Building upon Supramolecular Synthons: Some Aspects of Crystal Engineering

It has been 20 years since the concept of supramolecular synthon was introduced with the purpose of rational supramolecular synthesis. While this concept has been greatly successful in employing a retrosynthetic approach in crystal engineering, the past few years have seen a continuous evolution of supramolecular synthons from being a synthetic subunit to a basic unit for understanding the dynamics of crystallization. This review attempts to give a glimpse of such developments.

Systematic Analysis of Mycobacterial Acylation Reveals First Example of Acylation-mediated Regulation of Enzyme Activity of a Bacterial Phosphatase

Protein lysine acetylation is known to regulate multiple aspects of bacterial metabolism. However, its presence in mycobacterial signal transduction and virulence-associated proteins has not been studied. In this study, analysis of mycobacterial proteins from different cellular fractions indicated dynamic and widespread occurrence of lysine acetylation. Mycobacterium tuberculosis proteins regulating diverse physiological processes were then selected and expressed in the surrogate host Mycobacterium smegmatis. The purified proteins were analyzed for the presence of lysine acetylation, leading to the identification of 24 acetylated proteins. In addition, novel lysine succinylation and propionylation events were found to co-occur with acetylation on several proteins. Protein-tyrosine phosphatase B (PtpB), a secretory phosphatase that regulates phosphorylation of host proteins and plays a critical role in Mycobacterium infection, is modified by acetylation and succinylation at Lys-224. This residue is situated in a lid region that covers the enzyme's active site. Consequently, acetylation and succinylation negatively regulate the activity of PtpB.

Physiological role of FolD (methylenetetrahydrofolate dehydrogenase), FchA (methenyltetrahydrofolate cyclohydrolase) and Fhs (formyltetrahydrofolate synthetase) from Clostridium perfringens in a heterologous model of Escherichia coli

Most organisms possess bifunctional FolD 5,10-methylenetetrahydrofolate (5,10-CH2-THF) dehydrogenase-cyclohydrolase] to generate NADPH and 10-formyltetrandrofolate (10-CHO-THF) required in various metabolic steps. In addition, some organisms including Clostridium perfringens possess another protein, Fhs (formyltetrahydrofolate synthetase), to synthesize 10-CHO-THF. Here, we show that unlike the bifunctional FolD of Escherichia coli (Eco FolD), and contrary to its annotated bifunctional nature, C. perfringens FolD (Cpe FoID) is a monofunctional 5,10-CH2-THF dehydrogenase. The dehydrogenase activity of Cpe FoID is about five times more efficient than that of Eco FolD. The 5,10-methenyltetrahydrofolate (5,10-CH+-THF) cyclohydrolase activity in C. perfringens is provided by another protein, FchA (5,10-CH+-THF cyclohydrolase), whose cyclohydrolase activity is similar to 10 times more efficient than that of Eco FolD. Kinetic parameters for Cpe Fhs were also determined for utilization of all of its substrates. Both Cpe FoID and Cpe FchA are required to substitute for the single bifunctional FolD in E. coli. The simultaneous presence of Cpe FoID and Cpe FchA is also necessary to rescue an E coli folD deletion strain (harbouring Cpe Fhs support) for its formate and glycine auxotrophies, and to alleviate its susceptibility to trimethoprim (an antifolate drug) or UV light. The presence of the three clostridial proteins (FolD, FchA and Fhs) is required to maintain folate homeostasis in the cell.

Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch.

Campylobacter jejuni is a prevalent cause of food-borne diarrhoeal illness in humans. Understanding of the physiological and metabolic capabilities of the organism is limited. We report a detailed analysis of the C. jejuni growth cycle in batch culture. Combined transcriptomic, phenotypic and metabolic analysis demonstrates a highly dynamic 'stationary phase', characterized by a peak in motility, numerous gene expression changes and substrate switching, despite transcript changes that indicate a metabolic downshift upon the onset of stationary phase. Video tracking of bacterial motility identifies peak activity during stationary phase. Amino acid analysis of culture supernatants shows a preferential order of amino acid utilization. Proton NMR (1H-NMR) highlights an acetate switch mechanism whereby bacteria change from acetate excretion to acetate uptake, most probably in response to depletion of other substrates. Acetate production requires pta (Cj0688) and ackA (Cj0689), although the acs homologue (Cj1537c) is not required. Insertion mutants in Cj0688 and Cj0689 maintain viability less well during the stationary and decline phases of the growth cycle than wild-type C. jejuni, suggesting that these genes, and the acetate pathway, are important for survival.

Large Eddy Simulation of Complex Turbulent Flows: Physical Aspects and Research Trends

In the current paper, we have primarily addressed one powerful simulation tool developed during the last decades-Large Eddy Simulation (LES), which is most suitable for unsteady three-dimensional complex turbulent flows in industry and natural environment. The main point in LES is that the large-scale motion is resolved while the small-scale motion is modeled or, in geophysical terminology, parameterized. With a view to devising a subgrid-scale(SGS) model of high quality, we have highlighted analyzing physical aspects in scale interaction and-energy transfer such as dissipation, backscatter, local and non-local interaction, anisotropy and resolution requirement. They are the factors responsible for where the advantages and disadvantages in existing SGS models come from. A case study on LES of turbulence in vegetative canopy is presented to illustrate that LES model is more based on physical arguments. Then, varieties of challenging complex turbulent flows in both industry and geophysical fields in the near future-are presented. In conclusion; we may say with confidence that new century shall see the flourish in the research of turbulence with the aid of LES combined with other approaches.

Computation of turbulent-flow in a square duct - aspects of the secondary flow and its origin

A numerical study of turbulent flow in a straight duct of square cross-section is made. An order-of-magnitude analysis of the 3-D, time-averaged Navier-Stokes equations resulted in a parabolic form of the Navier-Stokes equations. The governing equations, expressed in terms of a new vector-potential formulation, are expanded as a multi-deck structure with each deck characterized by its dominant physical forces. The resulting equations are solved using a finite-element approach with a bicubic element representation on each cross-sectional plane. The numerical integration along the streamwise direction is carried out with finite-difference approximations until a fully-developed state is reached. The computed results agree well with other numerical studies and compare very favorably with the available experimental data. One important outcome of the current investigation is the interpretation analytically that the driving force of the secondary flow in a square duct comes mainly from the second-order terms of the difference in the gradients of the normal and transverse Reynolds stresses in the axial vorticity equation.

Some theoretical aspects of the simplified Navier-Stokes(SNS) equations

This study deals with the formulation, mathematical property and physical meaning of the simplified Navier-Stokes (SNS) equations. The tensorial SNS equations proposed is the simplest in form and is applicable to flow fields with arbitrary body boundaries. The zones of influence and dependence of the SNS equations, which are of primary importance to numerical solutions, are expounded for the first time from the viewpoint of subcharacteristics. Besides, a detailed analysis of the diffusion process in flow fields shows that the diffusion effect has an influence zone globally windward and an upwind propagation greatly depressed by convection. The maximum upwind influential distance of the viscous effect and the relative importance of the viscous effect in the flow direction to that in the direction normal to the flow are represented by the Reynolds number, which illustrates the conversion of the complete Navier-Stokes (NS) equations to the SNS equations for flows with large Reynolds number.

Hydrologic aspects of freshening upper Old Tampa Bay, Florida

Upper Old Tampa Bay, a 17-square mile area of Old Tampa Bay, Florida, has been proposed for conversion to a fresh-water lake. The amount of runoff to the proposed lake and its chemical quality are both adequate to freshen and sustain a fresh-water lake in this part of the bay. During 1950-66 runoff to the proposed lake, including discharge from Lake Tarpon, would have averaged 134 mgd (million gallons per day) and would have displaced the volume of the proposed lake at normal pool stage (2.5 feet above mean sea level) about 1.7 times per year. Without discharge from Lake Tarpon, the volume of the proposed lake would have been displaced 1.2 times. If the lake level was initially at a normal pool stage during a critically dry year, such as 1956, the proposed lake would have declined 0.25 to 0.5 foot below the minimum design level, (1.5 feet above mean sea level). (44 page document)