The Influence of Heparan Sulfate on Breast Amyloidosis and the Toxicity of the Pre-fibrils Formed by β-casein

The Protein Journal - Heparan sulfate (HS) as a mediator is usually involved in both inflammation and fibrosis. Besides, pre-fibrils are the intermediates of amyloid fibrils that usually cause cell...     

The Influence of Study Schedules and Work on the Sleep–Wake Cycle of College Students

College students usually exhibit an irregular sleep-wake cycle characterized by great phase delays on weekends and short sleep length on weekdays. As the temporal organization of social activities is an important synchronizer of human biological rhythms, we investigated the role played by study's schedules and work on the sleep-wake cycle. Three groups of female college students were investigated: (1) no-job morning group, (2) no-job evening group, (3) job evening group. The volunteers answered a sleep questionnaire in the classroom. The effects of day of the week and group on the sleep schedules and sleep length were analyzed by a two way ANOVA for repeated measures. The three groups showed delays in the wake up time on weekends. No-job evening and morning groups also delayed bedtime, but the job evening group slept at the same time on weekdays as on weekends. Sleep length increased on weekends for morning group and job evening group, whereas the no-job evening group maintained the amount of sleep from weekdays to weekends. This survey showed that the tendency of phase delay on weekends was differently expressed according to study's schedules and work.     

The Influence of the Non‐Nucleotide Insert on the Hybridization Properties of Oligonucleotides

The effect of different non‐nucleotide inserts incorporated into oligonucleotide chains on their hybridization properties was studied by the method of thermal denaturation. Various types of alkyldiols and oligoethylene glycols were used as inserts modifying oligonucleotide backbone. Such modification of oligonucleotides caused the destabilization of their complementary complexes. It was shown that the hybridization properties of the modified oligonucleotides depend on several features of inserts: the type, number, length of insertions, and positions of interrupted dinucleotide steps in oligonucleotide chain.     

The AlphaFold Database of Protein Structures: A Biologist’s Guide

AlphaFold, the deep learning algorithm developed by DeepMind, recently released the three-dimensional models of the whole human proteome to the scientific community. Here we discuss the advantages, limitations and the still unsolved challenges of the AlphaFold models from the perspective of a biologist, who may not be an expert in structural biology.     

The Influence of Data Resolution on Predicted Distribution and Estimates of Extent of Current Protection of Three ‘Listed’ Deep-Sea Habitats

Modelling approaches have the potential to significantly contribute to the spatial management of the deep-sea ecosystem in a cost effective manner. However, we currently have little understanding of the accuracy of such models, developed using limited data, of varying resolution. The aim of this study was to investigate the performance of predictive models constructed using non-simulated (real world) data of different resolution. Predicted distribution maps for three deep-sea habitats were constructed using MaxEnt modelling methods using high resolution multibeam bathymetric data and associated terrain derived variables as predictors. Model performance was evaluated using repeated 75/25 training/test data partitions using AUC and threshold-dependent assessment methods. The overall extent and distribution of each habitat, and the percentage contained within an existing MPA network were quantified and compared to results from low resolution GEBCO models. Predicted spatial extent for scleractinian coral reef and Syringammina fragilissima aggregations decreased with an increase in model resolution, whereas Pheronema carpenteri total suitable area increased. Distinct differences in predicted habitat distribution were observed for all three habitats. Estimates of habitat extent contained within the MPA network all increased when modelled at fine scale. High resolution models performed better than low resolution models according to threshold-dependent evaluation. We recommend the use of high resolution multibeam bathymetry data over low resolution bathymetry data for use in modelling approaches. We do not recommend the use of predictive models to produce absolute values of habitat extent, but likely areas of suitable habitat. Assessments of MPA network effectiveness based on calculations of percentage area protection (policy driven conservation targets) from low resolution models are likely to be fit for purpose.     

Influence of Protein – Micelle Ratios and Cysteine Residues on the Kinetic Stability and Unfolding Rates of Human Mitochondrial VDAC-2

Delineating the kinetic and thermodynamic factors which contribute to the stability of transmembrane β-barrels is critical to gain an in-depth understanding of membrane protein behavior. Human mitochondrial voltage-dependent anion channel isoform 2 (hVDAC-2), one of the key anti-apoptotic eukaryotic β-barrel proteins, is of paramount importance, owing to its indispensable role in cell survival. We demonstrate here that the stability of hVDAC-2 bears a strong kinetic contribution that is dependent on the absolute micellar concentration used for barrel folding. The refolding efficiency and ensuing stability is sensitive to the lipid-to-protein (LPR) ratio, and displays a non-linear relationship, with both low and high micellar amounts being detrimental to hVDAC-2 structure. Unfolding and aggregation process are sequential events and show strong temperature dependence. We demonstrate that an optimal lipid-to-protein ratio of 2600∶1 – 13000∶1 offers the highest protection against thermal denaturation. Activation energies derived only for lower LPRs are ∼17 kcal mol⁻¹ for full-length hVDAC-2 and ∼23 kcal mol⁻¹ for the Cys-less mutant, suggesting that the nine cysteine residues of hVDAC-2 impart additional malleability to the barrel scaffold. Our studies reveal that cysteine residues play a key role in the kinetic stability of the protein, determine barrel rigidity and thereby give rise to strong micellar association of hVDAC-2. Non-linearity of the Arrhenius plot at high LPRs coupled with observation of protein aggregation upon thermal denaturation indicates that contributions from both kinetic and thermodynamic components stabilize the 19-stranded β-barrel. Lipid-protein interaction and the linked kinetic contribution to free energy of the folded protein are together expected to play a key role in hVDAC-2 recycling and the functional switch at the onset of apoptosis.     

The Influence of Minimum Sitting Period of the ActivPAL? on the Measurement of Breaks in Sitting in Young Children

Background

Sitting time and breaks in sitting influence cardio-metabolic health. New monitors (e.g. activPAL™) may be more accurate for measurement of sitting time and breaks in sitting although how to optimize measurement accuracy is not yet clear. One important issue is the minimum sitting/upright period (MSUP) to define a new posture. Using the activPAL™, we investigated the effect of variations in MSUP on total sitting time and breaks in sitting, and also determined the criterion validity of different activPAL™ settings for both constructs.

Methods

We varied setting of MSUP in 23 children (mean (SD) age 4.5 y (0.7)) who wore activPAL™ (24 hr/d) for 5–7 d. We first studied activPAL™ using the default setting of 10 s MSUP and then reduced this to 5 s, 2 s and 1 s. In a second study, in a convenience sample of 30 pre-school children (mean age 4.1 y (SD 0.5)) we validated the activPAL™ measures of sitting time and breaks in sitting at different MSUP settings against direct observation.

Results

Comparing settings of 10, 5, 2 and 1 s, there were no significant differences in sitting time (6.2 hr (1.0), 6.3 hr (1.0), 6.4 hr (1.0) and 6.3 hr (1.6), respectively) between settings but there were significant increases in the apparent number of breaks - (8(3), 14(2), 21(4) and 28 (6)/h) at 10, 5, 2 and 1 s settings, respectively. In comparison with direct observation, a 2 s setting had the smallest error relative to direct observation (95% limits of agreement: -14 to +17 sitting bouts/hr, mean difference 1.83, p = 0.2).

Conclusion

With activPAL™, breaks in sitting, but not total sitting time, are highly sensitive to the setting of MSUP, with 2 s optimal for young children. The MSUP to define a new posture will need to be empirically determined if accurate measurements of number of breaks in sitting are to be obtained.     

Do Seasons Have an Influence on the Incidence of Depression? The Use of an Internet Search Engine Query Data as a Proxy of Human Affect

Background

Seasonal depression has generated considerable clinical interest in recent years. Despite a common belief that people in higher latitudes are more vulnerable to low mood during the winter, it has never been demonstrated that human''s moods are subject to seasonal change on a global scale. The aim of this study was to investigate large-scale seasonal patterns of depression using Internet search query data as a signature and proxy of human affect.

Methodology/Principal Findings

Our study was based on a publicly available search engine database, Google Insights for Search, which provides time series data of weekly search trends from January 1, 2004 to June 30, 2009. We applied an empirical mode decomposition method to isolate seasonal components of health-related search trends of depression in 54 geographic areas worldwide. We identified a seasonal trend of depression that was opposite between the northern and southern hemispheres; this trend was significantly correlated with seasonal oscillations of temperature (USA: r = −0.872, p<0.001; Australia: r = −0.656, p<0.001). Based on analyses of search trends over 54 geological locations worldwide, we found that the degree of correlation between searching for depression and temperature was latitude-dependent (northern hemisphere: r = −0.686; p<0.001; southern hemisphere: r = 0.871; p<0.0001).

Conclusions/Significance

Our findings indicate that Internet searches for depression from people in higher latitudes are more vulnerable to seasonal change, whereas this phenomenon is obscured in tropical areas. This phenomenon exists universally across countries, regardless of language. This study provides novel, Internet-based evidence for the epidemiology of seasonal depression.     

The Specificity of Controlled Protein Disorder in the Photoprotection of?Plants

Light-harvesting pigment-protein complexes of photosystem II of plants have a dual function: they efficiently use absorbed energy for photosynthesis at limiting sunlight intensity and dissipate the excess energy at saturating intensity for photoprotection. Recent single-molecule spectroscopy studies on the trimeric LHCII complex showed that environmental control of the intrinsic protein disorder could in principle explain the switch between their light-harvesting and photoprotective conformations in vivo. However, the validity of this proposal depends strongly on the specificity of the protein dynamics. Here, a similar study has been performed on the minor monomeric antenna complexes of photosystem II (CP29, CP26, and CP24). Despite their high structural homology, similar pigment content and organization compared to LHCII trimers, the environmental response of these proteins was found to be rather distinct. A much larger proportion of the minor antenna complexes were present in permanently weakly fluorescent states under most conditions used; however, unlike LHCII trimers the distribution of the single-molecule population between the strongly and weakly fluorescent states showed no significant sensitivity to low pH, zeaxanthin, or low detergent conditions. The results support a unique role for LHCII trimers in the regulation of light harvesting by controlled fluorescence blinking and suggest that any contribution of the minor antenna complexes to photoprotection would probably involve a distinct mechanism.     

The Influence of Cosolvent on the Complexation of HP-β-cyclodextrins with Oleanolic Acid and Ursolic Acid

The present work was aimed at the influence of ethanol on the complex formation of hydroxypropyl-β-cyclodextrin (HP-β-CD) with oleanolic acid (OA) and ursolic acid (UA), two insoluble isomeric triterpenic acids. Phase solubility studies were carried out to evaluate the solubilizing power of HP-β-CD, in association with ethanol, toward OA and UA. A mathematical model was applied to explain and predict the solubility of OA and UA influenced by HP-β-CD and ethanol. The solid complexes were prepared by evaporating the filtrate of samples which was prepared in different complexing media. The solubility of OA is much higher than that of UA in all the tested aqueous solutions. The solubility of OA and UA can be increased over 900 and 200 times, respectively, by forming complex with HP-β-CD. Ethanol (0.5%, v/v) can help the formation of OA-HP-β-CD complex, but is harmful to the formation of UA-HP-β-CD complex. Increasing solubility in water can be achieved by adding ethanol into the complexing media, but the concentration of ethanol should be optimized. The ring E of the chemical compounds has a great influence on the complexing process.     

Influence of Cholesterol and ��-Sitosterol on the Structure of EYPC Bilayers

The influence of cholesterol and β-sitosterol on egg yolk phosphatidylcholine (EYPC) bilayers is compared. Different interactions of these sterols with EYPC bilayers were observed using X-ray diffraction. Cholesterol was miscible with EYPC in the studied concentration range (0-50 mol%), but crystallization of β-sitosterol in EYPC bilayers was observed at X ≥ 41 mol% as detected by X-ray diffraction. Moreover, the repeat distance (d) of the lamellar phase was similar upon addition of the two sterols up to mole fraction 17%, while for X ≥ 17 mol% it became higher in the presence of β-sitosterol compared to cholesterol. SANS data on suspensions of unilamellar vesicles showed that both cholesterol and β-sitosterol similarly increase the EYPC bilayer thickness. Cholesterol in amounts above 33 mol% decreased the interlamellar water layer thickness, probably due to "stiffening" of the bilayer. This effect was not manifested by β-sitosterol, in particular due to the lower solubility of β-sitosterol in EYPC bilayers. Applying the formalism of partial molecular areas, it is shown that the condensing effect of both sterols on the EYPC area at the lipid-water interface is small, if any. The parameters of ESR spectra of spin labels localized in different regions of the EYPC bilayer did not reveal any differences between the effects of cholesterol and β-sitosterol in the range of full miscibility.     

Influence of proline and β-turn mimetics on the cyclization of penta- and hexapeptides

Summary Proline and Pro-derived peptidomimetics, such as meoxPro-Oic (4-methoxy-proline-octahydro indolic acid), and DBF (2-aminoethyl-6-dibenzofuran propionic acid) were introduced into thymopentin-derived penta-[SP5-] and hexa-[SP6-] peptides and penta-, hexa- and hepta-alanine. Surprisingly, we found that cyclomonomer formation in the investigated penta- and hexapeptides was drastically hindered by the presence of proline regardless of position.     

Protein aggregation and amyloidosis: confusion of the kinds?

Recent years have witnessed major advances in our understanding of the structural basis of protein aggregation on several fronts. Firstly, high-resolution structural information that remained elusive for many years was provided by a series of studies of amyloid fibers using NMR, X-ray crystallography and electron microscopy, thereby confirming earlier models based on lower resolution observations. Secondly, studies of the sequence determinants of protein aggregation culminated in the development of computer algorithms that predict aggregation-prone sequences with good accuracy, allowing the design of mutations that reduce aggregation. Thirdly, based on the first results from such predictions and on statistical analysis of naturally occurring aggregating sequences, a picture is emerging in which aggregation-prone sequences are capped by gatekeeper residues that oppose aggregation. In addition to their aggregation-opposing function, it seems that gatekeeper residues are also important in determining chaperone selectivity for strongly aggregating regions. Finally, recent computational and experimental work shows that preventing aggregation does not necessarily mean that amyloid formation is prevented and vice versa. Thus, although aggregation and amyloidosis correlate to a certain extent, they are different processes and should be treated as such.