A numerical simulation of the flow in a T-type bifurcation and its application to an "end to side" fistula

Some recent surgical procedures such as arteriovenous fistula, or coronary and cerebral by-passes were observed to yield counterdirectional branching blood flows. There is a lack of knowledge about the role of the counterdirectional flow ratio, the angle of anastomosis and the shear stresses in the process of thrombogenesis that leads to shunt occlusion. The program developed to simulate these hemodynamic conditions uses an efficient numerical scheme for the solution of the 2-D Navier-Stokes equations and can be easily adapted to flows in other geometrical configurations.     

Tongue twisters: feeding enrichment to reduce oral stereotypy in giraffe

Stereotypic behavior has been well‐studied and documented in a variety of animals including primates, carnivores, and domesticated ungulates. However, very little information is known about stereotypic behavior of captive exotic ungulates. Giraffe have been found to perform a wide range of stereotypic behaviors. According to a survey of zoological institutions, oral stereotypies, specifically the licking of nonfood objects are the most prevalent stereotypic behaviors observed in giraffe. Their performance appears to be related to feeding and rumination and may be a result of the inability of a highly motivated feeding behavior pattern, tongue manipulation, to be successfully completed. To test this hypothesis, the indoor and outdoor feeders for three giraffe housed at Zoo Atlanta were modified to require the giraffe to perform more naturalistic and complex foraging behaviors. Data were collected using instantaneous scan sampling in both exhibit and holding areas. Our results showed that, for the giraffe that engaged in the highest rates of oral stereotypic behavior in the baseline, more complex feeders that required tongue use to access grain or alfalfa had the greatest effect on behavior. For the giraffe that performed low baseline rates of oral stereotypic behavior, adding slatted tops to the alfalfa feeders indoors virtually eliminated the behavior. Although some changes in ruminating and feeding behavior were observed, the decreases in stereotypic behavior were not associated with the changes in ruminating or feeding behavior. These results provide evidence for the hypothesis that oral stereotypy in herbivores can be reduced by encouraging giraffe to engage in more naturalistic foraging behavior. Zoo Biol 27:200–212, 2008. © 2008 Wiley‐Liss, Inc.     

Comparison of different strategies to reduce acetate formation in Escherichia coli

E. coli cells produce acetate as an extracellular coproduct of aerobic cultures. Acetate is undesirable because it retards growth and inhibits protein formation. Most process designs or genetic modifications to minimize acetate formation aim at balancing growth rate and oxygen consumption. In this research, three genetic approaches to reduce acetate formation were investigated: (1) direct reduction of the carbon flow to acetate (ackA-pta, poxB knock-out); (2) anticipation on the underlying metabolic and regulatory mechanisms that lead to acetate (constitutive ppc expression mutant); and (3) both (1) and (2). Initially, these mutants were compared to the wild-type E. coli via batch cultures under aerobic conditions. Subsequently, these mutants were further characterized using metabolic flux analysis on continuous cultures. It is concluded that a combination of directly reducing the carbon flow to acetate and anticipating on the underlying metabolic and regulatory mechanism that lead to acetate, is the most promising approach to overcome acetate formation and improve recombinant protein production. These genetic modifications have no significant influence on the metabolism when growing the micro-organisms under steady state at relatively low dilution rates (less than 0.4 h(-1)).     

Microbes in Helicoverpa armigera oral secretions contribute to increased senescence around plant wounds

1. Plants have long been exposed to insect herbivore attack. Crucial to the plant's ability to defend itself is its ability to identify specific signals associated with attacking insects. Distinctive chemical cues, such as those associated with chewing insect oral secretions (OS), activate targeted defence responses to chewing insect herbivores. 2. Herbivore-associated cues can be complicated by the fact that many herbivores form associations with microbes that produce their own specific signals, which may induce alternative defence processes. 3. Here we report that OS of the global pest, the cotton bollworm (Helicoverpa armigera), induce senescence around wounds in Brachypodium distachyon leaves. Crude OS activate greater levels of senescence than OS with reduced microbial abundance or mechanical wounding alone. Nonetheless, plants closed mechanical wounds more rapidly when treated with H. armigera OS regardless of the microbial component. 4. This study concludes that H. armigera OS can activate senescence and wound closure in plant tissues and that microbes within OS have an important role in shaping plant-herbivore interactions through additional increases in senescence.     

Simple approach to reduce PCR artefact formation leads to reliable genotyping of MHC and other highly polymorphic loci--implications for evolutionary analysis

Genetic variation in coding regions is of strong interest for biologists as it represents an important factor that drives evolution. To analyse polymorphic loci, researchers usually rely on commonly used typing techniques such as cloning, SSCP, DGGE or RSCA. However, there are potential pitfalls in screening multi-allelic templates, which are mainly the formation of sequence chimeras during PCR amplification, and mosaic sequences during cloning. One of the most challenging genomic regions to explore is the Major Histocompatibility Complex (MHC), which codes for peptide-binding proteins of the vertebrate's adaptive immune system and is well known for its exceptional polymorphism. We compared the effect of two different PCR amplification approaches in a study of the MHC class IIB genes of the three-spined stickleback (Gasterosteus aculeatus). One approach used standard PCR conditions and the other a combination of several measures to eliminate PCR artefacts. In both approaches, the amplicons obtained were cloned and sequenced. In the first, established approach, 24% of the clones represented artefacts, while in the second approach the number of artefacts were reduced ten-fold. Furthermore, it enabled easy differentiation between real alleles and artificial sequences. We also analysed the potential effects of such artefacts in genetic analysis and evolutionary interpretation, and found a slight reduction in the signature of positive selection and an increase in recombination events. Consequently, we strongly recommend to apply the new PCR approach described in this study when genotyping MHC or other polymorphic genes.     

A local approach to reduce industrial uranium wound contamination in rats

The aim of this work is to develop a new approach to partially decontaminate wounds after industrial uranium contamination, during the interval of time between contamination and transfer of the patient to the infirmary. A wound dressing and a paste mixed or not with uranium-chelating ligands, ethane-1-hydroxy-1,1-bisphosphonate (EHBP) and carballylic amido bis phosphonic acid (CAPBP), were tested in vitro on muscles and in vivo on rats after deposit of uranium oxide compounds. The dressing and the paste, composed of carboxymethylcellulose-based hydrocolloids known to be highly absorbent, were applied on simulated wounds a few minutes after the contamination. The incorporation of chelating ligands did not improve the efficacy of the dressing or paste, and the best results were obtained with the dressing. In vivo, after 1 h of contact with the wound, the dressing absorbed about 30% and 60% of a UO4 compound deposited intra- and intermuscularly, respectively. After intramuscular deposit, the efficacy of the dressing was not reduced if the contact time decreased from 1 h to 15 min. Therefore, this wound dressing could be a practical option to treat uranium-contaminated wounds, but its efficacy depends on the localization of the uranium deposit.     

Genetic engineering approach to reduce undesirable by-products in cephalosporin C fermentation

Deacetoxycephalosporin C (DAOC) is produced by Acremonium chrysogenum as an intermediate compound in the cephalosporin C biosynthetic pathway, and is present in small quantities in cephalosporin C fermentation broth. This compound forms an undesirable impurity, 7-aminodeacetoxycephalosporanic acid (7-ADCA), when the cephalosporin C is converted chemically or enzymatically to 7-aminocephalosporanic acid (7-ACA). In the cephalosporin C biosynthetic pathway of A. chrysogenum, the bifunctional expandase/hydroxylase enzyme catalyzes the conversion of penicillin N to DAOC and subsequently deacetylcephalosporin C (DAC). By genetically engineering strains for increased copy number of the expandase/hydroxylase gene, we were able to reduce the level of DAOC present in the fermentation broth to 50% of the control. CHEF gel electrophoresis and Southern analysis of DNA from two of the transformants revealed that one copy of the transforming plasmid had integrated into chromosome VIII (ie a heterologous site from the host expandase/hydroxylase gene situated on chromosome II). Northern analysis indicated that the amount of transcribed expandase/hydroxylase mRNA in one of the transformants is increased approximately two-fold over that in the untransformed host. Received 5 January 1998/ Accepted in revised form 29 May 1998     

A theoretical approach to cluster formation in biological membranes

A theoretical analysis of cluster formation within the lipid matrix of biological membranes is presented. Various models are analysed: (a) one-dimensional monolayer, (b) two-dimensional monolayer and (c) one dimensional bilayer. Furthermore, lipid-protein interactions are considered. The model is based on differential equations for the probabilities a_i and b₁ which characterize the occupation of the lattice site i by the lipids A and B, respectively. These differential equations are an approximation of the Master-equation. Steady states as well as time-dependent variations are analysed. Depending on the interaction energies of the two lipids, different stationary lipid distributions are obtained, including clusters of lipids A or B and alternating structures. The distributions may be dynamically stable or unstable. It is shown that phase transitions within the lipid matrix may be induced by alteration of the composition of the membrane, by changing the interaction energies of the lipids, by variation of the temperature or by lipid-protein interactions. The transitions between different stationary distributions are studied by use of bifurcation diagrams. The analysis of time-dependent states reveals that unstable structures of the membrane may be important for certain time periods. Consideration of the lipid bilayer leads to a great number of possible distributions, which may be symmetric or asymmetric with respect to the outer and inner leaflets of the membrane.     

A new approach to the side chain formation of 24-alkyl-22-hydroxy steroids: application to the preparation of early brassinolide biosynthetic precursors

A new synthetic route to 22S-hydroxy-24R-methyl steroids has been developed and applied for the preparation of cathasterone, (22S)-hydroxycampesterol, and 6-deoxocathasterone, which are precursors in the early stages of the biosynthesis of brassinolide. The construction of the steroid side chain with the correct stereochemistry at C-24 is based on the use of Claisen rearrangement. The introduction of the 22-hydroxyl group has been achieved by epoxidation of the Δ(22)-double bond, nucleophilic opening of the intermediate mesyl epoxide with sodium sulfide, and desulfurization of the formed tetrahydrothiophenes with Raney nickel.     

Technical strategies to reduce the amount of "false significant" results in quantitative proteomics

When the p-value is set at <0.05 in statistical group comparisons, a 5% rate of "false significant" results is expected. In order to test the reliability of our 2-DE method, we loaded each of 24 gels with equal-sized samples (200 mug protein from pooled rat brain, pH 4-7, stained with ruthenium fluorescent stain for visualization) and statistically compared the first 12 gels with the last 12. In numerous experiments the rate of significant differences found far exceeded 5%. Several factors were identified as causing the following rates of false significant differences in spot intensities: (i) running samples in two different 2-DE runs (42%), (ii) running second dimension gels produced in two different gel casters (16%), (iii) normalizing the entire gel instead of separately normalizing several different gel zones (11%), (iv) using IPG strips from different packages (19%), (v) dividing the whole sample into subgroups during software analysis (9%). After controlling for all these factors, the rates of "false positive" results in our experiments were regularly reduced to approximately 5%. This is an indispensable prerequisite for avoiding too high a rate of false positive results in experiments in which different subgroups are compared statistically.     

A first principles approach to differential expression in microarray data analysis

Background  

The disparate results from the methods commonly used to determine differential expression in Affymetrix microarray experiments may well result from the wide variety of probe set and probe level models employed. Here we take the approach of making the fewest assumptions about the structure of the microarray data. Specifically, we only require that, under the null hypothesis that a gene is not differentially expressed for specified conditions, for any probe position in the gene's probe set: a) the probe amplitudes are independent and identically distributed over the conditions, and b) the distributions of the replicated probe amplitudes are amenable to classical analysis of variance (ANOVA). Log-amplitudes that have been standardized within-chip meet these conditions well enough for our approach, which is to perform ANOVA across conditions for each probe position, and then take the median of the resulting (1 - p) values as a gene-level measure of differential expression.     

A physical approach to reduce nonspecific adhesion in molecular recognition atomic force microscopy.

Atomic force microscopy is one of the few techniques that allow analysis of biological recognition processes at the single-molecule level. A major limitation of this approach is the nonspecific interaction between the force sensor and substrate. We have modeled the nonspecific interaction by looking at the interaction potential between a conical Si3N4 tip with a spherical end face and a mica surface in solution, using DLVO (Derjaguin, Landau, Verwey, Overbeek) theory and numerical calculations. Insertion of the tip-sample potential in a simulation of an approach-retract cycle of the cantilever gives the well-known force-distance curve. Simulating a force-distance curve at low salt concentration predicts a discrete hopping of the tip, caused by thermal fluctuations. This hopping behavior was observed experimentally and gave rise to a novel approach to making measurements in adhesion mode that essentially works in the repulsive regime. The distance between tip and sample will still be small enough to allow spacer-involved specific interactions, and the percentage of nonspecific interactions of the bare tip with the mica is minimized. We have validated this physical model by imaging intercellular adhesion molecule 1 (ICAM-1) antigen with a tip functionalized with anti-ICAM-1 antibody. The measurement demonstrated that a significant decrease in the number of nonspecific interactions was realized, and the topographical image quality and the specific bonding capability of the tip were not affected.     

Lipid transport function is the main target of oral oleoylethanolamide to reduce adiposity in high-fat-fed mice

We evaluated the biological basis of reduced fat gain by oleoylethanolamide (OEA) in high-fat-fed mice and sought to determine how degradation of OEA affected its efficiency by comparing its effects to those of KDS-5104, a nonhydrolyzable lipid OEA analog. Mice were given OEA or KDS-5104 by the oral route (100 mg/kg body weight). Sixty-eight variables per mouse, describing six biological processes (lipid transport, lipogenesis, energy intake, energy expenditure, endocannabinoid signaling, and glucose metabolism), spanning gene expression of biochemical and physiological parameters were examined to determine the primary target whereby OEA reduces fat gain. Although KDS-5104 but not OEA was resistant to fatty acid amide hydrolase hydrolysis, OEA was degraded by an unidentified hydrolysis system in the liver. Nevertheless, both compounds equally decreased body fat pads after 5 weeks (20%; P < 0.05). The six biological functions constructed from the 68 initial variables predicted up to 58% of adipose fat variations. Lipid transport appeared central to the explanation for body fat deposition (16%; P < 0.0001), in which decreased expression of the FAT/CD36 gene was the component most related to adipose depots. Lipid transport appears to be a determinant player in the OEA fat-lowering response, with adipose tissue FAT/CD36 expression being the most relevant bioindicator of OEA action.     

A new approach to the problem of oxygen formation in photosynthesis

A detailed quantum-mechanical analysis of the model of water oxidizing complex, based on recent X-ray data on the structure of PSII, was made. A mechanism of water oxidation was suggested and explained for the first time. The role of three manganese atoms that are not involved directly in water oxidation, the role of the cubic structure of the complex, and the necessity of the presence of calcium and chlorine atoms during water oxidation are discussed. Theoretical computations of the energies of the complex in each S-state were made.     

Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast

Diacetyl causes an unwanted buttery off-flavor in lager beer. It is spontaneously generated from α-acetolactate, an intermediate of yeast's valine biosynthesis released during the main beer fermentation. Green lager beer has to undergo a maturation process lasting two to three weeks in order to reduce the diacetyl level below its taste-threshold. Therefore, a reduction of yeast's α-acetolactate/diacetyl formation without negatively affecting other brewing relevant traits has been a long-term demand of brewing industry. Previous attempts to reduce diacetyl production by either traditional approaches or rational genetic engineering had different shortcomings. Here, three lager yeast strains with marked differences in diacetyl production were studied with regard to gene copy numbers as well as mRNA abundances under conditions relevant to industrial brewing. Evaluation of data for the genes directly involved in the valine biosynthetic pathway revealed a low expression level of Sc-ILV6 as a potential molecular determinant for low diacetyl formation. This hypothesis was verified by disrupting the two copies of Sc-ILV6 in a commercially used lager brewers' yeast strain, which resulted in 65% reduction of diacetyl concentration in green beer. The Sc-ILV6 deletions did not have any perceptible impact on beer taste. To our knowledge, this has been the first study exploiting natural diversity of lager brewers' yeast strains for strain optimization.