Impact of hydrographic data assimilation on the modelled Atlantic meridional overturning circulation

Here we make an initial step toward the development of an ocean assimilation system that can constrain the modelled Atlantic Meridional Overturning Circulation (AMOC) to support climate predictions. A detailed comparison is presented of 1° and 1/4° resolution global model simulations with and without sequential data assimilation, to the observations and transport estimates from the RAPID mooring array across 26.5° N in the Atlantic. Comparisons of modelled water properties with the observations from the merged RAPID boundary arrays demonstrate the ability of in situ data assimilation to accurately constrain the east-west density gradient between these mooring arrays. However, the presence of an unconstrained "western boundary wedge" between Abaco Island and the RAPID mooring site WB2 (16 km offshore) leads to the intensification of an erroneous southwards flow in this region when in situ data are assimilated. The result is an overly intense southward upper mid-ocean transport (0–1100 m) as compared to the estimates derived from the RAPID array. Correction of upper layer zonal density gradients is found to compensate mostly for a weak subtropical gyre circulation in the free model run (i.e. with no assimilation). Despite the important changes to the density structure and transports in the upper layer imposed by the assimilation, very little change is found in the amplitude and sub-seasonal variability of the AMOC. This shows that assimilation of upper layer density information projects mainly on the gyre circulation with little effect on the AMOC at 26° N due to the absence of corrections to density gradients below 2000 m (the maximum depth of Argo). The sensitivity to initial conditions was explored through two additional experiments using a climatological initial condition. These experiments showed that the weak bias in gyre intensity in the control simulation (without data assimilation) develops over a period of about 6 months, but does so independently from the overturning, with no change to the AMOC. However, differences in the properties and volume transport of North Atlantic Deep Water (NADW) persisted throughout the 3 year simulations resulting in a difference of 3 Sv in AMOC intensity. The persistence of these dense water anomalies and their influence on the AMOC is promising for the development of decadal forecasting capabilities. The results suggest that the deeper waters must be accurately reproduced in order to constrain the AMOC.

Synthesis of a systolic array genetic algorithm

The paper presents a design for a hardware genetic algorithm which uses a pipeline of systolic arrays. These arrays have been designed using systolic synthesis techniques which involve expressing the algorithm as a set of uniform recurrence relations. The final design divorces the fitness function evaluation from the hardware and can process chromosomes of different lengths, giving the design a generic quality. The paper demonstrates the design methodology by progressively re-writing a simple genetic algorithm, expressed in C code, into a form from which systolic structures can be deduced. This paper extends previous work by introducing a simplification to a previous systolic design for the genetic algorithm. The simplification results in the removal of 2N 2 + 4N cells and reduces the time complexity by 3N + 1 cycles.

Implementing a generic systolic array for genetic algorithms

We have designed a highly parallel design for a simple genetic algorithm using a pipeline of systolic arrays. The systolic design provides high throughput and unidirectional pipelining by exploiting the implicit parallelism in the genetic operators. The design is significant because, unlike other hardware genetic algorithms, it is independent of both the fitness function and the particular chromosome length used in a problem. We have designed and simulated a version of the mutation array using Xilinix FPGA tools to investigate the feasibility of hardware implementation. A simple 5-chromosome mutation array occupies 195 CLBs and is capable of performing more than one million mutations per second. I. Introduction Genetic algorithms (GAs) are established search and optimization techniques which have been applied to a range of engineering and applied problems with considerable success [1]. They operate by maintaining a population of trial solutions encoded, using a suitable encoding scheme.

Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins

In this study, we demonstrate the suitability of the vertebrate Danio rerio (zebrafish) for functional screening of novel platelet genes in vivo by reverse genetics. Comparative transcript analysis of platelets and their precursor cell, the megakaryocyte, together with nucleated blood cell elements, endothelial cells, and erythroblasts, identified novel platelet membrane proteins with hitherto unknown roles in thrombus formation. We determined the phenotype induced by antisense morpholino oligonucleotide (MO)–based knockdown of 5 of these genes in a laser-induced arterial thrombosis model. To validate the model, the genes for platelet glycoprotein (GP) IIb and the coagulation protein factor VIII were targeted. MO-injected fish showed normal thrombus initiation but severely impaired thrombus growth, consistent with the mouse knockout phenotypes, and concomitant knockdown of both resulted in spontaneous bleeding. Knockdown of 4 of the 5 novel platelet proteins altered arterial thrombosis, as demonstrated by modified kinetics of thrombus initiation and/or development. We identified a putative role for BAMBI and LRRC32 in promotion and DCBLD2 and ESAM in inhibition of thrombus formation. We conclude that phenotypic analysis of MO-injected zebrafish is a fast and powerful method for initial screening of novel platelet proteins for function in thrombosis.

Modelling habitat selection and distribution of the critically endangered Jerdon's courser Rhinoptilus bitorquatus in scrub jungle: an application of a new tracking method

1. Jerdon's courser Rhinoptilus bitorquatus is a nocturnally active cursorial bird that is only known to occur in a small area of scrub jungle in Andhra Pradesh, India, and is listed as critically endangered by the IUCN. Information on its habitat requirements is needed urgently to underpin conservation measures. We quantified the habitat features that correlated with the use of different areas of scrub jungle by Jerdon's coursers, and developed a model to map potentially suitable habitat over large areas from satellite imagery and facilitate the design of surveys of Jerdon's courser distribution. 2. We used 11 arrays of 5-m long tracking strips consisting of smoothed fine soil to detect the footprints of Jerdon's coursers, and measured tracking rates (tracking events per strip night). We counted the number of bushes and trees, and described other attributes of vegetation and substrate in a 10-m square plot centred on each strip. We obtained reflectance data from Landsat 7 satellite imagery for the pixel within which each strip lay. 3. We used logistic regression models to describe the relationship between tracking rate by Jerdon's coursers and characteristics of the habitat around the strips, using ground-based survey data and satellite imagery. 4. Jerdon's coursers were most likely to occur where the density of large (>2 m tall) bushes was in the range 300-700 ha(-1) and where the density of smaller bushes was less than 1000 ha(-1). This habitat was detectable using satellite imagery. 5. Synthesis and applications. The occurrence of Jerdon's courser is strongly correlated with the density of bushes and trees, and is in turn affected by grazing with domestic livestock, woodcutting and mechanical clearance of bushes to create pasture, orchards and farmland. It is likely that there is an optimal level of grazing and woodcutting that would maintain or create suitable conditions for the species. Knowledge of the species' distribution is incomplete and there is considerable pressure from human use of apparently suitable habitats. Hence, distribution mapping is a high conservation priority. A two-step procedure is proposed, involving the use of ground surveys of bush density to calibrate satellite image-based mapping of potential habitat. These maps could then be used to select priority areas for Jerdon's courser surveys. The use of tracking strips to study habitat selection and distribution has potential in studies of other scarce and secretive species.

Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria

Identification of Fusarium species has always been difficult due to confusing phenotypic classification systems. We have developed a fluorescent-based polymerase chain reaction assay that allows for rapid and reliable identification of five toxigenic and pathogenic Fusarium species. The species includes Fusarium avenaceum, F. culmorum, F. equiseti, F. oxysporum and F. sambucinum. The method is based on the PCR amplification of species-specific DNA fragments using fluorescent oligonucleotide primers, which were designed based on sequence divergence within the internal transcribed spacer region of nuclear ribosomal DNA. Besides providing an accurate, reliable, and quick diagnosis of these Fusaria, another advantage with this method is that it reduces the potential for exposure to carcinogenic chemicals as it substitutes the use of fluorescent dyes in place of ethidium, bromide. Apart from its multidisciplinary importance and usefulness, it also obviates the need for gel electrophoresis. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments

The distribution and activity of communities of sulfate-reducing bacteria (SRB) and methanogenic archaea in two contrasting Antarctic sediments were investigated. Methanogenesis dominated in freshwater Lake Heywood, while sulfate reduction dominated in marine Shallow Bay. Slurry experiments indicated that 90% of the methanogenesis in Lake Heywood was acetoclastic. This finding was supported by the limited diversity of clones detected in a Lake Heywood archaeal clone library, in which most clones were closely related to the obligate acetate-utilizing Methanosaeta concilii. The Shallow Bay archaeal clone library contained clones related to the C-1-utilizing Methanolobus and Methanococcoides and the H-2-utilizing Methanogenium. Oligonucleotide probing of RNA extracted directly from sediment indicated that archaea represented 34% of the total prokaryotic signal in Lake Heywood and that Methanosaeta was a major component (13.2%) of this signal. Archaea represented only 0.2% of the total prokaryotic signal in RNA extracted from Shallow Bay sediments. In the Shallow Bay bacterial clone library, 10.3% of the clones were SRB-like, related to Desulfotalea/Desulforhopalus, Desulfofaba, Desulfosarcina, and Desulfobacter as well as to the sulfur and metal oxidizers comprising the Desulfuromonas cluster. Oligonucleotide probes for specific SRB clusters indicated that SRB represented 14.7% of the total prokaryotic signal, with Desulfotalea/Desulforhopalus being the dominant SRB group (10.7% of the total prokaryotic signal) in the Shallow Bay sediments; these results support previous results obtained for Arctic sediments. Methanosaeta and Desulfotalea/Desulforhopalus appear to be important in Lake Heywood and Shallow Bay, respectively, and may be globally important in permanently low-temperature sediments.

Construction of Helical Nanofibers from Self-Assembling Pseudopeptide Building Blocks: Modulating the Handedness and Breaking the Helicity

Helical nanofibers are successfully constructed from suitable self-assembling pseudopeptide-based molecular building blocks. The handedness of these nanofibers can be reversed by using mirror-imaged pseudopeptide-based building blocks. Straight nanofibers are also constructed by modulating the molecular and supramolecular structures by the proper choice of the stereochemical nature of the molecular scaffolds. This study demonstrates that molecular structure and chirality are not the only determining factors for tuning the morphology and chirality of nanostructures; the nature of the supramolecular structures formed from the corresponding molecular scaffolds also plays a key role in dictating the shape and chirality of nanostructures. Helical nanofibers are suitable templates for fabricating dipeptide-capped gold nanoparticles, indicating a possible use of these nanofibers in the construction of arrays of gold nanoparticles.

Solvent-induced dynamic single-crystal-to-single-crystal transformation of a synthetic peptide-based cyclic compound

Solvent induced single-crystal-to-single-crystal transformation has been demonstrated indicating the dynamic behavior of one dimensional arrays obtained from a self-assembled new synthetic cyclic peptide.

Macrocyclic amines as structure-directing agents for the synthesis of three-dimensional antimony-sulfide frameworks

A new family of antimony sulfides, incorporating the macrocyclic tetramine 1,4,8,11-tetraazacyclotetradecane ( cyclam), has been prepared by a hydrothermal method. [C10N4H26][Sb4S7] (1), [Ni(C10N4H24)][Sb4S7] (2), and [Co(C10N4H24)](x)[C10N4H26](1-x)[Sb4S7] (0.08 <= x <= 0.74) (3) have been characterized by single-crystal X-ray diffraction, elemental analysis, thermogravimetry, and analytical electron microscopy. All three materials possess the same novel three-dimensional Sb4S72- framework, constructed from layers of parallel arrays of Sb4S84- chains stacked at 90 to one another. In 1, doubly protonated macrocyclic cations reside in the channel structure of the antimonysulfide framework. In 2 and 3, the cyclam acts as a ligand, chelating the divalent transition- metal cation. Analytical and X-ray diffraction data indicate that the level of metal incorporation in 2 is effectively complete, whereas in 3, both metalated and nonmetalated forms of the macrocycle coexist within the structure.

DNA cleavage and antitumour activity of platinum(II) and copper(II) compounds derived from 4-methyl-2-N-(2-pyridylmethyl)aminophenol: spectroscopic, electrochemical and biological investigation

The reaction of the redox-active ligand, Hpyramol (4-methyl-2-N-(2-pyridylmethyl)aminophenol) with K2PtCl4 yields monofunctional square-planar [Pt(pyrimol)Cl], PtL-Cl, which was structurally characterised by single-crystal X-ray diffraction and NMR spectroscopy. This compound unexpectedly cleaves supercoiled double-stranded DNA stoichiometrically and oxidatively, in a non-specific manner without any external reductant added, under physiological conditions. Spectro-electrochemical investigations of PtL-Cl were carried out in comparison with the analogue CuL-Cl as a reference compound. The results support a phenolate oxidation, generating a phenoxyl radical responsible for the ligand-based DNA cleavage property of the title compounds. Time-dependent in vitro cytotoxicity assays were performed with both PtL-Cl and CuL-Cl in various cancer cell lines. The compound CuL-Cl overcomes cisplatin-resistance in ovarian carcinoma and mouse leukaemia cell lines, with additional activity in some other cells. The platinum analogue, PtL-Cl also inhibits cell-proliferation selectively. Additionally, cellular-uptake studies performed for both compounds in ovarian carcinoma cell lines showed that significant amounts of Pt and Cu were accumulated in the A2780 and A2780R cancer cells. The conformational and structural changes induced by PtL-Cl and CuL-Cl on calf thymus DNA and phi X174 supercoiled phage DNA at ambient conditions were followed by electrophoretic mobility assay and circular dichroism spectroscopy. The compounds induce extensive DNA degradation and unwinding, along with formation of a monoadduct at the DNA minor groove. Thus, hybrid effects of metal-centre variation, multiple DNA-binding modes and ligand-based redox activity towards cancer cell-growth inhibition have been demonstrated. Finally, reactions of PtL-Cl with DNA model bases (9-Ethylguanine and 5'-GMP) followed by NMR and MS showed slow binding at Guanine-N7 and for the double stranded self complimentary oligonucleotide d(GTCGAC)(2) in the minor groove.

Modified rare earth semiconductor oxide as a new nucleotide probe

Recent rapid developments in biological analysis, medical diagnosis, pharmaceutical industry, and environmental control fuel the urgent need for recognition of particular DNA sequences from samples. Currently, DNA detection techniques use radiochemical, enzymatic, fluorescent, or electrochemiluminescent methods; however, these techniques require costly labeled DNA and highly skilled and cumbersome procedure, which prohibit any in-situ monitoring. Here, we report that hybridization of surface-immobilized single-stranded oligonucleotide on praseodymium oxide (evaluated as a biosensor surface for the first time) with complimentary strands in solution provokes a significant shift of electrical impedance curve. This shift is attributed to a change in electrical characteristics through modification of surface charge of the underlying modified praseodymium oxide upon hybridization with the complementary oligonucelotide strand. On the other hand, using a noncomplementary single strand in solution does not create an equivalent change in the impedance value. This result clearly suggests that a new and simple electrochemical technique based on the change in electrical properties of the modified praseodymium oxide semiconductor surface upon recognition and transduction of a biological event without using labeled species is revealed.

Synthesis and fabrication of a thin film containing silica-encapsulated face-centered tetragonal FePt nanoparticles

Self-assembly of monodisperse, silica-encapsulated, face-centered tetragonal FePt nanoparticles forms closely packed 2D arrays (see figure). Placing monodisperse FePt nanoparticles in silica nanocapsules allows the transition from a disordered face-centered cubic phase to a ferromagnetic crystalline face-centered tetragonal structure at elevated temperature without severe sintering. These materials are potential candidates for the generation of ultrahigh-density magnetic recording media.

Survivability of a probiotic Lactobacillus casei in the gastrointestinal tract of healthy human volunteers and its impact on the faecal microflora

Aim: The aim of this study was to measure the gastrointestinal survival of Lactobacillus casei and its impact on the gut microflora in healthy human volunteers. Methods and Results: Twenty healthy volunteers took part in a double-blind placebo-controlled probiotic feeding study (10 fed probiotic, 10 fed placebo). The probiotic was delivered in two 65 ml aliquots of fermented milk drink (FMD) daily for 21 days at a dose of 8.6 +/- 0.1 Log(10)Lact. casei CFU ml(-1) FMD. Faecal samples were collected before, during and after FMD or placebo consumption, and important groups of faecal bacteria enumerated by fluorescent in situ hybridization (FISH) using oligonucleotide probes targeting the 16S rRNA. The fed Lact. casei was enumerated using selective nutrient agar and colony identity confirmed by pulsed field gel electrophoresis. Seven days after ingestion of FMD, the Lact. casei was recovered from faecal samples taken from the active treatment group at 7.1 +/- 0.4 Log(10) CFU g(-1) faeces (mean +/- SD, n = 9) and numbers were maintained at this level until day 21. Lact. casei persisted in six volunteers until day 28 at 5.0 +/- 0.9 Log(10) CFU g(-1) faeces (mean +/- SD, n = 6). Numbers of faecal lactobacilli increased significantly upon FMD ingestion. In addition, the numbers of bifidobacteria were higher on days 7 and 21 than on days 0 and 28 in both FMD fed and placebo fed groups. Consumption of Lact. casei had little discernible effect on other bacterial groups enumerated. Conclusions: Daily consumption of FMD enabled a probiotic Lact. casei strain to be maintained in the gastrointestinal tract of volunteers at a stable relatively high population level during the probiotic feeding period. Significance and Impact of the Study: The study has confirmed that this probiotic version of Lact. casei survives well within the human gastrointestinal tract.

Exopolysaccharides produced by Bifidobacterium longum IPLA E44 and Bifidobacterium animalis subsp lactis IPLA R1 modify the composition and metabolic activity of human faecal microbiota in pH-controlled batch cultures

Exopolysaccharides (EPS) isolated from two Bifidobacterium strains, one of human intestinal origin (Bifidobacterium longum subsp. longum IPLA E44) and the other from dairy origin (Bifidobacterium animalis subsp. lactis IPLA R1), were subjected to in vitro chemically simulated gastrointestinal digestion. which showed the absence of degradation of both polymers in these conditions. Polymers were then used as carbon sources in pH-controlled faecal batch cultures and compared with the non-prebiotic carbohydrate glucose and the prebiotic inulin to determine changes in the composition of faecal bacteria. A set of eight fluorescent in situ hybridisation oligonucleotide probes targeting 16S rRNA sequences was used to quantify specific groups of microorganisms. Growth of the opportunistic pathogen Clostridium histolyticum occurred with all carbohydrates tested similarly to that found in negative control cultures without added carbohydrate and was mainly attributed to the culture conditions used rather than enhancement of growth by these substrates. Polymers E44 and RI stimulated growth of Lactobacillus/Enterococcus, Bifidobacterium, and Bacteroides/Prevotella in a similar way to that seen with inulin. The EPS RI also promoted growth of the Atopobium cluster during the first 24 h of fermentation. An increase in acetic and lactic acids was found during early stages of fermentation (first 10-24 h) correlating with increases of Lactobacillus, Bifidobacterium, and Atopobium. Propionic acid concentrations increased in old cultures, which was coincident with the enrichment of Clostridium cluster IX in cultures with EPS RI and with the increases in Bacteroides in cultures with both microbial EPS (RI and E44) and inulin. The lowest acetic to propionic acid ratio was obtained for EPS E44. None of the carbohydrates tested supported the growth of microorganisms from Clostridium clusters XIVa+b and IV, results that correlate with the poor butyrate production in the presence of EPS. Thus, EPS synthesized by bifidobacteria from dairy and intestinal origins can modulate the intestinal microbiota in vitro, promoting changes in some numerically and metabolically relevant microbial populations and shifts in the production of short chain fatty acids. (C) 2009 Elsevier B.V. All rights reserved.