Effects of salts on internal DNA pressure and mechanical properties of phage capsids

Based on atomic force microscopy nanoindentation measurements of phage λ, we previously proposed a minimal model describing the effect of water hydrating DNA that strengthens viral capsids against external deformation at wild-type DNA packing density. Here, we report proof of this model by testing the prediction that DNA hydration forces can be dramatically decreased by addition of multivalent ions (Mg²⁺ and Sp⁴⁺). These results are explained using a DNA hydration model without adjustable parameters. The model also predicts the stiffness of other DNA-filled capsids, which we confirm using bacteriophage ?29 and herpes simplex virus type 1 particles.     

Heterogeneity in viral populations increases the rate of deleterious mutation accumulation

RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection and heterogeneity in viral output affect these patterns. Specifically, using agent-based intercellular simulations we find, in agreement with previous studies, that coinfection of cells by viruses relaxes the strength of purifying selection and thereby increases the rate of deleterious mutation accumulation. We further find that cellular heterogeneity in viral output exacerbates the rate of deleterious mutation accumulation, regardless of whether this heterogeneity in viral output is stochastic or is due to variation in the cellular multiplicity of infection. These results highlight the need to consider the unique life histories of viruses and their population structure to better understand observed patterns of viral evolution.     

Tuning the activity of iminosugars: novel N-alkylated deoxynojirimycin derivatives as strong BuChE inhibitors

We have designed unprecedented cholinesterase inhibitors based on 1-deoxynojirimycin as potential anti-Alzheimer’s agents. Compounds are comprised of three key structural motifs: the iminosugar, for interaction with cholinesterase catalytic anionic site (CAS); a hydrocarbon tether with variable lengths, and a fragment derived from 2-phenylethanol for promoting interactions with peripheral anionic site (PAS). Title compounds exhibited good selectivity towards BuChE, strongly depending on the substitution pattern and the length of the tether. The lead compounds were found to be strong mixed inhibitors of BuChE (IC₅₀ = 1.8 and 1.9 µM). The presumptive binding mode of the lead compound was analysed using molecular docking simulations, revealing H-bond interactions with the catalytic subsite (His438) and CAS (Trp82 and Glu197) and van der Waals interactions with PAS (Thr284, Pro285, Asn289). They also lacked significant antiproliferative activity against tumour and non-tumour cells at 100 µM, making them promising new agents for tackling Alzheimer’s disease through the cholinergic approach.     

Three-dimensional finite element simulations of the mechanical response of the fingertip to static and dynamic compressions

The analysis of the mechanics of the contact interactions of fingers/handle and the stress/strain distributions in the soft tissues in the fingertip is essential to optimize design of tools to reduce many occupation-related hand disorders. In the present study, a three-dimensional (3D) finite element (FE) model for the fingertip is proposed to simulate the nonlinear and time-dependent responses of a fingertip to static and dynamic loadings. The proposed FE model incorporates the essential anatomical structures of a finger: skin layers (outer and inner skins), subcutaneous tissue, bone and nail. The soft tissues (inner skin and subcutaneous tissue) are considered to be nonlinearly viscoelastic, while the hard tissues (outer skin, bone and nail) are considered to be linearly elastic. The proposed model has been used to simulate two loading scenarios: (a) the contact interactions between the fingertip and a flat surface and (b) the indentation of the fingerpad via a sharp wedge. For case (a), the predicted force/displacement relationships and time-dependent force responses are compared with the published experimental data; for case (b), the skin surface deflection profiles were predicted and compared with the published experimental observations. Furthermore, for both cases, the time-dependent stress/strain distributions within the tissues of the fingertip were calculated. The good agreement between the model predictions and the experimental observations indicates that the present model is capable of predicting realistic time-dependent force/displacement responses and stress/strain distributions in the soft tissues for dynamic loading conditions.     

Finite element simulation of the mechanical impact of computer work on the carpal tunnel syndrome

Carpal tunnel syndrome (CTS) is a clinical disorder resulting from the compression of the median nerve. The available evidence regarding the association between computer use and CTS is controversial. There is some evidence that computer mouse or keyboard work, or both are associated with the development of CTS. Despite the availability of pressure measurements in the carpal tunnel during computer work (exposure to keyboard or mouse) there are no available data to support a direct effect of the increased intracarpal canal pressure on the median nerve.     

Scanner influence on the mechanical response of QCT-based finite element analysis of long bones

Patient-specific QCT-based finite element (QCTFE) analyses enable highly accurate quantification of bone strength. We evaluated CT scanner influence on QCTFE models of long bones.A femur, humerus, and proximal femur without the head were scanned with K₂HPO₄ phantoms by seven CT scanners (four models) using typical clinical protocols. QCTFE models were constructed. The geometrical dimensions, as well as the QCT-values expressed in Hounsfield unit (HU) distribution was compared. Principal strains at representative regions of interest (ROIs), and maximum principal strains (associated with fracture risk) were compared. Intraclass correlation coefficients (ICCs) were calculated to evaluate strain prediction reliability for different scanners. Repeatability was examined by scanning the femur twice and comparing resulting QCTFE models.Maximum difference in geometry was 2.3%. HU histograms before phantom calibration showed wide variation between QCT scans; however, bone density histogram variability was reduced after calibration and algorithmic manipulation. Relative standard deviation (RSD) in principal strains at ROIs was <10.7%. ICC estimates between scanners were >0.9. Fracture-associated strain had 6.7%, 8.1%, and 13.3% maximum RSD for the femur, humerus, and proximal femur, respectively. The difference in maximum strain location was <2 mm. The average difference with repeat scans was 2.7%.Quantification of strain differences showed mean RSD bounded by ∼6% in ROIs. Fracture-associated strains in “regular” bones showed a mean RSD bounded by ∼8%. Strains were obtained within a ±10% difference relative to the mean; thus, in a longitudinal study only changes larger than 20% in the principal strains may be significant. ICCs indicated high reliability of QCTFE models derived from different scanners.     

Insights from the docking and molecular dynamics simulation of the Phosphopantetheinyl transferase (PptT) structural model from Mycobacterium tuberculosis

A great challenge is posed to the treatment of tuberculosis due to the evolution of multidrug-resistant (MDR) and extensively drugresistant (XDR) strains of Mycobacterium tuberculosis in recent times. The complex cell envelope of the bacterium contains unusual structures of lipids which protects the bacterium from host enzymes and escape immune response. To overcome the drug resistance, targeting “drug targets” which have a critical role in growth and virulence factor is a novel approach for better tuberculosis treatment. The enzyme Phosphopantetheinyl transferase (PptT) is an attractive drug target as it is primarily involved in post translational modification of various types-I polyketide synthases and assembly of mycobactin, which is required for lipid virulence factors. Our in silico studies reported that the structural model of M.tuberculosis PptT characterizes the structure-function activity. The refinement of the model was carried out with molecular dynamics simulations and was analyzed with root mean square deviation (RMSD), and radius of gyration (Rg). This confirmed the structural behavior of PptT in dynamic system. Molecular docking with substrate coenzyme A (CoA) identified the binding pocket and key residues His93, Asp114 and Arg169 involved in PptT-CoA binding. In conclusion, our results show that the M.tuberculosis PptT model and critical CoA binding pocket initiate the inhibitor design of PptT towards tuberculosis treatment.     

Radioimmunotherapy of non-Hodgkin's lymphoma: from the 'magic bullets' to 'radioactive magic bullets'

Radioimmunotherapy (RIT) of lymphoma with Zevalin and Bexxar was approved by FDA in 2002 and 2003, respectively, for the treatment of relapsed or refractory CD20+ follicular B-cell non-Hodgkin′s lymphoma. In 2009, Zevalin was also approved for consolidation therapy in patients with follicular non-Hodgkin's lymphoma that achieve a partial or complete response to first-line chemotherapy. For follicular lymphoma patients, the overall response and progression-free survival rates have significantly improved since the implementation of RIT. The predominant complication of RIT is hematological toxicity that is usually manageable. There are ongoing trials to further define the expanding role of RIT as first line or concomitant therapy in the treatment of lymphoma as well as for certain antibiotic resistant infections and aggressive malignancies. There is also growing interest in the development of newer protocols for increased and more uniform dose delivery resulting in better outcomes and improved patient survival. This review will primarily focus on the role of RIT in treatment of non-Hodgkin's lymphoma, which is of established clinical utility and FDA approved. The mechanism of RIT, available radionuclides and pharmacokinetics, therapy administration, clinical utility and toxicities, and future directions would be discussed.     

Loss of neuronal Miro1 disrupts mitophagy and induces hyperactivation of the integrated stress response

Clearance of mitochondria following damage is critical for neuronal homeostasis. Here, we investigate the role of Miro proteins in mitochondrial turnover by the PINK1/Parkin mitochondrial quality control system in vitro and in vivo. We find that upon mitochondrial damage, Miro is promiscuously ubiquitinated on multiple lysine residues. Genetic deletion of Miro or block of Miro1 ubiquitination and subsequent degradation lead to delayed translocation of the E3 ubiquitin ligase Parkin onto damaged mitochondria and reduced mitochondrial clearance in both fibroblasts and cultured neurons. Disrupted mitophagy in vivo, upon post‐natal knockout of Miro1 in hippocampus and cortex, leads to a dramatic increase in mitofusin levels, the appearance of enlarged and hyperfused mitochondria and hyperactivation of the integrated stress response (ISR). Altogether, our results provide new insights into the central role of Miro1 in the regulation of mitochondrial homeostasis and further implicate Miro1 dysfunction in the pathogenesis of human neurodegenerative disease.     

Recognizing the cooperative and independent mitochondrial functions of Parkin and PINK1

Comment on: Johnson BN, et al. Proc Natl Acad Sci USA 2012; 109:6283-8.     

Thematic Review Series: Calorie Restriction and Ketogenic Diets: Ketone body therapy: from the ketogenic diet to the oral administration of ketone ester

Ketone bodies (KBs), acetoacetate and β-hydroxybutyrate (βHB), were considered harmful metabolic by-products when discovered in the mid-19th century in the urine of patients with diabetic ketoacidosis. It took physicians many years to realize that KBs are normal metabolites synthesized by the liver and exported into the systemic circulation to serve as an energy source for most extrahepatic tissues. Studies have shown that the brain (which normally uses glucose for energy) can readily utilize KBs as an alternative fuel. Even when there is diminished glucose utilization in cognition-critical brain areas, as may occur early in Alzheimer’s disease (AD), there is preliminary evidence that these same areas remain capable of metabolizing KBs. Because the ketogenic diet (KD) is difficult to prepare and follow, and effectiveness of KB treatment in certain patients may be enhanced by raising plasma KB levels to ≥2 mM, KB esters, such as 1,3-butanediol monoester of βHB and glyceryl-tris-3-hydroxybutyrate, have been devised. When administered orally in controlled dosages, these esters can produce plasma KB levels comparable to those achieved by the most rigorous KD, thus providing a safe, convenient, and versatile new approach to the study and potential treatment of a variety of diseases, including epilepsy, AD, and Parkinson’s disease.     

湖北五峰后河国家级自然保护区鸟类多样性

为了解湖北五峰后河国家级自然保护区(以下简称后河保护区)鸟类物种多样性及其区系组成的变化, 我们通过样线、红外相机调查和检索文献资料相结合的方法获得了后河保护区鸟类名录, 并将其与后河保护区1999年科学考察结果进行对比分析。本研究于2017-2019年共在后河保护区内设置了82 km的鸟类调查样线, 共在309个位点上放置了红外相机, 累计99,586个相机日。我们用“后河” “鸟类” “湖北省”等关键词搜索相关出版物, 并查阅中国观鸟记录中心经审核后发布的鸟类信息, 结合样线和红外相机调查结果形成后河保护区鸟类名录。共整理得到后河保护区鸟类255种, 隶属于16目55科。其中, 国家I级重点保护野生鸟类2种, 包括中华秋沙鸭(Mergus squamatus)和金雕(Aquila chrysaetos); 国家II级重点保护野生鸟类46种, 包括红腹角雉(Tragopan temminckii)、棉凫(Nettapus coromandelianus)、松雀鹰(Accipiter virgatus)、灰林鸮(Strix aluco)、蓝鹀(Emberiza siemsseni)等。此外, 后河保护区有11种中国特有鸟类, 占我国特有鸟类种数(n = 93)的11.83%。在区系成分上, 后河保护区鸟类以东洋种为主(151种, 占59.22%), 其次为广布种(55种, 占21.57%)。与1999年科学考察结果相比, 鸟类增加了116种, 其中有15种国家重点保护野生鸟类。在区系组成上, 后河保护区内东洋种占比增加, 包括分布区向北扩散的物种成分。此外, 本次调查未记录到20世纪在保护区内有分布的白冠长尾雉(Syrmaticus reevesii)和海南鳽(Gorsachius magnificus)。本研究表明, 后河保护区鸟类物种多样性高、特有种及珍稀濒危物种丰富, 具有极高的保护价值和意义。通过对比分析后河保护区内野生鸟类动态变化, 可为保护区生物多样性监测方案设计和保护对策的制定提供科学依据。     

Pretransition and progressive softening of bovine carbonic anhydrase II as probed by single molecule atomic force microscopy

To develop a simple method for probing the physical state of surface adsorbed proteins, we adopted the force curve mode of an atomic force microscope (AFM) to extract information on the mechanical properties of surface immobilized bovine carbonic anhydrase II under native conditions and in the course of guanidinium chloride-induced denaturation. A progressive increase in the population of individually softened molecules was probed under mildly to fully denaturing conditions. The use of the approach regime of force curves gave information regarding the height and rigidity of the molecule under compressive stress, whereas use of the retracting regime of the curves gave information about the tensile characteristics of the protein. The results showed that protein molecules at the beginning of the transition region possessed slightly more flattened and significantly more softened conformations compared with that of native molecules, but were still not fully denatured, in agreement with results based on solution studies. Thus the force curve mode of an AFM was shown to be sensitive enough to provide information concerning the different physical states of single molecules of globular proteins.     

Gene Expression Profiles of Human Mesenchymal Stromal Cells Derived from Wharton’s Jelly and Amniotic Membrane before and after Osteo-Induction Using NanoString Platform

The use of perinatal mesenchymal stem cells (MSCs) in bone tissue regeneration and engineering to substitute bone marrow MSCs has drawn great interest due to their high yield, ease of procurement, multilineage differentiation potential and lack of ethical concerns. Although amniotic membrane (AM) and Wharton’s jelly (WJ)-derived MSCs have been widely shown to possess osteogenic differentiation potential, the intrinsic properties determining their osteogenic capacity remain unclear. Here, we compared gene expression profiles of AM- and WJ-MSCs at basal and osteogenic conditions by using the NanoString Stem Cell Panel containing regulatory genes associated with stemness, self-renewal, Wnt, Notch and Hedgehog signalling pathways. At basal condition, WJ-MSCs displayed higher expression in most genes regardless of their functional roles in self-renewal, adhesion, or differentiation signalling pathways. After osteo-induction, elevated expression of self-renewal genes ADAR and PAFAH1B1 was observed in AM-MSCs, while stemness genes MME and ALDH1A1 were upregulated in WJ-MSC. Both MSCs showed differences in genes associated with ligands, receptors and ubiquitin ligases of the Notch pathway. In addition, further evidence was demonstrated in some signalling molecules including CTBPs, protein kinases, phosphatases, RHOA, RAC1. Downstream targets HES1 and JUN especially showed higher expression in non-induced WJ-MSCs. Hedgehog genes initially expressed in both MSCs were downregulated in WJ-MSCs during osteogenesis. This study has provided insights into the intrinsic biological differences that may lead to their discrimination in therapeutic intervention.     

Biomechanical and mechanical behavior of the plantar fascia in macro and micro structures

Plantar fascia (PF) is a heterogeneous thickness structure across plantar foot. It is important significance to investigate the biomechanical behavior of the medial, middle and lateral PF regions. To investigate the non-uniform macro/micro structures of the different PF regions, the uniaxial tensile test of PF strips were performed to assess the mechanical behavior of PF. A scanning electron microscope (SEM) was used to visualize and measure the micro morphology of PF associated with collagen fibers. A three-dimensional foot finite element (FE) model was developed to quantify the tensile behavior of the internal PF. The elastic modulus of the lateral PF component (1560 MPa) was observed, followed by the medial (701 MPa), the central (1100 MPa) and the lateral (714 MPa) portions in the central component. Elongation of the central portion (0.192) was lower than the medial (0.223) and the lateral (0.227) portions. The corresponding SEM images showed that the fibers of the central portion were more densely packed and thicker compared to the ambilateral portions in the central component. While the FE model prediction also suggested that the greater elastic modulus of the central PF portion had lower strain (0.192) versus the ambilateral portions. Therefore, the lower elongation and greater elastic modulus at the central portion of PF would probably have a high risk of PF injury. The findings showed a relation between the mechanical tension and fibrous morphology of PF. This information would have a better understanding of the PF pathophysiology diseases related to tear and injury of PF.     

Computer simulation of feeding behaviour in the thylacine and dingo as a novel test for convergence and niche overlap

The extinct marsupial thylacine (Thylacinus cynocephalus) and placental grey wolf (Canis lupus) are commonly presented as an iconic example of convergence. However, various analyses suggest distinctly different behaviours and specialization towards either relatively small or large prey in the thylacine, bringing the degree of apparent convergence into question. Here we apply a powerful engineering tool, three-dimensional finite element analysis incorporating multiple material properties for bone, to examine mechanical similarity and niche overlap in the thylacine and the wolf subspecies implicated in its extinction from mainland Australia, Canis lupus dingo. Comparisons of stress distributions not only reveal considerable similarity, but also informative differences. The thylacine's mandible performs relatively poorly where only the actions of the jaw muscles are considered, although this must be considered in the light of relatively high bite forces. Stresses are high in the posterior of the thylacine's cranium under loads that simulate struggling prey. We conclude that relative prey size may have been comparable where both species acted as solitary predators, but that the dingo is better adapted to withstand the high extrinsic loads likely to accompany social hunting of relatively large prey. It is probable that there was considerable ecological overlap. As a large mammalian hypercarnivore adapted to taking small-medium sized prey, the thylacine may have been particularly vulnerable to disturbance.