Contribution of myocardium hydraulic skeleton to left ventricular wall interaction and synergy in dogs

The most premature motion change after coronary occlusion is early diastolic thinning of the ischemic left ventricular (LV) wall, with concomitant thickening of the normoperfused wall. We aimed 1). to demonstrate that these early changes are the result of the absence of fluid within the ischemic myocardium (hydraulic skeleton) rather than to cell anoxia and 2). to quantitate the contribution of the lack of hydraulic skeleton to left ventricular asynergy of contraction in seven anesthetized dogs submitted to acute, short-lasting circumflex artery (Cx) occlusion (ischemia) and to perfusion of the Cx with an oxygen-free solution (anoxia). We analyzed the time course of regional work index (WI, area of the LV pressure-wall thickness loop) and regional efficiency (defined as the ratio of WI to the maximum possible work). Interwall asynergy was defined as the difference between the regional efficiency of the anterior and posterior walls. After 9-10 s, posterior wall efficiency decreased 37 +/- 6% with anoxia and 72 +/- 3% with ischemia (P < 0.025), and interwall asynergy was 0 +/- 6% with anoxia and 32 +/- 5% with ischemia (P < 0.05). The contribution of absent hydraulic skeleton to interwall asynergy (calculated as the difference between %asynergy in anoxia and %asynergy in ischemia) was 30 +/- 8% (P < 0.05). In conclusion, the earliest wall motion change observed after acute coronary occlusion, namely ischemic wall thinning concomitant with normoperfused wall thickening during isovolumic relaxation, is the result of the absence of intracoronary fluid. The lack of hydraulic skeleton within the myocardium contributes approximately 30% to interwall asynergy.     

Buckling analysis of defective cross-linked functionalized single- and double-walled carbon nanotubes with polyethylene chains using molecular dynamics simulations

Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two different configurations with the consideration of vacancy defects, namely mapped and wrapped, are selected. According to the results, critical buckling force of cross-linked functionalized CNTs with PE chains increases as compared to pure CNTs, especially in the case of double-walled carbon nanotubes (DWCNTs). By contrast, it is demonstrated that critical strain of cross-linked functionalized CNTs decreases as compared to that of pristine CNTs. Also, it is observed that increasing the weight percentage leads to the higher increase and the decrease in critical buckling force and strain of cross-linked functionalized CNTs, respectively. Moreover, the presence of defect considerably reduces both critical buckling force and strain of cross-linked functionalized CNTs. Finally, it is shown that the critical buckling strain is more sensitive to the presence of defects as compared to critical buckling force.     

Frequent alterations of visual pigment genes in adrenoleukodystrophy.

Both adrenoleukodystrophy (ALD) and red/green color blindness have been mapped to the distal long arm of the human X chromosome (Xq28). Color-vision defects are frequently associated with ALD, and study of the red and green visual pigment genes in eight ALD kindreds has shown frequent structural changes including deletions and possible intragenic recombinations. Such changes may reflect chromosomal events underlying both ALD and the associated visual defects and should help define both the structural gene responsible for ALD and physical genetic relationships in the Xq28 region.     

Translational dynamic friction analysis of double-walled carbon nanotubes

Conflicting results on the effects of commensurability, overlap area, helicity and end configuration of double-walled carbon nanotubes (DWCNTs) on translational intertube friction have been reported. We perform molecular dynamics simulations on DWCNTs with different commensurabilities, overlap areas, helicities and end configurations to analyse the intertube friction behaviour and clarify these results. It is found that commensurability and overlap area play an insignificant role, while the atomic configurations of nanotube ends play a dominant role: armchair, normal and reconstructed zigzag ends contribute little to intertube friction; while the irregular ends with dangling atoms greatly increase the friction force. This end effect may also explain the role of helicity in the intertube friction. Implications of the end effect on experimental observations are also discussed.     

The Pcdp1 complex coordinates the activity of dynein isoforms to produce wild-type ciliary motility

Generating the complex waveforms characteristic of beating cilia requires the coordinated activity of multiple dynein isoforms anchored to the axoneme. We previously identified a complex associated with the C1d projection of the central apparatus that includes primary ciliary dyskinesia protein 1 (Pcdp1). Reduced expression of complex members results in severe motility defects, indicating that C1d is essential for wild-type ciliary beating. To define a mechanism for Pcdp1/C1d regulation of motility, we took a functional and structural approach combined with mutants lacking C1d and distinct subsets of dynein arms. Unlike mutants completely lacking the central apparatus, dynein-driven microtubule sliding velocities are wild type in C1d- defective mutants. However, coordination of dynein activity among microtubule doublets is severely disrupted. Remarkably, mutations in either outer or inner dynein arm restore motility to mutants lacking C1d, although waveforms and beat frequency differ depending on which isoform is mutated. These results define a unique role for C1d in coordinating the activity of specific dynein isoforms to control ciliary motility.     

A model of temporomandibular joint function in anthropoid primates based on condylar movements during mastication

The hypothesis that the shape of the bony temporomandibular joint (TMJ) is functionally related to sagittal sliding of the condyle during mastication is tested, and a model of the relation of sagittal sliding to mandibular size, TMJ shape, and diet is developed. Sagittal sliding is defined as fore-aft motion of the condyle during mandibular translation and/or angular rotation. Ascending ramus height is used as a structural correlate of the distance between the condyle and the mandibular axis of rotation (CR). Cineradiographic data on sagittal sliding and gape during mastication in Ateles spp., Macaca fascicularis, Papio anubis, and Pan troglodytes in conjunction with comparative data on mandibular size and TMJ shape are used to evaluate the hypothesis. The results show that 1) linear and angular gape are highly positively correlated with sagittal sliding, 2) pure mandibular translation is rare during mastication, 3) the CR is rarely if ever located at the condyle during mastication, 4) angular gape should be standardized in interindividual comparisons of sagittal sliding, and 5) the height of the ascending ramus (and by inference the CR-to-condyle distance) is highly positively correlated with absolute sagittal sliding. Sagittal sliding relative to the length of the articular eminence was the variable used to explore the relation between TMJ shape and sliding. This variable standardized absolute sagittal sliding relative to joint size. The relative depth and orientation of the articular eminence were not correlated with relative sagittal sliding. The anteroposterior curvature of the condyle was highly negatively correlated with relative sagittal sliding. Flat condyles are associated with large amounts of relative sagittal sliding. A flat condyle increases joint contact area, which reduces joint stress. A flat condyle also increases joint congruence, and this may facilitate the combined sliding and rolling motion of the condyle when the sliding motion is relatively large. The shape of the entoglenoid process was also positively correlated with relative sagittal sliding. A relatively large entoglenoid process may help to guide sagittal sliding and prevent excessive mediolateral sliding of the condyle. The functional model makes a number of predictions about the correlations between food consistency and food object size, mandibular size, TMJ shape, and sagittal sliding of the condyle during mastication and incision. Am J Phys Anthropol 109:67–88, 1999. © 1999 Wiley-Liss, Inc.     

Detailed structural and biochemical characterization of the nexin-dynein regulatory complex

The nexin-dynein regulatory complex (N-DRC) forms a cross-bridge between the outer doublet microtubules of the axoneme and regulates dynein motor activity in cilia/flagella. Although the molecular composition and the three-dimensional structure of N-DRC have been studied using mutant strains lacking N-DRC subunits, more accurate approaches are necessary to characterize the structure and function of N-DRC. In this study, we precisely localized DRC1, DRC2, and DRC4 using cryo–electron tomography and structural labeling. All three N-DRC subunits had elongated conformations and spanned the length of N-DRC. Furthermore, we purified N-DRC and characterized its microtubule-binding properties. Purified N-DRC bound to the microtubule and partially inhibited microtubule sliding driven by the outer dynein arms (ODAs). Of interest, microtubule sliding was observed even in the presence of fourfold molar excess of N-DRC relative to ODA. These results provide insights into the role of N-DRC in generating the beating motions of cilia/flagella.     

Sliding osteotomies in mandibular reconstruction

The aim of this article is to describe a few simple and atraumatic methods for mandibular reconstruction following the ablation of tumors or traumas. These reconstruction techniques are indicated for rebuilding short mandibular defects (less than 4 cm) or for patients in poor general condition with larger defects that cannot be remedied using longer and more complicated procedures. Five types of osteotomies were used: "C," single, double, bilateral sliding, and sagittal sliding.Osteotomies were performed on 14 patients, 13 with malignant tumors and one with a gunshot wound. Good results were obtained in 10 patients, total failure occurred in two, and complications without failure of the reconstruction arose in the other two.     

Structural Insights into Saccharomyces cerevisiae Msh4–Msh5 Complex Function Using Homology Modeling

The Msh4–Msh5 protein complex in eukaryotes is involved in stabilizing Holliday junctions and its progenitors to facilitate crossing over during Meiosis I. These functions of the Msh4–Msh5 complex are essential for proper chromosomal segregation during the first meiotic division. The Msh4/5 proteins are homologous to the bacterial mismatch repair protein MutS and other MutS homologs (Msh2, Msh3, Msh6). Saccharomyces cerevisiae msh4/5 point mutants were identified recently that show two fold reduction in crossing over, compared to wild-type without affecting chromosome segregation. Three distinct classes of msh4/5 point mutations could be sorted based on their meiotic phenotypes. These include msh4/5 mutations that have a) crossover and viability defects similar to msh4/5 null mutants; b) intermediate defects in crossing over and viability and c) defects only in crossing over. The absence of a crystal structure for the Msh4–Msh5 complex has hindered an understanding of the structural aspects of Msh4–Msh5 function as well as molecular explanation for the meiotic defects observed in msh4/5 mutations. To address this problem, we generated a structural model of the S. cerevisiae Msh4–Msh5 complex using homology modeling. Further, structural analysis tailored with evolutionary information is used to predict sites with potentially critical roles in Msh4–Msh5 complex formation, DNA binding and to explain asymmetry within the Msh4–Msh5 complex. We also provide a structural rationale for the meiotic defects observed in the msh4/5 point mutations. The mutations are likely to affect stability of the Msh4/5 proteins and/or interactions with DNA. The Msh4–Msh5 model will facilitate the design and interpretation of new mutational data as well as structural studies of this important complex involved in meiotic chromosome segregation.     

Clamp loaders and sliding clamps

A coherent view of the structure and function of DNA polymerase processivity factors (sliding clamps and clamp loaders) is emerging from recent structural studies. Crystal structures of sliding clamps from the T4 and RB69 bacteriophages, and from an archaebacterium expand the gallery of ring-shaped processivity factors and clarify how the clamp interacts with the DNA polymerase. Crystallographic and electron microscopic views of clamp loaders from bacteria, archaebacteria and eukaryotes emphasize their common architecture and have produced models of how ATPbinding might be coupled to clamp opening/loading.     

Evaluation of the head-helmet sliding properties in an impact test

The scalp plays a crucial role in head impact biomechanics, being the first tissue involved in the impact and providing a sliding interface between the impactor and/or helmet and the skull. It is important to understand both the scalp-skull and the scalp-helmet sliding in order to determine the head response due to an impact. However, experimental data on the sliding properties of the scalp is lacking. The aim of this work was to identify the sliding properties of the scalp using cadaver heads, in terms of scalp-skull and scalp-liner (internal liner of the helmet) friction and to compare these values with that of widely used artificial headforms (HIII and magnesium EN960). The effect of the hair, the direction of sliding, the speed of the test and the normal load were considered. The experiments revealed that the sliding behaviour of the scalp under impact loading is characterised by three main phases: (1) the low friction sliding of the scalp over the skull (scalp-skull friction), (2) the tensioning effect of the scalp and (3) the sliding of the liner fabric over the scalp (scalp-liner friction). Results showed that the scalp-skull coefficient of friction (COF) is very low (0.06 ± 0.048), whereas the scalp-liner COF is 0.29 ± 0.07. The scalp-liner COF is statistically different from the value of the HIII-liner (0.75 ± 0.06) and the magnesium EN960-liner (0.16 ± 0.026). These data will lead to the improvement of current headforms for head impact standard tests, ultimately leading to more realistic head impact simulations and the optimization of helmet designs.     

Structure–property relation and relevance of beam theories for microtubules: a coupled molecular and continuum mechanics study

Quasi-one-dimensional microtubules (MTs) in cells enjoy high axial rigidity but large transverse flexibility due to the inter-protofilament (PF) sliding. This study aims to explore the structure–property relation for MTs and examine the relevance of the beam theories to their unique features. A molecular structural mechanics (MSM) model was used to identify the origin of the inter-PF sliding and its role in bending and vibration of MTs. The beam models were then fitted to the MSM to reveal how they cope with the distinct mechanical responses induced by the inter-PF sliding. Clear evidence showed that the inter-PF sliding is due to the soft inter-PF bonds and leads to the length-dependent bending stiffness. The Euler beam theory is found to adequately describe MT deformation when the inter-PF sliding is largely prohibited. Nevertheless, neither shear deformation nor the nonlocal effect considered in the ‘more accurate’ beam theories can fully capture the effect of the inter-PF sliding. This reflects the distinct deformation mechanisms between an MT and its equivalent continuous body.     

Water transport through carbon nanotubes with defects

Non-equilibrium molecular dynamics simulations are performed to investigate how changing the number of structural defects in the wall of a (7,7) single-walled carbon nanotube (CNT) affects water transport and internal fluid dynamics. Structural defects are modelled as vacancy sites (missing carbon atoms). We find that, while fluid flow rates exceed continuum expectations, increasing numbers of defects lead to significant reductions in fluid velocity and mass flow rate. The inclusion of such defects causes a reduction in the water density inside the nanotubes and disrupts the nearly frictionless water transport commonly attributed to CNTs.     

Defective structural RNA processing in relapsing-remitting multiple sclerosis

BackgroundSurveillance of integrity of the basic elements of the cell including DNA, RNA, and proteins is a critical element of cellular physiology. Mechanisms of surveillance of DNA and protein integrity are well understood. Surveillance of structural RNAs making up the vast majority of RNA in a cell is less well understood. Here, we sought to explore integrity of processing of structural RNAs in relapsing remitting multiple sclerosis (RRMS) and other inflammatory diseases.ResultsWe employed mononuclear cells obtained from subjects with RRMS and cell lines. We used quantitative-PCR and whole genome RNA sequencing to define defects in structural RNA surveillance and siRNAs to deplete target proteins. We report profound defects in surveillance of structural RNAs in RRMS exemplified by elevated levels of poly(A) + Y1-RNA, poly(A) + 18S rRNA and 28S rRNAs, elevated levels of misprocessed 18S and 28S rRNAs and levels of the U-class of small nuclear RNAs. Multiple sclerosis is also associated with genome-wide defects in mRNA splicing. Ro60 and La proteins, which exist in ribonucleoprotein particles and play different roles in quality control of structural RNAs, are also deficient in RRMS. In cell lines, silencing of the genes encoding Ro60 and La proteins gives rise to these same defects in surveillance of structural RNAs.ConclusionsOur results establish that profound defects in structural RNA surveillance exist in RRMS and establish a causal link between Ro60 and La proteins and integrity of structural RNAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0629-x) contains supplementary material, which is available to authorized users.     

Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides

Human defensins play important roles in a broad range of biological functions, such as microbial defense and immunity. Yet, little is known about their molecular properties, i.e. secondary structure stability, structural variability, important side chain interactions, surface charge distribution, and resistance to thermal fluctuations, and how these properties are related to their functions. To assess these factors, we studied the native human β-defensin-1 monomer and dimer as well as several single-site mutants using molecular dynamics simulations. The results showed that disulfide bonds are important determinants in maintaining the defensins’ structural integrity, as no structural transitions were observed at 300?K and only minor structural unfolding was detected upon heating to 500?K. The α-helix was less thermally stable than the core β-sheet structure held together by hydrogen bonds and hydrophobic interactions. The monomer α-helix stability was directly correlated, whereas the end-to-end distance was inversely correlated to the experimentally measured β-defensin-1 chemotactic activity, in the order: mutant 2 (Gln24Glu)?>?mutant 3 (Lys31Ala)?=?wild type?>?mutant 1 (Asn4Ala). The structural stability of the β-defensin-1 dimer species exhibited an inverse correlation to their chemotactic activity. In dimers formed by mutants 2 and 3, we observed sliding of one monomer upon the surface of the other in the absence of unbinding. This dynamic sliding feature may enhance the molecular oligomerization of β-defensin-1 peptides contributing to their antibacterial activity. It could also help these peptides orient correctly in the CC chemokine receptor 6 binding site, thereby initiating their chemotactic activity. In agreement with this notion, the remarkable sliding behavior was observed only for the mutants with the highest chemotactic activity.     

Theory of nucleosome corkscrew sliding in the presence of synthetic DNA ligands

Histone octamers show a heat-induced mobility along DNA. Recent theoretical studies have established two mechanisms that are qualitatively and quantitatively compatible with in vitro experiments on nucleosome sliding: octamer repositioning through one-base-pair twist defects and through ten-base-pair bulge defects. A recent experiment demonstrated that the repositioning is strongly suppressed in the presence of minor-groove binding DNA ligands. In the present study, we give a quantitative theory for nucleosome repositioning in the presence of such ligands. We show that the experimentally observed octamer mobilities are consistent with the picture of bound ligands blocking the passage of twist defects through the nucleosome. This strongly supports the model of twist defects inducing a corkscrew motion of the nucleosome as the underlying mechanism of nucleosome sliding. We provide a theoretical estimate of the nucleosomal mobility without adjustable parameters, as a function of ligand concentration, binding affinity, binding site orientation, temperature and DNA anisotropy. Having this mobility in hand, we speculate on the interaction between a nucleosome and a transcribing RNA polymerase, and suggest a novel mechanism that might account for polymerase-induced nucleosome repositioning on short DNA templates.     

Roles of the hydrophobic triplet in the motor domain of myosin in the interaction between myosin and actin

Myosin is a molecular motor and a member of a protein family comprising at least 18 classes. There is an about 1,000-fold difference in the in vitro sliding velocity between the fastest myosin and the slowest one. Previous studies revealed that the hydrophobic triplet in the motor domain (Val534, Phe535, and Pro536 in Dictyostelium myosin) is important for the strong binding of myosin to actin. We studied the role of the triplet in the sliding motion of myosin by means of site directed mutagenesis because the sliding velocity is determined by the time that myosin interacts with actin strongly. We produced mutant Dictyostelium myosins and subfragment-1s that have the triplet sequences of various classes of myosin with different sliding velocities. The V(max) and K(actin) values of the actin-activated ATPase for all these mutant subfragment-1s were lower than those of the wild-type Dictyostelium myosin. The mutant myosins exhibited much lower sliding velocities than the wild type. The time that the mutant subfragment-1s are in the strongly bound state did not correlate well with the sliding velocity. Our results suggested that (i) the hydrophobic triplet alone does not determine the sliding velocity of myosin, (ii) the size of the amino acid side chain in the triplet is crucial for the ATPase activity and the motility of myosin, and (iii) the hydrophobic triplet is important not only for strong binding to actin but also for the structural change of the myosin motor domain during the power stroke.     

Hypolipidemic therapy modulates expression of apolipoprotein B epitopes on low density lipoproteins. Studies in mild to moderate hypertriglyceridemic patients

Low density lipoproteins (LDL) of untreated moderate to severe hypertriglyceridemic patients (HTG-LDL) are smaller in size and are relatively enriched in triglycerides and proteins compared with normal LDL (N-LDL). HTG-LDL also manifest defective binding to the LDL receptors of normal cultured human fibroblasts. These structural and functional defects are reversible by effective hypolipidemic therapy. The aims of the present study were to confirm the reversibility of the structural and functional defects in mild to moderate hypertriglyceridemic patients and also to test the hypothesis that therapy improved the binding of HTG-LDL to cells by modulating epitopes of apolipoprotein B (apoB-100) on the surfaces of LDL particles. Fasting plasma samples were obtained from five mild to moderate hypertriglyceridemic patients before and 3 weeks after bezafibrate therapy when mean triglyceride levels were 436 and 157 mg/dl (P less than 0.01), respectively. LDL particles were isolated by zonal ultracentrifugation, characterized chemically, and assayed for cell association and proteolytic degradation in-up regulated normal human skin fibroblasts. LDL immunoreactivity was tested in solid phase competitive binding radioimmunoassays (RIA) using three monoclonal antiLDL antibodies (Mab). Mab 464B1B3 and Mab 465B6C3 react against epitopes in the COOH-terminal (T2/K4) fragment of apoB-100. Mab D7.1 reacts with an epitope in the midportion (T3/K3) fragment. Mab 464B1B3 inhibits the binding of LDL to the LDL receptor. Hypolipidemic treatment altered the composition of LDL. Mean LDL triglycerides fell from 9.4 to 5.8% of LDL mass (P less than 0.025).(ABSTRACT TRUNCATED AT 250 WORDS)