Dynamic changes in carbohydrate metabolism and endogenous hormones during <Emphasis Type="Italic">Tulipa edulis</Emphasis> stolon development into a new bulb

The stolon is the main asexual reproductive organ of Tulipa edulis (Miq.) Baker. It has a special morphology and can develop into a new bulb for propagation. In the current greenhouse experiment, the dynamic changes in carbohydrates and related enzymes, protein and endogenous hormones during T. edulis stolon development were investigated. The results showed that soluble sugar levels were basically declining, whereas starch and protein content rose continuously during stolon development. The adenosine diphosphoglucose pyrophosphorylase (AGPase) activity peaked in the initial swelling stage and stayed a relative high level in the middle swelling stage; sucrose synthase (SS), soluble starch synthase (SSS) and granule-bound starch synthase (GBSS) activities followed the same law that showed rising trends during stolon development. SS activity was significantly inversely related to sucrose content but had significantly positive relations with starch content, SSS and GBSS activities. Gibberellin (GA), indole-3-acetic acid (IAA) and zeatin riboside (ZR) peaked in the initial swelling stage and maintained high levels in the middle swelling stage; they then decreased significantly in the later swelling stage. A substantial increase was observed in abscisic acid (ABA) content until the middle swelling stage, followed by a significant reduction in the later swelling stage. The ratios of ABA to IAA, GA and ZR reached their lowest levels in the initial swelling stage. In conclusion, T. edulis stolon development is a process of new bulb morphogenesis along with the starch accumulation catalyzed by AGPase, SSS and GBSS, using the product of sucrose cleavage caused by SS. Initial low ABA content and low ratios of ABA to IAA, GA and ZR, together with the GA, IAA and ZR of high-content, soluble sugars worked more efficiently to induce new bulb formation.     

Identification of β-glucosidase 1 as a biomarker and its high expression in hepatocellular carcinoma is associated with resistance to chemotherapy drugs

Context and objective: Long-term prognosis of hepatocellular carcinoma (HCC) patients is challenging, and novel biomarkers are needed to predict patient risk and serve as potential therapeutic target.

Results: We found β-glucosidase 1 is significantly overexpressed and activated in primary HCC tissue and multiple HCC cell lines. β-Glucosidase 1 expression is associated with predicting prognosis of HCC patients under chemotherapy. Silencing β-glucosidase 1 inhibits growth and survival of HCC cells, with preferential inhibitory effects on high β-glucosidase 1-expressing cells. Combination of chemo drug with β-glucosidase 1 inhibitor sensitized HCC cells to chemotherapy.

Conclusion: Our data support β-glucosidase 1 as a HCC biomarker due to its prognosis significance.     

Genetic analysis and fine mapping of <Emphasis Type="Italic">Watermelon mosaic virus</Emphasis> resistance gene in cucumber

Watermelon mosaic virus (WMV) is an important disease of cucumber (Cucumis sativus L.) that is difficult to control in the field. Some resistant lines are available, and understanding the inheritance of the disease and mapping the gene or genes that confer resistance will facilitate the development of further resistant varieties. In this study, the inheritance and gene mapping for resistance to WMV in cucumber were conducted using populations derived from the cross between susceptible ‘65G’ and resistant ‘02245’ inbred lines. Genetic analysis showed that resistance to WMV in ‘02245’ is controlled by a single recessive gene designated as wmv ⁰²²⁴⁵ mapped to chromosome 6 (Chr.6). The region was flanked by the molecular markers SSRWMV60-23 and CAPS-W1 with genetic distances of 0.34 and 1.19 cM from the wmv ⁰²²⁴⁵ locus, respectively. The 134.7 kb physical distance of this region includes 21 candidate genes. Comparison of the genotypic and phenotypic results showed that the accuracy rate of the most closely linked marker SSRWMV60-23 was 94.0 %. This marker will be used for molecular marker-assisted selection to select resistant lines, and future research will be directed at identifying and cloning the resistance gene.     

General trends of dihedral conformational transitions in a globular protein

Dihedral conformational transitions are analyzed systematically in a model globular protein, cytochrome P450cam, to examine their structural and chemical dependences through combined conventional molecular dynamics (cMD), accelerated molecular dynamics (aMD) and adaptive biasing force (ABF) simulations. The aMD simulations are performed at two acceleration levels, using dihedral and dual boost, respectively. In comparison with cMD, aMD samples protein dihedral transitions approximately two times faster on average using dihedral boost, and ～3.5 times faster using dual boost. In the protein backbone, significantly higher dihedral transition rates are observed in the bend, coil, and turn flexible regions, followed by the β bridge and β sheet, and then the helices. Moreover, protein side chains of greater length exhibit higher transition rates on average in the aMD‐enhanced sampling. Side chains of the same length (particularly N_χ = 2) exhibit decreasing transition rates with residues when going from hydrophobic to polar, then charged and aromatic chemical types. The reduction of dihedral transition rates is found to be correlated with increasing energy barriers as identified through ABF free energy calculations. These general trends of dihedral conformational transitions provide important insights into the hierarchical dynamics and complex free energy landscapes of functional proteins. Proteins 2016; 84:501–514. © 2016 Wiley Periodicals, Inc.     

Unconstrained enhanced sampling for free energy calculations of biomolecules: a review

Abstract

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.     

Revised Absolute Configuration of Sibiricumin A: Substituent Effects in Simplified Model Structures Used for Quantum Mechanical Predictions of Chiroptical Properties

This study discusses the choice of different simplified models used in computations of electronic circular dichroism (ECD) spectra and other chiroptical characteristics used to determine the absolute configuration (AC) of the complex natural product sibiricumin A. Sections of molecules containing one chiral center with one near an aromatic group have large effects on the ECD spectra. Conversely, when the phenyl group is present on a substituent without a nonstereogenic center, removal of this section will have little effect on ECD spectra. However, these nonstereogenic‐center‐containing sections have large effects on calculated optical rotations (OR) values since the OR value is more sensitive to the geometries of sections in a molecule. In this study, the wrong AC of sibiricumin A was reassigned as (7R,8S,1'R,7'R,8'S)‐ 11 . Chirality 28:612–617, 2016. © 2016 Wiley Periodicals, Inc.     

The genetic diversity of SMLS (Sitobion miscanthi L type symbiont) and its effect on the fitness,mitochondrial DNA diversity and Buchnera aphidicola dynamic of wheat aphid,Sitobion miscanthi (Hemiptera: Aphididae)

SMLS (Sitobion miscanthi L type symbiont) is a recently discovered aphid secondary symbiont. Using evidence extracted from 16S rRNA sequences, previous studies indicate that SMLS is the most widely distributed and most recently transferred secondary symbiont in Chinese Sitobion miscanthi populations. Here, we further investigated genetic diversity among SMLS geographic strains with multiloci data. Furthermore, the influence of SMLS on S. miscanthi was uncovered with ecological and evolutionary evidence. The results indicated that there was limited influence of infection with SMLS on variation and evolutionary patterns of S. miscanthi mitochondrial DNA. By hemolymph injection, the SMLS‐infected and SMLS‐uninfected S. miscanthi clones with the identical genetic background were built in this study. Although similar Buchnera aphidicola dynamics were observed between SMLS‐infected and SMLS‐uninfected S. miscanthi population, B. aphidicola density of SMLS‐infected S. miscanthi population was always significantly higher than SMLS‐uninfected ones. The results of fitness measurements indicated that under laboratory rearing conditions, transfection of SMLS could confer modest advantages to some fitness components of S. miscanthi, that is, total number of offspring, longevity, age of first reproduction and weight of adult. However, as SMLS is not strictly associated with S. miscanthi, further investigations are needed to uncover the mechanisms responsible for this inconceivable association.