Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution

Holliday junction (HJ) resolvases are structure-specific endonucleases that cleave four-way DNA junctions (HJs) generated during DNA recombination and repair. Bacterial RuvC, a prototypical HJ resolvase, functions as homodimer and nicks DNA strands precisely across the junction point. To gain insights into the mechanisms underlying symmetrical strand cleavages by RuvC, we performed crystallographic and biochemical analyses of RuvC from Thermus thermophilus (T.th. RuvC). The crystal structure of T.th. RuvC shows an overall protein fold similar to that of Escherichia coli RuvC, but T.th. RuvC has a more tightly associated dimer interface possibly reflecting its thermostability. The binding mode of a HJ-DNA substrate can be inferred from the shape/charge complementarity between the T.th. RuvC dimer and HJ-DNA, as well as positions of sulfate ions bound on the protein surface. Unexpectedly, the structure of T.th. RuvC homodimer refined at 1.28 Å resolution shows distinct asymmetry near the dimer interface, in the region harboring catalytically important aromatic residues. The observation suggests that the T.th. RuvC homodimer interconverts between two asymmetric conformations, with alternating subunits switched on for DNA strand cleavage. This model provides a structural basis for the ‘nick-counter-nick’ mechanism in HJ resolution, a mode of HJ processing shared by prokaryotic and eukaryotic HJ resolvases.     

Improving ecophysiological simulation models to predict the impact of elevated atmospheric CO2 concentration on crop productivity

Background

Process-based ecophysiological crop models are pivotal in assessing responses of crop productivity and designing strategies of adaptation to climate change. Most existing crop models generally over-estimate the effect of elevated atmospheric [CO₂], despite decades of experimental research on crop growth response to [CO₂].

Analysis

A review of the literature indicates that the quantitative relationships for a number of traits, once expressed as a function of internal plant nitrogen status, are altered little by the elevated [CO₂]. A model incorporating these nitrogen-based functional relationships and mechanisms simulated photosynthetic acclimation to elevated [CO₂], thereby reducing the chance of over-estimating crop response to [CO₂]. Robust crop models to have small parameterization requirements and yet generate phenotypic plasticity under changing environmental conditions need to capture the carbon–nitrogen interactions during crop growth.

Conclusions

The performance of the improved models depends little on the type of the experimental facilities used to obtain data for parameterization, and allows accurate projections of the impact of elevated [CO₂] and other climatic variables on crop productivity.     

Production of transgenic mice expressing the goat H-FABP gene by intratesticular injection

The objective of this study was to explore the possibility of obtaining stable transgenic animals by intratesticular injection. The recombinant vector pEGFP-H-FABP expressing the goat heart-type fatty acid binding protein and green fluorescent protein was mixed with liposome complexes and randomly injected into the testes of mice. Testicular section, fluorescence, and DNA detection assays of mouse sperm were performed to determine the integration of foreign DNA. The results showed that foreign DNA was successfully expressed in the treated mice. Furthermore, the expression and function of the foreign gene were analyzed in F₁ generation and F₂ generation mice at different levels, with the positive rates of foreign gene transfer into the F₁ and F₂ generations being 4.0 and 30.23 %, respectively. These results strongly support testicular injection as an effective method of producing transgenic animals and indicate that foreign genes can be stably passed on to the offspring. This research has theoretical and practical implications for the improvement in the quality of laboratory animals and for gene therapy.     

The association between CD14 gene C-260T polymorphism and coronary heart disease risk: a meta-analysis

Monocyte differentiation antigen CD14 is considered an important cell-activating mediator of inflammatory responses that may result in atherosclerosis, coronary heart disease (CHD), thrombus formation, and myocardial infarction (MI). A common C-260T polymorphism in the promoter of the CD14 gene, the trans-membrane receptor of lipopolysaccharides, has been inconsistently associated with CHD. To investigate this inconsistency, we performed a meta-analysis of 28 studies involving a total of 13,335 CHD cases and 7,979 controls for C-260T of the CD14 gene to evaluate the effect of CD14 on genetic susceptibility for CHD. An overall random effects odds ratio of 1.24 (95 % CI: 1.12–1.36, P < 10^?5) was found for T allele. Significant results were also observed using dominant (OR = 1.34, 95 % CI: 1.17–1.54, P < 10^?4) or recessive genetic model (OR = 1.25, 95 % CI: 1.10–1.41, P = 0.0004). There was strong evidence of heterogeneity (P < 10^?5), which largely disappeared after stratification by ethnicity. After stratified by ethnicity, significant results were found in East Asians; whereas no significant associations were found among Caucasians and other ethnic populations in all genetic models. In the stratified analysis according to sample size, CHD endpoints, and HWE status, significantly increased risks for the polymorphism were found in all genetic models. In conclusion, our results indicate that the CD14 C-260T polymorphism is a risk factor of CHD, especially in East Asians. However, additional very large-scale studies are warranted to confirm our results.     

Effect of luteinizing hormone/choriogonadotropin receptor (LHCGR) gene on chicken reproductive traits

Luteinizing hormone/choriogonadotropin receptor (LHCGR) gene, potentially related to reproductive traits in chickens, was genotyped by using the Pooled DNA Sequencing, PCR–SSCP and Directing Sequencing techniques. 306 Erlang Mountain chickens form one line (SD03, a line that has been selected for egg quality from a local chicken breed in Sichuan province, China) were genotyped in this study. The associations between LHCGR polymorphisms and six reproductive traits [body weight at first egg (BWAFE), weight of first egg, age at first egg (AFE), number of eggs at 300 days of age (EN), body weight at 300 days of age and egg weight at 300 days of age (EWTA)] were estimated using the one-way analysis of variance method. Results showed that SNP +G4058A and SNP +T4099G of the LHCGR gene were significantly associated with BWFE and AFE. Birds with the AG genotype for the +G4058A SNP exhibited shorter AFE (P < 0.05) and greater EN than those of the GG and AA genotypes, suggesting a balancing selection (overdominance); the effect of allele C in SNP +C3021T and allele C in SNP +T4490C on EN and AFE is additive and may reflect the influence of positive selection. These alleles have promise as genetic markers for future marker-assisted selection.     

Bacteria-mediated bisphenol A degradation

Bisphenol A (BPA) is an important monomer in the manufacture of polycarbonate plastics, food cans, and other daily used chemicals. Daily and worldwide usage of BPA and BPA-contained products led to its ubiquitous distribution in water, sediment/soil, and atmosphere. Moreover, BPA has been identified as an environmental endocrine disruptor for its estrogenic and genotoxic activity. Thus, BPA contamination in the environment is an increasingly worldwide concern, and methods to efficiently remove BPA from the environment are urgently recommended. Although many factors affect the fate of BPA in the environment, BPA degradation is mainly depended on the metabolism of bacteria. Many BPA-degrading bacteria have been identified from water, sediment/soil, and wastewater treatment plants. Metabolic pathways of BPA degradation in specific bacterial strains were proposed, based on the metabolic intermediates detected during the degradation process. In this review, the BPA-degrading bacteria were summarized, and the (proposed) BPA degradation pathway mediated by bacteria were referred.