Discovering functions and revealing mechanisms at molecular level from biological networks

With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein-protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools.     

塞来昔布诱导前列腺癌细胞凋亡及其机制研究

目的:研究塞来昔布对前列腺癌DU-145细胞凋亡及侵袭力的影响,并探讨其可能作用机制.方法:应用Hoechst 33342/PI染色检测细胞凋亡形态;Annexin V-FITC/PI双染色流式细胞术检测不同浓度塞来昔布诱导细胞凋亡能力;RT-PCR法检测塞来昔布作用后Bcl-2、E-cadherin、ICE及COX-2 mRNA表达水平的变化.结果:Hoechst 33342/PI双染色可观察到药物作用后.细胞呈现明显凋亡现象.流式细胞术证实塞来昔布能有效诱导细胞凋亡,0、25、50、100、200μmol/L塞来昔布诱导细胞凋亡率分别为(1.10±0.15)%,(3.87±0.79)%,(10.59±1.58)%,(22.50±3.30)%,(33.85±2.71)%,细胞凋亡率呈现浓度依赖性递增.RT-PCR显示Bcl-2mRNA表达水平下调,E-cadherin mRNA表达水平上调,ICE mRNA表达水平无明显变化,COX-2 mRNA未检测到.结论:塞采昔布能有效诱导前列腺癌DU-145细胞凋亡并使其侵袭力降低.     

Baroreceptor mechanisms at the cellular level

Nothing is known of transduction mechanisms of baroreceptors in vivo. Not even the site of transduction is known. However, there are mechanotransducer ion channels that provide a useful model system of transduction. In these channels, transduction is accomplished by a strain-dependent increase in the probability of being open. Membrane tension is coupled to the channel by cytoskeletal strands that concentrate the strain energy from a large (approximately equal to 4000 A diameter) area of membrane and thereby provide high sensitivity. The channel is fast and does not inactivate, but viscoelastic coupling to the channel can dramatically alter the transfer function.     

Modulation of molecular signaling mechanisms in excitable cells by toxins and bacterial substances

The mechanisms of bacterial substances (protein A, peptidoglican Staphylococcus aureus), bacterium toxins (St. aureus, Corynebacterium diphtheriae, Shigella dysenteriae, Clostridium botulinum, Clostridium tetani, Vibrio choleral), transfer factor of immune reactivity to Staphylococcus aureus upon the key link (acetylcholine-, ATP-, inositol-1,4,5-triphosphate-, ryanodin-sensitive receptors, G-proteins, Ca2+, K(+)-transporting systems, second messengers) in the chain of signal conduction of excitatory and inhibitory agonists in excitable cells were examined. The action of these immune-active substances upon contractile proteins ATP-ase activity and protein synthesis was also discussed.     

Change of waveform in bacterial flagella: The role of mechanics at the molecular level

The flagella of Salmonella and other bacteria are constructed from molecules of the protein flagellin in a way which permits relatively easy transition between members of a family of distinct stable left and right-handed helical waveforms. Changes of waveform, particularly between “normal” (left-handed) and “curly” (right-handed) play an important role in the switch from smooth swimming to tumbling in chemotaxis. This paper establishes some mechanical properties of model flagella built from bi-stable subunits, which in turn clarifies the mechanics of the changes of waveform which occur, in a viscous fluid environment, at various points in the swimming cycle.Available data on the joining of different helical waveforms in a single filament, supplemented by information on the way in which helical filaments flatten down in preparation for electron microscopy, are well-fitted by the mechanical behaviour of an assembly of mechanical subunits having some simple distinctive design features. The same arrangement makes possible an explanation for the formation of flagellar-like but straight polymers from Salmonella flagellin in the presence of high concentrations of NaCl.     

Respiratory actions induced by cholecystokinin at the brainstem level

A functional differentiation of the action of cholecystokinin octapeptide (CCK-8) on the respiratory centers was accomplished by the topical application to the ventral surface of the medulla and to the dorso-rostral pontine surface in cats. In the medulla, CCK-8S at doses ranging from 0.09 nmol to 0.88 nmol, stimulated tidal volume in a dose-dependent fashion, with minimal or no changes in frequency. The antagonist proglumide (30 nmol) inhibited specifically the action on the respiratory amplitude. In the pons, CCK-8S did not modify the respiratory activity even at the dose of 8.8 nmol. The results suggest a specific involvement of CCK-8S in the mechanisms controlling respiratory amplitude, which appear mostly restricted to the medullary level. The lack of effect of the peptide in the pons is in agreement with the absence of CCK receptors in the respiration related nuclei located at that level, as evidenced by autoradiographic studies.     

Modern variations of human influenza group A viruses at the molecular level]

The authors own results on the variety of the genomic primary structures in human influenza A viruses participating in the epidemic process, including the atypical viruses. The comparative studies revealed new trends in the HA gene antigenic drift on the late stages and the PB1 gene shift. Modifications occurring in the primary structure of the influenza A viruses native genomes during laboratory treatment (adaptation to new hosts, vaccine preparation, egg passaging) have been analyzed. Sequencing of several types of "antigenic anachronisms" revealed the direct links between some of such viruses and the anthropogenic pollution of the biosphere by vaccine strains. Modifications in the HA genes of influenza A viruses during the persistent infection have also been studied.     

Exaptation at the molecular genetic level

The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA—including transposed elements, formerly considered junk DNA—for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.     

Pathogenesis of experimentally induced bacterial cold water disease in ayu Plecoglossus altivelis

Ayu Plecoglossus altivelis were experimentally infected with Flavobacterium psychrophilum, which is the causative agent of bacterial cold water disease (CWD). The fish infected by immersion usually died within an hour after they became moribund. The blood volume and haematocrit values of moribund fish were low, while those values of many infected fish that were not moribund were in the range of controls. Most of the affected fish in the immersion-infected groups had ulcerative lesions on their lower jaw. No histological evidence of haemolysis was observed. These results suggest that rapid bleeding occurred through ulcerative lesions, probably causing hypoxia which killed the fish. Ulcerative lesions developed on the dorsal skin when this area had been slightly abraded artificially prior to immersion challenge. Histologically, F. psychrophilum was initially found on the skin that had microscopic injuries, but not on normal skin. The bacterium then entered the dermis and migrated through connective tissues. The lesions subsequently expanded into the underlying musculature through the myosepta, developed necrotic myositis and formed externally open ulcers. Only in later stages of infection did mild lesions develop in the internal organs and the gill, probably caused by the bacterium migrating through blood vessels. This suggests that infection with CWD through the gill or digestive tract is unlikely. Virtually no open lesions were found in ayu challenged by intramuscular injections except at the injection sites. The results suggest that skin injuries are major portals of entry for F. psychrophilum in ayu, and the bacterium has affinity for collagenous connective tissues.     

Elucidating the molecular mechanisms of bacterial virulence using non-mammalian hosts

Several strains of the human opportunistic pathogen Pseudomonas aeruginosa infect plants, nematodes and insects. Our laboratory has developed a multihost pathogenesis system based on the P. aeruginosa clinical isolate PA14, in which non-mammalian hosts are used to screen directly for virulence-attenuated mutants. The majority of PA14 mutants isolated using non-mammalian hosts also displayed reduced virulence in a burned mouse model. Surprisingly, only a few host-specific virulence factors were identified, and many of the P. aeruginosa mutants were attenuated in virulence in all the hosts. These studies illustrate the extensive conservation in the virulence mechanisms used by P. aeruginosa to infect evolutionarily diverged hosts, and validate the multihost method of screening for virulence factors relevant to mammalian pathogenesis. Through the use of genetically tractable hosts, the multihost pathogenesis model also provides tools for elucidating host responses and dissecting the fundamental molecular interactions that underlie bacterial pathogenesis.     

Changes in bacterial cells induced by high pressure at subzero temperature

The aim of this study was to examine the effect of pressure treatment at 193 MPa and −20 °C on membrane damage, changes in activity of membrane-bound ATPases and degradation of nucleic acids. The experiments were carried out with three Escherichia coli strains, in the exponential and stationary phases of growth, and differing in sensitivity to pressure. All E. coli strains subjected to pressure in the exponential phase of growth were inactivated by 6 log cycles, independently of the strain, which was accompanied by a total loss of ability to plasmolyse, an increase in irreversible membrane permeability to PI, and a reduction of cellular ATP by more than 80%. After pressure treatment of stationary phase cells, the relationship between the inactivation level and the ability to plasmolyse was not as evident as in the case of exponential phase cells. Pressure treatment of two strains of E. coli K-12 and Ec160/59 in the stationary phase that decreased viability by no more than one log cycle led only to reversible permeabilization of bacterial membranes, while irreversible permeabilization was observed in the pressure sensitive E. coli IBA72 strain phase that was inactivated by 4.6 log cycles. The reduction of ATP and changes in ATPase activity after pressure treatment of tested E. coli strains in the stationary phase of growth depended on the stage of inactivation of the particular strain. Electrophoretic analysis showed degradation of RNA isolated after pressure treatment from cells of all E. coli strains tested in the exponential phase of growth. The changes of RNA induced by pressure were not visible in the case of cells in the stationary phase. The degradation of DNA isolated from pressure treated E. coli strains from the exponential as well as from the stationary phase of growth was not observed.     

Plant-pathogen arms races at the molecular level

Advances in research into the genetics of plant-pathogen interactions include an embracing of evolutionary ideas and methodologies. Recent studies reveal positive selection and selective maintenance of variation in plant resistance and defense-related genes. Coevolution between plants and their enemies involves many interactions at the molecular level.