Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys

Using the strictly neutral model as a null hypothesis, we tested for deviations from expected levels of nucleotide polymorphism at the alcohol dehydrogenase locus (Adh-1) within and among four species of pocket gophers (Geomys bursarius major, G. knoxjonesi, G. texensis llanensis, and G. attwateri). The complete protein-encoding region was examined, and 10 unique alleles, representing both electromorphic and cryptic alleles, were used to test hypotheses (e.g., the neutral model) concerning the maintenance of genetic variation. Nineteen variable sites were identified among the 10 alleles examined, including 9 segregating sites occurring in synonymous positions and 10 that were nonsynonymous. Several statistical methods, including those that test for within-species variation as well as those that examine variation within and among species, failed to reject the null hypothesis that variation (both within and between species of Geomys) at the Adh locus is consistent with the neutral theory. However, there was significant heterogeneity in the ratio of polymorphism to divergence across the gene, with polymorphisms clustered in the first half of the coding region and fixed differences clustered in the second half of the gene. Two alternative hypotheses are discussed as possible explanations for this heterogeneity: an old balanced polymorphism in the first half of the gene or a recent selective sweep in the second half of the gene.      

Carbon payback period and carbon offset parity point of wood pellet production in the South‐eastern United States

This study examines the effect of methodological choices to determine the carbon payback time and the offset parity point for wood pellet production from softwood plantations in the South‐eastern United States. Using the carbon accounting model GORCAM we model low‐, medium‐ and high‐intensity plantation management scenarios for a single stand level, an increasing stand level and a landscape level. Other variables are the fossil‐fuel reference system and the electrical conversion efficiency. Due to the large amount of possible methodological choices and reference systems, there is a wide range of payback times (≤1 year at landscape to 27 years at stand level) and offset parity points (2–106 years). Important aspects impacting on the carbon balances are yield, carbon replacement factor, system boundaries and the choice of reference scenario used to determine the parity point. We consider the landscape‐level carbon debt approach more appropriate for the situation in the South‐eastern United States, where softwood plantation is already in existence, and under this precondition, we conclude that the issue of carbon payback is basically nonexistent. If comparison against a protection scenario is deemed realistic and policy relevant, and assuming that wood pellets directly replace coal in an average coal power plant, the carbon offset parity point is in the range 12–46 years; i.e. one or two rotations. Switching to intensively managed plantations yields most drastic reduction in the time to parity points (≤17 years in 9 of 12 cases).     

Purification and characterization of the enzymes of fructan biosynthesis in tubers of Helianthus tuberosus 'Colombia': I. Fructan: fructan fructosyl transferase

Fructan: fructan fructosyl transferase (FFT), one of the enzymesinvolved in the synthesis of ß-2,1 linked fructosepolymers has been purified 205-fold from tubers of Helianthustuberosus harvested in the accumulation phase. The molecularweight of the native as well as the SDS-denatured protein isapproximately 70 kDa. On IEF, the protein was separated intofive molecular species with pl values between pH 4.5–5.0.The optimum pH for fructosyl transfer activity was between 5.5–7.0.Temperature optimum was in the range of 25-35° C; the Q10value between 25 and 5° C was 1.14. FTT catalysed the self-transferof fructosyl groups with GF₂, GF₃, GF₄ or GF₅ as substrate andacceptor. The rate of elf-transfer with both GF₂ and GF₃ increasedlinearly with substrate concentration up to 100 mol m^–3and was still not saturated at 600 and 300 mol m^–3, respectively.FFT was unable to hydrolyse GF or to catalyse the self-transferwith GF but could mediate the transfer of fructosyl units frominulin on to GF. Key words: Fructan: fructan fructosyl transferase, Helianthus tuberosus, Jerusalem artichoke, purification, kinetics     

Selective grazing by adults and larvae of the zebra mussel (Dreissena polymorpha): application of flow cytometry to natural seston

1. Selective grazing of adults and larvae of the zebra mussel (Dreissena polymorpha) on phytoplankton and detritus from both laboratory cultures and natural seston was quantified using flow cytometry. 2. Mean clearance rate of adult zebra mussels was higher on a mixture of the green alga Scenedesmus and the cyanobacterium Microcystis than when Scenedesmus was offered as single food, suggesting selective feeding by the mussels. 3. Feeding on lake seston both adults and larvae showed a higher clearance rate on phytoplankton than on detritus particles, suggesting that zebra mussels select for phytoplankton. Furthermore, it was noted that adults preferred seston particles in the 0–1 and 30–100 μm size ranges. 4. In our study, zebra mussels did not discriminate against cyanobacteria, and our results indicate that they may even ingest them preferentially.     

Multidrug transporter ABCG2/breast cancer resistance protein secretes riboflavin (vitamin B2) into milk

The multidrug transporter breast cancer resistance protein (BCRP/ABCG2) is strongly induced in the mammary gland during pregnancy and lactation. We here demonstrate that BCRP is responsible for pumping riboflavin (vitamin B(2)) into milk, thus supplying the young with this important nutrient. In Bcrp1(-/-) mice, milk secretion of riboflavin was reduced >60-fold compared to that in wild-type mice. Yet, under laboratory conditions, Bcrp1(-/-) pups showed no riboflavin deficiency due to concomitant milk secretion of its cofactor flavin adenine dinucleotide, which was not affected. Thus, two independent secretion mechanisms supply vitamin B(2) equivalents to milk. BCRP is the first active riboflavin efflux transporter identified in mammals and the first transporter shown to concentrate a vitamin into milk. BCRP activity elsewhere in the body protects against xenotoxins by reducing their absorption and mediating their excretion. Indeed, Bcrp1 activity increased excretion of riboflavin into the intestine and decreased its systemic availability in adult mice. Surprisingly, the paradoxical dual utilization of BCRP as a xenotoxin and a riboflavin pump is evolutionarily conserved among mammals as diverse as mice and humans. This study establishes the principle that an ABC transporter can transport a vitamin into milk and raises the possibility that other vitamins and nutrients are likewise secreted into milk by ABC transporters.     

Nuclear expression of thymidylate synthase in colorectal cancer cell lines and clinical samples.

Thymidylate synthase (TS) [TYMS; OMIM reference number (188,350)] is normally considered to be a cytoplasmic enzyme. However, a few reports have suggested it may also be present in the nucleus. To explore this in more detail, we used a highly specific polyclonal antibody to TS and a combination of techniques, including immunocytochemistry, confocal microscopy, cell fractionation, and Western blotting. We developed cell line HeLa-55, a HeLa derivative that grossly overexpresses TS. Although the vast majority of TS was in the cytoplasm, some TS also was seen in the nucleus. TS in parental HeLa cells and in normal human fibroblasts was seen exclusively in the cytoplasm. HeLa-55 cells exposed to 5-fluorodeoxyuridine were fractionated and examined by Western blotting. Interestingly, both free TS and the ternary complex of TS were seen in the cytoplasmic fraction but only free TS was detected in the nuclear fraction. Amongst different cell lines examined, HCT-15 and normal fibroblasts showed no nuclear TS, HCC-2998 and SW-620 showed a small amount of nuclear TS, and HT-29, RKO, and HCT-116 showed a strong nuclear TS signal. Nuclear staining was clearly evident in some clinical colorectal specimens, both normal and malignant. This staining was definitively shown to be TS by competition with recombinant TS protein. A putative leucine-rich nuclear export sequence was identified but its function could not be confirmed. We conclude that small amounts of TS protein is present in the nucleus of some cell types but further work is needed to determine the significance of this observation.     

Evolutionary relationships among the primate Mhc-DQA1 and DQA2 alleles

The variation of the Mhc-DQA1 and DQA2 loci of ten different primate species (hominoids and Old World monkeys) was studied in order to obtain an insight in the processes that generate polymorphism of major histocompatibility complex (Mhc) class II genes and to establish the evolutionary relationships of their alleles. To that end nucleotide sequences of 36 Mhc class II DQA1 and seven DQA2 second exons were determined and phylogenetic trees that illustrate their evolutionary relationships were constructed. We demonstrate the existence of four primate Mhc-DQA1 allele lineages, two of which probably existed before the separation of the ancestors of the hominoids and Old World monkeys (approximately 22–28 million years ago). Mhc-DQA2 sequences were found only in the hominoid species and showed little diversity. We found no evidence for a major contribution of recombinational events to the generation of allelic diversity of the primate Mhc-DQA1 locus. Instead, our data suggest that the primate Mhc-DQA1 and DQA2 loci are relatively stable entities that mutated primarily as a result of point mutations.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M76186-M76229.     

Basic strategies for valid cytometry using image analysis

The present review provides a starting point for setting up an image analysis system for quantitative densitometry and absorbance or fluorescence measurements in cell preparations, tissue sections or gels. Guidelines for instrumental settings that are essential for the valid application of image analysis in cytophotometry and cytofluorometry are described. The general principles of the working mechanism of CCD cameras in combination with general methods to improve the behaviour of the cameras are presented. Optimization of illumination of microscopical and macroscopical objects receives special attention because of its importance for valid cytometry. Sources of errors in quantitative measurements are listed and step-by-step charts for tuning the CCD camera, frame grabber and illumination for the optimal use of the systems are described. Suggestions are given for improvement of image arithmetics in difficult imaging situations, such as low fluorescence signals and high absorbance signals. This revised version was published online in November 2006 with corrections to the Cover Date.