Gene Function Hypotheses for the Campylobacter jejuni Glycome Generated by a Logic-Based Approach

Increasingly, experimental data on biological systems are obtained from several sources and computational approaches are required to integrate this information and derive models for the function of the system. Here, we demonstrate the power of a logic-based machine learning approach to propose hypotheses for gene function integrating information from two diverse experimental approaches. Specifically, we use inductive logic programming that automatically proposes hypotheses explaining the empirical data with respect to logically encoded background knowledge. We study the capsular polysaccharide biosynthetic pathway of the major human gastrointestinal pathogen Campylobacter jejuni. We consider several key steps in the formation of capsular polysaccharide consisting of 15 genes of which 8 have assigned function, and we explore the extent to which functions can be hypothesised for the remaining 7. Two sources of experimental data provide the information for learning—the results of knockout experiments on the genes involved in capsule formation and the absence/presence of capsule genes in a multitude of strains of different serotypes. The machine learning uses the pathway structure as background knowledge. We propose assignments of specific genes to five previously unassigned reaction steps. For four of these steps, there was an unambiguous optimal assignment of gene to reaction, and to the fifth, there were three candidate genes. Several of these assignments were consistent with additional experimental results. We therefore show that the logic-based methodology provides a robust strategy to integrate results from different experimental approaches and propose hypotheses for the behaviour of a biological system.     

Osteoprotegerin: Multiple partners for multiple functions

Osteoprotegerin (OPG) is an essential secreted protein in bone turnover due to its role as a decoy receptor for the Receptor Activator of Nuclear Factor-kB ligand (RANKL) in the osteoclasts, thus inhibiting their differentiation. However, there are additional ligands of OPG that confer various biological functions. OPG can promote cell survival, cell proliferation and facilitates migration by binding TNF-related apoptosis inducing ligand (TRAIL), glycosaminoglycans or proteoglycans. A large number of in vitro, pre-clinical and clinical studies provide evidences of OPG involvement in vascular, bone, immune and tumor biology. This review describes an overview of the different OPG ligands regulating its biological functions.     

Mono- and dicarboxylic polypyridyl-Ru complexes as potential cell DNA dyes and transfection agents

A ruthenium coordination complex, incorporating two highly extended pi-systems DIP and two carboxylic groups: [Ru(DIP)2(L-L)]2+ where DIP=4,7-diphenyl-1,10-phenanthroline and L-L=4,4'-dicarboxy-2,2'-bipyridine, is found to be of biological interest. It constitutes an effective nuclear DNA dye for living cells: fluorescent, permeant, biocompatible, high Stokes shift. These features are commented in terms of hydrophobicity and DNA binding. In addition, this complex is shown to internalize a plasmid carrying the enhanced green fluorescent protein (EGFP) gene. Positive results are obtained for gene expression, which is related to condensation of the DNA by this ruthenium agent. This opens up an innovative transfection route based on metal complexes.     

Health Literacy,Computer Skills and Quality of Patient-Physician Communication in Chinese Patients with Cataract

Purpose

The aim of the study was to assess levels of health literacy and computer skills in Chinese patients with cataract, and their impact on the doctor-patient relationship.

Methods

We undertook a cross-sectional study of cataract patients scheduled for cataract extraction procedures in Guangdong Province, China. Generic health literacy was assessed using 3 established screening questions. Adequate computer skills was determined if patients had used a computer and routinely used search engines on the Internet. Socio-demographic measures (e.g., age, sex, education) were obtained from a standardized interview. Participants who indicated that they could not understand what their doctors mean were considered to have had poor patient-physician communications.

Results

Of the 211 participants, 92 (43.6%) had inadequate health literacy and 204 (96.7%) inadequate computer skills. In multivariate analysis, females were more likely to have inadequate health literacy (odds ratio = 2.5, 95% confidence intervals [CI]: 1.3 to 4.7). People with inadequately health literacy were more likely to have a poor patient-physician communication (odds ratio = 3.5, 95% CIs: 1.3 to 9.0). Similar associations were found for inadequate computer skills.

Conclusion

Chinese elderly patients with cataract have inadequate health literacy and very limited computer skills, which place them at high risk of misunderstanding and mismanaging their ocular conditions. Patient education information other than online materials may improve the eye care and outcomes of these patients.     

Identification of a Cholesterol-Binding Pocket in Inward Rectifier K+ (Kir) Channels

Cholesterol is the major sterol component of all mammalian plasma membranes. Recent studies have shown that cholesterol inhibits both bacterial (KirBac1.1 and KirBac3.1) and eukaryotic (Kir2.1) inward rectifier K⁺ (Kir) channels. Lipid-sterol interactions are not enantioselective, and the enantiomer of cholesterol (ent-cholesterol) does not inhibit Kir channel activity, suggesting that inhibition results from direct enantiospecific binding to the channel, and not indirect effects of changes to the bilayer. Furthermore, conservation of the effect of cholesterol among prokaryotic and eukaryotic Kir channels suggests an evolutionary conserved cholesterol-binding pocket, which we aimed to identify. Computational experiments were performed by docking cholesterol to the atomic structures of Kir2.2 (PDB: 3SPI) and KirBac1.1 (PDB: 2WLL) using Autodock 4.2. Poses were assessed to ensure biologically relevant orientation and then clustered according to location and orientation. The stability of cholesterol in each of these poses was then confirmed by molecular dynamics simulations. Finally, mutation of key residues (S95H and I171L) in this putative binding pocket found within the transmembrane domain of Kir2.1 channels were shown to lead to a loss of inhibition by cholesterol. Together, these data provide support for this location as a biologically relevant pocket.     

Tooth germ initiation patterns in a developing dentition: An in vivo study of Xenopus laevis tadpoles

The transparency of soft tissue in Xenopus laevis tadpoles and the anterior‐posterior orientation of their developing tooth germs in the upper jaw offer a unique opportunity for the in vivo charting of the first 15–20 days of the developing dentition. Twenty‐two X. laevis tadpoles were anesthetized daily and their mouths opened to record the first appearance, position, and development of tooth germs in the upper jaw. The initiation patterns revealed considerable variability between animals, and even between the jaw quadrants in the same animal. This variability appears within a structural boundary and the results are consistent with the presence of an odontogenic band. The final length of dental rows far exceeded the jaw growth for each quadrant during the recording period. This in vivo investigation underlines the limits of cross‐sectional studies, and in particular the assumption that tooth germs initiate at the same position in the dental row. The tooth germ initiation patterns in this study did not align with the predictions of standard models for the development of the dentition—Zahnreihen, Clone, and New Progress Zone theories.     

Factors influencing the in vitro growth of Mycobacterium leprae: effect of sulfhydryl compounds

In an attempt to determine the factors that influence the in vitro growth of Mycobacterium leprae in DH medium, the effects of sulfhydryl compounds were studied. Growth of M. leprae was monitored using two biochemical indicators. Only the sulfhydryl compounds, in reduced form, containing carboxyl group could support the growth of M. leprae. Higher cell yields were obtained when these sulfhydryl compounds were supplemented with dithiothreitol, presumable to keep the monothiols in reduced state during long incubation periods. Ascorbic acid could not replace dithiothreitol for this purpose. It is suggested that these carboxylated sulfhydryl compounds play a role in the metabolic activity of M. leprae along with maintaining low redox potential of the medium.     

Lipopolysaccharide-Induced Dynamic Lipid Membrane Reorganization: Tubules,Perforations, and Stacks

Lipopolysaccharide (LPS) is a unique lipoglycan, with two major physiological roles: 1), as a major structural component of the outer membrane of Gram-negative bacteria and 2), as a highly potent mammalian toxin when released from cells into solution (endotoxin). LPS is an amphiphile that spontaneously inserts into the outer leaflet of lipid bilayers to bury its hydrophobic lipidic domain, leaving the hydrophilic polysaccharide chain exposed to the exterior polar solvent. Divalent cations have long been known to neutralize and stabilize LPS in the outer membrane, whereas LPS in the presence of monovalent cations forms highly mobile negatively-charged aggregates. Yet, much of our understanding of LPS and its interactions with the cell membrane does not take into account its amphiphilic biochemistry and charge polarization. Herein, we report fluorescence microscopy and atomic force microscopy analysis of the interaction between LPS and fluid-phase supported lipid bilayer assemblies (sLBAs), as model membranes. Depending on cation availability, LPS induces three remarkably different effects on simple sLBAs. Net-negative LPS-Na⁺ leads to the formation of 100-μm-long flexible lipid tubules from surface-associated lipid vesicles and the destabilization of the sLBA resulting in micron-size hole formation. Neutral LPS-Ca²⁺ gives rise to 100-μm-wide single- or multilamellar planar sheets of lipid and LPS formed from surface-associated lipid vesicles. Our findings have important implications about the physical interactions between LPS and lipids and demonstrate that sLBAs can be useful platforms to study the interactions of amphiphilic virulence factors with cell membranes. Additionally, our study supports the general phenomenon that lipids with highly charged or bulky headgroups can promote highly curved membrane architectures due to electrostatic and/or steric repulsions.