Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin

Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.Comment: to appear in Biophysical Journal (2009). to appear in Biophysical Journal (2009

Subchronic Exposure to TCDD, PeCDF, PCB126, and PCB153: Effect on Hepatic Gene Expression

We employed DNA microarray to identify unique hepatic gene expression patterns associated with subchronic exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and other halogenated aromatic hydrocarbons (HAHs). Female Harlan Sprague-Dawley rats were exposed for 13 weeks to toxicologically equivalent doses of four different HAHs based on the toxic equivalency factor of each chemical: TCDD (100 ng/kg/day), 2,3,4,7,8-pentachlorodibenzofuran (PeCDF; 200 ng/kg/day), 3,3′,4,4′,5-pentachlorobiphenyl (PCB126; 1,000 ng/kg/day), or 2,2′,4,4′,5,5′-hexachlorobiphenyl (PCB153; 1,000 μg/kg/day). Global gene expression profiles for each exposure, which account for 8,799 gene probe sets contained on Affymetrix RGU34A GeneChips, were compared by principal components analysis. The aryl hydrocarbon receptor (AhR) ligands TCDD, PeCDF, and PCB126 produced very similar global gene expression profiles that were unique from the nonAhR ligand PCB153, underscoring the extensive impact of AhR activation and/or the resulting hepatic injury on global gene expression in female rat liver. Many genes were co-expressed during the 13-week TCDD, PeCDF, or PCB126 exposures, including classical AhR-regulated genes and some genes not previously characterized as being AhR regulated, such as carcinoembryonic-cell adhesion molecule 4 (C-CAM4) and adenylate cyclase-associated protein 2 (CAP2). Real-time reverse-transcriptase polymerase chain reaction confirmed the increased expression of these genes in TCDD-, PeCDF-, and PCB126-exposed rats as well as the up- or down-regulation of several other novel dioxin-responsive genes. In summary, DNA microarray successfully identified dioxin-responsive genes expressed after exposure to AhR ligands (TCDD, PeCDF, PCB126) but not after exposure to the non-AhR ligand PCB153. Together, these findings may help to elucidate some of the fundamental features of dioxin toxicity and may further clarify the biologic role of the AhR signaling pathway

Delayed onset of tricuspid valve flow in repaired tetralogy of Fallot: an additional mechanism of diastolic dysfunction and interventricular dyssynchrony

<p>Abstract</p> <p>Background</p> <p>Diastolic dysfunction of the right ventricle (RV) is common after repair of tetralogy of Fallot. While restrictive physiology in late diastole has been well known, dysfunction in early diastole has not been described. The present study sought to assess the prevalence and mechanism of early diastolic dysfunction of the RV defined as delayed onset of the tricuspid valve (TV) flow after TOF repair.</p> <p>Methods</p> <p>The study population consisted of 31 children with repaired TOF (mean age ± SD, 12.3 ± 4.1 years) who underwent postoperative cardiovascular magnetic resonance (CMR). The CMR protocol included simultaneous phase-contrast velocity mapping of the atrioventricular valves, which enabled direct comparison of the timing and patterns of tricuspid (TV) and mitral (MV) valve flow. The TV flow was defined to have delayed onset when its onset was > 20 ms later than the onset of the MV flow. The TV and MV flow from 14 normal children was used for comparison. The CMR results were correlated with the findings on echocardiography and electrocardiography.</p> <p>Result</p> <p>Delayed onset of the TV flow was observed in 16/31 patients and in none of the controls. The mean delay time was 64.81 ± 27.07 ms (8.7 ± 3.2% of R-R interval). The delay time correlated with the differences in duration of the TV and MV flow (55.94 ± 32.88 ms) (r = 0.90, <it>p </it>< 0.001). Delayed onset was associated with prolongation of the RV ejection time in 9 and delayed onset and cessation of the pulmonary arterial flow in 4. Delayed onset was not associated with timing changes in the pulmonary artery in 3. The patients with delayed onset showed reduced RV ejection fraction (p = 0.01). However, the two groups did not show significant differences in TV E/A ratio, ventricular end-diastolic volumes, left ventricular ejection fraction, pulmonary regurgitant fraction, heart rate, PR interval and QRS duration.</p> <p>Conclusions</p> <p>Early diastolic dysfunction with delayed onset of TV flow is common after TOF repair, and is associated with reduced RV ejection fraction. It is a further manifestation of interventricular dyssynchrony and represent an additional mechanism of ventricular diastolic dysfunction.</p

The information needs of people living with ankylosing spondylitis: a questionnaire survey

&lt;p&gt;BACKGROUND:Today, health care is patient-centred with patients more involved in medical decision making and taking an active role in managing their disease. It is important that patients are appropriately informed about their condition and that their health care needs are met. We examine the information utilisation, sources and needs of people with ankylosing spondylitis (AS).&lt;/p&gt; &lt;p&gt;METHODS: Participants in an existing AS cohort study were asked to complete a postal or online questionnaire containing closed and open-ended questions, regarding their information access and needs. Participants were stratified by age and descriptive statistics were performed using STATA 11, while thematic analysis was performed on open-ended question narratives. Qualitative data was handled in Microsoft Access and explored for emerging themes and patterns of experiences.&lt;/p&gt; &lt;p&gt;RESULTS: Despite 73% of respondents having internet access, only 49% used the internet to access information regarding AS. Even then, this was only infrequently. Only 50% of respondents reported accessing written information about AS, which was obtained mainly in specialist clinics. Women were more likely than men to access information (63% (women) 46% (men)) regardless of the source, while younger patients were more likely to use online sources. The main source of non-written information was the rheumatologist. Overall, the respondents felt there was sufficient information available, but there was a perception that the tone was often too negative. The majority (95%) of people would like to receive a regular newsletter about AS, containing positive practical and local information. Suggestions were also made for more information about AS to be made available to non-specialist medical professionals and the general public.&lt;/p&gt; &lt;p&gt;CONCLUSIONS: There appears to be sufficient information available for people with AS in the UK and this is mostly accessed by younger AS patients. Many patients, particularly men, choose not to access AS information and concerns were raised about its negative tone. Patients still rely on written and verbal information from their specialists. Future initiatives should focus on the delivery of more positive information, targeting younger participants in particular and increasing the awareness in the general population and wider non-specialist medical community.&lt;/p&gt

Ameliorating effect of Erxian decoction combined with Fructus Schisandrae chinensis (Wu Wei Zi) on menopausal sweating and serum hormone profiles in a rat model

Additional file 3. The animal studies were performed following the ARRIVE guideline

Folding, Stability and Shape of Proteins in Crowded Environments: Experimental and Computational Approaches

How the crowded environment inside cells affects folding, stability and structures of proteins is a vital question, since most proteins are made and function inside cells. Here we describe how crowded conditions can be created in vitro and in silico and how we have used this to probe effects on protein properties. We have found that folded forms of proteins become more compact in the presence of macromolecular crowding agents; if the protein is aspherical, the shape also changes (extent dictated by native-state stability and chemical conditions). It was also discovered that the shape of the macromolecular crowding agent modulates the folding mechanism of a protein; in addition, the extent of asphericity of the protein itself is an important factor in defining its folding speed

An Exactly Solvable Model for the Integrability-Chaos Transition in Rough Quantum Billiards

A central question of dynamics, largely open in the quantum case, is to what extent it erases a system's memory of its initial properties. Here we present a simple statistically solvable quantum model describing this memory loss across an integrability-chaos transition under a perturbation obeying no selection rules. From the perspective of quantum localization-delocalization on the lattice of quantum numbers, we are dealing with a situation where every lattice site is coupled to every other site with the same strength, on average. The model also rigorously justifies a similar set of relationships recently proposed in the context of two short-range-interacting ultracold atoms in a harmonic waveguide. Application of our model to an ensemble of uncorrelated impurities on a rectangular lattice gives good agreement with ab initio numerics.Comment: 29 pages, 5 figure

New criteria for assessing low wind environment at pedestrian level in Hong Kong

The choice of proper wind comfort criterion is considered to be crucial to reliable assessment of pedestrian level wind comfort. This paper aims to propose a wind comfort criterion that can be applied to Hong Kong, in which the wind comfort is seriously deteriorated by the moderated airflow, particularly in the hot and humid summer. By thoroughly reviewing and comparing exiting wind comfort criteria, the parameters in Lawson (1978) criterion are adopted for acceptable, tolerable and intolerable category and the parameters in NEN8100 (2006) criterion are adopted for danger category in the proposed criteria. Besides, a low wind parameter suggested by AVA scheme (2005) is adopted for unfavourable category in summer criterion. The adopted parameters provide scientific foundations and they are carefully chosen to adapt the weak wind conditions. The prominent features of the criteria are proposed seasonally (summer and winter, respectively) and the overall mean wind velocity ratio (OMVR) is used as threshold wind velocity parameter. The wind tunnel tests of Hong Kong Polytechnic University (HKPolyU) campus model were used as a case study. The results show that the proposed criteria can reasonably represent the weak wind condition and provide suitable assessments of the wind comfort in Hong Kong. Moreover, the findings in this study provide scientific basis for future policy-making and the proposed criteria can also help city planners to improve the pedestrian level wind comfort.Department of Building Services Engineering2016-2017 > Academic research: refereed > Publication in refereed journalbcr

Genetic analysis of variation in human meiotic recombination

The number of recombination events per meiosis varies extensively among individuals. This recombination phenotype differs between female and male, and also among individuals of each gender. In this study, we used high-density SNP genotypes of over 2,300 individuals and their offspring in two datasets to characterize recombination landscape and to map the genetic variants that contribute to variation in recombination phenotypes. We found six genetic loci that are associated with recombination phenotypes. Two of these (RNF212 and an inversion on chromosome 17q21.31) were previously reported in the Icelandic population, and this is the first replication in any other population. Of the four newly identified loci (KIAA1462, PDZK1, UGCG, NUB1), results from expression studies provide support for their roles in meiosis. Each of the variants that we identified explains only a small fraction of the individual variation in recombination. Notably, we found different sequence variants associated with female and male recombination phenotypes, suggesting that they are regulated by different genes. Characterization of genetic variants that influence natural variation in meiotic recombination will lead to a better understanding of normal meiotic events as well as of non-disjunction, the primary cause of pregnancy loss. © 2009 Chowdhury et al

Genome-wide Haplotype Association Mapping in mice identifies a genetic variant in CER1 associated with bone mineral density and fracture in southern Chinese women

INTRODUCTION: Osteoporosis is characterized by a decrease in bone mass, deterioration of bone tissue, impaired bone strength and increased fracture risk. It is a medically, socially, and economically important disease, especially among the aging population. Bone Mass Density (BMD) is a quantitative index of osteoporosis. Acquisition of bone mineral is a complex process involving genetics and environmental factors. METHODS: A genome-wide Haplotype Association Mapping (HAM) approach was performed by using inbred mice strains which had been genotyped and phenotyped in the Mouse Phenome Project. In HAM, a dense SNPs map was first partitioned into blocks of three SNPs with an average length of 1Mb. Modified F-statistics were calculated for the whole genome to test if blocks exist where the haplotypes can partition inbred strains into high and low BMD groups. In this study, the candidate gene Cerberus 1 (Cer1) suggested from HAM analysis was eventually tested by a human case-control cohort of 1,083 subjects. RESULTS AND CONCLUSION: In this study, we used a HAM approach to identify a haplotype block within Cer1 that partitions inbred mice strains into high and low BMD groups. A cohort of 1083 high and low BMD human subjects were studied and a non-synonymous SNP (rs3747532) in human CER1 was identified to be associated with increased risk of both low BMD in premenopausal women (OR 2.2; 95% confidence interval: 1.0 - 4.6; p < 0.05) and increased risk of vertebral fractures (OR 1.82, p=0.025) in the post-menopausal cohort. We also showed that Cer1 is expressed in mouse bone and growth plate by RT-PCR, immunohistochemistry and in situ hybridization, consistent with polymorphisms potentially influencing bone mineral density. Our successful identification of an association with CER1 in humans together with our mouse study suggests that CER1 may play a role in the development of bone or its metabolism.postprintThe 59th Annual Meeting of The American Society of Human Genetics (ASHG), Honolulu, HI., 20-24 October 2009