I. Studies on bacteriophage DNA's and minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow dichroism of DNA solutions

Part I

Chapter 1.....A physicochemical study of the DNA molecules from the three bacteriophages, N1, N5, and N6, which infect the bacterium, M. lysodeikticus, has been made. The molecular weights, as measured by both electron microscopy and sedimentation velocity, are 23 x 10⁶ for N5 DNA and 31 x 10⁶ for N1 and N6 DNA's. All three DNA's are capable of thermally reversible cyclization. N1 and N6 DNA's have identical or very similar base sequences as judged by membrane filter hybridization and by electron microscope heteroduplex studies. They have identical or similar cohesive ends. These results are in accord with the close biological relation between N1 and N6 phages. N5 DNA is not closely related to N1 or N6 DNA. The denaturation T_m of all three DNA's is the same and corresponds to a (GC) content of 70%. However, the buoyant densities in CsCl of Nl and N6 DNA's are lower than expected, corresponding to predicted GC contents of 64 and 67%. The buoyant densities in Cs₂SO₄ are also somewhat anomalous. The buoyant density anomalies are probably due to the presence of odd bases. However, direct base composition analysis of N1 DNA by anion exchange chromatography confirms a GC content of 70%, and, in the elution system used, no peaks due to odd bases are present.

Chapter 2.....A covalently closed circular DNA form has been observed as an intracellular form during both productive and abortive infection processes in M. lysodeikticus. This species has been isolated by the method of CsC1-ethidium bromide centrifugation and examined with an electron microscope.

Chapter 3.....A minute circular DNA has been discovered as a homogeneous population in M. lysodeikticus. Its length and molecular weight as determined by electron microscopy are 0.445 μ and 0.88 x 10⁶ daltons respectively. There is about one minicircle per bacterium.

Chapter 4.....Several strains of E. coli 15 harbor a prophage. Viral growth can be induced by exposing the host to mitomycin C or to uv irradiation. The coliphage 15 particles from E. coli 15 and E, coli 15 T^- appear as normal phage with head and tail structure; the particles from E. coli 15 TAU are tailless. The complete particles exert a colicinogenic activity on E.coli 15 and 15 T^-, the tailless particles do not. No host for a productive viral infection has been found and the phage may be defective. The properties of the DNA of the virus have been studied, mainly by electron microscopy. After induction but before lysis, a closed circular DNA with a contour length of about 11.9 μ is found in the bacterium; the mature phage DNA is a linear duplex and 7.5% longer than the intracellular circular form. This suggests the hypothesis that the mature phage DNA is terminally repetitious and circularly permuted. The hypothesis was confirmed by observing that denaturation and renaturation of the mature phage DNA produce circular duplexes with two single-stranded branches corresponding to the terminal repetition. The contour length of the mature phage DNA was measured relative to φX RFII DNA and λ DNA; the calculated molecular weight is 27 x 10⁶. The length of the single-stranded terminal repetition was compared to the length of φX 174 DNA under conditions where single-stranded DNA is seen in an extended form in electron micrographs. The length of the terminal repetition is found to be 7.4% of the length of the nonrepetitious part of the coliphage 15 DNA. The number of base pairs in the terminal repetition is variable in different molecules, with a fractional standard deviation of 0.18 of the average number in the terminal repetition. A new phenomenon termed "branch migration" has been discovered in renatured circular molecules; it results in forked branches, with two emerging single strands, at the position of the terminal repetition. The distribution of branch separations between the two terminal repetitions in the population of renatured circular molecules was studied. The observed distribution suggests that there is an excluded volume effect in the renaturation of a population of circularly permuted molecules such that strands with close beginning points preferentially renature with each other. This selective renaturation and the phenomenon of branch migration both affect the distribution of branch separations; the observed distribution does not contradict the hypothesis of a random distribution of beginning points around the chromosome.

Chapter 5....Some physicochemical studies on the minicircular DNA species in E. coli 15 (0.670 μ, 1.47 x 10⁶ daltons) have been made. Electron microscopic observations showed multimeric forms of the minicircle which amount to 5% of total DNA species and also showed presumably replicating forms of the minicircle. A renaturation kinetic study showed that the minicircle is a unique DNA species in its size and base sequence. A study on the minicircle replication has been made under condition in which host DNA synthesis is synchronized. Despite experimental uncertainties involved, it seems that the minicircle replication is random and the number of the minicircles increases continuously throughout a generation of the host, regardless of host DNA synchronization.

Part II

The flow dichroism of dilute DNA solutions (A₂₆₀≈0.1) has been studied in a Couette-type apparatus with the outer cylinder rotating and with the light path parallel to the cylinder axis. Shear gradients in the range of 5-160 sec.^-1 were studied. The DNA samples were whole, "half," and "quarter" molecules of T4 bacteriophage DNA, and linear and circular λb₂b₅c DNA. For the linear molecules, the fractional flow dichroism is a linear function of molecular weight. The dichroism for linear A DNA is about 1.8 that of the circular molecule. For a given DNA, the dichroism is an approximately linear function of shear gradient, but with a slight upward curvature at low values of G, and some trend toward saturation at larger values of G. The fractional dichroism increases as the supporting electrolyte concentration decreases.

Studies on the submerged plant community in Lake Biwa. I. Distribution and productivity of Egeria densa. A submerged plant invader in the south basin [Translation from: Physiol.Ecol.Japan 17, 283-290, 1976]

Egeria densa (PLANCH.) ST. JOHN, a submerged plant invader, forms a wide submerged plant zone, particularly along the west coast of the south basin, Lake Biwa. The macrophyte occupies over 82% of the plant zone in the basin and its biomass reaches 93% of the total. The estimated annual net production was approximately 1 kg dry wt./m2 in a dense area, which is about 4.5 times as much as the net production by phytoplankton in an offshore area of the basin. Although the area covered by the macrophyte is only 5.8% of the total of the basin, it produced about one-tenth of the total annual primary production. In the most productive season Egeria produced 46% of the total primary productivity. Thus, the macrophyte never be neglected when one considers the energy flow or material circulation in the basin. This study was initiated in order to clarify the role of submerged macrophytes, particularly E. densa, in Lake Biwa. The following points are reported in this paper: the distribution of macrophytes in the south basin; seasonal change in standing crop of E. densa; seasonal change in values related to production, utilizing a model proposed by Ikushima with its parameters experimentally determined.

Steady surface wave pattern in a shear flow

The subject under investigation concerns the steady surface wave patterns created by small concentrated disturbances acting on a non-uniform flow of a heavy fluid. The initial value problem of a point disturbance in a primary flow having an arbitrary velocity distribution (U(y), 0, 0) in a direction parallel to the undisturbed free surface is formulated. A geometric optics method and the classical integral transformation method are employed as two different methods of solution for this problem. Whenever necessary, the special case of linear shear (i.e. U(y) = 1+ϵy)) is chosen for the purpose of facilitating the final integration of the solution.

The asymptotic form of the solution obtained by the method of integral transforms agrees with the leading terms of the solution obtained by geometric optics when the latter is expanded in powers of small ϵ r.

The overall effect of the shear is to confine the wave field on the downstream side of the disturbance to a region which is smaller than the wave region in the case of uniform flows. If U(y) vanishes, and changes sign at a critical plane y = y_cr (e.g. ϵy_cr = -1 for the case of linear shear), then the boundary of this asymmetric wave field approaches this critical vertical plane. On this boundary the wave crests are all perpendicular to the x-axis, indicating that waves are reflected at this boundary.

Inside the wave field, as in the case of a point disturbance in a uniform primary flow, there exist two wave systems. The loci of constant phases (such as the crests or troughs) of these wave systems are not symmetric with respect to the x-axis. The geometric optics method and the integral transform method yield the same result of these loci for the special case of U(y) = U_o(1 + ϵy) and for large Kr (ϵr ˂˂ 1 ˂˂ Kr).

An expression for the variation of the amplitude of the waves in the wave field is obtained by the integral transform method. This is in the form of an expansion in small ϵr. The zeroth order is identical to the expression for the uniform stream case and is thus not applicable near the boundary of the wave region because it becomes infinite in that neighborhood. Throughout this investigation the viscous terms in the equations of motion are neglected, a reasonable assumption which can be justified when the wavelengths of the resulting waves are sufficiently large.

I. Stokes flow past a thin screen. II. Viscous flows past porous bodies of finite size

Part I

The slow, viscous flow past a thin screen is analyzed based on Stokes equations. The problem is reduced to an associated electric potential problem as introduced by Roscoe. Alternatively, the problem is formulated in terms of a Stokeslet distribution, which turns out to be equivalent to the first approach.

Special interest is directed towards the solution of the Stokes flow past a circular annulus. A "Stokeslet" formulation is used in this analysis. The problem is finally reduced to solving a Fredholm integral equation of the second kind. Numerical data for the drag coefficient and the mean velocity through the hole of the annulus are obtained.

Stokes flow past a circular screen with numerous holes is also attempted by assuming a set of approximate boundary conditions. An "electric potential" formulation is used, and the problem is also reduced to solving a Fredholm integral equation of the second kind. Drag coefficient and mean velocity through the screen are computed.

Part II

The purpose of this investigation is to formulate correctly a set of boundary conditions to be prescribed at the interface between a viscous flow region and a porous medium so that the problem of a viscous flow past a porous body can be solved.

General macroscopic equations of motion for flow through porous media are first derived by averaging Stokes equations over a volume element of the medium. These equations, including viscous stresses for the description, are more general than Darcy's law. They reduce to Darcy's law when the Darcy number becomes extremely small.

The interface boundary conditions of the first kind are then formulated with respect to the general macroscopic equations applied within the porous region. An application of such equations and boundary conditions to a Poiseuille shear flow problem demonstrates that there usually exists a thin interface layer immediately inside the porous medium in which the tangential velocity varies exponentially and Darcy's law does not apply.

With Darcy's law assumed within the porous region, interface boundary conditions of the second kind are established which relate the flow variables across the interface layer. The primary feature is a jump condition on the tangential velocity, which is found to be directly proportional to the normal gradient of the tangential velocity immediately outside the porous medium. This is in agreement with the experimental results of Beavers, et al.

The derived boundary conditions are applied in the solutions of two other problems: (1) Viscous flow between a rotating solid cylinder and a stationary porous cylinder, and (2) Stokes flow past a porous sphere.

Self-Similarity and helical symmetry in vortex generator flow simulations

According to experimental observations, the vortices generated by vortex generators have previously been observed to be self-similar for both the axial (u(z)) and azimuthal (u(circle minus)) velocity profiles. Further, the measured vortices have been observed to obey the criteria for helical symmetry. This is a powerful result, since it reduces the highly complex flow to merely four parameters. In the present work, corresponding computer simulations using Reynolds-Averaged Navier-Stokes equations have been carried out and compared to the experimental observations. The main objective of this study is to investigate how well the simulations can reproduce the physics of the flow and if the same analytical model can be applied. Using this model, parametric studies can be significantly reduced and, further, reliable simulations can substantially reduce the costs of the parametric studies themselves.

Multimode radiation from an unflanged, semi-infinite circular duct with uniform flow.

Multimode sound radiation from an unflanged, semi-infinite, rigid-walled circular duct with uniform subsonic mean flow everywhere is investigated theoretically. The multimode directivity depends on the amplitude and directivity function of each individual cut-on mode. The amplitude of each mode is expressed as a function of cut-on ratio for a uniform distribution of incoherent monopoles, a uniform distribution of incoherent axial dipoles, and for equal power per mode. The directivity function of each mode is obtained by applying a Lorentz transformation to the zero-flow directivity function, which is given by a Wiener-Hopf solution. This exact numerical result is compared to an analytic solution, valid in the high-frequency limit, for multimode directivity with uniform flow. The high-frequency asymptotic solution is derived assuming total transmission of power at the open end of the duct, and gives the multimode directivity function with flow in the forward arc for a general family of mode amplitude distribution functions. At high frequencies the agreement between the exact and asymptotic solutions is shown to be excellent.

Electroosmotic flow analysis of a branched U-turn nanofluidic device.

In this paper, we present the analysis of electroosmotic flow in a branched -turn nanofluidic device, which we developed for detection and sorting of single molecules. The device, where the channel depth is only 150 nm, is designed to optically detect fluorescence from a volume as small as 270 attolitres (al) with a common wide-field fluorescent setup. We use distilled water as the liquid, in which we dilute 110 nm fluorescent beads employed as tracer-particles. Quantitative imaging is used to characterize the pathlines and velocity distribution of the electroosmotic flow in the device. Due to the device's complex geometry, the electroosmotic flow cannot be solved analytically. Therefore we use numerical flow simulation to model our device. Our results show that the deviation between measured and simulated data can be explained by the measured Brownian motion of the tracer-particles, which was not incorporated in the simulation.

Project neptune: Improved operation of water distribution networks

Water service providers (WSPs) in the UK have statutory obligations to supply drinking water to all customers that complies with increasingly stringent water quality regulations and minimum flow and pressure criteria. At the same time, the industry is required by regulators and investors to demonstrate increasing operational efficiency and to meet a wide range of performance criteria that are expected to improve year-on-year. Most WSPs have an ideal for improving the operation of their water supply systems based on increased knowledge and understanding of their assets and a shift to proactive management followed by steadily increasing degrees of system monitoring, automation and optimisation. The fundamental mission is, however, to ensure security of supply, with no interruptions and water quality of the highest standard at the tap. Unfortunately, advanced technologies required to fully understand, manage and automate water supply system operation either do not yet exist, are only partially evolved, or have not yet been reliably proven for live water distribution systems. It is this deficiency that the project NEPTUNE seeks to address by carrying out research into 3 main areas; these are: data and knowledge management; pressure management (including energy management); and the associated complex decision support systems on which to base interventions. The 3-year project started in April of 2007 and has already resulted in a number of research findings under the three main research priority areas (RPA). The paper summarises in greater detail the overall project objectives, the RPA activities and the areas of research innovation that are being undertaken in this major, UK collaborative study. Copyright 2009 ASCE.

High frequency multimode radiation from ducts with flow

Multimode sound radiation from hard-walled semi-infinite ducts with uniform subsonic flow is investigated theoretically. An analytic expression, valid in the high frequency limit, is derived for the multimode directivity function in the forward arc for a general family of mode distribution functions. The multimode directivity depends on the amplitude and directivity function of each individual mode. The amplitude of each mode is expressed as a function of cut-off ratio for a uniform distribution of incoherent monopoles, a uniform distribution of incoherent axial dipoles and for equal power per mode. The modes' directivity functions are obtained analytically by applying a Lorentz transformation to the zero flow solution. The analytic formula for the multimode directivity with flow is derived assuming total transmission of power at the open-end of the duct. This formula is compared to the exact numerical result for an unflanged duct, computed utilizing a Wiener-Hopf solution. The agreement is shown to be excellent. Copyright © 2008 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.

The biology, ecology, distribution and conservation of surviving haplochromine cichlids in Lakes Victoria, Kyoga and Nabugabo

Haplochrmine cichlids were the most abundant taxa in Lakes Victoria, Kyoga and Nabugabo prior to introduction of the Nile perch. As stocks of the introduced predator increased, these taxa were depleted to such an extent that they are now virtually absent from the lake. The haplochromine cichlids played an important role in the ecology of Lakes Victoria, Kyoga and Nabugabo. They occupied virtually all trophic levels in the lake and facilitated an efficient flow of energy through the ecosystem. Their depletion seem to have left much organic matter whose decomposition has contributed to accumulation of dead organic matter which may be contributing to prolonged anoxia in Lake Victoria. The haplochromines formed an important small-scale fishery. Fishermen formerly subsisting on this fishery have been driven out of business because they cannot afford the expensive nets required for Nile perch fishery. In addition to providing a cheap source of fish protein to humans, the species were an important source of Scientific material for students of genetics antd adaptive radiation.

Effect of bend orientation on life and puncture point location due to solid particle erosion of a high concentration flow in pneumatic conveyors

An investigation into predicting failure of pneumatic conveyor pipe bends due to hard solid particle impact erosion has been carried out on an industrial scale test rig. The bend puncture point locations may vary with many factors. However, bend orientation was suspected of being a main factor due to the biased particle distribution pattern of a high concentration flow. In this paper, puncture point locations have been studied with different pipe bend orientations and geometry (a solids loading ratio of 10 being used for the high concentration flow). Test results confirmed that the puncture point location is indeed most significantly influenced by the bend orientation (especially for a high concentration flow) due to the biased particle distribution and biased particle flux distribution. © 2004 Elsevier B.V. All rights reserved.

Numerical computation of laminar flow in a heated rotating cavity with an axial throughflow of air

A heated rotating cavity with an axial throughflow of cooling air is used as a model for the flow in the cylindrical cavities between adjacent discs of a high-pressure gas-turbine compressor. In an engine the flow is expected to be turbulent, the limitations of this laminar study are fully realised but it is considered an essential step to understand the fundamental nature of the flow. The three-dimensional, time-dependent governing equations are solved using a code based on the finite volume technique and a multigrid algorithm. The computed flow structure shows that flow enters the cavity in one or more radial arms and then forms regions of cyclonic and anticyclonic circulation. This basic flow structure is consistent with existing experimental evidence obtained from flow visualization. The flow structure also undergoes cyclic changes with time. For example, a single radial arm, and pair of recirculation regions can commute to two radial arms and two pairs of recirculation regions and then revert back to one. The flow structure inside the cavity is found to be heavily influenced by the radial distribution of surface temperature imposed on the discs. As the radial location of the maximum disc temperature moves radially outward, this appears to increase the number of radial arms and pairs of recirculation regions (from one to three for the distributions considered here). If the peripheral shroud is also heated there appear to be many radial arms which exchange fluid with a strong cyclonic flow adjacent to the shroud. One surface temperature distribution is studied in detail and profiles of the relative tangential and radial velocities are presented. The disc heat transfer is also found to be influenced by the disc surface temperature distribution. It is also found that the computed Nusselt numbers are in reasonable accord over most of the disc surface with a correlation found from previous experimental measurements. © 1994, MCB UP Limited.

Flow field measurements of pulverized coal combustion using optical diagnostic techniques

This paper demonstrates the application of laser Doppler velocimetry (LDV) and particle image velocimetry (PIV) techniques to a particle-laden reacting flow of pulverized coal. A laboratory-scale open-type annular burner is utilized to generate velocity profiles of coal particles and micrometric alumina particles. Pair-wise two-component LDV measurements and high-speed stereo PIV measurements provide three-dimensional velocity components of the flow field. A detailed comparison of velocities for alumina and coal particle seeding revealed differences attributed to the wide size distribution of coal particles. In addition, the non-spherical shape and high flame luminosity associated with coal particle combustion introduces noise to the Mie scatter images. The comparison of mean and RMS velocities measured by LDV and PIV techniques showed that PIV measurements are affected by the wide size distribution of coal particles, whereas LDV measurements become biased toward the velocity of small particles, as signals from large particles are rejected. This small-particle bias is also reflected in the spectral characteristics for both techniques, which are in good agreement within the range of frequencies accessible. PIV measurements showed an expected lack of response of large coal particles to the turbulence fluctuations. The overall good agreement between LDV and PIV measurements demonstrates the applicability of the high-speed PIV technique to a particle-laden, high luminosity coal flame while highlighting some of its limitations. © 2013 Springer-Verlag Berlin Heidelberg.