Development of a multiplex PCR for identification of vineyard mealybugs

A simple molecular tool was developed and tested to identify seven mealybug species found in North American vineyards: Pseudococcus maritimus Ehrhorn, Pseudococcus viburni (Signoret), Pseudococcus longispinus (Targioni-Tozzeti), Pseudococcus calceolariae (Maskell), Planococcus ficus (Signoret), Planococcus citri (Risso), and Ferrisia gilli Gullan. The developed multiplex PCR is based on the mitochondrial cytochrome c oxidase subunit one gene. In tests, this single-step multiplex PCR correctly identified 95 of 95 mealybug samples, representing all seven species and collected from diverse geographic regions. To test the sensitivity, single specimen samples with different Pl. ficus developmental stages (egg to adult female and adult male) were processed PCR and the resulting output provided consistent positive identification. To test the utility of this protocol for adult males caught in sex baited pheromone traps, Pl. ficus adult males were placed in pheromone traps, aged at a constant temperature of 26±2°C, and processed with the multiplex each day thereafter for 8 d. Results showed consistent positive identification for up to 6 d (range, 6-8 d). Results are discussed with respect to the usefulness of this molecular tool for the identification of mealybugs in pest management programs and biosecurity of invasive mealybugs.     

Elevated levels of fibrinogen-derived endogenous citrullinated peptides in synovial fluid of rheumatoid arthritis patients

Introduction

Rheumatoid arthritis (RA) is an autoimmune disease characterized by inflammation of the joints and the presence of autoantibodies directed against proteins containing the non-standard arginine-derived amino acid citrulline. The protein fibrinogen, which has an essential role in blood clotting, is one of the most prominent citrullinated autoantigens in RA, particularly because it can be found in the inflamed tissue of affected joints. Here, we set out to analyze the presence of citrullinated endogenous peptides in the synovial fluid of RA and arthritic control patients.

Methods

Endogenous peptides were isolated from the synovial fluid of RA patients and controls by filtration and solid phase extraction. The peptides were identified and quantified using high-resolution liquid chromatography-mass spectrometry.

Results

Our data reveal that the synovial fluid of RA patients contains soluble endogenous peptides, derived from fibrinogen, containing significant amounts of citrulline residues and, in some cases, also phosphorylated serine. Several citrullinated peptides are found to be more abundantly present in the synovial fluid of RA patients compared to patients suffering from other inflammatory diseases affecting the joints.

Conclusions

The increased presence of citrullinated peptides in RA patients points toward a possible specific role of these peptides in the immune response at the basis of the recognition of citrullinated peptides and proteins by RA patient autoantibodies.     

A METHOD FOR ISOLATION OF CAMPYLOBACTER SPP. (JEJUNI, COLI AND LARI) FROM SHELLFISH AND THE MARINE ENVIRONMENT

A method has been developed to detect thermophilic species of Campylobacter in shellfish, marine and tributary waters, sediment and farm runoff by-products such as manure and silage. The method consists of a 48 h enrichment incubation and subcultured to selective agars. Presumptive colonies confirmed with a latex agglutination (antibodies) to common flagellar antigens of C. jejuni, C. coli and C. lardi. Over an 8 year period, West Coast estuaries (Washington, Oregon, and California) were sampled, resulting in analysis of a total of 512 samples. Results suggest that Campylobacter spp. are well distributed in the marine environment. Two enrichment broths were compared for the recovery of campylobacters from environmental samples. The method described in the Food and Drug Administration Bacteriological Analytical Manual (FDA/BAM) (1984), was compared to a modified method. Use of the modified method described here resulted in higher recovery rates of Campylobacter spp. Recoveries of campylobacters from sediment, shellfish, and water were 10,13, and 28% higher for the modified method, respectively.     

A theoretical entropy score as a single value to express inhibitor selectivity

Background  

Designing maximally selective ligands that act on individual targets is the dominant paradigm in drug discovery. Poor selectivity can underlie toxicity and side effects in the clinic, and for this reason compound selectivity is increasingly monitored from very early on in the drug discovery process. To make sense of large amounts of profiling data, and to determine when a compound is sufficiently selective, there is a need for a proper quantitative measure of selectivity.     

Artifactual phosphate binding due to impurities in [32P]orthophosphate

Many commercial preparations of [32P]orthophosphate contain radioactive impurities that interfere with binding and transport studies in biological systems. One type of impurity is micro-particulate whereas another may be pyrophosphate. Methods of removing these impurities from radiolabeled orthophosphate solutions are described.     

Restriction endonuclease mapping of ribosomal RNA genes: Sequence divergence and the origin of the tetraploid treefrog Hyla versicolor

Hyla chrysoscelis (2n=24) and H. versicolor (2n=48) are a diploid-tetraploid species pair of treefrogs. Restriction endonuclease mapping of ribosomal RNA (rRNA) gene repeat units of diploids collected from eastern and western populations reveals no differences within rRNA gene coding regions but distinctive differences within the nontranscribed spacers. A minimum of two physical maps is required to construct an rRNA gene map for the tetraploid, whose repeat units appear to be a composite, with about 50% of the elements resembling the western diploid population and about 50% resembling the eastern population. These results imply that this population of the tetraploid species may have arisen from a genetically hybrid diploid. Alternatively, the dual level of sequence heterogeneity in H. versicolor may reflect some type of gene flow between the two species. The coding region of the rRNA genes in the tetraploid differs from that in either diploid in about 20% of all repeat units, as exemplified by a BamHI site located near the 5 terminus of the 28 S rRNA gene. If the 20% variant class of 28 S rRNA gene coding sequences is expressed, then there must be two structural classes of ribosomes; if only the 80% sequence class is expressed, then a genetic control mechanism must be capable of distinguishing between the two different sequence variants. It is postulated that the 20% variant sequence class may be correlated with a partial functional diploidization of rRNA genes in the tetraploid species.This research was supported, in part, by NSF Grants CDP-8002341 and PRM-8106947 and by faculty research grants from Miami University to J.C.V.     

Inter‐regional comparison of land‐use effects on stream metabolism

1. Rates of whole‐system metabolism (production and respiration) are fundamental indicators of ecosystem structure and function. Although first‐order, proximal controls are well understood, assessments of the interactions between proximal controls and distal controls, such as land use and geographic region, are lacking. Thus, the influence of land use on stream metabolism across geographic regions is unknown. Further, there is limited understanding of how land use may alter variability in ecosystem metabolism across regions. 2. Stream metabolism was measured in nine streams in each of eight regions (n = 72) across the United States and Puerto Rico. In each region, three streams were selected from a range of three land uses: agriculturally influenced, urban‐influenced, and reference streams. Stream metabolism was estimated from diel changes in dissolved oxygen concentrations in each stream reach with correction for reaeration and groundwater input. 3. Gross primary production (GPP) was highest in regions with little riparian vegetation (sagebrush steppe in Wyoming, desert shrub in Arizona/New Mexico) and lowest in forested regions (North Carolina, Oregon). In contrast, ecosystem respiration (ER) varied both within and among regions. Reference streams had significantly lower rates of GPP than urban or agriculturally influenced streams. 4. GPP was positively correlated with photosynthetically active radiation and autotrophic biomass. Multiple regression models compared using Akaike’s information criterion (AIC) indicated GPP increased with water column ammonium and the fraction of the catchment in urban and reference land‐use categories. Multiple regression models also identified velocity, temperature, nitrate, ammonium, dissolved organic carbon, GPP, coarse benthic organic matter, fine benthic organic matter and the fraction of all land‐use categories in the catchment as regulators of ER. 5. Structural equation modelling indicated significant distal as well as proximal control pathways including a direct effect of land‐use on GPP as well as SRP, DIN, and PAR effects on GPP; GPP effects on autotrophic biomass, organic matter, and ER; and organic matter effects on ER. 6. Overall, consideration of the data separated by land‐use categories showed reduced inter‐regional variability in rates of metabolism, indicating that the influence of agricultural and urban land use can obscure regional differences in stream metabolism.     

Comparative adaptations of Aphanizomenon and Anabaena for nitrogen fixation under weak irradiance

1. In situ measurements of nitrogen fixation rates for Aphanizomenon in fertile Colorado lakes with low inorganic nitrogen concentrations demonstrated high efficiency of nitrogen fixation at low irradiance. 2. For study populations, rates of N₂ fixation in darkness and with alternating exposure to light and darkness were a higher percentage of light‐saturated rates for Aphanizomenon than for Anabaena, suggesting storage of reduced metabolites at high irradiance that are used subsequently by Aphanizomenon when cells are forced by mixing into zones of low irradiance. Also, saturation of N₂ fixation occurred over a lower range of irradiance for Aphanizomenon than for Anabaena. 3. High efficiency of N₂ fixation in Aphanizomenon at low or fluctuating irradiance is complementary to its previously demonstrated high efficiency of photosynthesis at low irradiance. Nitrogen fixation rate was also strongly related to DIN concentration; fixation was highest at low DIN (maximum < 5 μg L^?1) but was also most vulnerable to photoinhibition under such conditions. 4. The fixation capabilities of Aphanizomenon under weak or varying irradiance could explain its commonly observed domination over Anabaena when transparency is low and available nitrogen is scarce.     

Leaf breakdown in an Atlantic Rain Forest stream

The hypothesis of this study was that colonizers in decaying leaf litter prefer native species (Erythrina verna) to exotic ones (Eucalyptus camaldulensis and Protium heptaphyllum). Therefore, native species are expected to show higher breakdown rates, increased biomass, richness and density of invertebrate species, and increased biomass of decomposer fungi. Breakdown of leaf litter from these three species was assessed in an Atlantic Rain Forest stream. Four samples were collected during a period of 90 days and washed on a sieve to separate the invertebrates. Then, a series of leaf disks were cut to determine ash‐free dry mass and fungal biomass, and the remaining material was oven‐dried to determine the dry weight. Eucalyptus camaldulensis and E. verna showed higher breakdown rates than P. heptaphyllum, due to differences in leaf physical and chemical characteristics. The harder detritus (P. heptaphyllum) broke down more slowly than detritus with high concentrations of labile compounds (E. camaldulensis). The density of the invertebrates associated with detritus increased with time. There were no differences in density, taxonomic richness or biomass of invertebrates among the leaf types, which indicated that the invertebrates did not distinguish between exotic and native detritus. Fungal colonization varied among samples; E. camaldulensis showed the lowest ergosterol concentrations, mainly due to a high concentration of total phenolics. The detritus with the highest hardness value was colonized most slowly by fungi. These results showed that leaf breakdown in Atlantic Rain Forest streams could be affected either by changes in riparian vegetation, or by becoming more savanna‐like process due to climate change.     

Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Presence of the dihydrouridine (D) stem in the mitochondrial cysteine tRNA is unusually variable among lepidosaurian reptiles. Phylogenetic and comparative analyses of cysteine tRNA gene sequences identify eight parallel losses of the D-stem, resulting in D-arm replacement loops. Sampling within the monophyletic Acrodonta provides no evidence for reversal. Slipped-strand mispairing of noncontiguous repeated sequences during replication or direct replication slippage can explain repeats observed within cysteine tRNAs that contain a D-arm replacement loop. These two mechanisms involving replication slippage can account for the loss of the cysteine tRNA D-stem in several lepidosaurian lineages, and may represent general mechanisms by which the secondary structures of mitochondrial tRNAs are altered.