Combined monte carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers

We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature.     

Prefused lysosomes cluster on autophagosomes regulated by VAMP8

Lysosome–autophagosome fusion is critical to autophagosome maturation. Although several proteins that regulate this fusion process have been identified, the prefusion architecture and its regulation remain unclear. Herein, we show that upon stimulation, multiple lysosomes form clusters around individual autophagosomes, setting the stage for membrane fusion. The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein on lysosomes—vesicle-associated membrane protein 8 (VAMP8)—plays an important role in forming this prefusion state of lysosomal clusters. To study the potential role of phosphorylation on spontaneous fusion, we investigated the effect of phosphorylation of C-terminal residues of VAMP8. Using a phosphorylation mimic, we observed a decrease of fusion in an ensemble lipid mixing assay and an increase of unfused lysosomes associated with autophagosomes. These results suggest that phosphorylation not only reduces spontaneous fusion for minimizing autophagic flux under normal conditions, but also preassembles multiple lysosomes to increase the fusion probability for resuming autophagy upon stimulation. VAMP8 phosphorylation may thus play an important role in chemotherapy drug resistance by influencing autophagosome maturation.Subject terms: Cancer therapeutic resistance, Membrane fusion     

Calcium imaging in Arabidopsis pollen cells using G-CaMP5

Calcium(Ca~(2+)) signaling has been implicated in pollen germination and pollen tube growth. To date,however, we still know very little about how exactly Ca~(2+) signaling links to various physiological subcellular processes during pollen germination and pollen tube growth.Given that Ca~(2+) signaling is tightly related to the cytosolic concentration and dynamics of Ca~(2+), it is vital to trace the dynamic changes in Ca~(2+) levels in order to decode Ca~(2+) signaling. Here, we demonstrate that G-Ca MP5 serves well as an indicator for monitoring cytosolic Ca~(2+) dynamics in pollen cells. Using this probe, we show that cytosolic Ca~(2+) changes dramatically during pollen germination, and, asreported previously, Ca~(2+) forms a tip-focused gradient in the pollen tube and undergoes oscillation in the tip region during pollen tube growth. In particular, using G-CaMP5 allowed us to capture the dynamic changes in the cytosolic Ca~(2+) concentration([Ca~(2+)]_(cyt)) in pollen tubes in response to various exogenous treatments. Our data suggest that G-CaMP5 is a suitable probe for monitoring the dynamics of[Ca~(2+)]_(cyt) in pollen cells.     

PMicroRNA-124a regulates LPS-induced septic cardiac dysfunction by targeting STX2

Objective

To examine the role of miR-124a in LPS-induced septic cardiac insufficiency where underlying mechanism is unclear.

Results

Expression of miR-124a was decreased in myocardium of LPS-induced septic cardiac dysfunction model. miR-124a antagomiR or agomiR were injected via tail vein to induce miR-124a-dysregulated model. miR-124a antagomiR aggravated LPS-induced cardiac dysfunction and apoptosis, while miR-124a agomiR had the opposite effect. Syntaxin-2 (STX2) was indicated as a candidate target gene by bioinformatic software. Further experiments confirmed that STX2 was downregulated in miR-124a agomiR-treated rats but upregulated in miR-124a antagomiR-treated rats, and STX2 inhibition could strongly block the miR-124a antagomiR-associated increase in cell apoptosis. Luciferase reporter activity assay indicated that STX2 was a direct target of miR-124a. Serological detection reveled that miR-124a was down-regulated in the plasma of septic cardiac dysfunction rats.

Conclusions

miR-124a aggravates LPS-induced cardiac dysfunction and the miR-124a/STX2 pathway might serve as the potential diagnostic and therapeutic targets for septic cardiac dysfunction.

     

Enzymatic Process Enhances the Flavour Profile and Increases the Proportion of Esters in Citrus Essential Oils

Citrus essential oils (CEOs) are important flavors in the food and confectionary industries. A lipase process was proposed for enhancing the flavor profiles and increasing the proportions of esters in CEOs. The effects of the enzymatic process were explored by detecting the constituents of the CEOs of American sweet orange oil (ASO) and Brazil mandarin oil (BMO) through GC/MS and sensory evaluation by a trained panel, and positive effects were confirmed by both methods. A further eleven kinds of CEOs were treated via the lipase process and increments of 10 – 1170% were achieved in the proportions of esters, which were mostly ethyl esters. Enhancement in fruity odor, especially the top note, was demonstrated by all CEOs after enzymatic processing. All CEOs were tested for antimicrobial activities, and only ASO displayed fairly ideal antimicrobial activities. Meanwhile, modified ASO showed a certain increase in antimicrobial activities. This methodology might be considered a sustainable route for acquiring ‘natural’ essential oils with enhanced flavor profiles and simultaneously enhancing the comprehensive utilization of citrus fruits.     

秦岭辛家山林区锐齿栎外生菌根真菌多样性

以秦岭辛家山林区锐齿栎为研究对象,通过野外调查结合形态学和分子生物学方法,观察和鉴定与其共生的外生菌根真菌。结果确定了3种子囊菌和48种担子菌,分属于10科14属,其中毛革菌属Tomentella是优势类群,丝伞盖属1 Inocybe 1、Russula persicina、毛革菌属1 Tomentella 1、毛革菌属2 Tomentella 2、块菌属Tuber、绒盖牛肝菌属Xerocomus是常见种,其余都为稀有种。两样地锐齿栎外生菌根真菌除丰富度指数外,Simpson指数、Shannon指数以及Pielou均匀度指数差异不显著;Jaccard相似性指数和Sorenson相似性指数分别为0.1154和0.2069。     

秦岭典型林分土壤活性有机碳及碳储量垂直分布特征

采用野外调查结合室内分析的方法,2013年8月分析了秦岭典型林分锐齿栎(马头滩林区,Ⅰ)、油松(Ⅱ)、华山松(Ⅲ)、松栎混交林(Ⅳ)、云杉(Ⅴ)、锐齿栎(辛家山林区,Ⅵ)土壤剖面上活性有机碳及碳储量的分布规律.结果表明: 研究区各林分土壤的有机碳、微生物生物量碳、水溶性碳、易氧化态碳含量均随着土层深度的增加而不断减小;在整个土壤剖面(0～60 cm)上,云杉和松栎混交林的土壤有机碳和水溶性碳含量明显高于其余林分,不同林分的土壤有机碳和水溶性碳含量的平均值大小均为Ⅴ＞Ⅳ＞Ⅰ＞Ⅱ＞Ⅲ＞Ⅵ;各林分不同土层的微生物生物量碳在71.25～710.05 mg·kg^-1,不同林分的土壤微生物生物量碳大小依次为Ⅰ＞Ⅴ＞Ⅳ＞Ⅲ＞Ⅱ＞Ⅵ;整个土壤剖面上,松栎混交林的土壤易氧化态碳含量降幅最大,不同林分土壤易氧化态碳含量的平均值大小为Ⅳ＞Ⅴ＞Ⅰ＞Ⅱ＞Ⅲ＞Ⅵ.3种活性有机碳占有机碳的比例在不同林分类型中没有表现出一致的规律性.各林分0～60 cm土层的有机碳储量大小为Ⅴ＞Ⅰ＞Ⅳ＞Ⅲ＞Ⅵ＞Ⅱ.各林分的土壤微生物生物量碳、水溶性碳、易氧化态碳两两之间均表现为极显著相关,各林分的土壤微生物生物量碳、水溶性碳、易氧化态碳与土壤有机碳、全氮之间的相关性均表现为显著或极显著水平,与碳氮比、pH、土壤水分、土壤容重的相关关系不显著.     

Expression of a cytotoxic cationic antibacterial peptide in Escherichia coli using two fusion partners

It has been reported that it is difficult to express cationic antibacterial peptides in engineered bacteria because such peptides are highly toxic to the host bacteria cells and sensitive to intracellular proteases. Antibacterial peptide CM4 (ABP-CM4) is a small cationic peptide with broad-spectrum activities against bacteria, fungi and tumor cells, which may possibly be used as an antimicrobial agent. Here we tried to express ABP-CM4 in Escherichia coli cells using either the GST fusion system or the intein-mediated fusion expression system. In order to investigate the possible use of these two fusion partners in cationic small peptide expression and purification, a mutant ABP-CMt, which is a highly positively charged peptide with +9 charges at neutral pH, was designed. In the present study, we have shown that both ABP-CM4 and ABP-CMt peptides can be expressed and purified by the intein-mediated expression system but not by the GST fusion expression system. Thus the intein-mediated peptide expression and purification system potentially could be employed for the production of recombinant protease-sensitive and cytotoxic peptides.     

Preparation and characterization of two novel three-dimensional supramolecular networks with blue photoluminescence

Two novel photoluminescent coordination polymers of formula [Cd(atpt)(H₂O)₂] · 2H₂O (1) and [Zn(atpt)(H₂O)₂] (2) (H₂atpt = 2-aminoterephthalic acid), in which the amino group of the atpt ligand coordinates to the metal(II) ions for the first time, have been synthesized through the self-assemblies of H₂atpt and N-containing ligands [nicotiamide for 1 and imidazole for 2, respectively] with the metal(II) ions in the presence of NaOH. These complexes were characterized by FT-IR spectroscopy, thermogravimetric analysis (TG), elemental analysis and X-ray analysis. X-ray crystallographic studies of the complexes reveal that complex 1 is a double stranded one-dimensional chain, which further assembles into a three-dimensional supramolecular network via the interchain π-π stacking interaction and strong hydrogen bonds, while complex 2 exhibits a two-dimensional porous architecture. The extensively strong hydrogen bonds in complex 2 lead to the formation of three-dimensional supramolecular framework. Photoluminescence properties of the compounds 1 and 2 have been examined in solid state at room temperature. These compounds have been found to exhibit blue photoluminescence and may be good candidates for photoactive materials.