Proteomic analysis of the defense response to Magnaporthe oryzae in rice harboring the blast resistance gene Piz-t

BACKGROUND

Rice blast (caused by Magnaporthe oryzae) is one of the most destructive diseases of rice. While many blast resistance (R) genes have been identified and deployed in rice cultivars, little is known about the R gene-mediated defense mechanism. We used a rice transgenic line harboring the resistance gene Piz-t to investigate the R gene-mediated resistance response to infection.

RESULTS

We conducted comparative proteome profiling of the Piz-t transgenic Nipponbare line (NPB-Piz-t) and wild-type Nipponbare (NPB) inoculated with M. oryzae at 24, 48, 72 h post-inoculation (hpi) using isobaric tags for relative and absolute quantification (iTRAQ) analysis. Comparative analysis of the response of NPB-Piz-t to the avirulent isolate KJ201 and the virulent isolate RB22 identified 114 differentially expressed proteins (DEPs) between KJ201-inoculated NPB-Piz-t (KJ201-Piz-t) and mock-treated NPB-Piz-t (Mock-Piz-t), and 118 DEPs between RB22-inoculated NPB-Piz-t (RB22-Piz-t) and Mock-Piz-t. Among the DEPs, 56 occurred commonly in comparisons KJ201-Piz-t/Mock-Piz-t and RB22-Piz-t/Mock-Piz-t. In a comparison of the responses of NPB and NPB-Piz-t to isolate KJ201, 93 DEPs between KJ201-Piz-t and KJ201-NPB were identified. DEPs in comparisons KJ201-Piz-t/Mock-Piz-t, RB22-Piz-t/Mock-Piz-t and KJ201-Piz-t/KJ201-NPB contained a number of proteins that may be involved in rice response to pathogens, including pathogenesis-related (PR) proteins, hormonal regulation-related proteins, defense and stress response-related proteins, receptor-like kinase, and cytochrome P450. Comparative analysis further identified 7 common DEPs between the comparisons KJ201-Piz-t/KJ201-NPB and KJ201-Piz-t/RB22-Piz-t, including alcohol dehydrogenase I, receptor-like protein kinase, endochitinase, similar to rubisco large subunit, NADP-dependent malic enzyme, and two hypothetical proteins.

CONCLUSIONS

Our results provide a valuable resource for discovery of complex protein networks involved in the resistance response of rice to blast fungus.

The importance of mechanical constraints for proper polarization and psuedo-cleavage furrow generation in the early Caenorhabditis elegans embryo

Intracellular polarization, where a cell specifies a spatial axis by segregation of specific factors, is a fundamental biological process. In the early embryo of the nematode worm Caenorhabditis elegans (C. elegans), polarization is often accompanied by deformations of the cortex, a highly contractile structure consisting of actin filaments cross-linked by the motor protein myosin (actomyosin). It has been suggested that the eggshell surrounding the early embryo plays a role in polarization although its function is not understood. Here we develop a mathematical model which couples a reaction-diffusion model of actomyosin dynamics with a phase field model of the cell cortex to implicitly track cell shape changes in the early C. elegans embryo. We investigate the potential rigidity effect of the geometric constraint imposed by the presence and size of the eggshell on polarization dynamics. Our model suggests that the geometric constraint of the eggshell is essential for proper polarization and the size of the eggshell also affects the dynamics of polarization. Therefore, we conclude that geometric constraint on a cell might affect the dynamics of a biochemical process.

Polarization, whereby molecules and proteins are asymmetrically distributed throughout the cell, is a vital process for many cellular functions. In the early C. elegans embryo the asymmetric distribution of cell cytoskeleton during the initiation of polarization leads to asymmetric contractions which are higher in the anterior and lower in the posterior of a cell. The C. elegans embryo is surrounded by a rigid body, the eggshell, which functions in numerous cell processes. We investigate the structural support of eggshell during the establishment phase by tracking the moving cell surface. We incorporate protein dynamics involved in polarization into the membrane evolution. We conclude that eggshell might have a role in cell polarization by preventing the distortion of cell surface.

[Strategy in management of adjacent organ lesion during laparoscopic pancreaticoduodenectomy]

Objective: To evaluate the safety and feasible of adjacent organ resection during laparoscopic pancreaticoduodenectomy(LPD), and summary the surgical strategies. Methods: Clinical data of 15 adjacent organ resections combined with LPD from March 2013 to September 2017 were reviewed.There were 10 male and 5 female patients aging from 20 to 86 years, and the body mass index ranged from 19.6 to 34.5 kg/m(2).Two patients had previous abdominal surgical history.Two patients underwent preoperative chemotherapy. Results: The resected adjacent organs included liver(n=4), stomach(n=3), colon(n=6), right kidney with embolectomy and vasoplastic of inferior vena cava(n=1), and spleen artery aneurysms(n=1). The operative time ranged from 280 to 450 minutes, and the blood loss ranged from 100 to 450 ml.The total complication rate was 5/15 and no one died in 90 days after surgery.The postoperative hospital stay ranged from 10 to 42 days with medium 18 days.The pathology included adenocarcinoma of stomach and duodenum(n=1), gastric cancer invading pancreas or duodenum(n=2), ampullary adenocarcinoma with left hepatolithiasis(n=1), ampullary adenocarcinoma with a benign lesion in left liver(n=1), ampullary adenocarcinoma with single liver metastasis(n=1), ampullary adenocarcinoma(n=1), pancreatic intraductal papillary mucinous neoplasm with splenic artery aneurysms(n=1), pancreatic neuroendocrine neoplasm with colon cancer(n=1), distal common bile duct adenocarcinoma involving righ hepatic duct(n=1), pancreatic neuroendocrine neoplasm invading inferior vena cava and right renal vein(n=1), duodenal adnocarcinoma(n=1), duodenal ewing's sarcoma(n=1), duodenal intesititialoma(n=2). The follow-up was from 3 to 40 months with the medium survival of 17.5 months. Conclusions: The oncological outcomes of PD combined with adjacent organ resection is acceptable.Surgical treatment for those patients with periampullary neoplasma and adjacent organ lesions should be aggressive.

Dehiscence method: a seed-saving, quick and simple viability assessment in rice

BACKGROUND

Seed viability monitoring is very important in ex situ germplasm preservation to detect germplasm deterioration. This requires seed-, time- and labor- saving methods with high precision to assess seed germination as viability. Although the current non-invasive, rapid, sensing methods (NRSs) are time- and labor-saving, they lack the precision and simplicity which are the virtues of traditional germination. Moreover, they consume a considerable amount of seeds to adjust sensed signals to germination percentage, which disregards the seed-saving objective. This becomes particularly severe for rare or endangered species whose seeds are already scarce. Here we propose a new method that is precise, low-invasive, simple, and quick, which involves analyzing the pattern of dehiscence (seed coat rupture), followed by embryonic protrusion.

RESULTS

Dehiscence proved simple to identify. After the trial of 20 treatments from 3 rice varieties, we recognized that dehiscence percentage at the 48th hour of germination (D(48)) correlates significantly with germination rate for tested seed lots. In addition, we found that the final germination percentage corresponded to D(48) plus 5. More than 70% of the seeds survived post-dehiscence desiccation for storage. Hydrogen peroxide (1 mM) as the solution for imbibition could further improve the survival. The method also worked quicker than tetrazolium which is honored as a fast, traditional method, in detecting less vigorous but viable seeds.

CONCLUSION

We demonstrated the comprehensive virtues of dehiscence method in assessing rice seed: it is more precise and easier to use than NRSs and is faster and more seed-saving than traditional methods. We anticipate modifications including artificial intelligence to extend our method to increasingly diverse circumstances and species.

CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE

This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization.

[Laparoscopic pancreaticoduodenectomy: a report of 233 cases by a single team]

Objective: To summary the experience of 233 cases of laparoscopic pancreaticoduodenectomy (LPD) performed by a single surgical team. Methods: Data of patients undergoing LPD from September 2012 to October 2016 were reviewed. There were 145 males and 88 females with the mean age of(60.3±13.0)years old, ranging from 19 to 92 years old, and the mean body mass index of (22.8±3.5)kg/m(2,) ranging from 16.3 to 36.8 kg/m(2). There were 195 patients with clinical manifestation and 54 patients who had the history of abdominal surgery. Results: LPD were performed on 233 patients by same surgical team consecutively. The mean operative time was(368.0±57.4)minutes. Mean blood loss was(203.8±138.6)ml. The postoperative morbidity rate was 33.5%, with 6.9% of grade B or C pancreatic fistula and 9.9% of bleeding. The reoperation rate was 5.6%. The mortality during 30 days after operation was 0.9%. Mean postoperative hospital stay was (18.1±11.2)days. Mean tumor size was (3.9±2.4)cm, and the mean number of lymph nodes harvested was 21.3±11.9.One hundred and sixty-three patients were diagnosed as malignant tumor, including pancreatic adenocarcinoma(n=84), cholangiocarcinoma(n=17), ampullary adenocarcinoma(n=55), duodenal adenocarcinoma(n=5), gastric cancer(n=1)and duel cancer (n=1) located in distal stomach and duodenum. Conclusion: The key point to make laparoscopic pancreaticduodenectomy a routine safe procedure is to operate the procedure under skilled hands in selected patients via suitable surgical approaches.

Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi2 and Pi9 have not been widely deployed in Chinese indica rice cultivars

BACKGROUND

The most sustainable approach to control rice blast disease is to develop durably resistant cultivars. In molecular breeding for rice blast resistance, markers developed based on polymorphisms between functional and non-functional alleles of resistance genes, can provide precise and accurate selection of resistant genotypes without the need for difficult, laborious and time-consuming phenotyping. The Pi2 and Pi9 genes confer broad-spectrum resistance against diverse blast isolates. Development of allele-specific markers for Pi2 and Pi9 would facilitate breeding of blast resistant rice by using the two blast resistance genes.

RESULT

In this work, we developed two new markers, named Pi9-Pro and Pi2-LRR respectively, targeting the unique polymorphisms of the resistant and susceptible alleles of Pi2 and of Pi9. The InDel marker Pi9-Pro differentiates three different genotypes corresponding to the Pi2/Piz-t, Pi9 and non-Pi2/Piz-t/Pi9 alleles, and the CAPS marker Pi2-LRR differentiates the Pi2 allele from the non-Pi2 allele. Based on the two newly developed markers and two available markers Pi2SNP and Pi9SNP, the presence of Pi2 and Pi9 was assessed in a set of 434 rice accessions consisting of 377 Chinese indica cultivars/breeding materials and 57 Chinese japonica cultivars/breeding materials. Of the 434 accessions tested, while one indica restorer line Huazhan was identified harboring the Pi2 resistance allele, no other rice line was identified harboring the Pi2 or Pi9 resistance alleles.

CONCLUSIONS

Allele-specific marker-based assessment revealed that Pi2 and Pi9 have not been widely incorporated into diverse Chinese indica rice cultivars. Thus, the two blast resistance genes can be new gene sources for developing blast resistant rice, especially indica rice, in China. The two newly developed markers should be highly useful for using Pi2 and Pi9 in marker-assisted selection (MAS) breeding programs.

[Estradiol stimulates the growth and biofilm formation of clinical Staphylococcus epidermidis]

Objective: To investigate the effect of steroid hormones on the growth and biofilm formation of S. epidermidis. Methods: In all experiments, two S. epidermidis standard strains (ATCC12228 and ATCC35984) and two S. epidermidis clinical strains (SE101 and SE40) were incubated on the surface of silica gel in estradiol concentrations of 0, 50, 125, 250 and 500 pmol/L at 4, 6, 12, 24, 48 and 72 hours. Growth curve were drawn by means of the OD value. Formed biofilms were assessed by crystal violet staining methods. In order to observe the processes and structures of biofilm, the confocal laser scanning microscopy (CLSM) and scanning electron microscope (SEM) were used. Results: All of the four strains which were incubated with the concentrations of 125 pmol/L of estradiol had entered the logarithmic growth stage ahead of the blank control (3 h and 4 h). Crystal violet staining indicated that there was no biofilm for ATCC12228. Improved primary attachment abilities were found for ATCC35984 and SE101 in the presence of estradiol, and the OD values were 0 pmol/L (0.081±0.015 and 0.082±0.011), 50 pmol /L (0.087±0.013 and 0.088±0.010), 125 pmol/L (0.175±0.052 and 0.091±0.012), 250 pmol/L (0.153±0.036 and 0.090±0.006), 500 pmol/L (0.157±0.050 and 0.082±0.032), respectively. The thickness of biofilm reached the peak in 125 pmol/L estradiol at 24 h. CLSM and SEM found estradiol promoted the biofilm maturity and the biofilm of 125 pmol/L group was denser and thicker than that of the other concentration groups. Conclusions: Our in vitro experiments indicate that estradiol could promote the growth of S. epidermidis which exit on the surface of silica gel, and improve the ability of biofilm formation of S. epidermidis.

Dwarf and deformed flower 1, encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativa L.)

Recent studies have shown that F-box proteins constitute a large family in eukaryotes, and play pivotal roles in regulating various developmental processes in plants. However, their functions in monocots are still obscure. In this study, we characterized a recessive mutant dwarf and deformed flower 1-1 (ddf1-1) in Oryza sativa (rice). The mutant is abnormal in both vegetative and reproductive development, with significant size reduction in all organs except the spikelet. DDF1 controls organ size by regulating both cell division and cell expansion. In the ddf1-1 spikelet, the specification of floral organs in whorls 2 and 3 is altered, with most lodicules and stamens being transformed into glume-like organs and pistil-like organs, respectively, but the specification of lemma/palea and pistil in whorls 1 and 4 is not affected. DDF1 encodes an F-box protein anchored in the nucleolus, and is expressed in almost all vegetative and reproductive tissues. Consistent with the mutant floral phenotype, DDF1 positively regulates B-class genes OsMADS4 and OsMADS16, and negatively regulates pistil specification gene DL. In addition, DDF1 also negatively regulates the Arabidopsis LFY ortholog APO2, implying a functional connection between DDF1 and APO2. Collectively, these results revealed that DDF1, as a newly identified F-box gene, is a crucial genetic factor with pleiotropic functions for both vegetative growth and floral organ specification in rice. These findings provide additional insights into the molecular mechanism controlling monocot vegetative and reproductive development.

Characterization of yellow grouper Epinephelus awoara (Serranidae) karyotype by chromosome bandings and fluorescence in situ hybridization

The cytogenetics of yellow grouper Epinephelus awoara was studied using multiple cytogenetic markers [Giemsa staining, C-banding, Ag-NORs and fluorescence in situ hybridization (FISH)]. Giemsa staining results showed that the karyotypic formula of E. awoara was 2n = 48a, FN (fundamental number) = 48. Faint C-bandings were only detected at the centromeric regions of chromosome pair number 24, being almost indiscernible on the other chromosome pairs. After Ag-NOR staining, one pair of nucleolar organizer regions (NOR) was observed in the subcentromeric region of pair number 24. FISH results showed that 5S rDNA was located at a pair of medium-sized chromosomes, while 18S rDNA appeared at the same location in the subcentromeric region of pair number 24 where Ag-NORs were detected. The telomeric sequence (TTAGGG)(n) detected by FISH was located at both ends of each chromosome. The results suggested that E. awoara has retained general karyotypic structure stability during the evolutionary diversification process.

A rare Y chromosome constitutional rearrangement: a partial AZFb deletion and duplication within chromosome Yp in an infertile man with severe oligoasthenoteratozoospermia

We report a case of an infertile man with severe oligoasthenoteratozoospermia with a partial azoospermia factor b (AZFb) deletion and duplication region within chromosome Yp11.2. The hormonal profile was normal for serum concentrations of follicle-stimulating hormone, luteinizing hormone, testosterone and oestradiol. The patient, who showed a 46,XY karyotype, had an approximate 2.4 Mb inherited duplication region in Yp11.2 and a de novo partial AZFb deletion, which spanned 5.25 Mb including eight protein coding genes and four non-coding transcripts, but did not remove the RBMY gene family. Both proximal and distal breakpoints of the deletion were outside any palindromic region or inverted repeat sequence and intra-chromosomal non-allelic homologous recombination could not have been the deletion mechanism. The partial AZFb deletion in our case diminished sperm production, but did not completely extinguish spermatogenesis. Considering severe oligozoospermia, spermatozoa in the patient's ejaculate were used for intracytoplasmic sperm injection, resulting in two twin pregnancies.

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: size effects on ionic distributions and diffusion-reaction rates

The effects of finite particle size on electrostatics, density profiles, and diffusion have been a long existing topic in the study of ionic solution. The previous size-modified Poisson-Boltzmann and Poisson-Nernst-Planck models are revisited in this article. In contrast to many previous works that can only treat particle species with a single uniform size or two sizes, we generalize the Borukhov model to obtain a size-modified Poisson-Nernst-Planck (SMPNP) model that is able to treat nonuniform particle sizes. The numerical tractability of the model is demonstrated as well. The main contributions of this study are as follows. 1), We show that an (arbitrarily) size-modified PB model is indeed implied by the SMPNP equations under certain boundary/interface conditions, and can be reproduced through numerical solutions of the SMPNP. 2), The size effects in the SMPNP effectively reduce the densities of highly concentrated counterions around the biomolecule. 3), The SMPNP is applied to the diffusion-reaction process for the first time, to our knowledge. In the case of low substrate density near the enzyme reactive site, it is observed that the rate coefficients predicted by SMPNP model are considerably larger than those by the PNP model, suggesting both ions and substrates are subject to finite size effects. 4), An accurate finite element method and a convergent Gummel iteration are developed for the numerical solution of the completely coupled nonlinear system of SMPNP equations.

Genetic analysis and mapping of gene fzp(t) controlling spikelet differentiation in rice

A mutant of spikelet differentiation in rice called frizzle panicle (fzp) was discovered in the progeny of a cross between Oryza sativa ssp. indica cv. V20B and cv. Hua1B. The mutant exhibits normal plant morphology but has apparently fewer tillers. The most striking change in fzp is that its spikelet differentiation is completely blocked, with unlimited subsequent rachis branches generated from the positions where spikelets normally develop in wild-type plants. Genetic analysis suggests that fzp is controlled by a single recessive gene, which is temporarily named fzp(t). Based on its mutant phenotype, fzp(t) represents a key gene controlling spikelet differentiation. Some F(2) mutant plants derived from various genetic background appeared as the "middle type", suggesting that the action of fzp(t) is influenced by the presence of redundant, modifier or interactive genes. By using simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) method, fzp(t) gene was mapped in the terminal region of the long arm of chromosome 7, with RM172 and RM248 on one side, 3.2 cM and 6.4 cM from fzp(t), and RM18 and RM234 on the other side, 23.1 cM and 26.3 cM from fzp(t), respectively. These results will facilitate the positional cloning and function studies of the gene.

Effect of daidzein on egg-laying performance in Shaoxing duck breeders during different stages of the egg production cycle

The effect of a phyto-oestrogen, daidzein, on the laying performance of Shaoxing female ducks was examined in three experiments performed at different stages of the egg production cycle. Egg-laying rate, egg weight, egg composition, feed conversion ratio, hatchability characteristics of eggs and body weight, ovary and oviduct weight, as well as changes in serum concentrations of T3, T4 and E2 were recorded as response criteria. In the first experiment, 68 young ducks, 100 d of age, were given a basal diet (maize-soybean meal) with or without 3 mg of daidzein/kg diet for 42 d. Daidzein did not affect the onset of lay but apparently decreased egg-laying rate and mean egg weight as well as the feed conversion ratio. In the second experiment, 240 breeding ducks, 402 d of age, were allotted at random to three groups and given the basal diet containing daidzein at 0 (control), 3 (Da1) and 5mg/kg (Da2) for 35d. Egg-laying rate, mean egg weight and feed conversion ratio increased in both Da1 and Da2 groups. However, an adverse effect of daidzein on fertility and hatchability was observed. In the third experiment, 320 breeding ducks, 415 d of age, were fed on the basal diet with or without 5mg of daidzein/kg diet for 63 d. Egg-laying rate increased by 7.7%, average egg weight tended to increase, whereas yolk/albumen ratio decreased. Daidzein-treated ducks had higher body weight and oviduct weight compared with their controls. Elevated plasma T4 and E2 concentrations accompanied these phenotypic changes, but serum T3 was not affected. It is suggested that daidzein exerts divergent effects on the egg-laying performance of Shaoxing ducks under different physiological conditions and this action is dose-dependent. The changes in circulating E2 imply possible participation of endogenous oestrogen in the mechanism of daidzein action.

Continuum electromechanical modeling of protein-membrane interactions

A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the electrostatic solvation energy of the system, and equilibrium membrane deformation is obtained by minimizing the electroelastic energy functional with respect to the dielectric interface. The model is illustrated with the systems with increasing geometry complexity and captures the sensitivity of membrane curvature to the permanent and mobile charge distributions.

Considerable Enhancement of Field Emission of SnO(2) Nanowires by Post-Annealing Process in Oxygen at High Temperature

The field emission properties of SnO(2) nanowires fabricated by chemical vapor deposition with metallic catalyst-assistance were investigated. For the as-fabricated SnO(2) nanowires, the turn-on and threshold field were 4.03 and 5.4 V/mum, respectively. Considerable enhancement of field emission of SnO(2) nanowires was obtained by a post-annealing process in oxygen at high temperature. When the SnO(2) nanowires were post-annealed at 1,000 degrees C in oxygen, the turn-on and threshold field were decreased to 3.77 and 4.4 V/mum, respectively, and the current density was increased to 6.58 from 0.3 mA/cm(2) at the same applied electric field of 5.0 V/mum.

Cluster characterization of mouse embryonic stem cell-derived pluripotent embryoid bodies in four distinct developmental stages

The formation of embryoid bodies (EBs) is the principal step in the differentiation of embryonic stem (ES) cells. In this study, the morphological characteristics and gene expression patterns of EBs related to the sequential stages of embryonic development were well defined in four distinct developmental groups over 112 days of culture: early-stage EBs groups (1-7 days of differentiation), mid-stage EBs groups (9-15 days of differentiation), maturing EBs groups (17-45 days of differentiation) and matured EBs groups (50 days of differentiation). We first determined definite histological location of apoptosis within EBs and the sequential expression of molecular markers representing stem cells (Oct4, SSEA-1, Sox-2 and AKP), germ cells (Fragilis, Dazl, c-kit, StellaR, Mvh and Stra8), ectoderm (Neurod, Nestin and Neurofilament), mesoderm (Gata-1, Flk-1 and Hbb) and endoderm (AFP and Transthyretin). Our results revealed that developing EBs possess either pluripotent stem cell or germ cell states and that three-dimensional aggregates of EBs initiate mES cell differentiation during prolonged culture in vitro. Therefore, we suggest that this EB system to some extent recapitulates the early developmental processes occurring in vivo.

A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces corresponding to four types of perturbations to an electrostatic potential field, and establish the existance of an equilibrium configuration using a fixed-point argument, under the assumption that the change in the ionic strength and charges due to the additional molecules causing the deformation are sufficiently small. The results are valid for elastic models with arbitrarily complex dielectric interfaces and cavities, and can be generalized to large elastic deformation caused by high ionic strength, large charges, and strong external fields by using continuation methods.

Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach

The Poisson-Nernst-Planck (PNP) equation provides a continuum description of electrostatic-driven diffusion and is used here to model the diffusion and reaction of acetylcholine (ACh) with acetylcholinesterase (AChE) enzymes. This study focuses on the effects of ion and substrate concentrations on the reaction rate and rate coefficient. To this end, the PNP equations are numerically solved with a hybrid finite element and boundary element method at a wide range of ion and substrate concentrations, and the results are compared with the partially coupled Smoluchowski-Poisson-Boltzmann model. The reaction rate is found to depend strongly on the concentrations of both the substrate and ions; this is explained by the competition between the intersubstrate repulsion and the ionic screening effects. The reaction rate coefficient is independent of the substrate concentration only at very high ion concentrations, whereas at low ion concentrations the behavior of the rate depends strongly on the substrate concentration. Moreover, at physiological ion concentrations, variations in substrate concentration significantly affect the transient behavior of the reaction. Our results offer a reliable estimate of reaction rates at various conditions and imply that the concentrations of charged substrates must be coupled with the electrostatic computation to provide a more realistic description of neurotransmission and other electrodiffusion and reaction processes.

Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution

A computational framework is presented for the continuum modeling of cellular biomolecular diffusion influenced by electrostatic driving forces. This framework is developed from a combination of state-of-the-art numerical methods, geometric meshing, and computer visualization tools. In particular, a hybrid of (adaptive) finite element and boundary element methods is adopted to solve the Smoluchowski equation (SE), the Poisson equation (PE), and the Poisson-Nernst-Planck equation (PNPE) in order to describe electrodiffusion processes. The finite element method is used because of its flexibility in modeling irregular geometries and complex boundary conditions. The boundary element method is used due to the convenience of treating the singularities in the source charge distribution and its accurate solution to electrostatic problems on molecular boundaries. Nonsteady-state diffusion can be studied using this framework, with the electric field computed using the densities of charged small molecules and mobile ions in the solvent. A solution for mesh generation for biomolecular systems is supplied, which is an essential component for the finite element and boundary element computations. The uncoupled Smoluchowski equation and Poisson-Boltzmann equation are considered as special cases of the PNPE in the numerical algorithm, and therefore can be solved in this framework as well. Two types of computations are reported in the results: stationary PNPE and time-dependent SE or Nernst-Planck equations solutions. A biological application of the first type is the ionic density distribution around a fragment of DNA determined by the equilibrium PNPE. The stationary PNPE with nonzero flux is also studied for a simple model system, and leads to an observation that the interference on electrostatic field of the substrate charges strongly affects the reaction rate coefficient. The second is a time-dependent diffusion process: the consumption of the neurotransmitter acetylcholine by acetylcholinesterase, determined by the SE and a single uncoupled solution of the Poisson-Boltzmann equation. The electrostatic effects, counterion compensation, spatiotemporal distribution, and diffusion-controlled reaction kinetics are analyzed and different methods are compared.

Highly accurate biomolecular electrostatics in continuum dielectric environments

Implicit solvent models based on the Poisson-Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson-Boltzmann solver is developed based on the matched interface and boundary (MIB) method, which rigorously enforces the continuity conditions of both the electrostatic potential and its flux at the molecular surface. The MIB based PB solver attains much better convergence rates as a function of mesh size compared to conventional finite difference and finite element based PB solvers. Consequently, highly accurate electrostatic potentials and solvation energies are obtained at coarse mesh sizes. In the context of biomolecular electrostatic calculations it is demonstrated that the MIB method generates substantially more accurate solutions of the PB equation than other established methods, thus providing a new level of reference values for such models. Initial results also indicate that the MIB method can significantly improve the quality of electrostatic surface potentials of biomolecules that are frequently used in the study of biomolecular interactions based on experimental structures.

[Studies on the sex difference in proteins between male and female adult worm of Schistosoma japonicum]

OBJECTIVE

To explore the sex difference in proteins between male and female adult worm of Schistosoma japonicum.

METHODS

Two-electrophoresis was used to analyse the difference of protein between the male and female adult worm of S. japonicum (Chinese strain).

RESULTS

Two-dimensional electrophoresis analysis revealed that at the site of 43 kDa and an isoelectric point (pI) of 5.60-5.90 the male worm exhibited a band carrying a number of spots and dots, being longer and wider than that exhibited by the female worm. The female worm exhibited 7 specific dots.

CONCLUSION

The sex differences in proteins between male and female adult worms of S. japonicum are significant.

[Purification and characterization of L-amino acid oxidase from Agkistrodon halys pallas venom]

L-amino acid oxidase (LAO, EC 1.4.3.2) is widely found in snake venoms and is thought to contribute to the toxicity in envenoming. By using of Sephadex G-150, DEAE-Sepharose CL-6B and FPLC Superose 12 chromatography, a protein with L-amino acid oxidase activity was purified and characterized from Agkistrodon haly Pallas venom. Its molecular mass was 57 kD as determined by SDS-PAGE analysis under both reducing and non-reducing conditions, and its pI was about 4.9. The protein catalysed the stereospecific oxidative deamination of L-amino acid substrate. It inhibited the platelet aggregation induced by ADP and collagen dose-dependently, even at low concentrations of 0.2 micromol/L and 0.08 micromol/L, respectively. The LAO had antibacterial effect to E.coli K12D31, and the effective concentration was as low as 0.03 g/L. Furthermore, the LAO showed cytotoxicity in crystal violet assay and apoptosis-inducing activity in the A549 cells. After 24h treatment with 5 mg/L LAO, the typical DNA fragmentation pattern of apoptotic cells was observed by using of agrose gel electrophoresis.

Structure of an acidic phospholipase A(2) from the venom of Deinagkistrodon acutus in a new crystal form

The three-dimensional structure of an acidic phospholipase A(2) purified from the venom of Deinagkistrodon acutus (Agkistrodon acutus) was determined in a new crystal form by molecular replacement at 0.28 nm resolution with a crystallographic R factor of 21.9% (R-free=25.7%) and reasonable stereochemistry. Being similar to the previous reported crystal form, a significant conformational adaptation of segment 14-23 at the dimer interface was observed. This segment was related to the "interface recognition site" (IRS). It was found that a positively charged residue at position 34 seems to be a common feature for most of hemolytic PLA(2)s belonging to group II. Structural comparison between the two crystal forms showed that NaCl had significant effects on the crystal packing, thus leading to dramatic changes of the unit cell parameters. In the new crystal form, MPD (2-methyl-2, 4-pentanediol) molecules exist in the hydrophobic channel of the enzyme.

[Cloning and expression of gynecophoral canal protein gene of Schistosoma japonicum (Chinese strain)]

A 1949 bp cDNA fragment was amplified by RT-PCR from adult Schistosoma japonicum (Chinese strain) mRNA with 3 pair of primers that were designed according to published SmGCP gene encoding gynecophoral canal protein of Schistosoma mansoni and SjGCP1 gene encoding the conservative region of gynecophoral canal protein of Schistosoma japonicum. Sequence analysis indicated that this fragment, named SjGCP, with 85% identity to SmGCP, contained a complete open reading frame (ORF) of gynecophoral canal protein gene of Schistosoma japonicum (Chinese strain). The amino acid sequence shared 83.7% identity with gynecophoral canal protein of Schistosoma mansoni. This fragment was cloned into the expression vector pET28c(+) and subsequently expressed in Escherichia coli. SDS-PAGE revealed that the molecular weight of this expressed product was 80 kD. Western blotting showed that the recombinant protein reacted well with the rabbit serum immunized with Sj worm antigen, indicating that this expressed product had good antigenicity.