Localization of thymosin β10 in breast cancer cells: relationship to actin cytoskeletal remodeling and cell motility

Beta-thymosins are polypeptides involved in the regulation of actin polymerization and thymosin β10 and β4 have been implicated in sequestration of monomeric (G-) actin. Additionally, experimental overexpression of thymosin β10 has been found to result in increases in F-actin bundles as well as in cell motility and spreading. We have studied the distribution of endogenously expressed thymosin β10 in cultured human breast cancer cell lines. Both unperturbed monolayer cultures and wound-healing models were examined using double-staining for thymosin β10 and polymerized (F-) actin. Our findings show that thymosin β10 is expressed in all three-cancer cell lines (SK-BR-3, MCF-7 and MDA-MB-231) studied. No or little staining was detected in confluent cells, whereas strong staining occurred in semiconfluent cells and in cells populating monolayer wounds. Importantly, the distribution of staining for thymosin β10 was inverse of staining for F-actin. These data support a physiological role for thymosin β10 in sequestration of G-actin as well as in cancer cell motility.     

The metabolic impact of β‐hydroxybutyrate on neurotransmission: Reduced glycolysis mediates changes in calcium responses and KATP channel receptor sensitivity

Glucose is the main energy substrate for neurons, and ketone bodies are known to be alternative substrates. However, the capacity of ketone bodies to support different neuronal functions is still unknown. Thus, a change in energy substrate from glucose alone to a combination of glucose and β‐hydroxybutyrate might change neuronal function as there is a known coupling between metabolism and neurotransmission. The purpose of this study was to shed light on the effects of the ketone body β‐hydroxybutyrate on glycolysis and neurotransmission in cultured murine glutamatergic neurons. Previous studies have shown an effect of β‐hydroxybutyrate on glucose metabolism, and the present study further specified this by showing attenuation of glycolysis when β‐hydroxybutyrate was present in these neurons. In addition, the NMDA receptor‐induced calcium responses in the neurons were diminished in the presence of β‐hydroxybutyrate, whereas a direct effect of the ketone body on transmitter release was absent. However, the presence of β‐hydroxybutyrate augmented transmitter release induced by the K_ATP channel blocker glibenclamide, thus giving an indirect indication of the involvement of K_ATP channels in the effects of ketone bodies on transmitter release.

     

Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity

The recently discovered lytic polysaccharide monooxygenases (LPMOs) carry out oxidative cleavage of polysaccharides and are of major importance for efficient processing of biomass. NcLPMO9C from Neurospora crassa acts both on cellulose and on non-cellulose β-glucans, including cellodextrins and xyloglucan. The crystal structure of the catalytic domain of NcLPMO9C revealed an extended, highly polar substrate-binding surface well suited to interact with a variety of sugar substrates. The ability of NcLPMO9C to act on soluble substrates was exploited to study enzyme-substrate interactions. EPR studies demonstrated that the Cu²⁺ center environment is altered upon substrate binding, whereas isothermal titration calorimetry studies revealed binding affinities in the low micromolar range for polymeric substrates that are due in part to the presence of a carbohydrate-binding module (CBM1). Importantly, the novel structure of NcLPMO9C enabled a comparative study, revealing that the oxidative regioselectivity of LPMO9s (C1, C4, or both) correlates with distinct structural features of the copper coordination sphere. In strictly C1-oxidizing LPMO9s, access to the solvent-facing axial coordination position is restricted by a conserved tyrosine residue, whereas access to this same position seems unrestricted in C4-oxidizing LPMO9s. LPMO9s known to produce a mixture of C1- and C4-oxidized products show an intermediate situation.     

Fatty acid composition of the blubber in white whales (Delphinapterus leucas)

Fatty acid (FA) composition of the blubber in free-ranging white whales (Delphinapterus leucas) from Svalbard's waters was determined and compared with the fatty acid composition of potential prey species in an attempt to assess diet. This methodology is based on the common assumption that unique arrays of FAs found within groups of organisms are transferred, largely unaltered, up marine food chains and thus may be useful for assessment of diet composition. Complete-column blubber biopsies were sampled from white whales (n=7) during the summers of 1996 and 1997. All captured animals were adult males. FAs were extracted from 2–4 replicates taken from an area about 10 cm in front of the mid-dorsal ridge. FA data from a total of 12 potential prey species from the Svalbard area were compared to the white-whale blubber samples. Twenty-two FAs were consistently found in relative amounts >0.5% of the total FA composition in white whales. These FAs accounted for 94–96% of the total FAs present. The blubber was composed almost entirely of triacylglycerols. The major saturated FAs were 14:0 and 16:0; 16:1(n-7), 18:1(n-9) and 20:1(n-9) were the major monounsaturated FAs and 20:5(n-3) and 22:6(n-3) were the major polyunsaturated FAs. Sixteen of the 22 FAs consistently found in the white-whale blubber were also found in considerable amounts (>0.5% of total FAs) in most of the potential species. Principal Component Analysis run on these 16 FAs suggests that polar cod (Boreogadus saida) had the most similar FA composition to the white-whale blubber, followed by capelin (Mallotus villosus), the copepod Calanus hyperboreus and the shrimp Pandalus borealis. Accepted: 27 November 1999     

The pathway from arachidonic to docosapentaenoic acid (20:4n-6 to 22:5n-6) and from eicosapentaenoic to docosahexaenoic acid (20:5n-3 to 22:6n-3) studied in testicular cells from immature rats

The concentration-dependent metabolism of 1-¹⁴C-labelled precursors of 22:5n-6 and 22:6n-3 was compared in rat testis cells. The amounts of [¹⁴C]22- and 24-carbon metabolites were measured by HPLC. The conversion of [1-¹⁴C]20:5n-3 to [3-¹⁴C]22:6n-3 was more efficient than that of [1-¹⁴C]20:4n-6 to [3-¹⁴C]22:5n-6. At low substrate concentration (4 μM) it was 3.4 times more efficient, reduced to 2.3 times at high substrate concentration (40 μM). The conversion of [1-¹⁴C]22:5n-3 to [1-¹⁴C]22:6n-3 was 1.7 times more efficient than that of [1-¹⁴C]22:4n-6 to [1-¹⁴C]22:5n-6 using a low, but almost equally efficient using a high substrate concentration. When unlabelled 20:5n-3 was added to a cell suspension incubated with [1-¹⁴C]20:4n-6 or unlabelled 22:5n-3 to a cell suspension incubated with [1-¹⁴C]22:4n-6, the unlabelled n-3 fatty acids strongly inhibited the conversion of [1-¹⁴C]20:4n-6 or [1-¹⁴C]22:4n-6 to [¹⁴C]22:5n-6. In the reciprocal experiment, unlabelled 20:4n-6 and 22:4n-6 only weakly inhibited the conversion of [1-¹⁴C]20:5n-3 and [1-¹⁴C]22:5n-3 to [¹⁴C]22:6n-3. The results indicate that if both n-6 and n-3 fatty acids are present, the n-3 fatty acids are preferred over the n-6 fatty acids in the elongation from 20- to 22- and from 22- to 24-carbon atom fatty acids. In vivo the demand for 22-carbon fatty acids for spermatogenesis in the rat may exceed the supply of n-3 precursors and thus facilitate the formation of 22:5n-6 from the more abundant n-6 precursors.     

Strong impact on the polycyclic aromatic hydrocarbon (PAH)-degrading community of a PAH-polluted soil but marginal effect on PAH degradation when priming with bioremediated soil dominated by mycobacteria

Bioaugmentation of soil polluted with polycyclic aromatic hydrocarbons (PAHs) is often disappointing because of the low survival rate and low activity of the introduced degrader bacteria. We therefore investigated the possibility of priming PAH degradation in soil by adding 2% of bioremediated soil with a high capacity for PAH degradation. The culturable PAH-degrading community of the bioremediated primer soil was dominated by Mycobacterium spp. A microcosm containing pristine soil artificially polluted with PAHs and primed with bioremediated soil showed a fast, 100- to 1,000-fold increase in numbers of culturable phenanthrene-, pyrene-, and fluoranthene degraders and a 160-fold increase in copy numbers of the mycobacterial PAH dioxygenase gene pdo1. A nonpolluted microcosm primed with bioremediated soil showed a high rate of survival of the introduced degrader community during the 112 days of incubation. A nonprimed control microcosm containing pristine soil artificially polluted with PAHs showed only small increases in the numbers of culturable PAH degraders and no pdo1 genes. Initial PAH degradation rates were highest in the primed microcosm, but later, the degradation rates were comparable in primed and nonprimed soil. Thus, the proliferation and persistence of the introduced, soil-adapted degraders had only a marginal effect on PAH degradation. Given the small effect of priming with bioremediated soil and the likely presence of PAH degraders in almost all PAH-contaminated soils, it seems questionable to prime PAH-contaminated soil with bioremediated soil as a means of large-scale soil bioremediation.     

Brown hares on the edge: Genetic population structure of the Danish brown hare

Denmark lies on the edge of the distributional range of the brown hareLepus europaeus Pallas, 1778, where population differentiation is most likely to occur. A total of 369 brown hares from eight geographically distinct Danish European brown hare populations were used to study the genetic population structure. In all, 480bp of the mitochondrial D-loop were sequenced in both directions. Observed genetic diversity (π) was relatively low (π=0.41%) while haplotype diversity (h=0.808) and the number of unique haplotypes (19) were similar to levels found in other European brown hare populations. The observed population structure was pronounced (pairwise conventionalF _ST and ϕ _st ranged between 6.9–57% and 5–69.8%, respectively). There was no correlation between the geographic and the genetic distance. Population structure was influenced by genetic drift, anthropogenic effects (eg translocation and escapes from hare-farms) and by post-glacial recolonization from southern refuges or refuges north east of the Black Sea. Analysis of historical population expansion/fluctuation events indicated that the populations have experienced different demographic events in the recent past. Relatively high sequence divergence between some populations might be explained by multiple recolonization events after the last Pleistocene glaciations or by stocking effects. Colonization from southern refuges was supported by the observation that haplotype 2 in the Danish brown hare was identical to the central European ancestral haplotype c07.     

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs was selected for experimental validation by resequencing and genotyping. This study provides a web-based DNA chromatogram and contig browser that facilitates the evaluation and selection of candidate SNPs, which can be applied as genetic markers for genome wide genetic studies. AVAILABILITY: The stand-alone version of MAVIANT program for local use is freely available under GPL license terms at http://snp.agrsci.dk/maviant. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.