Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method

Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes.

[The clinical features of patients with lymphoplasmacytic diseases harboring MyD88 L265P mutation]

Objective: To explore the clinical features of lymphoplasmacytic diseases with MyD88 L265P mutation. Methods: To analyze the distribution of MYD88 L265P mutation in patients with lymphoplasmacytic diseases by using of ARMS PCR-CE. Results: There were 25(30.9%) MyD88 L265P mutated patients in 81 patients. The mutation was frequently observed in 14 patients with WM (77.8%, 14/18), 2 patients with lymphoplasmacytic lymphoma (66.7%, 2/3), 1 acute lymphocytic leukemia patient (50.0%, 1/2), 3 multiple myeloma patients (30.0%, 3/10), 1 patient with monoclonal gammopathy of undetermined significance (25%, 1/4), 3 patients with chronic lymphocytic leukemia (13.0%, 3/23) and 1 lymphoma patient (4.8%, 1/21). 20 (80%, 20/25) patients were identified with IgM subtype. Compared with wild-type group of 56 cases, mutated patients were older (median age: 67 years vs 55 years, P< 0.001), with lower WBC count (median count: 5.23 × 109/L vs 10.80 × 109/L, P=0.001), lower HGB level (median count: 85 g/L vs 119 g/L, P<0.001). Conclusion: MyD88 L265P mutation was mainly observed in patients with IgM subtype lymphoplasmacytic diseases, and Waldenstrom' s macroglobulinemia was the most common disease. Compared with the wild-type group, patients with MyD88 L265P mutation were older and had lower WBC count, lower level of HGB. However, further studies were needed to test the prognostic value of MyD88 L265P mutation.

FOXK1 interaction with FHL2 promotes proliferation, invasion and metastasis in colorectal cancer

The transcriptional factor Forkhead box k1 (FOXK1) is a member of the FOX family. The abnormal expression of FOXK1 may have an important role in tumour development. Our previous studies showed that four-and-a-half LIM protein 2 (FHL2) is a critical inducer of the epithelial-to-mesenchymal transition (EMT) and invasion. However, the molecular mechanism by which FOXK1 synergizes with FHL2 tumour proliferation, EMT and metastasis is not well defined. We evaluated that messenger RNA (mRNA) and protein expression levels by quantitative RT–PCR, western blot, immunofluorescence and immunohistochemistry (IHC) assays. The migration and invasive abilities of colorectal cancer (CRC) cells were evaluated using short hairpin RNA (shRNA)-mediated inhibition in vitro and in vivo. We showed that FOXK1 expression was upregulated in CRC compared with matched normal tissues. FOXK1 physically interacts with FHL2 in CRC. Moreover, higher expression levels of the two proteins were significantly associated with differentiation, lymph node metastasis, AJCC stage and poorer prognosis. Furthermore, the overexpression of FOXK1 in CRC cells is associated with EMT, invasion and metastasis. However, the siRNA-mediated repression of FHL2 in FOXK1-overexpressing cells reversed EMT and both the proliferative and metastatic phenotypes in vitro and in vivo. These data identified that the co-expression of FOXK1 and FHL2 enhances cell proliferation and metastasis through the induction of EMT. Thus, FOXK1 and FHL2 may serve as putative targets in the combined therapy of CRC.

Histone H3K9 acetylation influences growth characteristics of goat adipose-derived stem cells in vitro

Adipose-derived stem cells (ADSCs) show nearly unlimited potential in medical and animal science. Currently, understanding of the biological mechanisms regulating ADSC growth in vitro remains very limited. Histone acetylation, an epigenetic modification, plays a key role in maintaining stem cell properties. To further study its effect on ADSC growth characteristics in vitro, we treated goat ADSCs with the histone deacetylase inhibitors trichostatin A (TSA) and vorinostat (SAHA). This inhibited SIRT1 expression and increased histone H3K9 acetylation, leading to decreased cell viability, cell cycle arrest, and apoptosis. Quantitative real-time polymerase chain reaction revealed that H3K9 hyperacetylation stimulated transcription of NANOG, OCT4, SOX2, and TERT, but inhibited that of PCNA, P53, and BAX. Western blotting indicated that TSA and SAHA increased protein expression of NANOG, reduced that of SOX2, TERT, PCNA, P53, and BAX, and did not change that of OCT4. These findings provide new experimental evidence contributing to our understanding of the mechanisms underlying ADSC growth characteristics in vitro.

Far-infrared tangential interferometer/polarimeter design and installation for NSTX-U

The Far-infrared Tangential Interferometer/Polarimeter (FIReTIP) system has been refurbished and is being reinstalled on the National Spherical Torus Experiment-Upgrade (NSTX-U) to supply real-time line-integrated core electron density measurements for use in the NSTX-U plasma control system (PCS) to facilitate real-time density feedback control of the NSTX-U plasma. Inclusion of a visible light heterodyne interferometer in the FIReTIP system allows for real-time vibration compensation due to movement of an internally mounted retroreflector and the FIReTIP front-end optics. Real-time signal correction is achieved through use of a National Instruments CompactRIO field-programmable gate array.

Maternal dietary linoleic acid supplementation promotes muscle fibre type transformation in suckling piglets

As meat quality is basically dependent on muscle fibre characteristics, it is important to know how muscle fibres are regulated and transformed. This study aimed to investigate the effect of maternal dietary supplementation on muscle fibre types using 3% saturated fatty acid (palmitic acid, PA) or 3% unsaturated fatty acid (linoleic acid, LA) from 80 days of gestation to the weaning of offspring (25 days post-natal). The results indicated that higher mRNA levels of MyHCI type genes were found in the soleus muscles of piglets that suckled from LA-supplemented sows than from PA-supplemented sows. In addition, LA treatment increased the gene expression of the type I muscle fibre marker troponin I (p < 0.01), suggesting that LA promoted muscle fibre type transformation to type I fibres. Moreover, PGC-1α (p < 0.01) and MEF2c (p < 0.05) mRNA levels were higher in the piglets from the LA treatment group than in those from the PA treatment group. Furthermore, LA supplementation also significantly increased AMP-activated protein kinase (AMPK) mRNA levels (p < 0.05), which is an upstream regulator of PGC-1α. Collectively, these findings demonstrated that maternal dietary LA supplementation promoted muscle fibre transformation to type I fibre and that this process may be mediated through an AMPK-dependent pathway.

A crucial role for spatial distribution in bacterial quorum sensing

Quorum sensing (QS) is a process that enables bacteria to communicate using secreted signaling molecules, and then makes a population of bacteria to regulate gene expression collectively and control behavior on a community-wide scale. Theoretical studies of efficiency sensing have suggested that both mass-transfer performance in the local environment and the spatial distribution of cells are key factors affecting QS. Here, an experimental model based on hydrogel microcapsules with a three-dimensional structure was established to investigate the influence of the spatial distribution of cells on bacterial QS. Vibrio harveyi cells formed different spatial distributions in the microcapsules, i.e., they formed cell aggregates with different structures and sizes. The cell aggregates displayed stronger QS than did unaggregated cells even when equal numbers of cells were present. Large aggregates (LA) of cells, with a size of approximately 25 μm, restricted many more autoinducers (AIs) than did small aggregates (SA), with a size of approximately 10 μm, thus demonstrating that aggregate size significantly affects QS. These findings provide a powerful demonstration of the fact that the spatial distribution of cells plays a crucial role in bacterial QS.

Novel function of FAXDC2 in megakaryopoiesis

FAXDC2 (fatty acid hydroxylase domain containing 2) is a member of the fatty acid hydroxylase superfamily. Given the important role of fatty acids in megakaryocytes, we have studied the role of this gene in the development of this lineage. Here we show that the expression of FAXDC2 is constantly elevated during megakaryocyte maturation. In contrast, FAXDC2 is significantly downregulated in acute myeloid leukemia and acute megakaryoblastic leukemia. Moreover, FAXDC2 overexpression promotes the differentiation of megakaryocytic cell lines and primary cells, whereas its knockdown disrupts their maturation. Mechanism study shows that FAXDC2 overexpression enhances extracellular signal-regulated kinase (ERK) signaling and increases RUNX1 (Runt-related transcription factor 1) expression. FAXDC2 also restores megakaryocytic differentiation in cells exposed to an ERK inhibitor or those expressing a dominant negative form of RUNX1. Finally, FAXDC2 overexpression leads to an increase in sphingolipid GM3 synthase, suggesting a potential role of FAXDC2 in lipid metabolism that increases ERK signaling and facilitates megakaryocyte differentiation. Together, these results show that FAXDC2 plays a novel role in development of megakaryocytes and its dysregulation may contribute to abnormal hematopoietic cell development in leukemia.

Alginate-based microcapsules with galactosylated chitosan internal for primary hepatocyte applications

Alginate-galactosylated chitosan/polylysine (AGCP) microcapsules with excellent stability and high permeability were developed and employed in primary hepatocyte applications. The galactosylated chitosan (GC), synthesized via the covalent coupling of lactobionic acid (LA) with low molecular weight and water-soluble chitosan (CS), was ingeniously introduced into the core of alginate microcapsules by regulating the pH of gelling bath. The internal GC of the microcapsules simultaneously provided a large number of binding sites for the hepatocytes and further promoted the hepatocyte-matrix interactions via the recognition of asialoglycoprotein receptors (ASGPRs) on the hepatocyte surface, and afforded the AGCP microcapsules an excellent stability via the electrostatic interactions with alginate. As a consequence, primary hepatocytes in AGCP microcapsules demonstrated enhanced viability, urea synthesis, albumin secretion, and P-450 enzyme activity, showing great prospects for hepatocyte applications in microcapsule system.

Controlling Gel Structure to Modulate Cell Adhesion and Spreading on the Surface of Microcapsules

The surface properties of implanted materials or devices play critical roles in modulating cell behavior. However, the surface properties usually affect cell behaviors synergetically so that it is still difficult to separately investigate the influence of a single property on cell behavior in practical applications. In this study, alginate-chitosan (AC) microcapsules with a dense or loose gel structure were fabricated to understand the effect of gel structure on cell behavior. Cells preferentially adhered and spread on the loose gel structure microcapsules rather than on the dense ones. The two types of microcapsules exhibited nearly identical surface positive charges, roughness, stiffness, and hydrophilicity; thus, the result suggested that the gel structure was the principal factor affecting cell behavior. X-ray photoelectron spectroscopy analyses demonstrated that the overall percentage of positively charged amino groups was similar on both microcapsules. The different gel structures led to different states and distributions of the positively charged amino groups of chitosan, so we conclude that the loose gel structure facilitated greater cell adhesion and spreading mainly because more protonated amino groups remained unbound and exposed on the surface of these microcapsules.

Curcumin ameliorates insulin signalling pathway in brain of Alzheimer's disease transgenic mice

Deficits in glucose, impaired insulin signalling and brain insulin resistance are common in the pathogenesis of Alzheimer's disease (AD); therefore, some scholars even called AD type 3 diabetes mellitus. Curcumin can reduce the amyloid pathology in AD. Moreover, it is a well-known fact that curcumin has anti-oxidant and anti-inflammatory properties. However, whether or not curcumin could regulate the insulin signal transduction pathway in AD remains unclear. In this study, we used APPswe/PS1dE9 double transgenic mice as the AD model to investigate the mechanisms and the effects of curcumin on AD. Immunohistochemical (IHC) staining and a western blot analysis were used to test the major proteins in the insulin signal transduction pathway. After the administration of curcumin for 6 months, the results showed that the expression of an insulin receptor (InR) and insulin receptor substrate (IRS)-1 decreased in the hippocampal CA1 area of the APPswe/PS1dE9 double transgenic mice, while the expression of phosphatidylinositol-3 kinase (PI3K), phosphorylated PI3K (p-PI3K), serine-threonine kinase (AKT) and phosphorylated AKT (p-AKT) increased. Among the curcumin groups, the medium-dose group was the most effective one. Thus, we believe that curcumin may be a potential therapeutic agent that can regulate the critical molecules in brain insulin signalling pathways. Furthermore, curcumin could be adopted as one of the AD treatments to improve a patient's learning and memory ability.

Small-molecule inhibitor sorafenib regulates immunoreactions by inducing survival and differentiation of bone marrow cells

Sorafenib has been used for the treatment of liver cancer. However, its clinical impact on human immunity system remains poorly known. Our previous study has shown that sorafenib modulates immunosuppressive cell populations in murine liver cancer models. Here, we continue to report that low doses of sorafenib promotes the survival of murine bone marrow cells (BMCs) in a dose-dependent manner by up-regulating the anti-apoptotic protein survivin. Sorafenib induces differentiation of BMCs into suppressive dendritic cells that inhibit autologous T-cell proliferation and stimulate CD4+ T cells to express increased IL-1β, IL-2, IL-4, IL-10, IFN-γ and TNF-α, and reduced levels of IL-6 and CD25, which indicates that sorafenib-induced dendritic cells represent a distinct cellular subset with unique properties. Taken together, our findings suggest that in addition to its anticancer effects, sorafenib has an immunoregulatory property that is apparent at low doses.

Deubiquitinase USP2a Sustains Interferons Antiviral Activity by Restricting Ubiquitination of Activated STAT1 in the Nucleus

STAT1 is a critical transcription factor for regulating host antiviral defenses. STAT1 activation is largely dependent on phosphorylation at tyrosine 701 site of STAT1 (pY701-STAT1). Understanding how pY701-STAT1 is regulated by intracellular signaling remains a major challenge. Here we find that pY701-STAT1 is the major form of ubiquitinated-STAT1 induced by interferons (IFNs). While total STAT1 remains relatively stable during the early stages of IFNs signaling, pY701-STAT1 can be rapidly downregulated by the ubiquitin-proteasome system. Moreover, ubiquitinated pY701-STAT1 is located predominantly in the nucleus, and inhibiting nuclear import of pY701-STAT1 significantly blocks ubiquitination and downregulation of pY701-STAT1. Furthermore, we reveal that the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1, and inhibits K48-linked ubiquitination and degradation of pY701-STAT1. Importantly, USP2a sustains IFNs-induced pY701-STAT1 levels, and enhances all three classes of IFNs- mediated signaling and antiviral activity. To our knowledge, this is the first identified deubiquitinase that targets activated pY701-STAT1. These findings uncover a positive mechanism by which IFNs execute efficient antiviral signaling and function, and may provide potential targets for improving IFNs-based antiviral therapy.

Phosphorylated STAT1 at tyrosine 701 site (pY701-STAT1) is critical for regulating many cellular functions including antiviral immunity. Maintaining sufficient pY701-STAT1 levels in the nucleus is essential to sustain efficient interferons (IFNs) signaling and antiviral functions. Therefore, it is important to clarify how pY701-STAT1 levels are positively regulated in the nucleus. Here, we demonstrated for the first time that IFNs-induced pY701-STAT1 largely raised STAT1 ubiquitination, and ubiquitinated-pY701-STAT1 is located predominantly in the nucleus and regulated by proteasome-dependent degradation. In IFNs signaling, the deubiquitinase USP2a translocates into the nucleus and binds to pY701-STAT1. USP2a positively regulates pY701-STAT1 levels through inhibiting its K48-linked ubiquitination and degradation. Importantly, USP2a sustains all three classes of IFNs-mediated signaling and antiviral function. Our studies uncover an important positive mechanism in the nucleus by which IFNs can execute efficient antiviral signaling and functions.

Tuning the formation and stability of microcapsules by environmental conditions and chitosan structure

The goal of this work is to tune the formation and stability of the alginate-chitosan (AC) polyelectrolyte complexes (PECs) and microcapsules. Particularly, we explore the role of the conformation of chitosan on its interaction with alginate to understand the mechanism underpinning their interactions at the molecular level. Reducing the charge density by increasing pH will increase the compactness of chitosan, the values of the enthalpy (H) and stoichiometry (N) of binding between chitosan and alginate. Consequently, chitosan has advantage in being adsorbed on alginate beads to form microcapsules, including the binding rate and binding amount. Though the total heat release remain similar in the range of ionic strength, chitosan diffuses much easier into alginate hydrogels when in higher ionic strength. Increasing pH and ionic strength both help AC microcapsules to have higher stability. The results indicate that the formation and stability of AC microcapsules are related to the rigidity and conformations of chitosan molecules. After increasing acetylation degree (DA) of chitosan, the binding rate of chitosan and mechanical strength of AC microcapsules are both reduced. This work demonstrates the versatility and feasibility of tuning the formation and stability of polysaccharide microcapsules by physical factors and chitosan chemical structures.

Notch signaling in postnatal joint chondrocytes, but not subchondral osteoblasts, is required for articular cartilage and joint maintenance

OBJECTIVE

Notch signaling has been identified as a critical regulator in cartilage development and joint maintenance, and loss of Notch signaling in all joint tissues results in an early and progressive osteoarthritis (OA)-like pathology. This study investigated the targeted cell population within the knee joint in which Notch signaling is required for normal cartilage and joint integrity.

METHODS

Two loss-of-function mouse models were generated with tissue-specific knockout of the core Notch signaling component, RBPjκ. The AcanCre(ERT2) transgene specifically removed Rbpjκ floxed alleles in postnatal joint chondrocytes, while the Col1Cre(2.3kb) transgene deleted Rbpjκ in osteoblast populations, including subchondral osteoblasts. Mutant and control mice were analyzed via histology, immunohistochemistry (IHC), real-time quantitative polymerase chain reaction (qPCR), X-ray, and microCT imaging at multiple time-points.

RESULTS

Loss of Notch signaling in postnatal joint chondrocytes results in a progressive OA-like pathology, and triggered the recruitment of non-targeted fibrotic cells into the articular cartilage potentially due to mis-regulated chemokine expression from within the cartilage. Upon recruitment, these fibrotic cells produced degenerative enzymes that may lead to the observed cartilage degradation and contribute to a significant portion of the age-related OA-like pathology. On the contrary, loss of Notch signaling in subchondral osteoblasts did not affect normal cartilage development or joint maintenance.

CONCLUSIONS

RBPjκ-dependent Notch signaling in postnatal joint chondrocytes, but not subchondral osteoblasts, is required for articular cartilage and joint maintenance.

MiR-485-3p and miR-485-5p suppress breast cancer cell metastasis by inhibiting PGC-1α expression

Breast cancer is the worldwide leading cause of cancer mortality in women. The majority of deaths from breast cancer arise from metastasis of local tumors. Cancer cells support their rapid proliferation by diverting metabolites into anabolic pathways, but during cancer metastasis, the proliferative program of invasive cancer cells is suspended for a migratory phenotype. In this study, we demonstrated that both mature forms of miRNA-485, miR-485-3p and miR-485-5p were involved in regulating mitochondrial respiration, cell migration and cell invasion in breast cancer cells by directly targeting and inhibiting the expression of PGC-1α. Specifically, the expression levels of both miR-485-3p and miR-485-5p were decreased in breast cancer tissues. Overexpression of miR-485-3p and miR-485-5p suppressed mitochondrial respiration and potential for cell migration and invasion in vitro, and also inhibited spontaneous metastasis of breast cancer cells in vivo. The suppression of mitochondrial respiration and cell invasion could be partially relieved by restoration of PGC-1α expression.