Pairing of single-cell RNA analysis and T cell antigen receptor profiling indicates breakdown of T cell tolerance checkpoints in atherosclerosis.

Atherosclerotic plaques form in the inner layer of arteries triggering heart attacks and strokes. Although T cells have been detected in atherosclerosis, tolerance dysfunction as a disease driver remains unexplored. Here we examine tolerance checkpoints in atherosclerotic plaques, artery tertiary lymphoid organs and lymph nodes in mice burdened by advanced atherosclerosis, via single-cell RNA sequencing paired with T cell antigen receptor sequencing. Complex patterns of deteriorating peripheral T cell tolerance were observed being most pronounced in plaques followed by artery tertiary lymphoid organs, lymph nodes and blood. Affected checkpoints included clonal expansion of CD4+, CD8+ and regulatory T cells; aberrant tolerance-regulating transcripts of clonally expanded T cells; T cell exhaustion; Treg-TH17 T cell conversion; and dysfunctional antigen presentation. Moreover, single-cell RNA-sequencing profiles of human plaques revealed that the CD8+ T cell tolerance dysfunction observed in mouse plaques was shared in human coronary and carotid artery plaques. Thus, our data support the concept of atherosclerosis as a bona fide T cell autoimmune disease targeting the arterial wall.

Photodynamic Therapy and Its Synergism with Melittin Against Drug-Resistant Acinetobacter baumannii Isolates with High Biofilm Formation Ability.

Drug-resistant biofilm producer A. baumannii isolates are a global concern that warns researchers about the development of new treatments. This study was designed to analyze the effect of photodynamic therapy (PDT) as monotherapy and associated with melittin on multidrug-resistant A. baumannii isolates. Sub-lethal doses of photosensitizer, LED, and PDT were determined. The PDT effect on the biofilm and expression of biofilm-associated genes was evaluated by scanning electron microscopy and quantitative real-time PCR (qRT-PCR) methods, respectively. The synergistic effect of PDT and melittin on the survival of MDR/XDR strong biofilm producer isolates was evaluated by checkerboard assay. Survival rates were significantly decreased at the lowest concentration of 12.5-50 µg/ml in 4 min at an energy density of 93.75 J/cm2 (P < 0.05). The optimized PDT method had a bactericidal effect against all tested groups, and the mean expression levels of csu, abaI, bap, and ompA genes in the strong biofilm producers were decreased significantly compared to the control group. The combined effect of LED and melittin successfully reduced the MDR/XDR A. baumannii strong biofilm producers' growth from 3.1 logs. MB-mediated aPDT and combined treatment of PDT with melittin, which has been investigated for the first time in this study, can be an efficient strategy against MDR/XDR A. baumannii isolates with strong biofilm production capacity.

Role of particle local curvature in cellular wrapping.

Cellular uptake through membranes plays an important role in adsorbing nutrients and fighting infection and can be used for nanomedicine developments. Endocytosis is one of the pathways of cellular uptake which associate with elastic deformation of the membrane wrapping around the foreign particle. The deformability of the membrane is strongly regulated by the presence of a cortical cytoskeleton placed underneath the membrane. It is shown that shape and orientation of the particles influence on their internalization. Here, we study the role of particle local curvature in cellular uptake by investigating the wrapping of an elastic membrane around a long cylindrical object with an elliptical cross-section. The membrane itself is adhered to a substrate mimicking the cytoskeleton. Membrane wrapping proceeds differently whether the initial contact occurs at the target's highly curved part (vertical) or along its long side (horizontal). We obtain a wrapping phase diagram as a function of the membrane-cytoskeleton and the membrane-target adhesion energy, which includes three distinct regimes (unwrapped, partially wrapped and fully wrapped), separated by two phase transitions. We also provide analytical expressions for the boundaries between the different regimes which confirm that the transitions strongly depend on the orientation and aspect ratio of the nanowire.

Theoretical study of RNA-polymerase behavior considering the backtracking state.

The dynamical behavior of the RNA polymerase in the transcription process is vital to gene expression. During the transcription process, the 3' end of the transcribed RNA can be dislocated from the active site of the enzyme and as a result, the RNA polymerase goes to the backtracked state. Here, we develop a theoretical model to study the transcription process considering the backtracking state. We aim at describing the behavior of the enzyme in the backtracking state in the presence of an external force, which leads to two possibilities: (i) rescuing from the backtracking state and, (ii) the arresting of the enzyme. We study the probability and the rate of the mentioned processes. In addition, we find that entering the backtracking state behaves like the Brownian ratchet mechanism. This model could shed some light on the modeling of the transcription process and further studies on the energy landscape of the backtracking channel and the gene regulation.

The Association Between Hepatitis B Virus Mutations and the Risk of Liver Disease and Hepatocellular Carcinoma.

Hepatitis B virus [HBV], the best-described hepadnavirus, is distributed all around the world and may lead to chronic and acute liver disease, cirrhosis, and hepatocellular carcinoma. Despite the advancement in treatment against HBV, an errorprone reverse transcriptase, which is required for HBV replication as well as host immune pressure, leads to constant evolution and emergence of genotypes, subgenotypes and mutant viruses; so, HBV will remain as a major healthcare problem around the world. This review article mainly focuses on the HBV mutations which correlated to occult HBV infection, immune escape, vaccine failure and eventually liver cirrhosis and HCC. The current study indicated that preS/S region mutations are related to vaccine failure, immune escape, occult HBV infection and the occurrence of HCC. Whereas P region Mutations may lead to drug resistance to NA antivirals. PreC/C region mutations are associated with HBeAg negativity, immune escape, and persistent hepatitis. Moreover, X region Mutations play an important role in HCC development.

The characteristics of nuclear membrane fluctuations in stem cells.

We analyse the stem cell nucleus shape fluctuation spectrum obtained from optical confocal microscopy on an hour time scale with 10 s resolution. In particular, we investigate the angular and time dependencies of these fluctuations, define appropriate correlation functions that reveal the fundamentally out of equilibrium nature of the observed fluctuations as well as their global anisotropy. Langevin equations respecting the symmetry of the system allow us to model the damped oscillatory behaviour of the time correlations.

Understanding the role of integrins in breast cancer invasion, metastasis, angiogenesis, and drug resistance.

Integrins are cell adhesion receptors, which are typically transmembrane glycoproteins that connect to the extracellular matrix (ECM). The function of integrins regulated by biochemical events within the cells. Understanding the mechanisms of cell growth by integrins is important in elucidating their effects on tumor progression. One of the major events in integrin signaling is integrin binding to extracellular ligands. Another event is distant signaling that gathers chemical signals from outside of the cell and transmit the signals upon cell adhesion to the inside of the cell. In normal breast tissue, integrins function as checkpoints to monitor effects on cell proliferation, while in cancer tissue these functions altered. The combination of tumor microenvironment and its associated components determines the cell fate. Hypoxia can increase the expression of several integrins. The exosomal integrins promote the growth of metastatic cells. Expression of certain integrins is associated with increased metastasis and decreased prognosis in cancers. In addition, integrin-binding proteins promote invasion and metastasis in breast cancer. Targeting specific integrins and integrin-binding proteins may provide new therapeutic approaches for breast cancer therapies. This review will examine the current knowledge of integrins' role in breast cancer.

Insight into the unwrapping of the dinucleosome.

Dynamics of nucleosomes, the building blocks of chromatin, has crucial effects on the expression, replication and repair of genomes in eukaryotes. Beside the constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin remodelling complexes cause their active displacements. Here we propose a theoretical analysis of dinucleosome wrapping and unwrapping dynamics in the presence of an external force. We explore the energy landscape and configurations of a dinucleosome in different unwrapped states. Moreover, using a dynamical Monte-Carlo simulation algorithm, we demonstrate the dynamical features of the system such as the unwrapping force for partial and full wrapping processes. Furthermore, we show that in the short length of linker DNA (∼10-90 bp), asymmetric unwrapping occurs. These findings could shed some light on chromatin dynamics and gene accessibility.

Achieving an Ultrahigh Power Factor in Sb2Te2Se Monolayers via Valence Band Convergence.

An efficient approach to improve the thermoelectric performance of materials is to converge their electronic bands, which is known as band engineering. In this regard, lots of effort has been made to further improve the thermoelectric efficiency of bulk and exfoliated monolayers of Bi2Te3 and Sb2Te3. However, ultrahigh band degeneracy and thus significant improvement of the power factor have not yet been realized in these materials. Using first-principles methods, we demonstrate that the valley degeneracy of Bi2Te3 and Sb2Te3 can be largely improved upon substitution of the middle-layer Te atoms with the more electronegative S or Se atoms. Our detailed analysis reveals that in this family of materials, two out of four possible valence band valleys merely depend on the electronegativity of the middle-layer chalcogen atoms, which makes the independent modulation of the valleys' position feasible. As such, band alignment of Bi2Te3 and Sb2Te3 largely improves upon substitution of the middle-layer Te atoms with more electronegative, yet chemically similar, S and Se ones. A superior valence band alignment is attained in Sb2Te2Se monolayers where three out of four possible valleys are well aligned, resulting in a giant band degeneracy of 18 that holds the record among all thermoelectric materials. As a result, an outstanding power factor for the hole-doped monolayers is achieved, indicating a highly efficient p-type thermoelectric material.

Wrapping of a nanowire by a supported lipid membrane.

Internalization of particles by cells plays a crucial role for adsorbing nutrients and fighting infection. Endocytosis is one of the most important mechanisms of particle uptake, which encompasses multiple pathways. Although endocytosis is a complex mechanism involving biochemical signaling and active force generation, the energetic cost associated with the large deformations of the cell membrane wrapping around a foreign particle is an important factor controlling this process, which can be studied using quantitative physical models. Of particular interest is the competition between membrane-cytoskeleton and membrane-target adhesion. This competitive adhesion mechanism can be reproduced to some extent by studying particle wrapping by a membrane adhered to a substrate. We propose a theoretical analysis of this process. Here, we explore the wrapping of a lipid membrane around a long cylindrical object in the presence of a substrate mimicking the cytoskeleton. Using discretization of the Helfrich elastic energy, which accounts for the membrane bending rigidity and surface tension, we obtain a wrapping phase diagram as a function of the membrane-cytoskeleton and the membrane-target adhesion energy, which includes unwrapped, partially wrapped and fully wrapped states. We provide an analytical expression for the boundary between the different regimes. While the transition to partial wrapping is independent of the membrane tension, the transition to full wrapping is very much influenced by the membrane tension. We also show that target wrapping may proceed in an asymmetric fashion in the full wrapping regime.

Influence of cross-linking and retrograde flow on formation and dynamics of lamellipodium.

The forces that arise from the actin cortex play a crucial role in determining the membrane deformation. These include protrusive forces due to actin polymerization, pulling forces due to transient attachment of actin filaments to the membrane, retrograde flow powered by contraction of actomyosin network, and adhesion to the extracellular matrix. Here we present a theoretical model for membrane deformation resulting from the feedback between the membrane shape and the forces acting on the membrane. We model the membrane as a series of beads connected by springs and determine the final steady-state shape of the membrane arising from the interplay between pushing/pulling forces of the actin network and the resisting membrane tension. We specifically investigate the effect of the gel dynamics on the spatio-temporal deformation of the membrane until a stable lamellipodium is formed. We show that the retrograde flow and the cross-linking velocity play an essential role in the final elongation of the membrane. Interestingly, in the simulations where motor-induced contractility is switched off, reduced retrograde flow results in an increase in the rate and amplitude of membrane protrusion. These simulations are consistent with experimental observations that report an enhancement in protrusion efficiency as myosin II molecular motors are inhibited.

Effects of dielectric inhomogeneity on electrostatic twist rigidity of a helical biomolecule in Debye-Hückel regime.

The electrostatic interactions play a crucial role in biological systems. Here we consider an impermeable dielectric molecule in the solvent with a different dielectric constant. The electrostatic free energy in the problem is studied in the Debye-Hückel regime using the analytical Green function that is calculated in the paper. Using this electrostatic free energy, we study the electrostatic contribution to the twist rigidity of a double stranded helical molecule such as a DNA and an actin filament. The dependence of the electrostatic twist rigidity of the molecule to the dielectric inhomogeneity, structural parameters, and the salt concentration is studied. It is shown that, depending on the parameters, the electrostatic twist rigidity could be positive or negative.

Modelling of Dictyostelium discoideum movement in a linear gradient of chemoattractant.

Chemotaxis is a ubiquitous biological phenomenon in which cells detect a spatial gradient of chemoattractant, and then move towards the source. Here we present a position-dependent advection-diffusion model that quantitatively describes the statistical features of the chemotactic motion of the social amoeba Dictyostelium discoideum in a linear gradient of cAMP (cyclic adenosine monophosphate). We fit the model to experimental trajectories that are recorded in a microfluidic setup with stationary cAMP gradients and extract the diffusion and drift coefficients in the gradient direction. Our analysis shows that for the majority of gradients, both coefficients decrease over time and become negative as the cells crawl up the gradient. The extracted model parameters also show that besides the expected drift in the direction of the chemoattractant gradient, we observe a nonlinear dependency of the corresponding variance on time, which can be explained by the model. Furthermore, the results of the model show that the non-linear term in the mean squared displacement of the cell trajectories can dominate the linear term on large time scales.

Modeling of ribosome dynamics on a ds-mRNA under an external load.

Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions.

Elastic model for dinucleosome structure and energy.

The equilibrium structure of a dinucleosome is studied using an elastic model that takes into account the force and torque balance conditions. Using the proper boundary conditions, it is found that the conformational energy of the problem does not depend on the length of the linker DNA. In addition it is shown that the two histone octamers are almost perpendicular to each other, and the linker DNA in short lengths is almost straight. These findings could shed some light on the role of DNA elasticity in the chromatin structure.

Regulation of the membrane wrapping transition of a cylindrical target by cytoskeleton adhesion.

The adsorption of external objects to the cell membrane often triggers cellular responses involving large deformations. In phagocytosis, upon contact with the target, the cell creates large extensions that wrap around the target and ultimately lead to its engulfment. Although active force generation, in particular by actin polymerization, is required for completion of this process, the elastic deformation of the cell membrane upon adhesion to an external object might play an important part in its initiation. In this paper, the elastic deformation of a bilayer owing to the binding of a cylindrical object is studied, taking into account the membrane bending rigidity and the surface tension, the membrane adhesion to both the external target and inner cytoskeleton. The problem is studied within the framework of the Helfrich-Hamiltonian and using force balance relations and the proper boundary conditions that are related to the adhesion energy coefficients. It is shown that membrane wrapping around the target may be a continuous or abrupt transition upon increasing the target binding energy, depending on the value of the parameter. The degree of wrapping and the shape of the membrane in the vicinity of the object are computed numerically, and analytical expressions are given for the boundaries separating the different wrapping regimes in the parameter space.

DNA conformation and energy in nucleosome core: a theoretical approach.

DNA conformation in complex with proteins is far from its canonical B-form. The affinity of complex formation and structure of DNA depend on its attachment configuration and sequence. In this article, we develop a mechanical model to address the problem of DNA structure and energy under deformation. DNA in nucleosome core particle is described as an example. The structure and energy of nucleosomal DNA is calculated based on its sequence and positioning state. The inferred structure has remarkable similarity with X-ray data. Although there is no sequence-specific interaction of bases and the histone core, we found considerable sequence dependency for the nucleosomal DNA positioning. The affinity of nucleosome formation for several sequences is examined and the differences are compatible with observations. We argue that structural energy determines the natural state of nucleosomal DNA and is the main reason for affinity differences in vitro. This theory can be utilized for the DNA structure and energy determination in protein-DNA complexes in general. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:17.

Impact of Metabolic Syndrome on Response to Medical Treatment of Benign Prostatic Hyperplasia

PURPOSE: To investigate the effect of metabolic syndrome (MetS) on the response to medical therapy of benign prostatic hyperplasia (BPH) after a 3-month period of treatment. MATERIALS AND METHODS: This was a cohort study of 100 patients, 47 with MetS and 53 without MetS, referred to either the primary care unit or referral hospital with BPH who had moderate lower urinary tract symptoms of prostate involvement and were candidates for medical treatment. Our main outcome was response to medical treatment with prazosin 1 mg twice a day and finasteride 5 mg daily in patients with BPH on the basis of International Prostate Symptom Score (IPSS). Multivariate analysis of covariance was used to compare BPH treatment response in patients with and without MetS before and after receiving treatment. RESULTS: The mean volume of the prostate was significantly higher in MetS patients than in patients without MetS (57+/-32.65 mL compared with 46.00+/-20.19 mL, p=0.036). The control group demonstrated an 11-unit reduction in IPSS, whereas those with MetS showed a reduction in the symptom score of only 6 units (p<0.001). Regarding the components of MetS separately, triglyceride (p<0.001), fasting blood sugar (p=0.001), and waist circumference (p=0.028) significantly affected the clinical progression of BPH. The observational nature of this study may be a limitation in comparison with an interventional study. CONCLUSIONS: The results of the present study showed that MetS can negatively affect the response to medical treatment of BPH. Therefore, it is necessary to consider MetS in selecting patients with BPH for drug therapy.

Impact of glibenclamide versus Insulin on neurological and functional outcomes of hemorrhagic stroke in diabetic patients

Background & Objective: Stroke is one of the common leading causes of morbidity and mortality worldwide. Diabetes is one of the modifi able risk factors of stroke which is related to a higher mortality and a poorer outcome. We aimed to evaluate the protective effect of Insulin versus glibenclamide on the improvement of neurological and functional outcomes of hemorrhagic stroke. Methods: The present single blind clinical trial was conducted on 100 patients with stroke and diabetes who had referred to Neurology Emergency Department of Vali-e-Asr hospital, Arak, Iran. The patients were categorized into two groups according to the glucose control treatment before stroke. Without any randomization, glibenclamide was used in 45 patients, while others (55 ones) received insulin. National Institute of Health Stroke Scale (NIHSS) and modifi ed Rankin scale (MRS) systems were used for evaluating the neurological and functional outcomes. Results: Hemiparesis was the most common sign of the patients. The mean of changes in NIHSS and MRS scores of the two groups were -29.69±21.4 and -17.24±21, respectively. Although Insulin group had a higher decrease in NIHSS and MRS scores, no signifi cant difference was found between the two groups. Both treatment methods had a signifi cant decreasing effect on NIHSS and MRS scores (p<0.001). Conclusion: Patients treated with both glibenclamide and insulin had similar decrease in their one week NIHSS and MRS scores with no signifi cant difference in the two treatment groups.