Employment of 16S rDNA gene sequencing techniques for improved identification of difficult-to-identify bacterial veterinary pathogens

To employ 16S rDNA PCR and automated sequencing techniques to identify a collection of bacterial veterinary pathogens from avian, equine, canine and ovine sources, that have proven difficult to identify, employing conventional cultural techniques. Universal or “broad-range” eubacterial PCR was performed on a collection of 46 difficult-to-identify bacterial isolates originating from clinical veterinary specimens. 16S rDNA PCR was performed using two sets of universal primers to successfully generate a composite amplicon of 1,068 bp, which was sequenced to obtain each isolate’s identity. Sequence analysis was able to identify all isolates examined with relative ease. Where the use of molecular identification methods is justified, such as in outbreak control or bioterrorism in animal health, employment of partial 16S rDNA PCR and sequencing employing universal or “broad-range” 16S rDNA, provides a valuable and reliable method of identification of such pathogens.     

Effect of ultrasound on a bilayer lipid membrane.

The effects of continuous wave ultrasound at a frequency of 1 MHz in the intensity range of 0-1.4 W/cm2 on an oxidized cholesterol bilayer lipid membrane (BLM) were observed. Ultrasound at 1.5 W/cm2 broke the membrane; in the range from 0.5 to 1.4 W/cm2, it accelerated the draining of the bulk lipid solution from the annulus to the Teflon support. At all intensities it has no effect on the conductance, the capacitance, or the dependence of each on the voltage applied across the membrane. Electrical parameters were measured in the presence of aqueous solutions of NaCl, KCl, and distilled water. The motivation and results of this project are explained in relation to an overall objective of determining the specific effects of ultrasound on biological membranes.     

Differences in above-ground resource acquisition and niche overlap between a model invader (Phragmites australis) and resident plant species: measuring the role of fitness and niche differences in the field

Biological Invasions - Identifying the mechanisms that result in a “high impact” invasive species can be difficult. Coexistence theory suggests that detrimental invasive species can be...     

The more food webs change,the more they stay the same

Here, we synthesize a number of recent empirical and theoretical papers to argue that food-web dynamics are characterized by high amounts of spatial and temporal variability and that organisms respond predictably, via behaviour, to these changing conditions. Such behavioural responses on the landscape drive a highly adaptive food-web structure in space and time. Empirical evidence suggests that underlying attributes of food webs are potentially scale-invariant such that food webs are characterized by hump-shaped trophic structures with fast and slow pathways that repeat at different resolutions within the food web. We place these empirical patterns within the context of recent food-web theory to show that adaptable food-web structure confers stability to an assemblage of interacting organisms in a variable world. Finally, we show that recent food-web analyses agree with two of the major predictions of this theory. We argue that the next major frontier in food-web theory and applied food-web ecology must consider the influence of variability on food-web structure.     

In Vitro and Ex Vivo Testing of Tenofovir Shows It Is Effective As an HIV-1 Microbicide

Background

Tenofovir gel has entered into clinical trials for use as a topical microbicide to prevent HIV-1 infection but has no published data regarding pre-clinical testing using in vitro and ex vivo models. To validate our findings with on-going clinical trial results, we evaluated topical tenofovir gel for safety and efficacy. We also modeled systemic application of tenofovir for efficacy.

Methods and Findings

Formulation assessment of tenofovir gel included osmolality, viscosity, in vitro release, and permeability testing. Safety was evaluated by measuring the effect on the viability of vaginal flora, PBMCs, epithelial cells, and ectocervical and colorectal explant tissues. For efficacy testing, PBMCs were cultured with tenofovir or vehicle control gels and HIV-1 representing subtypes A, B, and C. Additionally, polarized ectocervical and colorectal explant cultures were treated apically with either gel. Tenofovir was added basolaterally to simulate systemic application. All tissues were challenged with HIV-1 applied apically. Infection was assessed by measuring p24 by ELISA on collected supernatants and immunohistochemistry for ectocervical explants. Formulation testing showed the tenofovir and vehicle control gels were >10 times isosmolar. Permeability through ectocervical tissue was variable but in all cases the receptor compartment drug concentration reached levels that inhibit HIV-1 infection in vitro. The gels were non-toxic toward vaginal flora, PBMCs, or epithelial cells. A transient reduction in epithelial monolayer integrity and epithelial fracture for ectocervical and colorectal explants was noted and likely due to the hyperosmolar nature of the formulation. Tenofovir gel prevented HIV-1 infection of PBMCs regardless of HIV-1 subtype. Topical and systemic tenofovir were effective at preventing HIV-1 infection of explant cultures.

Conclusions

These studies provide a mechanism for pre-clinical prediction of safety and efficacy of formulated microbicides. Tenofovir was effective against HIV-1 infection in our algorithm. These data support the use of tenofovir for pre-exposure prophylaxis.     

Identification of genomic regions that affect grain-mould incidence and other traits of agronomic importance in sorghum

Grain-mould is a major problem in grain sorghum utilization as mouldy grain has a reduced quality due to the deterioration of the endosperm and reduced embryo viability. Here, our objective was to use genome mapping to improve knowledge of genetic variation and co-variation for grain-mould incidence and other inter-related agronomic traits. Grain-mould incidence, kernel-milling hardness, grain density, plant height, panicle peduncle length, foliar-disease incidence, and plant color were measured on 125 F₅ genotypes derived from a cross of Sureño and RTx430. Quantitative trait loci were detected by means of 130 mapped markers (44 microsatellites, 85 AFLPs, one morphological-trait locus) distributed among ten linkage groups covering 970 cM. One to five QTLs affected each trait, with the exception of grain density for which no QTLs were detected. Grain-mould incidence was affected by five QTLs each accounting for between 10 and 23% of the phenotypic variance. The effects and relative positions of QTLs for grain-mould incidence were in accordance with the QTL distribution of several inter-related agronomic traits (e.g., plant height, peduncle length) and with the correlation between these phenotypic traits and grain-mould incidence. The detection of QTLs for grain-mould incidence was dependent on the environment, which is consistent with heritibility estimates that show strong environmental and genotype × environment effects. Several genomic regions affected multiple traits including one region that affected grain-mould incidence, plant height, panicle peduncle length, and grain-milling hardness, and a second region that influenced grain-mould (in four environments) and plant height. One genomic region, which harbors loci for plant color, influenced the severity of foliar disease symptoms and the incidence of grain-mould in one environment. Collectively QTLs detected in the present population explained between 10% and 55% of the phenotypic variance observed for a given trait.     

A molecular cytogenetic map of sorghum chromosome 1. Fluorescence in situ hybridization analysis with mapped bacterial artificial chromosomes

We used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum. Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH). Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR). The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map. In addition, the order of several tightly linked molecular markers was clarified by FISH analysis. The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1. The centromere and NOR were located in a large heterochromatic region that spans approximately 60% of chromosome 1. In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome. Variation in recombination frequency among euchromatic chromosomal regions also was apparent. The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions. The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific "paints" from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping. Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application of genomic resources, cloning, transgene localization, development of plant "chromonomics," germplasm introgression, and marker-assisted breeding. In combination with previously reported work, the results indicate that a sorghum cytogenomics system would be partially applicable to other gramineous genera.     

Purinoceptor agonists stimulate phosphatidylcholine secretion in primary cultures of adult rat type II pneumocytes

We examined the effect of purinoceptor agonists on phosphatidylcholine secretion in primary cultures of type II pneumocytes from adult rats. Surfactant is a major product of the type II cell and phosphatidylcholine is its principal component. Adenosine, AMP, ADP and ATP stimulated phosphatidylcholine secretion in a concentration-dependent manner. At the optimum concentration (1 mM), adenosine and AMP stimulated phosphatidylcholine secretion more than 2-fold, while ATP stimulated 5-fold and ADP almost 7-fold. Because of the magnitude of the response it is tempting to speculate that secretion of surfactant may be under purinoceptor regulation. None of these agents influenced cellular phosphatidylcholine synthesis or lactate dehydrogenase release into the medium, so the effects were primarily on secretion and were not secondary to effects on synthesis or cell damage. Non-metabolizable analogs of adenosine, 5'-N-ethyl-carboxyamidoadensoine (NECA) and L-N6-phenylisopropyladenosine (L-PIA), stimulated secretion to the same extent as adenosine and the effect of NECA was antagonized by 8-phenyltheophylline, suggesting a P1 purinoceptor-mediated mechanism. The stimulatory effect of ATP was diminished by alpha, beta-methylene ATP but only slightly by 8-phenyltheophylline, suggesting that, although part of the ATP effect could be explained by catabolism to adenosine, the P2 purinoceptor may also be involved in regulation of surfactant secretion.     

Surfactant secretion in a newborn rabbit lung slice model

We describe a slice model for the study of pulmonary surfactant secretion in newborn rabbits. Full term rabbits were delivered by cesarean section and injected intraperitoneally with [Me-3H]choline. Four hours later they were killed, the lungs were perfused to remove blood, slices (0.5 mm thick) were prepared and incubated in buffer at 37 degrees C. The composition of the lipids initially released into the medium resembled those of lung tissue rather than surfactant. Following 3 changes of medium, however, the composition of the lipids released was very similar to that of lung lavage. Phosphatidylcholine accounted for over 70% of the total while phosphatidylethanolamine and sphingomyelin accounted for only 7% and 4%, respectively. 52% of the phosphatidylcholine was disaturated. Less than 5% of the tissue lactate dehydrogenase was released into the medium. The rate of phosphatidyl[Me-3H]choline release during this period was, therefore, measured. Release of phosphatidyl[Me-3H]choline was linear with time and was temperature-dependent. Prostaglandin E2 stimulated its rate of release by 20% while indomethacin and flufenamic acid, inhibitors of prostaglandin synthesis, inhibited it by 52% and 37%, respectively. The calcium ionophore A23187 in the presence of Ca2+ stimulated release by 40% while colchicine an cytochalasin B inhibited it by 36% and 32%, respectively. These data suggest that both prostaglandins and Ca2+ are involved in surfactant release and that intact microtubular and microfilament systems may also be necessary.     

Oxygenated cholesterols synergistically immobilize acyl chains and enhance protein helical structure in human erythrocyte membranes

Fourier transform infrared spectroscopy revealed that insertion of 20 alpha-hydroxycholesterol into human erythrocyte membranes (10% of total membrane sterol) immobilized the lipid acyl chains to a degree equivalent to enriching total membrane cholesterol by 50% (Rooney, M.W., Lange, Y. and Kauffman, J.W. (1984) J. Biol. Chem. 259, 8281-8285). Raman spectroscopy showed that the amount of acyl chain rotamers was not significantly altered by the presence of 20 alpha-hydroxycholesterol, indicating that acyl chain immobilization was limited to an inhibition of lateral motion. The presence of 20 alpha-hydroxycholesterol may synergistically enhance the acyl-chain-immobilizing behavior of membrane cholesterol. In addition, protein helical structure was not altered by 20 alpha-hydroxycholesterol. The insertion of 7 alpha-hydroxycholesterol into erythrocyte membranes resulted in an increase in protein helical structure which was comparable to that observed for erythrocyte membranes enriched with pure cholesterol by 50%. However, both acyl chain mobility and conformation were unchanged. These results suggest a synergistic behavior between oxysterols and cholesterol in modifying erythrocyte membrane packing.