iTRAQ Protein Profiling of Adventitious Root Formation in Mulberry Hardwood Cuttings

The ability to form mature adventitious roots (AR) provides a competitive advantage for clonal multiplication of elite genotypic plant species, because high economic losses occur as a result of insufficient rooting. To better understand potential mechanisms involved in AR formation, we utilized an iTRAQ-based proteomic approach on mulberry hardwood cuttings. A total of 4427 proteins were identified from the base of cuttings, of which 595 and 231 proteins showed differential accumulations in the two periods of rooting, respectively. Three differentially expressed enzyme proteins were validated by an enzyme assay and qPCR. Functional annotation analysis showed that dysregulated proteins were involved in glucose metabolism, flavonoids biosynthesis, cell wall modification, and hormone regulation, indicating potential contributions to adventitious rooting. These results provide fundamental and important information for research on the molecular mechanism of AR development in mulberry cuttings and facilitate rooting efficiency in agricultural practice.     

Protective effects of intermittent hypoxic adaptation on myocardium and its mechanisms.

Intermittent hypoxic adaptation offers as many beneficial effects in protecting against myocardial injuries as chronic continuous hypoxic adaptation. However, chronic continuous hypoxic adaptation readily causes some adverse effects on the organism, which may be prevented by intermittent hypoxic adaptation. As an approach to potentiate the protective effects, intermittent hypoxic adaptation is also much easier to apply to subjects who are not living at high altitude. The mechanisms underlying the cardioprotective effects of intermittent hypoxic adaptation are less understood, although great similarities exist between chronic continuous and intermittent hypoxic adaptation. The participation of several factors, such as myocardial vascularity, coronary blood flow, and cardiomyoglobin, which comprise the oxygen uptake system is not apparent, while the more efficient energetic metabolism after intermittent hypoxic adaptation may be a mechanism for cardioprotection. The possible roles of several signaling transduction pathways, including adrenoceptors, prostaglandins, and the adenosinergic system, in the beneficial effects of intermittent hypoxia are compared to those of chronic continuous hypoxic adaptation. Antioxidant enzymes and stress proteins may also be part of the mechanisms contributing to the cardioprotection of the intermittent hypoxic adaptation. As the cardioprotective effects of intermittent hypoxic adaptation employ multifold mechanisms, their clear elucidation needs more efforts.     

<Emphasis Type="Italic">Flavobacterium zaozhuangense</Emphasis> sp. nov., a new member of the family <Emphasis Type="Italic">Flavobacteriaceae</Emphasis>, isolated from metolachlor-contaminated soil

Strain ZZ-8^T, a Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented, rod-shaped bacterium, was isolated from metolachlor-contaminated soil in China. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZZ-8^T is a member of the genus Flavobacterium and shows high sequence similarity to Flavobacterium humicola UCM-46^T (97.2%) and Flavobacterium pedocola UCM-R36^T (97.1%), and lower (<?97%) sequence similarity to other known Flavobacterium species. Chemotaxonomic analysis revealed that strain ZZ-8^T possessed MK-6 as the major respiratory quinone; and iso-C_15:0 (28.5%), summed feature 9 (iso-C_17:1 w9c/C_16:0 10-methyl, 22.9%), iso-C_17:0 3-OH (17.0%), iso-C_15:0 3-OH (8.9%), iso-C_15:1 G (8.6%) and summed feature 3 (C_16:1 w7c/C_16:1 w6c, 5.7%) as the predominant fatty acids. The polar lipids of strain ZZ-8^T were determined to be lipids, a glycolipid, aminolipids and phosphatidylethanolamine. Strain ZZ-8^T showed low DNA–DNA relatedness with F. pedocola UCM-R36^T (43.23?±?4.1%) and F. humicola UCM-46^T (29.17?±?3.8%). The DNA G+C content was 43.3 mol%. Based on the phylogenetic and phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization, strain ZZ-8^T is considered a novel species of the genus Flavobacterium, for which the name Flavobacterium zaozhuangense sp. nov. (type strain ZZ-8^T?=?KCTC 62315 ^T?=?CCTCC AB 2017243^T) is proposed.     

Chemical gene synthesis: strategies, softwares, error corrections, and applications

Chemical synthesis of DNA sequences provides a powerful tool for modifying genes and for studying gene structure, expression and function. Modified genes and consequently protein/enzymes can bridge genomics and proteomics research or facilitate commercial applications of gene and protein technologies. In this review, we will summarize various strategies, designing softwares and error correction methods for chemical gene synthesis, particularly for the synthesis and assembly of long DNA molecules based on polymerase cycling assembly. Also, we will briefly discuss some of the major applications of chemical synthesis of DNA sequences in basic research and applied areas.     

Modulating the Mechanical Stability of Extracellular Matrix Protein Tenascin-C in a Controlled and Reversible Fashion

Stretching force can induce conformational changes of proteins and is believed to be an important biological signal in the mechanotransduction network. Tenascin-C is a large extracellular matrix protein and is subject to stretching force under its physiological condition. Regulating the mechanical properties of the fibronectin type III domains of tenascin-C will alter its response to mechanical stretching force and thus may provide the possibility of regulating the biological activities of tenascin-C in living cells. However, tuning the mechanical stability of proteins in a rational and systematic fashion remains challenging. Using the third fibronectin type III domain (TNfn3) of tenascin-C as a model system, here we report a successful engineering of a mechanically stronger extracellular matrix protein via engineered metal chelation. Combining steered molecular dynamics simulations, protein engineering and single-molecule atomic force microscopy, we have rationally engineered a bihistidine-based metal chelation site into TNfn3. We used its metal chelation capability to selectively increase the unfolding energy barrier for the rate-limiting step during the mechanical unfolding of TNfn3. The resultant TNfn3 mutant exhibits enhanced mechanical stability. Using a stronger metal chelator, one can convert TNfn3 back to a state of lower mechanical stability. This is the first step toward engineering extracellular matrix proteins with defined mechanical properties, which can be modulated reversibly by external stimuli, and will provide the possibility of using external stimuli to regulate the biological functions of extracellular matrix proteins.     

Divalent Metal Transporter 1 Expression and Regulation in Human Placenta

Divalent metal transporter 1 (DMT1) is likely responsible for the release of iron from endosomes to the cytoplasm in placental syncytiotrophoblasts (STB). To determine the localization and the regulation of DMT1 expression by iron directly in placenta, the expression of DMT1 in human term placental tissues and BeWo cells (human placental choriocarcinoma cell line) was detected and the change in expression in response to different iron treatments on BeWo cells was observed. DMT1 was shown to be most prominent near the maternal side in human term placenta and predominantly in the cytoplasm of BeWo cells. BeWo cells were treated with desferrioxamine (DFO) and human holotransferrin (hTf-2Fe) and it was found that both DMT1 mRNA and protein increased significantly with DFO treatment and decreased with hTf-2Fe treatment. Further, DMT1 mRNA responded more significantly to treatments if it possessed an iron-responsive element than mRNA without this element. This study indicated that DMT1 is likely involved in endosomal iron transport in placental STB and placental DMT1 + IRE expression was primarily regulated by the IRE/IRP mechanism.