The functional roles of the unstructured N- and C-terminal regions in αB-crystallin and other mammalian small heat-shock proteins

Small heat-shock proteins (sHsps), such as αB-crystallin, are one of the major classes of molecular chaperone proteins. In vivo, under conditions of cellular stress, sHsps are the principal defence proteins that prevent large-scale protein aggregation. Progress in determining the structure of sHsps has been significant recently, particularly in relation to the conserved, central and β-sheet structured α-crystallin domain (ACD). However, an understanding of the structure and functional roles of the N- and C-terminal flanking regions has proved elusive mainly because of their unstructured and dynamic nature. In this paper, we propose functional roles for both flanking regions, based around three properties: (i) they act in a localised crowding manner to regulate interactions with target proteins during chaperone action, (ii) they protect the ACD from deleterious amyloid fibril formation and (iii) the flexibility of these regions, particularly at the extreme C-terminus in mammalian sHsps, provides solubility for sHsps under chaperone and non-chaperone conditions. In the eye lens, these properties are highly relevant as the crystallin proteins, in particular the two sHsps αA- and αB-crystallin, are present at very high concentrations.     

Age-dependent deamidation of glutamine residues in human γS crystallin: deamidation and unstructured regions

Human aging is associated with the deterioration of long-lived proteins. Gradual cumulative modifications to the life-long proteins of the lens may ultimately be responsible for the pronounced alterations to the optical and physical properties that characterize lenses from older people. γS crystallin, a major human lens protein, is known to undergo several age-dependent changes. Using proteomic techniques, a site of deamidation involving glutamine 92 has been characterized and its time course established. The proportion of deamidation increased from birth to teen-age years and then plateaud. Deamidation at this site increased again in the eighth decade of life. There was no significant difference in the extent of deamidation between cataract and age-matched normal lenses. Gln92 is located in the linker region between the two domains, and the introduction of a negative charge at this site may alter the interaction between the two regions of the protein. Gln170, which is located in another unstructured part of γS crystallin, showed a similar deamidation profile to that of Gln92. As the other Gln residues in β-sheet regions of γS crystallin appear to remain as amides, modification of Gln92 and Gln170 thus conforms to a pattern whereby deamidation is localized to the unstructured regions of long-lived proteins.     

Phylogenomics and rapid diversification of the genus Eutrema on the Qinghai–Tibet Plateau and adjacent regions

Both geographic isolation and polyploidization are assumed to play an important role in driving species diversification. However, this is rarely illustrated through phylogenomic analyses. The genus Eutrema (Brassicaceae), which also includes the salt-resistant species, are distributed mainly in Asia with extensive species diversification in the Qinghai–Tibet Plateau (QTP) and adjacent regions. In this study, we revealed almost fully resolved backbone relationships of the genus with genome re-sequencing data for genomes of 168 individuals from 28 species. Phylogenetic analyses of both plastomes and single-copy nuclear genes from the whole genome recovered six well-supported clades with almost consistent relationships. The first two clades are mainly distributed in central China and central Asia, while the other four in the QTP and adjacent regions. All of them diversified within 12 million years. Within each clade, we recovered numerous conflicts in the interspecific relationships between nuclear and plastome phylogenies, likely suggesting hybridization and incomplete lineage sorting during species diversification. Our estimation of genome size and comparison of the number of the single-copy nuclear genes demonstrated frequent occurrences of polyploids in the genus. Except for an establishment of the backbone phylogeny, our phylogenomic analyses suggest that in addition to strong geographic isolation, polyploidization may have played an important role in species diversification of this genus.     

Strong oligomerization behavior of PDGFβ ?receptor transmembrane domain and its regulation by the juxtamembrane regions

The platelet-derived growth factor β-receptor (PDGFβR) represents an important subclass of receptor tyrosine kinase (RTK) thought to be activated by ligand-induced dimerization. Interestingly, the receptor is also activated by the bovine papillomavirus E5 oncoprotein, an interaction involving the transmembrane domains of both proteins and resulting in constitutive downstream signalling. This unique mode of activation along with emerging data for other RTKs raises important questions about the role of the PDGFβR transmembrane domain in signalling. To address this, we have investigated the murine PDGFβR transmembrane and juxtamembrane domains. We show for the first time the strong oligomerization behavior of PDGFβR transmembrane domain, forming dimers and trimers in natural membranes and detergents; and that these self-interactions are mediated by a leucine-zipper-like motif. The juxtamembrane regions are found to regulate these helix-helix interactions and select specifically for dimer formation. These data provide evidence that PDGFβR is able to form ligand-independent dimers, supporting similar observations in a number of other RTK's. A point mutant in the PDGFβR juxtamembrane domain previously shown to cause receptor activation was studied and yielded no change in oligomerization or folding, suggesting (in-line with observations of the c-Kit receptor) that it may moderate interactions with other regions of PDGFβR.     

Fluid–structure interactions in micro-interlocked regions of the cement–bone interface

Experimental tests and computational modelling were used to explore the fluid dynamics at the trabeculae–cement interlock regions found in the tibial component of total knee replacements. A cement–bone construct of the proximal tibia was created to simulate the immediate post-operative condition. Gap distributions along nine trabeculae–cement regions ranged from 0 to 50.4 μm (mean = 12 μm). Micro-motions ranged from 0.56 to 4.7 μm with a 1 MPa compressive load to the cement. Fluid–structure analysis between the trabeculae and the cement used idealised models with parametric evaluation of loading direction, gap closing fraction (GCF), gap thickness, loading frequency and fluid viscosity. The highest fluid shear stresses (926 Pa) along the trabecular surface were found for conditions with very thin and large GCFs, much larger than reported physiological levels (～1–5 Pa). A second fluid–structure model was created with a provision for bone resorption using a constitutive model with resorption velocity proportional to fluid shear rate. A lower cut-off was used, below which bone resorption would not occur (50 s^? 1). Results showed that there was initially high shear rates (>1000 s^? 1) that diminished after initial trabecular resorption. Resorption continued in high shear rate regions, resulting in a final shape with bone left deep in the cement layer, and is consistent with morphology found in post-mortem retrievals. Small gaps between the trabecular surface and the cement in the immediate post-operative state produce fluid flow conditions that appear to be supra-physiologic; these may cause fluid-induced lysis of trabeculae in the micro-interlock regions.     

Study of rheological properties of açai berry pulp: an analysis of its time-dependent behavior and the effect of temperature

The industry of açai-based products has been growing in the last few years. Knowledge about the physical properties of açai pulp, including its rheology, is essential to the optimization of industrial processes. This work presents the rheological behavior of açai berry pulp in relation to the effects of shear rate, temperature, and time of shearing. The entire study was carried out in the temperature range of 10–70 °C. Açai pulp showed a non-Newtonian, pseudoplastic, and time-dependent behavior. Four upward and backward shear rate cycles were evaluated, resulting in complex hysteresis loops, in which thixotropy and anti-thixotropy zones were observed. Downward flow curves could be satisfactorily represented by the Power-Law rheological model. The stress profiles as a function of shear rate obtained in the first upward curves suggest a breakdown of the initial fluid structure at low shear rates. Tests were also carried out at a constant shear rate of 20 s^?1 and, in this case, the Weltman model of thixotropy satisfactorily fit the experimental data. The activation energy, which was calculated by the Arrhenius equation, was 29.0 kJ/mol. The achievements of this work may be useful to further studies about açai pulp rheology and may contribute to process design in the açai industry.     

The effects of ambient temperature,nature and temperature of the floor and radiant heat on the metabolic rate of the new—born pig

Using a closed circuit technique, the oxygen consumption of 108 piglets below one week of age have been measured while modifying the physical attributes of the thermal environment. Moving the piglets onto a wooden floor from concrete reduced the oxygen consumption rate from 37.8 ml to 34.5 ml/kg. min) at 10°C, and from 33.7 to 31.4 ml/(kg. min) on a rubber floor at the same temperature. Oxygen consumption was also significantly reduced when the piglets were placed on a straw floor, were supplied with radiant heat and when the floor temperature was raised independently of chamber temperature. It is concluded that the provision of supplementary heating either in the floor or by overhead radiation can greatly reduce the effects of a cold environment on the new-born pig and so enhance the animal's viability.

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Zusammenfassung Der Sauerstoff-Umsatz von 108 Ferkeln, die jünger als eine Woche waren, wurde unter wechselnden Bedingungen der thermischen Umwelt gemessen. Das Verlegen der Ferkel von einem Zement- auf einen Holzboden führte zur Senkung des 0₂-Umsatzes von 37,8 auf 34,5 ml O₂/kg. min) und von 33,7 auf 31,4 ml O₂/(kg. min) bei 10°C auf einem Gummiboden. Auf einem strohbedecktem Boden war der O₂-Umsatz ebenfalls vermindert. Den gleichen Effekt hatte die Anwendung von Strahlungswärme oder die Erhöhung der Bodentemperatur. Danach kann zusätzliche Erwärmung vom Boden oder von der Decke die Kälteeinwirkung auf das Ferkel aus der Umgebung stark reduzieren und die Lebensfähigkeit der Tiere erhöhen.

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Resume Au moyen d'un appareil à circuit fermé, on a mesuré la consommation en oxygène le 108 porcelets âgés de moins d'une semaine soumis à divers régimes thermiques et cela dans une température ambiante constante. En transférant les porcelets d'un sol de béton à un plancher de bois, leur consommation d'oxygène a passé de 37,8 à 34,5 ml/(kg. min), et de 33,7 à 31,4 ml/(kg. min) en passant du béton à un sol recouvert de caoutchouc. La consommation d'oxygène a également été réduite de façon significative pour un sol recouvert de paille. Il en est allé de même pour des lampes à infra-rouge et si le sol était chauffé indépendamment du local. On en conclut qu'un chauffage supplémentaire soit dans le sol soit par rayonnement peut réduire sensiblement les effets néfastes d'une ambiance froide sur lesporcelets nouveau-nés et rehausser leurs chances de survie.

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Presented during the Fifth International Biometeorological Congress, 1–6 September 1969, Montreux, Switzerland.     

Vapor–liquid equilibria and thermophysical behavior of the SPC-HW model for heavy water

The vapor–liquid coexistence curve of the simple point charge heavy-water model (SPC-HW), [J. Chem. Phys., 114, 8064–8067 (2001)] is determined by Gibbs Ensemble Monte-Carlo (GEMC) simulation. The estimated critical conditions of the model based on the Wegner-type expansion for the order parameters and the rectilinear diameter are ρ_c = 0.300 g/cc, T _c = 661 K and P _c = 156 bars. The dielectric constant determined by isothermal–isochoric molecular dynamics is underpredicted along the coexistence curve by 29–44% in comparison with the experimental values. The analysis of the orthobaric temperature dependence of the system microstructure, in terms of the three site–site radial distribution functions, indicates that the first coordination numbers for the oxygen–oxygen and the oxygen–deuterium interactions are ～4.3 ± 0.1 and ～1.9 ± 0.1 at T = 300 K, and decrease by 15 and 55%, respectively, at criticality. The dipole–dipole correlation functions show that the orientational order in heavy water is quickly lost beyond the first oxygen–oxygen coordination shell. The model's second virial coefficient is determined by Monte-Carlo integration and used to aid the interpretation of the predicted phase equilibrium results.     

Source–Sink Relations in the Organs and Tissues of Silver Birch during Different Scenarios of Xylogenesis

Russian Journal of Plant Physiology - Source–sink relations in the “leaf–stem–root” system at the time of cambial growth were studied in two forms of silver birch:...     

Testing the drivers of the temperature–size covariance using artificial selection

Body size often declines with increasing temperature. Although there is ample evidence for this effect to be adaptive, it remains unclear whether size shrinking at warmer temperatures is driven by specific properties of being smaller (e.g., surface to volume ratio) or by traits that are correlated with size (e.g., metabolism, growth). We used 290 generations (22 months) of artificial selection on a unicellular phytoplankton species to evolve a 13-fold difference in volume between small-selected and large-selected cells and tested their performance at 22°C (usual temperature), 18°C (−4), and 26°C (+4). Warmer temperatures increased fitness in small-selected individuals and reduced fitness in large-selected ones, indicating changes in size alone are sufficient to mediate temperature-dependent performance. Our results are incompatible with the often-cited geometric argument of warmer temperature intensifying resource limitation. Instead, we find evidence that is consistent with larger cells being more vulnerable to reactive oxygen species. By engineering cells of different sizes, our results suggest that smaller-celled species are pre-adapted for higher temperatures. We discuss the potential repercussions for global carbon cycles and the biological pump under climate warming.     

Ab initio and molecular dynamics studies of solid β-HMX: effects of hydrostatic pressure and high temperature

Using first-principles density functional theory and classical molecular dynamics (MD), the structural, electronic and mechanical properties of the energetic material β-HMX have been studied. The crystal structure optimised by the local density approximation calculations compares reasonably with the experimental data. Electronic band structure and density of states indicate that β-HMX is an insulator with a band gap of 3.059 eV. The pressure effect on the crystal structure and physical properties has been investigated in the range of 0–40 GPa. The crystal structure and electronic properties change slightly as the pressure increases from 0 to 2.5 GPa; when the pressure is above 2.5 GPa, further increment of the pressure results in significant changes in crystal structure. There is a larger compression along the b-axis than along the a- and c-axes. Isothermal–isobaric MD simulations on β-HMX were performed in the temperature range of 5–400 K. Phase transition at 360 K, corresponding to a volume interrupt, was found. The computed thermal expansion coefficients show anisotropic behaviour with a slightly larger expansion along the b- and c-axes than along the a-axis. In the temperature range of 5–360 K, β-HMX possesses good plasticity and its stiffness decreases with increasing the temperature.     

Coexistence of competing juvenile–adult structured populations

The Leslie-Gower model is a discrete time analog of the competition Lotka–Volterra model and is known to possess the same dynamic scenarios of that famous model. The Leslie–Gower model played a historically significant role in the history of competition theory in its application to classic laboratory experiments of two competing species of flour beetles (carried out by Park in the 1940s–1960s). While these experiments generally supported what became the Competitive Exclusion Principle, Park observed an anomalous coexistence case. Recent literature has discussed Park’s ‘coexistence case’ by means of non-Lotka–Volterra, non-equilibrium dynamics that occur in a high dimensional model with life cycle stages. We study this dynamic possibility in the lowest possible dimension, that is to say, by means of a model involving only two species each with two life cycle stages. We do this by extending the Leslie–Gower model so as to describe the competitive interaction of two species with juvenile and adult classes. We give a complete account of the global dynamics of the resulting model and show that it allows for non-equilibrium competitive coexistence as competition coefficients are increased. We also show that this phenomenon occurs in a general class of models for competing populations structured by juvenile and adult life cycle stages.     

Efficient cap-dependent translation of mammalian mRNAs with long and highly structured 5′-untranslated regions in vitro and in vivo

According to the generally accepted scanning model proposed by M. Kozak, the secondary structure of the 5′-untranslated region (5′-UTR) of eukaryotic mRNA can only inhibit the translation initiation by counteracting migration of the 40S ribosomal subunit along the mRNA polynucleotide chain. The existence of efficiently translatable mRNAs with long and highly structured 5′-UTRs is incompatible with the cap-dependent scanning mechanism. Such mRNAs are expected to use alternative ways of translation initiation to be efficiently translated, primarily the mechanism of internal ribosome entry mediated by internal ribosome entry sites (IRESs), special RNA structures that reside in the 5′-UTR. The paper shows that this viewpoint is incorrect and is probably based on experiments with mRNA translation in rabbit reticulocyte lysate. This cell-free system fails to adequately reflect the relative translation efficiencies observed for different mRNAs in vivo. Five structurally similar mRNAs with either short leaders of the β-globin and β-actin mRNAs or long and highly structured 5′-UTRs of the c-myc, LINE-1, and Apaf-1 mRNAs displayed comparable translation activities in transfected cells and an entire cytoplasmic extract of cultivated cells. Translation activity proved to strongly depend on the presence of a cap at the 5′ end.     

Does titin regulate the length of muscle thick filaments?

The protein titin has been localized by electron microscopy of myofibrils labelled with monoclonal antibodies. The data are consistent with individual titin molecules extending from near the M-line to beyond the ends of thick filaments, a distance of approximately 1 micron. In the A-band, titin appears to be bound to thick filaments, probably to the outside of the filament shaft. Molecules of titin in this configuration provided an obvious mechanism by which the length of thick filaments could be regulated accurately.     

Physical Activity and Different Concepts of Fall Risk Estimation in Older People–Results of the ActiFE-Ulm Study

Objectives

To investigate the relationship between physical activity and two measures of fall incidence in an elderly population using person-years as well as hours walked as denominators and to compare these two approaches.

Design

Prospective cohort study with one-year follow-up of falls using fall calendars. Physical activity was defined as walking duration and recorded at baseline over one week using a thigh-worn uni-axial accelerometer (activPAL; PAL Technologies, Glasgow, Scotland). Average daily physical activity was extracted from these data and categorized in low (0–59 min), medium (60–119 min) and high (120 min and more) activity.

Setting

The ActiFE Ulm study located in Ulm and adjacent regions in Southern Germany.

Participants

1,214 community-dwelling older people (≥65 years, 56.4% men).

Measurements

Negative-binomial regression models were used to calculate fall rates and incidence rate ratios for each activity category each with using (1) person-years and (2) hours walked as denominators stratified by gender, age group, fall history, and walking speed. All analyses were adjusted either for gender, age, or both.

Results

No statistically significant association was seen between falls per person-year and average daily physical activity. However, when looking at falls per 100 hours walked, those who were low active sustained more falls per hours walked. The highest incidence rates of falls were seen in low-active persons with slow walking speed (0.57 (95% confidence interval (95% CI): 0.33 to 0.98) falls per 100 hours walked) or history of falls (0.60 (95% CI: 0.36 to 0.99) falls per 100 hours walked).

Conclusion

Falls per hours walked is a relevant and sensitive outcome measure. It complements the concept of incidence per person years, and gives an additional perspective on falls in community-dwelling older people.     

Electron diffraction study of hydrated phospholipid single bilayers. Effects of temperature,hydration and surface pressure of the “precursor” monolayer

The molecular packing and phase transition of hydrated dipalmitoylphosphatidylcholine single bilayers are studied by electron diffraction, using an electron microscope equipped with a hydration stage. The phase transition and area per molecule are measured as functions of temperature, hydration and the surface pressure of the monolayer from which the bilayer is formed. The transition temperature of a bilayer agrees with calorimetric measurements on bulk lipid/water mixtures. The molecular packing of a bilayer corresponds to that of the precursor monolayer at a surface pressure of 47 dyne/cm.     

Enthalpy–entropy compensation and the isokinetic temperature in enzyme catalysis

Enthalpy–entropy compensation supposes that differences in activation enthalpy ?H ^? for different reactions (or, typically in biochemistry, the same reaction catalysed by enzymes obtained from different species) may be compensated for by differences in activation entropy ?S ^?. At the isokinetic temperature the compensation is exact, so that all samples have the same activity. These ideas have been controversial for several decades, but examples are still frequently reported as evidence of a real phenomenon, nearly all of the reports ignoring or discounting the possibility of a statistical artefact. Even for measurements in pure chemistry artefacts occur often, and they are almost inescapable in enzyme kinetics and other fields that involve biological macromolecules, on account of limited stability and the fact that kinetic equations are normally valid only over a restricted range of temperature. Here I review the current status and correct an error in a recent book chapter.     

An historical perspective of the discovery of titin filaments –Part 2

In 2017, a Special Issue of Biophysical Reviews was devoted to “Titin and Its Binding Partners. The issue contained a review: “An historical perspective of the discovery of titin filaments” by dos Remedios and Gilmour that was intended to be a history of the discovery of the giant protein titin, previously named connectin. The review took readers back to the earliest discovery of the so-called third filament component of skeletal and cardiac muscle sarcomeres and ended in 1969. Recently, my colleague Shin’ichi Ishiwata gently reminded me of two papers published in 1990 and 1993 that were unwittingly omitted from the original historical perspective. In the first paper (J Cell Biol 110:53–62, 1990), Funatsu et al. examined the elastic filaments in skeletal muscle using a combination of light and electron microscopy, but they also measured resting as well as passive stiffness mechanical measurements to establish that connectin (titin) is responsible for both stiffness and fiber tension. In the second paper (J Cell Biol 120:711–724, 1993), Funatsu et al. used permeabilised cardiac muscle myocytes (from rabbit papillary muscles) and focussed on filament ultrastructure using either freeze-substitution or deep-etched replica methods to visualise connectin/titin filaments in fibers with and without actin and myosin filaments.