ALBERT

Description: The mer operon confers bacterial resistance to inorganic mercury (Hg 2+ ) and organomercurials by encoding proteins involved in sensing, transport and detoxification of these cytotoxic agents. Expression of the mer operon is under tight control by the dual-function transcriptional regulator MerR. The metal-free, apo MerR binds to the mer operator/promoter region as a repressor to block transcription initiation, but is converted into an activator upon Hg 2+ -binding. To understand how MerR interacts with Hg 2+ and how Hg 2+ -binding modulates MerR function, we report here the crystal structures of apo and Hg 2+ -bound MerR from Bacillus megaterium , corresponding respectively to the repressor and activator conformation of MerR. To our knowledge, the apo-MerR structure represents the first visualization of a MerR family member in its intact and inducer-free form. And the Hg 2+ -MerR structure offers the first view of a triligated Hg 2+ -thiolate center in a metalloprotein, confirming that MerR binds Hg 2+ via trigonal planar coordination geometry. Structural comparison revealed the conformational transition of MerR is coupled to the assembly/disassembly of a buried Hg 2+ binding site, thereby providing a structural basis for the Hg 2+ -mediated functional switching of MerR. The pronounced Hg 2+ -induced repositioning of the MerR DNA-binding domains suggests a plausible mechanism for the transcriptional regulation of the mer operon.

Description: The human JC virus (JCV) is potentially carcinogenic to humans as a Group 2B carcinogen, and it is ubiquitous in human populations. To investigate whether the small tumour (ST) antigen of the JCV contributes to genomic instability, we established cell lines stably expressing the JCV ST and examined its role in DNA repair. Results from host cell reactivation (HCR) assay revealed that the established cell lines exhibited lower nucleotide excision repair (NER) activity than the vector control cells did. The presence of -H2AX, a marker of DNA damage, indicated that the established cell line contained more DNA damage foci compared with vector control cells. Furthermore, the results of clonogenic analyses indicated that the JCV ST-expressing cells were more sensitive than the vector control cells to ultraviolet (UV) irradiation and cisplatin treatment. Micronuclei formation assay revealed that the JCV ST-positive cells presented more chromosomal breakages than did the JCV ST-negative cells, particularly after exposure to DNA-damaging agents. The xeroderma pigmentosum Group D protein, a DNA helicase involved in NER, was downregulated in the JCV ST-positive cells in response to UV irradiation. The effect of the protein phosphatase 2A (PP2A) inhibitor okadaic acid on NER was similar to that of the ST, which is a PP2A-binding protein. Therefore, the deactivation of the PP2A might underlie ST-mediated NER inhibition. The results of this study indicate that exposing JCV ST-positive cells to DNA-damaging agents causes genomic instability, which contributes to carcinogenesis. Our data provide further evidence on the association between the JCV ST and human cancer.

Description: Most authentication protocols are used for remote users, in which the registration is achieved through a secure channel and the authentication is achieved through an insecure channel. However, in real life, there are many applications in which the registration is implemented remotely through an insecure channel and the authentication is achieved through a secure channel. In this paper, a novel authentication protocol that is suitable for the insecure registration is proposed. There are three main contributions, i.e. (i) the registration can be implemented through an insecure channel, (ii) the authentication is achieved by image exchange between the registration center and the user and (iii) a proxy user authentication mechanism is proposed, which allows a proxy user to act on behalf of the primary user. The correctness and security of the proposed authentication protocol are proved by both theoretical analysis and experimental simulations.

Description: G-quadruplex (G4) is a promising target for anti-cancer treatment. In this paper, we provide the first evidence supporting the presence of G4 in the mitochondrial DNA (mtDNA) of live cells. The molecular engineering of a fluorescent G4 ligand, 3,6-bis(1-methyl-4-vinylpyridinium) carbazole diiodide (BMVC), can change its major cellular localization from the nucleus to the mitochondria in cancer cells, while remaining primarily in the cytoplasm of normal cells. A number of BMVC derivatives with sufficient mitochondrial uptake can induce cancer cell death without damaging normal cells. Fluorescence studies of these anti-cancer agents in live cells and in isolated mitochondria from HeLa cells have demonstrated that their major target is mtDNA. In this study, we use fluorescence lifetime imaging microscopy to verify the existence of mtDNA G4s in live cells. Bioactivity studies indicate that interactions between these anti-cancer agents and mtDNA G4 can suppress mitochondrial gene expression. This work underlines the importance of fluorescence in the monitoring of drug-target interactions in cells and illustrates the emerging development of drugs in which mtDNA G4 is the primary target.

Description: Although the objective of secure communication can be achieved by using cryptographic tools, the undeniability that results from cryptographic properties may create a potential threat to the sender of the message. Unfortunately, most existing deniable protocols only provide 1-out-of-2 deniability. When both parties (the sender and the receiver) are allowed to deny generating the message, a dispute might occur between these two parties. The 1-out-of-2 deniable protocol can result in an unfair resolution of the dispute. Therefore, we propose a new model of deniability, called 1-out-of- deniability, that can provide full deniability. The 1-out-of- deniability protocol allows the originator of the message to deny that he or she generated the message, since there are an infinite number of possible message generators; at the same time, all transmitted messages can be protected and authenticated between the sender and the intended receiver. Our design can be implemented by using any public-key cryptography technique. We also analyze the correctness of the proposed protocols based on logical rules, and two practical examples are given to illustrate our design.

Description: The understanding of protein-folding mechanisms is often considered to be an important goal that will enable structural biologists to discover the mysterious relationship between the sequence, structure and function of proteins. The ability to predict protein-folding rates without the need for actual experimental work will assist the research work of structural biologists in many ways. Many bioinformatics tools have emerged in the past decade, and each has showcased different features. In this article, we review and compare eight web-based prediction tools that are currently available and that predominantly predict the protein-folding rate. The prediction performance, usability and utility, together with the prediction tool development and validation methodologies for these tools, are critically reviewed. This article is presented in a comprehensible manner to assist readers in the process of selecting the most appropriate bioinformatics tools to meet their needs.

Description: The solubility of recombinant protein expressed in Escherichia coli often represents the production yield. However, up-to-date, instances of successful production of soluble recombinant proteins in E. coli expression system with high yield remain scarce. This is mainly due to the difficulties in improving the overall production capacity, as most of the well-established strategies usually involve a series of trial and error steps with unguaranteed success. One way to concurrently improve the production yield and minimize the production cost would be incorporating the potency of bioinformatics tools to conduct in silico studies, which forecasts the outcome before actual experimental work. In this article, we review and compare seven prediction tools available, which predict the solubility of protein expressed in E. coli , using the following criteria: prediction performance, usability, utility, prediction tool development and validation methodologies. This comprehensive review will be a valuable resource for researchers with limited prior experience in bioinformatics tools. As such, this will facilitate their choice of appropriate tools for studies related to enhancement of intracellular recombinant protein production in E. coli .

Description: With the rapid development of cloud computing technologies, more and more service providers place their services in clouds for users. In the cloud environment, users can access the resources and services without knowing the location of data, computing devices and platforms. With the popularity of cloud computing applications, authentication and security issues of cloud computing have become important research topics. Considering the benefits of implementing a service system in the cloud environment and the convenience of the integration of different ticket-sale systems, we propose a novel and secure diverse ticket-sale system (DTS) in hybrid cloud using smart cards. The accuracy of involved participant authentication is demonstrated according to the BAN logic. The DTS contains a ticket integration platform that the service providers can delegate the sale of their service tickets to the integrated server, and the customers can freely browse and purchase electronic service tickets from the system in any networked place. We also show that the DTS system possesses many good features and can effectively resist a number of potential attacks.

Description: Aims and Methods Diversity-disturbance research has focused on community diversity, but disturbance frequency could impact diversity within species as well, with important consequences for community diversity and ecosystem function. We examined patterns of genetic diversity of a dominant grass species, Andropogon gerardii , in native North American tallgrass prairie sites located in eastern Kansas that have been subjected to a gradient of fire frequency treatments (burned every 1, 2, 4 or 20 years) since the 1970s. In addition, we were able to assess the relationships between genetic diversity of A. gerardii , species diversity and productivity across this range of fire frequencies. Important Findings We found no significant relationships between genetic diversity of A. gerardii at the local scale (1 m 2 plot level) and disturbance frequency (burned 2 to 32 times over a 38-year period). However, at the site level (i.e. across all plots sampled within a site, ~100 m 2 ) there were differences in genotype richness and composition, as well as genomic dissimilarity among individuals of A. gerardii . Genotype richness was greatest for the site burned at an intermediate (4-year) frequency and lowest for the infrequently (20-year) burned site. In addition, genotypes found in the frequently burned sites were more similar from each other than expected by random chance than those found in the infrequently burned sites. Genotype composition of A. gerardii was not significantly different between the frequently burned sites (annual vs. 2 year) but did differ between frequently burned and infrequently burned sites (1 and 2 year vs. 4 and 20 year, etc.). Together, these results suggest site-level ecological sorting of genotypes in intact prairie across a broad gradient of disturbance frequencies, likely driven by alterations in environmental conditions. Frequent fire promotes the abundance of dominant grass species, reduces plant community diversity and impacts ecosystem processes such as productivity. Our study suggests that genetic diversity within dominant grass species also may be affected by disturbance frequency, which could have important implications for how species are able to respond to disturbance.

Description: Motivation: p38 mitogen-activated protein kinase activation plays an important role in resistance to chemotherapeutic cytotoxic drugs in treating multiple myeloma (MM). However, how the p38 mitogen-activated protein kinase signaling pathway is involved in drug resistance, in particular the roles that the various p38 isoforms play, remains largely unknown. Method: To explore the underlying mechanisms, we developed a novel systems biology approach by integrating liquid chromatography–mass spectrometry and reverse phase protein array data from human MM cell lines with computational pathway models in which the unknown parameters were inferred using a proposed novel algorithm called modularized factor graph. Results: New mechanisms predicted by our models suggest that combined activation of various p38 isoforms may result in drug resistance in MM via regulating the related pathways including extracellular signal-regulated kinase (ERK) pathway and NFB pathway. ERK pathway regulating cell growth is synergistically regulated by p38 isoform, whereas nuclear factor kappa B (NFB) pathway regulating cell apoptosis is synergistically regulated by p38α isoform. This finding that p38 isoform promotes the phosphorylation of ERK1/2 in MM cells treated with bortezomib was validated by western blotting. Based on the predicted mechanisms, we further screened drug combinations in silico and found that a promising drug combination targeting ERK1/2 and NFB might reduce the effects of drug resistance in MM cells. This study provides a framework of a systems biology approach to studying drug resistance and drug combination selection. Availability and implementation: RPPA experimental Data and Matlab source codes of modularized factor graph for parameter estimation are freely available online at http://ctsb.is.wfubmc.edu/publications/modularized-factor-graph.php Contact: xizhou@wakehealth.edu or zhanglcq@swu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.