Phylogenetic analysis of microbial communities in different regions of the gastrointestinal tract in Panaque nigrolineatus, a wood-eating fish

The Neotropical detritivorous catfish Panaque nigrolineatus imbibes large quantities of wood as part of its diet. Due to the interest in cellulose, hemi-cellulose and lignin degradation pathways, this organism provides an interesting model system for the detection of novel microbial catabolism. In this study, we characterize the microbial community present in different regions of the alimentary tract of P. nigrolineatus fed a mixed diet of date palm and palm wood in laboratory aquaria. Analysis was performed on 16S rRNA gene clone libraries derived from anterior and posterior regions of the alimentary tract and the auxiliary lobe (AL), an uncharacterized organ that is vascularly attached to the midgut. Sequence analysis and phylogenetic reconstruction revealed distinct microbial communities in each tissue region. The foregut community shared many phylotypes in common with aquarium tank water and included Legionella and Hyphomicrobium spp. As the analysis moved further into the gastrointestinal tract, phylotypes with high levels of 16S rRNA sequence similarity to nitrogen-fixing Rhizobium and Agrobacterium spp. and Clostridium xylanovorans and Clostridium saccharolyticum, dominated midgut and AL communities. However, the hindgut was dominated almost exclusively by phylotypes with the highest 16S rRNA sequence similarity to the Cytophaga-Flavobacterium-Bacteroides phylum. Species richness was highest in the foregut (Chao(1) = 26.72), decreased distally through the midgut (Chao(1) = 25.38) and hindgut (Chao(1) = 20.60), with the lowest diversity detected in the AL (Chao(1) = 18.04), indicating the presence of a specialized microbial community. Using 16S rRNA gene phylogeny, we report that the P. nigrolineatus gastrointestinal tract possesses a microbial community closely related to microorganisms capable of cellulose degradation and nitrogen fixation. Further studies are underway to determine the role of this resident microbial community in Panaque nigrolineatus

Examination of a culturable microbial population from the gastrointestinal tract of the wood-eating loricariid catfish Panaque nigrolineatus

Fish play a critical role in nutrient cycling and organic matter flow in aquatic environments. However, little is known about the microbial diversity within the gastrointestinal tracts that may be essential in these degradation activities. Panaque nigrolineatus is a loricariid catfish found in the Neotropics that have a rare dietary strategy of consuming large amounts of woody material in its natural environment. As a consequence, the gastrointestinal (GI) tract of P. nigrolineatus is continually exposed to high levels of cellulose and other recalcitrant wood compounds and is, therefore, an attractive, uncharacterized system to study microbial community diversity. Our previous 16S rRNA gene surveys demonstrated that the GI tract microbial community includes phylotypes having the capacity to degrade cellulose and fix molecular nitrogen. In the present study we verify the presence of a resident microbial community by fluorescence microscopy and focus on the cellulose-degrading members by culture-based and 13C-labeled cellulose DNA stable-isotope probing (SIP) approaches. Analysis of GI tract communities generated from anaerobic microcrystalline cellulose enrichment cultures by 16S rRNA gene analysis revealed phylotypes sharing high sequence similarity to known cellulolytic bacteria including Clostridium, Cellulomonas, Bacteroides, Eubacterium and Aeromonas spp. Related bacteria were identified in the SIP community, which also included nitrogen-fixing Azospirillum spp. Our ability to enrich for specialized cellulose-degrading communities suggests that the P. nigrolineatus GI tract provides a favorable environment for this activity and these communities may be involved in providing assimilable carbon under challenging dietary conditions

Development of a three-dimensional turbulent duct flow analysis

A method for computing three-dimensional turbulent subsonic flow in curved ducts is described. An approximate set of governing equations is given for viscous flows which have a primary flow direction. The derivation is coordinate invariant, and the resulting equations are expressed in terms of tensors. General tube-like coordinates were developed for a general class of geometries applicable to many internal flow problems. The coordinates are then particularized to pipes having superelliptic cross sections whose shape can vary continuously between a circle and a near rectangle. The analysis is applied to a series of relevant aerodynamic problems including transition from nearly square to round pipes and flow through a pipe with an S-shaped bend

Derivation and evaluation of an approximate analysis for three-dimensional viscous subsonic flow with large secondary velocities

An approximate analysis is presented for calculating three-dimensional, low Mach number, laminar viscous flows in curved passages with large secondary flows and corner boundary layers. The analysis is based on the decomposition of the overall velocity field into inviscid and viscous components with the overall velocity being determined from superposition. An incompressible vorticity transport equation is used to estimate inviscid secondary flow velocities to be used as corrections to the potential flow velocity field. A parabolized streamwise momentum equation coupled to an adiabatic energy equation and global continuity equation is used to obtain an approximate viscous correction to the pressure and longitudinal velocity fields. A collateral flow assumption is invoked to estimate the viscous correction to the transverse velocity fields. The approximate analysis is solved numerically using an implicit ADI solution for the viscous pressure and velocity fields. An iterative ADI procedure is used to solve for the inviscid secondary vorticity and velocity fields. This method was applied to computing the flow within a turbine vane passage with inlet flow conditions of M = 0.1 and M = 0.25, Re = 1000 and adiabatic walls, and for a constant radius curved rectangular duct with R/D = 12 and 14 and with inlet flow conditions of M = 0.1, Re = 1000, and adiabatic walls

Turbofan forced mixer-nozzle internal flowfield. Volume 3: A computer code for 3-D mixing in axisymmetric nozzles

A finite difference method is developed for making detailed predictions of three dimensional subsonic turbulent flow in turbofan lobe mixers. The governing equations are solved by a forward-marching solution procedure which corrects an inviscid potential flow solution for viscous and thermal effects, secondary flows, total pressure distortion and losses, internal flow blockage and pressure drop. Test calculations for a turbulent coaxial jet flow verify that the turbulence model performs satisfactorily for this relatively simple flow. Lobe mixer flows are presented for two geometries typical of current mixer design. These calculations included both hot and cold flow conditions, and both matched and mismatched Mach number and total pressure in the fan and turbine streams

Prediction of laminar and turbulent primary and secondary flows in strongly curved ducts

The analysis is based on a primary secondary velocity decomposition in a given coordinate system, and leads to approximate governing equations which correct an a priori inviscid solution for viscous effects, secondary flows, total pressure distortion, heat transfer, and internal flow blockage and losses. Solution of the correction equations is accomplished as an initial value problem in space using an implicit forward marching technique. The overall solution procedure requires significantly less computational effort than Navier-Stokes algorithms. The solution procedure is effective even with the extreme local mesh resolution which is necessary to solve near wall sublayer regions in turbulent flow calculations. Computed solutions for both laminar and turbulent flow compared very favorably with available analytical and experimental results. The overall method appears very promising as an economical procedure for making detailed predictions of viscous primary and secondary flows in highly curved passages

Development of a three-dimensional supersonic inlet flow analysis

A method for computing three dimensional flow in supersonic inlets is described. An approximate set of governing equations is given for viscous flows which have a primary flow direction. The governing equations are written in general orthogonal coordinates. These equations are modified in the subsonic region of the flow to prevent the phenomenon of branching. Results are presented for the two sample cases: a Mach number equals 2.5 flow in a square duct, and a Mach number equals 3.0 flow in a research jet engine inlet. In the latter case the computed results are compared with the experimental data. A users' manual is included

Suppressing Proton Decay By Separating Quarks And Leptons

Arkani-Hamed and Schmaltz (AS) have shown that proton stability need not originate from symmetries in a high energy theory. Instead the proton decay rate is suppressed if quarks and leptons are spatially separated in a compact extra dimension. This separation may be achieved by coupling five dimensional fermions to a bulk scalar field with a non-trivial vacuum profile and requires relationships between the associated quark and lepton Yukawa couplings. We hypothesise that these relationships are the manifestation of an underlying symmetry. We further show that the AS proposal may suggest that proton stability \emph{is} the result of an underlying symmetry, though not necessarily the traditional baryon number symmetry.Comment: 4 pages, references added to match published versio

Turbine stator flow field simulations

The increased capability and accessibility of modern computers, coupled with increasingly sophisticated and accurate numerical and physical modeling, has led to a marked impact of numerical simulations upon current turbine design and research problems. The turbine section represents a considerable challenge as it contains significant regions of complex three-dimensional flow, including both aerodynamic and heat transfer phenomena. The focus of the present effort is the development of an efficient and accurate three-dimensional Navier-Stokes calculation procedure for application to the turbine stator and rotor problems. In particular, an effective procedure is sought which: (1) adequately represents the flow physics, (2) allows for sufficient resolution in regions of small length scale, and (3) has sufficiently good convergence properties so as to allow use on a regular basis