Chip calorimetry and biomagnetic separation: Fast detection of bacterial contamination at low cell titers

We present a new chip calorimeter for fast and quantitative measurement of metabolic heat rates of microorganisms attached to magnetic beads. In biomagnetic separation (BMS) experiments, Escherichia coli K12 immobilized on nonspecifically functionalized beads has a specific heat rate of around 1 pW per cell at 37°C. Therefore, at least 2 × 10⁴ bacteria are required to exceed the calorimetric signal resolution of 20 nW. If the samples to be analyzed have the original volume of 4 mL, bacteria at less than 10⁴ cells mL^?1 should be detectable. In practice, we achieved the detection of approximately 2 × 10⁴ cells mL^?1. The method presented here might also find some applications in the investigation of biofilms and study of biomolecular interactions.     

Host behaviour drives parasite genetics at multiple geographic scales: population genetics of the chewing louse,Thomomydoecus minor

Pocket gophers and their symbiotic chewing lice form a host–parasite assemblage known for a high degree of cophylogeny, thought to be driven by life history parameters of both host and parasite that make host switching difficult. However, little work to date has focused on determining whether these life histories actually impact louse populations at the very fine scale of louse infrapopulations (individuals on a single host) at the same or at nearby host localities. We used microsatellite and mtDNA sequence data to make comparisons of chewing‐louse (Thomomydoecus minor) population subdivision over time and over geographic space where there are different potential amounts of host interaction surrounding a zone of contact between two hybridizing pocket‐gopher subspecies. We found that chewing lice had high levels of population isolation consistent with a paucity of horizontal transmission even at the very fine geographic scale of a single alfalfa field. We also found marked genetic discontinuity in louse populations corresponding with host subspecies and little, if any, admixture in the louse genetic groups even though the lice are closely related. The correlation of louse infrapopulation differentiation with host interaction at multiple scales, including across a discontinuity in pocket‐gopher habitat, suggests that host behaviour is the primary driver of parasite genetics. This observation makes sense in light of the life histories of both chewing lice and pocket gophers and provides a powerful explanation for the well‐documented pattern of parallel cladogenesis in pocket gophers and chewing lice.     

High-affinity AKAP7delta-protein kinase A interaction yields novel protein kinase A-anchoring disruptor peptides

PKA (protein kinase A) is tethered to subcellular compartments by direct interaction of its regulatory subunits (RI or RII) with AKAPs (A kinase-anchoring proteins). AKAPs preferentially bind RII subunits via their RII-binding domains. RII-binding domains form structurally conserved amphipathic helices with unrelated sequences. Their binding affinities for RII subunits differ greatly within the AKAP family. Amongst the AKAPs that bind RIIalpha subunits with high affinity is AKAP7delta [AKAP18delta; K(d) (equilibrium dissociation constant) value of 31 nM]. An N-terminally truncated AKAP7delta mutant binds RIIalpha subunits with higher affinity than the full-length protein presumably due to loss of an inhibitory region [Henn, Edemir, Stefan, Wiesner, Lorenz, Theilig, Schmidtt, Vossebein, Tamma, Beyermann et al. (2004) J. Biol. Chem. 279, 26654-26665]. In the present study, we demonstrate that peptides (25 amino acid residues) derived from the RII-binding domain of AKAP7delta bind RIIalpha subunits with higher affinity (K(d)=0.4+/-0.3 nM) than either full-length or N-terminally truncated AKAP7delta, or peptides derived from other RII binding domains. The AKAP7delta-derived peptides and stearate-coupled membrane-permeable mutants effectively disrupt AKAP-RII subunit interactions in vitro and in cell-based assays. Thus they are valuable novel tools for studying anchored PKA signalling. Molecular modelling indicated that the high affinity binding of the amphipathic helix, which forms the RII-binding domain of AKAP7delta, with RII subunits involves both the hydrophobic and the hydrophilic faces of the helix. Alanine scanning (25 amino acid peptides, SPOT technology, combined with RII overlay assays) of the RII binding domain revealed that hydrophobic amino acid residues form the backbone of the interaction and that hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction.     

Energy metabolism and evaporative water loss in the European free-tailed bat and Hemprich's long-eared bat (Microchiroptera): species sympatric in the Negev Desert

We compared the thermoregulatory abilities of two insectivorous bat species, Tadarida teniotis (mean body mass 32 g) and Otonycteris hemprichii (mean body mass 25 g), that are of different phylogenetic origins and zoogeographic distributions but are sympatric in the Negev Desert. At night, both were normothermic. By day, both were torpid when exposed to ambient temperatures (T(a)) below 25 degrees Celsius, with concomitant adjustments in metabolic rate (MR). Otonycteris hemprichii entered torpor at higher T(a) than T. teniotis, and, when torpid, their body temperatures (T(b)) were 1 degrees -2 degrees Celsius and 5 degrees -8 degrees Celsius above T(a), respectively; MR was correspondingly reduced. At night, the lower critical temperature of T. teniotis was 31.5 degrees Celsius, and that of O. hemprichii was 33 degrees Celsius. Mean nocturnal thermoneutral MR of T. teniotis was 37% greater than that of O. hemprichii. At high T(a), evaporative water loss (EWL) increased markedly in both species, but it was significantly higher in T. teniotis above 38 degrees Celsius. In both species, the dry heat transfer coefficient (thermal conductance) followed the expected pattern for small mammals, by day and by night. Total EWL was notably low in normothermic and torpid animals of both species, much lower than values reported for other bats, indicating efficient water conservation mechanisms in the study species. Comparing thermoregulatory abilities suggests that O. hemprichii is better adapted to hot, arid environments than T. teniotis, which may explain its wider desert distribution. By both standard and phylogenetically informed ANCOVA, we found no differences in basal metabolic rate (BMR) between desert and nondesert species of insectivorous bats, substantiating previous studies suggesting that low BMR is a characteristic common to insectivorous bats in general.     

A high-throughput Arabidopsis reverse genetics system

A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymmetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from approximately 100000 transformed lines. A total of 85108 TAIL-PCR products from 52964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org.     

Thermodynamic and electrostatic properties of ternary Oxytricha nova TEBP-DNA complex

Telomeres constitute the nucleoprotein ends of eukaryotic chromosomes which are essential for their proper function. Telomere end binding protein (TEBP) from Oxytricha nova was among the first telomeric proteins, which were well characterized biologically. TEBP consists of two protein subunits (alpha, beta) and forms a ternary complex with single stranded telomeric DNA containing tandem repeats TTTTGGGG. This work presents the characterization of the thermodynamic and electrostatic properties of this complex by computational chemistry methods (continuum Poisson-Boltzmann and solvent accessible surface calculations). Our calculations give a new insight into molecular properties of studied system. Based on the thermodynamic analysis we provide a rationale for the experimental observation that alpha and ssDNA forms a binary complex and the beta subunit joins alpha:ssDNA complex only after the latter is formed. Calculations of distribution of the molecular electrostatic potential for protein subunits alone and for all possible binary complexes revealed the important role of the "guiding funnel" potential generated by alpha:ssDNA complex. This potential may help the beta subunit to dock to the already formed alpha:DNA intermediate in highly steric and electrostatic favorable manner. Our pK(a) calculations of TEBP are able to explain the experimental mobility shifts of the complex in electrophoretic non-denaturating gels.     

Cephalopod remains from stomachs of sperm whales (Physeter macrocephalus) that mass‐stranded along the Oregon coast

On 16 June 1979, a herd of 41 sperm whales stranded near the mouth of the Siuslaw River in Florence, Oregon. The stomach contents from 32 whales were collected, identified to the lowest taxonomic level possible, enumerated, and measured. A total of 20,247 cephalopod lower beaks that represented 24 species from 14 different families were recovered. The most numerous species were Histioteuthis hoylei (25.9%), Taonius borealis (12.9%), Galiteuthis phyllura (11.2%), Gonatopsis/Berryteuthis type (10.9%), and Moroteuthis robusta (10.7%). Reconstructed estimates of mass indicated that M. robusta contributed almost 50% of the total mass of cephalopods consumed, followed by H. hoylei (19.3%), and T. borealis (7.0%). The most important species in the diet of stranded whales were M. robusta, H. hoylei, T. borealis, G. phyllura, Octopoteuthis deletron, and Gonatopsis/Berryteuthis type. There were significant differences in the diet of males and females, but no differences between sperm whales of different age groups. Overall, sperm whales primarily consumed small cephalopods that were likely eaten south of 45ºN in or near the California Current System. This study provides new estimates of the food habits of sperm whales in the northeast Pacific from one of the largest strandings of this species.     

Investigating the activity of quinine analogues versus chloroquine resistant Plasmodium falciparum

Plasmodium falciparum, the deadliest malarial parasite species, has developed resistance against nearly all man-made antimalarial drugs within the past century. However, quinine (QN), the first antimalarial drug, remains efficacious worldwide. Some chloroquine resistant (CQR) P. falciparum strains or isolates show mild cross resistance to QN, but many do not. Further optimization of QN may provide a well-tolerated therapy with improved activity versus CQR malaria. Thus, using the Heck reaction, we have pursued a structure-activity relationship study, including vinyl group modifications of QN. Certain derivatives show good antiplasmodial activity in QN-resistant and QN-sensitive strains, with lower IC(50) values relative to QN.     

Extrachromosomal Recombinant Adeno-Associated Virus Vector Genomes Are Primarily Responsible for Stable Liver Transduction In Vivo

Recombinant adeno-associated virus (rAAV) vectors stably transduce hepatocytes in experimental animals. Although the vector genomes are found both as extrachromosomes and as chromosomally integrated forms in hepatocytes, the relative proportion of each has not yet been clearly established. Using an in vivo assay based on the induction of hepatocellular regeneration via a surgical two-thirds partial hepatectomy, we have determined the proportion of integrated and extrachromosomal rAAV genomes in mouse livers and their relative contribution to stable gene expression in vivo. Plasma human coagulation factor IX (hF.IX) levels in mice originating from a chromosomally integrated hF.IX-expressing transposon vector remained unchanged with hepatectomy. This was in sharp contrast to what was observed when a surgical partial hepatectomy was performed in mice 6 weeks to 12 months after portal vein injection of a series of hF.IX-expressing rAAV vectors. At doses of 2.4 x 10(11) to 3.0 x 10(11) vector genomes per mouse (n = 12), hF.IX levels and the average number of stably transduced vector genomes per cell decreased by 92 and 86%, respectively, after hepatectomy. In a separate study, one of three mice injected with a higher dose of rAAV had a higher proportion (67%) of integrated genomes, the significance of which is not known. Nevertheless, in general, these results indicate that, in most cases, no more than approximately 10% of stably transduced genomes integrated into host chromosomes in vivo. Additionally, the results demonstrate that extrachromosomal, not integrated, genomes are the major form of rAAV in the liver and are the primary source of rAAV-mediated gene expression. This small fraction of integrated genomes greatly decreases the potential risk of vector-related insertional mutagenesis associated with all integrating vectors but also raises uncertainties as to whether rAAV-mediated hepatic gene expression can persist lifelong after a single vector administration.