Spatio-temporal distribution patterns of three stream-dwelling freshwater mussel species: towards a strategy for representative surveys

Conservation efforts for freshwater mussels (Unionoida) require a priori assessments of their populations’ status quo. Unfortunately, collection of representative census and other data for most European species is currently hampered by an insufficient understanding of inter- and intra-specific variation in distribution patterns. We assessed distribution and movement in three Unio crassus populations and one sympatric population of Anodonta anatina and Unio pictorum, respectively. We surveyed vertical movement across four sediment depths, and horizontal movement by mark-recapture technique in 3-month intervals. For all the populations, movement and the proportion inhabiting surface layers increased considerably from winter to spring/summer. Spatial aggregation levels remained stable for some populations, while others became increasingly randomly distributed during the study. One U. crassus population exhibited elevated mortality and displayed movement rates exceeding twice those of conspecific populations. The visible proportion of U. crassus populations differed by up to 69% between sites. Current monitoring guidelines in Europe often insufficiently account for the extensive inter- and intra-specific differences in spatio-temporal distribution patterns observed. We suggest developing internationally standardised protocols that specify sampling season and methodology. In particular, U. crassus surveys should be restricted to summer months, and hand-sampling is crucial for some populations.     

Single-step Strep-tag purification for the isolation and identification of protein complexes from mammalian cells

Identification of protein complexes is the key to understanding cellular functions. In this study, we present a novel method for the identification of multiprotein complexes from mammalian cells. By using the Strep-tag affinity chromatography method, enabling fast and simple one-step purification, coupled with competitive elution under physiological conditions, we successfully purified a PP2A holoenzyme protein complex from a cultured mammalian cancer cell line. We identified, by mass spectrometry, both known and novel interacting proteins for PP2A, and demonstrate that the purified PP2A complex is functional. The benefits and potential applications of the Strep-tag method for protein complex purification are discussed.     

Expression, purification, crystallization and preliminary X-ray analysis of strictosidine glucosidase, an enzyme initiating biosynthetic pathways to a unique diversity of indole alkaloid skeletons

Strictosidine beta-D-glucosidase, a plant enzyme initiating biosynthetic pathways to about 2000 monoterpenoid indole alkaloids with an extremely large number of various carbon skeletons, has been functionally expressed in Escherichia coli and purified to homogeneity in mg scale. Crystals suitable for X-ray analysis were found by robot-mediated screening. Using the hanging-drop technique, optimum conditions were 0.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6 and PEG 4000 (10%) as precipitant buffer. The crystals of strictosidine glucosidase belong to the space group P42(1)2 with unit cell dimensions of a=157.63, c=103.59 A and diffract X-rays to 2.48-A resolution.     

Determination and evaluation of an optimal dosage of carfentanil and xylazine for the immobilization of white-tailed deer (Odocoileus virginianus)

Using an iteration method, optimal hand-injected immobilization dosages of carfentanil/xylazine (CAR/XYL) were determined for 13 adult white-tailed deer (Odocoileus virginianus). Deer were temporarily restrained in a squeeze chute and were repeatedly immobilized one to four times at 2-5-wk intervals from December 2002 to March 2003. A fixed ratio of 1 mg CAR:10 mg XYL intramuscularly was used, increasing or decreasing the dosage until the optimal dosage (defined by an induction time < 3 min and PaCO(2)< 60 mmHg) was reached for each animal. Inductions were video-recorded and reviewed by observers blinded to drugs and dosages, who rated qualitative aspects of each induction. There were significant (P < 0.05) dosage-dependent decreases in induction time, time to first effect, PaO(2), SaO(2), and arterial pH, and significant dosage-dependent increases in PaCO(2) and quality ratings. The median optimal dosage (mOD) was 0.03 (range, 0.015-0.06) mg/kg CAR+0.3 (range, 0.15-0.6) mg/kg XYL. Induction times using the mOD were rapid (median 3.0 min [range, 1.8-10.0]), but quality ratings were considered undesirable for nine of 13 deer. Increased rectal body temperatures of 40.6+/-0.5 C (mean +/- SD) were noted in all deer and hyperthermia (T > 41 C) was noted in three. There was a positive correlation between body temperature and induction time (r=0.44). Heart rates significantly decreased from 5 to 15 min postinduction and remained decreased at the 20-min reading; there was occasional bradycardia. There was a significant increase in pH from 10 to 20 min postinduction, but metabolic acidemia (pH<7.3) persisted throughout the immobilization periods for all deer. Possible hypoxemia (SaO(2) and SpO(2)<90 mmHg but PaO(2)>60 mmHg) was present after induction, while hypercapnea (PaCO(2) > 60 mmHg) did not occur. Reversal times with naltrexone and yohimbine were rapid (mean 3.7+/-1.5 min) and uneventful, with no evidence of renarcotization. Although the median optimal dosage produced rapid inductions, no respiratory depression, complete reversal after antagonist administration, and no renarcotization, negative attributes included elevated body temperatures, acidemia, and undesirable induction qualities.     

Hypochlorite-oxidized low-density lipoprotein upregulates CD36 and PPARγ mRNA expression and modulates SR-BI gene expression in murine macrophages

Huntington's disease (HD) is associated with expansion of polyglutamine tract in a protein named huntingtin (htt) that is expressed in virtually all body tissues. Thus mutated htt (HD-htt) might affect all organs, although clinical manifestations of HD are associated with selective loss of corticostriatal neurons of the brain. In this work we studied how HD-htt affects mitochondria in human peripheral blood cells. We compared various functions of mitochondria isolated from cultured lymphoblastoid cells derived from three HD patients with juvenile onset of the disease (HD-LBM) and three age-matched control (C-LBM) individuals. Respiratory parameters in different metabolic states, with succinate and glutamate plus malate were the same for all control and HD cell lines. State 4 membrane potential in HD-LBM was slightly lower than in C-LBM. The calcium retention capacity (CRC) of mitochondria was estimated using simultaneously several methods to register permeability transition (PT). We found that LBM do not undergo swelling upon Ca2+-induced PT, and do not increase CRC in the presence of ADP + oligomycin. Although each cell line had different CRC values, qualitatively PT was different in C-LBM and HD-LBM. With C-LBM cyclosporin A (CsA) increased CRC significantly, while with HD-LBM CsA was ineffective. In C-LBM depolarization of mitochondria and a large pore opening (PT) always occurred simultaneously. In HD-LBM depolarization occurred at 20-50% lower Ca2+ loads than PT. We suggest that HD-htt promotes low H+ conductance of the mitochondria by interacting with proteins at the contacts sites without directly promoting PT or hampering mitochondrial oxidative phosphorylation.     

Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6 A resolution

Sanglifehrin A (SFA) is a novel immunosuppressant isolated from Streptomyces sp. that binds strongly to the human immunophilin cyclophilin A (CypA). SFA exerts its immunosuppressive activity through a mode of action different from that of all other known immunophilin-binding substances, namely cyclosporine A (CsA), FK506, and rapamycin. We have determined the crystal structure of human CypA in complex with SFA at 1.6 A resolution. The high resolution of the structure revealed the absolute configuration at all 17 chiral centers of SFA as well as the details of the CypA/SFA interactions. In particular, it was shown that the 22-membered macrocycle of SFA is deeply embedded in the same binding site as CsA and forms six direct hydrogen bonds with CypA. The effector domain of SFA, on the other hand, has a chemical and three-dimensional structure very different from CsA, already strongly suggesting different immunosuppressive mechanisms. Furthermore, two CypA.SFA complexes form a dimer in the crystal as well as in solution as shown by light scattering and size exclusion chromatography experiments. This observation raises the possibility that the dimer of CypA.SFA complexes is the molecular species mediating the immunosuppressive effect.     

Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin

A new group of anaerobic thermophilic bacteria was isolated from enrichment cultures obtained from deep sea sediments of Peru Margin collected during Leg 201 of the Ocean Drilling Program. A total of ten isolates were obtained from cores of 1–2 m below seafloor (mbsf) incubated at 60°C: three isolates came from the sediment 426 m below sea level with a surface temperature of 9°C (Site 1227), one from 252 m below sea level with a temperature of 12°C (Site 1228), and six isolates under sulfate-reducing condition from the lower slope of the Peru Trench (Site 1230). Strain JW/IW-1228P from the Site 1228 and strain JW/YJL-1230-7/2 from the Site 1230 were chosen as representatives of the two identified clades. Based on the 16S rDNA sequence analysis, these isolates represent a novel group with Thermovenabulum and Caldanaerobacter as their closest relatives. The temperature range for growth was 52–76°C with an optimum at around 68°C for JW/IW-1228P and 43–76°C with an optimum at around 64°C for JW/YJL-1230-7/2. The pH^25C range for growth was from 6.3 to 9.3 with an optimum at 7.5 for JW/IW-1228P and from 5 to 9.5 with an optimum at 7.9–8.4 for JW/YJL-1230-7/2. The salinity range for growth was from 0% to 6% (w/v) for JW/IW-1228P and from 0% to 4.5% (w/v) for JW/YJL-1230-7/2. The G+C content of the DNA was 50 mol% for both JW/IW-1228P and JW/YJL-1230-7/2. DNA–DNA hybridization yielded 52% similarity between the two strains. According to 16S rRNA gene sequence analysis, the isolates are located within the family, Thermoanaerobacteriaceae. Based on their morphological and physiological properties and phylogenetic analysis, it is proposed that strain JW/IW-1228P^T is placed into a novel taxa, Thermosediminibacter oceani, gen. nov., sp. nov. (DSM 16646^T=ATCC BAA-1034^T), and JW/YJL-1230-7/2^T into Thermosediminibacter litoriperuensis sp. nov. (DSM 16647^T =ATCC BAA-1035^T).An erratum to this article can be found at     

Distribution of genes encoding the microbial non-oxidative reversible hydroxyarylic acid decarboxylases/phenol carboxylases

Bacterial non-oxidative, reversible multi subunit hydroxyarylic acid decarboxylases/phenol carboxylases are encoded by the three clustered genes, B, C, and D, of approximately 0.6, 1.4, and 0.2 kb, respectively. There are more than 160 homologues in the database with significant similarity to gene B (homology to ubiX) and C (ubiD) distributed in all three microbial domains, however, homologues to gene D, are not numerous ( approximately 15). The occurrence of the entire BCD gene cluster encoding for either identified or presumptive hydroxyarylic acid decarboxylase to date has been revealed in Sedimentibacter hydroxybenzoicus (unique genes arrangement CDB), Streptomyces sp. D7, Bacillus subtilis, B. licheniformis, E. coli O157:H7, Klebsiella pneumoniae, Enterobacter cloacae, Shigella dysenteriae, Salmonella enterica, S. paratyphi, S. typhimurium, S. bongori, and S. diarizonae. The corresponding genes from S. hydroxybenzoicus, B. subtilis, Streptomyces sp. D7, E. coli O157:H7, K. pneumoniae, and S. typhimurium were cloned and expressed in E. coli DH5alpha (void of analogous genes), and shown to code for proteins exhibiting non-oxidative hydroxyarylic acid decarboxylase activity.     

Impact of remote mutations on metallo-beta-lactamase substrate specificity: implications for the evolution of antibiotic resistance

Metallo-beta-lactamases have raised concerns due to their ability to hydrolyze a broad spectrum of beta-lactam antibiotics. The G262S point mutation distinguishing the metallo-beta-lactamase IMP-1 from IMP-6 has no effect on the hydrolysis of the drugs cephalothin and cefotaxime, but significantly improves catalytic efficiency toward cephaloridine, ceftazidime, benzylpenicillin, ampicillin, and imipenem. This change in specificity occurs even though residue 262 is remote from the active site. We investigated the substrate specificities of five other point mutants resulting from single-nucleotide substitutions at positions near residue 262: G262A, G262V, S121G, F218Y, and F218I. The results suggest two types of substrates: type I (nitrocefin, cephalothin, and cefotaxime), which are converted equally well by IMP-6, IMP-1, and G262A, but even more efficiently by the other mutants, and type II (ceftazidime, benzylpenicillin, ampicillin, and imipenem), which are hydrolyzed much less efficiently by all the mutants. G262V, S121G, F218Y, and F218I improve conversion of type I substrates, whereas G262A and IMP-1 improve conversion of type II substrates, indicating two distinct evolutionary adaptations from IMP-6. Substrate structure may explain the catalytic efficiencies observed. Type I substrates have R2 electron donors, which may stabilize the substrate intermediate in the binding pocket. In contrast, the absence of these stabilizing interactions with type II substrates may result in poor conversion. This observation may assist future drug design. As the G262A and F218Y mutants confer effective resistance to Escherichia coli BL21(DE3) cells (high minimal inhibitory concentrations), they are likely to evolve naturally.