Dynamic changes of histone H3 lysine 9 following trimethylation in bovine oocytes and pre-implantation embryos

Objectives

We have examined dynamic changes of histone H3 lysine 9 following trimethylation (H3K9me3), the mRNA expression levels of SUV39H1 and SUV39H2 in bovine oocytes and the role in the development of in vitro fertilization (IVF) pre-implantation embryos.

Results

There were strong H3K9me3 signals in germinal vesicle (GV) oocytes but no signals in MII oocytes. H3K9me3 signals were maintained during IVF pre-implantation embryo development. SUV39H1 and SUV39H2 showed significantly higher mRNA expression levels in GV oocytes than MII oocytes (P < 0.01). SUV39H1 showed high mRNA expression level in two-cell embryos, however, SUV39H2 showed high mRNA expression level in four-cell embryos. In other development stage, SUV39H1 and SUV39H2 showed low expression levels.

Conclusion

Bovine IVF pre-implantation embryos maintain strong H3K9me3 signals and SUV39H1 and SUV39H2 are highly expressed at the early development stage of pre-implantation embryos.

     

Rats with Malformations of Cortical Development Exhibit Decreased Length of AIS and Hypersensitivity to Pilocarpine-Induced Status Epilepticus

Malformations of cortical development (MCD) are critical brain development disorders associated with varied abnormalities in both anatomic structures and neural functioning. It is also a very common etiology to the epilepsy, in which the alteration on excitability of cortical neurons is hypothesized as one of important causes to the epileptic seizures. Due to the key role in regulating neuron firing properties, the plasticity of axon initial segment (AIS) was investigated in present study to further determine the relation between MCD and epilepsy. Our results showed a prolonged decrease in the length of AIS occurred in MCD animal models. Besides, the AIS was also found greatly shortened in MCD models during the acute, but not chronic phase of status epileptics compared with intact controls. Our findings of identification of AIS plasticity in MCD animal models and its hypersensitivity to status epilepsy are significant in furthering our understanding of the pathophysiological mechanisms involved in this disorder.     

Investigation of peat sediments from Daiyun Mountain in southeast China: late Holocene vegetation,climate and human impact

In this study, late Holocene vegetation, climate and human impacts were investigated using multiproxy data-pollen percentages, pollen accumulation rates (PAR), humification and loss-on-ignition (LOI)—measured from peat sediments from Daiyun Mountain, southeast China. A stratigraphic chronology was established on the basis of four radiocarbon dates. The 4,350 year sequence of vegetation history and climate change exhibits three distinctive stages: (1) 4,350–1,000 cal bp, during which the vegetation was dominated by evergreen forests mainly composed of broad-leaf trees, indicating a warm and wet climate; (2) 1,000–550 cal bp, during which the climate was thought to be cool and dry, based on a decrease in pollen percentages and the PARs of trees, shrubs and wetland herbs, and an increase in the pollen percentage and PAR of dry land herbs, as well as high overall LOI values; and (3) 550 cal bp to modern times, during which higher pollen percentages of dry land and wetland herbs, along with low pollen percentage and PAR of trees and shrubs, as well as low absorbance and LOI values, suggest relatively cooler but wetter climate conditions. In addition, major climatic events, such as the warm period from ad 670–960, the Medieval Warm Period (ad 1050–1520) and the Little Ice Age (ad 1580–1850), could be identified within the peat sediments in this study, with climatic conditions at these times being characteristically warm and wet, warm and dry, and cold and wet, respectively. Pollen signals indicate significant human impact since 1,000 cal bp, which may be linked to the development of the local porcelain industry and a rapid increase in the population in the study region.     

Simulation of 3D tumor cell growth using nonlinear finite element method

We propose a novel parallel computing framework for a nonlinear finite element method (FEM)-based cell model and apply it to simulate avascular tumor growth. We derive computation formulas to simplify the simulation and design the basic algorithms. With the increment of the proliferation generations of tumor cells, the FEM elements may become larger and more distorted. Then, we describe a remesh and refinement processing of the distorted or over large finite elements and the parallel implementation based on Message Passing Interface to improve the accuracy and efficiency of the simulation. We demonstrate the feasibility and effectiveness of the FEM model and the parallelization methods in simulations of early tumor growth.     

Lipopolysaccharide Structure and Biosynthesis in Helicobacter pylori

This review covers the current knowledge and gaps in Helicobacter pylori lipopolysaccharide (LPS) structure and biosynthesis. H. pylori is a Gram‐negative bacterium which colonizes the luminal surface of the human gastric epithelium. Both a constitutive alteration of the lipid A preventing TLR4 elicitation and host mimicry of the Lewis antigen decorated O‐antigen of H. pylori LPS promote immune escape and chronic infection. To date, the complete structure of H. pylori LPS is not available, and the proposed model is a linear arrangement composed of the inner core defined as the hexa‐saccharide (Kdo‐LD‐Hep‐LD‐Hep‐DD‐Hep‐Gal‐Glc), the outer core composed of a conserved trisaccharide (‐GlcNAc‐Fuc‐DD‐Hep‐) linked to the third heptose of the inner core, the glucan, the heptan and a variable O‐antigen, generally consisting of a poly‐LacNAc decorated with Lewis antigens. Although the glycosyltransferases (GTs) responsible for the biosynthesis of the H. pylori O‐antigen chains have been identified and characterized, there are many gaps in regard to the biosynthesis of the core LPS. These limitations warrant additional mutagenesis and structural studies to obtain the complete LPS structure and corresponding biosynthetic pathway of this important gastric bacterium.     

Characteristic Steroids from the South China Sea Gorgonian Muricella sibogae and Their Cytotoxicities

Twenty‐four steroid‐based natural products, 9,10‐secosteroids ( 1 – 10 ), 1,4‐dien‐3‐one steroids ( 11 – 19 ), and 4‐en‐3‐one steroids ( 20 – 24 ), containing varying side‐chains, were isolated from the South China Sea gorgonian Muricella sibogae. The structures of one new 9,10‐secosteroid, sibogol D ( 1 ), and two new 1,4‐dien‐3‐one steroids, sibogols E and F ( 11 and 12 ), were elucidated by extensive spectroscopic analyses and by comparison with the literature data. Cytotoxicities for all the isolates were evaluated against four selected tumor cell lines, HL‐60, HCT116, K562, and P388. Compounds 3, 9 , and 13 exhibited potent cytotoxic activities against the HL‐60 cell line, with IC₅₀ values ranging from 1.27 to 10.05 μM , and compound 3 was also cytotoxic against HCT116 with an IC₅₀ value of 5.8 μM . The bioassay results also indicated a potential relationship between structural patterns and activity. The newly presented series of 1,4‐dien‐3‐one and 4‐en‐3‐one types of steroids relating to the unique 9,10‐secosteroids in biogenesis were found in this species for the first time, which is of considerable chemotaxonomic significance.     

Least squares regression methods for clustered ROC data with discrete covariates

The receiver operating characteristic (ROC) curve is a popular tool to evaluate and compare the accuracy of diagnostic tests to distinguish the diseased group from the nondiseased group when test results from tests are continuous or ordinal. A complicated data setting occurs when multiple tests are measured on abnormal and normal locations from the same subject and the measurements are clustered within the subject. Although least squares regression methods can be used for the estimation of ROC curve from correlated data, how to develop the least squares methods to estimate the ROC curve from the clustered data has not been studied. Also, the statistical properties of the least squares methods under the clustering setting are unknown. In this article, we develop the least squares ROC methods to allow the baseline and link functions to differ, and more importantly, to accommodate clustered data with discrete covariates. The methods can generate smooth ROC curves that satisfy the inherent continuous property of the true underlying curve. The least squares methods are shown to be more efficient than the existing nonparametric ROC methods under appropriate model assumptions in simulation studies. We apply the methods to a real example in the detection of glaucomatous deterioration. We also derive the asymptotic properties of the proposed methods.     

Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide libraries

Two targeted chromogenic octapeptide combinatorial libraries, comprised of 38 pools each containing 361 different peptides, were used to analyze the enzyme/substrate interactions of five plasmepsins. The first library (P1 library) was based on a good synthetic aspartic peptidase substrate [Westling, J., Cipullo, P., Hung, S. H., Saft, H., Dame, J. B., and Dunn, B. M. (1999) Protein Sci. 8, 2001-2009; Scarborough, P. E., and Dunn, B. M. (1994) Protein Eng. 7, 495-502] and had the sequence Lys-Pro-(Xaa)-Glu-P1*Nph-(Xaa)-Leu. The second library (P1' library) incorporated results with the plasmepsins from the first library and had the sequence Lys-Pro-Ile-(Xaa)-Nph*P1'-Gln-(Xaa). In both cases, P1 and P1' were fixed residues for a given peptide pool, where Nph was a para-nitrophenylalanine chromogenic reporter and Xaa was a mixture of 19 different amino acids. Kinetic assays monitoring the rates of cleavage of these libraries revealed the optimal P1 and P1' residues for the five plasmepsins as hydrophobic substitutions. Extended specificity preferences were obtained utilizing liquid chromatography-mass spectrometry (LC-MS) to analyze the cleavage products produced by enzyme-catalyzed digestion of the best pools of each peptide library. LC-MS analysis of the P1-Phe and P1'-Phe pools revealed the favored amino acids at the P3, P2, P2', and P3' positions. These analyses have provided new insights on the binding preferences of malarial digestive enzymes that were used to design specific methyleneamino peptidomimetic inhibitors of the plasmepsins. Some of these compounds were potent inhibitors of the five plasmepsins, and their possible binding modes were analyzed by computational methods.     

Fibrillogenesis of apomyoglobin facilitated by aggregation sequence of yeast Sup35 in various regions

To examine the effect of aggregation sequence QGGYQQQYNP from yeast Sup35 on fibril formation of sperm whale apomyoglobin (apoMb), we constructed several mutants via substitution. Urea-induced unfolding of apoMb confirms that the substitution of the aggregation sequence does not significantly affect the stability of the mutants compared to wild type (WT) at pH 4.2. Under this condition, however, despite the difference in rate most apoMb mutants form fibrils more readily than WT with distinct morphology. These results suggest that the aggregation sequence facilitates fibril assembly of apoMb at acidic pH in vitro and this facilitation depends on the regions replaced.