Loop Strands Research Articles

Understanding and manipulating the recognition of necrosis-inducing secreted protein 1 (NIS1) by BRI1-associated receptor kinase 1 (BAK1)

Necrosis-inducing secreted protein 1 (NIS1) is a core effector of Ascomycota and Basidiomycota fungi. They inhibit the immune responses of host plants mainly through interaction with the multi-functional coreceptor BRI1-associated receptor kinase 1 (BAK1). However, the structural mechanism of the NIS1 family and how they are recognized by BAK1 are unknown. Herein, we report the first crystal structure of the NIS1 family protein, the Magnaporthe oryzae NIS1 (MoNIS1), analyze the recognition mechanism of NIS1s by BAK1, and explore regulation of the NIS1-BAK1 interaction by a chemical compound. MoNIS1 exists as a β barrel formed by eight β strands, a folding mode that has not been reported. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) assay suggested that β4-β5 loop and β5 strand of MoNIS1 participate in OsBAK1 interaction, which was supported by further single-point mutational assays. For OsBAK1, HDX-MS assay suggested four regions involved in MoNIS1 interaction. Additionally, we identified a compound that blocks MoNIS1-OsBAK1 interaction in vitro and inhibits the virulence of M. oryzae on rice. Collectively, we determined the first structure of NIS1 family effectors, presented the recognition mechanism of NIS1 by BAK1, and showed that blocking NIS1-BAK1 interaction could be a new target for fungicide development.

Morphological evidence for nanoflares heating warm loops in the solar corona

Context. Nanoflares are impulsive energy releases that occur due to magnetic reconnection in the braided coronal magnetic field, which is a potential mechanism for heating the corona. However, there are still sporadic observations of the interchange of braiding structure segments and footpoints inside coronal loops, which is predicted to be the morphological evolution of the reconnecting magnetic bundles in the nanoflare picture. Aims. This work aims to detect the evolutions of the pairs of braiding strands within the apparent single coronal loops observed in Atmospheric Imaging Assembly (AIA) images. Methods. The loop strands were detected on two kinds of upsampled AIA 193 Å images, which were obtained by upscaling the point spread function matched AIA images via bicubic interpolation and were generated using a super-resolution convolutional neural network. The architecture of the network is designed to map the AIA images to unprecedentedly high spatial resolution coronal images taken by the High-resolution Coronal Imager (Hi-C) during its brief flight. Results. At times, pairs of separate strands that appear braided together later evolved into pairs of almost parallel strands with completely exchanged parts. These evolutions offer morphological evidence that magnetic reconnections between the braiding strands have taken place, which is further supported by the appearance of transient hot emissions containing significant high-temperature components (T > 5 MK) at the footpoints of the braiding structures. Conlusions. The brief appearances of the two rearranging strands support the idea that magnetic reconnections have occurred within what appears to be a single AIA loop.

Gallic acid inhibits Staphylococcus aureus RecA protein functions: role in countering antibiotic resistance in bacteria.

Recombinase RecA and its homologs play a key role in homologous recombination DNA repair and revive stalled replication fork DNA synthesis. RecA plays an essential role in the evolution of antibiotic-resistant strains via stress-induced DNA repair mechanisms during the SOS response. Accordingly, RecA has become an attractive target to slow down antibiotic resistance rates and prevent mutations in pathogenic bacterial species. We employed RecA conserved activities: DNA binding, displacement loop formation, strand exchange, ATP hydrolysis, and LexA cleavage, to elucidate the inhibitory role of gallic acid on S. aureus RecA functions. Gallic acid inhibition of the SOS response by western blot analysis and its antibacterial activity were measured. The gallic acid inhibited all the canonical activities of S. aureus RecA protein. The natural phenolic compound gallic acid interferes with RecA protein DNA complex formation and inhibits activities such as displacement loop formation, strand exchange reaction, ATP hydrolysis, and coprotease activity of S. aureus. Additionally, gallic acid can obstruct ciprofloxacin-induced RecA expression and eventually confer the inhibitory role of gallic acid in the SOS survival mechanism in S. aureus.

Multistep Transformations of DNA Origami Domino Array via Mechanical Forces

Nanostructures that display controllable motions and functions are indispensable to build molecular nanomachines. Structural DNA nanotechnology, enabling precise design of complex static and dynamic structures, can be used to construct molecular nanomachines. However, designing complex dynamic structures that present multiple motion behaviors with different stimuli‐responsiveness is full of challenges. Herein, multistep transformations of DNA origami domino array (DODA) triggered by mechanical forces are developed. The DODA consists of small, modular DNA units, which can be regulated by the external forces. Under the expanding and contraction forces exerted by the DNA trigger and G‐quadruplex (G4)‐functionalized loop strand, the units are reconfigured, leading to the programmable transformations of DODA among three conformations. This multistep transformation strategy is applied to construct chiral plasmonic metamolecules, and analyze K+ via fluorescence resonance energy transfer (FRET) analysis. Moreover, the strategy shows a diversified approach to build the DNA‐based nanodevices, and may find potential applications in various fields.

Structural analysis of human CEACAM1 oligomerization

The human (h) CEACAM1 GFCC’ face serves as a binding site for homophilic and heterophilic interactions with various microbial and host ligands. hCEACAM1 has also been observed to form oligomers and micro-clusters on the cell surface which are thought to regulate hCEACAM1-mediated signaling. However, the structural basis for hCEACAM1 higher-order oligomerization is currently unknown. To understand this, we report a hCEACAM1 IgV oligomer crystal structure which shows how GFCC’ face-mediated homodimerization enables highly flexible ABED face interactions to arise. Structural modeling and nuclear magnetic resonance (NMR) studies predict that such oligomerization is not impeded by the presence of carbohydrate side-chain modifications. In addition, using UV spectroscopy and NMR studies, we show that oligomerization is further facilitated by the presence of a conserved metal ion (Zn++ or Ni++) binding site on the G strand of the FG loop. Together these studies provide biophysical insights on how GFCC’ and ABED face interactions together with metal ion binding may facilitate hCEACAM1 oligomerization beyond dimerization.

Anglemetry of neural axis cell differentiation genes by structural pressurotopy of DNA loop strand segment tropy in reference to tissue macro-compliance

Even as the eukaryotic stranded DNA is known to heterochromatinize at the nuclear envelope in response to mechanical strain, the precise mechanistic basis for alterations in chromatin gene transcription in differentiating cell lineages has been difficult to determine due to limited spatial resolution for detection of shifts in reference to a specific gene in vitro. In this study, heterochromatin shift during euchromatin gene transcription has been studied by parallel determinations of DNA strand loop segmentation tropy nano-compliance (esebssiwaagoTQ units, linear nl), gene positioning angulation in linear normal two-dimensional (2-D) z, y-vertical plane (anglemetry, 0), horizontal alignment to the z, x-plane (vectormetry; mA, mM, a.u.), and by pressuromodulation mapping of differentiated neuron cell sub-class operating range for neuroaxis gene expression in reference to tissue macro-compliance (Peff). The esebssiwaagoTQ effective pressure unit (Peff) maxima and minima for horizontal gene intergene base segment tropy loop alignment were determined (n = 224); the Peff esebssiwaagoTQ quotient were determined (n = 28) for analysis of gene intergene base loop segment tropy structure nano-compliance (n = 28; n = 188); and gene positioning anglemetry and vectormetry was performed (n = 42). The sebs intercept-to-sebssiwa intercept quotient for linear normalization was determined (bsebs/bsebssiwa) by exponential plotting of sub-episode block sum (sebs) (x1, y1; x2, y2) and sub-episode block sum split integrated weighted average (sebssiwa) functions was performed, and the sebs – sebssiwa function residuals were determined. The effective cell pressure (Peff)-to-angle conversion factor was determined, ϴA = (1E + 02) {0.90 – [(0.000 + a ≥ x 0.200 ≤ 0.300; n = 6), between tier 1 and tier 3 (Peff > 0.300; n = 8), and between tier 3 and tier 2 (α = 0.05). Based on the results of this study, I) heterochromatin strand DNA loop micro-segmentation structural nano-compliance is either amorphousity, anisotropy or mesotropy loop segment forms perceiving various grades of the asymmetric tropy viscosity effect, where between 3-to-5 and 8-to-11 genes are arranged as one or two in-tandem alternating anisotropic and mesotropic gene(s), or as in-tandem anisotropic or mesotropic genes in juxtaposition separated by intergene tropy base distance; for example, the anisotropy loop segment form between positions − 12 to + 15 in reference LMNA (Peff, 0.184; θA = 68.40) on human 1q22 (+) is: 5′-0.234-(a− 12)-0.272 (m− 11)-0.229 (a− 10)-0.211 (a− 9)-0.269 (m− 8)-0.144 (a− 7)-0.314 (m− 6)-0.268 (m− 5)-0.176 (a− 4)-0.260 (m− 3)-0.259 (m− 2)-0.270 (m− 1)-0.184 (a0)-0.135 (m+ 1)-0.395 (m+ 2)-0.146 (a+ 3)-0.212 (a+ 4)-0.336 (m+ 5)-0.287 (m+ 6)-0.153 (a+ 7)-0.283 (m+ 8)-0.193 (a+ 9)-0.269 (m+ 10)-0.199 (a+ 11)-0.146 (a+ 12)-0.190 (a+ 13)-0.188 (a+ 14)-0.243 (a+ 15)-3′, which begins at the 5′ end with DAP3 (Peff 0.234); II) mesotropy loop form genes are positioned between 11.7 and 60.40 (CD34) in the z, y-vertical plane, whereas anisotropy loop form genes positioned between 60.5 and 82.30 (MIR4537) in the z, y-vertical plane; III) the relationship between effective pressure and momentum is inverse proportionality, Peff (0.064 ≥ x 0.305), between a Peff of 0.305 and 0.213 for cerebrocortical upper motor neurons, between a Peff of 0.318 and 0.203 for hippocampocortical neurons, and between a Peff of 0.298 and 0.217 for basal ganglia spiny neurons; therefore, there exists an inverse relationship between effective range of whole cell compliance and tissue macro-compliance (Reffective whole cell compliance ˑ Tmacro-compliance = k), in which case the range for mesenchymal cell (MSC) gene expression is delineable as being between a Peff of 0.648 and <= 0.118 esebssiwaagoTQ units; and V) RGS18 (Peff 0.205; θM = 65.20), RGS16 (Peff 0.251; θM = 59.70; human paralog of murine RGS4), lnc-RXFP4–5 (Peff, 0.314; θM = 52.10; pituit), RGS13 (Peff; 0.360, θM = 46.50), CEACAM1 (Peff, 0.384; θM = 43.60), SLC25A44 (Peff, 0.395; θM = 42.30) and RGS21 (Peff, 0.413; θM = 40.10) are expressed within the lower motor neuron (lmn)-upper motor neuron (umn) neural cell axis; and TSACC (Peff, 0.336; θM = 49.40) and JUND (Peff, 0.344; θM = 48.40) are non-cell specific developmental biomarkers. Based on the findings of this study considered together, the precise mechanistic basis for alterations in chromatin gene transcription eukaryotic stranded heterochromatin arranged by structural pressurotopy nano-compliance in DNA stand loop segments is effective cell pressure (Peff) regulated shifting of transcriptionally active DNA in-between the inner nuclear envelope margin and the peripheral nucleoplasm edge and the z, x-plane horizontal alignment of a gene by gene specific Peff within the cell specific effective range of whole cell compliance in reference to tissue macro-compliance. The findings of this study are therefore applicable to the further study of changes in gene transcription in response to applied mechanical strain-mediated alterations in nuclear envelope deformability in silico.

Can the Superposition of Evaporative Flows Explain Broad Fe xxi Profiles during Solar Flares?

Abstract The observation of the high-temperature (≳10 MK) Fe xxi 1354.1 Å line with the Interface Region Imaging Spectrograph has provided significant insights into the chromospheric evaporation process in flares. In particular, the line is often observed to be completely blueshifted, in contrast to previous observations at lower spatial and spectral resolution, and in agreement with predictions from theoretical models. Interestingly, the line is also observed to be mostly symmetric and significantly broader than expected from thermal motions (assuming the peak formation temperature of the ion is in equilibrium). One popular interpretation for the nonthermal broadening is the superposition of flows from different loop strands. In this work, we test this scenario by forward-modeling the Fe xxi line profile assuming different possible observational scenarios using hydrodynamic simulations of multi-thread flare loops with the 1D RADYN code. Our results indicate that the superposition of flows alone cannot easily reproduce both the symmetry and the significant broadening of the line and that some other physical process, such as turbulence, or a much larger ion temperature than previously expected, likely needs to be invoked in order to explain the observed profiles.

Helical Twisting Number and Braiding Linkage Number of Solar Coronal Loops

Abstract Coronal loops in active regions are often characterized by quasi-circular and helically twisted (sigmoidal) geometries, which are consistent with dipolar potential field (PF) models in the former case, and with nonlinear force-free field models with vertical currents in the latter case. Alternatively, Parker-type nanoflare models of the solar corona hypothesize that a braiding mechanism operates between unresolved loop strands, which is a more complex topological model. In this study we use the vertical-current approximation of a nonpotential magnetic field solution (that fulfils the divergence-free and force-free conditions) to characterize the number of helical turns N twist in twisted coronal loops. We measure the helical twist in 15 active regions observed with Atmospheric Imaging Assembly and Helioseismic and Magnetic Imager/SDO (Solar Dynamic Observatory) and find a mean nonpotentiality angle (between the potential and nonpotential field directions) of μ NP = 15° ± 3°. The resulting mean rotational twist angle is φ = 49° ± 11°, which corresponds to N twist = φ/360° = 0.14 ± 0.03 turns with respect to the untwisted PF, with an absolute upper limit of N twist ≲ 0.5, which is far below the kink instability limit of . The number of twist turns N twist corresponds to the Gauss linkage number N link in braiding topologies. We conclude that any braided topology (with ) cannot explain the observed stability of loops in a force-free corona, nor the observed low twist number. Parker-type nanoflaring can thus occur in non-force-free environments only, such as in the chromosphere and transition region.

Y-shaped DNA-Mediated hybrid nanoflowers as efficient gene carriers for fluorescence imaging of tumor-related mRNA in living cells

Organic-inorganic hybrid nanomaterial has gained much attention due to its excellent performances in bioanalysis and biomedicine. However, the preparation of DNA-inorganic hybrid nanomaterial with suitable size for cell uptake remains a huge challenge. Herein, a moderate biomineralization strategy for synthesis of Y-DNA@Cu3(PO4)2 (Y-DNA@CuP) hybrid nanoflowers is reported. Y-DNA with a loop structure is used as both the biomineralization template and the recognition unit for thymidine kinase 1 (TK1) mRNA. The Y-DNA probe can linearly response to TK1 mRNA target sequence in a range from 2 nM to 150 nM with the limit of detection as low as 0.56 nM. Interestingly, the presence of Y-DNA significantly decreases the size of Cu3(PO4)2 (CuP) particles, which allows them suitable for intracellular applications as gene nanocarriers. Once inside the cells, the hybrid nanoflowers dissolve and release the Y-DNA probes. Then, the intracellular TK1 mRNA hybridizes with the loop region of Y-DNA, which dissociates the Cy3-labeled loop strand and turns on the red fluorescence. Through the real-time imaging of the intracellular TK1 mRNA, the assessment of tumor cells before and after the treatment of drugs including β-estradiol and tamoxifen is achieved.

Epitopes for neutralizing antibodies induced by HIV-1 envelope glycoprotein BG505 SOSIP trimers in rabbits and macaques.

The native-like, soluble SOSIP.664 trimer based on the BG505 clade A env gene of HIV-1 is immunogenic in various animal species, of which the most studied are rabbits and rhesus macaques. The trimer induces autologous neutralizing antibodies (NAbs) consistently but at a wide range of titers and with incompletely determined specificities. A precise delineation of immunogenic neutralization epitopes on native-like trimers could help strategies to extend the NAb response to heterologous HIV-1 strains. One autologous NAb epitope on the BG505 Env trimer is known to involve residues lining a hole in the glycan shield that is blocked by adding a glycan at either residue 241 or 289. This glycan-hole epitope accounts for the NAb response of most trimer-immunized rabbits but not for that of a substantial subset. Here, we have used a large panel of mutant BG505 Env-pseudotyped viruses to define additional sites. A frequently immunogenic epitope in rabbits is blocked by adding a glycan at residue 465 near the junction of the gp120 V5 loop and β24 strand and is influenced by amino-acid changes in the structurally nearby C3 region. We name this new site the “C3/465 epitope”. Of note is that the C3 region was under selection pressure in the infected infant from whom the BG505 virus was isolated. A third NAb epitope is located in the V1 region of gp120, although it is rarely immunogenic. In macaques, NAb responses induced by BG505 SOSIP trimers are more often directed at the C3/465 epitope than the 241/289-glycan hole.

Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops.

Internal loops within structured nucleic acids disrupt local base stacking and destabilize neighboring helical domains; however, these structural motifs also expand the conformational and functional capabilities of structured nucleic acids. Variations in the size, distribution of loop nucleotides on opposing strands (strand asymmetry), and sequence alter their biophysical properties. Here, the thermodynamics and structural flexibility of oligo-T-rich DNA internal loops were systematically investigated in terms of loop size and strand asymmetry. From optical melting experiments, a thermodynamic prediction model is proposed for the energetic penalty of internal loops that accounts for diminishing enthalpic and increasing entropic contributions due to loop size and strand asymmetry for bulges, asymmetric loops, and symmetric loops. These single-stranded domains become less sequence-dependent and more polymeric as the loop size increases. Single-molecule fluorescence resonance energy transfer studies reveal a gradual transition in conformation and structural flexibility from an elongated domain to an increasingly flexible bend that results from increasing strand asymmetry. The findings provide a framework for understanding the thermodynamic and conformational effects of internal loops for the rational design of functional DNA nanostructures.

Fundamental and Harmonic Oscillations in Neighboring Coronal Loops

Abstract We present observations of multimode (fundamental and harmonic) oscillations in a loop system, which appear to be simultaneously excited by a GOES C-class flare. Analysis of the periodic oscillations reveals that (1) the primary loop with a period of P a ≈ 4 minutes and a secondary loop with two periods of P a ≈ 4 minutes and P b ≈ 2 minutes are detected simultaneously in closely spaced loop strands; (2) both oscillation components have their peak amplitudes near the loop apex, while in the second loop the low-frequency component P a dominates in a loop segment that is two times larger than the high-frequency component P b ; (3) the harmonic mode P b shows the largest deviation from a sinusoidal loop shape at the loop apex. We conclude that multiple harmonic modes with different displacement profiles can be excited simultaneously even in closely spaced strands, similar to the overtones of a violin string.

The Width Distribution of Loops and Strands in the Solar Corona—Are We Hitting Rock Bottom?

Abstract In this study, we analyze Atmospheric Imaging Assembly (AIA) and Hi-C images in order to investigate absolute limits for the finest loop strands. We develop a model of the occurrence–size distribution function of coronal loop widths, characterized by the lower limit of widths w min, the peak (or most frequent) width w p , the peak occurrence number n p , and a power-law slope a. Our data analysis includes automated tracing of curvilinear features with the OCCULT-2 code, automated sampling of the cross-sectional widths of coronal loops, and fitting of the theoretical size distribution to the observed distribution. With Monte Carlo simulations and variable pixel sizes , we derive a first diagnostic criterion to discriminate whether the loop widths are unresolved or fully resolved (if ). For images with resolved loop widths, we can apply a second diagnostic criterion that predicts the lower limit of loop widths as a function of the spatial resolution. We find that the loop widths are marginally resolved in AIA images but are fully resolved in Hi-C images, where our model predicts a most frequent (peak) value at , in agreement with recent results of Brooks et al. This result agrees with the statistics of photospheric granulation sizes and thus supports coronal heating mechanisms operating on the macroscopic scale of photospheric magneto-convection, rather than nanoflare braiding models on unresolved microscopic scales.

Multi-instrument observations of a failed flare eruption associated with MHD waves in a loop bundle

We present observations of a B7.9-class flare that occurred on the 24th January, 2015, using the Atmopsheric Imaging Assembly (AIA) of the Solar Dynamics Observatory (SDO), the EUV Imaging Spectrometer (EIS) and the X-Ray Telescope of Hinode. The flare triggers the eruption of a dense cool plasma blob as seen in AIA 171\AA,\, which is unable to completely break out and remains confined within a local bundle of active region loops. During this process, transverse oscillations of the threads are observed. The cool plasma is then observed to descend back to the chromosphere along each loop strand. At the same time, a larger diffuse co-spatial loop observed in the hot wavebands of SDO/AIA and Hinode/XRT is formed, exhibiting periodic intensity variations along its length. The formation and evolution of magnetohydrodynamic (MHD) waves depend upon the values of the local plasma parameters (e.g. density, temperature and magnetic field), which can hence be inferred by coronal seismology. In this study we aim to assess how the observed MHD modes are affected by the variation of density and temperature. We combined analysis of EUV/X-ray imaging and spectroscopy using SDO/AIA, Hinode/EIS and XRT. We show that the evolution of the detected waves is determined by the temporal variations of the local plasma parameters, caused by the flare heating and the consequent cooling. We apply coronal seismology to both waves obtaining estimations of the background plasma parameters.

Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade

The use of antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in the field of cancer immunotherapy. Here, we identified KN035, an anti-PD-L1 nanobody that can strongly induce T-cell responses and inhibit tumor growth. The crystal structures of KN035 complexed with PD-L1 and free PD-L1, solved here at 1.7 and 2.7 Å resolution, respectively, show that KN035 competes with PD-1 (programmed death protein 1) for the same flat surface on PD-L1, mainly through a single surface loop of 21 amino acids. This loop forms two short helices and develops key hydrophobic and ionic interactions with PD-L1 residues, such as Ile54, Tyr56 and Arg113, which are also involved in PD-1 binding. The detailed mutagenesis study identified the hotspot residues of the PD-L1 surface and provides an explanation for the stronger (~1 000-fold) binding of KN035 to PD-L1 than PD-1 and its lack of binding to PD-L2. Overall, this study reveals how a single immunoglobulin-variable scaffold of KN035 or PD-1 can bind to a flat protein surface through either a single surface loop or beta-sheet strands; and provides a basis for designing new immune checkpoint blockers and generating bi-specific antibodies for combination therapy.

Dilute oriented loop models

We study a model of dilute oriented loops on the square lattice, where each loop is compatible with a fixed, alternating orientation of the lattice edges. This implies that loop strands are not allowed to go straight at vertices, and results in an enhancement of the usual symmetry to . The corresponding transfer matrix acts on a number of representations (standard modules) that grows exponentially with the system size. We derive their dimension and those of the centralizer by both combinatorial and algebraic techniques. A mapping onto a field theory permits us to identify the conformal field theory governing the critical range, . We establish the phase diagram and the critical exponents of low-energy excitations. For generic n, there is a critical line in the universality class of the dilute model, terminating in an point. The case n = 1 maps onto the critical line of the six-vertex model, along which exponents vary continuously.

COOL TRANSITION REGION LOOPS OBSERVED BY THEINTERFACE REGION IMAGING SPECTROGRAPH

We report on the first Interface Region Imaging Spectrograph (IRIS) study of cool transition region loops. This class of loops has received little attention in the literature. A cluster of such loops was observed on the solar disk in active region NOAA11934, in the Si IV 1402.8 \AA\ spectral raster and 1400 \AA\ slit-jaw (SJ) images. We divide the loops into three groups and study their dynamics and interaction. The first group comprises relatively stable loops, with 382--626\,km cross-sections. Observed Doppler velocities are suggestive of siphon flows, gradually changing from -10 km/s at one end to 20 km/s at the other end of the loops. Nonthermal velocities from 15 to 25 km/s were determined. These physical properties suggest that these loops are impulsively heated by magnetic reconnection occurring at the blue-shifted footpoints where magnetic cancellation with a rate of $10^{15}$ Mx/s is found. The released magnetic energy is redistributed by the siphon flows. The second group corresponds to two footpoints rooted in mixed-magnetic-polarity regions, where magnetic cancellation occurred at a rate of $10^{15}$ Mx/s and line profiles with enhanced wings of up to 200 km/s were observed. These are suggestive of explosive-like events. The Doppler velocities combined with the SJ images suggest possible anti-parallel flows in finer loop strands. In the third group, interaction between two cool loop systems is observed. Evidence for magnetic reconnection between the two loop systems is reflected in the line profiles of explosive events, and a magnetic cancellation rate of $3\times10^{15}$ Mx/s observed in the corresponding area. The IRIS observations have thus opened a new window of opportunity for in-depth investigations of cool transition region loops. Further numerical experiments are crucial for understanding their physics and their role in the coronal heating processes.

Correlation between the genotoxicity endpoints measured by two different genotoxicity assays: comet assay and CBMN assay

Correlation between the genotoxicity endpoints measured by two different genotoxicity assays: comet assay and CBMN assay

Dynamics of a multi-thermal loop in the solar corona

Context. We present an observation of a long-living multi-thermal coronal loop, visible in different extreme ultra-violet wavebands of SDO/AIA in a quiet-Sun region close to the western solar limb. Aims. Analysis of persistent kink displacements of the loop seen in different bandpasses that correspond to different temperatures of the plasma allows sub-resolution structuring of the loop to be revealed. Methods. A vertically oriented slit is taken at the loop top, and time-distance maps are made from it. Loop displacements in time-distance maps are automatically tracked with the Gaussian fitting technique and fitted with a sinusoidal function that is “guessed”. Wavelet transforms are further used in order to quantify the periodicity variation in time of the kink oscillations. Results. The loop strands are found to oscillate with the periods ranging between 3 and 15 min. The oscillations are observed in intermittent regime with temporal changes in the period and amplitude. The oscillations are different at three analysed wavelengths. Conclusions. This finding suggests that the loop-like threads seen at different wavelengths are not co-spatial, hence that the loop consists of several multi-thermal strands. The detected irregularity of the oscillations can be associated with a stochastic driver acting at the footpoints of the loop.

Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations.

A critical step of β-amyloid fibril formation is fibril elongation in which amyloid-β monomers undergo structural transitions to fibrillar structures upon their binding to fibril tips. The atomic detail of the structural transitions remains poorly understood. Computational characterization of the structural transitions is limited so far to short Aβ segments (5–10 aa) owing to the long time scale of Aβ fibril elongation. To overcome the computational time scale limit, we combined a hybrid-resolution model with umbrella sampling and replica exchange molecular dynamics and performed altogether ∼1.3 ms of molecular dynamics simulations of fibril elongation for Aβ17–42. Kinetic network analysis of biased simulations resulted in a kinetic model that encompasses all Aβ segments essential for fibril formation. The model not only reproduces key properties of fibril elongation measured in experiments, including Aβ binding affinity, activation enthalpy of Aβ structural transitions and a large time scale gap (τlock/τdock = 103–104) between Aβ binding and its structural transitions, but also reveals detailed pathways involving structural transitions not seen before, namely, fibril formation both in hydrophobic regions L17-A21 and G37-A42 preceding fibril formation in hydrophilic region E22-A30. Moreover, the model identifies as important kinetic intermediates strand–loop–strand (SLS) structures of Aβ monomers, long suspected to be related to fibril elongation. The kinetic model suggests further that fibril elongation arises faster at the fibril tip with exposed L17-A21, rather than at the other tip, explaining thereby unidirectional fibril growth observed previously in experiments.