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At least 451 records · Page 25

Principles and biophysical applications of single particle super-localization and rotational tracking

While conventional Single Particle Tracking (SPT) techniques acquire 2D or 3D trajectories of particle probes, we have developed Single Particle Orientation and Rotational Tracking (SPORT) techniques to extract orientation and rotational information. Combined with DIC microscopy, the SPORT technique has been applied in biophysical studies, including membrane diffusion and intracellular transport. The rotational dynamics of nanoparticle vectors on live cell membranes was recorded and its influence on the fate of these nanoparticle vectors was elucidated. The rotational motions of gold nanorods with various surface modifiers were tracked continuously at a temporal resolution of 5 ms under a DIC microscope. We found that the rotational behaviors of gold nanorod vectors are strongly related to their surface charge, specific surface functional groups, and the availability of receptors on cell membranes. The study of rotational Brownian motion of nanoparticles on cell membranes will lead to a better understanding of the mechanisms of drug delivery and provide guidance in designing surface modification strategies for drug delivery vectors under various circumstances. To characterize the rotation mode of surface functionalized gold nanorods on cell membranes, the SPORT technique is combined with the correlation analysis of the bright and dark DIC intensities. The unique capabilities of visualizing and understanding rotational motions of functionalized nanoparticles on live cell membranes allow us to correlate rotational and translational dynamics in unprecedented detail and provide new insights for complex membrane processes, including electrostatic interactions, ligand-receptor binding, and lateral (confined and hopping) diffusion of membrane receptors. Surface-functionalized nanoparticles interact with the membrane in fundamentally different ways and exhibit distinct rotational modes. The early events of particle-membrane approach and attachment are directly visualized for the first time. The rotational dynamics of cargos in both active directional transport and pausing stages of axonal transport was also visualized using high-speed SPORT with a temporal resolution of 2 ms. Both long and short pauses are imaged, and the correlations between the pause duration, the rotational behaviour of the cargo at the pause, and the moving direction after the pause are established. Furthermore, the rotational dynamics leading to switching tracks are visualized in detail. These first-time observations of cargo's rotational dynamics provide new insights on how kinesin and dynein motors take the cargo through the alternating stages of active directional transport and pause. To improve the localization precision of the SPT technique with DIC microscopy, a precise three-dimensional (3D) localization method of spherical gold nanoparticle probes using model-based correlation coefficient mapping was introduced. To accomplish this, a stack of sample images at different z-positions are acquired, and a 3D intensity profile of the probe serving as the model is used to map out the positions of nanoparticles in the sample. By using this model-based correlation imaging method, precise localization can be achieved in imaging techniques with complicated point spread functions (PSF) such as differential interference contrast (DIC) microscopy. The 3D superlocalization method was applied to tracking gold nanospheres during live endocytosis events. Finally, a novel dual-modality imaging technique has been developed to super-localize a single gold nanorod while providing its orientation and rotational information. The super-localization of the gold nanorod can be accomplished by curve fitting the modified bright-field images generated by one of the two beams laterally shifted by the first Nomarski prism in a DIC microscope. The orientation and rotational information is derived from the DIC images of gold nanorods. The new imaging setup has been applied to study the steric hindrance induced by relatively large cargos in the microtubule gliding assay and to track nanocargos in the crowded cellular environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neural induced embryoid bodies present high levels of metals detected by x-ray microfluorescence

Molecular mechanisms driving neural differentiation in human embryonic stem cells are not completely elucidated, specially, the role of atomic elements within this process. In this work, we described the distribution of trace elements in those stem cells growing as embryoid bodies by using synchrotron radiation X-ray microfluorescence (SR-XRF). Naive and neural induced embryoid bodies derived from embryonic stem cells were irradiated with a spatial resolution of 20 {mu}m to make elemental maps and qualitative chemical analyses. We consistently detected metallic elements content raise on neural induced embryoid bodies, mimicking characteristic brain development. The use of SR-XRF reveals that human embryoid bodies exhibit self-organization at the atomic level, which is enhanced during neurogenesis triggered in vitro.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Blue crab larval dispersal highlights population connectivity and implications for fishery management

In the Western Atlantic and Gulf of Mexico (GOM), the blue crab Callinectes sapidus fishery is managed at regional scale and its assessment does not consider the population structure of the species. To understand connectivity of the blue crab population, we simulated larval dispersal using a biophysical model driven by high-resolution ocean currents and including early life-history traits of the species. Simulations were conducted during 2015 and 2016, and larvae were released from locations along Florida’s GOM and Atlantic coasts. A high degree of local larval retention was observed in Florida’s GOM waters, mainly during summer when weak southeastern winds tend to yield a shoreward net flow. Results demonstrated clear evidence of connectivity between the Gulf coast of Florida population and those of Mississippi, Alabama, and Louisiana, suggesting that the blue crab populations in the GOM are intermixed and the hypothesized boundary (in Florida) of two stocks needs further consideration. Outputs of the model also indicated connectivity between the blue crab populations of Florida’s Gulf coast and the South-Atlantic Bight (SAB). Larval trajectories show inter-annual variability driven by the interaction of winds, Loop Current (LC) intrusions in the northern GOM, LC eddies and their cyclonic counterparts, and the Mississippi River plume. The latter provides a conduit for larval transport from the GOM to the SAB. These findings provide evidence of the physical oceanographic processes that sustain the homogenous genetic population structure for blue crabs between SAB and GOM populations, highlighting the need for collaborative management in US waters.

Criales, Maria M.↗

Nature’s conductors: what can microbial multi-heme cytochromes teach us about electron transport and biological energy conversion?

Microorganisms can acquire energy from the environment by extending their electron transport chains to external solid electron donors or acceptors. This process, known as extracellular electron transfer (EET), is now being heavily pursued for wiring microbes to electrodes in bioelectrochemical renewable energy technologies. Recent studies highlight the crucial role of multi-heme cytochromes in facilitating biotic–abiotic EET both for cellular electron export and uptake. Here we explore progress in understanding the range and function of these biological electron conduits in the context of fuel-to-electricity and electricity-to-bioproduct conversion. We also highlight emerging topics, including the role of multi-heme cytochromes in inter-species electron transfer and in inspiring the design and synthesis of a new generation of protein-based bioelectronic components.

59 BASIC BIOLOGICAL SCIENCES↗

Gravitropism of cucumber hypocotyls: biophysical mechanism of altered growth

The biophysical basis for the changes in cell elongation rate during gravitropism was examined in aetiolated cucumber (Cucumis sativus L.) hypocotyls. Bulk osmotic pressures on the two sides of the stem and in the epidermal cells were not altered during the early time course of gravitropism. By the pressure-probe technique, a small increase in turgor (0.3 bar, 30 kPa) was detected on the upper (inhibited) side, whereas there was a negligible decrease in turgor on the lower (stimulated) side. These small changes in turgor and water potential appeared to be indirect, passive consequences of the altered growth and the small resistance for water movement from the xylem, and indicated that the change in growth was principally due to changes in wall properties. The results indicate that the hydraulic conductance of the water-transport pathway was large (.25 h-1 bar-1) and the water potential difference supporting cell expansion was no greater than 0.3 bar (30 kPa). From pressure-block experiments, it appeared that upon gravitropic stimulation (1) the yield threshold of the lower half of the stem did not decrease and (2) the wall on the upper side of the stem was not made more rigid by a cross-linking process. Mechanical measurements of the stress/strain properties of the walls showed that the initial development of gravitropism did not involve an alteration of the mechanical behaviour of the isolated walls. Thus, gravitropism in cucumber hypocotyls occurs principally by an alteration of the wall relaxation process, without a necessary change in wall mechanical properties.

Non-NASA Center↗

Mapping the body’s battle with Ebola and Zika

The viruses that cause Ebola and Zika, daunting diseases that inspire concern at every outbreak, share a strong similarity in how they first infiltrate a host’s cells. Through the computer modeling capabilities of Los Alamos National Laboratory, the molecular calisthenics involved in invading a cell are visually documented, an essential step toward vaccine and therapeutic medicine development. “The two very different viruses both use a surface protein to initiate a process called ‘membrane fusion,’ which allows the viral entry into the host cell,” said Chang-Shung Tung, the leading and corresponding author of the recent work in the journal Biomolecules. “Before the membrane fusion started, these two proteins went through large conformational changes that was not fully understood, as the proteins would take on the physical shape that would allow them to fuse with the cell and begin the infection. In this work, we modeled the structures of the two proteins in the fusion-initiation state. Then we used the structures to explain how four different antibodies in our bodies can fight the infection and block the viral entry, based on how they bind to these two proteins,” Tung said. The aim of the team’s work was to understand the specific structure-function relationship of the Ebola glycoprotein (EBOV GP) and Zika envelope (ZIKA E) proteins, the ones that are instrumental in the fusion with the host cell. “This computer modeling approach allowed us to generate atomic-level models of EBOV GP and ZIKV E proteins in the fusion state for the first time,” said Anna Lappala, a postdoctoral fellow at the Center for Nonlinear Studies and the Theoretical Biology & Biophysics Group at Los Alamos. “These models, together with the knowledge of the envelope proteins in the pre-fusion state, allowed us to study the function of neutralizing antibodies as they bind to the viral envelope proteins.” Read the published scientific paper here: http://www.mdpi.com/2218-273X/8/2/25/pdf

59 BASIC BIOLOGICAL SCIENCES↗

Targeting Aspergillus allergen oryzin with a chemical probe at atomic precision

We report the molecular basis of Aspergillus fumigatus oryzin, allergen Asp f 13, or alkaline proteinase ALP1, containing the sequence motif His–Asp–Ser of the subtilisin family, structure, and function at atomic detail. Given the resolution of the data (1.06 Å), we use fragment molecular replacement with ideal polyalanine α-helices to determine the first crystal structure of oryzin. We probe the catalytic serine through formation of an irreversible bond to a small molecule compound, specifically labeling it, describing the amino acid residues performing the catalytic function. Defined by a self-processed pro-peptide, the active site architecture shapes up pocket-like subsites that bind to and unveil the S1′–S4′ substrate binding preferences. We use molecular modeling to dock a model of the pro-peptide in the S1–S4 region and to dock collagen along the active site cleft. Opposite to the face harboring the catalytic serine, the enzyme binds to a calcium ion in a binding site created by backbone flipping. We use thermal unfolding to show that this metal ion provides structural stability. With no known host inhibitor identified thus far, this structure may hasten the progress of developing new therapeutic agents for diseases caused by pathogenic fungi.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum-mechanical predictions of electron-induced ionization cross sections of DNA components

Ionization of biomolecules remains still today rarely investigated on both the experimental and the theoretical sides. In this context, the present work appears as one of the first quantum mechanical approaches providing a multi-differential description of the electron-induced ionization process of the main DNA components for impact energies ranging from the target ionization threshold up to about 10 keV. The cross section calculations are here performed within the 1st Born approximation framework in which the ejected electron is described by a Coulomb wave whereas the incident and the scattered electrons are both described by a plane wave. The biological targets of interest, namely, the DNA nucleobases and the sugar-phosphate backbone, are here described by means of the GAUSSIAN 09 system using the restricted Hartree-Fock method with geometry optimization. The theoretical predictions also obtained have shown a reasonable agreement with the experimental total ionization cross sections while huge discrepancies have been pointed out with existing theoretical models, mainly developed within a semi-classical framework.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling Bird Migration under Climate Change: A Mechanistic Approach

How will migrating birds respond to changes in the environment under climate change? What are the implications for migratory success under the various accelerated climate change scenarios as forecast by the Intergovernmental Panel on Climate Change? How will reductions or increased variability in the number or quality of wetland stop-over sites affect migratory bird species? The answers to these questions have important ramifications for conservation biology and wildlife management. Here, we describe the use of continental scale simulation modeling to explore how spatio-temporal changes along migratory flyways affect en-route migration success. We use an individually based, biophysical, mechanistic, bird migration model to simulate the movement of shorebirds in North America as a tool to study how such factors as drought and wetland loss may impact migratory success and modify migration patterns. Our model is driven by remote sensing and climate data and incorporates important landscape variables. The energy budget components of the model include resting, foraging, and flight, but presently predation is ignored. Results/Conclusions We illustrate our model by studying the spring migration of sandpipers through the Great Plains to their Arctic breeding grounds. Why many species of shorebirds have shown significant declines remains a puzzle. Shorebirds are sensitive to stop-over quality and spacing because of their need for frequent refueling stops and their opportunistic feeding patterns. We predict bird "hydrographs that is, stop-over frequency with latitude, that are in agreement with the literature. Mean stop-over durations predicted from our model for nominal cases also are consistent with the limited, but available data. For the shorebird species simulated, our model predicts that shorebirds exhibit significant plasticity and are able to shift their migration patterns in response to changing drought conditions. However, the question remains as to whether this behavior can be maintained over increasing and sustained environmental change. Also, the problem is much more complex than described by the current processes captured in our model. We have taken some important and interesting steps, and our model does demonstrate how local scale information about individual stop-over sites can be linked into the migratory flyway as a whole. We are incorporating additional, species specific, mechanistic processes to better reflect different climate change scenarios

Smith, James A.↗

NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successful overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.

60 APPLIED LIFE SCIENCES↗

Statin-induced myotoxicity is exacerbated by aging: A biophysical and molecular biology study in rats treated with atorvastatin

Statin-induced skeletal muscle damage in rats is associated to the reduction of the resting sarcolemmal chloride conductance (gCl) and ClC-1 chloride channel expression. These drugs also affect the ClC-1 regulation by increasing protein kinase C (PKC) activity, which phosphorylate and close the channel. Also the intracellular resting calcium (restCa) level is increased. Similar alterations are observed in skeletal muscles of aged rats, suggesting a higher risk of statin myotoxicity. To verify this hypothesis, we performed a 4–5-weeks atorvastatin treatment of 24-months-old rats to evaluate the ClC-1 channel function by the two-intracellular microelectrodes technique as well as transcript and protein expression of different genes sensitive to statins by quantitative real-time-PCR and western blot analysis. The restCa was measured using FURA-2 imaging, and histological analysis of muscle sections was performed. The results show a marked reduction of resting gCl, in agreement with the reduced ClC-1 mRNA and protein expression in atorvastatin-treated aged rats, with respect to treated adult animals. The observed changes in myocyte-enhancer factor-2 (MEF2) expression may be involved in ClC-1 expression changes. The activity of PKC was also increased and further modulate the gCl in treated aged rats. In parallel, a marked reduction of the expression of glycolytic and mitochondrial enzymes demonstrates an impairment of muscle metabolism. No worsening of restCa or histological features was found in statin-treated aged animals. These findings suggest that a strong reduction of gCl and alteration of muscle metabolism coupled to muscle atrophy may contribute to the increased risk of statin-induced myopathy in the elderly. - Highlights: • This work characterizes the causes of atorvastatin related myotoxicity in aged rats. • Skeletal muscle chloride channel ClC-1 is a target of statin-induced side effects. • ClC-1 dysfunction is worsened by aging process. • Age-related changes of energy production contribute to statin-induced myotoxicity. • These findings suggest caution with statin therapy during aging.

60 APPLIED LIFE SCIENCES↗

Crystal structure of a plectonemic RNA supercoil

Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

59 BASIC BIOLOGICAL SCIENCES↗

Energy landscapes from cryo-EM snapshots: a benchmarking study

Abstract Biomolecules undergo continuous conformational motions, a subset of which are functionally relevant. Understanding, and ultimately controlling biomolecular function are predicated on the ability to map continuous conformational motions, and identify the functionally relevant conformational trajectories. For equilibrium and near-equilibrium processes, function proceeds along minimum-energy pathways on one or more energy landscapes, because higher-energy conformations are only weakly occupied. With the growing interest in identifying functional trajectories, the need for reliable mapping of energy landscapes has become paramount. In response, various data-analytical tools for determining structural variability are emerging. A key question concerns the veracity with which each data-analytical tool can extract functionally relevant conformational trajectories from a collection of single-particle cryo-EM snapshots. Using synthetic data as an independently known ground truth, we benchmark the ability of four leading algorithms to determine biomolecular energy landscapes and identify the functionally relevant conformational paths on these landscapes. Such benchmarking is essential for systematic progress toward atomic-level movies of continuous biomolecular function.

59 BASIC BIOLOGICAL SCIENCES↗

Biophysics Representation of the Two-Hit Model of Alzheimer's Disease for the Exploration of Late CNS Risks from Space Radiation

A concern for long-term space travel outside the Earth s magnetic field is the late effects to the central nervous system (CNS) from galactic cosmic ray (GCR) or solar particle events (SPE). Human epidemiology data is severely limited for making CNS risk estimates and it is not clear such effects occur following low LET exposures. We are developing systems biology models based on biological information on specific diseases, and experimental data for proton and heavy ion radiation. A two-hit model of Alzheimer s disease (AD) has been proposed by Zhu et al.(1), which is the framework of our model. Of importance is that over 50% of the US population over the age of 75-y have mild to severe forms of AD. Therefore we recommend that risk assessment for a potential AD risk from space radiation should focus on the projection of an earlier age of onset of AD and the prevention of this possible acceleration through countermeasures. In the two-hit model, oxidative stress and aberrant cell cycle-related abnormalities leading to amyloid-beta plaques and neurofibrillary tangles are necessary and invariant steps in AD. We have formulated a stochastic cell kinetics model of the two-hit AD model. In our model a population of neuronal cells is allowed to undergo renewal through neurogenesis and is susceptible to oxidative stress or cell cycle abnormalities with age-specific accumulation of damage. Baseline rates are fitted to AD population data for specific ages, gender, and for persons with an apolipoprotein 4 allele. We then explore how low LET or heavy ions may increase either of the two-hits or neurogenesis either through persistent oxidative stress, direct mutation, or through changes to the micro-environment, and suggest possible ways to develop accurate quantitative estimates of these processes for predicting AD risks following long-term space travel.

Cucinotta, Francis A.↗

Blood group typing based on recording the elastic scattering of laser radiation using the method of digital imaging

The possibility is demonstrated to determine the human blood group by recording the scattering of laser radiation with the help of the digital imaging method. It is experimentally shown that the action of a standing ultrasound wave leads to acceleration of the agglutination reaction of red blood cells, to formation of larger immune complexes of red blood cells, and, as a consequence, to acceleration of their sedimentation. In the absence of agglutination of red blood cells the ultrasound does not enhance the relevant processes. This difference in the results of ultrasound action on the mixture of blood and serum allows a method of blood typing to be offered. Theoretical modelling of the technique of the practical blood typing, carried out on the basis of the elastic light scattering theory, agrees well with the experimental results, which made it possible to plan further improvement of the proposed method. The studies of specific features of sedimentation of red blood cells and their immune complexes were aimed at the optimisation of the sample preparation, i.e., at the search for such experimental conditions that provide the maximal resolution of the method and the device for registering the reaction of red blood cells agglutination. The results of the study may be used in designing the instrumentation for blood group assessment in humans.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon

During ribosomal translation, nascent polypeptide chains (NCs) undergo a variety of physical processes that determine their fate in the cell. This study utilizes a combination of arrest peptide experiments and coarse-grained molecular dynamics to measure and elucidate the molecular origins of forces that are exerted on NCs during cotranslational membrane insertion and translocation via the Sec translocon. The approach enables deconvolution of force contributions from NC-translocon and NC-ribosome interactions, membrane partitioning, and electrostatic coupling to the membrane potential. In particular, we show that forces due to NC-lipid interactions provide a readout of conformational changes in the Sec translocon, demonstrating that lateral gate opening only occurs when a sufficiently hydrophobic segment of NC residues reaches the translocon. The combination of experiment and theory introduced here provides a detailed picture of the molecular interactions and conformational changes during ribosomal translation that govern protein biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Wall relaxation and the driving forces for cell expansive growth

When water uptake by growing cells is prevented, the turgor pressure and the tensile stress in the cell wall are reduced by continued wall loosening. This process, termed in vivo stress relaxation, provides a new way to study the dynamics of wall loosening and to measure the wall yield threshold and the physiological wall extensibility. Stress relaxation experiments indicate that wall stress supplies the mechanical driving force for wall yielding. Cell expansion also requires water absorption. The driving force for water uptake during growth is created by wall relaxation, which lowers the water potential of the expanding cells. New techniques for measuring this driving force show that it is smaller than believed previously; in elongating stems it is only 0.3 to 0.5 bar. This means that the hydraulic resistance of the water transport pathway is small and that rate of cell expansion is controlled primarily by wall loosening and yielding.

NASA Program Space Biology↗

The development and applications of multidimensional biomolecular spectroscopy illustrated by photosynthetic light harvesting

The parallel and synergistic developments of atomic resolution structural information, new spectroscopic methods, their underpinning formalism, and the application of sophisticated theoretical methods have led to a step function change in our understanding of photosynthetic light harvesting, the process by which photosynthetic organisms collect solar energy and supply it to their reaction centers to initiate the chemistry of photosynthesis. The new spectroscopic methods, in particular multidimensional spectroscopies, have enabled a transition from recording rates of processes to focusing on mechanism. We discuss two ultrafast spectroscopies – two-dimensional electronic spectroscopy and two-dimensional electronic-vibrational spectroscopy – and illustrate their development through the lens of photosynthetic light harvesting. Both spectroscopies provide enhanced spectral resolution and, in different ways, reveal pathways of energy flow and coherent oscillations which relate to the quantum mechanical mixing of, for example, electronic excitations (excitons) and nuclear motions. The new types of information present in these spectra provoked the application of sophisticated quantum dynamical theories to describe the temporal evolution of the spectra and provide new questions for experimental investigation. While multidimensional spectroscopies have applications in many other areas of science, we feel that the investigation of photosynthetic light harvesting has had the largest influence on the development of spectroscopic and theoretical methods for the study of quantum dynamics in biology, hence the focus of this review. We conclude with key questions for the next decade of this review.

59 BASIC BIOLOGICAL SCIENCES↗