Mechanisms of formation of the Arabian Sea mini warm pool in a high-resolution Ocean General Circulation Model

An Ocean General Circulation Model of the Indian Ocean with high horizontal (0.25 degrees x 0.25 degrees) and vertical (40 levels) resolutions is used to study the dynamics and thermodynamics of the Arabian Sea mini warm pool (ASMWP), the warmest region in the northern Indian Ocean during January-April. The model simulates the seasonal cycle of temperature, salinity and currents as well as the winter time temperature inversions in the southeastern Arabian Sea (SEAS) quite realistically with climatological forcing. An experiment which maintained uniform salinity of 35 psu over the entire model domain reproduces the ASMWP similar to the control run with realistic salinity and this is contrary to the existing theories that stratification caused by the intrusion of low-salinity water from the Bay of Bengal into the SEAS is crucial for the formation of ASMWP. The contribution from temperature inversions to the warming of the SEAS is found to be negligible. Experiments with modified atmospheric forcing over the SEAS show that the low latent heat loss over the SEAS compared to the surroundings, resulting from the low winds due to the orographic effect of Western Ghats, plays an important role in setting up the sea surface temperature (SST) distribution over the SEAS during November March. During March-May, the SEAS responds quickly to the air-sea fluxes and the peak SST during April-May is independent of the SST evolution during previous months. The SEAS behaves as a low wind, heat-dominated regime during November-May and, therefore, the formation and maintenance of the ASMWP is not dependent on the near surface stratification.

Some mechanisms of tribofilm formation in metal/metal and ceramic/metal sliding interactions

Tribological interaction often generates new structures and materials which form the interface between the sliding pair. The new material designated tribofilm here may be protective or tribologically deleterious. The tribofilm plays a major role in determining the friction and wear of the interaction. Here, we give three examples: mechanically mixed, chemically generated and thermally activated, of tribofilms formed in three different tribological systems and speculate on the mechanism of their formation.

Effect of strain rate response and pin diameter on mechanically mixed layer formation and wear mechanisms in a Ti6Al4V-SS316L pair

Three mechanisms operate during wear of materials. These mechanisms include the Strain Rate Response (SRR - effect of strain rate on plastic deformation), Tribo-Chemical Reactions (TCR) and formation of Mechanically Mixed Layers (MML). The present work investigates the effect of these three in context of the formation of MML. For this wear experiments are done on a pin-on-disc machine using Ti64 as the pin and SS316L as the disc. It is seen that apart from the speed and load, which control the SRR and TCR, the diameter of the pin controls the formation of MML, especially at higher speeds.

Engineering nucleic acid mechanisms for regulation and readout of gene expression : conditional Dicer substrate formation and sensitive multiplexed northern blots

Nucleic acids are most commonly associated with the genetic code, transcription and gene expression. Recently, interest has grown in engineering nucleic acids for biological applications such as controlling or detecting gene expression. The natural presence and functionality of nucleic acids within living organisms coupled with their thermodynamic properties of base-pairing make them ideal for interfacing (and possibly altering) biological systems. We use engineered small conditional RNA or DNA (scRNA, scDNA, respectively) molecules to control and detect gene expression. Three novel systems are presented: two for conditional down-regulation of gene expression via RNA interference (RNAi) and a third system for simultaneous sensitive detection of multiple RNAs using labeled scRNAs.

RNAi is a powerful tool to study genetic circuits by knocking down a gene of interest. RNAi executes the logic: If gene Y is detected, silence gene Y. The fact that detection and silencing are restricted to the same gene means that RNAi is constitutively on. This poses a significant limitation when spatiotemporal control is needed. In this work, we engineered small nucleic acid molecules that execute the logic: If mRNA X is detected, form a Dicer substrate that targets independent mRNA Y for silencing. This is a step towards implementing the logic of conditional RNAi: If gene X is detected, silence gene Y. We use scRNAs and scDNAs to engineer signal transduction cascades that produce an RNAi effector molecule in response to hybridization to a nucleic acid target X. The first mechanism is solely based on hybridization cascades and uses scRNAs to produce a double-stranded RNA (dsRNA) Dicer substrate against target gene Y. The second mechanism is based on hybridization of scDNAs to detect a nucleic acid target and produce a template for transcription of a short hairpin RNA (shRNA) Dicer substrate against target gene Y. Test-tube studies for both mechanisms demonstrate that the output Dicer substrate is produced predominantly in the presence of a correct input target and is cleaved by Dicer to produce a small interfering RNA (siRNA). Both output products can lead to gene knockdown in tissue culture. To date, signal transduction is not observed in cells; possible reasons are explored.

Signal transduction cascades are composed of multiple scRNAs (or scDNAs). The need to study multiple molecules simultaneously has motivated the development of a highly sensitive method for multiplexed northern blots. The core technology of our system is the utilization of a hybridization chain reaction (HCR) of scRNAs as the detection signal for a northern blot. To achieve multiplexing (simultaneous detection of multiple genes), we use fluorescently tagged scRNAs. Moreover, by using radioactive labeling of scRNAs, the system exhibits a five-fold increase, compared to the literature, in detection sensitivity. Sensitive multiplexed northern blot detection provides an avenue for exploring the fate of scRNAs and scDNAs in tissue culture.

Different mechanisms for the formation of acetaldehyde and ethanol on the Rh-based catalysts

Different mechanisms for the formation of acetaldehyde and ethanol on the Rh-based catalysts were investigated by the TPR (temperature programmed reaction) method, and the active sites were studied by CO-TPD, TPSR (temperature programmed surface reaction of preadsorbed CO by H-2) and XPS techniques. The TPR results indicated that ethanol and acetaldehyde might be formed through different intermediates, whereas ethanol and methanol might result from the same intermediate. Results of CO-TPD, TPSR, and XPS showed that on the Rh-based catalyst, the structure of the active sites for the formation of C-2-oxygenates is ((RhxRhy+)-Rh-0)-O-Mn+ (M=Mn or Zr, x>>y, 2 less than or equal ton less than or equal to4). The tilt-adsorbed CO species is the main precursor for CO dissociation and the precursor for the formation of ethanol and methanol. Most of the linear and geminal adsorbed CO species desorbed below 500 K. Based on the suggested model of the active sites, detailed mechanisms for the formation of acetaldehyde and ethanol are proposed. Ethanol is formed by direct hydrogenation of the tilt-adsorbed CO molecules, followed by CH2 insertion into the surface CH2-O species and the succeeding hydrogenation step. Acetaldehyde is formed through CO insertion into the surface CH3-Rh species followed by hydrogenation, and the role of the promoters was to stabilize the intermediate of the surface acetyl species. (C) 2000 Academic Press.

Biomolecular mechanisms of staphylococcal biofilm formation

The multitude of biomolecular and regulatory factors involved in staphylococcal adhesion and biofilm formation owe much to their ability to colonize surfaces, allowing the biofilm form to become the preferential bacterial phenotype. Judging by total number, biomass and variety of environments colonized, bacteria can be categorized as the most successful lifeform on earth. This is due to the ability of bacteria and other microorganisms to respond phenotypically via biomolecular processes to the stresses of their surrounding environment. This review focuses on the specific pathways involved in the adhesion of the Gram-positive bacteria Staphylococcus epidermidis and Staphylococcus aureus with reference to the role of specific cell surface adhesins, the ica operon, accumulation-associated proteins and quorum-sensing systems and their significance in medical device-related infection.

Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation

Pseudomonas aeruginosa and Escherichia coli are the most prevalent Gram-negative biofilm forming medical device associated pathogens, particularly with respect to catheter associated urinary tract infections. In a similar manner to Gram-positive bacteria, Gram-negative biofilm formation is fundamentally determined by a series of steps outlined more fully in this review, namely adhesion, cellular aggregation, and the production of an extracellular polymeric matrix. More specifically this review will explore the biosynthesis and role of pili and flagella in Gram-negative adhesion and accumulation on surfaces in Pseudomonas aeruginosa and Escherichia coli. The process of biofilm maturation is compared and contrasted in both species, namely the production of the exopolysaccharides via the polysaccharide synthesis locus (Psl), pellicle Formation (Pel) and alginic acid synthesis in Pseudomonas aeruginosa, and UDP-4-amino-4-deoxy-l-arabinose and colonic acid synthesis in Escherichia coli. An emphasis is placed on the importance of the LuxR homologue sdiA; the luxS/autoinducer-II; an autoinducer-III/epinephrine/norepinephrine and indole mediated Quorum sensing systems in enabling Gram-negative bacteria to adapt to their environments. The majority of Gram-negative biofilms consist of polysaccharides of a simple sugar structure (either homo- or heteropolysaccharides) that provide an optimum environment for the survival and maturation of bacteria, allowing them to display increased resistance to antibiotics and predation.

Biofilm formation by Bacillus subtilis: new insights into regulatory strategies and assembly mechanisms

Biofilm formation is a social behaviour that generates favourable conditions for sustained survival in the natural environment. For the Gram-positive bacterium Bacillus subtilis the process involves the differentiation of cell fate within an isogenic population and the production of communal goods that form the biofilm matrix. Here we review recent progress in understanding the regulatory pathways that control biofilm formation and highlight developments in understanding the composition, function and structure of the biofilm matrix.

Role of insulin and insulin-like peptides in bone formation: identification of bone-specific target genes and regulatory mechanisms, and characterization of the insulin-mimetic effect of vanadium

Tese de Doutoramento em Biologia, Especialidade em Biologia Molecular, Universidade do Algarve, 2008

Mechanisms for the formation of organic acids in the gas-phase ozonolysis of 3-carene

This paper describes experimental studies aimed at elucidating mechanisms for the formation of low-volatility organic acids in the gas-phase ozonolysis of 3-carene. Experiments were carried out in a static chamber under 'OH-free' conditions. A range of multifunctional acids-which are analogous to those observed from alpha-pinene ozonolysis-were identified in the condensed phase using gas chromatography coupled to mass spectrometry after derivation. Product yields were determined as a function of different OH radical scavengers and relative humidities to give mechanistic information about their routes of formation. Furthermore, an enone and an enal derived from 3-carene were ozonised in order to probe the early mechanistic steps in the reaction and, in particular, which of the two initially formed Criegee intermediates gives rise to which products. Branching ratios for the formation of the two Criegee Intermediates are determined. Similarities and differences in product formation from 3-carene and alpha-pinene ozonolysis are discussed and possible mechanisms-supported by experimental evidence-are developed for all acids investigated.