the binding processes suggests that a dissociative mechanism with the release of a coordinated water molecule as rate limiting step is operative in the binding of H 2 S to Mb-Fe III and that the binding of HS - is prevented in the access to the protein matrix. For the MP11-Fe III case, where no access restrictions for the ligands are present, an associative component in the mechanism seems to be operative. Overall, the results suggest that if accessing the active site then both H 2 S and HS - are capable of binding a ferric heme moiety.

Antibody binding in altered gravity: implications for immunosorbent assay during space flight

NASA Technical Reports Server (NTRS)

Maule, Jake; Fogel, Marilyn; Steele, Andrew; Wainwright, Norman; Pierson, Duane L.; McKay, David S.

2003-01-01

A single antibody-incubation step of an indirect, enzyme-linked immunosorbent assay (ELISA) was performed during microgravity, Martian gravity (0.38 G) and hypergravity (1.8 G) phases of parabolic flight, onboard the NASA KC-135 aircraft. Antibody-antigen binding occurred within 15 seconds; the level of binding did not differ between microgravity, Martian gravity and 1 G (Earth's gravity) conditions. During hypergravity and 1 G, antibody binding was directly proportional to the fluid volume (per microtiter well) used for incubation; this pattern was not observed during microgravity. These effects in microgravity may be due to "fluid spread" within the chamber (observed during microgravity with digital photography), leading to greater fluid-surface contact and subsequently antibody-antigen contact. In summary, these results demonstrate that: i) ELISA antibody-incubation and washing steps can be successfully performed by human operators during microgravity, Martian gravity and hypergravity; ii) there is no significant difference in antibody binding between microgravity, Martian gravity and 1 G conditions; and iii) a smaller fluid volume/well (and therefore less antibody) was required for a given level of binding during microgravity. These conclusions indicate that reduced gravity would not present a barrier to successful operation of immunosorbent assays during spaceflight.

Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator

PubMed Central

Rajasekar, Karthik V.; Lovering, Andrew L.; Dancea, Felician; Scott, David J.; Harris, Sarah A.; Bingle, Lewis E.H.; Roessle, Manfred; Thomas, Christopher M.; Hyde, Eva I.; White, Scott A.

2016-01-01

Abstract The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting cooperatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-amino acid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerization domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20-bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, nuclear magnetic resonance spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in cooperative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerization domain of the tumour suppressor p53. PMID:27016739

Light-dependent gene regulation by a coenzyme B12-based photoreceptor

PubMed Central

Ortiz-Guerrero, Juan Manuel; Polanco, María Carmen; Murillo, Francisco J.; Padmanabhan, S.; Elías-Arnanz, Montserrat

2011-01-01

Cobalamin (B12) typically functions as an enzyme cofactor but can also regulate gene expression via RNA-based riboswitches. B12-directed gene regulatory mechanisms via protein factors have, however, remained elusive. Recently, we reported down-regulation of a light-inducible promoter in the bacterium Myxococcus xanthus by two paralogous transcriptional repressors, of which one, CarH, but not the other, CarA, absolutely requires B12 for activity even though both have a canonical B12-binding motif. Unanswered were what underlies this striking difference, what is the specific cobalamin used, and how it acts. Here, we show that coenzyme B12 (5′-deoxyadenosylcobalamin, AdoB12), specifically dictates CarH function in the dark and on exposure to light. In the dark, AdoB12-binding to the autonomous domain containing the B12-binding motif foments repressor oligomerization, enhances operator binding, and blocks transcription. Light, at various wavelengths at which AdoB12 absorbs, dismantles active repressor oligomers by photolysing the bound AdoB12 and weakens repressor–operator binding to allow transcription. By contrast, AdoB12 alters neither CarA oligomerization nor operator binding, thus accounting for its B12-independent activity. Our findings unveil a functional facet of AdoB12 whereby it serves as the chromophore of a unique photoreceptor protein class acting in light-dependent gene regulation. The prevalence of similar proteins of unknown function in microbial genomes suggests that this distinct B12-based molecular mechanism for photoregulation may be widespread in bacteria. PMID:21502508

A comparative study of basal metabolism and thermoregulation in a folivorous (Colobus guereza) and an omnivorous (Cercopithecus mitis) primate species.

PubMed

Müller, E F; Kamau, J M; Maloiy, G M

1983-01-01

1. Abdominal temperatures (Tab) and oxygen consumption (VO2) were measured in two males each of colobus and Sykes monkeys. 2. Tab in both species had the same range (36 38.5 C), but there were marked differences in the daily rhythms. 3. Low ambient temperatures (Ta) had little effect on Tab; at Ta = 33.5 35.5 C. however, Tab rose quickly to above 40 C. 4. The thermoneutral zone (TNZ) extended from about 5 to 28 C in both species. 5. In the colobus monkeys the basal metabolic rate (BMR) was considerably lower than in the Sykes monkeys: 85% vs 113% of the value predicted from body mass.

FY2016 Advanced Batteries R&D Annual Progress Report - Part 5 of 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

None, None

The Advanced Batteries research and development (R&D) subprogram within the DOE Vehicle Technologies Office (VTO) provides support and guidance for projects focusing on batteries for plug-in electric vehicles. Program targets focus on overcoming technical barriers to enable market success including: (1) significantly reducing battery cost, (2) increasing battery performance (power, energy, durability), (3) reducing battery weight & volume, and (4) increasing battery tolerance to abusive conditions such as short circuit, overcharge, and crush. This report describes the progress made on the research and development projects funded by the Battery subprogram in 2016. This section cover Advanced Battery Materials Research (BMR)more » part 2, Battery500 Innovation Centers project summaries, and appendices.« less

Weak partitioning chromatography for anion exchange purification of monoclonal antibodies.

PubMed

Kelley, Brian D; Tobler, Scott A; Brown, Paul; Coffman, Jonathan L; Godavarti, Ranga; Iskra, Timothy; Switzer, Mary; Vunnum, Suresh

2008-10-15

Weak partitioning chromatography (WPC) is an isocratic chromatographic protein separation method performed under mobile phase conditions where a significant amount of the product protein binds to the resin, well in excess of typical flowthrough operations. The more stringent load and wash conditions lead to improved removal of more tightly binding impurities, although at the cost of a reduction in step yield. The step yield can be restored by extending the column load and incorporating a short wash at the end of the load stage. The use of WPC with anion exchange resins enables a two-column cGMP purification platform to be used for many different mAbs. The operating window for WPC can be easily established using high throughput batch-binding screens. Under conditions that favor very strong product binding, competitive effects from product binding can give rise to a reduction in column loading capacity. Robust performance of WPC anion exchange chromatography has been demonstrated in multiple cGMP mAb purification processes. Excellent clearance of host cell proteins, leached Protein A, DNA, high molecular weight species, and model virus has been achieved. (c) 2008 Wiley Periodicals, Inc.

46 CFR 308.539 - Application.

Code of Federal Regulations, 2014 CFR

2014-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Facultative War Risk Cargo Insurance § 308.539 Application. (a) Preliminary request. Application for a... bind war risk in writing; for security reasons, if the applicant is submitting the order to bind war...

dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes

PubMed Central

Korenjak, Michael; Kwon, Eunjeong; Morris, Robert T.; Anderssen, Endre; Amzallag, Arnaud; Ramaswamy, Sridhar; Dyson, Nicholas J.

2014-01-01

dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains. PMID:25053843

Isolation from genomic DNA of sequences binding specific regulatory proteins by the acceleration of protein electrophoretic mobility upon DNA binding.

PubMed

Subrahmanyam, S; Cronan, J E

1999-01-21

We report an efficient and flexible in vitro method for the isolation of genomic DNA sequences that are the binding targets of a given DNA binding protein. This method takes advantage of the fact that binding of a protein to a DNA molecule generally increases the rate of migration of the protein in nondenaturing gel electrophoresis. By the use of a radioactively labeled DNA-binding protein and nonradioactive DNA coupled with PCR amplification from gel slices, we show that specific binding sites can be isolated from Escherichia coli genomic DNA. We have applied this method to isolate a binding site for FadR, a global regulator of fatty acid metabolism in E. coli. We have also isolated a second binding site for BirA, the biotin operon repressor/biotin ligase, from the E. coli genome that has a very low binding efficiency compared with the bio operator region.

Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator

NASA Astrophysics Data System (ADS)

Deng, Zengqin; Wang, Qing; Liu, Zhao; Zhang, Manfeng; Machado, Ana Carolina Dantas; Chiu, Tsu-Pei; Feng, Chong; Zhang, Qi; Yu, Lin; Qi, Lei; Zheng, Jiangge; Wang, Xu; Huo, Xinmei; Qi, Xiaoxuan; Li, Xiaorong; Wu, Wei; Rohs, Remo; Li, Ying; Chen, Zhongzhou

2015-07-01

Ferric uptake regulator (Fur) plays a key role in the iron homeostasis of prokaryotes, such as bacterial pathogens, but the molecular mechanisms and structural basis of Fur-DNA binding remain incompletely understood. Here, we report high-resolution structures of Magnetospirillum gryphiswaldense MSR-1 Fur in four different states: apo-Fur, holo-Fur, the Fur-feoAB1 operator complex and the Fur-Pseudomonas aeruginosa Fur box complex. Apo-Fur is a transition metal ion-independent dimer whose binding induces profound conformational changes and confers DNA-binding ability. Structural characterization, mutagenesis, biochemistry and in vivo data reveal that Fur recognizes DNA by using a combination of base readout through direct contacts in the major groove and shape readout through recognition of the minor-groove electrostatic potential by lysine. The resulting conformational plasticity enables Fur binding to diverse substrates. Our results provide insights into metal ion activation and substrate recognition by Fur that suggest pathways to engineer magnetotactic bacteria and antipathogenic drugs.

Ribosomal proteins L5 and L11 co-operatively inactivate c-Myc via RNA-induced silencing complex.

PubMed

Liao, J-M; Zhou, X; Gatignol, A; Lu, H

2014-10-09

Oncogene MYC is highly expressed in many human cancers and functions as a global regulator of ribosome biogenesis. Previously, we reported that ribosomal protein (RP) L11 binds to c-Myc and inhibits its transcriptional activity in response to ribosomal stress. Here, we show that RPL5, co-operatively with RPL11, guides the RNA-induced silencing complex (RISC) to c-Myc mRNA and mediates the degradation of the mRNA, consequently leading to inhibition of c-Myc activity. Knocking down of RPL5 induced c-Myc expression at both mRNA and protein levels, whereas overexpression of RPL5 suppressed c-Myc expression and activity. Immunoprecipitation revealed that RPL5 binds to 3'UTR of c-Myc mRNA and two subunits of RISC, TRBP (HIV-1 TAR RNA-binding protein) and Ago2, mediating the targeting of c-Myc mRNA by miRNAs. Interestingly, RPL5 and RPL11 co-resided on c-Myc mRNA and suppressed c-Myc expression co-operatively. These findings uncover a mechanism by which these two RPs can co-operatively suppress c-Myc expression, allowing a tightly controlled ribosome biogenesis in cells.

Structural Basis of Transcriptional Regulation of the Proline Utilization Regulon by Multifunctional PutA

PubMed Central

Zhou, Yuzhen; Larson, John D.; Bottoms, Christopher A.; Arturo, Emilia C.; Henzl, Michael T.; Jenkins, Jermaine L.; Nix, Jay C.; Becker, Donald F.; Tanner, John J.

2009-01-01

Summary The multifunctional Escherichia coli PutA flavoprotein functions as both a membrane-associated proline catabolic enzyme and transcriptional repressor of the proline utilization genes putA and putP. To better understand the mechanism of transcriptional regulation by PutA, we have mapped the put regulatory region, determined a crystal structure of the PutA ribbon-helix-helix domain (PutA52) complexed with DNA and examined the thermodynamics of DNA binding to PutA52. Five operator sites, each containing the sequence motif 5′-GTTGCA-3′, were identified using gel-shift analysis. Three of the sites are shown to be critical for repression of putA, whereas the two other sites are important for repression of putP. The 2.25 Å resolution crystal structure of PutA52 bound to one of the operators (operator 2, 21-bp) shows that the protein contacts a 9-bp fragment, corresponding to the GTTGCA consensus motif plus three flanking base pairs. Since the operator sequences differ in flanking bases, the structure implies that PutA may have different affinities for the five operators. This hypothesis was explored using isothermal titration calorimetry. The binding of PutA52 to operator 2 is exothermic with an enthalpy of −1.8 kcal/mol and a dissociation constant of 210 nM. Substitution of the flanking bases of operator 4 into operator 2 results in an unfavorable enthalpy of 0.2 kcal/mol and 15-fold lower affinity, which shows that base pairs outside of the consensus motif impact binding. The structural and thermodynamic data suggest that hydrogen bonds between Lys9 and bases adjacent to the GTTGCA motif contribute to transcriptional regulation by fine-tuning the affinity of PutA for put control operators. PMID:18586269

The Case against Binding Interest Arbitration.

ERIC Educational Resources Information Center

Ecker, Charles I.

1984-01-01

The author contends that districts should reject binding interest arbitration as a means of resolving an impasse in contract negotiations, charging that it hampers good faith bargaining, adversely affects fiscal and operational management of the school system, and diminishes the governing role of the board of education. (MJL)

Influence of binding pH and protein solubility on the dynamic binding capacity in hydrophobic interaction chromatography.

PubMed

Baumann, Pascal; Baumgartner, Kai; Hubbuch, Jürgen

2015-05-29

Hydrophobic interaction chromatography (HIC) is one of the most frequently used purification methods in biopharmaceutical industry. A major drawback of HIC, however, is the rather low dynamic binding capacity (DBC) obtained when compared to e.g. ion exchange chromatography (IEX). The typical purification procedure for HIC includes binding at neutral pH, independently of the proteins nature and isoelectric point. Most approaches to process intensification are based on resin and salt screenings. In this paper a combination of protein solubility data and varying binding pH leads to a clear enhancement of dynamic binding capacity. This is shown for three proteins of acidic, neutral, and alkaline isoelectric points. High-throughput solubility screenings as well as miniaturized and parallelized breakthrough curves on Media Scout RoboColumns (Atoll, Germany) were conducted at pH 3-10 on a fully automated robotic workstation. The screening results show a correlation between the DBC and the operational pH, the protein's isoelectric point and the overall solubility. Also, an inverse relationship of DBC in HIC and the binding kinetics was observed. By changing the operational pH, the DBC could be increased up to 30% compared to the standard purification procedure performed at neutral pH. As structural changes of the protein are reported during HIC processes, the applied samples and the elution fractions were proven not to be irreversibly unfolded. Copyright © 2015 Elsevier B.V. All rights reserved.

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response

PubMed Central

Goldstein, Ido; Baek, Songjoon; Presman, Diego M.; Paakinaho, Ville; Swinstead, Erin E.; Hager, Gordon L.

2017-01-01

Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting. PMID:28031249

Altitudinal variation in parental energy expenditure by white-crowned sparrows.

PubMed

Weathers, Wesley W; Davidson, Charisse L; Olson, Christopher R; Morton, Martin L; Nur, Nadav; Famula, Thomas R

2002-09-01

We used the doubly labeled water technique to measure daily energy expenditure (DEE) during the incubation and feeding nestling stages in two populations of white-crowned sparrows (Zonotrichia leucophrys) - one montane and migratory, the other coastal and sedentary - that differ in thermal environment and clutch size. We assessed the birds' thermal environment by continuously monitoring (among other variables) operative temperature and wind speed both in the open and within bushes and willow thickets occupied by sparrows. From these measurements, we derived several estimates of the birds' thermal environment, including standard operative temperature (T(es)). Shade air temperature and T(es) averaged 6.6 and 10.3 degrees C lower, respectively, at the montane study site during DEE measurements. The montane population's DEE averaged 24% higher than that of the sea-level population (103.6+/-12.2 versus 83.7+/-9.6 kJ day(-1); means +/- S.D., N=31 and 22, respectively), reflecting both its larger brood size (3.7 versus 2.9) and the colder environment. The DEE:BMR ratio was lowest in the sea-level population (2.1 versus 2.6), but neither population worked to their physiological capacity to produce young. DEE was significantly correlated with temperature across populations, with T(es) explaining 42% of the variation in DEE. Statistically removing the effect of temperature by adjusting DEE to a common temperature reduced the difference in DEE between populations by 34% to 87.7 and 100.8 kJ day(-1), respectively, for sea-level and montane populations. Basal and resting metabolic rates were similar in both populations, implying that greater activity in the montane population accounted for its higher temperature-adjusted DEE. Our results indicate that the thermal context within which behavior occurs can significantly affect interindividual variation in DEE. Attempts to assess reproductive effort by measuring DEE should therefore account explicitly for the effect of temperature.

Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network.

PubMed

Culyba, Matthew J; Kubiak, Jeffrey M; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

2018-06-01

Biochemical pathways are often genetically encoded as simple transcription regulation networks, where one transcription factor regulates the expression of multiple genes in a pathway. The relative timing of each promoter's activation and shut-off within the network can impact physiology. In the DNA damage repair pathway (known as the SOS response) of Escherichia coli, approximately 40 genes are regulated by the LexA repressor. After a DNA damaging event, LexA degradation triggers SOS gene transcription, which is temporally separated into subsets of 'early', 'middle', and 'late' genes. Although this feature plays an important role in regulating the SOS response, both the range of this separation and its underlying mechanism are not experimentally defined. Here we show that, at low doses of DNA damage, the timing of promoter activities is not separated. Instead, timing differences only emerge at higher levels of DNA damage and increase as a function of DNA damage dose. To understand mechanism, we derived a series of synthetic SOS gene promoters which vary in LexA-operator binding kinetics, but are otherwise identical, and then studied their activity over a large dose-range of DNA damage. In distinction to established models based on rapid equilibrium assumptions, the data best fit a kinetic model of repressor occupancy at promoters, where the drop in cellular LexA levels associated with higher doses of DNA damage leads to non-equilibrium binding kinetics of LexA at operators. Operators with slow LexA binding kinetics achieve their minimal occupancy state at later times than operators with fast binding kinetics, resulting in a time separation of peak promoter activity between genes. These data provide insight into this remarkable feature of the SOS pathway by demonstrating how a single transcription factor can be employed to control the relative timing of each gene's transcription as a function of stimulus dose.

Lower critical temperature and cold-induced thermogenesis of lean and overweight humans are inversely related to body mass and basal metabolic rate.

PubMed

Nahon, Kimberly J; Boon, Mariëtte R; Doornink, Fleur; Jazet, Ingrid M; Rensen, Patrick C N; Abreu-Vieira, Gustavo

2017-10-01

It is colloquially stated that body size plays a role in the human response to cold, but the magnitude and details of this interaction are unclear. To explore the inherent influence of body size on cold-exposed metabolism, we investigated the relation between body composition and resting metabolic rate in humans at thermoneutrality and during cooling within the nonshivering thermogenesis range. Body composition and resting energy expenditure were measured in 20 lean and 20 overweight men at thermoneutrality and during individualized cold exposure. Metabolic rates as a function of ambient temperature were investigated considering the variability in body mass and composition. We observed an inverse relationship between body size and the lower critical temperature (LCT), i.e. the threshold where thermoneutrality ends and cold activates thermogenesis. LCT was higher in lean than overweight subjects (22.1 ± 0.6 vs 19.5 ± 0.5°C, p < 0.001). Below LCT, minimum conductance was identical between lean and overweight (100 ± 4 vs 97 ± 3kcal/°C/day respectively, p = 0.45). Overweight individuals had higher basal metabolic rate (BMR) explained mostly by the higher lean mass, and lower cold-induced thermogenesis (CIT) per degree of cold exposure. Below thermoneutrality, energy expenditure did not scale to lean body mass. Overweight subjects had lower heat loss per body surface area (44.7 ± 1.3 vs 54.7 ± 2.3kcal/°C/m 2 /day, p < 0.001). We conclude that larger body sizes possessed reduced LCT as explained by higher BMR related to more lean mass rather than a change in whole-body conductance. Thus, larger individuals with higher lean mass need to be exposed to colder temperatures to activate CIT, not because of increased insulation, but because of a higher basal heat generation. Our study suggests that the distinct effects of body size and composition on energy expenditure should be taken in account when exploring the metabolism of humans exposed to cold. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aerobic power, huddling and the efficiency of torpor in the South American marsupial, Dromiciops gliroides

PubMed Central

Franco, Marcela; Contreras, Carolina; Cortés, Pablo; Chappell, Mark A.; Soto-Gamboa, Mauricio; Nespolo, Roberto F.

2012-01-01

Summary During periods of cold, small endotherms depend on a continuous supply of food and energy to maintain euthermic body temperature (Tb), which can be challenging if food is limited. In these conditions, energy-saving strategies are critical to reduce the energetic requirements for survival. Mammals from temperate regions show a wide arrange of such strategies, including torpor and huddling. Here we provide a quantitative description of thermoregulatory capacities and energy-saving strategies in Dromiciops gliroides, a Microbiotherid marsupial inhabiting temperate rain forests. Unlike many mammals from temperate regions, preliminary studies have suggested that this species has low capacity for control and regulation of body temperature, but there is still an incomplete picture of its bioenergetics. In order to more fully understand the physiological capacities of this “living fossil”, we measured its scope of aerobic power and the interaction between huddling and torpor. Specifically, we evaluated: (1) the relation between basal (BMR) and maximum metabolic rate (MMR), and (2) the role of huddling on the characteristics of torpor at different temperatures. We found that BMR and MMR were above the expected values for marsupials and the factorial aerobic scope (from CO2) was 6.0±0.45 (using CO2) and 6.2±0.23 (using O2), an unusually low value for mammals. Also, repeatability of physiological variables was non-significant, as in previous studies, suggesting poor time-consistency of energy metabolism. Comparisons of energy expenditure and body temperature (using attached data-loggers) between grouped and isolated individuals showed that at 20°C both average resting metabolic rate and body temperature were higher in groups, essentially because animals remained non-torpid. At 10°C, however, all individuals became torpid and no differences were observed between grouped and isolated individuals. In summary, our study suggests that the main response of Dromiciops gliroides to low ambient temperature is reduced body temperature and torpor, irrespective of huddling. Low aerobic power and low time-consistency of most thermoregulatory traits of Dromiciops gliroides support the idea of poor thermoregulatory abilities in this species. PMID:23259051

Effects of high-intensity interval training on physical capacities and substrate oxidation rate in obese adolescents.

PubMed

Lazzer, S; Tringali, G; Caccavale, M; De Micheli, R; Abbruzzese, L; Sartorio, A

2017-02-01

To investigate the effects of a 3-week weight-management program entailing moderate energy restriction, nutritional education, psychological counseling and three different exercise training (a: low intensity, LI: 40 % V'O 2 max; b: high intensity, HI: 70 % V'O 2 max; c: high-intensity interval training, HIIT), on body composition, energy expenditure and fat oxidation rate in obese adolescents. Thirty obese adolescents (age: 15-17 years, BMI: 37.5 kg m -2 ) participated in this study. Before starting (week 0, W0) and at the end of the weight-management program (week 3, W3), body composition was assessed by an impedancemeter; basal metabolic rate (BMR), energy expenditure and substrate oxidation rate were measured during exercise and post-exercise recovery by indirect calorimetry. At W3, body mass (BM) and fat mass (FM) decreased significantly in all groups, the decreases being significantly greater in the LI than in the HI and HIIT subgroups (BM: -8.4 ± 1.5 vs -6.3 ± 1.9 vs -4.9 ± 1.3 kg and FM: -4.2 ± 1.9 vs -2.8 ± 1.2 vs -2.3 ± 1.4 kg, p < 0.05, respectively). V'O 2 peak, expressed in relative values, changed significantly only in the HI and HIIT groups by 0.009 ± 0.005 and 0.007 ± 0.004 L kg FFM -1  min -1 (p < 0.05). Furthermore, the HI and HIIT subgroups exhibited a greater absolute rate of fat oxidation between 50 and 70 % V'O 2 peak at W3. No significant changes were observed at W3 in BMR, energy expenditure during exercise and post-exercise recovery. A 3-week weight-management program induced a greater decrease in BM and FM in the LI than in the HI and HIIT subgroups, and greater increase in V'O 2 peak and fat oxidation rate in the HI and HIIT than in the LI subgroup.

Engineering Macaca fascicularis cytochrome P450 2C20 to reduce animal testing for new drugs.

PubMed

Rua, Francesco; Sadeghi, Sheila J; Castrignanò, Silvia; Di Nardo, Giovanna; Gilardi, Gianfranco

2012-12-01

In order to develop in vitro methods as an alternative to P450 animal testing in the drug discovery process, two main requisites are necessary: 1) gathering of data on animal homologues of the human P450 enzymes, currently very limited, and 2) bypassing the requirement for both the P450 reductase and the expensive cofactor NADPH. In this work, P450 2C20 from Macaca fascicularis, homologue of the human P450 2C8 has been taken as a model system to develop such an alternative in vitro method by two different approaches. In the first approach called "molecular Lego", a soluble self-sufficient chimera was generated by fusing the P450 2C20 domain with the reductase domain of cytochrome P450 BM3 from Bacillus megaterium (P450 2C20/BMR). In the second approach, the need for the redox partner and also NADPH were both obviated by the direct immobilization of the P450 2C20 on glassy carbon and gold electrodes. Both systems were then compared to those obtained from the reconstituted P450 2C20 monooxygenase in presence of the human P450 reductase and NADPH using paclitaxel and amodiaquine, two typical drug substrates of the human P450 2C8. The K(M) values calculated for the 2C20 and 2C20/BMR in solution and for 2C20 immobilized on electrodes modified with gold nanoparticles were 1.9 ± 0.2, 5.9 ± 2.3, 3.0 ± 0.5 μM for paclitaxel and 1.2 ± 0.2, 1.6±0.2 and 1.4 ± 0.2 μM for amodiaquine, respectively. The data obtained not only show that the engineering of M. fascicularis did not affect its catalytic properties but also are consistent with K(M) values measured for the microsomal human P450 2C8 and therefore show the feasibility of developing alternative in vitro animal tests. Copyright © 2012 Elsevier Inc. All rights reserved.

Functional linkages for the pace of life, life-history, and environment in birds.

PubMed

Williams, Joseph B; Miller, Richard A; Harper, James M; Wiersma, Popko

2010-11-01

For vertebrates, body mass underlies much of the variation in metabolism, but among animals of the same body mass, metabolism varies six-fold. Understanding how natural selection can influence variation in metabolism remains a central focus of Physiological Ecologists. Life-history theory postulates that many physiological traits, such as metabolism, may be understood in terms of key maturational and reproductive characteristics over an organism's life-span. Although it is widely acknowledged that physiological processes serve as a foundation for life-history trade-offs, the physiological mechanisms that underlie the diversification of life-histories remain elusive. Data show that tropical birds have a reduced basal metabolism (BMR), field metabolic rate, and peak metabolic rate compared with temperate counterparts, results consistent with the idea that a low mortality, and therefore increased longevity, and low productivity is associated with low mass-specific metabolic rate. Mass-adjusted BMR of tropical and temperate birds was associated with survival rate, in accordance with the view that animals with a slow pace of life tend to have increased life spans. To understand the mechanisms responsible for a reduced rate of metabolism in tropical birds compared with temperate species, we summarized an unpublished study, based on data from the literature, on organ masses for both groups. Tropical birds had smaller hearts, kidneys, livers, and pectoral muscles than did temperate species of the same body size, but they had a relatively larger skeletal mass. Direct measurements of organ masses for tropical and temperate birds showed that the heart, kidneys, and lungs were significantly smaller in tropical birds, although sample sizes were small. Also from an ongoing study, we summarized results to date on connections between whole-organism metabolism in tropical and temperate birds and attributes of their dermal fibroblasts grown in cell culture. Cells derived from tropical birds had a slower rate of growth, consistent with the hypothesis that these cells have a slower metabolism. We found that dermal fibroblasts from tropical birds resisted chemical agents that induce oxidative and non-oxidative stress better than do cells from temperate species, consistent with the hypothesis that birds that live longer invest more in self-maintenance such as antioxidant properties of cells.

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

The composition of genomes with respect to short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. The underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, which we detect in all species across domains of life. We hypothesize that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Alternative contributions may come from interference of protein-DNA binding with replication and mutational repair processes, which operates with similar rates. We conclude that genome-wide word compositions have been molded by DNA binding proteins through tiny evolutionary steps over timescales spanning millions of generations.

Structure of the C-terminal effector-binding domain of AhrC bound to its corepressor l-arginine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garnett, James A.; Baumberg, Simon; Stockley, Peter G.

2007-11-01

The crystal structure of the C-terminal domain hexameric core of AhrC, with bound corepressor (l-arginine), has been solved at 1.95 Å resolution. Binding of l-arginine results in a rotation between the two trimers of the hexamer, leading to the activation of the DNA-binding state. The arginine repressor/activator protein (AhrC) from Bacillus subtilis belongs to a large family of multifunctional transcription factors that are involved in the regulation of bacterial arginine metabolism. AhrC interacts with operator sites in the promoters of arginine biosynthetic and catabolic operons, acting as a transcriptional repressor at biosynthetic sites and an activator of transcription at catabolicmore » sites. AhrC is a hexamer of identical subunits, each having two domains. The C-terminal domains form the core of the protein and are involved in oligomerization and l-arginine binding. The N-terminal domains lie on the outside of the compact core and play a role in binding to 18 bp DNA operators called ARG boxes. The C-terminal domain of AhrC has been expressed, purified and characterized, and also crystallized as a hexamer with the bound corepressor l-arginine. Here, the crystal structure refined to 1.95 Å is presented.« less

Porphyrin-substrate binding to murine ferrochelatase: effect on the thermal stability of the enzyme

PubMed Central

2004-01-01

Ferrochelatase (EC 4.99.1.1), the terminal enzyme of the haem biosynthetic pathway, catalyses the chelation of Fe(II) into the protoporphyrin IX ring. The energetics of the binding between murine ferrochelatase and mesoporphyrin were determined using isothermal titration calorimetry, which revealed a stoichiometry of one molecule of mesoporphyrin bound per protein monomer. The binding is strongly exothermic, with a large intrinsic enthalpy (ΔH=−97.1 kJ · mol−1), and is associated with the uptake of two protons from the buffer. This proton transfer suggests that hydrogen bonding between ferrochelatase and mesoporphyrin is a key factor in the thermodynamics of the binding reaction. Differential scanning calorimetry thermograms indicated a co-operative two-state denaturation process with a single transition temperature of 56 °C for wild-type murine ferrochelatase. An increase in the thermal stability of ferrochelatase is dependent upon mesoporphyrin binding. Similarly, murine ferrochelatase variants, in which the active site Glu-289 was replaced by either glutamine or alanine and, when purified, contained specifically-bound protoporphyrin, exhibited enhanced protein stability when compared with wild-type ferrochelatase. However, in contrast with the wild-type enzyme, the thermal denaturation of ferrochelatase variants was best described as a non-co-operative denaturation process. PMID:15496139

On binding energy of trions in bulk materials

NASA Astrophysics Data System (ADS)

Filikhin, Igor; Kezerashvili, Roman Ya.; Vlahovic, Branislav

2018-03-01

We study the negatively T- and positively T+ charged trions in bulk materials in the effective mass approximation within the framework of a potential model. The binding energies of trions in various semiconductors are calculated by employing Faddeev equation in configuration space. Results of calculations of the binding energies for T- are consistent with previous computational studies and are in reasonable agreement with experimental measurements, while the T+ is unbound for all considered cases. The mechanism of formation of the binding energy of trions is analyzed by comparing contributions of a mass-polarization term related to kinetic energy operators and a term related to the Coulomb repulsion of identical particles.

Negative inotropic effect of carbachol and interaction between acetylcholine receptor-operated potassium channel (K.ACh channel) and GTP binding protein in mouse isolated atrium--a novel methodological trial.

PubMed

Okada, Muneyoshi; Noma, Chihiro; Yamawaki, Hideyuki; Hara, Yukio

2013-01-01

Interaction between acetylcholine receptor-operated potassium channel (K.ACh channel) and GTP binding protein was examined by an immunoprecipitation-Western blotting system in mouse isolated atrium. The carbachol-induced negative inotropic action in indomethacin-pretreated mouse atrium was significantly inhibited by a K.ACh channel blocker, tertiapin or atropine. Kir3.1 K.ACh channel (Kir3.1) was immunoprecipitated with a mouse anti-Kir3.1 antibody. Coprecipitating Gβ with Kir3.1, detected by Western blotting, was significantly augmented by carbachol. Atropine, but not tertiapin, significantly inhibited the carbachol-induced coprecipitating Gβ with Kir3.1. The data indicate that immunoprecipitation with Kir3.1 and Western blotting of Gβ system is a useful method for assessing interaction between K.ACh channel and GTP binding protein in mouse atrium.

Transcription factor assisted loading and enhancer dynamics dictate the hepatic fasting response.

PubMed

Goldstein, Ido; Baek, Songjoon; Presman, Diego M; Paakinaho, Ville; Swinstead, Erin E; Hager, Gordon L

2017-03-01

Fasting elicits transcriptional programs in hepatocytes leading to glucose and ketone production. This transcriptional program is regulated by many transcription factors (TFs). To understand how this complex network regulates the metabolic response to fasting, we aimed at isolating the enhancers and TFs dictating it. Measuring chromatin accessibility revealed that fasting massively reorganizes liver chromatin, exposing numerous fasting-induced enhancers. By utilizing computational methods in combination with dissecting enhancer features and TF cistromes, we implicated four key TFs regulating the fasting response: glucocorticoid receptor (GR), cAMP responsive element binding protein 1 (CREB1), peroxisome proliferator activated receptor alpha (PPARA), and CCAAT/enhancer binding protein beta (CEBPB). These TFs regulate fuel production by two distinctly operating modules, each controlling a separate metabolic pathway. The gluconeogenic module operates through assisted loading, whereby GR doubles the number of sites occupied by CREB1 as well as enhances CREB1 binding intensity and increases accessibility of CREB1 binding sites. Importantly, this GR-assisted CREB1 binding was enhancer-selective and did not affect all CREB1-bound enhancers. Single-molecule tracking revealed that GR increases the number and DNA residence time of a portion of chromatin-bound CREB1 molecules. These events collectively result in rapid synergistic gene expression and higher hepatic glucose production. Conversely, the ketogenic module operates via a GR-induced TF cascade, whereby PPARA levels are increased following GR activation, facilitating gradual enhancer maturation next to PPARA target genes and delayed ketogenic gene expression. Our findings reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis upon fasting. Published by Cold Spring Harbor Laboratory Press.

Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface.

PubMed

Moody, Colleen L; Tretyachenko-Ladokhina, Vira; Laue, Thomas M; Senear, Donald F; Cocco, Melanie J

2011-08-09

The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, spacing between the recognition half-sites. This suggests a strong likelihood that protein folding would be coupled to DNA binding as a mechanism to accommodate the variety of different operator architectures to which CytR is targeted. Such coupling is a common feature of sequence-specific DNA-binding proteins, including the LacR family repressors; however, there are no significant structural rearrangements upon DNA binding within the three-helix DNA-binding domains (DBDs) studied to date. We used nuclear magnetic resonance (NMR) spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue. This structural heterogeneity is previously unknown in the LacR family. These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif. However, this structure differs from all other LacR family members whose structures are known with regard to the packing of the helices and consequently their relative orientations. Aspects of CytR activity are unique among repressors; we identify here structural properties that are also distinct and that might underlie the different functional properties. © 2011 American Chemical Society

E2 Proteins from High- and Low-Risk Human Papillomavirus Types Differ in Their Ability To Bind p53 and Induce Apoptotic Cell Death

PubMed Central

Parish, Joanna L.; Kowalczyk, Anna; Chen, Hsin-Tien; Roeder, Geraldine E.; Sessions, Richard; Buckle, Malcolm; Gaston, Kevin

2006-01-01

The E2 proteins from oncogenic (high-risk) human papillomaviruses (HPVs) can induce apoptotic cell death in both HPV-transformed and non-HPV-transformed cells. Here we show that the E2 proteins from HPV type 6 (HPV6) and HPV11, two nononcogenic (low-risk) HPV types, fail to induce apoptosis. Unlike the high-risk HPV16 E2 protein, these low-risk E2 proteins fail to bind p53 and fail to induce p53-dependent transcription activation. Interestingly, neither the ability of p53 to activate transcription nor the ability of p53 to bind DNA, are required for HPV16 E2-induced apoptosis in non-HPV-transformed cells. However, mutations that reduce the binding of the HPV16 E2 protein to p53 inhibit E2-induced apoptosis in non-HPV-transformed cells. In contrast, the interaction between HPV16 E2 and p53 is not required for this E2 protein to induce apoptosis in HPV-transformed cells. Thus, our data suggest that this high-risk HPV E2 protein induces apoptosis via two pathways. One pathway involves the binding of E2 to p53 and can operate in both HPV-transformed and non-HPV-transformed cells. The second pathway requires the binding of E2 to the viral genome and can only operate in HPV-transformed cells. PMID:16611918

Peri-operative heart-type fatty acid binding protein is associated with acute kidney injury after cardiac surgery

PubMed Central

Schaub, Jennifer A.; Garg, Amit X.; Coca, Steven G.; Testani, Jeffrey M.; Shlipak, Michael G.; Eikelboom, John; Kavsak, Peter; McArthur, Eric; Shortt, Colleen; Whitlock, Richard; Parikh, Chirag R.

2015-01-01

Acute Kidney Injury (AKI) is a common complication after cardiac surgery and is associated with worse outcomes. Since heart fatty acid binding protein (H-FABP) is a myocardial protein that detects cardiac injury, we sought to determine if plasma H-FABP was associated with AKI in the TRIBE-AKI cohort; a multi-center cohort of 1219 patients at high risk for AKI who underwent cardiac surgery. The primary outcomes of interest were any AKI (Acute Kidney Injury Network (AKIN) stage 1 or higher) and severe AKI (AKIN stage 2 or higher). The secondary outcome was long-term mortality after discharge. Patients who developed AKI had higher levels of H-FABP pre- and post-operatively than patients who did not have AKI. In analyses adjusted for known AKI risk factors, first post-operative log(H-FABP) was associated with severe AKI (adjusted OR 5.39 [95% CI, 2.87-10.11] per unit increase), while pre-operative log(H-FABP) was associated with any AKI (2.07 [1.48-2.89]) and mortality (1.67 [1.17-2.37]). These relationships persisted after adjustment for change in serum creatinine (for first postoperative log(H-FABP)) and biomarkers of cardiac and kidney injury, including brain natriuretic peptide, cardiac troponin-I, interleukin-18, liver fatty acid binding protein, kidney injury molecule-1, and neutrophil gelatinase associated lipocalin. Thus, peri-operative plasma H-FABP levels may be used for risk-stratification of AKI and mortality following cardiac surgery. PMID:25830762

Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family

PubMed Central

Kumar, Yellapu Nanda; Kumar, Pasupuleti Santhosh; Sowjenya, Gopal; Rao, Valasani Koteswara; Yeswanth, Sthanikam; Prasad, Uppu Venkateswara; Pradeepkiran, Jangampalli Adi; Sarma, PVGK; Bhaskar, Matcha

2012-01-01

Hexokinases (HKs) are the enzymes that catalyses the ATP dependent phosphorylation of Hexose sugars to Hexose-6-Phosphate (Hex-6-P). There exist four different forms of HKs namely HK-I, HK-II, HK-III and HK-IV and all of them share a common ATP binding site core surrounded by more variable sequence that determine substrate affinities. Although they share a common binding site but they differ in their kinetic functions, hence the present study is aimed to analyze the binding mode of ATP. The analysis revealed that the four ATP binding domains are showing 13 identical, 7 similar and 6 dissimilar residues with similar structural conformation. Molecular docking of ATP into the kinase domains using Molecular Operating Environment (MOE) soft ware tool clearly showed the variation in the binding mode of ATP with variable docking scores. This probably explains the variable phosphorylation rates among hexokinases family. PMID:22829728

Untangling Locality and Orientation Constraints in the L2 Acquisition of Anaphoric Binding: A Feature-Based Approach

ERIC Educational Resources Information Center

Dominguez, Laura; Hicks, Glyn; Song, Hee-Jeong

2012-01-01

This study offers a Minimalist analysis of the L2 acquisition of binding properties whereby cross-linguistic differences arise from the interaction of anaphoric feature specifications and operations of the computational system (Reuland 2001, 2011; Hicks 2009). This analysis attributes difficulties in the L2 acquisition of locality and orientation…

Hoxa2 Selectively Enhances Meis Binding to Change a Branchial Arch Ground State

PubMed Central

Amin, Shilu; Donaldson, Ian J.; Zannino, Denise A.; Hensman, James; Rattray, Magnus; Losa, Marta; Spitz, François; Ladam, Franck; Sagerström, Charles; Bobola, Nicoletta

2015-01-01

Summary Hox transcription factors (TFs) are essential for vertebrate development, but how these evolutionary conserved proteins function in vivo remains unclear. Because Hox proteins have notoriously low binding specificity, they are believed to bind with cofactors, mainly homeodomain TFs Pbx and Meis, to select their specific targets. We mapped binding of Meis, Pbx, and Hoxa2 in the branchial arches, a series of segments in the developing vertebrate head. Meis occupancy is largely similar in Hox-positive and -negative arches. Hoxa2, which specifies second arch (IIBA) identity, recognizes a subset of Meis prebound sites that contain Hox motifs. Importantly, at these sites Meis binding is strongly increased. This enhanced Meis binding coincides with active enhancers, which are linked to genes highly expressed in the IIBA and regulated by Hoxa2. These findings show that Hoxa2 operates as a tissue-specific cofactor, enhancing Meis binding to specific sites that provide the IIBA with its anatomical identity. PMID:25640223

Scanpath memory binding: multiple read-out experiments

NASA Astrophysics Data System (ADS)

Stark, Lawrence W.; Privitera, Claudio M.; Yang, Huiyang; Azzariti, Michela; Ho, Yeuk F.; Chan, Angie; Krischer, Christof; Weinberger, Adam

1999-05-01

The scanpath theory proposed that an internal spatial- cognitive model controls perception and the active looking eye movements, EMs, of the scanpath sequence. Evidence for this came from new quantitative methods, experiments with ambiguous figures and visual imagery and from MRI studies, all on cooperating human subjects. Besides recording EMs, we introduce other experimental techniques wherein the subject must depend upon memory bindings as in visual imagery, but may call upon other motor behaviors than EMs to read-out the remembered patterns. How is the internal model distributed and operationally assembled. The concept of binding speaks to the assigning of values for the model and its execution in various parts of the brain. Current neurological information helps to localize different aspects of the spatial-cognitive model in the brain. We suppose that there are several levels of 'binding' -- semantic or symbolic binding, structural binding for the spatial locations of the regions-of-interest and sequential binding for the dynamic execution program that yields the sequence of EMs. Our aim is to dissect out respective contributions of these different forms of binding.

Probing the binding of fluoxetine hydrochloride to human serum albumin by multispectroscopic techniques

NASA Astrophysics Data System (ADS)

Katrahalli, Umesha; Jaldappagari, Seetharamappa; Kalanur, Shankara S.

2010-01-01

The interaction between human serum albumin (HSA) and fluoxetine hydrochloride (FLX) have been studied by using different spectroscopic techniques viz., fluorescence, UV-vis absorption, circular dichroism and FTIR under simulated physiological conditions. Fluorescence results revealed the presence of static type of quenching mechanism in the binding of FLX to HSA. The values of binding constant, K of FLX-HSA were evaluated at 289, 300 and 310 K and were found to be 1.90 × 10 3, 1.68 × 10 3 and 1.45 × 10 3 M -1, respectively. The number of binding sites, n was noticed to be almost equal to unity thereby indicating the presence of a single class of binding site for FLX on HSA. Based on the thermodynamic parameters, Δ H0 and Δ S0 nature of binding forces operating between HSA and FLX were proposed. Spectral results revealed the conformational changes in protein upon interaction. Displacement studies indicated the site I as the main binding site for FLX on HSA. The effect of common ions on the binding of FLX to HSA was also investigated.

A verotoxin 1 B subunit-lambda CRO chimeric protein specifically binds both DNA and globotriaosylceramide (Gb(3)) to effect nuclear targeting of exogenous DNA in Gb(3) positive cells.

PubMed

Facchini, L M; Lingwood, C A

2001-09-10

Inefficient nuclear incorporation of foreign DNA remains a critical roadblock in the development of effective nonviral gene delivery systems. DNA delivered by traditional protocols remains within endosomal/lysosomal vesicles, or is rapidly degraded in the cytoplasm. Verotoxin I (VT), an AB(5) subunit toxin produced by enterohaemorrhagic Escherichia coli, binds to the cell surface glycolipid, globotriaosylceramide (Gb(3)) and is internalized into preendosomes. VT is then retrograde transported to the Golgi, endoplasmic reticulum (ER), and nucleus of highly VT-sensitive cells. We have utilized this nuclear targeting of VT to design a unique delivery system which transports exogenous DNA via vesicular traffic to the nucleus. The nontoxic VT binding subunit (VTB) was fused to the lambda Cro DNA-binding repressor, generating a 14-kDa VTB-Cro chimera. VTB-Cro binds specifically via the Cro domain to a 25-bp DNA fragment containing the consensus Cro operator. VTB-Cro demonstrates simultaneous specific binding to Gb(3). Treatment of Vero cells with fluorescent-labeled Cro operator DNA in the presence of VTB-Cro, results in DNA internalization to the Golgi, ER, and nucleus, whereas fluorescent DNA alone is incorporated poorly and randomly within the cytoplasm. VTB-Cro mediated nuclear DNA transport is prevented by brefeldin A, consistent with Golgi/ER intracellular routing. Pretreatment with filipin had no effect, indicating that caveoli are not involved. This novel VTB-Cro shuttle protein may find practical applications in the fields of intracellular targeting, gene delivery, and gene therapy. Copyright 2001 Academic Press.

S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA

PubMed Central

Fuchs, Ryan T.; Grundy, Frank J.; Henkin, Tina M.

2007-01-01

The SMK box is a conserved riboswitch motif found in the 5′ untranslated region of metK genes [encoding S-adenosylmethionine (SAM) synthetase] in lactic acid bacteria, including Enterococcus, Streptococcus, and Lactococcus sp. Previous studies showed that this RNA element binds SAM in vitro, and SAM binding causes a structural rearrangement that sequesters the Shine–Dalgarno (SD) sequence by pairing with an anti-SD (ASD) element. A model was proposed in which SAM binding inhibits metK translation by preventing binding of the ribosome to the SD region of the mRNA. In the current work, the addition of SAM was shown to inhibit binding of 30S ribosomal subunits to SMK box RNA; in contrast, the addition of S-adenosylhomocysteine (SAH) had no effect. A mutant RNA, which has a disrupted SD-ASD pairing, was defective in SAM binding and showed no reduction of ribosome binding in the presence of SAM, whereas a compensatory mutation that restored SD-ASD pairing restored the response to SAM. Primer extension inhibition assays provided further evidence for SD-ASD pairing in the presence of SAM. These results strongly support the model that SMK box translational repression operates through occlusion of the ribosome binding site and that SAM binding requires the SD-ASD pairing. PMID:17360376

76 FR 60503 - Guidance for Industry on Target Animal Safety and Effectiveness Protocol Development and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-29

... regarding how and when data collection forms and standard operating procedures should be included with the... topic. It does not create or confer any rights for or on any person and does not operate to bind FDA or...

Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

NASA Astrophysics Data System (ADS)

Qian, Long; Kussell, Edo

2016-10-01

The composition of a genome with respect to all possible short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional DNA binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. We demonstrate that the underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, a signal that we detect in all species across domains of life. We consider the possibility that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Likewise, we show that evolutionary mechanisms based on interference of protein-DNA binding with replication and mutational repair processes could yield similar results and operate with similar rates. On the basis of these modeling and bioinformatic results, we conclude that genome-wide word compositions have been molded by DNA binding proteins acting through tiny evolutionary steps over time scales spanning millions of generations.

Environmental Assessment for Ongoing and Future Operations at U.S. Navy Dabob Bay and Hood Canal Military Operating Areas

DTIC Science & Technology

2002-05-01

well as being cultivated in aquaculture operations in Puget Sound, including Hood Canal and Dabob Bay (Figure 3.4-2). Pacific oysters (Crassostrea...gigas) are widely cultivated in aquaculture operations in Puget Sound. Commercial oyster beds exist in Dabob Bay, mostly at the north end. Dabob Bay... Ecotoxicology of metals in aquatic sediments: binding and release, bioavailability, risk assessment, and remediation. Canadian Journal of

Standards of nutrition for athletes in Germany.

PubMed

Diel, F; Khanferyan, R A

2013-01-01

The Deutscher Olympische Sportbund (DOSB) founded recently an advisory board for German elite athlete nutrition, the 'Arbeitsgruppe (AG) Ernahrungsberatung an den Olympiastutzpunkten'. The 'Performance codex and quality criteria for the food supply in facilities of German elite sports' have been established since 1997. The biochemical equivalent (ATP) for the energy demand is calculated using the DLW (Double Labeled Water)-method on the basis of RMR (Resting Metabolic Rate) and BMR (Basic Metabolic Rate) at sport type specific exercises and performances. Certain nutraceutical ingredients for dietary supplements can be recommended. However, quality criteria for nutrition, cooking and food supply are defined on the basis of Health Food and the individual physiological/social-psychological status of the athlete. Especially food supplements and instant food have to be avoided for young athletes. The German advisory board for elite athlete nutrition publishes 'colour lists' for highly recommended (green), acceptable (yellow), and less recommended (red) food stuff.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci.

PubMed

Milbredt, Sarah; Waldminghaus, Torsten

2017-06-07

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. Copyright © 2017 Milbredt and Waldminghaus.

BiFCROS: A Low-Background Fluorescence Repressor Operator System for Labeling of Genomic Loci

PubMed Central

Milbredt, Sarah; Waldminghaus, Torsten

2017-01-01

Fluorescence-based methods are widely used to analyze elementary cell processes such as DNA replication or chromosomal folding and segregation. Labeling DNA with a fluorescent protein allows the visualization of its temporal and spatial organization. One popular approach is FROS (fluorescence repressor operator system). This method specifically labels DNA in vivo through binding of a fusion of a fluorescent protein and a repressor protein to an operator array, which contains numerous copies of the repressor binding site integrated into the genomic site of interest. Bound fluorescent proteins are then visible as foci in microscopic analyses and can be distinguished from the background fluorescence caused by unbound fusion proteins. Even though this method is widely used, no attempt has been made so far to decrease the background fluorescence to facilitate analysis of the actual signal of interest. Here, we present a new method that greatly reduces the background signal of FROS. BiFCROS (Bimolecular Fluorescence Complementation and Repressor Operator System) is based on fusions of repressor proteins to halves of a split fluorescent protein. Binding to a hybrid FROS array results in fluorescence signals due to bimolecular fluorescence complementation. Only proteins bound to the hybrid FROS array fluoresce, greatly improving the signal to noise ratio compared to conventional FROS. We present the development of BiFCROS and discuss its potential to be used as a fast and single-cell readout for copy numbers of genetic loci. PMID:28450375

Diketo modification of curcumin affects its interaction with human serum albumin.

PubMed

Shaikh, Shaukat Ali M; Singh, Beena G; Barik, Atanu; Ramani, Modukuri V; Balaji, Neduri V; Subbaraju, Gottumukkala V; Naik, Devidas B; Indira Priyadarsini, K

2018-06-15

Curcumin isoxazole (CI) and Curcumin pyrazole (CP), the diketo modified derivatives of Curcumin (CU) are metabolically more stable and are being explored for pharmacological properties. One of the requirements in such activities is their interaction with circulatory proteins like human serum albumin (HSA). To understand this, the interactions of CI and CP with HSA have been investigated employing absorption and fluorescence spectroscopy and the results are compared with that of CU. The respective binding constants of CP, CI and CU with HSA were estimated to be 9.3×10 5 , 8.4×10 5 and 2.5×10 5 M -1 , which decreased with increasing salt concentration in the medium. The extent of decrease in the binding constant was the highest in CP followed by CI and CU. This revealed that along with hydrophobic interaction other binding modes like electrostatic interactions operate between CP/CI/CU with HSA. Fluorescence quenching studies of HSA with these compounds suggested that both static and dynamic quenching mechanisms operate, where the contribution of static quenching is higher for CP and CI than that for CU. From fluorescence resonance energy transfer studies, the binding site of CU, CI and CP was found to be in domain IIA of HSA. CU was found to bind in closer proximity with Trp214 as compared to CI and CP and the same was responsible for efficient energy transfer and the same was also established by fluorescence anisotropy measurements. Furthermore docking simulation complemented the experimental observation, where both electrostatic as well as hydrophobic interactions were indicated between HSA and CP, CI and CU. This study is useful in designing more stable CU derivatives having suitable binding properties with proteins like HSA. Copyright © 2018 Elsevier B.V. All rights reserved.

Diketo modification of curcumin affects its interaction with human serum albumin

NASA Astrophysics Data System (ADS)

Shaikh, Shaukat Ali M.; Singh, Beena G.; Barik, Atanu; Ramani, Modukuri V.; Balaji, Neduri V.; Subbaraju, Gottumukkala V.; Naik, Devidas B.; Indira Priyadarsini, K.

2018-06-01

Curcumin isoxazole (CI) and Curcumin pyrazole (CP), the diketo modified derivatives of Curcumin (CU) are metabolically more stable and are being explored for pharmacological properties. One of the requirements in such activities is their interaction with circulatory proteins like human serum albumin (HSA). To understand this, the interactions of CI and CP with HSA have been investigated employing absorption and fluorescence spectroscopy and the results are compared with that of CU. The respective binding constants of CP, CI and CU with HSA were estimated to be 9.3 × 105, 8.4 × 105 and 2.5 × 105 M-1, which decreased with increasing salt concentration in the medium. The extent of decrease in the binding constant was the highest in CP followed by CI and CU. This revealed that along with hydrophobic interaction other binding modes like electrostatic interactions operate between CP/CI/CU with HSA. Fluorescence quenching studies of HSA with these compounds suggested that both static and dynamic quenching mechanisms operate, where the contribution of static quenching is higher for CP and CI than that for CU. From fluorescence resonance energy transfer studies, the binding site of CU, CI and CP was found to be in domain IIA of HSA. CU was found to bind in closer proximity with Trp214 as compared to CI and CP and the same was responsible for efficient energy transfer and the same was also established by fluorescence anisotropy measurements. Furthermore docking simulation complemented the experimental observation, where both electrostatic as well as hydrophobic interactions were indicated between HSA and CP, CI and CU. This study is useful in designing more stable CU derivatives having suitable binding properties with proteins like HSA.

Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants

NASA Astrophysics Data System (ADS)

Einav, Tal; Duque, Julia; Phillips, Rob

2018-02-01

Allosteric transcription factors undergo binding events both at their inducer binding sites as well as at distinct DNA binding domains, and it is often difficult to disentangle the structural and functional consequences of these two classes of interactions. In this work, we compare the ability of two statistical mechanical models - the Monod-Wyman-Changeux (MWC) and the Koshland-N\\'emethy-Filmer (KNF) models of protein conformational change - to characterize the multi-step activation mechanism of the broadly acting cyclic-AMP receptor protein (CRP). We first consider the allosteric transition resulting from cyclic-AMP binding to CRP, then analyze how CRP binds to its operator, and finally investigate the ability of CRP to activate gene expression. In light of these models, we examine data from a beautiful recent experiment that created a single-chain version of the CRP homodimer, thereby enabling each subunit to be mutated separately. Using this construct, six mutants were created using all possible combinations of the wild type subunit, a D53H mutant subunit, and an S62F mutant subunit. We demonstrate that both the MWC and KNF models can explain the behavior of all six mutants using a small, self-consistent set of parameters. In comparing the results, we find that the MWC model slightly outperforms the KNF model in the quality of its fits, but more importantly the parameters inferred by the MWC model are more in line with structural knowledge of CRP. In addition, we discuss how the conceptual framework developed here for CRP enables us to not merely analyze data retrospectively, but has the predictive power to determine how combinations of mutations will interact, how double mutants will behave, and how each construct would regulate gene expression.

Daily torpor and hibernation in birds and mammals.

PubMed

Ruf, Thomas; Geiser, Fritz

2015-08-01

Many birds and mammals drastically reduce their energy expenditure during times of cold exposure, food shortage, or drought, by temporarily abandoning euthermia, i.e. the maintenance of high body temperatures. Traditionally, two different types of heterothermy, i.e. hypometabolic states associated with low body temperature (torpor), have been distinguished: daily torpor, which lasts less than 24 h and is accompanied by continued foraging, versus hibernation, with torpor bouts lasting consecutive days to several weeks in animals that usually do not forage but rely on energy stores, either food caches or body energy reserves. This classification of torpor types has been challenged, suggesting that these phenotypes may merely represent extremes in a continuum of traits. Here, we investigate whether variables of torpor in 214 species (43 birds and 171 mammals) form a continuum or a bimodal distribution. We use Gaussian-mixture cluster analysis as well as phylogenetically informed regressions to quantitatively assess the distinction between hibernation and daily torpor and to evaluate the impact of body mass and geographical distribution of species on torpor traits. Cluster analysis clearly confirmed the classical distinction between daily torpor and hibernation. Overall, heterothermic endotherms tend to be small; hibernators are significantly heavier than daily heterotherms and also are distributed at higher average latitudes (∼35°) than daily heterotherms (∼25°). Variables of torpor for an average 30 g heterotherm differed significantly between daily heterotherms and hibernators. Average maximum torpor bout duration was >30-fold longer, and mean torpor bout duration >25-fold longer in hibernators. Mean minimum body temperature differed by ∼13°C, and the mean minimum torpor metabolic rate was ∼35% of the basal metabolic rate (BMR) in daily heterotherms but only 6% of BMR in hibernators. Consequently, our analysis strongly supports the view that hibernators and daily heterotherms are functionally distinct groups that probably have been subject to disruptive selection. Arguably, the primary physiological difference between daily torpor and hibernation, which leads to a variety of derived further distinct characteristics, is the temporal control of entry into and arousal from torpor, which is governed by the circadian clock in daily heterotherms, but apparently not in hibernators. © 2014 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Metal site occupancy and allosteric switching in bacterial metal sensor proteins.

PubMed

Guerra, Alfredo J; Giedroc, David P

2012-03-15

All prokaryotes encode a panel of metal sensor or metalloregulatory proteins that govern the expression of genes that allows an organism to quickly adapt to toxicity or deprivation of both biologically essential transition metal ions, e.g., Zn, Cu, Fe, and heavy metal pollutants. As such, metal sensor proteins can be considered arbiters of intracellular transition metal bioavailability and thus potentially control the metallation state of the metalloproteins in the cell. Metal sensor proteins are specialized allosteric proteins that regulate transcription as a result direct binding of one or two cognate metal ions, to the exclusion of all others. In most cases, the binding of the cognate metal ion induces a structural change in a protein oligomer that either activates or inhibits operator DNA binding. A quantitative measure of the degree to which a particular metal drives metalloregulation of operator DNA-binding is the allosteric coupling free energy, ΔGc. In this review, we summarize recent work directed toward understanding metal occupancy and metal selectivity of these allosteric switches in selected families of metal sensor proteins and examine the structural origins of ΔGc in the functional context a thermodynamic "set-point" model of intracellular metal homeostasis. Copyright © 2011 Elsevier Inc. All rights reserved.

How aromatic compounds block DNA binding of HcaR catabolite regulator

DOE PAGES

Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance; ...

2016-04-25

Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Åmore » resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. Furthermore, the current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.« less

Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription

PubMed Central

Weihofen, Wilhelm Andreas; Cicek, Aslan; Pratto, Florencia; Alonso, Juan Carlos; Saenger, Wolfram

2006-01-01

Repressor ω regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ω belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-A/TATCACA/T-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω2 and contrasting other RHH2 repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω2 binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω2 passes the central C–G base pair of each heptad with ∼0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (→→), ∼0.6 Å shorter in (→←) but would be ∼0.6 Å longer in (←→). These variations grade interactions between adjacent ω2 and explain modulations in cooperative binding affinity of ω2 to operators with different heptad orientations. PMID:16528102

Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bacik, John-Paul; Yeager, Chris M.; Twary, Scott N.

FadR is a versatile global regulator in Escherichia coli that controls fatty acid metabolism and thereby modulates the ability of this bacterium to grow using fatty acids or acetate as the sole carbon source. FadR regulates fatty acid metabolism in response to intra-cellular concentrations of acyl-CoA lipids. The ability of FadR to bind acyl-CoA fatty acids is hence of significant interest for the engineering of biosynthetic pathways for the production of lipid-based biofuels and commodity chemicals. Based on the available crystal structure of E. coli bound to myristoyl- CoA, we predicted amino acid positions within the effector binding pocket thatmore » would alter the ability of FadR to bind acyl-CoA fatty acids without affecting DNA binding. We utilized fluorescence polarization to characterize the in-vitro binding properties of wild type and mutant FadR. We found that a Leu102Ala mutant enhanced binding of the effector, likely by increasing the size of the binding pocket for the acyl moiety of the molecule. Conversely, the elimination of the guanidine side chain (Arg213Ala and Arg213Met mutants) of the CoA moiety binding site severely diminished the ability of FadR to bind the acyl-CoA effector. These results demonstrate the ability to fine tune FadR binding capacity. The validation of an efficient method to fully characterize all the binding events involved in the specific activity (effector and DNA operator binding) of FadR has allowed us to increase our understanding of the role of specific amino acids in the binding and recognition of acyl-CoA fatty acids and will greatly facilitate efforts aimed at engineering tunable FadR regulators for synthetic biology.« less

Modulation of FadR Binding Capacity for Acyl-CoA Fatty Acids Through Structure-Guided Mutagenesis

DOE PAGES

Bacik, John-Paul; Yeager, Chris M.; Twary, Scott N.; ...

2015-09-18

FadR is a versatile global regulator in Escherichia coli that controls fatty acid metabolism and thereby modulates the ability of this bacterium to grow using fatty acids or acetate as the sole carbon source. FadR regulates fatty acid metabolism in response to intra-cellular concentrations of acyl-CoA lipids. The ability of FadR to bind acyl-CoA fatty acids is hence of significant interest for the engineering of biosynthetic pathways for the production of lipid-based biofuels and commodity chemicals. Based on the available crystal structure of E. coli bound to myristoyl- CoA, we predicted amino acid positions within the effector binding pocket thatmore » would alter the ability of FadR to bind acyl-CoA fatty acids without affecting DNA binding. We utilized fluorescence polarization to characterize the in-vitro binding properties of wild type and mutant FadR. We found that a Leu102Ala mutant enhanced binding of the effector, likely by increasing the size of the binding pocket for the acyl moiety of the molecule. Conversely, the elimination of the guanidine side chain (Arg213Ala and Arg213Met mutants) of the CoA moiety binding site severely diminished the ability of FadR to bind the acyl-CoA effector. These results demonstrate the ability to fine tune FadR binding capacity. The validation of an efficient method to fully characterize all the binding events involved in the specific activity (effector and DNA operator binding) of FadR has allowed us to increase our understanding of the role of specific amino acids in the binding and recognition of acyl-CoA fatty acids and will greatly facilitate efforts aimed at engineering tunable FadR regulators for synthetic biology.« less

ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins.

PubMed

Konc, Janez; Janežič, Dušanka

2017-09-01

ProBiS (Protein Binding Sites) Tools consist of algorithm, database, and web servers for prediction of binding sites and protein ligands based on the detection of structurally similar binding sites in the Protein Data Bank. In this article, we review the operations that ProBiS Tools perform, provide comments on the evolution of the tools, and give some implementation details. We review some of its applications to biologically interesting proteins. ProBiS Tools are freely available at http://probis.cmm.ki.si and http://probis.nih.gov. Copyright © 2017 Elsevier Ltd. All rights reserved.

Operational Plasticity Enables Hsp104 to Disaggregate Diverse Amyloid and Non-Amyloid Clients

PubMed Central

DeSantis, Morgan E.; Leung, Eunice H.; Sweeny, Elizabeth A.; Jackrel, Meredith E.; Cushman-Nick, Mimi; Neuhaus-Follini, Alexandra; Vashist, Shilpa; Sochor, Matthew A.; Knight, M. Noelle; Shorter, James

2012-01-01

Summary It is not understood how Hsp104, a hexameric AAA+ ATPase from yeast, disaggregates diverse structures including stress-induced aggregates, prions, and α-synuclein conformers connected to Parkinson disease. Here, we establish that Hsp104 hexamers adapt different mechanisms of intersubunit collaboration to disaggregate stress-induced aggregates versus amyloid. To resolve disordered aggregates, Hsp104 subunits collaborate non-co-operatively via probabilistic substrate binding and ATP hydrolysis. To disaggregate amyloid, several subunits co-operatively engage substrate and hydrolyze ATP. Importantly, Hsp104 variants with impaired intersubunit communication dissolve disordered aggregates but not amyloid. Unexpectedly, prokaryotic ClpB subunits collaborate differently than Hsp104 and couple probabilistic substrate binding to cooperative ATP hydrolysis, which enhances disordered aggregate dissolution but sensitizes ClpB to inhibition and diminishes amyloid disaggregation. Finally, we establish that Hsp104 hexamers deploy more subunits to disaggregate Sup35 prion strains with more stable ‘cross-β’ cores. Thus, operational plasticity enables Hsp104 to robustly dissolve amyloid and non-amyloid clients, which impose distinct mechanical demands. PMID:23141537

A Smad action turnover switch operated by WW domain readers of a phosphoserine code

PubMed Central

Aragón, Eric; Goerner, Nina; Zaromytidou, Alexia-Ileana; Xi, Qiaoran; Escobedo, Albert; Massagué, Joan; Macias, Maria J.

2011-01-01

When directed to the nucleus by TGF-β or BMP signals, Smad proteins undergo cyclin-dependent kinase 8/9 (CDK8/9) and glycogen synthase kinase-3 (GSK3) phosphorylations that mediate the binding of YAP and Pin1 for transcriptional action, and of ubiquitin ligases Smurf1 and Nedd4L for Smad destruction. Here we demonstrate that there is an order of events—Smad activation first and destruction later—and that it is controlled by a switch in the recognition of Smad phosphoserines by WW domains in their binding partners. In the BMP pathway, Smad1 phosphorylation by CDK8/9 creates binding sites for the WW domains of YAP, and subsequent phosphorylation by GSK3 switches off YAP binding and adds binding sites for Smurf1 WW domains. Similarly, in the TGF-β pathway, Smad3 phosphorylation by CDK8/9 creates binding sites for Pin1 and GSK3, then adds sites to enhance Nedd4L binding. Thus, a Smad phosphoserine code and a set of WW domain code readers provide an efficient solution to the problem of coupling TGF-β signal delivery to turnover of the Smad signal transducers. PMID:21685363

Feature binding in visual short-term memory is unaffected by task-irrelevant changes of location, shape, and color.

PubMed

Logie, Robert H; Brockmole, James R; Jaswal, Snehlata

2011-01-01

Three experiments used a change detection paradigm across a range of study-test intervals to address the respective contributions of location, shape, and color to the formation of bindings of features in sensory memory and visual short-term memory (VSTM). In Experiment 1, location was designated task irrelevant and was randomized between study and test displays. The task was to detect changes in the bindings between shape and color. In Experiments 2 and 3, shape and color, respectively, were task irrelevant and randomized, with bindings tested between location and color (Experiment 2) and location and shape (Experiment 3). At shorter study-test intervals, randomizing location was most disruptive, followed by shape and then color. At longer intervals, randomizing any task-irrelevant feature had no impact on change detection for bindings between features, and location had no special role. Results suggest that location is crucial for initial perceptual binding but loses that special status once representations are formed in VSTM, which operates according to different principles, than do visual attention and perception.

Development of operational models of receptor activation including constitutive receptor activity and their use to determine the efficacy of the chemokine CCL17 at the CC chemokine receptor CCR4

PubMed Central

Slack, RJ; Hall, DA

2012-01-01

BACKGROUND AND PURPOSE The operational model provides a key conceptual framework for the analysis of pharmacological data. However, this model does not include constitutive receptor activity, a frequent phenomenon in modern pharmacology, particularly in recombinant systems. Here, we developed extensions of the operational model which include constitutive activity and applied them to effects of agonists at the chemokine receptor CCR4. EXPERIMENTAL APPROACH The effects of agonists of CCR4 on [35S]GTPγS binding to recombinant cell membranes and on the filamentous (F-) actin content of human CD4+ CCR4+ T cells were determined. The basal [35S]GTPγS binding was changed by varying the GDP concentration whilst the basal F-actin contents of the higher expressing T cell populations were elevated, suggesting constitutive activity of CCR4. Both sets of data were analysed using the mathematical models. RESULTS The affinity of CCL17 (also known as TARC) derived from analysis of the T cell data (pKa= 9.61 ± 0.17) was consistent with radioligand binding experiments (9.50 ± 0.11) while that from the [35S]GTPγS binding experiments was lower (8.27 ± 0.09). Its intrinsic efficacy differed between the two systems (110 in T cells vs. 11). CONCLUSIONS AND IMPLICATIONS The presence of constitutive receptor activity allows the absolute intrinsic efficacy of agonists to be determined without a contribution from the signal transduction system. Intrinsic efficacy estimated in this way is consistent with Furchgott's definition of this property. CCL17 may have a higher intrinsic efficacy at CCR4 in human T cells than that expressed recombinantly in CHO cells. PMID:22335621

Reversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain: possible allosteric regulation and a conserved structural motif for the chloride-binding site.

PubMed

Ogawa, Haruo; Qiu, Yue; Philo, John S; Arakawa, Tsutomu; Ogata, Craig M; Misono, Kunio S

2010-03-01

The binding of atrial natriuretic peptide (ANP) to its receptor requires chloride, and it is chloride concentration dependent. The extracellular domain (ECD) of the ANP receptor (ANPR) contains a chloride near the ANP-binding site, suggesting a possible regulatory role. The bound chloride, however, is completely buried in the polypeptide fold, and its functional role has remained unclear. Here, we have confirmed that chloride is necessary for ANP binding to the recombinant ECD or the full-length ANPR expressed in CHO cells. ECD without chloride (ECD(-)) did not bind ANP. Its binding activity was fully restored by bromide or chloride addition. A new X-ray structure of the bromide-bound ECD is essentially identical to that of the chloride-bound ECD. Furthermore, bromide atoms are localized at the same positions as chloride atoms both in the apo and in the ANP-bound structures, indicating exchangeable and reversible halide binding. Far-UV CD and thermal unfolding data show that ECD(-) largely retains the native structure. Sedimentation equilibrium in the absence of chloride shows that ECD(-) forms a strongly associated dimer, possibly preventing the structural rearrangement of the two monomers that is necessary for ANP binding. The primary and tertiary structures of the chloride-binding site in ANPR are highly conserved among receptor-guanylate cyclases and metabotropic glutamate receptors. The chloride-dependent ANP binding, reversible chloride binding, and the highly conserved chloride-binding site motif suggest a regulatory role for the receptor bound chloride. Chloride-dependent regulation of ANPR may operate in the kidney, modulating ANP-induced natriuresis.

Reversibly Bound Chloride in the Atrial Natriuretic Peptide Receptor Hormone Binding Domain: Possible Allosteric Regulation and a Conserved Structural Motif for the Chloride-binding Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogawa, H.; Qiu, Y; Philo, J

2010-01-01

The binding of atrial natriuretic peptide (ANP) to its receptor requires chloride, and it is chloride concentration dependent. The extracellular domain (ECD) of the ANP receptor (ANPR) contains a chloride near the ANP-binding site, suggesting a possible regulatory role. The bound chloride, however, is completely buried in the polypeptide fold, and its functional role has remained unclear. Here, we have confirmed that chloride is necessary for ANP binding to the recombinant ECD or the full-length ANPR expressed in CHO cells. ECD without chloride (ECD(-)) did not bind ANP. Its binding activity was fully restored by bromide or chloride addition. Amore » new X-ray structure of the bromide-bound ECD is essentially identical to that of the chloride-bound ECD. Furthermore, bromide atoms are localized at the same positions as chloride atoms both in the apo and in the ANP-bound structures, indicating exchangeable and reversible halide binding. Far-UV CD and thermal unfolding data show that ECD(-) largely retains the native structure. Sedimentation equilibrium in the absence of chloride shows that ECD(-) forms a strongly associated dimer, possibly preventing the structural rearrangement of the two monomers that is necessary for ANP binding. The primary and tertiary structures of the chloride-binding site in ANPR are highly conserved among receptor-guanylate cyclases and metabotropic glutamate receptors. The chloride-dependent ANP binding, reversible chloride binding, and the highly conserved chloride-binding site motif suggest a regulatory role for the receptor bound chloride. Chloride-dependent regulation of ANPR may operate in the kidney, modulating ANP-induced natriuresis.« less

Reversibly bound chloride in the atrial natriuretic peptide receptor hormone-binding domain: Possible allosteric regulation and a conserved structural motif for the chloride-binding site

PubMed Central

Ogawa, Haruo; Qiu, Yue; Philo, John S; Arakawa, Tsutomu; Ogata, Craig M; Misono, Kunio S

2010-01-01

The binding of atrial natriuretic peptide (ANP) to its receptor requires chloride, and it is chloride concentration dependent. The extracellular domain (ECD) of the ANP receptor (ANPR) contains a chloride near the ANP-binding site, suggesting a possible regulatory role. The bound chloride, however, is completely buried in the polypeptide fold, and its functional role has remained unclear. Here, we have confirmed that chloride is necessary for ANP binding to the recombinant ECD or the full-length ANPR expressed in CHO cells. ECD without chloride (ECD(−)) did not bind ANP. Its binding activity was fully restored by bromide or chloride addition. A new X-ray structure of the bromide-bound ECD is essentially identical to that of the chloride-bound ECD. Furthermore, bromide atoms are localized at the same positions as chloride atoms both in the apo and in the ANP-bound structures, indicating exchangeable and reversible halide binding. Far-UV CD and thermal unfolding data show that ECD(−) largely retains the native structure. Sedimentation equilibrium in the absence of chloride shows that ECD(−) forms a strongly associated dimer, possibly preventing the structural rearrangement of the two monomers that is necessary for ANP binding. The primary and tertiary structures of the chloride-binding site in ANPR are highly conserved among receptor-guanylate cyclases and metabotropic glutamate receptors. The chloride-dependent ANP binding, reversible chloride binding, and the highly conserved chloride-binding site motif suggest a regulatory role for the receptor bound chloride. Chloride-dependent regulation of ANPR may operate in the kidney, modulating ANP-induced natriuresis. PMID:20066666

Modulation of ouabain binding and potassium pump fluxes by cellular sodium and potassium in human and sheep erythrocytes.

PubMed Central

Joiner, C H; Lauf, P K

1978-01-01

1. Erythrocytes were treated with nystatin to alter internal Na (Nai) and K (Ki) composition. Although the rates of K pumping and [3H]ouabain binding were altered dramatically, the relationship between glycoside binding and K pump inhibition was unaffected. 2. Human cells with high Nai and low Ki exhibited an increased rate of ouabain binding as compared to high Ki, low Nai cells; this paralleled the stimulated K pump activity of high Nai cells. 3. At constant Ki, increasing internal Na stimulated K pump and ouabain binding rates concomitantly. 4. At low Nai, increasing Ki inhibited both K pumping and ouabain binding. However, at high Nai, increasing Ki from 4 to 44 mM stimulated the rate of glycoside binding, parallel to its effect of increasing the rate of active K influx. 5. Anti-L, an isoantibody to low K (LK) sheep red cells, increased the rate of ouabain binding via its stimulation of K pump turnover. Since the latter effect is the result of affinity changes at the internal cation activation site(s) of the pump (Lauf, Rasmusen, Hoffman, Dunham, Cook, Parmelee & Tosteson, 1970), the antibody's effect on ouabain binding reflected the positive correlation between the rates of K pump turnover and glycoside binding. 6. These data provide the first evidence in intact cells for the occurrence of a Nai-induced conformational change in the Na/K pump during its normal operational cycle. PMID:722574

Mobile magnetic particles as solid-supports for rapid surface-based bioanalysis in continuous flow.

PubMed

Peyman, Sally A; Iles, Alexander; Pamme, Nicole

2009-11-07

An extremely versatile microfluidic device is demonstrated in which multi-step (bio)chemical procedures can be performed in continuous flow. The system operates by generating several co-laminar flow streams, which contain reagents for specific (bio)reactions across a rectangular reaction chamber. Functionalized magnetic microparticles are employed as mobile solid-supports and are pulled from one side of the reaction chamber to the other by use of an external magnetic field. As the particles traverse the co-laminar reagent streams, binding and washing steps are performed on their surface in one operation in continuous flow. The applicability of the platform was first demonstrated by performing a proof-of-principle binding assay between streptavidin coated magnetic particles and biotin in free solution with a limit of detection of 20 ng mL(-1) of free biotin. The system was then applied to a mouse IgG sandwich immunoassay as a first example of a process involving two binding steps and two washing steps, all performed within 60 s, a fraction of the time required for conventional testing.

Reverse spin-crossover and high-pressure kinetics of the heme iron center relevant for the operation of heme proteins under deep-sea conditions.

PubMed

Troeppner, Oliver; Lippert, Rainer; Shubina, Tatyana E; Zahl, Achim; Jux, Norbert; Ivanović-Burmazović, Ivana

2014-10-20

By design of a heme model complex with a binding pocket of appropriate size and flexibility, and by elucidating its kinetics and thermodynamics under elevated pressures, some of the pressure effects are demonstrated relevant for operation of heme-proteins under deep-sea conditions. Opposite from classical paradigms of the spin-crossover and reaction kinetics, a pressure increase can cause deceleration of the small-molecule binding to the vacant coordination site of the heme-center in a confined space and stabilize a high-spin state of its Fe center. This reverse high-pressure behavior can be achieved only if the volume changes related to the conformational transformation of the cavity can offset the volume changes caused by the substrate binding. It is speculated that based on these criteria nature could make a selection of structures of heme pockets that assist in reducing metabolic activity and enzymatic side reactions under extreme pressure conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

In vitro selection of zinc fingers with altered DNA-binding specificity.

PubMed

Jamieson, A C; Kim, S H; Wells, J A

1994-05-17

We have used random mutagenesis and phage display to alter the DNA-binding specificity of Zif268, a transcription factor that contains three zinc finger domains. Four residues in the helix of finger 1 of Zif268 that potentially mediate DNA binding were identified from an X-ray structure of the Zif268-DNA complex. A library was constructed in which these residues were randomly mutated and the Zif268 variants were fused to a truncated version of the gene III coat protein on the surface of M13 filamentous phage particles. The phage displayed the mutant proteins in a monovalent fashion and were sorted by repeated binding and elution from affinity matrices containing different DNA sequences. When the matrix contained the natural nine base pair operator sequence 5'-GCG-TGG-GCG-3', native-like zinc fingers were isolated. New finger 1 variants were found by sorting with two different operators in which the singly modified triplets, GTG and TCG, replaced the native finger 1 triplet, GCG. Overall, the selected finger 1 variants contained a preponderance of polar residues at the four sites. Interestingly, the net charge of the four residues in any selected finger never derived more that one unit from neutrality despite the fact that about half the variants contained three or four charged residues over the four sites. Measurements of the dissociation constants for two of these purified finger 1 variants by gel-shift assay showed their specificities to vary over a 10-fold range, with the greatest affinity being for the DNA binding site for which they were sorted.(ABSTRACT TRUNCATED AT 250 WORDS)

Vaccinia virus proteins A36 and F12/E2 show strong preferences for different kinesin light chain isoforms.

PubMed

Gao, William N D; Carpentier, David C J; Ewles, Helen A; Lee, Stacey-Ann; Smith, Geoffrey L

2017-08-01

Vaccinia virus (VACV) utilizes microtubule-mediated trafficking at several stages of its life cycle, of which virus egress is the most intensely studied. During egress VACV proteins A36, F12 and E2 are involved in kinesin-1 interactions; however, the roles of these proteins remain poorly understood. A36 forms a direct link between virions and kinesin-1, yet in its absence VACV egress still occurs on microtubules. During a co-immunoprecipitation screen to seek an alternative link between virions and kinesin, A36 was found to bind isoform KLC1 rather than KLC2. The F12/E2 complex associates preferentially with the C-terminal tail of KLC2, to a region that overlaps the binding site of cellular 14-3-3 proteins. F12/E2 displaces 14-3-3 from KLC and, unlike 14-3-3, does not require phosphorylation of KLC for its binding. The region determining the KLC1 specificity of A36 was mapped to the KLC N-terminal heptad repeat region that is responsible for its association with kinesin heavy chain. Despite these differing binding properties F12/E2 can co-operatively enhance A36 association with KLC, particularly when using a KLC1-KLC2 chimaera that resembles several KLC1 spliceforms and can bind A36 and F12/E2 efficiently. This is the first example of a pathogen encoding multiple proteins that co-operatively associate with kinesin-1. © 2017 The Authors. Traffic published by John Wiley & Sons Ltd.

General transfer matrix formalism to calculate DNA-protein-drug binding in gene regulation: application to OR operator of phage lambda.

PubMed

Teif, Vladimir B

2007-01-01

The transfer matrix methodology is proposed as a systematic tool for the statistical-mechanical description of DNA-protein-drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the O(R) operator of phage lambda. The transfer matrix formalism allowed the description of the lambda-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI-Cro-RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the O(R) and O(L) operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters P(R) and P(RM) becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed.

General transfer matrix formalism to calculate DNA–protein–drug binding in gene regulation: application to OR operator of phage λ

PubMed Central

Teif, Vladimir B.

2007-01-01

The transfer matrix methodology is proposed as a systematic tool for the statistical–mechanical description of DNA–protein–drug binding involved in gene regulation. We show that a genetic system of several cis-regulatory modules is calculable using this method, considering explicitly the site-overlapping, competitive, cooperative binding of regulatory proteins, their multilayer assembly and DNA looping. In the methodological section, the matrix models are solved for the basic types of short- and long-range interactions between DNA-bound proteins, drugs and nucleosomes. We apply the matrix method to gene regulation at the OR operator of phage λ. The transfer matrix formalism allowed the description of the λ-switch at a single-nucleotide resolution, taking into account the effects of a range of inter-protein distances. Our calculations confirm previously established roles of the contact CI–Cro–RNAP interactions. Concerning long-range interactions, we show that while the DNA loop between the OR and OL operators is important at the lysogenic CI concentrations, the interference between the adjacent promoters PR and PRM becomes more important at small CI concentrations. A large change in the expression pattern may arise in this regime due to anticooperative interactions between DNA-bound RNA polymerases. The applicability of the matrix method to more complex systems is discussed. PMID:17526526

Restructuring Schools in Chester Upland, Pennsylvania: An Analysis of State and District Efforts. ECS Policy Brief

ERIC Educational Resources Information Center

Rhim, Lauren Morando

2005-01-01

Restructuring is a process initiated to substantively change the governance, operation and instruction of public schools or districts identified as failing. There are multiple definitions of restructuring, but the common thread binding all restructuring models is a substantive change of the standard operating procedures of a school or an entire…

Prediction of 3- to 5-Month Outcomes from Signs of Acute Bilirubin Toxicity in Newborn Infants.

PubMed

El Houchi, Salma Z; Iskander, Iman; Gamaleldin, Rasha; El Shenawy, Amira; Seoud, Iman; Abou-Youssef, Hazem; Wennberg, Richard P

2017-04-01

To evaluate the ability of the bilirubin-induced neurologic dysfunction (BIND) score to predict residual neurologic and auditory disability and to document the relationship of BIND score to total serum bilirubin (TSB) concentration. The BIND score (assessing mental status, muscle tone, and cry patterns) was obtained serially at 6- to 8-hour intervals in 220 near-term and full-term infants with severe hyperbilirubinemia. Neurologic and/or auditory outcomes at 3-5 months of age were correlated with the highest calculated BIND score. The BIND score was also correlated with TSB. Follow-up neurologic and auditory examinations were performed for 145/202 (72%) surviving infants. All infants with severe acute bilirubin encephalopathy (BIND scores 7-9) either died or suffered residual neurologic and auditory impairment. Of 24 cases with moderate encephalopathy (BIND 4-6), 15 (62.5%) resolved following aggressive intervention and were normal at follow-up. Three of 73 infants with mild encephalopathy (BIND scores 1-3) but severe jaundice (TSB ranging 33.5-38 mg/dL; 573-650 µmol/L) had residual neurologic and/or auditory impairment. A BIND score ≥4 had a specificity of 87.3% and a sensitivity of 97.4% for predicting poor neurologic outcomes (receiver operating characteristic analysis). BIND scores trended higher with severe hyperbilirubinemia (r 2  = 0.54, P < .005), but 5/39 (13%) infants with TSB ≥36.5 mg/dL (624 µmol/L) had BIND scores ≤3, and normal outcomes at 3-5 months. The BIND score can be used to evaluate the severity of acute bilirubin encephalopathy and predict residual neurologic and hearing dysfunction. Copyright © 2017 Elsevier Inc. All rights reserved.

A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

DOE PAGES

Dossani, Zain Y.; Reider Apel, Amanda; Szmidt-Middleton, Heather; ...

2017-10-30

Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domainmore » of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. Finally, this set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.« less

Specific DNA binding of a potential transcriptional regulator, inosine 5'-monophosphate dehydrogenase-related protein VII, to the promoter region of a methyl coenzyme m reductase I-encoding operon retrieved from Methanothermobacter thermautotrophicus strain DeltaH.

PubMed

Shinzato, Naoya; Enoki, Miho; Sato, Hiroaki; Nakamura, Kohei; Matsui, Toru; Kamagata, Yoichi

2008-10-01

Two methyl coenzyme M reductases (MCRs) encoded by the mcr and mrt operons of the hydrogenotrophic methanogen Methanothermobacter thermautotrophicus DeltaH are expressed in response to H(2) availability. In the present study, cis elements and trans-acting factors responsible for the gene expression of MCRs were investigated by using electrophoretic mobility shift assay (EMSA) and affinity particle purification. A survey of their operator regions by EMSA with protein extracts from mrt-expressing cultures restricted them to 46- and 41-bp-long mcr and mrt upstream regions, respectively. Affinity particle purification of DNA-binding proteins conjugated with putative operator regions resulted in the retrieval of a protein attributed to IMP dehydrogenase-related protein VII (IMPDH VII). IMPDH VII is predicted to have a winged helix-turn-helix DNA-binding motif and two cystathionine beta-synthase domains, and it has been suspected to be an energy-sensing module. EMSA with oligonucleotide probes with unusual sequences showed that the binding site of IMPDH VII mostly overlaps the factor B-responsible element-TATA box of the mcr operon. The results presented here suggest that IMPDH VII encoded by MTH126 is a plausible candidate for the transcriptional regulator of the mcr operon in this methanogen.

A combinatorial approach to synthetic transcription factor‐promoter combinations for yeast strain engineering

PubMed Central

Dossani, Zain Y.; Reider Apel, Amanda; Szmidt‐Middleton, Heather; Hillson, Nathan J.; Deutsch, Samuel; Keasling, Jay D.

2017-01-01

Abstract Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domain of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. This set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain. PMID:29084380

A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dossani, Zain Y.; Reider Apel, Amanda; Szmidt-Middleton, Heather

Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domainmore » of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. Finally, this set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.« less

Urate is a ligand for the transcriptional regulator PecS.

PubMed

Perera, Inoka C; Grove, Anne

2010-09-24

PecS is a member of the MarR (multiple antibiotic resistance regulator) family, which has been shown in Erwinia to regulate the expression of virulence genes. MarR homologs typically bind a small molecule ligand, resulting in attenuated DNA binding. For PecS, the natural ligand has not been identified. We have previously shown that urate is a ligand for the Deinococcus radiodurans-encoded MarR homolog HucR (hypothetical uricase regulator) and identified residues responsible for ligand binding. We show here that all four residues involved in urate binding and propagation of conformational changes to DNA recognition helices are conserved in PecS homologs, suggesting that urate is the ligand for PecS. Consistent with this prediction, Agrobacterium tumefaciens PecS specifically binds urate, and urate attenuates DNA binding in vitro. PecS binds two operator sites in the intergenic region between the divergent pecS gene and pecM genes, one of which features two partially overlapping repeats to which PecS binds as a dimer on opposite faces of the duplex. Notably, urate dissociates PecS from cognate DNA, allowing transcription of both genes in vivo. Taken together, our data show that urate is a ligand for PecS and suggest that urate serves a novel function in signaling the colonization of a host plant. Copyright © 2010 Elsevier Ltd. All rights reserved.

Cyclophilin B binding to platelets supports calcium-dependent adhesion to collagen.

PubMed

Allain, F; Durieux, S; Denys, A; Carpentier, M; Spik, G

1999-08-01

We have recently reported that cyclophilin B (CyPB), a secreted cyclosporine-binding protein, could bind to T lymphocytes through interactions with two types of binding sites. The first ones, referred to as type I, involve interactions with the conserved domain of CyPB and promote the endocytosis of surface-bound ligand, while the second type of binding sites, termed type II, are represented by glycosaminoglycans (GAG). Here, we further investigated the interactions of CyPB with blood cell populations. In addition to lymphocytes, CyPB was found to interact mainly with platelets. The binding is specific, with a dissociation constant (kd) of 9 +/- 3 nmol/L and the number of sites estimated at 960 +/- 60 per cell. Platelet glycosaminoglycans are not required for the interactions, but the binding is dramatically reduced by active cyclosporine derivatives. We then analyzed the biologic effects of CyPB and found a significant increase in platelet adhesion to collagen. Concurrently, CyPB initiates a transmembranous influx of Ca(2+) and induces the phosphorylation of the P-20 light chains of myosin. Taken together, the present results demonstrate for the first time that extracellular CyPB specifically interacts with platelets through a functional receptor related to the lymphocyte type I binding sites and might act by regulating the activity of a receptor-operated membrane Ca(2+) channel.

Nanofiber adsorbents for high productivity continuous downstream processing.

PubMed

Hardick, Oliver; Dods, Stewart; Stevens, Bob; Bracewell, Daniel G

2015-11-10

An ever increasing focus is being placed on the manufacturing costs of biotherapeutics. The drive towards continuous processing offers one opportunity to address these costs through the advantages it offers. Continuous operation presents opportunities for real-time process monitoring and automated control with potential benefits including predictable product specification, reduced labour costs, and integration with other continuous processes. Specifically to chromatographic operations continuous processing presents an opportunity to use expensive media more efficiently while reducing their size and therefore cost. Here for the first time we show how a new adsorbent material (cellulosic nanofibers) having advantageous convective mass transfer properties can be combined with a high frequency simulated moving bed (SMB) design to provide superior productivity in a simple bioseparation. Electrospun polymeric nanofiber adsorbents offer an alternative ligand support surface for bioseparations. Their non-woven fiber structure with diameters in the sub-micron range creates a remarkably high surface area material that allows for rapid convective flow operations. A proof of concept study demonstrated the performance of an anion exchange nanofiber adsorbent based on criteria including flow and mass transfer properties, binding capacity, reproducibility and life-cycle performance. Binding capacities of the DEAE adsorbents were demonstrated to be 10mg/mL, this is indeed only a fraction of what is achievable from porous bead resins but in combination with a very high flowrate, the productivity of the nanofiber system is shown to be significant. Suitable packing into a flow distribution device has allowed for reproducible bind-elute operations at flowrates of 2,400 cm/h, many times greater than those used in typical beaded systems. These characteristics make them ideal candidates for operation in continuous chromatography systems. A SMB system was developed and optimised to demonstrate the productivity of nanofiber adsorbents through rapid bind-elute cycle times of 7s which resulted in a 15-fold increase in productivity compared with packed bed resins. Reproducible performance of BSA purification was demonstrated using a 2-component protein solution of BSA and cytochrome c. The SMB system exploits the advantageous convective mass transfer properties of nanofiber adsorbents to provide productivities much greater than those achievable with conventional chromatography media. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Impaired visual search in rats reveals cholinergic contributions to feature binding in visuospatial attention.

PubMed

Botly, Leigh C P; De Rosa, Eve

2012-10-01

The visual search task established the feature integration theory of attention in humans and measures visuospatial attentional contributions to feature binding. We recently demonstrated that the neuromodulator acetylcholine (ACh), from the nucleus basalis magnocellularis (NBM), supports the attentional processes required for feature binding using a rat digging-based task. Additional research has demonstrated cholinergic contributions from the NBM to visuospatial attention in rats. Here, we combined these lines of evidence and employed visual search in rats to examine whether cortical cholinergic input supports visuospatial attention specifically for feature binding. We trained 18 male Long-Evans rats to perform visual search using touch screen-equipped operant chambers. Sessions comprised Feature Search (no feature binding required) and Conjunctive Search (feature binding required) trials using multiple stimulus set sizes. Following acquisition of visual search, 8 rats received bilateral NBM lesions using 192 IgG-saporin to selectively reduce cholinergic afferentation of the neocortex, which we hypothesized would selectively disrupt the visuospatial attentional processes needed for efficient conjunctive visual search. As expected, relative to sham-lesioned rats, ACh-NBM-lesioned rats took significantly longer to locate the target stimulus on Conjunctive Search, but not Feature Search trials, thus demonstrating that cholinergic contributions to visuospatial attention are important for feature binding in rats.

Structural basis of redox-dependent substrate binding of protein disulfide isomerase

PubMed Central

Yagi-Utsumi, Maho; Satoh, Tadashi; Kato, Koichi

2015-01-01

Protein disulfide isomerase (PDI) is a multidomain enzyme, operating as an essential folding catalyst, in which the b′ and a′ domains provide substrate binding sites and undergo an open–closed domain rearrangement depending on the redox states of the a′ domain. Despite the long research history of this enzyme, three-dimensional structural data remain unavailable for its ligand-binding mode. Here we characterize PDI substrate recognition using α-synuclein (αSN) as the model ligand. Our nuclear magnetic resonance (NMR) data revealed that the substrate-binding domains of PDI captured the αSN segment Val37–Val40 only in the oxidized form. Furthermore, we determined the crystal structure of an oxidized form of the b′–a′ domains in complex with an undecapeptide corresponding to this segment. The peptide-binding mode observed in the crystal structure with NMR validation, was characterized by hydrophobic interactions on the b′ domain in an open conformation. Comparison with the previously reported crystal structure indicates that the a′ domain partially masks the binding surface of the b′ domain, causing steric hindrance against the peptide in the reduced form of the b′–a′ domains that exhibits a closed conformation. These findings provide a structural basis for the mechanism underlying the redox-dependent substrate binding of PDI. PMID:26350503

Modified high-affinity binding of Ni2+, Ca2+ and Zn2+ to natural mutants of human serum albumin and proalbumin.

PubMed

Kragh-Hansen, U; Brennan, S O; Minchiotti, L; Galliano, M

1994-07-01

High-affinity binding of radioactive Ni2+, Ca2+ and Zn2+ to six genetic albumin variants and to normal albumin isolated from the same heterozygote carriers was studied by equilibrium dialysis at pH 7.4. The three cations bind differently to albumin. Ni2+ binds to a site in the N-terminal region of the protein which is partially blocked by the presence of a propeptide as in proalbumin (proAlb) Varese (Arg-2-->His), proAlb Christchurch (Arg-1-->Gln) and proAlb Blenheim (Asp1-->Val) and by the presence of only an extra Arg residue (Arg-1) as in Arg-Alb and albumin (Alb) Redhill. The association constants are decreased by more than one order of magnitude in these cases, suggesting biological consequences for the ligand. The additional structural changes in Alb Redhill have no effect on Ni2+ binding. Finally, the modification of Alb Blenheim (Asp1-->Val) reduces the binding constant to 50%. Ca2+ binding is decreased to about 60-80% by the presence of a propeptide and the mutation Asp1-->Val. Arg-1 alone does not affect binding, whereas Alb Redhill binds Ca2+ more strongly than the normal protein (125%). In contrast with binding of Ni2+ and Ca2+, albumin shows heterogeneity with regard to binding of Zn2+, i.e. the number of high-affinity sites was calculated to be, on average, 0.43. The binding constant for Zn2+ is increased to 125% in the case of proAlb Varese, decreased to 50-60% for proAlb Christchurch and Alb Redhill but is normal for proAlb Blenheim, Alb Blenheim and Arg-Alb. The effects of the mutations on binding of Ca2+ and Zn2+ indicate that primary binding, when operative, is to as yet unidentified sites in domain I of the albumin molecule.

Probing the interaction of anticancer drug temsirolimus with human serum albumin: molecular docking and spectroscopic insight.

PubMed

Shamsi, Anas; Ahmed, Azaj; Bano, Bilqees

2018-05-01

The binding interaction between temsirolimus, an important antirenal cancer drug, and HSA, an important carrier protein was scrutinized making use of UV and fluorescence spectroscopy. Hyper chromaticity observed in UV spectroscopy in the presence of temsirolimus as compared to free HSA suggests the formation of complex between HSA and temsirolimus. Fluorescence quenching experiments clearly showed quenching in the fluorescence of HSA in the presence of temsirolimus confirming the complex formation and also confirmed that static mode of interaction is operative for this binding process. Binding constant values obtained through UV and fluorescence spectroscopy reveal strong interaction; temsirolimus binds to HSA at 298 K with a binding constant of 2.9 × 10 4  M -1 implying the strength of interaction. The negative Gibbs free energy obtained through Isothermal titration calorimetry as well as quenching experiments suggests that binding process is spontaneous. Molecular docking further provides an insight of various residues that are involved in this binding process; showing the binding energy to be -12.9 kcal/mol. CD spectroscopy was retorted to analyze changes in secondary structure of HSA; increased intensity in presence of temsirolimus showing changes in secondary structure of HSA induced by temsirolimus. This study is of importance as it provides an insight into the binding mechanism of an important antirenal cancer drug with an important carrier protein. Once temsirolimus binds to HSA, it changes conformation of HSA which in turn can alter the functionality of this important carrier protein and this altered functionality of HSA can be highlighted in variety of diseases.

FY2017 Defense Appropriations Fact Sheet: Selected Highlights of H.R. 5293 and S. 3000

DTIC Science & Technology

2016-06-17

legally binding caps on discretionary spending for defense programs and for non-defense programs, which were established by P.L. 114-74, the Bipartisan...funding for FY2017 that (1) exceeds the relevant BBA cap ; and (2) is also exempt from that spending cap because it is classified as funding for so-called...Overseas Contingency Operations (OCO). The 2015 BBA increased binding caps on defense and non-defense discretionary appropriations for FY2016 and

Fact Sheet: Selected Highlights of the FY2017 National Defense Authorization Act (H.R. 4909)

DTIC Science & Technology

2016-05-12

shaped by the legally binding caps on discretionary spending for defense programs and for non-defense programs, which were established by P.L. 114-74...of Defense (DOD) funding for FY2017 that (1) exceeds the relevant BBA cap ; and (2) is exempt from that spending cap because it is classified as...funding for so- called Overseas Contingency Operations (OCO). The 2015 BBA increased binding caps on defense and non-defense discretionary appropriations

Optimized Standard Operating Procedures for the Analysis of Cerebrospinal Fluid Aβ42 and the Ratios of Aβ Isoforms Using Low Protein Binding Tubes.

PubMed

Vanderstichele, Hugo Marcel Johan; Janelidze, Shorena; Demeyer, Leentje; Coart, Els; Stoops, Erik; Herbst, Victor; Mauroo, Kimberley; Brix, Britta; Hansson, Oskar

2016-05-31

Reduced cerebrospinal fluid (CSF) concentration of amyloid-β1-42 (Aβ1-42) reflects the presence of amyloidopathy in brains of subjects with Alzheimer's disease (AD). To qualify the use of Aβ1-42/Aβ1-40 for improvement of standard operating procedures (SOP) for measurement of CSF Aβ with a focus on CSF collection, storage, and analysis. Euroimmun ELISAs for CSF Aβ isoforms were used to set up a SOP with respect to recipient properties (low binding, polypropylene), volume of tubes, freeze/thaw cycles, addition of detergents (Triton X-100, Tween-20) in collection or storage tubes or during CSF analysis. Data were analyzed with linear repeated measures and mixed effects models. Optimization of CSF analysis included a pre-wash of recipients (e.g., tubes, 96-well plates) before sample analysis. Using the Aβ1-42/Aβ1-40 ratio, in contrast to Aβ1-42, eliminated effects of tube type, additional freeze/thaw cycles, or effect of CSF volumes for polypropylene storage tubes. 'Low binding' tubes reduced the loss of Aβ when aliquoting CSF or in function of additional freeze/thaw cycles. Addition of detergent in CSF collection tubes resulted in an almost complete absence of variation in function of collection procedures, but affected the concentration of Aβ isoforms in the immunoassay. The ratio of Aβ1-42/Aβ1-40 is a more robust biomarker than Aβ1-42 toward (pre-) analytical interfering factors. Further, 'low binding' recipients and addition of detergent in collection tubes are able to remove effects of SOP-related confounding factors. Integration of the Aβ1-42/Aβ1-40 ratio and 'low-binding tubes' into guidance criteria may speed up worldwide standardization of CSF biomarker analysis.

Effect of PEG-PDMAEMA Block Copolymer Architecture on Polyelectrolyte Complex Formation with Heparin.

PubMed

Välimäki, Salla; Khakalo, Alexey; Ora, Ari; Johansson, Leena-Sisko; Rojas, Orlando J; Kostiainen, Mauri A

2016-09-12

Heparin is a naturally occurring polyelectrolyte consisting of a sulfated polysaccharide backbone. It is widely used as an anticoagulant during major surgical operations. However, the associated bleeding risks require rapid neutralization after the operation. The only clinically approved antidote for heparin is protamine sulfate, which is, however, ineffective against low molecular weight heparin and can cause severe adverse reactions in patients. In this study, the facile synthesis of cationic-neutral diblock copolymers and their effective heparin binding is presented. Poly(ethylene glycol)-poly(2-(dimethylamino)ethyl methacrylate) (PEG-PDMAEMA) block copolymers were synthesized in two steps via atom-transfer radical polymerization (ATRP) using PEG as a macroinitiator. Solution state binding between heparin and a range of PEG-PDMAEMA block copolymers and one homopolymer was studied with dynamic light scattering and methylene blue displacement assay. Also in vitro binding in plasma was studied by utilizing a chromogenic heparin anti-Xa assay. Additionally, quartz crystal microbalance and multiparametric surface plasmon resonance were used to study the surface adsorption kinetics of the polymers on a heparin layer. It was shown that the block copolymers and heparin form electrostatically bound complexes with varying colloidal properties, where the block lengths play a key role in controlling the heparin binding affinity, polyelectrolyte complex size and surface charge. With the optimized polymers (PEG114PDMAEMA52 and PEG114PDMAEMA100), heparin could be neutralized in a dose-dependent manner, and bound efficiently into small neutral complexes, with a hydrodynamic radius less than 100 nm. These complexes had only a limited effect on cell viability. Based on these studies, our approach paves the way for the development of new polymeric heparin binding agents.

Geomagnetic Workshop, Canberra

NASA Astrophysics Data System (ADS)

Barton, C. E.; Lilley, F. E. M.; Milligan, P. R.

On May 14-15, 1985, 63 discerning geomagnetists flocked to Canberra to attend the Geomagnetic Workshop coorganized by the Australian Bureau of Mineral Resources (BMR) and the Research School of Earth Sciences, Australian National University (ANU). With an aurorally glowing cast that included an International Association of Geomagnetism and Aeronomy (IAGA) president, former president, and division chairman, the Oriental Magneto-Banquet (which was the center of the meeting), was assured of success. As a cunning ploy to mask the true nature of this gastronomic extravagance from the probings of income tax departments, a presentation of scientific papers on Australian geomagnetism in its global setting was arranged.The Australian region, including New Zealand, Papua New Guinea, Indonesia, and a large sector of the Antarctic, covers one eighth of the Earth's surface and historically has played an important role in the study of geomagnetism. The region contains both the south magnetic and geomagnetic poles, and two Australian Antarctic stations (Casey and Davis) are situated in the region of the south polar cusp (see Figure 1).

Interactions of the Metalloregulatory Protein SloR from Streptococcus mutans with Its Metal Ion Effectors and DNA Binding Site

PubMed Central

Corbett, John; Cornacchione, Louis; Daly, William; Galan, Diego; Wysota, Michael; Tivnan, Patrick; Collins, Justin; Nye, Dillon; Levitz, Talya; Breyer, Wendy A.; Glasfeld, Arthur

2015-01-01

ABSTRACT Streptococcus mutans is the causative agent of dental caries, a significant concern for human health, and therefore an attractive target for therapeutics development. Previous work in our laboratory has identified a homodimeric, manganese-dependent repressor protein, SloR, as an important regulator of cariogenesis and has used site-directed mutagenesis to map functions to specific regions of the protein. Here we extend those studies to better understand the structural interaction between SloR and its operator and its effector metal ions. The results of DNase I assays indicate that SloR protects a 42-bp region of DNA that overlaps the sloABC promoter on the S. mutans UA159 chromosome, while electrophoretic mobility shift and solution binding assays indicate that each of two SloR dimers binds to this region. Real-time semiquantitative reverse transcriptase PCR (real-time semi-qRT-PCR) experiments were used to determine the individual base pairs that contribute to SloR-DNA binding specificity. Solution studies indicate that Mn2+ is better than Zn2+ at specifically activating SloR to bind DNA, and yet the 2.8-Å resolved crystal structure of SloR bound to Zn2+ provides insight into the means by which selective activation by Mn2+ may be achieved and into how SloR may form specific interactions with its operator. Taken together, these experimental observations are significant because they can inform rational drug design aimed at alleviating and/or preventing S. mutans-induced caries formation. IMPORTANCE This report focuses on investigating the SloR protein as a regulator of essential metal ion transport and virulence gene expression in the oral pathogen Streptococcus mutans and on revealing the details of SloR binding to its metal ion effectors and binding to DNA that together facilitate this expression. We used molecular and biochemical approaches to characterize the interaction of SloR with Mn2+ and with its SloR recognition element to gain a clearer picture of the regulatory networks that optimize SloR-mediated metal ion homeostasis and virulence gene expression in S. mutans. These experiments can have a significant impact on caries treatment and/or prevention by revealing the S. mutans SloR-DNA binding interface as an appropriate target for the development of novel therapeutic interventions. PMID:26350131

[The influence of cardiosurgical intervention type and conditions of artificial blood circulation of perioperative dynamics of cardiac biomarkers].

PubMed

Dement'eva, I I; Morozov, Iu A; Charnaia, M A

2013-01-01

125 patients after cardiac surgery operated on with the use of artificial blood circulation (ABC) were followed-up. Blood levels of cardiac protein, binding aliphatic acids and troponin 1 and 3 days after the operation were registered. The study showed that aorta clamping more then 90 minutes and hypothermic perfusion regimen influence cardiomyocites negatively. The state of "surgical trauma" and reperfusional myocardium damage was approximately the same during aortic surgery, myocardium revascularization with the use of aortic clamping and cardioplegia, and correction of the acquired heart disease, according to the dynamics of the studied proteins in blood. The minimal blood level of cardiac protein, binding aliphatic acids after coronary by-pass surgery on the working heart witnesses about negative influence of crystalloid hypothermic cardioplegia on coronary microcirculation.

Evaluation of galectin binding by frontal affinity chromatography (FAC).

PubMed

Iwaki, Jun; Hirabayashi, Jun

2015-01-01

Frontal affinity chromatography (FAC) is a simple and versatile procedure enabling quantitative determination of diverse biological interactions in terms of dissociation constants (K d), even though these interactions are relatively weak. The method is best applied to glycans and their binding proteins, with the analytical system operating on the basis of highly reproducible isocratic elution by liquid chromatography. Its application to galectins has been successfully developed to characterize their binding specificities in detail. As a result, their minimal requirements for recognition of disaccharides, i.e., β-galactosides, as well as characteristic features of individual galectins, have been elucidated. In this chapter, we describe standard procedures to determine the K d's for interactions between a series of standard glycans and various galectins.

The ebolavirus VP24 interferon antagonist

PubMed Central

Zhang, Adrianna P.P.; Abelson, Dafna M.; Bornholdt, Zachary A.; Liu, Tong; Woods, Jr, Virgil L.; Saphire, Erica Ollmann

2012-01-01

Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways.1,2 The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation.3 A more recent discovery is that VP24 also binds STAT1 directly,4 suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses. PMID:23076242

Allosteric control of transcription in GntR family of transcription regulators: A structural overview.

PubMed

Jain, Deepti

2015-07-01

The GntR family of transcription regulators constitutes one of the most abundant family of transcription factors. These modulators are involved in a variety of mechanisms controlling various metabolic processes. GntR family members are typically two domain proteins with a smaller N-terminus domain (NTD) with conserved architecture of winged-helix-turn-helix (wHTH) for DNA binding and a larger C-terminus domain (CTD) or the effector binding domain which is also involved in oligomerization. Interestingly, the CTD shows structural heterogeneity depending upon the type of effector molecule that it binds and displays structural homology to various classes of proteins. Binding of the effector molecule to the CTD brings about a conformational change in the transcription factor such that its affinity for its cognate DNA sequence is altered. This review summarizes the structural information available on the members of GntR family and discusses the common features of the DNA binding and operator recognition within the family. The variation in the allosteric mechanism employed by the members of this family is also discussed. © 2015 International Union of Biochemistry and Molecular Biology.

Selected wheat seed defense proteins exhibit competitive binding to model microbial lipid interfaces.

PubMed

Sanders, Michael R; Clifton, Luke A; Neylon, Cameron; Frazier, Richard A; Green, Rebecca J

2013-07-17

Puroindolines (Pins) and purothionins (Pths) are basic, amphiphilic, cysteine-rich wheat proteins that play a role in plant defense against microbial pathogens. This study examined the co-adsorption and sequential addition of Pins (Pin-a, Pin-b, and a mutant form of Pin-b with Trp-44 to Arg-44 substitution) and β-purothionin (β-Pth) model anionic lipid layers using a combination of surface pressure measurements, external reflection FTIR spectroscopy, and neutron reflectometry. Results highlighted differences in the protein binding mechanisms and in the competitive binding and penetration of lipid layers between respective Pins and β-Pth. Pin-a formed a blanket-like layer of protein below the lipid surface that resulted in the reduction or inhibition of β-Pth penetration of the lipid layer. Wild-type Pin-b participated in co-operative binding with β-Pth, whereas the mutant Pin-b did not bind to the lipid layer in the presence of β-Pth. The results provide further insight into the role of hydrophobic and cationic amino acid residues in antimicrobial activity.

Comparative analysis the binding affinity of mycophenolic sodium and meprednisone with human serum albumin: Insight by NMR relaxation data and docking simulation.

PubMed

Ma, Xiaoli; He, Jiawei; Yan, Jin; Wang, Qing; Li, Hui

2016-03-25

Mycophenolic sodium is an immunosuppressive agent that is always combined administration with corticosteroid in clinical practice. Considering the distribution and side-effect of the drug may change when co-administrated drug exist, this paper comparatively analyzed the binding ability of mycophenolic sodium and meprednisone toward human serum albumin by nuclear magnetic resonance relaxation data and docking simulation. The nuclear magnetic resonance approach was based on the analysis of proton selective and non-selective relaxation rate enhancement of the ligand in the absence and presence of macromolecules. The contribution of the bound ligand fraction to the observed relaxation rate in relation to protein concentration allowed the calculation of the affinity index. This approach allowed the comparison of the binding affinity of mycophenolic sodium and meprednisone. Molecular modeling was operated to simulate the binding model of ligand and albumin through Autodock 4.2.5. Competitive binding of mycophenolic sodium and meprednisone was further conducted through fluorescence spectroscopy. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion

PubMed Central

Rui, Huan; Artigas, Pablo; Roux, Benoît

2016-01-01

The Na+/K+-pump maintains the physiological K+ and Na+ electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E1 and E2. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle. DOI: http://dx.doi.org/10.7554/eLife.16616.001 PMID:27490484

The monomeric form of Neisseria DNA mimic protein DMP19 prevents DNA from binding to the histone-like HU protein

PubMed Central

Ko, Tzu-Ping; Liao, Yi-Ting; Hsu, Kai-Cheng

2017-01-01

DNA mimicry is a direct and effective strategy by which the mimic competes with DNA for the DNA binding sites on other proteins. Until now, only about a dozen proteins have been shown to function via this strategy, including the DNA mimic protein DMP19 from Neisseria meningitides. We have shown previously that DMP19 dimer prevents the operator DNA from binding to the transcription factor NHTF. Here, we provide new evidence that DMP19 monomer can also interact with the Neisseria nucleoid-associated protein HU. Using BS3 crosslinking, gel filtration and isothermal titration calorimetry assays, we found that DMP19 uses its monomeric form to interact with the Neisseria HU dimer. Crosslinking conjugated mass spectrometry was used to investigate the binding mode of DMP19 monomer and HU dimer. Finally, an electrophoretic mobility shift assay (EMSA) confirmed that the DNA binding affinity of HU is affected by DMP19. These results showed that DMP19 is bifunctional in the gene regulation of Neisseria through its variable oligomeric forms. PMID:29220372

Saccharin and Cyclamate Inhibit Binding of Epidermal Growth Factor

NASA Astrophysics Data System (ADS)

Lee, L. S.

1981-02-01

The binding of 125I-labeled mouse epidermal growth factor (EGF) to 18 cell lines, including HeLa (human carcinoma), MDCK (dog kidney cells), HTC (rat hepatoma), K22 (rat liver), HF (human foreskin), GM17 (human skin fibroblasts), XP (human xeroderma pigmentosum fibroblasts), and 3T3-L1 (mouse fibroblasts), was inhibited by saccharin and cyclamate. The human cells were more sensitive to inhibition by these sweeteners than mouse or rat cells. EGF at doses far above the physiological levels reversed the inhibition in rodent cells but not in HeLa cells. In HeLa cells, the doses of saccharin and cyclamate needed for 50% inhibition were 3.5 and 9.3 mg/ml, respectively. Glucose, 2-deoxyglucose, sucrose, and xylitol did not inhibit EGF binding. Previous studies have shown that phorbol esters, strongly potent tumor promoters, also inhibit EGF binding to tissue culture cells. To explain the EGF binding inhibition by such greatly dissimilar molecules as phorbol esters, saccharin, and cyclamate, it is suggested that they operate through the activation of a hormone response control unit.

The ebolavirus VP24 interferon antagonist: know your enemy.

PubMed

Zhang, Adrianna P P; Abelson, Dafna M; Bornholdt, Zachary A; Liu, Tong; Woods, Virgil L; Saphire, Erica Ollmann

2012-08-15

Suppression during the early phases of the immune system often correlates directly with a fatal outcome for the host. The ebolaviruses, some of the most lethal viruses known, appear to cripple initial stages of the host defense network via multiple distinct paths. Two of the eight viral proteins are critical for immunosuppression. One of these proteins is VP35, which binds double-stranded RNA and antagonizes several antiviral signaling pathways. The other protein is VP24, which binds transporter molecules to prevent STAT1 translocation. A more recent discovery is that VP24 also binds STAT1 directly, suggesting that VP24 may operate in at least two separate branches of the interferon pathway. New crystal structures of VP24 derived from pathogenic and nonpathogenic ebolaviruses reveal its novel, pyramidal fold, upon which can be mapped sites required for virulence and for STAT1 binding. These structures of VP24, and new information about its direct binding to STAT1, provide avenues by which we may explore its many roles in the viral life cycle, and reasons for differences in pathogenesis among the ebolaviruses.

Microbubble Enzyme-Linked Immunosorbent Assay for the Detection of Targeted Microbubbles in in Vitro Static Binding Assays.

PubMed

Wischhusen, Jennifer; Padilla, Frederic

2017-07-01

Targeted microbubbles (MBs) are ultrasound contrast agents that are functionalized with a ligand for ultrasound molecular imaging of endothelial markers. Novel targeted MBs are characterized in vitro by incubation in protein-coated wells, followed by binding quantification by microscopy or ultrasound imaging. Both methods provide operator-dependent results: Between 3 and 20 fields of view from a heterogeneous sample are typically selected for analysis by microscopy, and in ultrasound imaging, different acoustic settings affect signal intensities. This study proposes a new method to reproducibly quantify MB binding based on enzyme-linked immunosorbent assay (ELISA), in which bound MBs are revealed with an enzyme-linked antibody. MB-ELISA was adapted to in vitro static binding assays, incubating the MBs in inverted position or by agitation, and compared with microscopy. The specificity and sensitivity of MB-ELISA enable the reliable quantification of MB binding in a rapid, high-throughput and whole-well analysis, facilitating the characterization of new targeted contrast agents. Copyright © 2017 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Light-induced carotenogenesis in Myxococcus xanthus: evidence that CarS acts as an anti-repressor of CarA.

PubMed

Whitworth, D E; Hodgson, D A

2001-11-01

In the bacterium Myxococcus xanthus, carotenoids are produced in response to illumination, as a result of expression of the crt carotenoid biosynthesis genes. The majority of crt genes are clustered in the crtEBDC operon, which is repressed in the dark by CarA. Genetic data suggest that, in the light, CarS is synthesized and achieves activation of the crtEBDC operon by removing the repressive action of CarA. As CarS contains no known DNA-binding motif, the relief of CarA-mediated repression was postulated to result from a direct interaction between these two proteins. Use of the yeast two-hybrid system demonstrated direct interaction between CarA and CarS. The two-hybrid system also implied that CarA and, possibly, CarS are capable of homodimerization. Direct evidence for CarS anti-repressor action was provided in vitro. A glutathione S-transferase (GST)-CarA protein fusion was shown to bind specifically to a palindromic operator sequence within the crtEBDC promoter. CarA was prevented from binding to its operator, and prebound CarA was removed by the addition of purified CarS. CarS is therefore an anti-repressor.

Purification and DNA-binding properties of the cro-type regulatory repressor protein cng encoded by the Lactobacillus plantarum phage phi g1e.

PubMed

Kakikawa, M; Ohkubo, S; Sakate, T; Sayama, M; Taketo, A; Kodaira, K

2000-05-16

The putative repressor protein Cng (10kDa on an SDS gel) for the lytic pathway of Lactobacillus plantarum phage φg1e was purified using the Escherichia coli Pt7 system, and its DNA-binding ability for the seven operator-like sequences, the GATAC-boxes (Gb1 to Gb7), was investigated in vitro. In gel-shift assays, Cng selectively bound to the DNA fragments containing the GATAC-box(es). In addition, DNase I footprinting analysis with supercoiled DNA demonstrated that Cng can specifically cover about a 25bp region centered around each of the GATAC-boxes, although two boxes, Gb4 and Gb6, were only partially protected. Moreover, protein crosslinking experiments using glutaraldehyde suggested that Cng most likely functions as a dimer. On the other hand, the binding ability of Cpg for the GATAC-boxes in supercoiled DNA was also examined under the same conditions as in Cng; unlike Cng, Cpg covered Gb4 and Gb6 completely sufficiently as well as the other five boxes. Thus, the present and previous [Kakikawa et al., Gene 215 (1998) 371-379; 242 (2000) 155-166] results indicate a possibility that the two proteins Cng and Cpg selectively bind to the GATAC-boxes that act as operators, and can decide between the lytic or lysogenic pathways through repression of the promoter activity of P(R) as well as P(L).

Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

PubMed Central

Gillard, Nathalie; Goffinont, Stephane; Buré, Corinne; Davidkova, Marie; Maurizot, Jean-Claude; Cadene, Martine; Spotheim-Maurizot, Melanie

2007-01-01

Understanding the cellular effects of radiation-induced oxidation requires the unravelling of key molecular events, particularly damage to proteins with important cellular functions. The Escherichia coli lactose operon is a classical model of gene regulation systems. Its functional mechanism involves the specific binding of a protein, the repressor, to a specific DNA sequence, the operator. We have shown previously that upon irradiation with γ-rays in solution, the repressor loses its ability to bind the operator. Water radiolysis generates hydroxyl radicals (OH· radicals) which attack the protein. Damage of the repressor DNA-binding domain, called the headpiece, is most likely to be responsible of this loss of function. Using CD, fluorescence spectroscopy and a combination of proteolytic cleavage with MS, we have examined the state of the irradiated headpiece. CD measurements revealed a dose-dependent conformational change involving metastable intermediate states. Fluorescence measurements showed a gradual degradation of tyrosine residues. MS was used to count the number of oxidations in different regions of the headpiece and to narrow down the parts of the sequence bearing oxidized residues. By calculating the relative probabilities of reaction of each amino acid with OH· radicals, we can predict the most probable oxidation targets. By comparing the experimental results with the predictions we conclude that Tyr7, Tyr12, Tyr17, Met42 and Tyr47 are the most likely hotspots of oxidation. The loss of repressor function is thus correlated with chemical modifications and conformational changes of the headpiece. PMID:17263689

Identification of thyroid hormone receptor binding sites and target genes using ChIP-on-chip in developing mouse cerebellum.

PubMed

Dong, Hongyan; Yauk, Carole L; Rowan-Carroll, Andrea; You, Seo-Hee; Zoeller, R Thomas; Lambert, Iain; Wade, Michael G

2009-01-01

Thyroid hormone (TH) is critical to normal brain development, but the mechanisms operating in this process are poorly understood. We used chromatin immunoprecipitation to enrich regions of DNA bound to thyroid receptor beta (TRbeta) of mouse cerebellum sampled on post natal day 15. Enriched target was hybridized to promoter microarrays (ChIP-on-chip) spanning -8 kb to +2 kb of the transcription start site (TSS) of 5000 genes. We identified 91 genes with TR binding sites. Roughly half of the sites were located in introns, while 30% were located within 1 kb upstream (5') of the TSS. Of these genes, 83 with known function included genes involved in apoptosis, neurodevelopment, metabolism and signal transduction. Two genes, MBP and CD44, are known to contain TREs, providing validation of the system. This is the first report of TR binding for 81 of these genes. ChIP-on-chip results were confirmed for 10 of the 13 binding fragments using ChIP-PCR. The expression of 4 novel TH target genes was found to be correlated with TH levels in hyper/hypothyroid animals providing further support for TR binding. A TRbeta binding site upstream of the coding region of myelin associated glycoprotein was demonstrated to be TH-responsive using a luciferase expression system. Motif searches did not identify any classic binding elements, indicating that not all TR binding sites conform to variations of the classic form. These findings provide mechanistic insight into impaired neurodevelopment resulting from TH deficiency and a rich bioinformatics resource for developing a better understanding of TR binding.

Architecture of a Fur Binding Site: a Comparative Analysis

PubMed Central

Lavrrar, Jennifer L.; McIntosh, Mark A.

2003-01-01

Fur is an iron-binding transcriptional repressor that recognizes a 19-bp consensus site of the sequence 5′-GATAATGATAATCATTATC-3′. This site can be defined as three adjacent hexamers of the sequence 5′-GATAAT-3′, with the third being slightly imperfect (an F-F-F configuration), or as two hexamers in the forward orientation separated by one base pair from a third hexamer in the reverse orientation (an F-F-x-R configuration). Although Fur can bind synthetic DNA sequences containing the F-F-F arrangement, most natural binding sites are variations of the F-F-x-R arrangement. The studies presented here compared the ability of Fur to recognize synthetic DNA sequences containing two to four adjacent hexamers with binding to sequences containing variations of the F-F-x-R arrangement (including natural operator sequences from the entS and fepB promoter regions of Escherichia coli). Gel retardation assays showed that the F-F-x-R architecture was necessary for high-affinity Fur-DNA interactions and that contiguous hexamers were not recognized as effectively. In addition, the stoichiometry of Fur at each binding site was determined, showing that Fur interacted with its minimal 19-bp binding site as two overlapping dimers. These data confirm the proposed overlapping-dimer binding model, where the unit of interaction with a single Fur dimer is two inverted hexamers separated by a C:G base pair, with two overlapping units comprising the 19-bp consensus binding site required for the high-affinity interaction with two Fur dimers. PMID:12644489

Bone sialoprotein-collagen interaction promotes hydroxyapatite nucleation.

PubMed

Baht, Gurpreet S; Hunter, Graeme K; Goldberg, Harvey A

2008-09-01

In bone, hydroxyapatite (HA) crystals are deposited onto the type I collagen scaffold by a mechanism that has yet to be elucidated. Bone sialoprotein (BSP) is an acidic phosphoprotein that is expressed at high levels in mineralized tissues, capable of binding type I collagen, and nucleating HA. Both bone-extracted and recombinant BSP (rBSP) bind with equal affinity to collagen. The nature of the BSP-collagen interaction and its role in HA nucleation are not known. We have used a solid-phase binding assay and affinity chromatography to characterize the BSP-collagen interaction. rBSP-binding affinities of triple-helical and fibrillar type I collagen were similar (K(D) approximately 13 nM), while that of heat-denatured type I collagen was lower (K(D) approximately 44 nM), indicating the importance of triple-helical structure in binding BSP. Pepsin treatment of collagen had no effect on rBSP binding, demonstrating that the telopeptides of collagen are not involved. The majority of collagen-bound rBSP was eluted by acetonitrile, indicating that hydrophobic interactions are principally responsible for binding. Using an HA-nucleation assay, it was shown that rBSP is ten-fold more potent in reconstituted fibrillar collagen gels than in agarose gels. Nucleating potency of a non-collagen-binding, HA-nucleating peptide [rBSP(134-206)] showed no difference in the two gel systems. The work here shows that optimal binding of rBSP requires collagen to be in a native, triple-helical structure, does not require the telopeptides, and is stabilized by hydrophobic interactions. Upon binding to collagen, rBSP displays an increase in nucleation potency, implying a co-operative effect of BSP and collagen in mineral formation.

Antigenic modulation of the cytophilic binding of guinea-pig IgG and IgM antibodies to homologous macrophages.

PubMed Central

Webster, R O; Lawrence, D A

1979-01-01

The cytophilic binding of immune complexes by peritoneal exudate cells (PEC) from adjuvant-stimulated guinea-pigs was studied using 125I-labelled guinea-pig IgG1, IgG2 and IgM antibodies to the dinitrophenyl (DNP) group. The influence of hapten density upon cytophilic activity was studied by the addition of DNP-conjugated antigens to antibody in 2-200 molar ratios of DNP:antibody. Only IgG2 binding was enhanced by immune complex formation, and the increased binding of IgG2 anti-DNP was dependent on the number of DNP determinants per antigen molecule. Cytophilic activity with epsilon-DNP-L-lysine (DNP-LYS), alpha,epsilon-di-DNP-L-lysine (DNP-LYS-DNP), or DNP1-8-BSA was no greater than that seen in the absence of hapten. Increased cytophilic binding was noted only with DNP20-41-BSA. The binding of IgG2 and IgG2 anti-DNP:DNP-bovine serum albumin (BSA) complexes was inhibited by monomeric IgG2. The relative cytophilic capacities of guinea-pig immunoglobulins appeared as follows: IgG greater than IgG1 greater than IgM. IgG1 and IgM binding of DNP conjugates did not enhance their cytophilic activity; therefore, IgG1 and IgM cytophilic binding to PEC was considered biologically insignificant. This investigation provides further evidence that cytophilic binding of immune complexes to macrophages is due to the co-operative action of multiple Fc sites rather than a conformational change in the IgG2 antibodies, and serum proteins, notably complement components, can alter the binding and/or phagocytosis of IgG2 anti-DNP:DNP-BSA complexes. PMID:86509

SB265610 is an allosteric, inverse agonist at the human CXCR2 receptor

PubMed Central

Bradley, ME; Bond, ME; Manini, J; Brown, Z; Charlton, SJ

2009-01-01

Background and purpose: In several previous studies, the C-X-C chemokine receptor (CXCR)2 antagonist 1-(2-bromo-phenyl)-3-(7-cyano-3H-benzotriazol-4-yl)-urea (SB265610) has been described as binding competitively with the endogenous agonist. This is in contrast to many other chemokine receptor antagonists, where the mechanism of antagonism has been described as allosteric. Experimental approach: To determine whether it displays a unique mechanism among the chemokine receptor antagonists, the mode of action of SB265610 was investigated at the CXCR2 receptor using radioligand and [35S]-GTPγS binding approaches in addition to chemotaxis of human neutrophils. Key results: In equilibrium saturation binding studies, SB265610 depressed the maximal binding of [125I]-interleukin-8 ([125I]-IL-8) without affecting the Kd. In contrast, IL-8 was unable to prevent binding of [3H]-SB265610. Kinetic binding experiments demonstrated that this was not an artefact of irreversible or slowly reversible binding. In functional experiments, SB265610 caused a rightward shift of the concentration-response curves to IL-8 and growth-related oncogene α, but also a reduction in maximal response elicited by each agonist. Fitting these data to an operational allosteric ternary complex model suggested that, once bound, SB265610 completely blocks receptor activation. SB265610 also inhibited basal [35S]-GTPγS binding in this preparation. Conclusions and implications: Taken together, these data suggest that SB265610 behaves as an allosteric inverse agonist at the CXCR2 receptor, binding at a region distinct from the agonist binding site to prevent receptor activation, possibly by interfering with G protein coupling. PMID:19422399

The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

PubMed

Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi

2016-01-01

The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

Early-developmental stress, repeatability, and canalization in a suite of physiological and behavioral traits in female zebra finches.

PubMed

Careau, Vincent; Buttemer, William A; Buchanan, Katherine L

2014-10-01

Adaptive developmental plasticity allows individuals experiencing poor environmental conditions in early life to adjust their life-history strategy in order to prioritize short-term fitness benefits and maximize reproductive output in challenging environments. Much research has been conducted to test whether such adoption of a "faster" life-history strategy is accompanied by concordant changes in behavior and physiology, with mixed results. As research in this field has focused on comparison of mean-level responses of treatment groups, few studies include repeated measures of response variables and the effect that developmental stress may have on repeatability per se. We investigated how early-developmental stress affects the mean expression of (and repeatability in) a variety of behavioral and physiological traits in female zebra finches. We predicted that: (1) individuals subjected to nutritional restriction in the nestling phase would have higher feeding and activity rates, with associated increases in hematocrit and basal metabolic rates (BMRs), (2) nutritional restriction in early life would alter adults' stress-induced corticosterone level, and (3) developmental stress would, respectively, influence the amount of among-individual and within-individual variation in behavioral and physiological traits, hence affecting the repeatability of these traits. In comparison to control females, stressed females did not differ in activity rate or stress-induced corticosterone level, but they did have higher levels of feeding, hematocrit, and BMR. Among-individual variance and repeatability were generally higher in stressed females than in controls. Finally, we found that developmental dietary restriction significantly reduced the amount of within-individual variance both in activity rate in the novel environment and in stress-induced corticosterone level. Our results not only confirm previous findings on the effect of early-developmental stress on BMR, but also extend its effect to feeding rate and hematocrit, suggesting that developmental plasticity in these traits is ontogenetically linked. Early-developmental stress may disable particular genetic canalizing processes, which would release cryptic genetic variation and explain why repeatability and among-individual variance were generally higher in the stressed groups than in controls. For activity rate in the novel environment and with stress-induced corticosterone level, however, early-developmental stress significantly reduced within-individual variance, which may be a consequence of increased canalization of these traits at the micro-environmental level. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Nutrition in advanced age: dietary assessment in the Newcastle 85+ study.

PubMed

Adamson, A J; Collerton, J; Davies, K; Foster, E; Jagger, C; Stamp, E; Mathers, J C; Kirkwood, T

2009-02-01

Assessing food choice and/or nutrient intake in older people, particularly the oldest old (85 years and over), presents particular challenges. In some cases the respondent may have little or no involvement in food acquisition or preparation, in others, cognitive/memory impairment may restrict the ability to recall intake, or physical limitations may affect the ability to record intake. The assessment may therefore need to involve whoever provides care for the older person, of whom there may be more than one. For these reasons, there is a need for validated methods for dietary assessment in large populations within this age range. The need is particularly acute in view of the secular increase in the numbers of older people and the interest in the role of nutrition in maintaining health and ameliorating age-related decline. This paper describes a comparison of two different methods of dietary assessment within the Newcastle 85+ Study; a UK cohort study of health and ageing in the oldest old. Two methods, the food frequency questionnaire (FFQ) (based on broad recall of the previous 12 months intake) and the repeated multiple pass recall (MPR) tool (based on detailed recall of the previous day's intake on two separate occasions), were applied in two different groups of approximately 85 individuals aged 85 years. FFQ data were collected during a pilot study conducted between 2003 and 2004, MPR data were collected in the main Newcastle study in 2006. Relative validity was measured by calculation of the ratio of reported energy intake to estimated basal metabolic rate (EI/BMR) and by comparison with dietary intakes reported for subjects of similar age in the UK National Diet and Nutrition Survey. EI/BMR ratios for MPR were 1.56 and 1.39 for men and women, respectively, and for FFQ were 2.18 and 2.14. The FFQ was found to overestimate energy and nutrient intake considerably. The MPR gave more realistic estimates of energy and nutrient intakes, and was found to be acceptable for use in this population group. However, use of this tool required greater investigator (nurse) time, extra resources for training and quality assurance and additional time and expertise in data processing. In the Newcastle 85+ Study, where the overall aims include detailed investigation of diet in relation to many variables describing biological, clinical and psychosocial status, we concluded that MPR was the preferable method, although there remains a need for non-subjective methods for assessing dietary intake, that is, biomarker approaches, which can give a comprehensive and objective assessment of dietary exposure.

Spontaneous activity responses to exercise in males and females.

PubMed

McLaughlin, R; Malkova, D; Nimmo, M A

2006-09-01

This study examines the impact of a short-term exercise programme, prescribed on the basis of current exercise recommendations, on energy balance in males and females to assess whether this type of exercise induces compensatory changes in spontaneous activity energy expenditure (SAEE) and energy intake (EI). Individuals were monitored for 16 days, 8 days of habitual physical activity (C) and 8 days when exercise was imposed (E). Total energy expenditure (TEE) was calculated from individual relationships of VO2 and VCO2 to heart rate (HR) records of HR and physical activity obtained during waking hours of the C and E periods and basal metabolic rate (BMR) measurements (Deltatrac System, Datex Instrumentation). Changes in nude body mass (BM) were estimated by using a digital scale (Sartorius AG, Gottigen, Germany). Laboratory and free-living. Eight lean females (body fat: 17.5+/-4.5%) and eight males of similar percentage body fat participated in this study. All subjects were Caucasian and aged between 20 and 25 years. During the E period, a supervised exercise session was conducted every second day, each consisting of a total net energy expenditure of 2092 kJ+BMR at 90% lactate threshold. During the E period, TEE was higher than C in males and females (exercise: 95.2+/-13.9, 78.3+/-15.9 MJ; control: 82.4+/-10.4, 68.8+/-16.7 MJ, respectively; P<0.00; P=0.02). SAEE, calculated as TEE minus the energy expended during exercise, was not significantly different between C (males: 82.4+/-4.8 MJ; females: 68.8+/-7.6 MJ) and E (males: 86.8+/-6.3 MJ; females: 70.0+/-7.2 MJ) periods in either gender. Males showed no change in BM over the C (pre-intervention: 83.4+/-7.2 kg; post-intervention: 83.1+/-6.8 kg) or E (pre-intervention: 83.4+/-6.8 kg; post-intervention: 83.4+/-6.8 kg) periods. Females' BM over the C period did not alter (pre-intervention: 63.3+/-2.8 kg; post-intervention 63.7+/-3.1 kg); however, there was a significant decrease (P<0.00) in BM over the E period (pre-intervention: 63.0+/-2.7 kg; post-intervention: 62.4+/-2.7 kg). The exercise programme was achieved in males and females without any impact on SAEE. Therefore, differences between genders in relation to BM reduction can be explained by differences in the EI response to exercise. Published online 22 February 2006.

1-3-A Resolution Structure of Human Glutathione S-Transferase With S-Hexyl Glutathione Bound Reveals Possible Extended Ligandin Binding Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trong, I.Le; Stenkamp, R.E.; Ibarra, C.

2005-08-22

Cytosolic glutathione S-transferases (GSTs) play a critical role in xenobiotic binding and metabolism, as well as in modulation of oxidative stress. Here, the high-resolution X-ray crystal structures of homodimeric human GSTA1-1 in the apo form and in complex with S-hexyl glutathione (two data sets) are reported at 1.8, 1.5, and 1.3A respectively. At this level of resolution, distinct conformations of the alkyl chain of S-hexyl glutathione are observed, reflecting the nonspecific nature of the hydrophobic substrate binding site (H-site). Also, an extensive network of ordered water, including 75 discrete solvent molecules, traverses the open subunit-subunit interface and connects the glutathionemore » binding sites in each subunit. In the highest-resolution structure, three glycerol moieties lie within this network and directly connect the amino termini of the glutathione molecules. A search for ligand binding sites with the docking program Molecular Operating Environment identified the ordered water network binding site, lined mainly with hydrophobic residues, suggesting an extended ligand binding surface for nonsubstrate ligands, the so-called ligandin site. Finally, detailed comparison of the structures reported here with previously published X-ray structures reveal a possible reaction coordinate for ligand-dependent conformational changes in the active site and the C-terminus.« less

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

Development of operational models of receptor activation including constitutive receptor activity and their use to determine the efficacy of the chemokine CCL17 at the CC chemokine receptor CCR4.

PubMed

Slack, R J; Hall, D A

2012-07-01

BACKGROUND AND PURPOSE The operational model provides a key conceptual framework for the analysis of pharmacological data. However, this model does not include constitutive receptor activity, a frequent phenomenon in modern pharmacology, particularly in recombinant systems. Here, we developed extensions of the operational model which include constitutive activity and applied them to effects of agonists at the chemokine receptor CCR4. EXPERIMENTAL APPROACH The effects of agonists of CCR4 on [(35) S]GTPγS binding to recombinant cell membranes and on the filamentous (F-) actin content of human CD4(+) CCR4(+) T cells were determined. The basal [(35) S]GTPγS binding was changed by varying the GDP concentration whilst the basal F-actin contents of the higher expressing T cell populations were elevated, suggesting constitutive activity of CCR4. Both sets of data were analysed using the mathematical models. RESULTS The affinity of CCL17 (also known as TARC) derived from analysis of the T cell data (pK(a) = 9.61 ± 0.17) was consistent with radioligand binding experiments (9.50 ± 0.11) while that from the [(35) S]GTPγS binding experiments was lower (8.27 ± 0.09). Its intrinsic efficacy differed between the two systems (110 in T cells vs. 11). CONCLUSIONS AND IMPLICATIONS The presence of constitutive receptor activity allows the absolute intrinsic efficacy of agonists to be determined without a contribution from the signal transduction system. Intrinsic efficacy estimated in this way is consistent with Furchgott's definition of this property. CCL17 may have a higher intrinsic efficacy at CCR4 in human T cells than that expressed recombinantly in CHO cells. © 2012 GSK Services Unlimited. British Journal of Pharmacology © 2012 The British Pharmacological Society.

Functional asymmetry in the lysyl-tRNA synthetase explored by molecular dynamics, free energy calculations and experiment

PubMed Central

Hughes, Samantha J; Tanner, Julian A; Hindley, Alison D; Miller, Andrew D; Gould, Ian R

2003-01-01

Background Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. Results Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. Conclusions The asymmetry uncovered here appears to be a common feature of oligomeric aminoacyl-tRNA synthetases, and may play an important functional role. We suggest a manner in which catalytic efficiency could be improved by LysU operating in an alternating sites mechanism. PMID:12787471

The role of criteria in design and management of space systems

NASA Technical Reports Server (NTRS)

Blair, J. C.; Ryan, R. S.

1992-01-01

Explicit requirements and standards arising in connection with space systems management serve as a framework for technical management and furnish legally binding control of development, verification, and operations. As a project develops, additional requirements are derived which are unique to the system in question; these are designated 'derived requirements'. The reliability and cost-effectiveness of a space system are best ensured where a balance has arisen between formal (legally binding) and informal. Attention is presently given to the development of criteria consistent with total quality management.

Discovery of d-amino acid oxidase inhibitors based on virtual screening against the lid-open enzyme conformation.

PubMed

Szilágyi, Bence; Skok, Žiga; Rácz, Anita; Frlan, Rok; Ferenczy, György G; Ilaš, Janez; Keserű, György M

2018-06-01

d-Amino acid oxidase (DAAO) inhibitors are typically small polar compounds with often suboptimal pharmacokinetic properties. Features of the native binding site limit the operational freedom of further medicinal chemistry efforts. We therefore initiated a structure based virtual screening campaign based on the X-ray structures of DAAO complexes where larger ligands shifted the loop (lid opening) covering the native binding site. The virtual screening of our in-house collection followed by the in vitro test of the best ranked compounds led to the identification of a new scaffold with micromolar IC 50 . Subsequent SAR explorations enabled us to identify submicromolar inhibitors. Docking studies supported by in vitro activity measurements suggest that compounds bind to the active site with a salt-bridge characteristic to DAAO inhibitor binding. In addition, displacement of and interaction with the loop covering the active site contributes significantly to the activity of the most potent compounds. Copyright © 2018 Elsevier Ltd. All rights reserved.

Multiple Ion Binding Equilibria, Reaction Kinetics, and Thermodynamics in Dynamic Models of Biochemical Pathways

PubMed Central

Vinnakota, Kalyan C.; Wu, Fan; Kushmerick, Martin J.; Beard, Daniel A.

2009-01-01

The operation of biochemical systems in vivo and in vitro is strongly influenced by complex interactions between biochemical reactants and ions such as H+, Mg2+, K+, and Ca2+. These are important second messengers in metabolic and signaling pathways that directly influence the kinetics and thermodynamics of biochemical systems. Herein we describe the biophysical theory and computational methods to account for multiple ion binding to biochemical reactants and demonstrate the crucial effects of ion binding on biochemical reaction kinetics and thermodynamics. In simulations of realistic systems, the concentrations of these ions change with time due to dynamic buffering and competitive binding. In turn, the effective thermodynamic properties vary as functions of cation concentrations and important environmental variables such as temperature and overall ionic strength. Physically realistic simulations of biochemical systems require incorporating all of these phenomena into a coherent mathematical description. Several applications to physiological systems are demonstrated based on this coherent simulation framework. PMID:19216922

Lis1 acts as a "clutch" between the ATPase and microtubule-binding domains of the dynein motor.

PubMed

Huang, Julie; Roberts, Anthony J; Leschziner, Andres E; Reck-Peterson, Samara L

2012-08-31

The lissencephaly protein Lis1 has been reported to regulate the mechanical behavior of cytoplasmic dynein, the primary minus-end-directed microtubule motor. However, the regulatory mechanism remains poorly understood. Here, we address this issue using purified proteins from Saccharomyces cerevisiae and a combination of techniques, including single-molecule imaging and single-particle electron microscopy. We show that rather than binding to the main ATPase site within dynein's AAA+ ring or its microtubule-binding stalk directly, Lis1 engages the interface between these elements. Lis1 causes individual dynein motors to remain attached to microtubules for extended periods, even during cycles of ATP hydrolysis that would canonically induce detachment. Thus, Lis1 operates like a "clutch" that prevents dynein's ATPase domain from transmitting a detachment signal to its track-binding domain. We discuss how these findings provide a conserved mechanism for dynein functions in living cells that require prolonged microtubule attachments. Copyright © 2012 Elsevier Inc. All rights reserved.

The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic.

PubMed

Walbott, Hélène; Machado-Pinilla, Rosario; Liger, Dominique; Blaud, Magali; Réty, Stéphane; Grozdanov, Petar N; Godin, Kate; van Tilbeurgh, Herman; Varani, Gabriele; Meier, U Thomas; Leulliot, Nicolas

2011-11-15

SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA-protein-binding sites to achieve a specific protein-protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins.

The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic

PubMed Central

Walbott, Hélène; Machado-Pinilla, Rosario; Liger, Dominique; Blaud, Magali; Réty, Stéphane; Grozdanov, Petar N.; Godin, Kate; van Tilbeurgh, Herman; Varani, Gabriele; Meier, U. Thomas; Leulliot, Nicolas

2011-01-01

SHQ1 is an essential assembly factor for H/ACA ribonucleoproteins (RNPs) required for ribosome biogenesis, pre-mRNA splicing, and telomere maintenance. SHQ1 binds dyskerin/NAP57, the catalytic subunit of human H/ACA RNPs, and this interaction is modulated by mutations causing X-linked dyskeratosis congenita. We report the crystal structure of the C-terminal domain of yeast SHQ1, Shq1p, and its complex with yeast dyskerin/NAP57, Cbf5p, lacking its catalytic domain. The C-terminal domain of Shq1p interacts with the RNA-binding domain of Cbf5p and, through structural mimicry, uses the RNA–protein-binding sites to achieve a specific protein–protein interface. We propose that Shq1p operates as a Cbf5p chaperone during RNP assembly by acting as an RNA placeholder, thereby preventing Cbf5p from nonspecific RNA binding before association with an H/ACA RNA and the other core RNP proteins. PMID:22085966

Lis1 Acts as a “Clutch” between the ATPase and Microtubule-Binding Domains of the Dynein Motor

PubMed Central

Huang, Julie; Roberts, Anthony J.; Leschziner, Andres E.; Reck-Peterson, Samara L.

2012-01-01

Summary The lissencephaly protein Lis1 has been reported to regulate the mechanical behavior of cytoplasmic dynein, the primary minus-end-directed microtubule motor. However, the regulatory mechanism remains poorly understood. Here, we address this issue using purified proteins from Saccharomyces cerevisiae and a combination of techniques, including single-molecule imaging and single-particle electron microscopy. We show that rather than binding to the main ATPase site within dynein's AAA+ ring or its microtubule-binding stalk directly, Lis1 engages the interface between these elements. Lis1 causes individual dynein motors to remain attached to microtubules for extended periods, even during cycles of ATP hydrolysis that would canonically induce detachment. Thus, Lis1 operates like a “clutch” that prevents dynein's ATPase domain from transmitting a detachment signal to its track-binding domain. We discuss how these findings provide a conserved mechanism for dynein functions in living cells that require prolonged microtubule attachments. PMID:22939623

Evaluation of a novel virtual screening strategy using receptor decoy binding sites.

PubMed

Patel, Hershna; Kukol, Andreas

2016-08-23

Virtual screening is used in biomedical research to predict the binding affinity of a large set of small organic molecules to protein receptor targets. This report shows the development and evaluation of a novel yet straightforward attempt to improve this ranking in receptor-based molecular docking using a receptor-decoy strategy. This strategy includes defining a decoy binding site on the receptor and adjusting the ranking of the true binding-site virtual screen based on the decoy-site screen. The results show that by docking against a receptor-decoy site with Autodock Vina, improved Receiver Operator Characteristic Enrichment (ROCE) was achieved for 5 out of fifteen receptor targets investigated, when up to 15 % of a decoy site rank list was considered. No improved enrichment was seen for 7 targets, while for 3 targets the ROCE was reduced. The extent to which this strategy can effectively improve ligand prediction is dependent on the target receptor investigated.

Unraveling the B. pseudomallei Heptokinase WcbL: From Structure to Drug Discovery

PubMed Central

Vivoli, Mirella; Isupov, Michail N.; Nicholas, Rebecca; Hill, Andrew; Scott, Andrew E.; Kosma, Paul; Prior, Joann L.; Harmer, Nicholas J.

2015-01-01

Summary Gram-negative bacteria utilize heptoses as part of their repertoire of extracellular polysaccharide virulence determinants. Disruption of heptose biosynthesis offers an attractive target for novel antimicrobials. A critical step in the synthesis of heptoses is their 1-O phosphorylation, mediated by kinases such as HldE or WcbL. Here, we present the structure of WcbL from Burkholderia pseudomallei. We report that WcbL operates through a sequential ordered Bi-Bi mechanism, loading the heptose first and then ATP. We show that dimeric WcbL binds ATP anti-cooperatively in the absence of heptose, and cooperatively in its presence. Modeling of WcbL suggests that heptose binding causes an elegant switch in the hydrogen-bonding network, facilitating the binding of a second ATP molecule. Finally, we screened a library of drug-like fragments, identifying hits that potently inhibit WcbL. Our results provide a novel mechanism for control of substrate binding and emphasize WcbL as an attractive anti-microbial target for Gram-negative bacteria. PMID:26687481

Convection, diffusion and reaction in a surface-based biosensor: modeling of cooperativity and binding site competition on the surface and in the hydrogel.

PubMed

Lebedev, Konstantin; Mafé, Salvador; Stroeve, Pieter

2006-04-15

We study theoretically the transport and kinetic processes underlying the operation of a biosensor (particularly the surface plasmon sensor "Biacore") used to study the surface binding kinetics of biomolecules in solution to immobilized receptors. Unlike previous studies, we concentrate mainly on the modeling of system-specific phenomena rather than on the influence of mass transport limitations on the intrinsic kinetic rate constants determined from binding data. In the first problem, the case of two-site binding where each receptor unit on the surface can accommodate two analyte molecules on two different sites is considered. One analyte molecule always binds first to a specific site. Subsequently, the second analyte molecule can bind to the adjacent unoccupied site. In the second problem, two different analytes compete for one binding site on the same surface receptor. Finally, the third problem considers the case of positive cooperativity among bound molecules in the hydrogel using a simple mean-field approach. The transport in both the flow channel and the hydrogel phases of the biosensor is taken into account in this case (with few exceptions, most previous studies assume a simpler model in which the hydrogel is treated as a planar surface with the receptors). We consider simultaneously diffusion and convection through the flow channel together with diffusion and cooperativity binding on the surface and in the hydrogel. In each case, typical results for the concentration contours of the free and bound molecules in the flow channel and hydrogel regions are presented together with the time-dependent association/dissociation curves and reaction rates. For binding site competition, the analysis predicts overshoot phenomena.

Gold Binding by Native and Chemically Modified Hops Biomasses

PubMed Central

López, M. Laura; Peralta-Videa, J. R.; de la Rosa, G.; Armendáriz, V.; Herrera, I.; Troiani, H.; Henning, J.

2005-01-01

Heavy metals from mining, smelting operations and other industrial processing facilities pollute wastewaters worldwide. Extraction of metals from industrial effluents has been widely studied due to the economic advantages and the relative ease of technical implementation. Consequently, the search for new and improved methodologies for the recovery of gold has increased. In this particular research, the use of cone hops biomass (Humulus lupulus) was investigated as a new option for gold recovery. The results showed that the gold binding to native hops biomass was pH dependent from pH 2 to pH 6, with a maximum percentage binding at pH 3. Time dependency studies demonstrated that Au(III) binding to native and modified cone hops biomasses was found to be time independent at pH 2 while at pH 5, it was time dependent. Capacity experiments demonstrated that at pH 2, esterified hops biomass bound 33.4 mg Au/g of biomass, while native and hydrolyzed hops biomasses bound 28.2 and 12.0 mg Au/g of biomass, respectively. However, at pH 5 the binding capacities were 38.9, 37.8 and 11.4 mg of Au per gram of native, esterified and hydrolyzed hops biomasses, respectively. PMID:18365087

Mapping the signal peptide binding and oligomer contact sites of the core subunit of the pea twin arginine protein translocase.

PubMed

Ma, Xianyue; Cline, Kenneth

2013-03-01

Twin arginine translocation (Tat) systems of thylakoid and bacterial membranes transport folded proteins using the proton gradient as the sole energy source. Tat substrates have hydrophobic signal peptides with an essential twin arginine (RR) recognition motif. The multispanning cpTatC plays a central role in Tat operation: It binds the signal peptide, directs translocase assembly, and may facilitate translocation. An in vitro assay with pea (Pisum sativum) chloroplasts was developed to conduct mutagenesis and analysis of cpTatC functions. Ala scanning mutagenesis identified mutants defective in substrate binding and receptor complex assembly. Mutations in the N terminus (S1) and first stromal loop (S2) caused specific defects in signal peptide recognition. Cys matching between substrate and imported cpTatC confirmed that S1 and S2 directly and specifically bind the RR proximal region of the signal peptide. Mutations in four lumen-proximal regions of cpTatC were defective in receptor complex assembly. Copurification and Cys matching analyses suggest that several of the lumen proximal regions may be important for cpTatC-cpTatC interactions. Surprisingly, RR binding domains of adjacent cpTatCs directed strong cpTatC-cpTatC cross-linking. This suggests clustering of binding sites on the multivalent receptor complex and explains the ability of Tat to transport cross-linked multimers. Transport of substrate proteins cross-linked to the signal peptide binding site tentatively identified mutants impaired in the translocation step.

Evidence for a kinetic heterogeneity in ligand binding to R-state haemoglobin Kempsey [Asp-G1(99) beta----Asn].

PubMed Central

Coletta, M; Brittain, T; Brunori, M

1986-01-01

Thermodynamic and kinetic properties of O2 and CO binding to haemoglobin (Hb) Kempsey [Asp-G1(99) beta----Asn] were investigated and the activation parameters for the two ligands were determined. At every temperature the O2-binding isotherms display a weak co-operativity, n ranging between 1.1 and 1.2, and dissociation kinetics show a single-exponential behaviour. O2-binding kinetics were studied at 25 degrees C by temperature jump and are characterized at each saturation (from Y = 0.31 to Y = 1.0) by two processes, a fast bimolecular one and a slow monomolecular one (tau -1 = 20 s-1), which contributes to approx. 30% of the whole relaxation amplitude at every Y. CO-binding kinetics to Hb Kempsey were followed at several temperatures by flash photolysis and stopped flow. The process is biphasic, as reported elsewhere [Bunn, Wohl, Bradley, Cooley & Gibson (1974) J. Biol. Chem. 249, 7402-7409], and the relative contributions of the two bimolecular rates to the whole process are only slightly affected by temperature. On taking account for the fraction of dimers at every protein concentration, the slow phase corresponds to approx. 50% of the ligand binding to tetramers. Correlation of these results with previous spectroscopic data leads to the hypothesis that the biphasic time course of CO binding may be attributed to alpha/beta heterogeneity of the R-state of tetrameric Hb Kempsey. PMID:3800943

Specific binding of PCBP1 to heavily oxidized RNA to induce cell death.

PubMed

Ishii, Takashi; Hayakawa, Hiroshi; Igawa, Tatsuhiro; Sekiguchi, Takeshi; Sekiguchi, Mutsuo

2018-06-26

In aerobically growing cells, the guanine base of RNA is oxidized to 8-oxo-7,8-dihydroguanine (8-oxoG), which induces alteration in their gene expression. We previously demonstrated that the human AUF1 protein binds to 8-oxoG in RNA to induce the selective degradation of oxidized messenger RNA. We herein report that the poly(C)-binding protein PCBP1 binds to more severely oxidized RNA to activate apoptosis-related reactions. While AUF1 binds to oligoribonucleotides carrying a single 8-oxoG, PCBP1 does not bind to such oligoribonucleotides but instead binds firmly to oligoribonucleotides in which two 8-oxoG residues are located nearby. PCBP1-deficient cells, constructed from the human HeLa S3 line using the CRISPR-Cas9 system, exhibited higher survival rates than HeLa S3 cells when small doses of hydrogen peroxide were applied. The levels of caspase-3 activation and PARP-1 cleavage in the PCBP1-deficient cells were significantly lower than those in wild-type cells. The structure-function relationship of PCBP1 was established with the use of PCBP1 mutant proteins in which the conserved KH domains were defective. Human cells appear to possess two distinct mechanisms, one controlled by AUF1 and the other by PCBP1, with the former functioning when messenger RNA is moderately oxidized and the latter operating when the RNA is more severely damaged.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Youngchang; Joachimiak, Grazyna; Bigelow, Lance

Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9-2.4 Åmore » resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. Furthermore, the current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.« less

Elevated mitochondrial gene expression during rat liver regeneration after portal vein ligation.

PubMed

Shimizu, Y; Suzuki, H; Nimura, Y; Onoue, S; Nagino, M; Tanaka, M; Ozawa, T

1995-10-01

We explored the molecular basis of mitochondrial energy production during rat liver regeneration after portal vein ligation. Ligation of the left branch of the portal vein induces an increase in the weight of the nonligated lobe, counterbalancing the reduced weight of the ligated lobe. Using this model, we investigated changes in mitochondrial DNA-binding proteins, mitochondrial DNA, and mitochondrial messenger RNA (mRNA) in rat hepatocytes of the nonligated lobes. The amount of mitochondrial DNA-binding protein increased maximally (200% to 300% of the preoperative level) at 12 hours after the operation, before an increase (390%) in mitochondrial DNA content at 24 hours, and parallel to an increase (240%) in mitochondrial mRNA levels at 12 hours. These results suggest that the energy supply for liver regeneration is achieved through enhancement of mitochondrial DNA replication as well as transcription, in which the mitochondrial DNA-binding proteins probably play regulatory roles. We also found that in the nonligated lobes, mRNA levels of hepatocyte growth factor increased to a detectable level only 12 hours after the operation. These molecular biochemical data help explain why preoperative portal vein embolization, which is a modification of portal vein branch ligation, is an effective method to prevent posthepatectomy liver failure.

Enhanced catalyst stability for cyclic co methanation operations

DOEpatents

Risch, Alan P.; Rabo, Jule A.

1983-01-01

Carbon monoxide-containing gas streams are passed over a catalyst to deposit a surface layer of active surface carbon thereon essentially without the formation of inactive coke. The active carbon is thereafter reacted with steam or hydrogen to form methane. Enhanced catalyst stability for long term, cyclic operation is obtained by the incorporation of an alkali or alkaline earth dopant in a silica binding agent added to the catalyst-support additive composition.

Multiple elements regulate nuclear/cytoplasmic shuttling of FOXO1: characterization of phosphorylation- and 14-3-3-dependent and -independent mechanisms.

PubMed Central

Zhao, Xiangshan; Gan, Lixia; Pan, Haiyun; Kan, Donghui; Majeski, Michael; Adam, Stephen A; Unterman, Terry G

2004-01-01

FOXO1, a Forkhead transcription factor, is an important target of insulin and growth factor action. Phosphorylation of Thr-24, Ser-256 and Ser-319 promotes nuclear exclusion of FOXO1, yet the mechanisms regulating nuclear/cytoplasmic shuttling of FOXO1 are poorly understood. Previous studies have identified an NLS (nuclear localization signal) in the C-terminal basic region of the DBD (DNA-binding domain), and a leucine-rich, leptomycin-B sensitive NES (nuclear export signal) located further downstream. Here, we find that other elements in the DBD also contribute to nuclear localization, and that multiple mechanisms contribute to nuclear exclusion of FOXO1. Phosphorylation of Ser-319 and a cluster of nearby residues (Ser-322, Ser-325 and Ser-329) functions co-operatively with the nearby NES to promote nuclear exclusion. The N-terminal region of FOXO1 (amino acids 1-149) also is sufficient to promote nuclear exclusion, and does so through multiple mechanisms. Amino acids 1-50 are sufficient to promote nuclear exclusion of green fluorescent protein fusion proteins, and the phosphorylation of Thr-24 is required for this effect. A leucine-rich, leptomycin B-sensitive export signal is also present nearby. Phosphorylated FOXO1 binds 14-3-3 proteins, and co-precipitation studies with tagged proteins indicate that 14-3-3 binding involves co-operative interactions with both Thr-24 and Ser-256. Ser-256 is located in the C-terminal region of the DBD, where 14-3-3 proteins may interfere both with DNA-binding and with nuclear-localization functions. Together, these studies demonstrate that multiple elements contribute to nuclear/cytoplasmic shuttling of FOXO1, and that phosphorylation and 14-3-3 binding regulate the cellular distribution and function of FOXO1 through multiple mechanisms. The presence of these redundant mechanisms supports the concept that the regulation of FOXO1 function plays a critical role in insulin and growth factor action. PMID:14664696

Clostridium Perfringens Enterotoxin (CPE) and CPE-Binding Domain (c-CPE) for the Detection and Treatment of Gynecologic Cancers

PubMed Central

Black, Jonathan D.; Lopez, Salvatore; Cocco, Emiliano; Schwab, Carlton L.; English, Diana P.; Santin, Alessandro D.

2015-01-01

Clostridium perfringens enterotoxin (CPE) is a three-domain polypeptide, which binds to Claudin-3 and Claudin-4 with high affinity. Because these receptors are highly differentially expressed in many human tumors, claudin-3 and claudin-4 may provide an efficient molecular tool to specifically identify and target biologically aggressive human cancer cells for CPE-specific binding and cytolysis. In this review we will discuss these surface proteins as targets for the detection and treatment of chemotherapy-resistant gynecologic malignancies overexpressing claudin-3 and -4 using CPE-based theranostic agents. We will also discuss the use of fluorescent c-CPE peptide in the operative setting for real time detection of micro-metastatic tumors during surgery and review the potential role of CPE in other medical applications. PMID:25835384

Executive Resources and Item-Context Binding: Exploring the Influence of Concurrent Inhibition, Updating, and Shifting Tasks on Context Memory

PubMed Central

Nieznański, Marek; Obidziński, Michał; Zyskowska, Emilia; Niedziałkowska, Daria

2015-01-01

Previous research has demonstrated that context memory performance decreases as a result of cognitive load. However, the role of specific executive resources availability has not been specified yet. In a dual-task experiment, participants performed three kinds of concurrent task engaging: inhibition, updating, or shifting operations. In comparison with a no-load single-task condition, a significant decrease in item and context memory was observed, regardless of the kind of executive task. When executive load conditions were compared with non-specific cognitive load conditions, a significant interference effect was observed in the case of the inhibition task. The inhibition process appears to be an aspect of executive control, which relies on the same resource as item-context binding does, especially when binding refers to associations retrieved from long-term memory. PMID:26435761

Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12.

PubMed

Sellars, Laura E; Bryant, Jack A; Sánchez-Romero, María-Antonia; Sánchez-Morán, Eugenio; Busby, Stephen J W; Lee, David J

2017-08-03

In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DNA bound proteins in the folded bacterial nucleoid, fluorescent reporters have been developed which can be targeted to specific DNA operator sites. Such Fluorescent Reporter-Operator System (FROS) probes consist of a fluorescent protein fused to a DNA binding protein, which binds to an array of DNA operator sites located within the genome. Here we have developed a new FROS probe using the Escherichia coli MalI transcription factor, fused to mCherry fluorescent protein. We have used this in combination with a LacI repressor::GFP protein based FROS probe to assess the cellular location of commonly regulated transcription units that are distal on the Escherichia coli genome. We developed a new DNA binding fluorescent reporter, consisting of the Escherichia coli MalI protein fused to the mCherry fluorescent protein. This was used in combination with a Lac repressor:green fluorescent protein fusion to examine the spatial positioning and possible co-localisation of target genes, regulated by the Escherichia coli AraC protein. We report that induction of gene expression with arabinose does not result in co-localisation of AraC-regulated transcription units. However, measurable repositioning was observed when gene expression was induced at the AraC-regulated promoter controlling expression of the araFGH genes, located close to the DNA replication terminus on the chromosome. Moreover, in dividing cells, arabinose-induced expression at the araFGH locus enhanced chromosome segregation after replication. Regions of the chromosome regulated by AraC do not colocalise, but transcription events can induce movement of chromosome loci in bacteria and our observations suggest a role for gene expression in chromosome segregation.

Diversity of the luciferin binding protein gene in bioluminescent dinoflagellates--insights from a new gene in Noctiluca scintillans and sequences from gonyaulacoid genera.

PubMed

Valiadi, Martha; Iglesias-Rodriguez, Maria Debora

2014-01-01

Dinoflagellate bioluminescence systems operate with or without a luciferin binding protein, representing two distinct modes of light production. However, the distribution, diversity, and evolution of the luciferin binding protein gene within bioluminescent dinoflagellates are not well known. We used PCR to detect and partially sequence this gene from the heterotrophic dinoflagellate Noctiluca scintillans and a group of ecologically important gonyaulacoid species. We report an additional luciferin binding protein gene in N. scintillans which is not attached to luciferase, further to its typical combined bioluminescence gene. This supports the hypothesis that a profound re-organization of the bioluminescence system has taken place in this organism. We also show that the luciferin binding protein gene is present in the genera Ceratocorys, Gonyaulax, and Protoceratium, and is prevalent in bioluminescent species of Alexandrium. Therefore, this gene is an integral component of the standard molecular bioluminescence machinery in dinoflagellates. Nucleotide sequences showed high within-strain variation among gene copies, revealing a highly diverse gene family comprising multiple gene types in some organisms. Phylogenetic analyses showed that, in some species, the evolution of the luciferin binding protein gene was different from the organism's general phylogenies, highlighting the complex evolutionary history of dinoflagellate bioluminescence systems. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

Affinity-purified tetanus neurotoxin interaction with synaptic membranes: properties of a protease-sensitive receptor component

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lazarovici, P.; Yavin, E.

1986-11-04

The pharmacokinetic interaction of an affinity-purified /sup 125/I-labeled tetanotoxin fraction with guinea pig brain synaptosomal preparations was investigated. Binding of tetanotoxin was time- and temperature-dependent, was proportional to protein concentration, and was saturable at about 8 x 10/sup -9/ M as estimated by a solid-surface binding assay. Binding was optimal at pH 6.5 under low ionic strength buffer and was almost entirely blocked by gangliosides or antitoxin. In analogy to intact nerve cells, binding of toxin to membranes resulted in a tight association operationally defined as sequestration. Binding and sequestration were abolished after membrane pretreatment with sialidase. The enzyme couldmore » not dissociate the membrane-bound toxin formed at 4 or 37/sup 0/C under low ionic strength conditions, which is in part compatible with internalization as defined in nerve cell cultures. In the latter system the toxin could be removed at 4/sup 0/C but not at 37/sup 0/C. Binding was significantly reduced upon pretreatment of guinea pig brain membranes by a variety of hydrolytic enzymes. It is proposed that, in addition to a ganglioside, interaction of tetanotoxin with synaptic membranes is facilitated by a protein and may also require an appropriate lipid environment. These latter membrane constituents may play a pivotal role in the sequestration of the toxin.« less

Crystal Structure of the Arginine Repressor Protein in Complex With the DNA Operator From Mycobacterium Tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherney, L.T.; Cherney, M.M.; Garen, C.R.

2009-05-12

The Mycobacterium tuberculosis (Mtb) gene product encoded by open reading frame Rv1657 is an arginine repressor (ArgR). All genes involved in the L-arginine (hereafter arginine) biosynthetic pathway are essential for optimal growth of the Mtb pathogen, thus making MtbArgR a potential target for drug design. The C-terminal domains of arginine repressors (CArgR) participate in oligomerization and arginine binding. Several crystal forms of CArgR from Mtb (MtbCArgR) have been obtained. The X-ray crystal structures of MtbCArgR were determined at 1.85 {angstrom} resolution with bound arginine and at 2.15 {angstrom} resolution in the unliganded form. These structures show that six molecules ofmore » MtbCArgR are arranged into a hexamer having approximate 32 point symmetry that is formed from two trimers. The trimers rotate relative to each other by about 11{sup o} upon binding arginine. All residues in MtbCArgR deemed to be important for hexamer formation and for arginine binding have been identified from the experimentally determined structures presented. The hexamer contains six regular sites in which the arginine molecules have one common binding mode and three sites in which the arginine molecules have two overlapping binding modes. The latter sites only bind the ligand at high (200 mM) arginine concentrations.« less

On the mechanism of energy transduction in myosin subfragment 1.

PubMed Central

Botts, J; Takashi, R; Torgerson, P; Hozumi, T; Muhlrad, A; Mornet, D; Morales, M F

1984-01-01

It is proposed that the myosin subfragment 1 moiety of the muscle contractile apparatus is a self-contained "engine" whose operational plan is based on the interactive nature of ATP (or degradation intermediate) binding and actin binding, made possible by an intersite communication system. It is suggested that the spatial information required for examining this engine can, at least provisionally, be derived from fluorescence resonance energy transfer measurements interpreted by the Förster equation and that the existence of an intersite communication system can be deduced from piece-wise detection of interacting pairs of points. PMID:6585786

Transmission Assessment Surveys (TAS) to Define Endpoints for Lymphatic Filariasis Mass Drug Administration: A Multicenter Evaluation

PubMed Central

Chu, Brian K.; Deming, Michael; Biritwum, Nana-Kwadwo; Bougma, Windtaré R.; Dorkenoo, Améyo M.; El-Setouhy, Maged; Fischer, Peter U.; Gass, Katherine; Gonzalez de Peña, Manuel; Mercado-Hernandez, Leda; Kyelem, Dominique; Lammie, Patrick J.; Flueckiger, Rebecca M.; Mwingira, Upendo J.; Noordin, Rahmah; Offei Owusu, Irene; Ottesen, Eric A.; Pavluck, Alexandre; Pilotte, Nils; Rao, Ramakrishna U.; Samarasekera, Dilhani; Schmaedick, Mark A.; Settinayake, Sunil; Simonsen, Paul E.; Supali, Taniawati; Taleo, Fasihah; Torres, Melissa; Weil, Gary J.; Won, Kimberly Y.

2013-01-01

Background Lymphatic filariasis (LF) is targeted for global elimination through treatment of entire at-risk populations with repeated annual mass drug administration (MDA). Essential for program success is defining and confirming the appropriate endpoint for MDA when transmission is presumed to have reached a level low enough that it cannot be sustained even in the absence of drug intervention. Guidelines advanced by WHO call for a transmission assessment survey (TAS) to determine if MDA can be stopped within an LF evaluation unit (EU) after at least five effective rounds of annual treatment. To test the value and practicality of these guidelines, a multicenter operational research trial was undertaken in 11 countries covering various geographic and epidemiological settings. Methodology The TAS was conducted twice in each EU with TAS-1 and TAS-2 approximately 24 months apart. Lot quality assurance sampling (LQAS) formed the basis of the TAS survey design but specific EU characteristics defined the survey site (school or community), eligible population (6–7 year olds or 1st–2nd graders), survey type (systematic or cluster-sampling), target sample size, and critical cutoff (a statistically powered threshold below which transmission is expected to be no longer sustainable). The primary diagnostic tools were the immunochromatographic (ICT) test for W. bancrofti EUs and the BmR1 test (Brugia Rapid or PanLF) for Brugia spp. EUs. Principal Findings/Conclusions In 10 of 11 EUs, the number of TAS-1 positive cases was below the critical cutoff, indicating that MDA could be stopped. The same results were found in the follow-up TAS-2, therefore, confirming the previous decision outcome. Sample sizes were highly sex and age-representative and closely matched the target value after factoring in estimates of non-participation. The TAS was determined to be a practical and effective evaluation tool for stopping MDA although its validity for longer-term post-MDA surveillance requires further investigation. PMID:24340120

Transmission assessment surveys (TAS) to define endpoints for lymphatic filariasis mass drug administration: a multicenter evaluation.

PubMed

Chu, Brian K; Deming, Michael; Biritwum, Nana-Kwadwo; Bougma, Windtaré R; Dorkenoo, Améyo M; El-Setouhy, Maged; Fischer, Peter U; Gass, Katherine; Gonzalez de Peña, Manuel; Mercado-Hernandez, Leda; Kyelem, Dominique; Lammie, Patrick J; Flueckiger, Rebecca M; Mwingira, Upendo J; Noordin, Rahmah; Offei Owusu, Irene; Ottesen, Eric A; Pavluck, Alexandre; Pilotte, Nils; Rao, Ramakrishna U; Samarasekera, Dilhani; Schmaedick, Mark A; Settinayake, Sunil; Simonsen, Paul E; Supali, Taniawati; Taleo, Fasihah; Torres, Melissa; Weil, Gary J; Won, Kimberly Y

2013-01-01

Lymphatic filariasis (LF) is targeted for global elimination through treatment of entire at-risk populations with repeated annual mass drug administration (MDA). Essential for program success is defining and confirming the appropriate endpoint for MDA when transmission is presumed to have reached a level low enough that it cannot be sustained even in the absence of drug intervention. Guidelines advanced by WHO call for a transmission assessment survey (TAS) to determine if MDA can be stopped within an LF evaluation unit (EU) after at least five effective rounds of annual treatment. To test the value and practicality of these guidelines, a multicenter operational research trial was undertaken in 11 countries covering various geographic and epidemiological settings. The TAS was conducted twice in each EU with TAS-1 and TAS-2 approximately 24 months apart. Lot quality assurance sampling (LQAS) formed the basis of the TAS survey design but specific EU characteristics defined the survey site (school or community), eligible population (6-7 year olds or 1(st)-2(nd) graders), survey type (systematic or cluster-sampling), target sample size, and critical cutoff (a statistically powered threshold below which transmission is expected to be no longer sustainable). The primary diagnostic tools were the immunochromatographic (ICT) test for W. bancrofti EUs and the BmR1 test (Brugia Rapid or PanLF) for Brugia spp. EUs. In 10 of 11 EUs, the number of TAS-1 positive cases was below the critical cutoff, indicating that MDA could be stopped. The same results were found in the follow-up TAS-2, therefore, confirming the previous decision outcome. Sample sizes were highly sex and age-representative and closely matched the target value after factoring in estimates of non-participation. The TAS was determined to be a practical and effective evaluation tool for stopping MDA although its validity for longer-term post-MDA surveillance requires further investigation.

Global Low Frequency Protein Motions in Long-Range Allosteric Signaling

NASA Astrophysics Data System (ADS)

McLeish, Tom; Rogers, Thomas; Townsend, Philip; Burnell, David; Pohl, Ehmke; Wilson, Mark; Cann, Martin; Richards, Shane; Jones, Matthew

2015-03-01

We present a foundational theory for how allostery can occur as a function of low frequency dynamics without a change in protein structure. Elastic inhomogeneities allow entropic ``signalling at a distance.'' Remarkably, many globular proteins display just this class of elastic structure, in particular those that support allosteric binding of substrates (long-range co-operative effects between the binding sites of small molecules). Through multi-scale modelling of global normal modes we demonstrate negative co-operativity between the two cAMP ligands without change to the mean structure. Crucially, the value of the co-operativity is itself controlled by the interactions around a set of third allosteric ``control sites.'' The theory makes key experimental predictions, validated by analysis of variant proteins by a combination of structural biology and isothermal calorimetry. A quantitative description of allostery as a free energy landscape revealed a protein ``design space'' that identified the key inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, by analyzing naturally occurring CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. The methodology establishes the means to engineer allosteric mechanisms that are driven by low frequency dynamics.

48 CFR 8.801 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Definitions. 8.801 Section 8.801 Federal Acquisition Regulations System FEDERAL ACQUISITION REGULATION ACQUISITION PLANNING..., means supplies that are used and equipment that is usable in printing and binding operations. [48 FR...

Intelligent transportation systems field operational test cross-cutting study : emergency notification and response

DOT National Transportation Integrated Search

2000-08-01

Transportation is vital to the social and economic health of the nation. Surface transportation systems ? the networks of highways, local streets, bus routes, and rail lines ? are the ties that bind communities and facilitate commerce. Despite the fa...

Dinosaur Metabolism and the Allometry of Maximum Growth Rate

PubMed Central

Myhrvold, Nathan P.

2016-01-01

The allometry of maximum somatic growth rate has been used in prior studies to classify the metabolic state of both extant vertebrates and dinosaurs. The most recent such studies are reviewed, and their data is reanalyzed. The results of allometric regressions on growth rate are shown to depend on the choice of independent variable; the typical choice used in prior studies introduces a geometric shear transformation that exaggerates the statistical power of the regressions. The maximum growth rates of extant groups are found to have a great deal of overlap, including between groups with endothermic and ectothermic metabolism. Dinosaur growth rates show similar overlap, matching the rates found for mammals, reptiles and fish. The allometric scaling of growth rate with mass is found to have curvature (on a log-log scale) for many groups, contradicting the prevailing view that growth rate allometry follows a simple power law. Reanalysis shows that no correlation between growth rate and basal metabolic rate (BMR) has been demonstrated. These findings drive a conclusion that growth rate allometry studies to date cannot be used to determine dinosaur metabolism as has been previously argued. PMID:27828977

Dinosaur Metabolism and the Allometry of Maximum Growth Rate.

PubMed

Myhrvold, Nathan P

2016-01-01

The allometry of maximum somatic growth rate has been used in prior studies to classify the metabolic state of both extant vertebrates and dinosaurs. The most recent such studies are reviewed, and their data is reanalyzed. The results of allometric regressions on growth rate are shown to depend on the choice of independent variable; the typical choice used in prior studies introduces a geometric shear transformation that exaggerates the statistical power of the regressions. The maximum growth rates of extant groups are found to have a great deal of overlap, including between groups with endothermic and ectothermic metabolism. Dinosaur growth rates show similar overlap, matching the rates found for mammals, reptiles and fish. The allometric scaling of growth rate with mass is found to have curvature (on a log-log scale) for many groups, contradicting the prevailing view that growth rate allometry follows a simple power law. Reanalysis shows that no correlation between growth rate and basal metabolic rate (BMR) has been demonstrated. These findings drive a conclusion that growth rate allometry studies to date cannot be used to determine dinosaur metabolism as has been previously argued.

A comparison of theory and experiment for coupled rotor body stability of a bearingless rotor model in hover and forward flight

NASA Technical Reports Server (NTRS)

Mirick, Paul H.

1988-01-01

Seven cases were selected for correlation from a 1/5.86 Froude-scale experiment that examined several rotor designs which were being considered for full-scale flight testing as part of the Bearingless Main Rotor (BMR) program. The model rotor hub used in these tests consisted of back-to-back C-beams as flexbeam elements with a torque tube for pitch control. The first four cases selected from the experiment were hover tests which examined the effects on rotor stability of variations in hub-to-flexbeam coning, hub-to-flexbeam pitch, flexbeam-to-blade coning, and flexbeam-to-blade pitch. The final three cases were selected from the forward flight tests of optimum rotor configuration as defined during the hover test. The selected cases examined the effects of variations in forward speed, rotor speed, and shaft angle. Analytical results from Bell Helicopter Textron, Boeing Vertol, Sikorsky Aircraft, and the U.S. Army Aeromechanics Laboratory were compared with the data and the correlations ranged from poor-to-fair to fair-to-good.

Continuous desalting of refolded protein solution improves capturing in ion exchange chromatography: A seamless process.

PubMed

Walch, Nicole; Jungbauer, Alois

2017-06-01

Truly continuous biomanufacturing processes enable an uninterrupted feed stream throughout the whole production without the need for holding tanks. We have utilized microporous anion and cation exchangers into which only salts, but not proteins, can penetrate into the pores for desalting of protein solutions, while diafiltration or dilution is usually employed for feed adjustments. Anion exchange and cation exchange chromatography columns were connected in series to remove both anions and cations. To increase operation performance, a continuous process was developed comprised of four columns. Continuous mode was achieved by staggered cycle operation, where one set of columns, consisting of one anion exchange and one cation exchange column, was loaded during the regeneration of the second set. Refolding, desalting and subsequent ion exchange capturing with a scFv as the model protein was demonstrated. The refolding solution was successfully desalted resulting in a consistent conductivity below 0.5 mS/cm from initial values of 10 to 11 mS/cm. With continuous operation process time could be reduced by 39% while productivity was increased to 163% compared to batch operation. Desalting of the protein solution resulted in up to 7-fold higher binding capacities in the subsequent ion exchange capture step with conventional protein binding resins. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Prediction of Nucleotide Binding Peptides Using Star Graph Topological Indices.

PubMed

Liu, Yong; Munteanu, Cristian R; Fernández Blanco, Enrique; Tan, Zhiliang; Santos Del Riego, Antonino; Pazos, Alejandro

2015-11-01

The nucleotide binding proteins are involved in many important cellular processes, such as transmission of genetic information or energy transfer and storage. Therefore, the screening of new peptides for this biological function is an important research topic. The current study proposes a mixed methodology to obtain the first classification model that is able to predict new nucleotide binding peptides, using only the amino acid sequence. Thus, the methodology uses a Star graph molecular descriptor of the peptide sequences and the Machine Learning technique for the best classifier. The best model represents a Random Forest classifier based on two features of the embedded and non-embedded graphs. The performance of the model is excellent, considering similar models in the field, with an Area Under the Receiver Operating Characteristic Curve (AUROC) value of 0.938 and true positive rate (TPR) of 0.886 (test subset). The prediction of new nucleotide binding peptides with this model could be useful for drug target studies in drug development. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Crystal Structure of the Intact E. coli RelBE Toxin-Antitoxin Complex Provides the Structural Basis for Conditional Cooperativity

PubMed Central

Bøggild, Andreas; Sofos, Nicholas; Andersen, Kasper R.; Feddersen, Ane; Easter, Ashley D.; Passmore, Lori A.; Brodersen, Ditlev E.

2012-01-01

Summary The bacterial relBE locus encodes a toxin-antitoxin complex in which the toxin, RelE, is capable of cleaving mRNA in the ribosomal A site cotranslationally. The antitoxin, RelB, both binds and inhibits RelE, and regulates transcription through operator binding and conditional cooperativity controlled by RelE. Here, we present the crystal structure of the intact Escherichia coli RelB2E2 complex at 2.8 Å resolution, comprising both the RelB-inhibited RelE and the RelB dimerization domain that binds DNA. RelE and RelB associate into a V-shaped heterotetrameric complex with the ribbon-helix-helix (RHH) dimerization domain at the apex. Our structure supports a model in which relO is optimally bound by two adjacent RelB2E heterotrimeric units, and is not compatible with concomitant binding of two RelB2E2 heterotetramers. The results thus provide a firm basis for understanding the model of conditional cooperativity at the molecular level. PMID:22981948

Haematoporphyrin and OO'-diacetylhaematoporphyrin binding by serum and cellular proteins. Implications for the clearance of these photochemotherapeutic agents by cells.

PubMed Central

Smith, A; Neuschatz, T

1983-01-01

Haematoporphyrin derivative (HpD), a mixture of porphyrins, is currently used as a photochemotherapeutic agent in the treatment of neoplasias. The interaction of purified components of HpD with serum and cellular proteins was investigated using absorption and fluorescence spectroscopy. The interactions of haematoporphyrin and OO'-diacetylhaematoporphyrin with human albumin and with haemopexin, the two major serum porphyrin-binding proteins, show stoichiometries of 1 mol of porphyrin bound per mol of protein. The apparent dissociation constants, Kd, are in the range of 1-2 microM for albumin and 3-4 microM for haemopexin. These two major components of HpD would, after intravenous injection, bind to albumin and circulate in serum as albumin complexes. Free porphyrin rather than porphyrin bound to albumin interacts with Morris hepatoma tissue culture cells. A rapid high-affinity saturable transport system operates at free porphyrin concentrations of less than 2 microM. In addition, fluorescence spectra show that components in rat liver cytosol can bind haematoporphyrin and OO'-diacetylhaematoporphyrin and distinguish these binders from those present in rat serum. PMID:6225429

BiodMHC: an online server for the prediction of MHC class II-peptide binding affinity.

PubMed

Wang, Lian; Pan, Danling; Hu, Xihao; Xiao, Jinyu; Gao, Yangyang; Zhang, Huifang; Zhang, Yan; Liu, Juan; Zhu, Shanfeng

2009-05-01

Effective identification of major histocompatibility complex (MHC) molecules restricted peptides is a critical step in discovering immune epitopes. Although many online servers have been built to predict class II MHC-peptide binding affinity, they have been trained on different datasets, and thus fail in providing a unified comparison of various methods. In this paper, we present our implementation of seven popular predictive methods, namely SMM-align, ARB, SVR-pairwise, Gibbs sampler, ProPred, LP-top2, and MHCPred, on a single web server named BiodMHC (http://biod.whu.edu.cn/BiodMHC/index.html, the software is available upon request). Using a standard measure of AUC (Area Under the receiver operating characteristic Curves), we compare these methods by means of not only cross validation but also prediction on independent test datasets. We find that SMM-align, ProPred, SVR-pairwise, ARB, and Gibbs sampler are the five best-performing methods. For the binding affinity prediction of class II MHC-peptide, BiodMHC provides a convenient online platform for researchers to obtain binding information simultaneously using various methods.

A Pro-Nerve Growth Factor (proNGF) and NGF Binding Protein, α2-Macroglobulin, Differentially Regulates p75 and TrkA Receptors and Is Relevant to Neurodegeneration Ex Vivo and In Vivo

PubMed Central

Barcelona, Pablo F.

2015-01-01

Nerve growth factor (NGF) is generated from a precursor, proNGF, that is proteolytically processed. NGF preferentially binds a trophic tyrosine kinase receptor, TrkA, while proNGF binds a neurotrophin receptor (NTR), p75NTR, that can have neurotoxic activity. Previously, we along with others showed that the soluble protein α2-macroglobulin (α2M) is neurotoxic. Toxicity is due in part to α2M binding to NGF and inhibiting trophic activity, presumably by preventing NGF binding to TrkA. However, the mechanisms remained unclear. Here, we show ex vivo and in vivo three mechanisms for α2M neurotoxicity. First, unexpectedly the α2M-NGF complexes do bind TrkA receptors but do not induce TrkA dimerization or activation, resulting in deficient trophic support. Second, α2M makes stable complexes with proNGF, conveying resistance to proteolysis that results in more proNGF and less NGF. Third, α2M-proNGF complexes bind p75NTR and are more potent agonists than free proNGF, inducing tumor necrosis factor alpha (TNF-α) production. Hence, α2M regulates proNGF/p75NTR positively and mature NGF/TrkA negatively, causing neuronal death ex vivo. These three mechanisms are operative in vivo, and α2M causes neurodegeneration in a p75NTR- and proNGF-dependent manner. α2M could be exploited as a therapeutic target, or as a modifier of neurotrophin signals. PMID:26217017

Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea.

PubMed

Rivera-Gómez, Nancy; Martínez-Núñez, Mario Alberto; Pastor, Nina; Rodriguez-Vazquez, Katya; Perez-Rueda, Ernesto

2017-08-01

Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions. In this work, we systematically evaluated the distribution, abundance and domain organization of DNA-binding TFs in 799 non-redundant bacterial and archaeal genomes. We found that the distributions of the DBDs and their corresponding PaDos correlated with the size of the genome. We also identified specific combinations between the DBDs and their corresponding PaDos. Within each class of DBDs there are differences in the actual angle formed at the dimerization interface, responding to the presence/absence of ligands and/or crystallization conditions, setting the orientation of the resulting helices and wings facing the DNA. Our results highlight the importance of PaDos as central elements that enhance the diversity of regulatory functions in all bacterial and archaeal organisms, and our results also demonstrate the role of PaDos in sensing diverse signal compounds. The highly specific interactions between DBDs and PaDos observed in this work, together with our structural analysis highlighting the difficulty in predicting both inter-domain geometry and quaternary structure, suggest that these systems appeared once and evolved with diverse duplication events in all the analysed organisms.

The activity of CouR, a MarR family transcriptional regulator, is modulated through a novel molecular mechanism

DOE PAGES

Otani, Hiroshi; Stogios, Peter J.; Xu, Xiaohui; ...

2015-09-22

CouR, a MarR-type transcriptional repressor, regulates the cou genes, encoding p-hydroxycinnamate catabolism in the soil bacterium Rhodococcus jostii RHA1. The CouR dimer bound two molecules of the catabolite p-coumaroyl–CoA (K d = 11 ± 1 μM). The presence of p-coumaroyl–CoA, but neither p-coumarate nor CoASH, abrogated CouR's binding to its operator DNA in vitro. The crystal structures of ligand-free CouR and its p-coumaroyl–CoA-bound form showed no significant conformational differences, in contrast to other MarR regulators. The CouR– p-coumaroyl–CoA structure revealed two ligand molecules bound to the CouR dimer with their phenolic moieties occupying equivalent hydrophobic pockets in each protomer andmore » their CoA moieties adopting non-equivalent positions to mask the regulator's predicted DNA-binding surface. More specifically, the CoA phosphates formed salt bridges with predicted DNA-binding residues Arg36 and Arg38, changing the overall charge of the DNA-binding surface. The substitution of either arginine with alanine completely abrogated the ability of CouR to bind DNA. By contrast, the R36A/R38A double variant retained a relatively high affinity for p-coumaroyl–CoA (K d = 89 ± 6 μM). Altogether, our data point to a novel mechanism of action in which the ligand abrogates the repressor's ability to bind DNA by steric occlusion of key DNA-binding residues and charge repulsion of the DNA backbone.« less

The prognostic and risk-stratified value of heart-type fatty acid-binding protein in septic patients in the emergency department.

PubMed

Chen, Yun-Xia; Li, Chun-Sheng

2014-08-01

To evaluate the prognostic and risk-stratified ability of heart-type fatty acid-binding protein (H-FABP) in septic patients in the emergency department (ED). From August to November 2012, 295 consecutive septic patients were enrolled. Circulating H-FABP was measured. The predictive value of H-FABP for 28-day mortality, organ dysfunction on ED arrival, and requirement for mechanical ventilation or a vasopressor within 6 hours after ED arrival was assessed by the receiver operating characteristic curve and logistic regression and was compared with Acute Physiology and Chronic Health Evaluation (APACHE) II score, Mortality in Emergency Department Sepsis (MEDS) score, and Sequential Organ Failure Assessment score. The 28-day mortality, APACHE II, MEDS, and Sequential Organ Failure Assessment scores were much higher in H-FABP-positive patients. The incidence of organ dysfunction at ED arrival and requirement for mechanical ventilation or a vasopressor within 6 hours after ED arrival was higher in H-FABP-positive patients. Heart-type fatty acid-binding protein was an independent predictor of 28-day mortality and organ dysfunction. The area under the receiver operating characteristic curve for H-FABP predicting 28-day mortality and organ dysfunction was 0.784 and 0.755, respectively. Combination of H-FABP and MEDS improved the performance of MEDS in predicting organ dysfunction, and the difference of AUC was statistically significant (P<.05). The combinations of H-FABP and MEDS or H-FABP and APACHE II also improved the prognostic value of MEDS and APACHE II, but the areas under the curve were not statistically different. Heart-type fatty acid-binding protein was helpful for prognosis and risk stratification of septic patients in the ED. Copyright © 2014 Elsevier Inc. All rights reserved.

AtSPX1 affects the AtPHR1-DNA-binding equilibrium by binding monomeric AtPHR1 in solution.

PubMed

Qi, Wanjun; Manfield, Iain W; Muench, Stephen P; Baker, Alison

2017-10-23

Phosphorus is an essential macronutrient for plant growth and is deficient in ∼50% of agricultural soils. The transcription factor phosphate starvation response 1 (PHR1) plays a central role in regulating the expression of a subset of phosphate starvation-induced (PSI) genes through binding to a cis -acting DNA element termed P1BS (PHR1-binding sequences). In Arabidopsis and rice, activity of AtPHR1/OsPHR2 is regulated in part by their downstream target SPX ( S yg1, P ho81, X pr1) proteins through protein-protein interaction. Here, we provide kinetic and affinity data for interaction between AtPHR1 and P1BS sites. Using surface plasmon resonance, a tandem P1BS sequence showed ∼50-fold higher affinity for MBPAtdPHR1 (a fusion protein comprising the DNA-binding domain and coiled-coil domain of AtPHR1 fused to maltose-binding protein) than a single site. The affinity difference was largely reflected in a much slower dissociation rate from the 2× P1BS-binding site, suggesting an important role for protein co-operativity. Injection of AtSPX1 in the presence of phosphate or inositol hexakisphosphate (InsP6) failed to alter the MBPAtdPHR1-P1BS dissociation rate, while pre-mixing of these two proteins in the presence of either 5 mM Pi or 500 µM InsP6 resulted in a much lower DNA-binding signal from MBPAtdPHR1. These data suggest that, in the Pi-restored condition, AtSPX1 can bind to monomeric AtPHR1 in solution and therefore regulate PSI gene expression by tuning the AtPHR1-DNA-binding equilibrium. This Pi-dependent regulation of AtPHR1-DNA-binding equilibrium also generates a negative feedback loop on the expression of AtSPX1 itself, providing a tight control of PSI gene expression. © 2017 The Author(s).

Gold Binding by Native and Chemically Modified Hops Biomasses

DOE PAGES

López, M. Laura; Gardea-Torresdey, J. L.; Peralta-Videa, J. R.; ...

2005-01-01

Heavy metals from mining, smelting operations and other industrial processing facilities pollute wastewaters worldwide. Extraction of metals from industrial effluents has been widely studied due to the economic advantages and the relative ease of technical implementation. Consequently, the search for new and improved methodologies for the recovery of gold has increased. In this particular research, the use of cone hops biomass ( Humulus lupulus ) was investigated as a new option for gold recovery. The results showed that the gold binding to native hops biomass was pH dependent from pH 2 to pH 6, with a maximum percentage binding atmore » pH 3. Time dependency studies demonstrated that Au(III) binding to native and modified cone hops biomasses was found to be time independent at pH 2 while at pH 5, it was time dependent. Capacity experiments demonstrated that at pH 2, esterified hops biomass bound 33.4 mg Au/g of biomass, while native and hydrolyzed hops biomasses bound 28.2 and 12.0 mg Au/g of biomass, respectively. However, at pH 5 the binding capacities were 38.9, 37.8 and 11.4 mg of Au per gram of native, esterified and hydrolyzed hops biomasses, respectively.« less

Accurate prediction of RNA-binding protein residues with two discriminative structural descriptors.

PubMed

Sun, Meijian; Wang, Xia; Zou, Chuanxin; He, Zenghui; Liu, Wei; Li, Honglin

2016-06-07

RNA-binding proteins participate in many important biological processes concerning RNA-mediated gene regulation, and several computational methods have been recently developed to predict the protein-RNA interactions of RNA-binding proteins. Newly developed discriminative descriptors will help to improve the prediction accuracy of these prediction methods and provide further meaningful information for researchers. In this work, we designed two structural features (residue electrostatic surface potential and triplet interface propensity) and according to the statistical and structural analysis of protein-RNA complexes, the two features were powerful for identifying RNA-binding protein residues. Using these two features and other excellent structure- and sequence-based features, a random forest classifier was constructed to predict RNA-binding residues. The area under the receiver operating characteristic curve (AUC) of five-fold cross-validation for our method on training set RBP195 was 0.900, and when applied to the test set RBP68, the prediction accuracy (ACC) was 0.868, and the F-score was 0.631. The good prediction performance of our method revealed that the two newly designed descriptors could be discriminative for inferring protein residues interacting with RNAs. To facilitate the use of our method, a web-server called RNAProSite, which implements the proposed method, was constructed and is freely available at http://lilab.ecust.edu.cn/NABind .

The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeon Pyrococcus furiosus in complex with sucrose

PubMed Central

Krug, Michael; Lee, Sung-Jae; Boos, Winfried; Diederichs, Kay; Welte, Wolfram

2013-01-01

TrmB is a repressor that binds maltose, maltotriose, and sucrose, as well as other α-glucosides. It recognizes two different operator sequences controlling the TM (Trehalose/Maltose) and the MD (Maltodextrin) operon encoding the respective ABC transporters and sugar-degrading enzymes. Binding of maltose to TrmB abrogates repression of the TM operon but maintains the repression of the MD operon. On the other hand, binding of sucrose abrogates repression of the MD operon but maintains repression of the TM operon. The three-dimensional structure of TrmB in complex with sucrose was solved and refined to a resolution of 3.0 Å. The structure shows the N-terminal DNA binding domain containing a winged-helix-turn-helix (wHTH) domain followed by an amphipathic helix with a coiled-coil motif. The latter promotes dimerization and places the symmetry mates of the putative recognition helix in the wHTH motif about 30 Å apart suggesting a canonical binding to two successive major grooves of duplex palindromic DNA. This suggests that the structure resembles the conformation of TrmB recognizing the pseudopalindromic TM promoter but not the conformation recognizing the nonpalindromic MD promoter. PMID:23576322

Specific and non-specific interactions of ParB with DNA: implications for chromosome segregation

PubMed Central

Taylor, James A.; Pastrana, Cesar L.; Butterer, Annika; Pernstich, Christian; Gwynn, Emma J.; Sobott, Frank; Moreno-Herrero, Fernando; Dillingham, Mark S.

2015-01-01

The segregation of many bacterial chromosomes is dependent on the interactions of ParB proteins with centromere-like DNA sequences called parS that are located close to the origin of replication. In this work, we have investigated the binding of Bacillus subtilis ParB to DNA in vitro using a variety of biochemical and biophysical techniques. We observe tight and specific binding of a ParB homodimer to the parS sequence. Binding of ParB to non-specific DNA is more complex and displays apparent positive co-operativity that is associated with the formation of larger, poorly defined, nucleoprotein complexes. Experiments with magnetic tweezers demonstrate that non-specific binding leads to DNA condensation that is reversible by protein unbinding or force. The condensed DNA structure is not well ordered and we infer that it is formed by many looping interactions between neighbouring DNA segments. Consistent with this view, ParB is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from two different DNA molecules in trans. The experiments provide no evidence for the promotion of non-specific DNA binding and/or condensation events by the presence of parS sequences. The implications of these observations for chromosome segregation are discussed. PMID:25572315

Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR.

PubMed

McDermott, Geoffrey P; Do, Duc; Litterst, Claudia M; Maar, Dianna; Hindson, Christopher M; Steenblock, Erin R; Legler, Tina C; Jouvenot, Yann; Marrs, Samuel H; Bemis, Adam; Shah, Pallavi; Wong, Josephine; Wang, Shenglong; Sally, David; Javier, Leanne; Dinio, Theresa; Han, Chunxiao; Brackbill, Timothy P; Hodges, Shawn P; Ling, Yunfeng; Klitgord, Niels; Carman, George J; Berman, Jennifer R; Koehler, Ryan T; Hiddessen, Amy L; Walse, Pramod; Bousse, Luc; Tzonev, Svilen; Hefner, Eli; Hindson, Benjamin J; Cauly, Thomas H; Hamby, Keith; Patel, Viresh P; Regan, John F; Wyatt, Paul W; Karlin-Neumann, George A; Stumbo, David P; Lowe, Adam J

2013-12-03

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.

Trigger Factor and DnaK possess overlapping substrate pools and binding specificities.

PubMed

Deuerling, Elke; Patzelt, Holger; Vorderwülbecke, Sonja; Rauch, Thomas; Kramer, Günter; Schaffitzel, Elke; Mogk, Axel; Schulze-Specking, Agnes; Langen, Hanno; Bukau, Bernd

2003-03-01

Ribosome-associated Trigger Factor (TF) and the DnaK chaperone system assist the folding of newly synthesized proteins in Escherichia coli. Here, we show that DnaK and TF share a common substrate pool in vivo. In TF-deficient cells, deltatig, depleted for DnaK and DnaJ the amount of aggregated proteins increases with increasing temperature, amounting to 10% of total soluble protein (approximately 340 protein species) at 37 degrees C. A similar population of proteins aggregated in DnaK depleted tig+ cells, albeit to a much lower extent. Ninety-four aggregated proteins isolated from DnaK- and DnaJ-depleted deltatig cells were identified by mass spectrometry and found to include essential cytosolic proteins. Four potential in vivo substrates were screened for chaperone binding sites using peptide libraries. Although TF and DnaK recognize different binding motifs, 77% of TF binding peptides also associated with DnaK. In the case of the nascent polypeptides TF and DnaK competed for binding, however, with competitive advantage for TF. In vivo, the loss of TF is compensated by the induction of the heat shock response and thus enhanced levels of DnaK. In summary, our results demonstrate that the co-operation of the two mechanistically distinct chaperones in protein folding is based on their overlap in substrate specificities.

12 CFR 614.4350 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... and Banking FARM CREDIT ADMINISTRATION FARM CREDIT SYSTEM LOAN POLICIES AND OPERATIONS Lending and... indirectly. Excluded are a Farm Credit System association or other financing institution that comply with the... commitment to make a lease. (b) Commitment means a legally binding obligation to extend credit, enter into...

46 CFR 308.539 - Application.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.539 Application. (a) Preliminary request. Application for a... submitting the request to bind war risk in writing; for security reasons, if the applicant is submitting the...

46 CFR 308.539 - Application.

Code of Federal Regulations, 2013 CFR

2013-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.539 Application. (a) Preliminary request. Application for a... submitting the request to bind war risk in writing; for security reasons, if the applicant is submitting the...

46 CFR 308.539 - Application.

Code of Federal Regulations, 2012 CFR

2012-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.539 Application. (a) Preliminary request. Application for a... submitting the request to bind war risk in writing; for security reasons, if the applicant is submitting the...

46 CFR 308.539 - Application.

Code of Federal Regulations, 2011 CFR

2011-10-01

... ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.539 Application. (a) Preliminary request. Application for a... submitting the request to bind war risk in writing; for security reasons, if the applicant is submitting the...

Cronus: A Distributed Operating System.

DTIC Science & Technology

1983-11-01

general, support movement of arbitrary objects from one host to another; some specific object tye will give rise to mobile objects, however. -34...File hierarchy is achieved by binding file identifiers to symbolic names in a hierarchical name space. Cronus CMos Aplications Since CMOS is the GCE

Benchmarking database performance for genomic data.

PubMed

Khushi, Matloob

2015-06-01

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a novel region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).Inc. © 2015 Wiley Periodicals, Inc.

Fast Modeling of Binding Affinities by Means of Superposing Significant Interaction Rules (SSIR) Method

PubMed Central

Besalú, Emili

2016-01-01

The Superposing Significant Interaction Rules (SSIR) method is described. It is a general combinatorial and symbolic procedure able to rank compounds belonging to combinatorial analogue series. The procedure generates structure-activity relationship (SAR) models and also serves as an inverse SAR tool. The method is fast and can deal with large databases. SSIR operates from statistical significances calculated from the available library of compounds and according to the previously attached molecular labels of interest or non-interest. The required symbolic codification allows dealing with almost any combinatorial data set, even in a confidential manner, if desired. The application example categorizes molecules as binding or non-binding, and consensus ranking SAR models are generated from training and two distinct cross-validation methods: leave-one-out and balanced leave-two-out (BL2O), the latter being suited for the treatment of binary properties. PMID:27240346

Frizzled 7 and PIP2 binding by syntenin PDZ2 domain supports Frizzled 7 trafficking and signalling

NASA Astrophysics Data System (ADS)

Egea-Jimenez, Antonio Luis; Gallardo, Rodrigo; Garcia-Pino, Abel; Ivarsson, Ylva; Wawrzyniak, Anna Maria; Kashyap, Rudra; Loris, Remy; Schymkowitz, Joost; Rousseau, Frederic; Zimmermann, Pascale

2016-07-01

PDZ domain-containing proteins work as intracellular scaffolds to control spatio-temporal aspects of cell signalling. This function is supported by the ability of their PDZ domains to bind other proteins such as receptors, but also phosphoinositide lipids important for membrane trafficking. Here we report a crystal structure of the syntenin PDZ tandem in complex with the carboxy-terminal fragment of Frizzled 7 and phosphatidylinositol 4,5-bisphosphate (PIP2). The crystal structure reveals a tripartite interaction formed via the second PDZ domain of syntenin. Biophysical and biochemical experiments establish co-operative binding of the tripartite complex and identify residues crucial for membrane PIP2-specific recognition. Experiments with cells support the importance of the syntenin-PIP2 interaction for plasma membrane targeting of Frizzled 7 and c-jun phosphorylation. This study contributes to our understanding of the biology of PDZ proteins as key players in membrane compartmentalization and dynamics.

Principles of regulatory information conservation between mouse and human.

PubMed

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia; Lin, Shin; Lin, Yiing; Visel, Axel; Kawli, Trupti; Yang, Xinqiong; Patacsil, Dorrelyn; Keller, Cheryl A; Giardine, Belinda; Kundaje, Anshul; Wang, Ting; Pennacchio, Len A; Weng, Zhiping; Hardison, Ross C; Snyder, Michael P

2014-11-20

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human-mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and with genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.

Metalloregulatory Proteins: Metal Selectivity and Allosteric Switching

PubMed Central

Caballero, Hermes Reyes; Campanello, Gregory C.; Giedroc, David P.

2011-01-01

Prokaryotic organisms have evolved an impressive capacity to quickly adapt to a changing and challenging microenvironment in which the availability of both biologically required and non-essential transition metal ions can vary dramatically. In all bacteria, a panel of metalloregulatory proteins control the expression of genes encoding membrane transporters and metal trafficking proteins, that collectively manage metal homeostasis and resistance. These “metal sensors” are specialized allosteric proteins, in which the direct binding of a specific or small number of “cognate” metal ion(s) drives a conformational change in the regulator that allosterically activates or inhibits operator DNA binding, or alternatively, distorts the promoter structure thereby converting a poor promoter to a strong one. In this review, we discuss our current understanding of the features that control metal specificity of the allosteric response in these systems, and the role that structure, thermodynamics and conformational dynamics play in mediating allosteric activation or inhibition of DNA binding. PMID:21511390

Data to hardware binding with physical unclonable functions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamlet, Jason

The various technologies presented herein relate to binding data (e.g., software) to hardware, wherein the hardware is to utilize the data. The generated binding can be utilized to detect whether at least one of the hardware or the data has been modified between an initial moment (enrollment) and a later moment (authentication). During enrollment, an enrollment value is generated that includes a signature of the data, a first response from a PUF located on the hardware, and a code word. During authentication, a second response from the PUF is utilized to authenticate any of the content in the enrollment value,more » and based upon the authentication, a determination can be made regarding whether the hardware and/or the data have been modified. If modification is detected then a mitigating operation can be performed, e.g., the hardware is prevented from utilizing the data. If no modification is detected, the data can be utilized.« less

Real-Time Label-Free Direct Electronic Monitoring of Topoisomerase Enzyme Binding Kinetics on Graphene.

PubMed

Zuccaro, Laura; Tesauro, Cinzia; Kurkina, Tetiana; Fiorani, Paola; Yu, Hak Ki; Knudsen, Birgitta R; Kern, Klaus; Desideri, Alessandro; Balasubramanian, Kannan

2015-11-24

Monolayer graphene field-effect sensors operating in liquid have been widely deployed for detecting a range of analyte species often under equilibrium conditions. Here we report on the real-time detection of the binding kinetics of the essential human enzyme, topoisomerase I interacting with substrate molecules (DNA probes) that are immobilized electrochemically on to monolayer graphene strips. By monitoring the field-effect characteristics of the graphene biosensor in real-time during the enzyme-substrate interactions, we are able to decipher the surface binding constant for the cleavage reaction step of topoisomerase I activity in a label-free manner. Moreover, an appropriate design of the capture probes allows us to distinctly follow the cleavage step of topoisomerase I functioning in real-time down to picomolar concentrations. The presented results are promising for future rapid screening of drugs that are being evaluated for regulating enzyme activity.

Structural Basis for the ABO Blood-Group Dependence of Plasmodium falciparum Rosetting

PubMed Central

Hessel, Audrey; Raynal, Bertrand; England, Patrick; Cohen, Jacques H.; Bertrand, Olivier; Peyrard, Thierry; Bentley, Graham A.; Lewit-Bentley, Anita; Mercereau-Puijalon, Odile

2012-01-01

The ABO blood group influences susceptibility to severe Plasmodium falciparum malaria. Recent evidence indicates that the protective effect of group O operates by virtue of reduced rosetting of infected red blood cells (iRBCs) with uninfected RBCs. Rosetting is mediated by a subgroup of PfEMP1 adhesins, with RBC binding being assigned to the N-terminal DBL1α1 domain. Here, we identify the ABO blood group as the main receptor for VarO rosetting, with a marked preference for group A over group B, which in turn is preferred to group O RBCs. We show that recombinant NTS-DBL1α1 and NTS-DBL1α1-CIDR1γ reproduce the VarO-iRBC blood group preference and document direct binding to blood group trisaccharides by surface plasmon resonance. More detailed RBC subgroup analysis showed preferred binding to group A1, weaker binding to groups A2 and B, and least binding to groups Ax and O. The 2.8 Å resolution crystal structure of the PfEMP1-VarO Head region, NTS-DBL1α1-CIDR1γ, reveals extensive contacts between the DBL1α1 and CIDR1γ and shows that the NTS-DBL1α1 hinge region is essential for RBC binding. Computer docking of the blood group trisaccharides and subsequent site-directed mutagenesis localized the RBC-binding site to the face opposite to the heparin-binding site of NTS-DBLα1. RBC binding involves residues that are conserved between rosette-forming PfEMP1 adhesins, opening novel opportunities for intervention against severe malaria. By deciphering the structural basis of blood group preferences in rosetting, we provide a link between ABO blood grouppolymorphisms and rosette-forming adhesins, consistent with the selective role of falciparum malaria on human genetic makeup. PMID:22807674

Lactose-containing starburst dendrimers: influence of dendrimer generation and binding-site orientation of receptors (plant/animal lectins and immunoglobulins) on binding properties.

PubMed

André, S; Ortega, P J; Perez, M A; Roy, R; Gabius, H J

1999-11-01

Starburst glycodendrimers offer the potential to serve as high-affinity ligands for clinically relevant sugar receptors. In order to define areas of application, their binding behavior towards sugar receptors with differential binding-site orientation but identical monosaccharide specificity must be evaluated. Using poly(amidoamine) starburst dendrimers of five generations, which contain the p-isothiocyanato derivative of p-aminophenyl-beta-D-lactoside as ligand group, four different types of galactoside-binding proteins were chosen for this purpose, i.e., the (AB)(2)-toxic agglutinin from mistletoe, a human immunoglobulin G fraction, the homodimeric galectin-1 with its two binding sites at opposite ends of the jelly-roll-motif-harboring protein and monomeric galectin-3. Direct solid-phase assays with surface-immobilized glycodendrimers resulted in obvious affinity enhancements by progressive core branching for the plant agglutinin and less pronounced for the antibody and galectin-1. High density of binding of galectin-3 with modest affinity increases only from the level of the 32-mer onwards points to favorable protein-protein interactions of the monomeric lectin and a spherical display of the end groups without a major share of backfolding. When the inhibitory potency of these probes was evaluated as competitor of receptor binding to an immobilized neoglycoprotein or to asialofetuin, a marked selectivity was detected. The 32- and 64-mers were second to none as inhibitors for the plant agglutinin against both ligand-exposing matrices and for galectin-1 on the matrix with a heterogeneous array of interglycoside distances even on the per-sugar basis. In contrast, a neoglycoprotein with the same end group was superior in the case of the antibody and, less pronounced, monomeric galectin-3. Intimate details of topological binding-site presentation and the ligand display on different generations of core assembly are major operative factors which determine the potential of dendrimers for applications as lectin-targeting device, as attested by these observations.

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach.

PubMed

Nielsen, Morten; Lundegaard, Claus; Worning, Peder; Hvid, Christina Sylvester; Lamberth, Kasper; Buus, Søren; Brunak, Søren; Lund, Ole

2004-06-12

Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates novel features optimized for the task of recognizing the binding motif of MHC classes I and II. The method locates the binding motif in a set of sequences and characterizes the motif in terms of a weight-matrix. Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design. We apply the motif sampler method to the complex problem of MHC class II binding. The input to the method is amino acid peptide sequences extracted from the public databases of SYFPEITHI and MHCPEP and known to bind to the MHC class II complex HLA-DR4(B1*0401). Prior identification of information-rich (anchor) positions in the binding motif is shown to improve the predictive performance of the Gibbs sampler. Similarly, a consensus solution obtained from an ensemble average over suboptimal solutions is shown to outperform the use of a single optimal solution. In a large-scale benchmark calculation, the performance is quantified using relative operating characteristics curve (ROC) plots and we make a detailed comparison of the performance with that of both the TEPITOPE method and a weight-matrix derived using the conventional alignment algorithm of ClustalW. The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method.

Comparison of crystal structures of human type 3 3α-hydroxysteroid dehydrogenase reveals an “induced-fit” mechanism and a conserved basic motif involved in the binding of androgen

PubMed Central

Couture, Jean-François; Pereira De Jésus-Tran, Karine; Roy, Anne-Marie; Cantin, Line; Côté, Pierre-Luc; Legrand, Pierre; Luu-The, Van; Labrie, Fernand; Breton, Rock

2005-01-01

The aldo-keto reductase (AKR) human type 3 3α-hydroxysteroid dehydrogenase (h3α–HSD3, AKR1C2) plays a crucial role in the regulation of the intracellular concentrations of testosterone and 5α-dihydrotestosterone (5α-DHT), two steroids directly linked to the etiology and the progression of many prostate diseases and cancer. This enzyme also binds many structurally different molecules such as 4-hydroxynonenal, polycyclic aromatic hydrocarbons, and indanone. To understand the mechanism underlying the plasticity of its substrate-binding site, we solved the binary complex structure of h3α–HSD3-NADP(H) at 1.9 Å resolution. During the refinement process, we found acetate and citrate molecules deeply engulfed in the steroid-binding cavity. Superimposition of this structure with the h3α–HSD3-NADP(H)-testosterone/acetate ternary complex structure reveals that one of themobile loops forming the binding cavity operates a slight contraction movement against the citrate molecule while the side chains of many residues undergo numerous conformational changes, probably to create an optimal binding site for the citrate. These structural changes, which altogether cause a reduction of the substrate-binding cavity volume (from 776 Å3 in the presence of testosterone/acetate to 704 Å3 in the acetate/citratecomplex), are reminiscent of the “induced-fit” mechanism previously proposed for the aldose reductase, another member of the AKR superfamily. We also found that the replacement of residues Arg301 and Arg304, localized near the steroid-binding cavity, significantly affects the 3α–HSD activity of this enzyme toward 5α-DHT and completely abolishes its 17β–HSD activity on 4-dione. All these results have thus been used to reevaluate the binding mode of this enzyme for androgens. PMID:15929998

Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters.

PubMed

Feng, Youjun; Cronan, John E

2011-04-01

Two transcriptional regulators, the FadR activator and the FabR repressor, control biosynthesis of unsaturated fatty acids in Escherichia coli. FabR represses expression of the two genes, fabA and fabB, required for unsaturated fatty acid synthesis and has been reported to require the presence of an unsaturated thioester (of either acyl carrier protein or CoA) in order to bind the fabA and fabB promoters in vitro. We report in vivo experiments in which unsaturated fatty acid synthesis was blocked in the absence of exogenous unsaturated fatty acids in a ΔfadR strain and found that the rates of transcription of fabA and fabB were unaffected by the lack of unsaturated thioesters. To examine the discrepancy between our in vivo results and the prior in vitro results we obtained active, natively folded forms of the E. coli and Vibrio cholerae FabRs by use of an in vitro transcription-translation system. We report that FabR bound the intact promoter regions of both fabA and fabB in the absence of unsaturated acyl thioesters, but bound the two promoters differently. Native FabR bound the fabA promoter region provided that the canonical FabR binding site is extended by inclusion of flanking sequences that overlap the neighbouring FadR binding site. In contrast, although binding to the fabB operator also required a flanking sequence, a non-specific sequence could suffice. However, unsaturated thioesters did allow FabR binding to the minimal FabR operator sites of both promoters which otherwise were not bound. Thus unsaturated thioester ligands were not essential for FabR/target DNA interaction, but acted to enhance binding. The gel mobility shift data plus in vivo expression data indicate that despite the remarkably similar arrangements of promoter elements, FadR predominately regulates fabA expression whereas FabR is the dominant regulator of fabB expression. We also report that E. coli fabR expression is not autoregulated. Complementation, qRT-PCR and fatty acid composition analyses demonstrated that V. cholerae FabR was a functional repressor of unsaturated fatty acid synthesis. However, in contrast to E. coli, gel mobility shift assays indicated that neither E. coli nor V. cholerae FabRs bound the V. cholerae fabB promoter, although both proteins efficiently bound the V. cholerae fabA promoter. This asymmetry was shown to be due to the lack of a FabR binding site within the V. cholerae fabB promoter region. © 2011 Blackwell Publishing Ltd.

The mechanism and high-free-energy transition state of lac repressor–lac operator interaction

PubMed Central

Sengupta, Rituparna; Capp, Michael W.; Shkel, Irina A.

2017-01-01

Abstract Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce kd without affecting ka significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO. PMID:29036376

The Mannitol Operon Repressor MTIR belongs to a new class of transcription regulators in bacteria.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, K.; Borovilos, M.; Zhou, M

2009-12-25

Many bacteria express phosphoenolpyruvate-dependent phosphotransferase systems (PTS). The mannitol-specific PTS catalyze the uptake and phosphorylation of d-mannitol. The uptake system comprises several genes encoded in the single operon. The expression of the mannitol operon is regulated by a proposed transcriptional factor, mannitol operon repressor (MtlR) that was first studied in Escherichia coli. Here we report the first crystal structures of MtlR from Vibrio parahemeolyticus (Vp-MtlR) and its homolog YggD protein from Shigella flexneri (Sf-YggD). MtlR and YggD belong to the same protein family (Pfam05068). Although Vp-MtlR and Sf-YggD share low sequence identity (22%), their overall structures are very similar, representingmore » a novel all {alpha}-helical fold, and indicate similar function. However, their lack of any known DNA-binding structural motifs and their unfavorable electrostatic properties imply that MtlR/YggD are unlikely to bind a specific DNA operator directly as proposed earlier. This structural observation is further corroborated by in vitro DNA-binding studies of E. coli MtlR (Ec-MtlR), which detected no interaction of Ec-MtlR with the well characterized mannitol operator/promoter region. Therefore, MtlR/YggD belongs to a new class of transcription factors in bacteria that may regulate gene expression indirectly as a part of a larger transcriptional complex.« less

[Changes of monocyte and monocyte-platelet aggregates in different subgroups of thrombotic events in patients with acute myocardial infarction during PCI].

PubMed

Wang, Sheng; Sun, Cuifang; Liao, Wang; Wu, Zhongwei; Wang, Yudai; Huang, Xiuxian; Lu, Sijia; Dong, Xiaoli; Shuai, Fujie; Li, Bin

2017-07-01

Objective To investigate the impact of thrombotic events on the alterations of monocyte and monocyte-platelet aggregates (MPAs) in patients with acute myocardial infarction (AMI) during percutaneous coronary intervention (PCI). Methods Blood was collected before PCI for flow cytometry. Monocyte subsets and MPAs were detected by four-color platform (CDl4-APC, CDl6-PE-Cy7, CD86-PE and CD41-Alexa Fluor R 488). According to the expression of the platelet surface marker CD41, the number of monocyte subsets and MPAs was analyzed using the fluorescent microspheres of absolute counting tube. The Wilcoxon rank sum test and receiver operating characteristic (ROC) curve analysis were performed. Results CD14 + CD16 ++ monocytes in intraprocedural thrombotic events (IPTE) group were significantly fewer than those in non-IPTE group, and the percentage in total mononuclear cells decreased. Compared with non-IPTE group, MPA binding ratio and monocyte subset MPA binding ratio were significantly higher in IPTE group. ROC analysis showed that MPA binding ratio and subgroup MPA binding ratio had a better predictive value for IPTE in patients with AMI. Conclusion The CD14 + CD16 ++ monocytes in IPTE group were significantly fewer than those in the non-IPTE group. MPA binding ratio and MPA binding ratio of monocyte subsets were significantly higher in the IPTE group than in the non-IPTE group, so they have a good predictive value for IPTE in patients with AMI.

High glucose disrupts oligosaccharide recognition function via competitive inhibition: a potential mechanism for immune dysregulation in diabetes mellitus.

PubMed

Ilyas, Rebecca; Wallis, Russell; Soilleux, Elizabeth J; Townsend, Paul; Zehnder, Daniel; Tan, Bee K; Sim, Robert B; Lehnert, Hendrik; Randeva, Harpal S; Mitchell, Daniel A

2011-01-01

Diabetic complications include infection and cardiovascular disease. Within the immune system, host-pathogen and regulatory host-host interactions operate through binding of oligosaccharides by C-type lectin. A number of C-type lectins recognise oligosaccharides rich in mannose and fucose - sugars with similar structures to glucose. This raises the possibility that high glucose conditions in diabetes affect protein-oligosaccharide interactions via competitive inhibition. Mannose-binding lectin, soluble DC-SIGN and DC-SIGNR, and surfactant protein D, were tested for carbohydrate binding in the presence of glucose concentrations typical of diabetes, via surface plasmon resonance and affinity chromatography. Complement activation assays were performed in high glucose. DC-SIGN and DC-SIGNR expression in adipose tissues was examined via immunohistochemistry. High glucose inhibited C-type lectin binding to high-mannose glycoprotein and binding of DC-SIGN to fucosylated ligand (blood group B) was abrogated in high glucose. Complement activation via the lectin pathway was inhibited in high glucose and also in high trehalose - a nonreducing sugar with glucoside stereochemistry. DC-SIGN staining was seen on cells with DC morphology within omental and subcutaneous adipose tissues. We conclude that high glucose disrupts C-type lectin function, potentially illuminating new perspectives on susceptibility to infectious and inflammatory disease in diabetes. Mechanisms involve competitive inhibition of carbohydrate binding within sets of defined proteins, in contrast to broadly indiscriminate, irreversible glycation of proteins. Copyright © 2010 Elsevier GmbH. All rights reserved.

The global repressor FliZ antagonizes gene expression by σS-containing RNA polymerase due to overlapping DNA binding specificity.

PubMed

Pesavento, Christina; Hengge, Regine

2012-06-01

FliZ, a global regulatory protein under the control of the flagellar master regulator FlhDC, was shown to antagonize σ(S)-dependent gene expression in Escherichia coli. Thereby it plays a pivotal role in the decision between alternative life-styles, i.e. FlhDC-controlled flagellum-based motility or σ(S)-dependent curli fimbriae-mediated adhesion and biofilm formation. Here, we show that FliZ is an abundant DNA-binding protein that inhibits gene expression mediated by σ(S) by recognizing operator sequences that resemble the -10 region of σ(S)-dependent promoters. FliZ does so with a structural element that is similar to region 3.0 of σ(S). Within this element, R108 in FliZ corresponds to K173 in σ(S), which contacts a conserved cytosine at the -13 promoter position that is specific for σ(S)-dependent promoters. R108 as well as C(-13) are also crucial for DNA binding by FliZ. However, while a number of FliZ binding sites correspond to known σ(S)-dependent promoters, promoter activity is not a prerequisite for FliZ binding and repressor function. Thus, we demonstrate that FliZ also feedback-controls flagellar gene expression by binding to a site in the flhDC control region that shows similarity only to a -10 element of a σ(S)-dependent promoter, but does not function as a promoter.

Entropy-enthalpy compensation at the single protein level: pH sensing in the bacterial channel OmpF.

PubMed

Alcaraz, Antonio; Queralt-Martín, María; Verdiá-Báguena, Carmina; Aguilella, Vicente M; Mafé, Salvador

2014-12-21

The pH sensing mechanism of the OmpF channel operates via ligand modification: increasing acidity induces the replacement of cations with protons in critical binding sites decreasing the channel conductance. Aside from the change in enthalpy associated with the binding, there is also a change in the microscopic arrangements of ligands, receptors and the surrounding solvent. We show that the pH-modulation of the single channel conduction involves small free energy changes because large enthalpic and entropic contributions change in opposite ways, demonstrating an approximate enthalpy-entropy compensation for different salts and concentrations.

Rapid incremental methods for the determination of serum iron and iron-binding capacity

PubMed Central

Beale, R. N.; Bostrom, J. O.; Taylor, R. F.

1961-01-01

Rapid methods depending on differential absorptiometry are described for the determination of the transferrin iron content and the latent iron-binding capacity of blood serum. Each determination requires as little as 0·5 ml. serum. The methods are well adapted for routine use in the `average' laboratory. Three or four sera may be completely analysed in 30 minutes. All operations are carried out in the cells or tubes used for the colorimetric measurements, no precipitation or heating being employed at any stage. Critical investigations of the reliability of the methods are attempted and ranges of normal values are included. PMID:13866116

Expression of Plant Receptor Kinases in Tobacco BY-2 Cells.

PubMed

Shinohara, Hidefumi; Matsubayashi, Yoshikatsu

2017-01-01

Although more than 600 single-transmembrane receptor kinase genes have been found in the Arabidopsis genome, only a few of them have known physiological functions, and even fewer plant receptor kinases have known specific ligands. Ligand-binding analysis must be operated using the functionally expressed receptor form. However, the relative abundance of native receptor kinase molecules in the plasma membrane is often quite low. Here, we present a method for stable and functional expression of plant receptor kinases in tobacco BY-2 cells that allows preparation of microsomal fractions containing the receptor. This procedure provides a sufficient amount of receptor proteins while maintaining its ligand-binding activities.

40 CFR 52.1488 - Visibility protection.

Code of Federal Regulations, 2011 CFR

2011-07-01

... substituting equivalent or superior control technology, provided such technology meets applicable emission... operator shall meet the following deadlines for design and construction of the emission control equipment... binding contract to design the SO2, opacity and NOX control systems for Unit 1 and Unit 2 by March 1, 2003...

40 CFR 52.1488 - Visibility protection.

Code of Federal Regulations, 2012 CFR

2012-07-01

... substituting equivalent or superior control technology, provided such technology meets applicable emission... operator shall meet the following deadlines for design and construction of the emission control equipment... binding contract to design the SO2, opacity and NOX control systems for Unit 1 and Unit 2 by March 1, 2003...

40 CFR 52.1488 - Visibility protection.

Code of Federal Regulations, 2013 CFR

2013-07-01

... substituting equivalent or superior control technology, provided such technology meets applicable emission... operator shall meet the following deadlines for design and construction of the emission control equipment... binding contract to design the SO2, opacity and NOX control systems for Unit 1 and Unit 2 by March 1, 2003...

40 CFR 52.1488 - Visibility protection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... substituting equivalent or superior control technology, provided such technology meets applicable emission... operator shall meet the following deadlines for design and construction of the emission control equipment... binding contract to design the SO2, opacity and NOX control systems for Unit 1 and Unit 2 by March 1, 2003...

46 CFR 308.542 - Warranty regarding thirty-day shipments.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 308.542 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Facultative War Risk Cargo Insurance § 308.542 Warranty regarding thirty-day shipments. If, after an effective binding of war risk insurance on a shipment of cargo, the...

Engineering cofactor and ligand binding in an artificial neuroglobin

NASA Astrophysics Data System (ADS)

Zhang, Lei

HP-7 is one artificial mutated oxygen transport protein, which operates via a mechanism akin to human neuroglobin and cytoglobin. This protein destabilizes one of two heme-ligating histidine residues by coupling histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Replacement of these glutamate residues with alanine, which has a neutral hydrophobicity, slows gaseous ligand binding 22-fold, increases the affinity of the distal histidine ligand by a factor of thirteen, and decreases the binding affinity of carbon monoxide, a nonreactive oxygen analogue, three-fold. Paradoxically, it also decreases heme binding affinity by a factor of three in the reduced state and six in the oxidized state. Application of a two-state binding model, in which an initial pentacoordinate binding event is followed by a protein conformational change to hexacoordinate, provides insight into the mechanism of this seemingly counterintuitive result: the initial pentacoordinate encounter complex is significantly destabilized by the loss of the glutamate side chains, and the increased affinity for the distal histidine only partially compensates. These results point to the importance of considering each oxidation and conformational state in the design of functional artificial proteins. We have also examined the effects these mutations have on function. The K d of the nonnreactive oxygen analogue carbon monoxide (CO) is only decreased three-fold, despite the large increase in distal histidine affinity engendered by the 22-fold decrease in the histidine ligand off-rate. This is a result of the four-fold increase in affinity for CO binding to the pentacoordinate state. Oxygen binds to HP7 with a Kd of 117 µM, while the mutant rapidly oxidizes when exposed to oxygen. EPR analysis of both ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation causes a large increase in water penetration into the protein core. The inability of the mutant protein may thus either be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors.

Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein‡

PubMed Central

Zhang, Lei; Andersen, Eskil M.E.; Khajo, Abdelahad; Magliozzo, Richard S.; Koder, Ronald L.

2013-01-01

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7 this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime which may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when when exposed to oxygen. Compared to HP7, distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off-rate. EPR comparison of these ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation greatly increases water penetration into the protein core. The inability of the mutant protein to bind oxygen may be due to increased water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together these data underline the importance of the control of protein dynamics in the design of functional artificial proteins. PMID:23249163

Dynamic factors affecting gaseous ligand binding in an artificial oxygen transport protein.

PubMed

Zhang, Lei; Andersen, Eskil M E; Khajo, Abdelahad; Magliozzo, Richard S; Koder, Ronald L

2013-01-22

We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7, this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities, and oxyferrous state lifetimes, of both heme binding sites in HP7. We find that despite the identical sequence of helices in both binding sites, there are differences in oxygen affinity and oxyferrous state lifetime that may be the result of differences in the freedom of motion imposed by the candelabra fold on the two sites of the protein. We further examine the effect of mutational removal of the buried glutamates on function. Heme iron in the ferrous state of this mutant is rapidly oxidized when exposed to oxygen. Compared to that of HP7, the distal histidine affinity is increased by a 22-fold decrease in the histidine ligand off rate. Electron paramagnetic resonance comparison of these ferric hemoproteins demonstrates that the mutation increases the level of disorder at the heme binding site. Nuclear magnetic resonance-detected deuterium exchange demonstrates that the mutation greatly increases the degree of penetration of water into the protein core. The inability of the mutant protein to bind oxygen may be due to an increased level of water penetration, the large decrease in binding rate caused by the increase in distal histidine affinity, or a combination of the two factors. Together, these data underline the importance of the control of protein dynamics in the design of functional artificial proteins.

Nanofiber adsorbents for high productivity downstream processing.

PubMed

Hardick, Oliver; Dods, Stewart; Stevens, Bob; Bracewell, Daniel G

2013-04-01

Electrospun polymeric nanofiber adsorbents offer an alternative ligand support surface for bioseparations. Their non-woven fiber structure with diameters in the sub-micron range creates a remarkably high surface area. To improve the purification productivity of biological molecules by chromatography, cellulose nanofiber adsorbents were fabricated and assembled into a cartridge and filter holder format with a volume of 0.15 mL, a bed height of 0.3 mm and diameter of 25 mm. The present study investigated the performance of diethylaminoethyl (DEAE) derivatized regenerated cellulose nanofiber adsorbents based on criteria including mass transfer and flow properties, binding capacity, and fouling effects. Our results show that nanofibers offer higher flow and mass transfer properties. The non-optimized DEAE-nanofiber adsorbents indicate a binding capacity of 10% that of packed bed systems with BSA as a single component system. However, they operate reproducibly at flowrates of a hundred times that of packed beds, resulting in a potential productivity increase of 10-fold. Lifetime studies showed that this novel adsorbent material operated reproducibly with complex feed material (centrifuged and 0.45 µm filtered yeast homogenate) and harsh cleaning-in-place conditions over multiple cycles. DEAE nanofibers showed superior operating performance in permeability and fouling over conventional adsorbents indicating their potential for bioseparation applications. Copyright © 2012 Wiley Periodicals, Inc.

40 CFR 98.4 - Authorization and responsibilities of the designated representative.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Administrator of a complete certificate of representation under this section for a facility or supplier, the designated representative identified in such certificate of representation shall represent and, by his or her representations, actions, inactions, or submissions, legally bind each owner and operator of such facility or...

50 CFR 600.1003 - Content of a request for a financed program.

Code of Federal Regulations, 2010 CFR

2010-10-01

... requester's endorsement in principle of the reduction amendment specifications in the business plan. Endorsement in principle is non-binding. (h) Request that NMFS conduct, at the appropriate time, a referendum... operating economics of typical harvesters in the reduction fishery, with particular emphasis on the extent...

40 CFR 63.3004 - What definitions apply to this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Requirements and Information § 63.3004 What definitions apply to this subpart? Terms used in this subpart are... application vacuum exhaust means the exhaust from the vacuum system used to remove excess resin solution from... binds the fibers. Emission limitation means an emission limit, operating limit, or work practice...

40 CFR 63.3004 - What definitions apply to this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... Requirements and Information § 63.3004 What definitions apply to this subpart? Terms used in this subpart are... application vacuum exhaust means the exhaust from the vacuum system used to remove excess resin solution from... binds the fibers. Emission limitation means an emission limit, operating limit, or work practice...

7 CFR 795.14 - Changes in farming operations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... existing under law, to divide, sell, transfer, rent, or lease his or her property if such division, sale, transfer, rental arrangement, or lease is legally binding as between the parties thereto. However, any document representing a division, sale, transfer, rental arrangement, or lease which is fictitious or not...

46 CFR 308.542 - Warranty re thirty-day shipments.

Code of Federal Regulations, 2011 CFR

2011-10-01

....542 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.542 Warranty re thirty-day shipments. If, after an effective binding of war risk insurance on a shipment of cargo, the assured believes...

46 CFR 308.542 - Warranty re thirty-day shipments.

Code of Federal Regulations, 2012 CFR

2012-10-01

....542 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.542 Warranty re thirty-day shipments. If, after an effective binding of war risk insurance on a shipment of cargo, the assured believes...

46 CFR 308.542 - Warranty re thirty-day shipments.

Code of Federal Regulations, 2010 CFR

2010-10-01

....542 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.542 Warranty re thirty-day shipments. If, after an effective binding of war risk insurance on a shipment of cargo, the assured believes...

46 CFR 308.542 - Warranty re thirty-day shipments.

Code of Federal Regulations, 2013 CFR

2013-10-01

....542 Shipping MARITIME ADMINISTRATION, DEPARTMENT OF TRANSPORTATION EMERGENCY OPERATIONS WAR RISK INSURANCE War Risk Cargo Insurance Iii-Facultative War Risk Cargo Insurance § 308.542 Warranty re thirty-day shipments. If, after an effective binding of war risk insurance on a shipment of cargo, the assured believes...

Cabin fuselage structural design with engine installation and control system

NASA Technical Reports Server (NTRS)

Balakrishnan, Tanapaal; Bishop, Mike; Gumus, Ilker; Gussy, Joel; Triggs, Mike

1994-01-01

Design requirements for the cabin, cabin system, flight controls, engine installation, and wing-fuselage interface that provide adequate interior volume for occupant seating, cabin ingress and egress, and safety are presented. The fuselage structure must be sufficient to meet the loadings specified in the appropriate sections of Federal Aviation Regulation Part 23. The critical structure must provide a safe life of 10(exp 6) load cycles and 10,000 operational mission cycles. The cabin seating and controls must provide adjustment to account for various pilot physiques and to aid in maintenance and operation of the aircraft. Seats and doors shall not bind or lockup under normal operation. Cabin systems such as heating and ventilation, electrical, lighting, intercom, and avionics must be included in the design. The control system will consist of ailerons, elevator, and rudders. The system must provide required deflections with a combination of push rods, bell cranks, pulleys, and linkages. The system will be free from slack and provide smooth operation without binding. Environmental considerations include variations in temperature and atmospheric pressure, protection against sand, dust, rain, humidity, ice, snow, salt/fog atmosphere, wind and gusts, and shock and vibration. The following design goals were set to meet the requirements of the statement of work: safety, performance, manufacturing and cost. To prevent the engine from penetrating the passenger area in the event of a crash was the primary safety concern. Weight and the fuselage aerodynamics were the primary performance concerns. Commonality and ease of manufacturing were major considerations to reduce cost.

FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis

PubMed Central

Deng, Weiwei; Ying, Hua; Helliwell, Chris A.; Taylor, Jennifer M.; Peacock, W. James; Dennis, Elizabeth S.

2011-01-01

FLOWERING LOCUS C (FLC) has a key role in the timing of the initiation of flowering in Arabidopsis. FLC binds and represses two genes that promote flowering, FT and SOC1. We show that FLC binds to many other genes, indicating that it has regulatory roles other than the repression of flowering. We identified 505 FLC binding sites, mostly located in the promoter regions of genes and containing at least one CArG box, the motif known to be associated with MADS-box proteins such as FLC. We examined 40 of the target genes, and 20 showed increased transcript levels in an flc mutant compared with the wild type. Five genes showed decreased expression in the mutant, indicating that FLC binding can result in either transcriptional repression or activation. The genes we identified as FLC targets are involved in developmental pathways throughout the life history of the plant, many of which are associated with reproductive development. FLC is also involved in vegetative development, as evidenced by its binding to SPL15, delaying the progression from juvenile to adult phase. Some of the FLC target genes are also bound by two other MADS-box proteins, AP1 and SEP3, suggesting that MADS-box genes may operate in a network of control at different stages of the life cycle, many ultimately contributing to the development of the reproductive phase of the plant. PMID:21464308

FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis.

PubMed

Deng, Weiwei; Ying, Hua; Helliwell, Chris A; Taylor, Jennifer M; Peacock, W James; Dennis, Elizabeth S

2011-04-19

FLOWERING LOCUS C (FLC) has a key role in the timing of the initiation of flowering in Arabidopsis. FLC binds and represses two genes that promote flowering, FT and SOC1. We show that FLC binds to many other genes, indicating that it has regulatory roles other than the repression of flowering. We identified 505 FLC binding sites, mostly located in the promoter regions of genes and containing at least one CArG box, the motif known to be associated with MADS-box proteins such as FLC. We examined 40 of the target genes, and 20 showed increased transcript levels in an flc mutant compared with the wild type. Five genes showed decreased expression in the mutant, indicating that FLC binding can result in either transcriptional repression or activation. The genes we identified as FLC targets are involved in developmental pathways throughout the life history of the plant, many of which are associated with reproductive development. FLC is also involved in vegetative development, as evidenced by its binding to SPL15, delaying the progression from juvenile to adult phase. Some of the FLC target genes are also bound by two other MADS-box proteins, AP1 and SEP3, suggesting that MADS-box genes may operate in a network of control at different stages of the life cycle, many ultimately contributing to the development of the reproductive phase of the plant.

Determination of binding affinity upon mutation for type I dockerin-cohesin complexes from Clostridium thermocellum and Clostridium cellulolyticum using deep sequencing.

PubMed

Kowalsky, Caitlin A; Whitehead, Timothy A

2016-12-01

The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

White collar 2, a partner in blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa.

PubMed Central

Linden, H; Macino, G

1997-01-01

A saturating genetic dissection of 'blind' mutants in Neurospora crassa has identified a total of two non-redundant loci (wc-1 and wc-2) each of which is required for blue-light perception/signal transduction. Previously, we demonstrated that WC1 is a putative zinc finger transcription factor able to bind specifically to a light-regulated promoter. Here, we present the cloning and characterization of the wc-2 gene. We demonstrate using mutation analysis and in vitro DNA-binding assays that WC2, the second partner of this light signal transduction system, encodes a functional zinc finger DNA-binding protein with putative PAS dimerization and transcription activation domains. This molecular genetic dissection of the second of two components of this light signal transduction system has enabled us to devise a model whereby WC1 and WC2 are proposed to interact via homologous PAS domains, bind to promoters of light-regulated genes and activate transcription. As such, this study provides the first insight into two co-operating partners in blue-light signal transduction in any organism and describes the molecular tools with which to dissect this enigmatic process. PMID:9009271

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires.

PubMed

Bergmann, Tobias; Moore, Carrie; Sidney, John; Miller, Donald; Tallmadge, Rebecca; Harman, Rebecca M; Oseroff, Carla; Wriston, Amanda; Shabanowitz, Jeffrey; Hunt, Donald F; Osterrieder, Nikolaus; Peters, Bjoern; Antczak, Douglas F; Sette, Alessandro

2015-11-01

Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25 % of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500 nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif.

The common equine class I molecule Eqca-1*00101 (ELA-A3.1) is characterized by narrow peptide binding and T cell epitope repertoires

PubMed Central

Bergmann, Tobias; Moore, Carrie; Sidney, John; Miller, Donald; Tallmadge, Rebecca; Harman, Rebecca M.; Oseroff, Carla; Wriston, Amanda; Shabanowitz, Jeffrey; Hunt, Donald F.; Osterrieder, Nikolaus; Peters, Bjoern; Antczak, Douglas F.; Sette, Alessandro

2016-01-01

Here we describe a detailed quantitative peptide-binding motif for the common equine leukocyte antigen (ELA) class I allele Eqca-1*00101, present in roughly 25 % of Thoroughbred horses. We determined a preliminary binding motif by sequencing endogenously bound ligands. Subsequently, a positional scanning combinatorial library (PSCL) was used to further characterize binding specificity and derive a quantitative motif involving aspartic acid in position 2 and hydrophobic residues at the C-terminus. Using this motif, we selected and tested 9- and 10-mer peptides derived from the equine herpesvirus type 1 (EHV-1) proteome for their capacity to bind Eqca-1*00101. PSCL predictions were very efficient, with an receiver operating characteristic (ROC) curve performance of 0.877, and 87 peptides derived from 40 different EHV-1 proteins were identified with affinities of 500 nM or higher. Quantitative analysis revealed that Eqca-1*00101 has a narrow peptide-binding repertoire, in comparison to those of most human, non-human primate, and mouse class I alleles. Peripheral blood mononuclear cells from six EHV-1-infected, or vaccinated but uninfected, Eqca-1*00101-positive horses were used in IFN-γ enzyme-linked immunospot (ELISPOT) assays. When we screened the 87 Eqca-1*00101-binding peptides for T cell reactivity, only one Eqca-1*00101 epitope, derived from the intermediate-early protein ICP4, was identified. Thus, despite its common occurrence in several horse breeds, Eqca-1*00101 is associated with a narrow binding repertoire and a similarly narrow T cell response to an important equine viral pathogen. Intriguingly, these features are shared with other human and macaque major histocompatibility complex (MHC) molecules with a similar specificity for D in position 2 or 3 in their main anchor motif. PMID:26399241

Regulation of the aceI multidrug efflux pump gene in Acinetobacter baumannii.

PubMed

Liu, Qi; Hassan, Karl A; Ashwood, Heather E; Gamage, Hasinika K A H; Li, Liping; Mabbutt, Bridget C; Paulsen, Ian T

2018-06-01

To investigate the function of AceR, a putative transcriptional regulator of the chlorhexidine efflux pump gene aceI in Acinetobacter baumannii. Chlorhexidine susceptibility and chlorhexidine induction of aceI gene expression were determined by MIC and quantitative real-time PCR, respectively, in A. baumannii WT and ΔaceR mutant strains. Recombinant AceR was prepared as both a full-length protein and as a truncated protein, AceR (86-299), i.e. AceRt, which has the DNA-binding domain deleted. The binding interaction of the purified AceR protein and its putative operator region was investigated by electrophoretic mobility shift assays and DNase I footprinting assays. The binding of AceRt with its putative ligand chlorhexidine was examined using surface plasmon resonance and tryptophan fluorescence quenching assays. MIC determination assays indicated that the ΔaceI and ΔaceR mutant strains both showed lower resistance to chlorhexidine than the parental strain. Chlorhexidine-induced expression of aceI was abolished in a ΔaceR background. Electrophoretic mobility shift assays and DNase I footprinting assays demonstrated chlorhexidine-stimulated binding of AceR with two sites upstream of the putative aceI promoter. Surface plasmon resonance and tryptophan fluorescence quenching assays suggested that the purified ligand-binding domain of the AceR protein was able to bind with chlorhexidine with high affinity. This study provides strong evidence that AceR is an activator of aceI gene expression when challenged with chlorhexidine. This study is the first characterization, to our knowledge, of a regulator controlling expression of a PACE family multidrug efflux pump.

Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression.

PubMed

Le, Tung B K; Stevenson, Clare E M; Fiedler, Hans-Peter; Maxwell, Anthony; Lawson, David M; Buttner, Mark J

2011-04-22

Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to operators in the intergenic region between simR and simX. Previously, we have shown that the mature antibiotic SD8 or its biosynthetic intermediate, simocyclinone C4, can dissociate SimR from its operators, leading to derepression of simX and export of SD8 from the cell. This provides a mechanism that couples the biosynthesis of the antibiotic to its export. Here, we report the crystal structures of SimR alone and in complex with either SD8 or simocyclinone C4. The ligand-binding pocket is unusual compared to those of other characterized TetR-family transcriptional regulators: the structures show an extensive ligand-binding pocket spanning both monomers in the functional dimeric unit, with the aminocoumarin moiety of SD8 buried in the protein core, while the angucyclic polyketide moiety is partially exposed to bulk solvent. Through comparisons of the structures, we postulate a derepression mechanism for SimR that invokes rigid-body motions of the subunits relative to one another, coupled with a putative locking mechanism to restrict further conformational change. Copyright © 2011 Elsevier Ltd. All rights reserved.

Enzyme catalysis by entropy without Circe effect.

PubMed

Kazemi, Masoud; Himo, Fahmi; Åqvist, Johan

2016-03-01

Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.

Enzyme catalysis by entropy without Circe effect

PubMed Central

Kazemi, Masoud; Himo, Fahmi; Åqvist, Johan

2016-01-01

Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution. PMID:26755610

The Study of Stability of Compression-loaded Multispan Composite Panel Upon Failure of elements Binding it to Panel Supports

NASA Technical Reports Server (NTRS)

Zamula, G. N.; Ierusalimsky, K. M.; Fomin, V. P.; Grishin, V. I.; Kalmykova, G. S.

1999-01-01

The present document is a final technical report under the NCC-1-233 research program (dated September 15, 1998; see Appendix 5) carried out within co-operation between United States'NASA Langley RC and Russia's Goskomoboronprom in aeronautics, and continues similar programs, NCCW-73, NCC-1-233 and NCCW 1-233 accomplished in 1996, 1997, and 1998, respectively. The report provides results of "The study of stability of compression-loaded multispan composite panels upon failure of elements binding it to panel supports"; these comply with requirements established at TsAGI on 24 March 1998 and at NASA on 15 September 1998.

Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goffinont, S.; Davidkova, M.; Spotheim-Maurizot, M., E-mail: spotheim@cnrs-orleans.fr

2009-08-21

The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro {gamma}-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucinemore » residues of the tetramerization domain.« less

Doping of germanium and silicon crystals with non-hydrogenic acceptors for far infrared lasers

DOEpatents

Haller, Eugene E.; Brundermann, Erik

2000-01-01

A method for doping semiconductors used for far infrared lasers with non-hydrogenic acceptors having binding energies larger than the energy of the laser photons. Doping of germanium or silicon crystals with beryllium, zinc or copper. A far infrared laser comprising germanium crystals doped with double or triple acceptor dopants permitting the doped laser to be tuned continuously from 1 to 4 terahertz and to operate in continuous mode. A method for operating semiconductor hole population inversion lasers with a closed cycle refrigerator.

Application of ‘tying, binding and fixing operation’ in surgical treatment of severe mixed hemorrhoids

PubMed Central

Huang, Hong-Xiang; Yao, Yi-Bo; Tang, Ying

2016-01-01

The aim of the present study was to examine the clinical value of ‘tying, binding and fixing operation’ in treating severe mixed hemorrhoids. A total of 160 patients with severe mixed hemorrhoids were selected and randomly divided into the experimental (n=80) and control (n=80) groups. The groups were treated using ‘tying, binding and fixing operation’ and Doppler ultrasound-guided hemorrhoidal artery ligation (DG-HAL), respectively. The results showed that the average operative time of the experimental group (35.57±6.17) was significantly higher than that of the control group (12.73±4.92). There was no significant difference of blood loss during the operation between the two groups (P>0.05). There was also no significant difference in improving the hemorrhage symptom between the two groups (P>0.05). In addition, concerning improvement of prolapse symptoms and reduction of the volume of hemorrhoids, the experimental group were significantly improved as compared to the control group. No anal function damage in the two groups was identified, and the length of stay in hospital for the two groups was not significantly different (P>0.05). However, the hospitalization cost in the experimental group (5,334.77±875.54) was significantly lower than that of the control group (8,551.81±1,806.54) and satisfaction degree was significantly higher than that of the control group. The incidences of perianal pain, anal edema and dysuria between two groups were not significantly different (P>0.05). There were 10 cases of secondary hemorrhage and 18 cases of infection in the experimental group, and 12 cases of secondary hemorrhage and 14 cases of infection in the control group, although the differences between the two groups were not statistically significant (P>0.05). The incidence rate of local hematoma in the experimental group (1.2%) was significantly lower than that in the control group (15.0%). The recurrence rate of the control group (22.5%) was also significantly higher than that of the experimental group (2.5%). In conclusion, tying, binding and fixing operation is a promising method that may be employed for the treatment of sever mixed hemorrhoids, and it is better than DG-HAL in improving the prolapse and reducing the volume of hemorrhoids. PMID:27446315

Electrostatic occlusion and quaternary structural ion pairing are key determinants of Cu(I)-mediated allostery in the copper-sensing operon repressor (CsoR).

PubMed

Chang, Feng-Ming James; Martin, Julia E; Giedroc, David P

2015-04-21

The copper-sensing operon repressor (CsoR) is an all-α-helical disc-shaped D2-symmetric homotetramer that forms a 2:1 tetramer/DNA operator complex and represses the expression of copper-resistance genes in a number of bacteria. A previous bioinformatics analysis of CsoR-family repressors distributes Cu(I)-sensing CsoRs in four of seven distinct clades on the basis of global sequence similarity. In this work, we define energetically important determinants of DNA binding in the apo-state (ΔΔGbind), and for allosteric negative coupling of Cu(I) binding to DNA binding (ΔΔGc) in a model clade IV CsoR from Geobacillus thermodenitrificans (Gt) of known structure, by selectively targeting for mutagenesis those charged residues uniquely conserved in clade IV CsoRs. These include a folded N-terminal "tail" and a number of Cu(I)-sensor and clade-specific residues that when mapped onto a model of Cu(I)-bound Gt CsoR define a path across one face of the tetramer. We find that Cu(I)-binding prevents formation of the 2:1 "sandwich" complex rather than DNA binding altogether. Folding of the N-terminal tail (residues R18, E22, R74) upon Cu-binding to the periphery of the tetramer inhibits assembly of the 2:1 apoprotein-DNA complex. In contrast, Ala substitution of residues that surround the central "hole" (R65, K101) in the tetramer, as well R48, impact DNA binding. We also identify a quaternary structural ion-pair, E73-K101″, that crosses the tetramer interface, charge-reversal of which restores DNA binding activity, allosteric regulation by Cu(I), and transcriptional derepression by Cu(I) in cells. These findings suggest an "electrostatic occlusion" model, in which basic residues important for DNA binding and/or allostery become sequestered via ion-pairing specifically in the Cu(I)-bound state, and this aids in copper-dependent disassembly of a repression complex.

40 CFR 96.210 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2012 CFR

2012-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR SO2 source... a complete certificate of representation under § 96.213 for a CAIR designated representative of the...

40 CFR 96.210 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2013 CFR

2013-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR SO2 source... a complete certificate of representation under § 96.213 for a CAIR designated representative of the...

40 CFR 96.110 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2012 CFR

2012-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR NOX source... received a complete certificate of representation under § 96.113 for a CAIR designated representative of...

40 CFR 96.110 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2010 CFR

2010-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR NOX source... received a complete certificate of representation under § 96.113 for a CAIR designated representative of...

40 CFR 96.110 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2014 CFR

2014-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR NOX source... received a complete certificate of representation under § 96.113 for a CAIR designated representative of...

40 CFR 96.210 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2014 CFR

2014-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR SO2 source... a complete certificate of representation under § 96.213 for a CAIR designated representative of the...

40 CFR 96.110 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2011 CFR

2011-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR NOX source... received a complete certificate of representation under § 96.113 for a CAIR designated representative of...

40 CFR 96.210 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2011 CFR

2011-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR SO2 source... a complete certificate of representation under § 96.213 for a CAIR designated representative of the...

40 CFR 60.4110 - Authorization and Responsibilities of Hg designated representative.

Code of Federal Regulations, 2011 CFR

2011-07-01

... representation under § 60.4113, the Hg designated representative of the source shall represent and, by his or her representations, actions, inactions, or submissions, legally bind each owner and operator of the Hg Budget source... complete certificate of representation under § 60.4113 for a Hg designated representative of the source and...

40 CFR 96.110 - Authorization and responsibilities of CAIR designated representative.

Code of Federal Regulations, 2013 CFR

2013-07-01

...)(4)(iv). (c) Upon receipt by the Administrator of a complete certificate of representation under § 96... representations, actions, inactions, or submissions, legally bind each owner and operator of the CAIR NOX source... received a complete certificate of representation under § 96.113 for a CAIR designated representative of...

40 CFR 60.4110 - Authorization and Responsibilities of Hg designated representative.

Code of Federal Regulations, 2010 CFR

2010-07-01

... representation under § 60.4113, the Hg designated representative of the source shall represent and, by his or her representations, actions, inactions, or submissions, legally bind each owner and operator of the Hg Budget source... complete certificate of representation under § 60.4113 for a Hg designated representative of the source and...

40 CFR 63.4281 - Am I subject to this subpart?

Code of Federal Regulations, 2013 CFR

2013-07-01

... fabric, rainwear, sheets, tents, threads and V-belts. The coating and printing subcategory includes any... slashing process, sizing compounds are applied to warp yarn to bind the fiber together and stiffen the yarn..., sheets, towels, and threads. (b) You are subject to this subpart if you own or operate a new...

40 CFR 63.4281 - Am I subject to this subpart?

Code of Federal Regulations, 2014 CFR

2014-07-01

... fabric, rainwear, sheets, tents, threads and V-belts. The coating and printing subcategory includes any... slashing process, sizing compounds are applied to warp yarn to bind the fiber together and stiffen the yarn..., sheets, towels, and threads. (b) You are subject to this subpart if you own or operate a new...

40 CFR 63.4281 - Am I subject to this subpart?

Code of Federal Regulations, 2012 CFR

2012-07-01

... fabric, rainwear, sheets, tents, threads and V-belts. The coating and printing subcategory includes any... slashing process, sizing compounds are applied to warp yarn to bind the fiber together and stiffen the yarn..., sheets, towels, and threads. (b) You are subject to this subpart if you own or operate a new...

iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases

USDA-ARS?s Scientific Manuscript database

Transcription factors (TFs) are proteins that regulate the expression of target genes by binding to specific elements in their regulatory regions. Transcriptional regulators (TRs) also regulate the expression of target genes; however, they operate indirectly via interaction with the basal transcript...

Annual Report for Contract Number N00014-88-K-0641 (Carnegie Mellon Univ)

DTIC Science & Technology

1991-09-30

labor -intensive process of data conversion. " The described mechanism might provide a course of action for coping with the Software Release Problem, i.e...8217 reover alorihm wll uarmet:thedatbaseis estred All subsequent setq operations to variable will change the bind- to aprevousy saed onsiten stae. ng

76 FR 21044 - Notice of Entering Into a Compact With the Republic of Malawi

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-14

...) Operations: MCC funding will support change management efforts, designing human resources strategies... efforts to implement a suitable market model which will include efforts to: (a) Study and design a single... from time to time in accordance with the terms hereof, the ``Program'') to counter a key binding...

Gqalpha-linked PLCbeta and PLCgamma are essential components of the pheromone biosynthesis activating neuropeptide (PBAN) signal transduction cascade

USDA-ARS?s Scientific Manuscript database

Sex pheromone production for most moths is regulated by pheromone biosynthesis activating neuropeptide (PBAN). In Bombyx mori, PBAN binding triggers the opening of store-operated Ca2+ channels, suggesting the involvement of a receptor-activated phospholipase C (PLC). In this study, we found that P...

Singlet oxygen-dependent translational control in the tigrina-d.12 mutant of barley.

PubMed

Khandal, Dhriti; Samol, Iga; Buhr, Frank; Pollmann, Stephan; Schmidt, Holger; Clemens, Stephan; Reinbothe, Steffen; Reinbothe, Christiane

2009-08-04

The tigrina (tig)-d.12 mutant of barley is impaired in the negative control limiting excess protochlorophyllide (Pchlide) accumulation in the dark. Upon illumination, Pchlide operates as photosensitizer and triggers singlet oxygen production and cell death. Here, we show that both Pchlide and singlet oxygen operate as signals that control gene expression and metabolite accumulation in tig-d.12 plants. In vivo labeling, Northern blotting, polysome profiling, and protein gel blot analyses revealed a selective suppression of synthesis of the small and large subunits of ribulose-1,5-bisphosphate carboxylase/oxygenase (RBCSs and RBCLs), the major light-harvesting chlorophyll a/b-binding protein of photosystem II (LHCB2), as well as other chlorophyll-binding proteins, in response to singlet oxygen. In part, these effects were caused by an arrest in translation initiation of photosynthetic transcripts at 80S cytoplasmic ribosomes. The observed changes in translation correlated with a decline in the phosphorylation level of ribosomal protein S6. At later stages, ribosome dissociation occurred. Together, our results identify translation as a major target of singlet oxygen-dependent growth control and cell death in higher plants.

Nonlocal torque operators in ab initio theory of the Gilbert damping in random ferromagnetic alloys

NASA Astrophysics Data System (ADS)

Turek, I.; Kudrnovský, J.; Drchal, V.

2015-12-01

We present an ab initio theory of the Gilbert damping in substitutionally disordered ferromagnetic alloys. The theory rests on introduced nonlocal torques which replace traditional local torque operators in the well-known torque-correlation formula and which can be formulated within the atomic-sphere approximation. The formalism is sketched in a simple tight-binding model and worked out in detail in the relativistic tight-binding linear muffin-tin orbital method and the coherent potential approximation (CPA). The resulting nonlocal torques are represented by nonrandom, non-site-diagonal, and spin-independent matrices, which simplifies the configuration averaging. The CPA-vertex corrections play a crucial role for the internal consistency of the theory and for its exact equivalence to other first-principles approaches based on the random local torques. This equivalence is also illustrated by the calculated Gilbert damping parameters for binary NiFe and FeCo random alloys, for pure iron with a model atomic-level disorder, and for stoichiometric FePt alloys with a varying degree of L 10 atomic long-range order.

Pairing tendencies in a two-orbital Hubbard model in one dimension

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, Niravkumar D.; Nocera, Adriana; Alvarez, Gonzalo

The recent discovery of superconductivity under high pressure in the ladder compound BaFe2S3 has opened a new field of research in iron-based superconductors with focus on quasi-one-dimensional geometries. In this publication, using the density matrix renormalization group technique, we study a two-orbital Hubbard model defined in one-dimensional chains. Our main result is the presence of hole binding tendencies at intermediate Hubbard U repulsion and robust Hund coupling JH / U = 0.25. Binding does not occur either in weak coupling or at very strong coupling. The pair-pair correlations that are dominant near half-filling, or of similar strength as the chargemore » and spin correlation channels, involve hole-pair operators that are spin singlets, use nearest-neighbor sites, and employ different orbitals for each hole. As a result, the Hund coupling strength, presence of robust magnetic moments, and antiferromagnetic correlations among them are important for the binding tendencies found here.« less

Free Energy Wells and Barriers to Ion Transport Across Membranes

NASA Astrophysics Data System (ADS)

Rempe, Susan

2014-03-01

The flow of ions across cellular membranes is essential to many biological processes. Ion transport is also important in synthetic materials used as battery electrolytes. Transport often involves specific ions and fast conduction. To achieve those properties, ion conduction pathways must solvate specific ions by just the ``right amount.'' The right amount of solvation avoids ion traps due to deep free energy wells, and avoids ion block due to high free energy barriers. Ion channel proteins in cellular membranes demonstrate this subtle balance in solvation of specific ions. Using ab initio molecular simulations, we have interrogated the link between binding site structure and ion solvation free energies in biological ion binding sites. Our results emphasize the surprisingly important role of the environment that surrounds ion-binding sites for fast transport of specific ions. We acknowledge support from Sandia's LDRD program. Sandia National Labs is a multi-program laboratory operated by Sandia Corp., a wholly owned subsidiary of Lockheed Martin Corp., for the US DOE's NNSA under contract DE-AC04-94AL85000.

Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

PubMed

Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

Mechanistic determinants of the directionality and energetics of active export by a heterodimeric ABC transporter

DOE PAGES

Grossmann, Nina; Vakkasoglu, Ahmet S.; Hulpke, Sabine; ...

2014-11-07

The ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) participates in immune surveillance by moving proteasomal products into the endoplasmic reticulum (ER) lumen for major histocompatibility complex class I loading and cell surface presentation to cytotoxic T cells. Here we delineate the mechanistic basis for antigen translocation. Notably, TAP works as a molecular diode, translocating peptide substrates against the gradient in a strict unidirectional way. We reveal the importance of the D-loop at the dimer interface of the two nucleotide-binding domains (NBDs) in coupling substrate translocation with ATP hydrolysis and defining transport vectoriality. Substitution of the converved aspartate, whichmore » coordinates the ATP-binding site, decreases NBD dimerization affinity and turns the unidirectional primary active pump into a passive bidirectional nucleotide-gated facilitator. Thus, ATP hydrolysis is not required for translocation per se, but is essential for both active and unidirectional transport. As a result, our data provide detailed mechanistic insight into how heterodimeric ABC exporters operate.« less

A label-free approach to detect ligand binding to cell surface proteins in real time.

PubMed

Burtscher, Verena; Hotka, Matej; Li, Yang; Freissmuth, Michael; Sandtner, Walter

2018-04-26

Electrophysiological recordings allow for monitoring the operation of proteins with high temporal resolution down to the single molecule level. This technique has been exploited to track either ion flow arising from channel opening or the synchronized movement of charged residues and/or ions within the membrane electric field. Here, we describe a novel type of current by using the serotonin transporter (SERT) as a model. We examined transient currents elicited on rapid application of specific SERT inhibitors. Our analysis shows that these currents originate from ligand binding and not from a long-range conformational change. The Gouy-Chapman model predicts that adsorption of charged ligands to surface proteins must produce displacement currents and related apparent changes in membrane capacitance. Here we verified these predictions with SERT. Our observations demonstrate that ligand binding to a protein can be monitored in real time and in a label-free manner by recording the membrane capacitance. © 2018, Burtscher et al.

Role of riboswitches in gene regulation and their potential for algal biotechnology.

PubMed

Nguyen, Ginnie T D T; Scaife, Mark A; Helliwell, Katherine E; Smith, Alison G

2016-06-01

Riboswitches are regulatory elements in messenger RNA to which specific ligands can bind directly in the absence of proteins. Ligand binding alters the mRNA secondary structure, thereby affecting expression of the encoded protein. Riboswitches are widespread in prokaryotes, with over 20 different effector ligands known, including amino acids, cofactors, and Mg(2+) ions, and gene expression is generally regulated by affecting translation or termination of transcription. In plants, fungi, and microalgae, riboswitches have been found, but only those that bind thiamine pyrophosphate. These eukaryotic riboswitches operate by causing alternative splicing of the transcript. Here, we review the current status of riboswitch research with specific emphasis on microalgae. We discuss new riboswitch discoveries and insights into the underlying mechanism of action, and how next generation sequencing technology provides the motivation and opportunity to improve our understanding of these rare but important regulatory elements. We also highlight the potential of microalgal riboswitches as a tool for synthetic biology and industrial biotechnology. © 2016 Phycological Society of America.

Principles of regulatory information conservation between mouse and human

DOE PAGES

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; ...

2014-11-19

To broaden our understanding of the evolution of gene regulation mechanisms, we generated occupancy profiles for 34 orthologous transcription factors (TFs) in human–mouse erythroid progenitor, lymphoblast and embryonic stem-cell lines. By combining the genome-wide transcription factor occupancy repertoires, associated epigenetic signals, and co-association patterns, here we deduce several evolutionary principles of gene regulatory features operating since the mouse and human lineages diverged. The genomic distribution profiles, primary binding motifs, chromatin states, and DNA methylation preferences are well conserved for TF-occupied sequences. However, the extent to which orthologous DNA segments are bound by orthologous TFs varies both among TFs and withmore » genomic location: binding at promoters is more highly conserved than binding at distal elements. Notably, occupancy-conserved TF-occupied sequences tend to be pleiotropic; they function in several tissues and also co-associate with many TFs. Lastly, single nucleotide variants at sites with potential regulatory functions are enriched in occupancy-conserved TF-occupied sequences.« less

Pig liver pyruvate carboxylase. The reaction pathway for the decarboxylation of oxaloacetate

PubMed Central

Warren, Graham B.; Tipton, Keith F.

1974-01-01

1. The reaction pathway for the decarboxylation of oxaloacetate, catalysed by pig liver pyruvate carboxylase, was studied in the presence of saturating concentrations of K+ and acetyl-CoA. 2. Free Mg2+ binds to the enzyme in an equilibrium fashion and remains bound during all further catalytic cycles. MgADP− and Pi bind randomly, at equilibrium, followed by the binding of oxaloacetate. Pyruvate is released before the ordered steay-state release of HCO3− and MgATP2−. 3. These results are entirely consistent with studies on the carboxylation of pyruvate presented in the preceding paper (Warren & Tipton, 1974b) and together they allow a quantitative description of the reaction mechanism of pig liver pyruvate carboxylase. 4. In the absence of other substrates of the back reaction pig liver pyruvate carboxylase will decarboxylate oxaloacetate in a manner that is not inhibited by avidin. 5. Reciprocal plots involving oxaloacetate are non-linear curves, which suggest a negatively co-operative interaction between this substrate and the enzyme. PMID:4447613

GREEN: A program package for docking studies in rational drug design

NASA Astrophysics Data System (ADS)

Tomioka, Nobuo; Itai, Akiko

1994-08-01

A program package, GREEN, has been developed that enables docking studies between ligand molecules and a protein molecule. Based on the structure of the protein molecule, the physical and chemical environment of the ligand-binding site is expressed as three-dimensional grid-point data. The grid-point data are used for the real-time evaluation of the protein-ligand interaction energy, as well as for the graphical representation of the binding-site environment. The interactive docking operation is facilitated by various built-in functions, such as energy minimization, energy contribution analysis and logging of the manipulation trajectory. Interactive modeling functions are incorporated for designing new ligand molecules while considering the binding-site environment and the protein-ligand interaction. As an example of the application of GREEN, a docking study is presented on the complex between trypsin and a synthetic trypsin inhibitor. The program package will be useful for rational drug design, based on the 3D structure of the target protein.

A method for fast energy estimation and visualization of protein-ligand interaction

NASA Astrophysics Data System (ADS)

Tomioka, Nobuo; Itai, Akiko; Iitaka, Yoichi

1987-10-01

A new computational and graphical method for facilitating ligand-protein docking studies is developed on a three-dimensional computer graphics display. Various physical and chemical properties inside the ligand binding pocket of a receptor protein, whose structure is elucidated by X-ray crystal analysis, are calculated on three-dimensional grid points and are stored in advance. By utilizing those tabulated data, it is possible to estimate the non-bonded and electrostatic interaction energy and the number of possible hydrogen bonds between protein and ligand molecules in real time during an interactive docking operation. The method also provides a comprehensive visualization of the local environment inside the binding pocket. With this method, it becomes easier to find a roughly stable geometry of ligand molecules, and one can therefore make a rapid survey of the binding capability of many drug candidates. The method will be useful for drug design as well as for the examination of protein-ligand interactions.

Prospective study of the changes in thyrotropin binding inhibitory immunoglobulins in Graves' disease treated by subtotal thyroidectomy or radioactive iodine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teng, C.S.; Yeung, R.T.T.; Khoo, R.K.K.

1980-06-01

The effects of subtotal thyroidectomy and radioactive iodine on thyroid-stimulating immunoglobulins, as measured by a receptor assay, more appropriately termed TSH binding inhibitory immunoglobulins (TBII), were studied in 74 patients with Graves' disease. Fourty-four patients received radioactive iodine therapy, while 30 were subjected to subtotal thyroidectomy. After radioactive iodine, more patients were TBII-positive (90.5% vs 81.8%) than before treatment, and the mean TBII index decreased dramatically, the maximum decrease being 3 months. The mean TBI index subsequently returned gradually to the pretreatment level. Subtotal thyroidectomy had a different effect on TBII activity. TBII indices were positive in 89.3% of thesemore » patients before any treatment but were positive in only 40% (12 patients) after antithyroid drugs had been given before surgery. After surgery, TBII indices remained positive in 7 patients, while the remaining 5 patients became TBII negative. Seventeen patients (56.7%) were TBII negative before operation and remained so after surgery. One patient who was TBII negative before operation became TBII positive 2 months after operation. Interestingly, postoperative relapse of hyperthyroidism occurred in 3 patients who were TIBII positive, while hypothyroidism occurred in patients who were TBII negative. Thus, the TBII activity after subtotal thyroidectomy might be an important factor in determining the outcome of surgery.« less

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Changsoo; Tesar, Christine; Li, Xiaoqing

2015-10-04

Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraRmore » forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.« less

A novel transcriptional regulator of L-arabinose utilization in human gut bacteria

DOE PAGES

Chang, Changsoo; Tesar, Christine; Li, Xiaoqing; ...

2015-10-04

We report that carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specificmore » DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. In the structure of the BtAraR–DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA. L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding. Furthermore, our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.« less

Genome-wide DNA methylation measurements in prostate tissues uncovers novel prostate cancer diagnostic biomarkers and transcription factor binding patterns.

PubMed

Kirby, Marie K; Ramaker, Ryne C; Roberts, Brian S; Lasseigne, Brittany N; Gunther, David S; Burwell, Todd C; Davis, Nicholas S; Gulzar, Zulfiqar G; Absher, Devin M; Cooper, Sara J; Brooks, James D; Myers, Richard M

2017-04-17

Current diagnostic tools for prostate cancer lack specificity and sensitivity for detecting very early lesions. DNA methylation is a stable genomic modification that is detectable in peripheral patient fluids such as urine and blood plasma that could serve as a non-invasive diagnostic biomarker for prostate cancer. We measured genome-wide DNA methylation patterns in 73 clinically annotated fresh-frozen prostate cancers and 63 benign-adjacent prostate tissues using the Illumina Infinium HumanMethylation450 BeadChip array. We overlaid the most significantly differentially methylated sites in the genome with transcription factor binding sites measured by the Encyclopedia of DNA Elements consortium. We used logistic regression and receiver operating characteristic curves to assess the performance of candidate diagnostic models. We identified methylation patterns that have a high predictive power for distinguishing malignant prostate tissue from benign-adjacent prostate tissue, and these methylation signatures were validated using data from The Cancer Genome Atlas Project. Furthermore, by overlaying ENCODE transcription factor binding data, we observed an enrichment of enhancer of zeste homolog 2 binding in gene regulatory regions with higher DNA methylation in malignant prostate tissues. DNA methylation patterns are greatly altered in prostate cancer tissue in comparison to benign-adjacent tissue. We have discovered patterns of DNA methylation marks that can distinguish prostate cancers with high specificity and sensitivity in multiple patient tissue cohorts, and we have identified transcription factors binding in these differentially methylated regions that may play important roles in prostate cancer development.

Insight into the Interaction of Metal Ions with TroA from Streptococcus suis

PubMed Central

Zheng, Beiwen; Zhang, Qiangmin; Gao, Jia; Han, Huiming; Li, Ming; Zhang, Jingren; Qi, Jianxun; Yan, Jinghua; Gao, George F.

2011-01-01

Background The scavenging ability of sufficient divalent metal ions is pivotal for pathogenic bacteria to survive in the host. ATP-binding cassette (ABC)-type metal transporters provide a considerable amount of different transition metals for bacterial growth. TroA is a substrate binding protein for uptake of multiple metal ions. However, the function and structure of the TroA homologue from the epidemic Streptococcus suis isolates (SsTroA) have not been characterized. Methodology/Principal Findings Here we determined the crystal structure of SsTroA from a highly pathogenic streptococcal toxic shock syndrome (STSS)-causing Streptococcus suis in complex with zinc. Inductively coupled plasma mass spectrometry (ICP-MS) analysis revealed that apo-SsTroA binds Zn2+ and Mn2+. Both metals bind to SsTroA with nanomolar affinity and stabilize the protein against thermal unfolding. Zn2+ and Mn2+ induce distinct conformational changes in SsTroA compared with the apo form as confirmed by both circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra. NMR data also revealed that Zn2+/Mn2+ bind to SsTroA in either the same site or an adjacent region. Finally, we found that the folding of the metal-bound protein is more compact than the corresponding apoprotein. Conclusions/Significance Our findings reveal a mechanism for uptake of metal ions in S. suis and this mechanism provides a reasonable explanation as to how SsTroA operates in metal transport. PMID:21611125

Learning abstract visual concepts via probabilistic program induction in a Language of Thought.

PubMed

Overlan, Matthew C; Jacobs, Robert A; Piantadosi, Steven T

2017-11-01

The ability to learn abstract concepts is a powerful component of human cognition. It has been argued that variable binding is the key element enabling this ability, but the computational aspects of variable binding remain poorly understood. Here, we address this shortcoming by formalizing the Hierarchical Language of Thought (HLOT) model of rule learning. Given a set of data items, the model uses Bayesian inference to infer a probability distribution over stochastic programs that implement variable binding. Because the model makes use of symbolic variables as well as Bayesian inference and programs with stochastic primitives, it combines many of the advantages of both symbolic and statistical approaches to cognitive modeling. To evaluate the model, we conducted an experiment in which human subjects viewed training items and then judged which test items belong to the same concept as the training items. We found that the HLOT model provides a close match to human generalization patterns, significantly outperforming two variants of the Generalized Context Model, one variant based on string similarity and the other based on visual similarity using features from a deep convolutional neural network. Additional results suggest that variable binding happens automatically, implying that binding operations do not add complexity to peoples' hypothesized rules. Overall, this work demonstrates that a cognitive model combining symbolic variables with Bayesian inference and stochastic program primitives provides a new perspective for understanding people's patterns of generalization. Copyright © 2017 Elsevier B.V. All rights reserved.

Zonal Rate Model for Axial and Radial Flow Membrane Chromatography. Part I: Knowledge Transfer Across Operating Conditions and Scales

PubMed Central

Ghosh, Pranay; Vahedipour, Kaveh; Lin, Min; Vogel, Jens H; Haynes, Charles A; von Lieres, Eric

2013-01-01

The zonal rate model (ZRM) has previously been applied for analyzing the performance of axial flow membrane chromatography capsules by independently determining the impacts of flow and binding related non-idealities on measured breakthrough curves. In the present study, the ZRM is extended to radial flow configurations, which are commonly used at larger scales. The axial flow XT5 capsule and the radial flow XT140 capsule from Pall are rigorously analyzed under binding and non-binding conditions with bovine serum albumin (BSA) as test molecule. The binding data of this molecule is much better reproduced by the spreading model, which hypothesizes different binding orientations, than by the well-known Langmuir model. Moreover, a revised cleaning protocol with NaCl instead of NaOH and minimizing the storage time has been identified as most critical for quantitatively reproducing the measured breakthrough curves. The internal geometry of both capsules is visualized by magnetic resonance imaging (MRI). The flow in the external hold-up volumes of the XT140 capsule was found to be more homogeneous as in the previously studied XT5 capsule. An attempt for model-based scale-up was apparently impeded by irregular pleat structures in the used XT140 capsule, which might lead to local variations in the linear velocity through the membrane stack. However, the presented approach is universal and can be applied to different capsules. The ZRM is shown to potentially help save valuable material and time, as the experiments required for model calibration are much cheaper than the predicted large-scale experiment at binding conditions. Biotechnol. Bioeng. 2013; 110: 1129–1141. © 2012 Wiley Periodicals, Inc. PMID:23097218

Mass-action equilibrium and non-specific interactions in protein binding networks

NASA Astrophysics Data System (ADS)

Maslov, Sergei

2009-03-01

Large-scale protein binding networks serve as a paradigm of complex properties of living cells. These networks are naturally weighted with edges characterized by binding strength and protein-nodes -- by their concentrations. However, the state-of-the-art high-throughput experimental techniques generate just a binary (yes or no) information about individual interactions. As a result, most of the previous research concentrated just on topology of these networks. In a series of recent publications [1-4] my collaborators and I went beyond purely topological studies and calculated the mass-action equilibrium of a genome-wide binding network using experimentally determined protein concentrations, localizations, and reliable binding interactions in baker's yeast. We then studied how this equilibrium responds to large perturbations [1-2] and noise [3] in concentrations of proteins. We demonstrated that the change in the equilibrium concentration of a protein exponentially decays (and sign-alternates) with its network distance away from the perturbed node. This explains why, despite a globally connected topology, individual functional modules in such networks are able to operate fairly independently. In a separate study [4] we quantified the interplay between specific and non-specific binding interactions under crowded conditions inside living cells. We show how the need to limit the waste of resources constrains the number of types and concentrations of proteins that are present at the same time and at the same place in yeast cells. [1] S Maslov, I. Ispolatov, PNAS 104:13655 (2007). [2] S. Maslov, K. Sneppen, I. Ispolatov, New J. of Phys. 9: 273 (2007). [3] K-K. Yan, D. Walker, S. Maslov, PRL accepted (2008). [4] J. Zhang, S. Maslov, and E. I. Shakhnovich, Mol Syst Biol 4, 210 (2008).

Thermodynamics of the GTP-GDP-operated Conformational Switch of Selenocysteine-specific Translation Factor SelB*

PubMed Central

Paleskava, Alena; Konevega, Andrey L.; Rodnina, Marina V.

2012-01-01

SelB is a specialized translation factor that binds GTP and GDP and delivers selenocysteyl-tRNA (Sec-tRNASec) to the ribosome. By analogy to elongation factor Tu (EF-Tu), SelB is expected to control the delivery and release of Sec-tRNASec to the ribosome by the structural switch between GTP- and GDP-bound conformations. However, crystal structures of SelB suggested a similar domain arrangement in the apo form and GDP- and GTP-bound forms of the factor, raising the question of how SelB can fulfill its delivery function. Here, we studied the thermodynamics of guanine nucleotide binding to SelB by isothermal titration calorimetry in the temperature range between 10 and 25 °C using GTP, GDP, and two nonhydrolyzable GTP analogs, guanosine 5′-O-(γ-thio)triphosphate (GTPγS) and guanosine 5′-(β,γ-imido)-triphosphate (GDPNP). The binding of SelB to either guanine nucleotide is characterized by a large heat capacity change (−621, −467, −235, and −275 cal × mol−1 × K−1, with GTP, GTPγS, GDPNP, and GDP, respectively), associated with compensatory changes in binding entropy and enthalpy. Changes in heat capacity indicate a large decrease of the solvent-accessible surface area in SelB, amounting to 43 or 32 amino acids buried upon binding of GTP or GTPγS, respectively, and 15–19 amino acids upon binding GDP or GDPNP. The similarity of the GTP and GDP forms in the crystal structures can be attributed to the use of GDPNP, which appears to induce a structure of SelB that is more similar to the GDP than to the GTP-bound form. PMID:22740700

Different Fatty Acids Compete with Arachidonic Acid for Binding to the Allosteric or Catalytic Subunits of Cyclooxygenases to Regulate Prostanoid Synthesis*

PubMed Central

Dong, Liang; Zou, Hechang; Yuan, Chong; Hong, Yu H.; Kuklev, Dmitry V.; Smith, William L.

2016-01-01

Prostaglandin endoperoxide H synthases (PGHSs), also called cyclooxygenases (COXs), convert arachidonic acid (AA) to PGH2. PGHS-1 and PGHS-2 are conformational heterodimers, each composed of an (Eallo) and a catalytic (Ecat) monomer. Previous studies suggested that the binding to Eallo of saturated or monounsaturated fatty acids (FAs) that are not COX substrates differentially regulate PGHS-1 versus PGHS-2. Here, we substantiate and expand this concept to include polyunsaturated FAs known to modulate COX activities. Non-substrate FAs like palmitic acid bind Eallo of PGHSs stimulating human (hu) PGHS-2 but inhibiting huPGHS-1. We find the maximal effects of non-substrate FAs on both huPGHSs occurring at the same physiologically relevant FA/AA ratio of ∼20. This inverse allosteric regulation likely underlies the ability of PGHS-2 to operate at low AA concentrations, when PGHS-1 is effectively latent. Unlike FAs tested previously, we observe that C-22 FAs, including ω-3 fish oil FAs, have higher affinities for Ecat than Eallo subunits of PGHSs. Curiously, C-20 ω-3 eicosapentaenoate preferentially binds Ecat of huPGHS-1 but Eallo of huPGHS-2. PGE2 production decreases 50% when fish oil consumption produces tissue EPA/AA ratios of ≥0.2. However, 50% inhibition of huPGHS-1 itself is only seen with ω-3 FA/AA ratios of ≥5.0. This suggests that fish oil-enriched diets disfavor AA oxygenation by altering the composition of the FA pool in which PGHS-1 functions. The distinctive binding specificities of PGHS subunits permit different combinations of non-esterified FAs, which can be manipulated dietarily, to regulate AA binding to Eallo and/or Ecat thereby controlling COX activities. PMID:26703471

iDNA-Prot: Identification of DNA Binding Proteins Using Random Forest with Grey Model

PubMed Central

Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

2011-01-01

DNA-binding proteins play crucial roles in various cellular processes. Developing high throughput tools for rapidly and effectively identifying DNA-binding proteins is one of the major challenges in the field of genome annotation. Although many efforts have been made in this regard, further effort is needed to enhance the prediction power. By incorporating the features into the general form of pseudo amino acid composition that were extracted from protein sequences via the “grey model” and by adopting the random forest operation engine, we proposed a new predictor, called iDNA-Prot, for identifying uncharacterized proteins as DNA-binding proteins or non-DNA binding proteins based on their amino acid sequences information alone. The overall success rate by iDNA-Prot was 83.96% that was obtained via jackknife tests on a newly constructed stringent benchmark dataset in which none of the proteins included has pairwise sequence identity to any other in a same subset. In addition to achieving high success rate, the computational time for iDNA-Prot is remarkably shorter in comparison with the relevant existing predictors. Hence it is anticipated that iDNA-Prot may become a useful high throughput tool for large-scale analysis of DNA-binding proteins. As a user-friendly web-server, iDNA-Prot is freely accessible to the public at the web-site on http://icpr.jci.edu.cn/bioinfo/iDNA-Prot or http://www.jci-bioinfo.cn/iDNA-Prot. Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results. PMID:21935457