GENETIC AND QUANTITATIVE VARIATION IN WILD SOYBEAN (GLYCINE SOJA) POPULATIONS

Glycine soja seeds collected from South Korea and Japan were studied for their genetic structure and quantitative variation. Seventy two G. soja seed accessions were examined for genetic variation by gel electrophoresis. Based on a total of 43 loci of 15 enzymes and one protein, an average of 67.4% polymorphism (at 99% level) was observed. The expected heterozygosity is 0.160, and the number of alleles per locus is 2.14. Genetic purity of these seed accessions are very high. The four natural G. soja populations collected along the Kitakami river, Japan, showed 38.1% polymorphic loci, and the average number of alleles per locus is 1.55. Their overall expected heterozygosity is 0.114 which is much higher than the average observed heterozygosity (0.023). 19.8% of gene diversity of the four natural populations resides among populations and 81.2% within populations. The G(,ST) value calculated from isozyme and protein variation indicates that the four local populations are well differentiated isoenzymatically. The average Nei\u27s genetic distance between each pair of these four populations is 0.044. Four enzyme loci, Ap, Ti, Lap1 and Pgd2, belong to Linkage Group 9 of soybeans. The gene order of the four loci is Ap-Ti-Lap1-Pgd2, and the recombination frequency between each pair of loci Ap-Ti is 9.41% (+OR-) 1.07%, Ap-Lap1 22.65% (+OR-) 0.73%, Ap-Pgd2 39.78% (+OR-) 0.98%, Ti-Lap1 17.96% (+OR-) 1.33%, Ti-Pgd2 36.85% (+OR-) 1.39%, and Lap1-Pgd2 20.62% (+OR-) 0.99%. Another gene pair, Pgi1-Pgd2, is linked with a recombination frequency of 15.34% (+OR-) 0.74%. Twelve G. soja accessions were selected based on their latitudinal locations to study their genetic and quantitative variations. The measure of quantitative variation consists of morphological, agronomic, and phenological traits. These 12 seed accessions are significantly different from one another in most of the quantitative traits measured. The principal component analysis shows about 60% of the phenological variation and about 43% of the agronomic variation among these 12 G. soja seed accessions are highly associated with their latitudinal locations. Among three reproduction components only the number of pods per plant is positively correlated with the total yield per plant. The average number of nodules per plant is positively correlated with the percent of 3-seed pods and 4-seed pods. The congruence of population differentiation based on genetic (protein) and quantitative variations of these 12 seed accessions is low

New estimation and inference procedures for a single-index conditional distribution model

AbstractThis article employs a more flexible single-index regression model to characterize the conditional distribution. The pseudo least integrated squares approach is proposed to estimate the index coefficients. As shown in the numerical results, our estimator outperforms the existing ones in terms of the mean squared error. Moreover, we provide the generalized cross-validation criteria for bandwidth selection and utilize the frequency distributions of weighted bootstrap analogues for the estimation of asymptotic variance and the construction of confidence intervals. With a defined residual process, a test rule is built to check the correctness of an applied single-index conditional distribution model. To tackle the problem of sparse variables, a multi-stage adaptive Lasso algorithm is developed to enhance the ability of identifying significant variables. All of our procedures are found to be easily implemented, numerically stable, and highly adaptive to a variety of data structures. In addition, we assess the finite sample performances of the proposed estimation and inference procedures through extensive simulation experiments. Two empirical examples from the house-price study in Boston and the environmental study in New York are further used to illustrate applications of the methodology

SPT5 affects the rate of mRNA degradation and physically interacts with CCR4 but does not control mRNA deadenylation

The CCR4-NOT complex has been shown to have multiple roles in mRNA metabolism, including that of transcriptional elongation, mRNA transport, and nuclear exosome function, but the primary function of CCR4 and CAF1 is in the deadenylation and degradation of cytoplasmic mRNA. As previous genetic analysis supported an interaction between SPT5, known to be involved in transcriptional elongation, and that of CCR4, the physical association of SPT5 with CCR4 was examined. A two-hybrid screen utilizing the deadenylase domain of CCR4 as a bait identified SPT5 as a potential interacting protein. SPT5 at its physiological concentration was shown to immunoprecipitate CCR4 and CAF1, and in vitro purified SPT5 specifically could bind to CAF1 and the deadenylase domain of CCR4. We additionally demonstrated that mutations in SPT5 or an spt4 deletion slowed the rate of mRNA degradation, a phenotype associated with defects in the CCR4 mRNA deadenylase complex. Yet, unlike ccr4 and caf1 deletions, spt5 and spt4 defects displayed little effect on the rate of deadenylation. They also did not affect decapping or 5\u27 - 3\u27 degradation of mRNA. These results suggest that the interactions between SPT5/SPT4 and the CCR4-NOT complex are probably the consequences of effects involving nuclear events and do not involve the primary role of CCR4 in mRNA deadenylation and turnover

Stoichiometry and Change of the mRNA Closed-Loop Factors as Translating Ribosomes Transit from Initiation to Elongation

Protein synthesis is a highly efficient process and is under exacting control. Yet, the actual abundance of translation factors present in translating complexes and how these abundances change during the transit of a ribosome across an mRNA remains unknown. Using analytical ultracentrifugation with fluorescent detection we have determined the stoichiometry of the closed-loop translation factors for translating ribosomes. A variety of pools of translating polysomes and monosomes were identified, each containing different abundances of the closed-loop factors eIF4E, eIF4G, and PAB1 and that of the translational repressor, SBP1. We establish that closed-loop factors eIF4E/eIF4G dissociated both as ribosomes transited polyadenylated mRNA from initiation to elongation and as translation changed from the polysomal to monosomal state prior to cessation of translation. eIF4G was found to particularly dissociate from polyadenylated mRNA as polysomes moved to the monosomal state, suggesting an active role for translational repressors in this process. Consistent with this suggestion, translating complexes generally did not simultaneously contain eIF4E/eIF4G and SBP1, implying mutual exclusivity in such complexes. For substantially deadenylated mRNA, however, a second type of closed-loop structure was identified that contained just eIF4E and eIF4G. More than one eIF4G molecule per polysome appeared to be present in these complexes, supporting the importance of eIF4G interactions with the mRNA independent of PAB1. These latter closed-loop structures, which were particularly stable in polysomes, may be playing specific roles in both normal and disease states for specific mRNA that are deadenylated and/or lacking PAB1. These analyses establish a dynamic snapshot of molecular abundance changes during ribosomal transit across an mRNA in what are likely to be critical targets of regulation

Combined Phytochemistry and Chemotaxis Assays for Identification and Mechanistic Analysis of Anti-Inflammatory Phytochemicals in Fallopia japonica

Plants provide a rich source of lead compounds for a variety of diseases. A novel approach combining phytochemistry and chemotaxis assays was developed and used to identify and study the mechanisms of action of the active compounds in F. japonica, a medicinal herb traditionally used to treat inflammation. Based on a bioactivity-guided purification strategy, two anthranoids, emodin and physcion, were identified from F. japonica. Spectroscopic techniques were used to characterize its crude extract, fractions and phytochemicals. The crude extract, chloroform fraction, and anthranoids of F. japonica significantly inhibited CXCR4-mediated chemotaxis. Mechanistic studies showed that emodin and physcion inhibited chemotaxis via inactivating the MEK/ERK pathway. Moreover, the crude extract and emodin could prevent or treat type 1 diabetes in non-obese diabetic (NOD) mice. This study illustrates the applicability of a combinational approach for the study of anti-inflammatory medicine and shows the potential of F. japonica and its anthranoids for anti-inflammatory therapy

4β-Hydroxywithanolide E from Physalis peruviana (golden berry) inhibits growth of human lung cancer cells through DNA damage, apoptosis and G2/M arrest

<p>Abstract</p> <p>Background</p> <p>The crude extract of the fruit bearing plant, <it>Physalis peruviana </it>(golden berry), demonstrated anti-hepatoma and anti-inflammatory activities. However, the cellular mechanism involved in this process is still unknown.</p> <p>Methods</p> <p>Herein, we isolated the main pure compound, 4β-Hydroxywithanolide (4βHWE) derived from golden berries, and investigated its antiproliferative effect on a human lung cancer cell line (H1299) using survival, cell cycle, and apoptosis analyses. An alkaline comet-nuclear extract (NE) assay was used to evaluate the DNA damage due to the drug.</p> <p>Results</p> <p>It was shown that DNA damage was significantly induced by 1, 5, and 10 μg/mL 4βHWE for 2 h in a dose-dependent manner (<it>p </it>< 0.005). A trypan blue exclusion assay showed that the proliferation of cells was inhibited by 4βHWE in both dose- and time-dependent manners (<it>p </it>< 0.05 and 0.001 for 24 and 48 h, respectively). The half maximal inhibitory concentrations (IC₅₀) of 4βHWE in H1299 cells for 24 and 48 h were 0.6 and 0.71 μg/mL, respectively, suggesting it could be a potential therapeutic agent against lung cancer. In a flow cytometric analysis, 4βHWE produced cell cycle perturbation in the form of sub-G₁accumulation and slight arrest at the G₂/M phase with 1 μg/mL for 12 and 24 h, respectively. Using flow cytometric and annexin V/propidium iodide immunofluorescence double-staining techniques, these phenomena were proven to be apoptosis and complete G₂/M arrest for H1299 cells treated with 5 μg/mL for 24 h.</p> <p>Conclusions</p> <p>In this study, we demonstrated that golden berry-derived 4βHWE is a potential DNA-damaging and chemotherapeutic agent against lung cancer.</p

Women with endometriosis have higher comorbidities: Analysis of domestic data in Taiwan

AbstractEndometriosis, defined by the presence of viable extrauterine endometrial glands and stroma, can grow or bleed cyclically, and possesses characteristics including a destructive, invasive, and metastatic nature. Since endometriosis may result in pelvic inflammation, adhesion, chronic pain, and infertility, and can progress to biologically malignant tumors, it is a long-term major health issue in women of reproductive age. In this review, we analyze the Taiwan domestic research addressing associations between endometriosis and other diseases. Concerning malignant tumors, we identified four studies on the links between endometriosis and ovarian cancer, one on breast cancer, two on endometrial cancer, one on colorectal cancer, and one on other malignancies, as well as one on associations between endometriosis and irritable bowel syndrome, one on links with migraine headache, three on links with pelvic inflammatory diseases, four on links with infertility, four on links with obesity, four on links with chronic liver disease, four on links with rheumatoid arthritis, four on links with chronic renal disease, five on links with diabetes mellitus, and five on links with cardiovascular diseases (hypertension, hyperlipidemia, etc.). The data available to date support that women with endometriosis might be at risk of some chronic illnesses and certain malignancies, although we consider the evidence for some comorbidities to be of low quality, for example, the association between colon cancer and adenomyosis/endometriosis. We still believe that the risk of comorbidity might be higher in women with endometriosis than that we supposed before. More research is needed to determine whether women with endometriosis are really at risk of these comorbidities

Comparing differentiation of wild soybean (Glycine soja Sieb. & Zucc.) populations based on isozymes and quantitative traits

Comparison of differentiation of 12 populations of wild soybean (Glycine soja Sieb. & Zucc.) collected from Japan and South Korea based on isozymes and quantitative traits were made. The protein and quantitative phenograms were compared for congruence by calculating distortion coefficients. In general, the concordance of population differentiation among the 12 populations was not high, but it is remarkable that the population distance estimated on the basis of such a small number of protein loci showed a significant correlation with the distance estimated by phenological and agronomic characters. If many more protein loci were included, higher congruence may be observed

An Effective Semiparametric Estimation Approach for the Sufficient Dimension Reduction Model

<p>In the exploratory data analysis, the sufficient dimension reduction model has been widely used to characterize the conditional distribution of interest. Different from the existing approaches, our main achievement is to simultaneously estimate two essential elements, basis and structural dimension, of the central subspace and the bandwidth of a kernel distribution estimator through a single estimation criterion. With an appropriate order of kernel function, the proposed estimation procedure can be effectively carried out by starting with a dimension of zero until the first local minimum is reached. Meanwhile, the optimal bandwidth selector is ensured to be a valid tuning parameter for the central subspace estimator. An important advantage of this estimation technique is its flexibility to allow a response to be discrete and some of covariates to be discrete or categorical providing that a certain continuity condition holds. Under very mild assumptions, we further derive the uniform consistency of the introduced optimization function and the consistency of the resulting estimators. Moreover, the asymptotic normality of the central subspace estimator is established with an estimated rather than exact structural dimension. In extensive simulations, the developed approach generally outperforms the competitors. Data from previous studies are also used to illustrate the proposal. On the whole, our methodology is very effective in estimating the central subspace and conditional distribution, highly flexible in adapting diverse types of a response and covariates, and practically feasible in obtaining an asymptotically optimal and valid bandwidth estimator. Supplementary materials for this article are available online.</p