<Emphasis Type="Italic">Pichia stipitis</Emphasis> xylose reductase helps detoxifying lignocellulosic hydrolysate by reducing 5-hydroxymethyl-furfural (HMF)

Background  

Pichia stipitis xylose reductase (Ps-XR) has been used to design Saccharomyces cerevisiae strains that are able to ferment xylose. One example is the industrial S. cerevisiae xylose-consuming strain TMB3400, which was constructed by expression of P. stipitis xylose reductase and xylitol dehydrogenase and overexpression of endogenous xylulose kinase in the industrial S. cerevisiae strain USM21.     

Reduced natural selection associated with low recombination in Drosophila melanogaster

Synonymous codons are not used equally in many organisms, and the extent of codon bias varies among loci. Earlier studies have suggested that more highly expressed loci in Drosophila melanogaster are more biased, consistent with findings from several prokaryotes and unicellular eukaryotes that codon bias is partly due to natural selection for translational efficiency. We link this model of varying selection intensity to the population-genetics prediction that the effectiveness of natural selection is decreased under reduced recombination. In analyses of 385 D. melanogaster loci, we find that codon bias is reduced in regions of low recombination (i.e., near centromeres and telomeres and on the fourth chromosome). The effect does not appear to be a linear function of recombination rate; rather, it seems limited to regions with the very lowest levels of recombination. The large majority of the genome apparently experiences recombination at a sufficiently high rate for effective natural selection against suboptimal codons. These findings support models of the Hill-Robertson effect and genetic hitchhiking and are largely consistent with multiple reports of low levels of DNA sequence variation in regions of low recombination.      

Kappa-chain constant-region gene sequences in genus Rattus: coding regions are diverging more rapidly than noncoding regions

We have determined the nucleotide sequence of a 1,200-base pair (bp) genomic fragment that includes the kappa-chain constant-region gene (C kappa) from two species of native Australian rodents, Rattus leucopus cooktownensis and Rattus colletti. Comparison of these sequences with each other and with other rodent C kappa genes shows three surprising features. First, the coding regions are diverging at a rate severalfold higher than that of the nearby noncoding regions. Second, replacement changes within the coding region are accumulating at a rate at least as great as that of silent changes. Third, most of the amino acid replacements are localized in one region of the C kappa domain--namely, the carboxy-terminal "bends" in the alpha-carbon backbone. These three features have previously been described from comparisons of the two allelic forms of C kappa genes in R. norvegicus. These data imply the existence of considerable evolutionary constraints on the noncoding regions (based on as yet undetermined functions) or powerful positive selection to diversify a portion of the constant-region domain (whose physiological significance is not known). These surprising features of C kappa evolution appear to be characteristic only of closely related C kappa genes, since comparison of rodent with human sequences shows the expected greater conservation of coding regions, as well as a predominance of silent nucleotide substitutions within the coding regions.      

Use of medetomidine-ketamine and atipamezole for reversible immobilization of free-ranging hog deer (Axis porcinus) captured in drive nets

A combination of 0.05 mg/kg medetomidine and 1.5 mg/kg ketamine was used to immobilize nine adult free-ranging hog deer (Axis porcinus) captured in drive nets in the Royal Bardia National Park, Nepal, 22-23 February 2000. The drugs were administered intramuscularly from separate syringes and the mean time (+/-SD) to complete immobilization was 4.6+/-1.0 min. Muscle relaxation was good and no major clinical side effects were seen. Mean values for physiologic parameters, recorded at 10-12 and 18-20 min after drug administration, were 40.6+/-0.5 and 41.1+/-0.6 C, 87+/-5 and 84+/-4%, 107+/-16 and 113+/-16 beats/ min, and 46+/-9 and 40+/-8 breaths/min for rectal temperature, SpO2, pulse rate, and respiratory rate, respectively. All animals received 0.25 mg/ kg atipamezole intramuscularly 20-22 min after administration of medetomidine-ketamine and the mean time to coordinated running was 4.8+/-0.8 min. All animals survived for at least 5 mo post-capture. To reduce stress and to facilitate handling, medetomidine-ketamine and atipamezole are recommended for reversible immobilization of free-ranging hog deer captured in drive nets.     

Quantification of the virus-host interaction in human T lymphotropic virus I infection

Background

Cellular infection with human immunodeficiency virus (HIV) both in vitro and in vivo requires a member of the chemokine receptor family to act as a co-receptor for viral entry. However, it is presently unclear to what extent the interaction of HIV proteins with chemokine receptors generates intracellular signals that are important for productive infection.

Results

In this study we have used a recently described family of chemokine inhibitors, termed BSCIs, which specifically block chemokine-induced chemotaxis without affecting chemokine ligands binding to their receptors. The BSCI termed Peptide 3 strongly inhibited CCR5 mediated HIV infection of THP-1 cells (83 ± 7% inhibition assayed by immunofluoresence staining), but had no effect on gp120 binding to CCR5. Peptide 3 did not affect CXCR4-dependent infection of Jurkat T cells.

Conclusion

These observations suggest that, in some cases, intracellular signals generated by the chemokine coreceptor may be required for a productive HIV infection.     

Complex temporal decay: a complete analysis

Relaxation dynamics is universal in science and engineering; its study serves to parameterize a system's response and to help identify a microscopic model of the processes involved. When measured data for a phenomenon cannot be fitted using one exponential, the choice of an alternative function to describe the decay becomes nontrivial. Here, we contrast two different, but fundamentally related approaches to fitting nontrivial decay curves; exponential decomposition and the gamma probability density function. Copyright © 2013 John Wiley & Sons, Ltd.     

Kill rates and food consumption of leopards in Bardia National Park, Nepal

This is the first study presenting data on kill rates and food consumption among Asian leopardsPanthera pardus Linnaeus, 1758. In Bardia National Park, Nepal, we found leopard kills by searching within areas with clusters of locations from radio collared leopards (2 males and 1 female with 2 cubs aged 4–9 months). We used two tracking schemes, 24-h intensive radio-tracking and daily monitoring, and we defined food consumption as the product of average prey live weight and proportion consumed. The three leopards consumed 89.2 kg of meat from five chitalAxis axis, one domestic dog and two birds during 19 days of 24-h intensive tracking, rendering an average (± SE) daily food intake of 4.7 ± 0.3 kgper capita. Twenty-five prey items (14 chital, one muntjacMuntiacus muntjak, four primates and six birds) were found during 180 days of daily monitoring of the female. All edible biomass was consumed in all kills, except for three chital, and the rate of kill consumption was positively related to the age of her cubs. The average daily food consumption of the female was 4.0 ± 0.3 kg/day, the kill rate (days/kill) including all prey categories was 5.6 ± 0.4 days, and the kill rate of ungulates was 10.6 ±0.7 days. Our food consumption estimates are higher than reported from arid African environments. We suggest that the high food consumption rate in our study is a consequence of a release from time-energy constraints due to high prey abundance.     

Cortical potential imaging using L-curve and GCV method to choose the regularisation parameter

Background

The electroencephalography (EEG) is an attractive and a simple technique to measure the brain activity. It is attractive due its excellent temporal resolution and simple due to its non-invasiveness and sensor design. However, the spatial resolution of EEG is reduced due to the low conducting skull. In this paper, we compute the potential distribution over the closed surface covering the brain (cortex) from the EEG scalp potential. We compare two methods – L-curve and generalised cross validation (GCV) used to obtain the regularisation parameter and also investigate the feasibility in applying such techniques to N170 component of the visually evoked potential (VEP) data.

Methods

Using the image data set of the visible human man (VHM), a finite difference method (FDM) model of the head was constructed. The EEG dataset (256-channel) used was the N170 component of the VEP. A forward transfer matrix relating the cortical potential to the scalp potential was obtained. Using Tikhonov regularisation, the potential distribution over the cortex was obtained.

Results

The cortical potential distribution for three subjects was solved using both L-curve and GCV method. A total of 18 cortical potential distributions were obtained (3 subjects with three stimuli each – fearful face, neutral face, control objects).

Conclusions

The GCV method is a more robust method compared to L-curve to find the optimal regularisation parameter. Cortical potential imaging is a reliable method to obtain the potential distribution over cortex for VEP data.

     

The effect of recreational homes on willow ptarmigan (Lagopus lagopus) in a mountain area of Norway

The increasing development of recreational resorts and second homes in mountain regions worldwide require substantial infrastructure, and have large impact on habitats and ecosystems. We hypothesized that developed areas would attract predators and lead to higher predation on willow ptarmigan and lower their abundance. In a 500-km² study area in south-central Norway, we sampled the density of territorial cocks in spring and the breeding success of willow ptarmigan along a 3-km gradient extending out from clusters of cabins. We also sampled red fox scats and corvid birds and measured nest predation on artificial nests across this gradient. Densities of cocks in the spring and of adults and brood sizes in August did not vary along the gradient. However, the density of chicks in August was higher beyond 1.5 km from cabin areas, presumably because more hens lost their clutches in the vicinity of cabins. This was supported by the results from the artificial nest experiment where significantly more nests were depredated near cabin areas than further away. The number of scats of red fox along trails increased with distance from cabins, whereas more corvid birds were observed near cabins. We conclude that corvid birds were the main cause of higher loss of ptarmigan nests near cabin areas, which led to lower production of chicks. Breeding density, however, did not seem to vary along the gradient, presumably because of suitable habitat for breeding and little human activity in these areas during the period of pair formation and nesting.