Search

This first-in-human study of AGN1 LOEP demonstrated that this minimally-invasive treatment durably increased aBMD in femurs of osteoporotic postmenopausal women. AGN1 resorption was coupled with new bone formation by 12 weeks and that new bone was maintained for at least 5-7 years resulting in substantially increased FEA-estimated femoral strength.IntroductionThis first-in-human study evaluated feasibility, safety, and in vivo response to treating proximal femurs of postmenopausal osteoporotic women with a minimally-invasive local osteo-enhancement procedure (LOEP) to inject a resorbable triphasic osteoconductive implant material (AGN1).MethodsThis prospective cohort study enrolled 12 postmenopausal osteoporotic (femoral neck T-score ≤ - 2.5) women aged 56 to 89 years. AGN1 LOEP was performed on left femurs; right femurs were untreated controls. Subjects were followed-up for 5-7 years. Outcomes included adverse events, proximal femur areal bone mineral density (aBMD), AGN1 resorption, and replacement with bone by X-ray and CT, and finite element analysis (FEA) estimated hip strength.ResultsBaseline treated and control femoral neck aBMD was equivalent. Treated femoral neck aBMD increased by 68 ± 22%, 59 ± 24%, and 58 ± 27% over control at 12 and 24 weeks and 5-7 years, respectively (p < 0.001, all time points). Using conservative assumptions, FEA-estimated femoral strength increased by 41%, 37%, and 22% at 12 and 24 weeks and 5-7 years, respectively (p < 0.01, all time points). Qualitative analysis of X-ray and CT scans demonstrated that AGN1 resorption and replacement with bone was nearly complete by 24 weeks. By 5-7 years, AGN1 appeared to be fully resorbed and replaced with bone integrated with surrounding trabecular and cortical bone. No procedure- or device-related serious adverse events (SAEs) occurred.ConclusionsTreating femurs of postmenopausal osteoporotic women with AGN1 LOEP results in a rapid, durable increase in aBMD and femoral strength. These results support the use and further clinical study of this approach in osteoporotic patients at high risk of hip fracture.

Two-component signaling (TCS) is the primary means by which bacteria sense and respond to the environment. TCS involves two partner proteins working in tandem, which interact to perform cellular functions whereas limiting interactions with non-partners (i.e., cross-talk). We construct a Potts model for TCS that can quantitatively predict how mutating amino acid identities affect the interaction between TCS partners and non-partners. The parameters of this model are inferred directly from protein sequence data. This approach drastically reduces the computational complexity of exploring the sequence-space of TCS proteins. As a stringent test, we compare its predictions to a recent comprehensive mutational study, which characterized the functionality of 204 mutational variants of the PhoQ kinase in Escherichia coli We find that our best predictions accurately reproduce the amino acid combinations found in experiment, which enable functional signaling with its partner PhoP. These predictions demonstrate the evolutionary pressure to preserve the interaction between TCS partners as well as prevent unwanted cross-talk. Further, we calculate the mutational change in the binding affinity between PhoQ and PhoP, providing an estimate to the amount of destabilization needed to disrupt TCS.

Background: Older spine surgery patients have a high incidence of debilitation, which can be managed with certain exercises., Aim: To investigate the current status and influencing factors related to the knowledge of exercise intervention among patients and professionals., Methods: Descriptive research methods were used to classify and summarize patients and professionals' perceptions and factors affecting exercise interventions. Data were analysed using the Colaizzi seven-step analysis method to distill and refine themes., Results: A total of 7 themes were identified: (1) The current status of patients' exercise is unsatisfactory; (2) patients' health literacy is low, coupled with a lack of social and family support; (3) there are numerous challenges with systematic exercise interventions; (4) healthcare professionals acknowledge the importance and need for exercise interventions; (5) there's a pronounced willingness among patients to participate in exercise intervention programs; (6) healthcare professionals believe that exercise interventions are beneficial; and (7) participants offered invaluable insights and suggestions on perioperative exercise during spinal surgery., Conclusion: To investigate the current status and influencing factors related to the knowledge of exercise intervention among patients and the related healthcare professionals to provide a reference for the construction of exercise management programs for these patients., Competing Interests: Conflict-of-interest statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (©The Author(s) 2024. Published by Baishideng Publishing Group Inc. All rights reserved.)

DNA-binding response regulators (DBRRs) are a broad class of proteins that operate in tandem with their partner kinase proteins to form two-component signal transduction systems in bacteria. Typical DBRRs are composed of two domains where the conserved N-terminal domain accepts transduced signals and the evolutionarily diverse C-terminal domain binds to DNA. These domains are assumed to be functionally independent, and hence recombination of the two domains should yield novel DBRRs of arbitrary input/output response, which can be used as biosensors. This idea has been proved to be successful in some cases; yet, the error rate is not trivial. Improvement of the success rate of this technique requires a deeper understanding of the linker-domain and inter-domain residue interactions, which have not yet been thoroughly examined. Here, we studied residue coevolution of DBRRs of the two main subfamilies (OmpR and NarL) using large collections of bacterial amino acid sequences to extensively investigate the evolutionary signatures of linker-domain and inter-domain residue interactions. Coevolutionary analysis uncovered evolutionarily selected linker-domain and inter-domain residue interactions of known experimental structures, as well as previously unknown inter-domain residue interactions. We examined the possibility of these inter-domain residue interactions as contacts that stabilize an inactive conformation of the DBRR where DNA binding is inhibited for both subfamilies. The newly gained insights on linker-domain/inter-domain residue interactions and shared inactivation mechanisms improve the understanding of the functional mechanism of DBRRs, providing clues to efficiently create functional DBRR-based biosensors. Additionally, we show the feasibility of applying coevolutionary landscape models to predict the functionality of domain-swapped DBRR proteins. The presented result demonstrates that sequence information can be used to filter out bioengineered DBRR proteins that are predicted to be nonfunctional due to a high negative predictive value., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

A series of bifunctional Ln(III)-based coordination polymers (CPs) {Ln(L)(DMA) 2 (NO 3 )} n [Ln(III) = Eu ( 1 ), Gd ( 2 ), and Dy ( 3 ); organic ligand H 2 L = 2,2'-(1,3,5,7-tetrahydroxyoctahydro-4,8-ethanopyrrolo[3,4- f ]isoindole-2,6(1 H ,3 H )-diyl)diacetic acid)] have been successfully synthesized. CPs 1 - 3 are isostructural and constructed from the dimeric Ln 2 unit in which two adjacent Ln III ions are bridged by two μ 3 -carboxyl oxygens, and the Ln 2 dimeric unit is connected by two NO 3 - ions, four DMA molecules, and four completely protonated L 2- ligands forming a 2D layer structure. The magnetic research reveals that CP 2 shows a significant cryogenic magnetocaloric effect (-Δ S m = 22.9 J kg -1 K -1 ; T = 2.0 K and Δ H = 7.0 T), whereas CP 3 exhibits slow magnetic relaxation property under H dc = 0 Oe field. Additionally, the luminescence explorations revealed that CP 1 can act as a recyclable luminescent probe for pollutant acetylacetone among various small organic solvent molecules, and the corresponding detection limit is 10 -7 mol/L. More importantly, CP 1 also exhibits good catalytic performance in the cycloaddition reaction of CO 2 and epoxides or cyanamides under mild conditions. As far as we know, CP 1 represents the first bifunctional lanthanide homogeneous catalyst that can efficiently catalyze the reaction of cyanamides/epoxides with CO 2 simultaneously.

Chromosomes endure mechanical stresses throughout the cell cycle; for example, resulting from the pulling of chromosomes by spindle fibers during mitosis or deformation of the nucleus during cell migration. The response to physical stress is closely related to chromosome structure and function. Micromechanical studies of mitotic chromosomes have revealed them to be remarkably extensible objects and informed early models of mitotic chromosome organization. We use a data-driven, coarse-grained polymer modeling approach to explore the relationship between the spatial organization of individual chromosomes and their emergent mechanical properties. In particular, we investigate the mechanical properties of our model chromosomes by axially stretching them. Simulated stretching led to a linear force-extension curve for small strain, with mitotic chromosomes behaving about 10-fold stiffer than interphase chromosomes. Studying their relaxation dynamics, we found that chromosomes are viscoelastic solids with a highly liquid-like, viscous behavior in interphase that becomes solid-like in mitosis. This emergent mechanical stiffness originates from lengthwise compaction, an effective potential capturing the activity of loop-extruding SMC complexes. Chromosomes denature under large strains via unraveling, which is characterized by opening of large-scale folding patterns. By quantifying the effect of mechanical perturbations on the chromosome's structural features, our model provides a nuanced understanding of in vivo mechanics of chromosomes., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Neospora caninum is an important apicomplexan parasite causing neosporosis in cattle. The disease is recognized as one of the most important cause of reproductive problems and abortion in cattle worldwide. In this context, we developed an indirect enzyme-linked immunosorbent assays (ELISA) with chimeric protein rSRS2-SAG1-GRA7 to diagnose antibodies to Neospora -infection. This indirect ELISA was compared to indirect fluorescent antibody test (IFAT) and western blotting (WB), and the sensitivity and specificity results of ELISA were calculated to be 86.7 and 96.1%, respectively. The overall coincidence rate was 92.6% using IFAT and WB. Additionally, 329 aborting dairy cattle serum samples were tested using this ELISA to evaluate the prevalence of N. caninum in Ningxia, China. The positive rate of N. caninum in these farms was from 19.05 to 57.89%, and the mean rate was 41.64% (±11.01%), indicating that infection with N. caninum may be one of the important causes of cattle abortion in this region. This established rSRS2-SAG1-GRA7 indirect ELISA is capable for detecting the antibodies against N. caninum , and it could be a useful screening tool for monitoring the epidemiology of neosporosis in cattle., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Yang, Yang, Ayanniyi, Chen, Lu, Zhang, Liu, Hong, Cheng, Zhang, Zong, Zhao and Xu.)

In recent years, much effort has been devoted to understanding the three-dimensional (3D) organization of the genome and how genomic structure mediates nuclear function. The development of experimental techniques that combine DNA proximity ligation with high-throughput sequencing, such as Hi-C, have substantially improved our knowledge about chromatin organization. Numerous experimental advancements, not only utilizing DNA proximity ligation but also high-resolution genome imaging (DNA tracing), have required theoretical modeling to determine the structural ensembles consistent with such data. These 3D polymer models of the genome provide an understanding of the physical mechanisms governing genome architecture. Here, we present an overview of the recent advances in modeling the ensemble of 3D chromosomal structures by employing the maximum entropy approach combined with polymer physics. Particularly, we discuss the minimal chromatin model (MiChroM) along with the "maximum entropy genomic annotations from biomarkers associated with structural ensembles" (MEGABASE) model, which have been remarkably successful in the accurate modeling of chromosomes consistent with both Hi-C and DNA-tracing data., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Background: Ureteral identification is essential to performing safe colorectal surgery. Injected immunofluorescence may aid with ureteral identification, but feasibility without ureteral catheterization is not well described., Methods: Case series of robotic colorectal resections where indocyanine green (ICG) injection with or without ureteral catheter placement was performed. Imaging protocol, time to ureteral identification, and factors impacting visualization are reported., Results: From 2019 to 2020, 83 patients underwent ureteral ICG injection, 20 with catheterization and 63 with injection only. Main indications were diverticulitis (52%) and cancer (36%). Median time to instill ICG was faster with injection alone than with catheter placement (4min vs 13.5min, p < 0.001). Median time [IQR] to right ureter (0.3 [0.01-1.2] min after robot docking) and left ureter (5.5 [3.1-8.8] min after beginning dissection) visualization was not different between injection alone and catheterization., Conclusion: ICG injection alone is faster than with indwelling catheter placement and equally reliable at intraoperative ureteral identification., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Direct coupling analysis (DCA) is a global statistical approach that uses information encoded in protein sequence data to predict spatial contacts in a three-dimensional structure of a folded protein. DCA has been widely used to predict the monomeric fold at amino acid resolution and to identify biologically relevant interaction sites within a folded protein. Going beyond single proteins, DCA has also been used to identify spatial contacts that stabilize the interaction in protein complex formation. However, extracting this higher order information necessary to predict dimer contacts presents a significant challenge. A DCA evolutionary signal is much stronger at the single protein level (intraprotein contacts) than at the protein-protein interface (interprotein contacts). Therefore, if DCA-derived information is to be used to predict the structure of these complexes, there is a need to identify statistically significant DCA predictions. We propose a simple Z -score measure that can filter good predictions despite noisy, limited data. This new methodology not only improves our prediction ability but also provides a quantitative measure for the validity of the prediction.

We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. The NDB is available at https://ndb.rice.edu., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Objective: To preliminarily explore the treatment effect of nivolumab on Chinese non-small-cell lung cancer (NSCLC) patients with brain metastases, and further enrich the evidences of programmed death-ligand 1 (PD-1) monoclonal antibody in the treatment of NSCLC patients with brain metastases. Methods: The clinical and pathological data of 22 NSCLC patients with brain metastases treated with nivolumab were collected. The electronic imaging data were collected to confirm the treatment effect and time point of disease progression, and the survival data of the patients were obtained through follow-up. Results: Twenty-one patients were evaluated for the intracranial treatment effect. The intracerebral objective response rate (IORR) was 28.6%, the intracranial disease control rate (IDCR) was 47.6%. The median intracranial progression-free-survival (iPFS) of all the 22 patients was 5.2 months. Both the 1-year and 2-year survival rates were 56.7%. Conclusions: The treatment effect of PD-1 monoclonal antibody on NSCLC patients with brain metastases is similar as those without brain metastases.

Using computer simulations, we generate cell-specific 3D chromosomal structures and compare them to recently published chromatin structures obtained through microscopy. We demonstrate using machine learning and polymer physics simulations that epigenetic information can be used to predict the structural ensembles of multiple human cell lines. Theory predicts that chromosome structures are fluid and can only be described by an ensemble, which is consistent with the observation that chromosomes exhibit no unique fold. Nevertheless, our analysis of both structures from simulation and microscopy reveals that short segments of chromatin make two-state transitions between closed conformations and open dumbbell conformations. Finally, we study the conformational changes associated with the switching of genomic compartments observed in human cell lines. The formation of genomic compartments resembles hydrophobic collapse in protein folding, with the aggregation of denser and predominantly inactive chromatin driving the positioning of active chromatin toward the surface of individual chromosomal territories., Competing Interests: RC, VC, EL, PW, MD, JO No competing interests declared, (© 2020, Cheng et al.)

Amyotrophic lateral sclerosis is a disease characterized by progressive paralysis and death. Most ALS-cases are sporadic (sALS) and patient heterogeneity poses challenges for effective therapies. Applying metabolite profiling on 77-sALS patient-derived-fibroblasts and 43-controls, we found ~25% of sALS cases (termed sALS-1) are characterized by transsulfuration pathway upregulation, where methionine-derived-homocysteine is channeled into cysteine for glutathione synthesis. sALS-1 fibroblasts selectively exhibited a growth defect under oxidative conditions, fully-rescued by N-acetylcysteine (NAC). [U 13 C]-glucose tracing showed transsulfuration pathway activation with accelerated glucose flux into the Krebs cycle. We established a four-metabolite support vector machine model predicting sALS-1 metabotype with 97.5% accuracy. Both sALS-1 metabotype and growth phenotype were validated in an independent cohort of sALS cases. Importantly, plasma metabolite profiling identified a system-wide cysteine metabolism perturbation as a hallmark of sALS-1. Findings reveal that sALS patients can be stratified into distinct metabotypes with differential sensitivity to metabolic stress, providing novel insights for personalized therapy., Competing Interests: Declaration of Competing Interest Nothing to report., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Objective: The aim of present study was to investigate the influence of genetic variation of programmed death-ligand 1 (PD-L1) on the prognosis of patients with non-small cell lung cancer (NSCLC) who received platinum-based adjuvant chemotherapy. Methods: This study was designed as a retrospective analysis, and a total of 278 patients with postoperative NSCLC who received platinum-based adjuvant chemotherapy from January 2012 to December 2018 in the Department of Respiratory Medicine of the First affiliated Hospital of Zhengzhou University were included in this study. Biological specimens of the patients were collected during hospitalization. Recurrence status and adverse reactions were evaluated in the hospital during adjuvant chemotherapy. Survival data of the patients were obtained through telephone follow-up after completing the fixed cycle of adjuvant chemotherapy. DNA extracted from the collected hematological specimens was genotyped for PD-L1 gene polymorphism. Additionally, postoperative cancer tissue specimens from 68 patients were collected for RNA extraction in order to perform the PD-L1 mRNA expression analysis. The univariate analysis of genotypes and prognosis was carried out by Kaplan-Meier survival analysis. Results: Prognostic results indicated that the median disease-free survival (DFS) of the 278 patients with NSCLC was 3.2 years and the median overall survival (OS) was 4.9 years. The prevalence of -1813G>C polymorphism were: GG genotype 173 cases (62.23%), GC genotype 92 cases (33.09%), CC genotype 13 cases (4.68%), the minor allele frequency was 0.21, the distribution of the three genotypes was in accordance with Hardy-Weinberg Equilibrium ( P= 0.864). In view of the rare frequency of CC genotype, GC and CC genotype were merged in the following analysis. The survival analysis results of the two genotype groups suggested that the median DFS of patients with GG and GC/CC genotype was 2.7 and 4.0 years, which was statistically significant ( P= 0.013). Furthermore, the median OS of patients with GG and GC/CC was 4.0 and 5.4 years respectively, which was statistically significant as well ( P= 0.009). However, the safety analysis failed to find the significant association between the polymorphism and adverse events ( P> 0.05). Interestingly, expression analysis of RNA extracted from cancer tissues specimens indicated that the PD-L1 mRNA expression of the patients with GG genotype were significantly higher than those of the GC/CC genotype (3.67±0.65 vs 2.69±0.78, P< 0.001). Conclusion: The prognosis of patients with postoperative non-small cell lung cancer who received platinum-based adjuvant chemotherapy is influenced by -1813G>C polymorphism of PD-L1 gene.

Embryonic diapause is a maternally controlled phenomenon. The molecule controlling the onset of the phenomenon is unknown. We demonstrated that overexpression of microRNA let-7a or incubation with let-7g-enriched extracellular vesicles from endometrial epithelial cells prolonged the in vitro survival of mouse blastocysts, which developed into live pups after having been transferred to foster mothers. Similar to in vivo dormant blastocysts, let-7-induced dormant blastocysts exhibited low level of proliferation, apoptosis, and nutrient metabolism. Let-7 suppressed c-myc/mTORC1 and mTORC2 signaling to induce embryonic diapause. It also inhibited ODC1 expression reducing biosynthesis of polyamines, which are known to reactivate dormant embryos. Furthermore, the overexpression of let-7 blocked trophoblast differentiation and implantation potential of human embryo surrogates, and prolonged survival of human blastocysts in vitro, supporting the idea that embryonic diapause was an evolutionary conserved phenomenon. In conclusion, let-7 is the main factor inducing embryonic diapause., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).)

Blockade of the programmed cell death 1(PD-1)/PD-1 ligand-1(PD-L1) pathway has been exploited therapeutically in many cancer types. Upregulation of PD-L1 in tumor cells contributes to malignancy through suppression of the T cell-mediated antitumor response. Pyruvate dehydrogenase kinase 1 (PDK1), a glycolytic gate-keeping enzyme, is also known to promote tumor development. Here, we have uncovered a mechanism of regulation of PD-L1 by PDK1 through activation of c-Jun-NH 2 -kinase (JNK)-c-Jun in ovarian cancer cells. Elevated PDK1 expression was correlated with that of PD-L1 in the TCGA ovarian cancer dataset and ovarian cancer tissue array. Overexpression of PDK1 in ovarian cancer cells impaired CD8 + T cell function by suppressing IFN-γ secretion through the PD-1/PD-L1 pathway. Conversely, knockdown of PDK1 in ovarian cancer cells relieved suppression of CD8 + T cell function. CD8 + T cell apoptosis induced by binding of PD-1 with PD-L1 was increased after co-culture with ovarian cancer cells overexpressing PDK1, while depletion of PDK1 exerted the opposite effect. In vivo experiments revealed synergistic improved overall survival and enhanced inhibition of tumor growth upon co-treatment with dichloroacetate (DCA), a PDK inhibitor, and PD-L1 antibody, accompanied by increased IFN-γ secretion by monocytes infiltrating tumor islets. Moreover, PDK1 expression and CD8 + T cell infiltration were inversely correlated in the ovarian cancer tissue array. Our collective findings provide a novel explanation of how PDK1 contributes to upregulation of PD-L1 in ovarian cancer and highlight its potential as a target therapeutic molecule that cooperates with the immune checkpoint blockade., (© 2019 Taylor & Francis Group, LLC.)

Nigakialcohol A ( 1 ), as unusual cyclization ionone derivative, together with eight known ones ( 2 - 9 ), were isolated from the leaves of Picrasma quassioides (D. Don) Benn (Simaroubaceae). Their structures were elucidated by extensive spectroscopic analyses and comparison with literature data. Compound 2 showed a weak inhibitory effect on NO production at non-cytotoxic concentration (100 μM) with inhibitory rate of 59%, and thus it should be regarded as potential anti-inflammatory agents.

The Liulin Spring is one of the ten most famous karst springs in the Shanxi province. The abundant karst groundwater resources support the economic and social development in the Luliang Prefecture. Therefore, the study of evolution and control factors of karst groundwater is of great significance to the sustainable utilization of water resources in the watershed. For revealing the evolution and control factors of karst groundwater in the Liulin Spring area, the main ion components of 29 karst groundwater samples from spring supply area, runoff area, discharge area, and deep buried area were analyzed. The results showed that the temperature and Na + , Ca 2+ , Mg 2+ , Cl - , HCO 3 - , and SO 4 2- concentrations increased continuously along the runoff route, from the recharge area to the runoff area, to the discharge area, and then to the deep burial area. K + , Na + , and Cl - mainly come from salt rock dissolution, and Ca 2+ , Mg 2+ , HCO 3 - , and SO 4 2- mainly come from the dissolution of calcite, dolomite, and gypsum. Because they are controlled by the continuous dissolution of salt rock and gypsum, the concentration of Na + , Cl - , and SO 4 2- in groundwater has increased greatly, with the maximum value being 50 times, 80 times, and 32 times of the minimum value, respectively. Under the influence of dedolomitization, the concentration of Ca 2+ and HCO 3 - in groundwater does not change significantly, the maximum is 2-3 times of the minimum. In the recharge area and runoff area, Na + and Cl - amounts are lower, and Ca 2+ and HCO 3 - are the main cations and anions in the groundwater. However, in the discharge area and deep buried area, Cl - and Na + exceed HCO 3 - , Ca 2+ , and Mg 2+ and become the main anions and cations in the groundwater. The hydrochemical type changes from HCO 3 -Ca·Mg in the supply area to HCO 3 ·SO 4 -Ca·Mg in the runoff area, to HCO 3 ·SO 4 -Ca·Na·Mg in the recharge area, and finally to Cl·HCO 3 -Na·Ca, Cl·HCO 3 -Na, and Cl-Na·Ca in the deep burial area.

We develop a simple, coarse-grained approach for simulating the folding of the Beet Western Yellow Virus (BWYV) pseudoknot toward the goal of creating a transferable model that can be used to study other small RNA molecules. This approach combines a structure-based model (SBM) of RNA with an electrostatic scheme that has previously been shown to correctly reproduce ionic condensation in the native basin. Mg 2+ ions are represented explicitly, directly incorporating ion-ion correlations into the system, and K + is represented implicitly, through the mean-field generalized Manning counterion condensation theory. Combining the electrostatic scheme with a SBM enables the electrostatic scheme to be tested beyond the native basin. We calibrate the SBM to reproduce experimental BWYV unfolding data by eliminating overstabilizing backbone interactions from the molecular contact map and by strengthening base pairing and stacking contacts relative to other native contacts, consistent with the experimental observation that relative helical stabilities are central determinants of the RNA unfolding sequence. We find that this approach quantitatively captures the Mg 2+ dependence of the folding temperature and generates intermediate states that better approximate those revealed by experiment. Finally, we examine how our model captures Mg 2+ condensation about the BWYV pseudoknot and a U-tail variant, for which the nine 3' end nucleotides are replaced with uracils, and find our results to be consistent with experimental condensation measurements. This approach can be easily transferred to other RNA molecules by eliminating and strengthening the same classes of contacts in the SBM and including generalized Manning counterion condensation.

Protein assemblies consisting of structural maintenance of chromosomes (SMC) and kleisin subunits are essential for the process of chromosome segregation across all domains of life. Prokaryotic condensin belonging to this class of protein complexes is composed of a homodimer of SMC that associates with a kleisin protein subunit called ScpA. While limited structural data exist for the proteins that comprise the (SMC)-kleisin complex, the complete structure of the entire complex remains unknown. Using an integrative approach combining both crystallographic data and coevolutionary information, we predict an atomic-scale structure of the whole condensin complex, which our results indicate being composed of a single ring. Coupling coevolutionary information with molecular-dynamics simulations, we study the interaction surfaces between the subunits and examine the plausibility of alternative stoichiometries of the complex. Our analysis also reveals several additional configurational states of the condensin hinge domain and the SMC-kleisin interaction domains, which are likely involved with the functional opening and closing of the condensin ring. This study provides the foundation for future investigations of the structure-function relationship of the various SMC-kleisin protein complexes at atomic resolution., Competing Interests: The authors declare no conflict of interest.

Selecting amino acids to design novel protein-protein interactions that facilitate catalysis is a daunting challenge. We propose that a computational coevolutionary landscape based on sequence analysis alone offers a major advantage over expensive, time-consuming brute-force approaches currently employed. Our coevolutionary landscape allows prediction of single amino acid substitutions that produce functional interactions between non-cognate, interspecies signaling partners. In addition, it can also predict mutations that maintain segregation of signaling pathways across species. Specifically, predictions of phosphotransfer activity between the Escherichia coli histidine kinase EnvZ to the non-cognate receiver Spo0F from Bacillus subtilis were compiled. Twelve mutations designed to enhance, suppress, or have a neutral effect on kinase phosphotransfer activity to a non-cognate partner were selected. We experimentally tested the ability of the kinase to relay phosphate to the respective designed Spo0F receiver proteins against the theoretical predictions. Our key finding is that the coevolutionary landscape theory, with limited structural data, can significantly reduce the search-space for successful prediction of single amino acid substitutions that modulate phosphotransfer between the two-component His-Asp relay partners in a predicted fashion. This combined approach offers significant improvements over large-scale mutations studies currently used for protein engineering and design., Competing Interests: The authors have declared that no competing interests exist.

Bear Bile Powder contains bile acids, protein, amino acids, bilirubin and microelements and other compounds. Among them, the bile acids are the most active components. Currently, there are many studies on bile acids, but few reports on other components. Therefore, the purpose of this study is to carry out a systematical analysis of multiple components in drainage Bear Bile Powder from different sources. Bilirubin and protein were quantified by microplate spectrophotometer. The contents of bile acids and amino acids were determined by liquid chromatography coupled with mass spectrometry (LC-MS). The contents of microelements were determined by inductively coupled plasma mass spectrometry (ICP-MS) The result indicated that among 20 batches of bear bile powder from different sources there is high similarity (0.922-0.977). Tauroursodeoxycholic acid (TUDCA) and taurochenodeoxycholic acid (TCDCA) were the two most abundant components. The total contents of them were 41%-59% and met the current standard for quality control of bear bile powder. However, significant differences were found in their contents among samples from different sources. Besides, bilirubin, protein, amino acids and microelements also contributed to the differentiation of samples from different sources. The main components of bear bile powder from the different sources were with satisfactory similarity. But bile acids, bilirubin, protein, amino acids and microelements all contributed to the different among samples. Our present study provided a systematical approach for the better quality control and evaluation of bear bile powder., Competing Interests: The authors of this article and the planning committee members and staff have no relevant financial relationships with commercial interests to disclose., (Copyright© by the Chinese Pharmaceutical Association.)

Discovery of agents for oral infectious diseases is always encouraged in natural products chemistry. A bioassay-guided isolation led to the isolation of two new acetylenic acids (1, 2) along with seven known ones (3-9) from the ethanol extract of Thesium chinense Turcz, a commonly used oral anti-bacterial and anti-inflammatory herb. Their structures were elucidated on the basis of spectroscopic and chemical evidence. Exocarpic acid (3) demonstrated the most promising activity against three tested oral pathogenic bacterial strains, Porphyromonas gingivalis, Fusobacterium nucleatum, and Streptococcus mutans, with minimum inhibitory concentration values of 0.86, 3.43, and 13.70 μg/mL, respectively. Compounds 1, 2, 4, 5 and 7 also showed potential activities against periodontal bacteria (P. gingivalis, F. nucleatum).

Inside the cell nucleus, genomes fold into organized structures that are characteristic of cell type. Here, we show that this chromatin architecture can be predicted de novo using epigenetic data derived from chromatin immunoprecipitation-sequencing (ChIP-Seq). We exploit the idea that chromosomes encode a 1D sequence of chromatin structural types. Interactions between these chromatin types determine the 3D structural ensemble of chromosomes through a process similar to phase separation. First, a neural network is used to infer the relation between the epigenetic marks present at a locus, as assayed by ChIP-Seq, and the genomic compartment in which those loci reside, as measured by DNA-DNA proximity ligation (Hi-C). Next, types inferred from this neural network are used as an input to an energy landscape model for chromatin organization [Minimal Chromatin Model (MiChroM)] to generate an ensemble of 3D chromosome conformations at a resolution of 50 kilobases (kb). After training the model, dubbed Maximum Entropy Genomic Annotation from Biomarkers Associated to Structural Ensembles (MEGABASE), on odd-numbered chromosomes, we predict the sequences of chromatin types and the subsequent 3D conformational ensembles for the even chromosomes. We validate these structural ensembles by using ChIP-Seq tracks alone to predict Hi-C maps, as well as distances measured using 3D fluorescence in situ hybridization (FISH) experiments. Both sets of experiments support the hypothesis of phase separation being the driving process behind compartmentalization. These findings strongly suggest that epigenetic marking patterns encode sufficient information to determine the global architecture of chromosomes and that de novo structure prediction for whole genomes may be increasingly possible., Competing Interests: The authors declare no conflict of interest., (Copyright © 2017 the Author(s). Published by PNAS.)

A novel metal-organic framework {[Zn(XL) 2 ](ClO 4 ) 2 ⋅6 H 2 O} n (XL=N,N'-bicyclo[2.2.2]oct-7-ene-2,3,5,6-tetracarboxdiimide bi(1,2,4-triazole)) was synthesized and structurally characterized, presenting the first example of six-fold interpenetrating 3 D framework with the topology type of sqc6, which displays high thermostability and solvent stability. Additionally, the luminescence investigations reveal that this MOF can sensitively and selectively detect acetylacetone with a detection limit of 1.72 ppm. More importantly, it is rather rare for an MOF-based luminescence probe to serve as a sensor to effectively detect acetylacetone., (© 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Based on the data of the field investigation and laboratory and the database of the 8 th national forestry inventory, ecosystem carbon density, storage amount, and sequestration potential of tree layer were estimated for five typical plantation ecosystems (Robinia pseudoacacia, Populus spp., Pinus tabuliformis Pinus armandii, which were grouped as one kind of ecosystems, Larix principis-rupprechtii, and Picea asperata) in Gansu Province. The results showed that the average carbon density and total carbon storage of the five typical plantation ecosystems were 139.65 t·hm -2 and 85.78 Tg, respectively. Ecosystem carbon density varied among ecosystems. It followed the sequence of premature (250.70 t·hm -2 ) > mature (175.97 t·hm -2 ) > middle-aged (156.92 t·hm -2 ) > young (117.56 t·hm -2 ) forest. Meanwhile, carbon storage in these plantations ranked in the order of young (45.47 Tg) > middle-aged (19.54 Tg) > mature (11.84 Tg) > pre-mature (8.93 Tg) forest. Specifically, young and middle-aged plantations contributed the most and accounted for 75.9% of the total carbon storage. The realistic carbon sequestration potential (CP r ) by tree layer of the five typical plantation ecosystems in Gansu Province was estimated as 7.27 Tg. The two largest contributors toCP r were R. pseudoacacia (2.49 Tg) and Populus spp. (2.10 Tg). Young plantations (3.78 Tg) showed the largest CP r , followed by middle-aged plantations (2.04 Tg), and the value of premature plantations (0.45 Tg) was the smallest. The maximum carbon sequestration potential (CP max ) might be up to 27.55 Tg, the CP max with different plantations ranked in the order of R. pseudoacacia (9.42 Tg)> L. principis-rupprechtii (6.22 Tg) ≈ P. asperata (6.36 Tg) > Populus spp. (3.18 Tg) >P. tabuliformis P. armandii (2.37 Tg). The CP max of young and middle-aged plantations was estimated as 18.48 and 6.89 Tg, respectively, which accounted for 92% of the total maximum carbon sequestration potential.

Sixty-three amide alkaloids, including three new, piperflaviflorine A ( 1 ), piperflaviflorine B ( 2 ), and sarmentamide D ( 4 ), and two previously synthesized ones, (1 E ,3 S )-1-cinnamoyl-3- hydroxypyrrolidine ( 3 ) and N -[7'-(4'-methoxyphenyl)ethyl]-2-methoxybenzamide ( 5 ), were isolated from the aerial parts of Piper flaviflorum and Piper sarmentosum. Their structures were elucidated by detailed spectroscopic analysis and, in case of 3 , by single-crystal X-ray diffraction. Most of the isolates were tested for their antifungal and antibacterial activities. Ten amides ( 6 - 15 ) showed antifungal activity against Cryptococcus neoformans ATCC 90 113 with IC 50 values in the range between 4.7 and 20.0 µg/mL., (Georg Thieme Verlag KG Stuttgart · New York.)

Protein-protein interactions play a central role in cellular function. Improving the understanding of complex formation has many practical applications, including the rational design of new therapeutic agents and the mechanisms governing signal transduction networks. The generally large, flat, and relatively featureless binding sites of protein complexes pose many challenges for drug design. Fragment docking and direct coupling analysis are used in an integrated computational method to estimate druggable protein-protein interfaces. (i) This method explores the binding of fragment-sized molecular probes on the protein surface using a molecular docking-based screen. (ii) The energetically favorable binding sites of the probes, called hot spots, are spatially clustered to map out candidate binding sites on the protein surface. (iii) A coevolution-based interface interaction score is used to discriminate between different candidate binding sites, yielding potential interfacial targets for therapeutic drug design. This approach is validated for important, well-studied disease-related proteins with known pharmaceutical targets, and also identifies targets that have yet to be studied. Moreover, therapeutic agents are proposed by chemically connecting the fragments that are strongly bound to the hot spots., Competing Interests: The authors declare no conflict of interest.

Fifty-eight phenolic compounds isolated from Phyllanthus emblica were screened and compared for their in vitro and in vivo antioxidant properties, as well as hyaluronidase (HAase) inhibitory activities. Among them, 20 compounds showed to be promising antioxidants due to the stronger scavenging activity in both DPPH radical and Danio rerio reactive oxygen species assays, while nine compounds were potential HAase inhibitors with 100-fold stronger activities than that of the positive control, DSCG. The structure activity relationship was discussed.

Peripheral nerve involvement may be the first sign of systemic amyloid light-chain (AL) amyloidosis, a rare disease. Physical examination and electrodiagnostic testing are the mainstays of peripheral neuropathy evaluation at presentation. Sural nerve biopsy is performed in conjunction with serum and urine protein evaluation to differentiate between focal and systemic disease. Systemic disease is treated with a combination of chemotherapy, steroids, and stem cell transplantation. Isolated peripheral nerve disease is extremely rare. The authors here report the case of an 80-year-old woman who presented with progressive right upper-extremity weakness due to right radial neuropathy discovered upon electrodiagnostic testing. Magnetic resonance neurography (MRN) revealed a focal lesion within the right radial nerve. She underwent radial nerve exploration and excision of an intraneural mass consisting of amyloid on histopathology, with mass spectrometry analysis diagnostic for AL amyloidosis. Noninvasive testing and clinical history did not suggest systemic involvement. This unique case of isolated peripheral nerve AL amyloidosis in the absence of signs and symptoms of systemic disease is described, and the literature demonstrating peripheral nerve involvement in AL amyloidosis is reviewed.

Unlabelled: Two-component systems (TCS) that employ histidine kinases (HK) and response regulators (RR) are critical mediators of cellular signaling in bacteria. In the model cyanobacterium Synechococcus elongatus PCC 7942, TCSs control global rhythms of transcription that reflect an integration of time information from the circadian clock with a variety of cellular and environmental inputs. The HK CikA and the SasA/RpaA TCS transduce time information from the circadian oscillator to modulate downstream cellular processes. Despite immense progress in understanding of the circadian clock itself, many of the connections between the clock and other cellular signaling systems have remained enigmatic. To narrow the search for additional TCS components that connect to the clock, we utilized direct-coupling analysis (DCA), a statistical analysis of covariant residues among related amino acid sequences, to infer coevolution of new and known clock TCS components. DCA revealed a high degree of interaction specificity between SasA and CikA with RpaA, as expected, but also with the phosphate-responsive response regulator SphR. Coevolutionary analysis also predicted strong specificity between RpaA and a previously undescribed kinase, HK0480 (herein CikB). A knockout of the gene for CikB (cikB) in a sasA cikA null background eliminated the RpaA phosphorylation and RpaA-controlled transcription that is otherwise present in that background and suppressed cell elongation, supporting the notion that CikB is an interactor with RpaA and the clock network. This study demonstrates the power of DCA to identify subnetworks and key interactions in signaling pathways and of combinatorial mutagenesis to explore the phenotypic consequences. Such a combined strategy is broadly applicable to other prokaryotic systems., Importance: Signaling networks are complex and extensive, comprising multiple integrated pathways that respond to cellular and environmental cues. A TCS interaction model, based on DCA, independently confirmed known interactions and revealed a core set of subnetworks within the larger HK-RR set. We validated high-scoring candidate proteins via combinatorial genetics, demonstrating that DCA can be utilized to reduce the search space of complex protein networks and to infer undiscovered specific interactions for signaling proteins in vivo Significantly, new interactions that link circadian response to cell division and fitness in a light/dark cycle were uncovered. The combined analysis also uncovered a more basic core clock, illustrating the synergy and applicability of a combined computational and genetic approach for investigating prokaryotic signaling networks., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

Two new oleanane-type triterpenoid saponins (1 and 2) were isolated from the methanolyzed total saponins of the seeds of Momordica cochinchinensis (Lour.) Spreng, together with 16 known compounds (3-18). Their structures were elucidated on the basis of detailed spectroscopic, including 1D and 2D NMR, mass spectrometric, methanolysis and LC-MS analysis. All the isolates were tested for their cytotoxic activities against five human cancer cell lines (HL-60, SMMC-7721, PANC-1, A-549, and SW-480) and the glucose uptake activity. The known compound 6 exhibited toxic effects against HL-60 with an IC50 value of 18.1 μM, while 10 showed cytotoxicity against SMMC-7721 and A-549 cell lines, with IC50 values of 34.4 and 32.8 μM, respectively. In addition, the new compound 2 showed glucose uptake activity with a glucose consumption value of 0.29 μM at 10 μM concentration.

Background: Granular cell tumor (GCT) is a relatively uncommon predominantly benign lesion that usually presents as a solitary, painless cutaneous or submucosal nodule. Most of these tumors are found in the tongue. Although GCT is believed to have a Schwann cell origin, reports of GCT in peripheral and spinal nerves are uncommon., Case Description: We report the case of a 43-year-old man with neck pain and hand numbness who was found to have a heterogeneously enhancing left-sided C2 nerve sheath tumor on magnetic resonance imaging. He underwent C2 decompression and resection of the left-sided C2 nerve sheath tumor with subsequent C1-C2 arthrodesis and instrumentation. Histopathologic review showed GCT. Review of the literature yielded 4 other reported cases of GCT within the vicinity of a spinal nerve root. Only one of these explicitly showed spinal nerve root involvement. This is a rare case of a GCT presenting as cervical nerve root mass, and what we believe is the first reported case of this in the literature., Conclusions: The surgeon should be aware of GCT when encountering spinal nerve root tumors because it may alter the surgical approach necessary for adequate resection compared with more commonly encountered nerve sheath tumors., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Recent developments in global statistical methodologies have advanced the analysis of large collections of protein sequences for coevolutionary information. Coevolution between amino acids in a protein arises from compensatory mutations that are needed to maintain the stability or function of a protein over the course of evolution. This gives rise to quantifiable correlations between amino acid sites within the multiple sequence alignment of a protein family. Here, we use the maximum entropy-based approach called mean field Direct Coupling Analysis (mfDCA) to infer a Potts model Hamiltonian governing the correlated mutations in a protein family. We use the inferred pairwise statistical couplings to generate the sequence-dependent heterogeneous interaction energies of a structure-based model (SBM) where only native contacts are considered. Considering the ribosomal S6 protein and its circular permutants as well as the SH3 protein, we demonstrate that these models quantitatively agree with experimental data on folding mechanisms. This work serves as a new framework for generating coevolutionary data-enriched models that can potentially be used to engineer key functional motions and novel interactions in protein systems., (© 2015 The Protein Society.)

Glioblastoma (GB) is the most common malignant brain tumor. Drug resistance frequently develops in these tumors during chemotherapy. Therefore, predicting drug response in these patients remains a major challenge in the clinic. Thus, to improve the clinical outcome, more effective and tolerable combination treatment strategies are needed. Robust experimental evidence has shown that the main reason for failure of treatments is signal redundancy due to coactivation of several functionally linked receptor tyrosine kinases (RTKs), including anaplastic lymphoma kinase (ALK), c-Met (hepatocyte growth factor receptor), and oncogenic c-ros oncogene1 (ROS1: RTK class orphan) fusion kinase FIG (fused in GB)-ROS1. As such, these could be attractive targets for GB therapy. The study subjects consisted of 19 patients who underwent neurosurgical resection of GB tissues. Our in vitro and ex vivo models promisingly demonstrated that treatments with crizotinib (PF-02341066: dual ALK/c-Met inhibitor) and temozolomide in combination induced synergistic antitumor activity on FIG-ROS1-positive GB cells. Our results also showed that ex vivo FIG-ROS1+ slices (obtained from GB patients) when cultured were able to preserve tissue architecture, cell viability, and global gene-expression profiles for up to 14 days. Both in vitro and ex vivo studies indicated that combination blockade of FIG, p-ROS1, p-ALK, and p-Met augmented apoptosis, which mechanistically involves activation of Bim and inhibition of survivin, p-Akt, and Mcl-1 expression. However, it is important to note that we did not see any significant synergistic effect of crizotinib and temozolomide on FIG-ROS1-negative GB cells. Thus, these ex vivo culture results will have a significant impact on patient selection for clinical trials and in predicting response to crizotinib and temozolomide therapy. Further studies in different animal models of FIG-ROS1-positive GB cells are warranted to determine useful therapies for the management of human GBs.

In an effort to identify anti-viral and cytotoxic compounds from Phyllanthus spp., 14 highly oxygenated norbisabolane sesquiterpenoids, phyllaemblicins H1-H14, were isolated from the roots of Phyllanthus emblica Linn, along with phyllaemblicins B and C and glochicoccinoside D. Their structures were determined on the basis of detailed spectroscopic analysis and chemical methods. Determination of absolute configurations of these compounds was facilitated by theoretical calculations of electronic circular dichroism (ECD) spectra using time-dependent density functional theory (TDDFT) for the aglycone components, and pre-column derivative/chiral HPLC analysis for the monosaccharides. The known glochicoccinoside D displayed potent activity against influenza A virus strain H3N2 and hand, foot and mouth virus EV71, with IC50 values of 4.5±0.6 and 2.6±0.7 μg/ml, respectively. Phyllaemblicin H1 showed moderate cytotoxicity against human cancer cell lines A-549 and SMMC-7721, with IC50 values of 4.7±0.7 and 9.9±1.3 μM, respectively., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Two novel 3D frameworks were synthesized, and further nanosized to form nanospheres. Studies revealed that is the first MOF-based luminescent sensor for detecting cyclohexane, and this is also the first time that quick regeneration, high sensitivity, high yield, and easy nanocrystallization of MOF-based luminescent sensors have been simultaneously realized.

Ethnopharmacological Relevance: Piper wallichii (Miq.) Hand.-Mazz. is a medicinal plant used widely for the treatment of rheumatoid arthritis, inflammatory diseases, cerebral infarction and angina in China. Previous study showed that lignans and neolignans from Piper spp. had potential inhibitory activities on platelet aggregation. In the present study, we investigated the chemical constituents of Piper wallichii and their antithrombotic activities, to support its traditional uses., Materials and Methods: The methanolic extract of the air-dried stems of Piper wallichii was separated and purified using various chromatographic methods, including semi-preparative HPLC. The chemical structures of the isolates were determined by detailed spectroscopic analysis, and acidic hydrolysis in case of the new glycoside 2. Determination of absolute configurations of the new compound 1 was facilitated by calculated electronic circular dichroism using time-dependent density-functional theory. All compounds were tested for their inhibitory effects on platelet aggregation induced by platelet activating factor (PAF) in rabbits׳ blood model, from which the active ones were further evaluated the in vivo antithrombotic activity in zebrafish model., Results: A new neolignan, piperwalliol A (1), and four new aromatic glycosides, piperwalliosides A-D (2-5) were isolated from the stems of Piper wallichii, along with 25 known compounds, including 13 lignans, six aromatic glycosides, two phenylpropyl aldehydes, and four biphenyls. Five known compounds (6-10) showed in vitro antiplatelet aggregation activities. Among them, (-)-syringaresinol (6) was the most active compound with an IC50 value of 0.52 mM. It is noted that in zebrafish model, the known lignan 6 showed good in vivo antithrombotic effect with a value of 37% at a concentration of 30 μM, compared with the positive control aspirin with the inhibitory value of 74% at a concentration of 125μM., Conclusion: This study demonstrated that lignans, phenylpropanoid and biphenyl found in Piper wallichii may be responsible for antithrombotic effect of the titled plant., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)

During the process exploring anti-viral compounds from Phyllanthus species, eight new highly oxygenated bisabolane sesquiterpenoid glycoside phyllaemblicins G1–G8 (1–8) were isolated from Phyllanthus emblica, along with three known compounds, phyllaemblicin F (9), phyllaemblic acid (10) and glochicoccin D (11). Phyllaemblicin G2 (2), bearing a tricyclo [3.1.1.1] oxygen bridge ring system, is an unusual sesquiterpenoid glycoside, while phyllaemblicins G6–G8 (6–8) are dimeric sesquiterpenoid glycosides with two norbisabolane units connecting through a disaccharide. All the structures were elucidated by the extensive analysis of HRMS and NMR data. The relative configuration of phyllaemblicin G2 was constructed based on heteronuclear coupling constants measurement, and the absolute configurations for all new compounds were established by calculated electronic circular dichroism (ECD) using time dependent density functional theory. The sesquiterpenoid glycoside dimers 6–9 displayed potential anti-hepatitis B virus (HBV) activities, especially for the new compound 6 with IC50 of 8.53 ± 0.97 and 5.68 ± 1.75 μM towards the HBV surface antigen (HBsAg) and HBV excreted antigen (HBeAg) secretion, respectively.

The energy landscape used by nature over evolutionary timescales to select protein sequences is essentially the same as the one that folds these sequences into functioning proteins, sometimes in microseconds. We show that genomic data, physical coarse-grained free energy functions, and family-specific information theoretic models can be combined to give consistent estimates of energy landscape characteristics of natural proteins. One such characteristic is the effective temperature T(sel) at which these foldable sequences have been selected in sequence space by evolution. T(sel) quantifies the importance of folded-state energetics and structural specificity for molecular evolution. Across all protein families studied, our estimates for T(sel) are well below the experimental folding temperatures, indicating that the energy landscapes of natural foldable proteins are strongly funneled toward the native state.

Pu-er ripe tea is a special microbial post-fermented tea made from Pu-er raw tea, a kind of green tea produced from the leaves of Camellia sinensis var. assamica. It is one of the most consumed teas in the past two decades in China, due to its special flavor, taste, and beneficial effects. This work aimed to obtain diverse catechin structures from Pu-er ripe tea, which led to the isolation of four new phenylpropanoid-substituted flavan-3-ols, puerins C-F (1-4), together with four known flavan-3-ols, (+)-catechin (5), (-)-epicatechin (6), (+/-)-gallocatechin (7), and (-)-epigallocatechin (8). Their structures were elucidated on the basis of detailed spectroscopic analysis, including 1D and 2D NMR, mass and CD spectra. Compounds 1-4, which could be formed in the post-fermentative process of Pu-er tea, were isolated for the first time from tea and Theaceae plant.

Abstract: Two new highly oxygenated limonoids, flexuosoids A (1) and B (2), and three new arylnaphthalene lignan glycosides, phyllanthusmins D-F (3-5), were isolated from the roots of Phyllanthus flexuosus, in addition to three known lignans, phyllanthusmin C, arabelline, and (+)-diasyringaresinol. Their structures were elucidated on the basis of detailed spectroscopic analysis and chemical methods. Compounds 1 and 2, two new decaoxygenated limonoids with a C-19/29 lactol bridge and heptaoxygenated substituents at C-1, C-2, C-3, C-7, C-11, C-17, and C-30, represent the second example of limonoids in the Euphorbiaceae family. Most of the isolates were tested for their antifeedant, anti-herpes simplex virus 1, and cytotoxic activities. The new limonoids 1 and 2 showed promising antifeedant activity against the beet army worm (Spodoptera exigua) with EC50 values of 25.1 and 17.3 μg/cm(2), respectively. In addition, both of them displayed moderate cytotoxicity against the ECA109 human esophagus cancer cell line, along with the known lignan glycoside, phyllanthusmin C, with the IC50 values of 11.5 (1), 8.5 (2), and 7.8 (phyllanthusmin C) μM, respectively., Graphical Abstract: Two new highly oxygenated limonoids, flexuosoids A (1) and B (2), and three new arylnaphthalene lignan glycosides, phyllanthusmins D-F (3-5), were isolated from the roots of Phyllanthus flexuosus, along with three known lignans. Flexuosoids A (1) and B (2) showed promising antifeedant activity against the beet army worm (Spodoptera exigua) with EC50 values of 25.1 and 17.3 μg/cm(2), respectively. In addition, both of them and the known lignan glycoside, phyllanthusmin C, displayed moderate cytotoxicity against the ECA109 human esophagus cancer cell line, with the IC50 values of 11.5, 8.5, and 7.8 μM, respectively.

Nineteen new highly oxygenated norbisabolane sesquiterpenoids, phyllanthacidoid acid methyl ester (1), and C-T (4-21), were isolated from Phyllanthus acidus Skeels, together with two known ones, phyllanthusols A (2) and B (3), whose sugar moiety was revised as glucosamine-N-acetate, rather than the previously assigned mannosamine-N-acetate. Compounds 2 and 3 were renamed respectively as phyllanthacidoids A (2) and B (3) to avoid confusion. All of the isolates except for 1 are glycosides, whose saccharide moieties possess a pentaoxy cyclohexane (scyllo quercitol) connecting with glucosamine-N-acetate or glucosyl moieties, which are first examples in natural products. Phyllanthacidoids N-R (15-19) with 8R configurations and/or 5,8-diketal skeleton, are unprecedented structures among norbisabolane sesquiterpenoids. Phyllanthacidoids S (20) and T (21) have the unusual tricyclo [3.1.1.1] oxygen bridge skeleton formed by a diketal system, of which the relative configurations of the aliphatic chain were assigned on the basis of heteronuclear coupling constants. The absolute configurations of compounds (1-21) were established by means of calculated electronic circular dichroism (ECD) and coupling constants. Compounds 1-5, 7-9, 10, and 14 displayed potential anti-hepatitis B virus (HBV) activities, with IC50 values of 0.8-36 μM against HBV surface antigen (HBsAg) and HBV excreted antigen (HBeAg), and the results indicated that the 5-ketal group and sugar moieties had contributions to the selectivity of HBsAg and HBeAg.

A challenge in molecular biology is to distinguish the key subset of residues that allow two-component signaling (TCS) proteins to recognize their correct signaling partner such that they can transiently bind and transfer signal, i.e., phosphoryl group. Detailed knowledge of this information would allow one to search sequence space for mutations that can be used to systematically tune the signal transmission between TCS partners as well as potentially encode a TCS protein to preferentially transfer signals to a nonpartner. Motivated by the notion that this detailed information is found in sequence data, we explore the sequence coevolution between signaling partners to better understand how mutations can positively or negatively alter their ability to transfer signal. Using direct coupling analysis for determining evolutionarily conserved protein-protein interactions, we apply a metric called the direct information score to quantify mutational changes in the interaction between TCS proteins and demonstrate that it accurately correlates with experimental mutagenesis studies probing the mutational change in measured in vitro phosphotransfer. Furthermore, by subtracting from our metric an appropriate null model corresponding to generic, conserved features in TCS signaling pairs, we can isolate the determinants that give rise to interaction specificity and recognition, which are variable among different TCS partners. Our methodology forms a potential framework for the rational design of TCS systems by allowing one to quickly search sequence space for mutations or even entirely new sequences that can increase or decrease our metric, as a proxy for increasing or decreasing phosphotransfer ability between TCS proteins.

Through hydrothermal reactions with corresponding lanthanide nitrates and 4-(4-carboxyphenylsulfonyloxy)-3-metnoxybenzoic acid (H2vspc), seven novel three-dimensional (3D) lanthanide-organic frameworks ([Ln(vspc)(Hvspc)(H2O)]n [Ln = Pr (1), Eu (2), Gd (3), Tb (4), Dy (5), Ho (6) and Er (7)]) have been synthesized and structurally characterized. All of them are isostructural and crystallize in the monoclinic crystal system, P21/c space group. Their structures feature a (3,6)-connected topological network, in which Ln(3+) were connected by carboxylate groups to give a 1D lanthanide chain, and the adjacent chains are further spanned by vspc(2-) and Hvspc(-) anions to form a 3D framework. The luminescent properties and lifetimes of 2 (Eu(III)), 4 (Tb(III)), and 5 (Dy(III)) have been studied, and the corresponding luminescent lifetimes are 0.53, 0.99 and 0.014 ms, respectively. The magnetic investigations reveal that compound displays weak antiferromagnet interaction, 4 and 5 exhibit ferromagnetic coupling, and compound 5 exhibits slow magnetic relaxation behavior.