Identification and Genetic Analysis of a Novel Allelic Variation of <i>Brittle-1</i> with Endosperm Mutant in Maize

Endosperm mutants are critical to the studies on both starch synthesis and metabolism and genetic improvement of starch quality in maize. In the present study, a novel maize endosperm mutant A0178 of natural variation was used as the experimental material and identified and then characterized. Through phenotypic identification, genetic analysis, main ingredients measurement and embryo rescue, development of genetic mapping population from A0178, the endosperm mutant gene was located. The results showed that the mutant exhibited extremely low germination ability as attributed to the inhibited embryo development, and amounts of sugars were accumulated in the mutant seeds and more sugars content was detected at 23 days after pollination (DAP) in A0178 than B73. Employing genetic linkage analysis, the mutant trait was mapped in the bin 5.04 on chromosome 5. Sequence analysis showed that two sites of base transversion and insertion presented in the protein coding region and non-coding region of the mutant brittle-1 (bt1), the adenylate translocator encoding gene involved in the starch synthesis. The single base insertion in the coding region cause frameshift mutation, early termination and lose of function of Brittle-1 (BT1). All results suggested that bt1 is a novel allelic gene and the causal gene of this endosperm mutant, providing insights on the mechanism of endosperm formation in maize.     

Dietary adaptations and palaeoecology of Lophialetidae (Mammalia,Tapiroidea) from the Eocene of the Erlian Basin,China: combined evidence from mesowear and stable isotope analyses

Lophialetidae is an extinct group of endemic Asiatic tapiroids that are widely distributed in the Eocene sediments of Asia. Schlosseria magister and Lophialetes expeditus are the most abundant species in this family. However, their dietary and ecological characteristics are largely unknown. For the first time, we reconstruct the palaeodiet and habitat of these two lophialetids using a combination of mesowear and stable carbon isotope analysis of fossil teeth excavated from the Erlian Basin, China. Mesowear analysis (n = 141) suggests that the dietary structure of S. magister and L. expeditus shifted from less to more abrasive diets from ~52 to ~42 Ma. Stable carbon isotope analysis (n = 137) suggests that the habitats of S. magister and L. expeditus became drier and/or more open through time. The dietary shifts of the two lophialetids are consistent with evident changes in habitat. The changes in the diet and habitat were probably related to global climate change during that time period. The gradual drop in global temperatures during the early–middle Eocene led to a drier and more open terrestrial ecosystem in the Erlian Basin, probably resulting in changes in floral composition of the environment inhabited by S. magister and L. expeditus. Hence, herbivores highly susceptible to vegetation modification had to develop new resource exploitation strategies to adapt to these changes. Schlosseria magister, considered to be the sister-group of L. expeditus and with a low level of ecological flexibility, was unable to adapt to the habitat changes finally becoming extinct at ~45 Ma.     

Nicotinamide increases the sensitivity of chronic myeloid leukemia cells to doxorubicin via the inhibition of SIRT1

The NAD-dependent deacetylase Sirtuin 1 (SIRT1) plays a vital role in leukemogenesis. Nicotinamide (NAM) is the principal NAD⁺ precursor and a noncompetitive inhibitor of SIRT1. In our study, we showed that NAM enhanced the sensitivity of chronic myeloid leukemia (CML) to doxorubicin (DOX) via SIRT1. We found that SIRT1 high expression in CML patients was associated with disease progression and drug resistance. Exogenous NAM efficiently repressed the deacetylation activity of SIRT1 and induced the apoptosis of DOX-resistant K562 cells (K562R) in a dose-dependent manner. Notably, the combination of NAM and DOX significantly inhibited tumor cell proliferation and induced cell apoptosis. The knockdown of SIRT1 in K562R cells enhanced NAM+DOX-induced apoptosis. SIRT1 rescue in K562R reduced the NAM+DOX-induced apoptosis. Mechanistically, the combinatory treatment significantly increased the cleavage of caspase-3 and PARP in K562R in vitro and in vivo. These results suggest the potential role of NAM in increasing the sensitivity of CML to DOX via the inhibition of SIRT1.     

Bindings of PPARγ ligand-binding domain with 5-cholesten-3β, 25-diol, 3-sulfate: accurate prediction by molecular simulation

Abstract

Peroxisome proliferator-activated receptor gamma (PPAR_γ) has recently been identified as an attractive target for atherosclerosis intervention. Given potential relevance of 5-cholesten-3β, 25-diol, 3-sulphate (CHOS) and PPAR_γ, an integrated docking method was used to study their interaction mechanisms, with the full considerations to distinct CHOS conformations and dynamic ensembles of PPAR_γ ligand-binding domain (PPAR_γ-LBD). The results revealed that this novel platform is satisfactory to the accurate determination of binding profiles, and the binding pattern of CHOS is rather similar as those of current PPAR_γ full/partial agonists. CHOS contributes to the stabilization of the AF2 and β-sheet surfaces of PPAR_γ-LBD and promotes the configuration adjustment of Ω loop, in order to inhibit the Cdk5-mediated PPAR_γ phosphorylation. Nonetheless, there are clear differences in term of occupation of full or partial agonist-like binding models. The energetic and geometric analyses further revealed that CHOS may be fond of partial agonist-like binding, and its sulfonic group and carbon skeleton are helpful for the binding process. We hope that the results will aid our understanding of recognitions involving CHOS with PPAR_γ-LBD and warrant the further aspects to pharmacological experiments.

Communicated by Ramaswamy H. Sarma     

Molecular characterization and functional analysis of the vitellogenin receptor in the rice stem borer,Chilo suppressalis

As a member of the low-density lipoprotein receptor (LDLR) superfamily, vitellogenin (Vg) receptor (VgR) is responsible for the uptake of Vg into developing oocytes and is a potential target for pest control. Here, a full-length VgR complementary DNA (named as CsVgR) was isolated and characterized in the rice stem borer, Chilo suppressalis. The composite CsVgR gene contained an open reading frame of 5,484 bp encoding a protein of 1,827 amino acid residues. Structural analysis revealed that CsVgR contained two ligand-binding domains (LBDs) with four Class A (LDLR_A) repeats in LBD1 and seven in LBD2, which was structurally different from most non-Lepidopteran insect VgRs having five repeats in LBD1 and eight in LBD2. The developmental expression analysis showed that CsVgR messenger RNA expression was first detectable in 3-day-old pupae, sharply increased in newly emerged female adults, and reached a peak in 2-day-old female adults. Consistent with most other insects VgRs, CsVgR was exclusively expressed in the ovary. Notably, injection of dsCsVgR into late pupae resulted in fewer follicles in the ovarioles as well as reduced fecundity, suggesting a critical role of CsVgR in female reproduction. These results may contribute to the development of RNA interference-mediated disruption of reproduction as a control strategy of C. suppressalis.     

Effects of different 2A peptides on transgene expression mediated by tricistronic vectors in transfected CHO cells

Molecular Biology Reports - Multicistronic vectors can increase transgene expression and decrease the imbalance of gene expression in the Chinese hamster ovary (CHO) cell expression system. Small,...     

Genome Wide Identification of C2H2-Type Zinc Finger Proteins of Tomato and Expression Analysis Under Different Abiotic Stresses

In plants, C2H2-type zinc finger proteins play important roles in multiple processes, including plant growth and development, as well as biotic and abiotic responses. In the present study, based on the presence of the C2H2 domain (CX2~4CX3FX5LX2HX3~5H), 112 C2H2-type zinc finger proteins were predicted in tomato. Through gene and protein structures analyses and phylogenetic analysis, the 112 C2H2-type zinc finger proteins were divided into five subfamilies. Members of the same subfamily shared similarities in gene and protein structures, while members of different subfamilies contained different numbers of the C2H2 domain. The tissue expression pattern analysis showed that 24 C2H2-type zinc finger proteins are constitutively expressed in all tissues, indicating that they may play important roles in the growth and development of all tissues. In addition, under chilling (4 °C), heat (42 °C), high salinity (200 Mm NaCl), and osmotic (20% PEG) stresses, members of C2H2-type zinc finger family were induced to varying degrees, which suggested that these genes were involved in multiple abiotic stress responses. This study will provide theoretical basis for further research of C2H2-type zinc finger proteins in tomato.

     

Large scale maximum average power multiple inference on time-course count data with application to RNA-seq analysis

Experiments that longitudinally collect RNA sequencing (RNA-seq) data can provide transformative insights in biology research by revealing the dynamic patterns of genes. Such experiments create a great demand for new analytic approaches to identify differentially expressed (DE) genes based on large-scale time-course count data. Existing methods, however, are suboptimal with respect to power and may lack theoretical justification. Furthermore, most existing tests are designed to distinguish among conditions based on overall differential patterns across time, though in practice, a variety of composite hypotheses are of more scientific interest. Finally, some current methods may fail to control the false discovery rate. In this paper, we propose a new model and testing procedure to address the above issues simultaneously. Specifically, conditional on a latent Gaussian mixture with evolving means, we model the data by negative binomial distributions. Motivated by Storey (2007) and Hwang and Liu (2010), we introduce a general testing framework based on the proposed model and show that the proposed test enjoys the optimality property of maximum average power. The test allows not only identification of traditional DE genes but also testing of a variety of composite hypotheses of biological interest. We establish the identifiability of the proposed model, implement the proposed method via efficient algorithms, and demonstrate its good performance via simulation studies. The procedure reveals interesting biological insights, when applied to data from an experiment that examines the effect of varying light environments on the fundamental physiology of the marine diatom Phaeodactylum tricornutum.