Macromolecular structural dynamics visualized by pulsed dose control in 4D electron microscopy

Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy of conformations can be mapped in the nonequilibrium region of a “funnel-like” free-energy landscape. The T-jump is introduced through a substrate (a “hot plate” type arrangement) because only the substrate is made to absorb the pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer physics as well as in the visualization of biological phenomena

Capillary abnormalities in workers occupationally exposed to ionizing and nonionizing radiations

Cilj studije je bio metodom kapilaroskopije upozoriti na mogući utjecaj ionizacijskog i neionizacijskog zračenja na periferni krvotok profesionalno izloženih osoba. Kapilaroskopski smo pregledali 100 osoba profesionalno izloženih ionizacijskom zračenju, 110 osoba profesionalno izloženih neionizacijskom zračenju i 80 kontrolnih, neizloženih osoba. U obje test-skupine oštećenja mikrocirkulacije su bila statistički značajno učestalija nego u kontrolnoj skupini.The aim of the study was to determine a possible effect of ionizing and nonionizing radiations on peripheral blood flow in occupationally exposed persons by means of capillaroscopic analysis. Altogether 290 subjects were examined. Of these 100 were occupationally exposed to ionizing radiation, 110 were occupationally exposed to nonionizing radiation and 80 control subjects never worked with radiation sources. Statistical analysis showed that microvascular abnormalities occurred significantly more frequently among occupationally exposed persons than in the control group

Ab initio theory of helix-coil phase transition

In this paper we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix-random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).Comment: 24 pages, 3 figure

Egg characteristics vary longitudinally in Arctic shorebirds

Arctic environments are changing rapidly and if we are to understand the resilience of species to future changes, we need to investigate alterations in their life histories. Egg size and egg shape are key life-history traits, reflecting parental investment as well as influencing future reproductive success. Here we focus on egg characteristics in two Arctic shorebirds, the Dunlin (Calidris alpina) and the Temminck’s stint (Calidris temminckii). Using egg photos that encompass their full breeding ranges, we show that egg characteristics exhibit significant longitudinal variations, and the variation in the monogamous species (Dunlin) is significantly greater than the polygamous species (Temminck’s stint). Our finding is consistent with the recent “disperse-to-mate” hypothesis which asserts that polygamous species disperse further to find mates than monogamous species, and by doing so they create panmictic populations. Taken together, Arctic shorebirds offer excellent opportunities to understand evolutionary patterns in life history traits

Advances in multispectral and hyperspectral imaging for archaeology and art conservation

Multispectral imaging has been applied to the field of art conservation and art history since the early 1990s. It is attractive as a noninvasive imaging technique because it is fast and hence capable of imaging large areas of an object giving both spatial and spectral information. This paper gives an overview of the different instrumental designs, image processing techniques and various applications of multispectral and hyperspectral imaging to art conservation, art history and archaeology. Recent advances in the development of remote and versatile multispectral and hyperspectral imaging as well as techniques in pigment identification will be presented. Future prospects including combination of spectral imaging with other noninvasive imaging and analytical techniques will be discussed

The origins of the Selden map of China: scientific analysis of the painting materials and techniques using a holistic approach

Since the 'rediscovery' of the Selden map of China, an early seventeenth century map of Asia, in the Bodleian Library in Oxford, the importance of the map in our understanding of globalisation in the early seventeenth century has been recognised. One of the unresolved questions is the origin of the map. This paper addresses the question through material evidence provided by a holistic approach using a suite of complementary analytical techniques. The map was examined in situ and non-invasively by a remote spectral imaging instrument (PRISMS) modified for close range imaging, which was followed by a range of complementary techniques applied to a number of detached fragments, though most of the techniques are non-invasive and can be applied to the map directly in the future. The binding medium was found to be a gum, almost certainly gum Arabic, rather than the animal glue commonly used in Chinese paintings. Some of the pigments and their usage were found to be at odds with the common practice in paintings from China. The detection of gum Arabic, a binding medium used by the Europeans, South and West Asians and the use of a mixture of orpiment and indigo, commonly found in European, South and West Asian paintings gives further evidence on the unusual origins of this map. The likely detection of a basic copper chloride, such as atacamite, in the green areas suggests an influence from the South and West Asian rather than the European tradition. Detailed analysis of the various spectral bands of the spectral image cube along with visual inspection of the large scale colour image showed that the map was not fully planned at the beginning but rather painted in stages, at times by trial and error and that it was unfinished. A new hypothesis for the origin of the Selden map in Aceh Sumatra is proposed based on the new evidences

The N-terminal Domain Allosterically Regulates Cleavage and Activation of the Epithelial Sodium Channel

The epithelial sodium channel (ENaC) is activated upon endoproteolytic cleavage of specific segments in the extracellular domains of the α- and γ-subunits. Cleavage is accomplished by intracellular proteases prior to membrane insertion and by surface-expressed or extracellular soluble proteases once ENaC resides at the cell surface. These cleavage events are partially regulated by intracellular signaling through an unknown allosteric mechanism. Here, using a combination of computational and experimental techniques, we show that the intracellular N terminus of γ-ENaC undergoes secondary structural transitions upon interaction with phosphoinositides. From ab initio folding simulations of the N termini in the presence and absence of phosphatidylinositol 4,5-bisphosphate (PIP2), we found that PIP2 increases α-helical propensity in the N terminus of γ-ENaC. Electrophysiology and mutation experiments revealed that a highly conserved cluster of lysines in the γ-ENaC N terminus regulates accessibility of extracellular cleavage sites in γ-ENaC. We also show that conditions that decrease PIP2 or enhance ubiquitination sharply limit access of the γ-ENaC extracellular domain to proteases. Further, the efficiency of allosteric control of ENaC proteolysis is dependent on Tyr370 in γ-ENaC. Our findings provide an allosteric mechanism for ENaC activation regulated by the N termini and sheds light on a potential general mechanism of channel and receptor activation

Discrete Kinetic Models from Funneled Energy Landscape Simulations

A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an “inside-out”, nucleation-propagation like character

Space-borne Bose-Einstein condensation for precision interferometry

Space offers virtually unlimited free-fall in gravity. Bose-Einstein condensation (BEC) enables ineffable low kinetic energies corresponding to pico- or even femtokelvins. The combination of both features makes atom interferometers with unprecedented sensitivity for inertial forces possible and opens a new era for quantum gas experiments. On January 23, 2017, we created Bose-Einstein condensates in space on the sounding rocket mission MAIUS-1 and conducted 110 experiments central to matter-wave interferometry. In particular, we have explored laser cooling and trapping in the presence of large accelerations as experienced during launch, and have studied the evolution, manipulation and interferometry employing Bragg scattering of BECs during the six-minute space flight. In this letter, we focus on the phase transition and the collective dynamics of BECs, whose impact is magnified by the extended free-fall time. Our experiments demonstrate a high reproducibility of the manipulation of BECs on the atom chip reflecting the exquisite control features and the robustness of our experiment. These properties are crucial to novel protocols for creating quantum matter with designed collective excitations at the lowest kinetic energy scales close to femtokelvins.Comment: 6 pages, 4 figure

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

The use of molecular dynamics simulations to provide atomic-level descriptions of biological processes tends to be computationally demanding, and a number of approximations are thus commonly employed to improve computational efficiency. In the past, the effect of these approximations on macromolecular structure and stability has been evaluated mostly through quantitative studies of small-molecule systems or qualitative observations of short-timescale simulations of biological macromolecules. Here we present a quantitative evaluation of two commonly employed approximations, using a test system that has been the subject of a number of previous protein folding studies–the villin headpiece. In particular, we examined the effect of (i) the use of a cutoff-based force-shifting technique rather than an Ewald summation for the treatment of electrostatic interactions, and (ii) the length of the cutoff used to determine how many pairwise interactions are included in the calculation of both electrostatic and van der Waals forces. Our results show that the free energy of folding is relatively insensitive to the choice of cutoff beyond 9 Å, and to whether an Ewald method is used to account for long-range electrostatic interactions. In contrast, we find that the structural properties of the unfolded state depend more strongly on the two approximations examined here