A Stochastic Model for Helix Bending in B-DNA

Abstract

Bending in double-helical B-DNA apparently occurs only by rolling adjacent base pairs over one another along their long axes. The lifting apart of ends that would be required by tilt or wedge angle contributions is too costly in free energy and does not occur. Roll angles at base steps can be positive (compression of major groove) or negative (compression of minor groove); with the former somewhat easier.

Individual steps may advance or oppose the overall direction of bend, or make lateral excursions, but the result of this series of “random roll” steps is the production of a net bending in the helix axis. Because the natural roll points for bending in a given plane occur every 5 base pairs, one would expect that double-helical DNA wrapped around a nucleosome core would exhibit bends with the same periodicity. Alternate bends might be particularly acute where the major groove faced the nucleosome core and was compressed against it.

The “annealed kinking” model proposed by Fratini et al. (J. Biol. Chem. 257, 14686 (1982) was suggested from the observation that a major bend at a natural roll point is flanked by decreasing roll angles at the steps to either side, as though local strain was being minimized by somewhat blurring the bend out rather than keeping it localized. The random walk model suggested in this paper would describe this as a decreased roll angle as the helix step rotates toward a direction perpendicular to the overall bend. Bending of DNA is seen to be a more stochastic process than had been suspected. Detailed analysis of every helix step reveals both side excursions and backward or retrograde motion, as in any random walk situation. Yet these isolated steps counteract one another, to leave behind a residuum of overall bending in a specific direction.     

A Realistic Host-Vector Transmission Model for Describing Malaria Prevalence Pattern

Malaria continues to be a major public health concern all over the world even after effective control policies have been employed, and considerable understanding of the disease biology have been attained, from both the experimental and modelling perspective. Interactions between different general and local processes, such as dependence on age and immunity of the human host, variations of temperature and rainfall in tropical and sub-tropical areas, and continued presence of asymptomatic infections, regulate the host-vector interactions, and are responsible for the continuing disease prevalence pattern. In this paper, a general mathematical model of malaria transmission is developed considering short and long-term age-dependent immunity of human host and its interaction with pathogen-infected mosquito vector. The model is studied analytically and numerically to understand the role of different parameters related to mosquitoes and humans. To validate the model with a disease prevalence pattern in a particular region, real epidemiological data from the north-eastern part of India was used, and the effect of seasonal variation in mosquito density was modelled based on local climactic data. The model developed based on general features of host-vector interactions, and modified simply incorporating local environmental factors with minimal changes, can successfully explain the disease transmission process in the region. This provides a general approach toward modelling malaria that can be adapted to control future outbreaks of malaria.     

Contractile Mechanisms in Flagella

The elastic theory of flexural waves in thin rods accurately predicts the velocity of flagellar bending waves over a wide range of viscosities. This shows that flagella behave as a purely mechanical system for the transmission of these waves. An evaluation of the total bending moment reveals that this moment occurs in phase over the entire length of a flagellum. From this it is concluded that each contractile fiber in the flagella is activated simultaneously over its whole length. The magnitude of the bending moment decreases linearly along the flagellum. This is most easily explained by a sliding filament hypothesis in flagella with the elementary 9 + 2 fibers. The expression found for the bending moment explains logically that the wave velocity in flagella is determined by their mechanical properties and the outside viscosity only.     

A Flagella Staining Technic for Soil Bacteria

In an attempt to stain the flagella of soil bacteria, many of which have flagella so fine that they are hard to stain by most methods, a technic was developed which combines the best points of Hofer and Wilson's method with that of Bailey as developed by O'Toole. Satisfactory preparations have been obtained for organisms of the genera Pseudomonas, Phytomonas, Alcaligenes, Escherichia, Azotobacter, and Bacillus. This technic, therefore, is recommended as a rapid and constant method for routine flagella staining of all motile aerobic organisms; it combines Hofer and Wilson's method of cleaning the slides with O'Toole's technic of spreading the smears and with a modification of Bailey's mordant.     

Synthesis of Bacterial Flagella: Chromosomal Synchrony and Flagella Synthesis

Synchronous cultures of Bacillus subtilis 168 M were obtained from light-density spores germinated at 46 C and grown at 37 C. This procedure synchronizes both cell division and chromosome replication. The chromosome synchrony was demonstrated by using transformation to measure changes in marker frequency during the cell cycle. The synthesis of two enzymes and of bacterial flagellar protein was also followed. All of the proteins were found to be synthesized continuously with an abrupt doubling in the rate of synthesis at a specific time in the cell cycle. The time at which the doubling occurred for each enzyme corresponded to the time at which the structural gene for the enzyme was replicated. The doubling of the rate of flagella synthesis corresponded to the time of replication of the hisA1 gene. We conclude that the genetic locus for the factors involved in the rate-limiting steps in flagella synthesis are located on the genetic map near the hisA1 locus.     

A Method for the Staining of Bacterial Flagella

A modification of the Loeffler method of staining bacterial flagella is proposed. The chief points of the modification are: The cultures are inoculated into distilled water after two successive daily transfers on agar slants, and the distilled water cultures are incubated at optimum temperature for from 48 to 72 hours. The mordant (tannic acid, ferrous sulphate, basic fuchsin) is allowed to stand 18 to 24 hours before use, and then cleared by centrifuging or filtering. An anilin water fuchsin is used as a stain. No heat is used for either mordanting or staining; but both mordant and stain are allowed to act on the preparation for 15 minutes. The writer finds the method admirably adapted for use in class work, where nearly 100 per cent success has been obtained except in the case of some three or four species of bacteria that are especially difficult to stain.     

A Method for the Staining of Bacterial Flagella

A modification of the Loeffler method of staining bacterial flagella is proposed. The chief points of the modification are: The cultures are inoculated into distilled water after two successive daily transfers on agar slants, and the distilled water cultures are incubated at optimum temperature for from 48 to 72 hours. The mordant (tannic acid, ferrous sulphate, basic fuchsin) is allowed to stand 18 to 24 hours before use, and then cleared by centrifuging or filtering. An anilin water fuchsin is used as a stain. No heat is used for either mordanting or staining; but both mordant and stain are allowed to act on the preparation for 15 minutes. The writer finds the method admirably adapted for use in class work, where nearly 100 per cent success has been obtained except in the case of some three or four species of bacteria that are especially difficult to stain.     

A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System

Cells cope with the threat of xenobiotic stress by activating a complex molecular network that recognizes and eliminates chemically diverse toxic compounds. This “chemoimmune system” consists of cellular Phase I and Phase II metabolic enzymes, Phase 0 and Phase III ATP Binding Cassette (ABC) membrane transporters, and nuclear receptors regulating these components. In order to provide a systems biology characterization of the chemoimmune network, we designed a reaction kinetic model based on differential equations describing Phase 0–III participants and regulatory elements, and characterized cellular fitness to evaluate toxicity. In spite of the simplifications, the model recapitulates changes associated with acquired drug resistance and allows toxicity predictions under variable protein expression and xenobiotic exposure conditions. Our simulations suggest that multidrug ABC transporters at Phase 0 significantly facilitate the defense function of successive network members by lowering intracellular drug concentrations. The model was extended with a novel toxicity framework which opened the possibility of performing in silico cytotoxicity assays. The alterations of the in silico cytotoxicity curves show good agreement with in vitro cell killing experiments. The behavior of the simplified kinetic model suggests that it can serve as a basis for more complex models to efficiently predict xenobiotic and drug metabolism for human medical applications.     

Flagella and Motility in Actinobacillus pleuropneumoniae

Actinobacillus pleuropneumoniae has been considered nonmotile and nonflagellate. In this work, it is demonstrated that A. pleuropneumoniae produces flagella composed of a 65-kDa protein with an N-terminal amino acid sequence that shows 100% identity with those of Escherichia coli, Salmonella, and Shigella flagellins. The DNA sequence obtained through PCR of the fliC gene in A. pleuropneumoniae showed considerable identity (93%) in its 5' and 3' ends with the DNA sequences of corresponding genes in E. coli, Salmonella enterica, and Shigella spp. The motility of A. pleuropneumoniae was observed in tryptic soy or brain heart infusion soft agar media, and it is influenced by temperature. Flagella and motility may be involved in the survival and pathogenesis of A. pleuropneumoniae in pigs.     

Energy Conversion in Bull Sperm Flagella

With the use of a specially developed incubation chamber the rates of motility, respiration, and fructolysis were measured simultaneously on semen samples. By inhibiting the respiration with antimycin A, and/or the fructolysis with 2-deoxyglucose, the rates of each of the two ATP-producing pathways could be reduced independently. In this way the ratio of the amount of free energy produced by respiration and by fructolysis could be varied at will from 1 to 0. In uninhibited preparations approximately 75% of the free energy derives from respiration, and 25% from fructolysis. By the use of the absolute rates of respiration, fructolysis, and motility, the efficiency of the conversion of free energy into hydrodynamic work was calculated. After correction for the decay of the preparation during the experiment, this conversion efficiency was found to be 30–45% lower for free energy from respiration than for free energy from fructolysis. The difference in distribution of the enzymes for fructolysis and respiration over the flagellum was ruled out as the cause of the efficiency difference. The respiration could be 70% inhibited by oligomycin. It is concluded that approximately one-third of the free energy from respiration is used for maintenance of the mitochondria.     

A Simple, Rapid Method for Demonstrating Bacterial Flagella

We developed a simple, rapid method for demonstrating flagellation of bacteria using the fluorescent protein stain NanoOrange (Molecular Probes, Eugene, Oreg.). The NanoOrange reagent binds to hydrophobic regions of proteins, which results in substantial enhancement of fluorescence. Unbound reagent is essentially nonfluorescent. NanoOrange fluorescently stained bacterial cell bodies, as well as flagella and other appendages, which could be directly observed by epifluorescence microscopy. Detection of flagella was further improved by using a charge-coupled device camera for image capture and processing. The reliability of the method was tested by using 37 pure cultures of marine bacteria. Detection of flagella on the isolates by NanoOrange staining was compared to detection by transmission electron microscopy (TEM). For 36 of 37 cultures, the two methods yielded the same results. In one case, flagella were detected by TEM but not by NanoOrange, although the difference may be attributable to differences between the culture preparations. NanoOrange staining is rapid (10 to 15 min) and does not require fixation or dehydration, so live samples can be stained. Since NanoOrange is a general protein stain and works directly in seawater, it may also prove to be useful for staining other proteinaceous material that is of interest to aquatic microbial ecologists.     

The Flagella of Pseudomonas solanacearum

Summary: Electron microscopic examination of 5 strains of Pseudomonas solanacearum , including the proposed neotype, NCPPB 325, showed that the cells of these organisms possess polar flagella.     

Basal Organelles of Bacterial Flagella

Liberated by enzymatic lysis of the cells, the flagella of Rhodospirillum rubrum, R. molischianum, and R. fulvum all have a similar structure. The hook at the base of the flagellum is connected by a short, narrow collar to a paired disc in the basal organelle. This paired disc is in turn connected to a second paired disc. The disposition of flagella to which fragments of the cell membrane still adhere suggests that the narrow collar at the base of the hook traverses both the wall and the membrane, and that the upper pair of discs in the basal organelle lies just beneath the surface of the membrane.     

Flagella Overexpression Attenuates Salmonella Pathogenesis

Flagella are cell surface appendages involved in a number of bacterial behaviors, such as motility, biofilm formation, and chemotaxis. Despite these important functions, flagella can pose a liability to a bacterium when serving as potent immunogens resulting in the stimulation of the innate and adaptive immune systems. Previous work showing appendage overexpression, referred to as attenuating gene expression (AGE), was found to enfeeble wild-type Salmonella. Thus, this approach was adapted to discern whether flagella overexpression could induce similar attenuation. To test its feasibility, flagellar filament subunit FliC and flagellar regulon master regulator FlhDC were overexpressed in Salmonella enterica serovar Typhimurium wild-type strain H71. The results show that the expression of either FliC or FlhDC alone, and co-expression of the two, significantly attenuates Salmonella. The flagellated bacilli were unable to replicate within macrophages and thus were not lethal to mice. In-depth investigation suggests that flagellum-mediated AGE was due to the disruptive effects of flagella on the bacterial membrane, resulting in heightened susceptibilities to hydrogen peroxide and bile. Furthermore, flagellum-attenuated Salmonella elicited elevated immune responses to Salmonella presumably via FliC’s adjuvant effect and conferred robust protection against wild-type Salmonella challenge.