The CQ ratio of surface energy components influences adhesion and removal of fouling bacteria

The interaction energy between bacteria and substrata with different surface energies was modelled by the extended DLVO (Derjaguin, Landau, Verwey and Overbeek) theory. The modeling results revealed that the interaction energy has a strong correlation with the CQ (Chen and Qi) ratio, which is defined as the ratio of the Lifshitz–van der Waals (LW) apolar to the electron donor surface energy components of substrata. Both modeling and experimental results with different bacteria including P. fluorescens, Cobetia marina and Vibrio alginolyticus demonstrated that if the LW surface energy of bacteria is larger than that of water, which is the case for most bacteria, the number of adhered bacteria decreases with a decreasing CQ ratio while bacterial removal rate increases with a decreasing CQ ratio. However, if the LW surface energy of bacteria is less than that of water, the opposite results are obtained. The CQ ratio gives a clear direction for the design of anti-biofouling and biofouling-release coatings through surface modification.     

Optimization of Cross-Linked Lexitropsins

Abstract

In attempts to optimize the cross-linked lexitropsin design, a number of cross-linked dimers composed of two tris(N-methylpyrrolecarboxamide) strands were synthesized and their binding interactions with poly d(A)? poly d(T) and poly d(A-T)?poly d(A-T) were characterized by circular dichroism and ethidium fluorometry. While all alkanediyl-linked dimers showed a similar binding behavior to the homo AT polymer, particularly at low ligand concentrations, the decanediyl linker was found to be the optimal linker permitting the bidentate anti parallel side-by-side binding of the corresponding dimer to the alternating AT polymer. Thus, in comparison with the monomer, the decanediyl-linked dimer has a binding strength enhancement of about 1400 times in the I: I binding mode. Moreover, the hydrophilicity of the linker has a significant effect on the bidentate binding strength. The (3,6)-dioxaoctanediyl-linked dimer has a further binding strength enhancement of 10 times over the decanediyl-linked dimer. Overall, the best optimized dimer has a binding strength enhancement of over 14,000 times in comparison with the monomer in the I: I binding mode. This binding enhancement parallels that observed in the best optimized bisintercalators. Distance-restrained molecular modeling provides support for the experimental results. Dimers of longer linkers can readily accommodate a bidentate anti parallel side-by-side binding mode but those of shorter linkers necessitate marked structural distortions in the bound ligand molecules. It is further observed that the binding strength enhancement to the alternating AT polymer is not always accompanied by the binding specificity improvement. Our analysis suggests that the non-specific appendage-DNA backbone interaction is a key factor that controls the specificity improvement.     

Single-Molecule Force Spectroscopy Study on the Mechanism of RNA Disassembly in Tobacco Mosaic Virus

To explore the disassembly mechanism of tobacco mosaic virus (TMV), a model system for virus study, during infection, we have used single-molecule force spectroscopy to mimic and follow the process of RNA disassembly from the protein coat of TMV by the replisome (molecular motor) in vivo, under different pH and Ca²⁺ concentrations. Dynamic force spectroscopy revealed the unbinding free-energy landscapes as that at pH 4.7 the disassembly process is dominated by one free-energy barrier, whereas at pH 7.0 the process is dominated by one barrier and that there exists a second barrier. The additional free-energy barrier at longer distance has been attributed to the hindrance of disordered loops within the inner channel of TMV, and the biological function of those protein loops was discussed. The combination of pH increase and Ca²⁺ concentration drop could weaken RNA-protein interactions so much that the molecular motor replisome would be able to pull and disassemble the rest of the genetic RNA from the protein coat in vivo. All these facts provide supporting evidence at the single-molecule level, to our knowledge for the first time, for the cotranslational disassembly mechanism during TMV infection under physiological conditions.     

Conditional gene inactivation by combining tetracycline-mediated transcriptional repression and auxin-inducible degron-mediated degradation

Characterizing the functions of essential cell cycle control genes requires tight and rapid inducible gene inactivation. Drawbacks of current conditional depletion approaches include slow responses and incomplete depletion. We demonstrated that by integrating the tetracycline-controlled promoter system and the auxin-inducible degron (AID) system together, AID-tagged proteins can be downregulated more efficiently than the individual technology alone. When used in conjunction with CRISPR-Cas9-mediated disruption of the endogenous locus, this system facilitates the analysis of essential genes by allowing rapid and tight conditional depletion, as we have demonstrated using several cell cycle-regulatory genes including cyclin A, CDK2, and TRIP13. The vectors constructed in this study allow expression of AID-fusion proteins under the control of tetracycline-controlled promoters and should be useful in studies requiring rapid and tight suppression of gene expression in mammalian cells.     

Epstein–Barr virus noncoding RNAs from the extracellular vesicles of nasopharyngeal carcinoma (NPC) cells promote angiogenesis via TLR3/RIG-I-mediated VCAM-1 expression

Viral noncoding RNAs (Epstein–Barr virus-encoded RNAs, EBERs) are believed to play a critical role in the progression of lymphoma and nasopharyngeal carcinoma (NPC). However, the accurate mechanisms accounting for their oncogenic function have not been elucidated, especially in terms of interaction between tumor cells and mesenchymal cells. Here, we report that, in addition to NPC cells, EBERs are also found in endothelial cells in Epstein–Barr virus (EBV)-infected NPC parenchymal tissues, which implicates NPC-derived extracellular vesicles (EVs) in transmitting EBERs to endothelial cells. In support of this hypothesis, we first ascertained if EBERs could be transferred to endothelial cells via EVs isolated from NPC culture supernatant. Then, we clarified that EVs-derived EBERs could promote angiogenesis through stimulation of VCAM-1 expression. Finally, we explored the involvement of EBER recognition by TLR3 and RIG-I in NPC angiogenesis. Our observations collectively illustrate the significance and mechanism of EVs-derived EBERs in angiogenesis and underlie the interaction mechanisms between EBV-infected NPC cells and the tumor microenvironment.     

LMI1-like and KNOX1 genes coordinately regulate plant leaf development in dicotyledons

Plant Molecular Biology - This report reveals that the LMI1-like and KNOX1 genes coordinately control the leaf development and different combinations of those genes which produce diverse leaf...     

Mining frequent patterns for AMP-activated protein kinase regulation on skeletal muscle

Background  

AMP-activated protein kinase (AMPK) has emerged as a significant signaling intermediary that regulates metabolisms in response to energy demand and supply. An investigation into the degree of activation and deactivation of AMPK subunits under exercise can provide valuable data for understanding AMPK. In particular, the effect of AMPK on muscle cellular energy status makes this protein a promising pharmacological target for disease treatment. As more AMPK regulation data are accumulated, data mining techniques can play an important role in identifying frequent patterns in the data. Association rule mining, which is commonly used in market basket analysis, can be applied to AMPK regulation.     

Metabolic engineering of microbes for oligosaccharide and polysaccharide synthesis

Metabolic engineering has recently been embraced as an effective tool for developing whole-cell biocatalysts for oligosaccharide and polysaccharide synthesis. Microbial catalysts now provide a practical means to derive many valuable oligosaccharides, previously inaccessible through other methods, in sufficient quantities to support research and clinical applications. The synthesis process based upon these microbes is scalable as it avoids expensive starting materials. Most impressive is the high product concentrations (up to 188 g/L) achieved through microbe-catalyzed synthesis. The overall cost for selected molecules has been brought to a reasonable range (estimated $ 30–50/g).     

Development and characterization of cell lines from heart, liver, spleen and head kidney of sea perch Lateolabrax japonicus

Five cell lines (LJHK, LJS, LJL, LJH-1 and LJH-2) were established from the head kidney, spleen, liver and heart of sea perch Lateolabrax japonicus . The cell lines LJHK, LJS, LJL, LJH-1 and LJH-2 were subcultured 46, 32, 32, 36 and 34 times in minimum essential medium (MEM) supplemented with foetal bovine serum (FBS), sea perch serum and 10 ng ml⁻¹ basic fibroblast growth factor (bFGF). Morphology of primary cultures and subcultures of the five cell lines were observed continuously by microscopy. The suitable temperature for growth was 18 to 30° C for all of these cell lines with the optimum growth at 24° C and a reduced growth rate <18° C. The optimum concentration of FBS was found to be 10% and addition of bFGF to the medium significantly increased the growth rate of the cells. The doubling time of LJS, LJH-1, LJL, LJH-2 and LJHK cells was determined to be 52·7, 54·9, 57, 58·7 and 66 h at a plating density of 1 × 10⁵ cells ml⁻¹ at 24° C, respectively. Chromosome analysis revealed that 42, 48, 38, 43 and 45% cells maintained normal diploid chromosome number (48) in the LJH-1, LJH-2, LJHK, LJL and LJS cell lines, respectively. The LJHK cells were successfully transfected with green fluorescent protein (GFP) reporter plasmids and the expression of GFP gene in the cells indicated the possible utility of the cells in gene expression studies. Furthermore, treatment of the LJHK cells with lipopolysaccharide led to increased expression of IL-1β, demonstrating that LJHK cells might be a valuable tool for studying the expression and function of immunomodulatory gene in fishes.