High prevalence of fasciolosis and evaluation of drug efficacy against Fasciola hepatica in dairy cattle in the Maffra and Bairnsdale districts of Gippsland, Victoria, Australia.

Liver fluke (Fasciola hepatica) is a common parasite amongst grazing livestock in the south-eastern region of Australia and is responsible for significant production losses in the beef and dairy industries. Gippsland in Victoria is a major region for dairy production but no fluke prevalence data in livestock has been obtained in this region since the late 1970s prior to the introduction of Triclabendazole (TCBZ). TCBZ resistance is also now widespread in cattle in south east Australia. In this study, we evaluated the prevalence and intensity of liver fluke infections in dairy cattle in Gippsland and assessed the efficacy of TCBZ and other drenches against F. hepatica on one farm. We obtained 30 individual faecal samples from each of 15 different farms and, using the liver fluke coproantigen ELISA, tested bulk faecal samples pooled from each farm. Any farm that returned a positive bulk sample had all of the samples tested individually to assess the intra-herd prevalence. One farm in the Maffra district also had a coproantigen reduction test and faecal egg count reduction test to assess the efficacy of TCBZ, Clorsulon (CLOR) and Oxyclozanide (OXY). The coproantigen ELISA proved to be a highly sensitive test for liver fluke with a high correlation (R(2)=0.8849) observed between ELISA data from bulk samples and individual samples, suggesting that future larger scale screening on farms for fasciolosis could use the bulk analysis technique. The ELISA data revealed that animals on six of the 15 farms were infected with F. hepatica and the herd prevalence of the infected herds ranged from 47 to 100% (mean 81%) which exceeds the prevalence value for production losses of 25%. The intensity of fluke infection in cattle varied considerably both within and between herds with a proportion of animals exhibiting a positive control value in the coproantigen ELISA of 50-88%. We also confirmed that TCBZ resistance was present on one farm but that CLOR or OXY can be used to remove the adult stage of the TCBZ-resistant parasites. We conclude that fasciolosis is a significant disease and a likely cause of production losses in dairy cattle in the irrigation zones of Gippsland and that TCBZ resistance is a serious threat to fluke control. We suggest that more work needs to be performed in Gippsland to further define the extent of fasciolosis and drug resistance and to ensure that effective chemical and non-chemical methods of fluke control are incorporated on farms in order to improve animal welfare and reduce financial impacts on producers.

Placebo effect in burning mouth syndrome: a systematic review.

Placebo controls play a critical role in the evaluation of any pharmacotherapy. This review surveys the placebo arm in 12 randomized controlled trials (RCTs) investigating burning mouth syndrome (BMS) and documents a positive placebo response in 6 of them. On average, treatment with placebos produced a response that was 72% as large as the response to active drugs. The lack of homogeneity in the use of placebos adds to the difficulty in comparing results and aggregating data. Future RCTs investigating BMS would benefit from larger sample sizes, adequate follow-up periods, and use of a standard placebo.

Meta-analysis: the effects of placebo treatment on gastro-oesophageal reflux disease.

BACKGROUND: There appears to be a significant placebo response rate in clinical trials for gastro-oesophageal reflux disease. Little is known about the determinants and the circumstances associated with placebo response in the treatment of gastro-oesophageal reflux disease (GERD). AIMS: To estimate the magnitude of the placebo response rate in randomized controlled trials for GERD and to identify factors that influence this response. METHODS: A meta-analysis of randomized, double-blind, placebo-controlled trials, published in English language, which included >20 patients with GERD, treated with either a proton pump inhibitor or H(2)-receptor antagonist for at least 2 weeks. Medline, Cochrane and EMBASE databases were searched, considering only studies that reported a global response for 'heartburn'. RESULTS: A total of 24 studies included 9989 patients with GERD. The pooled odds ratio (OR) for response to active treatment vs. placebo was 3.71 (95% CI: 2.78-4.96). The pooled estimate of the overall placebo response was 18.85% (range 2.94%-47.06%). Patients with erosive oesophagitis had a non-significantly lower placebo response rate than patients without it (11.87% and 18.31%, respectively; P = 0.246). Placebo response was significantly lower in studies of PPI therapy vs. studies of H(2) RAs (14.51% vs. 24.69%, respectively; P = 0.05). CONCLUSIONS: The placebo response rate in randomized controlled trials for GERD is substantial. A lower placebo response was associated with the testing of PPIs, but not the presence of erosive oesophagitis.

Genetic association of htSNPs across the major histocompatibility complex with rheumatoid arthritis in an African-American population.

Notwithstanding the well-established association of HLA-DRB1 shared epitope alleles, interest remains in identifying additional major histocompatibility complex (MHC) region variants associated with rheumatoid arthritis (RA). We used a panel of 1201 haplotype-tagging single nucleotide polymorphisms (SNPs) designed for African Americans to find genetic variants associated with RA in a 3.8-Mb region encompassing the MHC. Conditioning on seven covariates, including HLA-DRB1 risk alleles and population structure, we identified an SNP in HLA-DOA (rs9276977) significantly associated with RA; minor allele frequency (MAF) 0.27 in cases versus 0.21 in controls, odds ratio (+/-95% confidence interval)=2.86 (1.61, 5.31). Genotyping of rs9276977 in an independent sample of African-American RA patients and controls did not replicate the association (MAF 0.28 in cases versus 0.27 in controls). This study points to the potential association of a SNP in the HLA-DOA gene with RA in African Americans, but also underscores the importance of replication of findings in larger patient cohorts.

Serum correlates of the placebo effect in irritable bowel syndrome.

BACKGROUND In diseases defined primarily by the subjective nature of patient self-report, placebo effects can overwhelm the capacity of randomized controlled trials to detect medication-placebo differences. Moreover, it is unclear whether such placebo effects represent genuine psychobiological phenomena or just shifts in selective attention. Knowledge of predictors of the placebo response could improve the design of clinical trials and the delivery of personalized medical care. METHODS In patients with irritable bowel syndrome (IBS), a subset of our previous study that were randomized to placebo treatment (sham acupuncture) or no-treatment group (waitlist), we tested an enriched panel of 10 serum biomarkers at the enrolment and the 3rd week of intervention, using a multiplex electrochemiluminescent immunoassay. KEY RESULTS More pronounced changes overtime in serum levels of osteoprotegerin (OPG) have been found in patients who received placebo treatment compared with the waitlist group (P = 0.039). Moreover, serum levels of OPG at baseline were found to be higher (P = 0.0167) in patients who subsequently achieved adequate relief (AR) of their IBS symptoms, independently of their treatment group. Besides, serum levels of TNF-related weak inducer of apoptosis (TWEAK) at baseline were also higher (P = 0.0144) in patients who reported AR and in particular in those who received the placebo treatment. CONCLUSIONS & INFERENCES These two measurable biological parameters associated with placebo, namely serum OPG and TWEAK, provide a proof of principle for discovering putative molecular signatures of placebo response in IBS and perhaps in other illnesses with patient self-reported outcomes.

Evaluating linkage disequilibrium and recombination provides a haplotype-tagging SNP panel of the major histocompatibility complex in African Americans.

The major histocompatibility complex (MHC) (Chromosome 6p21.3) is a dynamic, immune gene-rich region that is associated with multiple diseases. Haplotype-tagging single-nucleotide polymorphism (htSNP) panels for the MHC can aid association studies but have only been reported for African, Asian and Caucasian populations to date. We genotyped 2154 SNPs spanning a 3.8-Mb region of the classical MHC in 94 healthy African Americans using Illumina BeadArray technology. We describe the haplotype structure of the MHC in African Americans, calculate the recombination rate (0.35 cM Mb(-1)) across the region, identify recombination hot spots and develop a panel of htSNPs for future genetic association studies in this population. We conclude that while patterns of LD and recombination are similar within the MHC to that reported in other populations, differences in minor allele frequency at specific markers necessitates an htSNP panel unique to African Americans, which we provide here for use in future genetic association studies.

Interferon regulatory factor-5 is genetically associated with systemic lupus erythematosus in African Americans.

Increased expression of interferon (IFN)-inducible genes is implicated in the pathogenesis of systemic lupus erythematosus (SLE). One transcription factor responsible for regulating IFN, interferon regulatory factor-5 (IRF5), has been associated with SLE in genetic studies of Asian, Caucasian and Hispanic populations. We genotyped up to seven polymorphic loci in or near IRF5 in a total of 4870 African-American and Caucasian subjects (1829 SLE sporadic cases and 3041 controls) from two independent studies. Population-based case-control comparisons were performed using the Pearson's chi(2)-test statistics and haplotypes were inferred using HaploView. We observed significant novel associations with the IRF5 variants rs2004640 and rs3807306 in African Americans and replicated previously reported associations in Caucasians. While we identified risk haplotypes, the majority of haplotypic effects were accounted for by one SNP (rs3807306) in conditional analyses. We conclude that genetic variants of IRF5 associate with SLE in multiple populations, providing evidence that IRF5 is likely to be a crucial component in SLE pathogenesis among multiple ethnic groups.

Copy number variants in genetic susceptibility and severity of systemic lupus erythematosus.

Systemic lupus erythematosus (SLE) is a systemic autoimmune disorder characterized by the presence of auto-antibodies to nuclear antigens, immune complex deposition, and subsequent tissue destruction. Early studies in twins suggested that SLE has, at least in part, a genetic basis, and a role for class II alleles in the major histocompatibility complex has been known for over 30 years. Through both linkage studies and candidate gene studies, numerous additional genetic risk factors have been identified. The recent publication of two SNP-based genome-wide association studies (GWAS) has resulted in the confirmation of a number of previously identified genetic risk loci and has identified new previously unappreciated loci conferring risk for development of SLE. A role for gene copy number variation (CNV) in SLE has also been appreciated through studies of the complement component 4 (C4) loci and more recent work in the IgG Fc receptor loci. The availability of large SNP-based GWAS datasets will undoubtedly lead to the genome-wide analysis and identification of copy number variants related to genetic susceptibility for development of SLE. We review current studies of CNV in SLE susceptibility that include reports of association between SLE and CNV in C4, IgG Fc receptors, TLR7, and CCL3L1.

The perceived clarity and understandability of the DSM-IV personality disorder criteria sets.

One of the expressed aims of the DSM-IV revision process was to "increase the clarity" and the understandability of the personality disorder (PD) criteria. This was an important goal as previous research had showed the DSM-III-R PD criteria to have problems with clarity. To assess the degree to which this goal was achieved, we had two groups (psychiatrists and lay persons) rate the clarity of the DSM-IV PD criteria and the criteria for major depressive disorder (MDD) and post-traumatic stress disorder (PTSD). The lay group rated five of the 10 PDs criteria sets and the criteria for PTSD as being significantly more clear than did the mental health professionals. No difference was seen between the two groups on their ratings of the MDD criteria. In addition, the professional group rated two of the PD criteria sets (borderline and schizotypal) as being less clear than the MDD criteria, while the lay group rated eight of the PD criteria sets as being more clear than the MDD criteria.

Enhanced activity of antisense phosphorothioate oligos against leishmania amastigotes: augmented uptake of oligo, ribonuclease H activation, and efficient target intervention under altered growth conditions.

Leishmania, a parasitic protozoan, infects human macrophages, often causing severe morbidity and mortality. The pathogenic form of this parasite, the amastigote, lives inside the acidic phagolysosomes of infected macrophages. In our attempt to develop anti-miniexon phosphorothioate oligodeoxyribonucleotides (S-oligos) as an alternative chemotherapy against Leishmania, we found that intracellular as well as 'axenic' amastigotes were more susceptible to these S-oligos than were the cultured promastigotes. Lower pH (4.5) and elevated temperature (35 degrees) of the medium were among the direct enhancing factors for killing. Addition of the cationic polypeptide poly-l-lysine (PLL) to the growth medium further enhanced the killing effect of the S-oligo at pH 4.5. The enhancement of specific ablation of mRNA expression was directly correlated to the increased leishmanicidal activity of the S-oligo. This was shown by the increased inhibition of luciferase activity expressed in transgenic Leishmania amazonensis promastigotes by anti-miniexon S-oligo or anti-luciferase S-oligo at acidic pHs and in the presence of PLL. The leishmanicidal effects of S-oligos at acidic pH and in the presence of PLL were related to increased uptake of the S-oligos under these conditions. The rate of S-oligo uptake was enhanced up to 15-fold at pH 4.5. The addition of PLL to the assay medium at acidic pH further enhanced the uptake of S-oligo up to 80-fold. RNase H is known to accentuate the antisense action of S-oligos. We found that at an elevated temperature RNase H activity in Leishmania cell extracts increased about 5-fold. Thus, enhanced uptake of S-oligos at the acidic pH of macrophage phagolysosomes and activation of RNase H may explain the efficient killing of the parasite in macrophages, both in tissue culture and in the animal model, by antisense miniexon oligonucleotide/PLL, when targeted directly to the parasite-containing phagolysosomes.

Size-fractionated plutonium isotopes in a coastal environment.

We have examined the distribution of individual Pu isotopes (239Pu, 240Pu, and 241Pu) in seawater from the Gulf of Maine (GOM). Samples were size-fractionated with a 1 kD cross-flow ultrafiltration (CFF) membrane. Subfractioned samples were radiochemically purified and Pu isotopes were analyzed using a three-stage thermal ionization mass spectrometer (TIMS). To our knowledge, this is the first time that both size class and Pu isotopic data have been obtained for seawater samples. Within measurement uncertainties a single 240Pu/239Pu atom ratio of 0.18 was found for all sample collection depths and sample size fractions. This signifies a current, single Pu source in GOM waters, namely global fallout, and suggests that no measurable isotopic fractionation occurred during CFF processing. The majority of Pu was found in the low molecular weight fraction (< 1 kD). Colloidal Pu varied from 8% of the total in surface waters to < 1% in the deepest (250 m) seawater sample. Evidence suggests that the vertical distribution of Pu in GOM is primarily controlled by conservative mixing processes. The high Pu fraction found in the low molecular size fraction implies that most of the Pu is in the non-particle-reactive oxidized fraction, and is consistent with the conservative Pu behavior. The activity levels are in agreement with other studies which show a slow decrease in Pu with time due to continued mixing and relatively slow particle removal.

The restricted expression of granzyme M in human lymphocytes.

We have analyzed the expression of human granzyme M (Gzm M) in various human leukocyte subsets using the specific mAb 4H10. Using FACS and Western blotting analysis we compared the expression of Gzm M with that of other granzymes (Gzm A and Gzm B) and the lytic protein perforin. Human Gzm M was constitutively highly expressed in NK cells as was perforin and Gzm A. Surprisingly, freshly isolated NK cells had very low (sometimes undetectable) levels of Gzm B. In contrast to Gzm B and perforin, Gzm M was not detected in highly purified CD4(+) and CD8(+) T cells either constitutively or after short term activation in vitro. However, low levels of Gzm M were observed in some T cell clones on prolonged passage in vitro. Gzm M was not detected in highly purified neutrophils, monocytes, or tumor cells of the myelomonocytic lineage. Examination of minor T cell subsets from human peripheral blood showed detectable Gzm M in CD3(+), CD56(+) T cells and gammadelta T cells. A histological staining procedure was developed that demonstrated a granular staining pattern for Gzm M and a cellular distribution similar to that observed by Western blotting. These data indicate that the expression of Gzm M does not always correlate with the lytic activity of cytotoxic cells. However, expression of Gzm M in NK cells, CD3(+), CD56(+) T cells, and gammadelta T cells suggests that this enzyme may play some role in innate immune responses.

Possible relationship between degenerative cardiac valvular pathology and lyme disease.

We report an unusual clinical presentation of Lyme carditis in a previously healthy 20-year-old black woman without any epidemiologic history of Lyme disease, fulminant in nature, involving a heart valve necessitating emergent mitral valve replacement, and requiring further surgical intervention because of the development of pericardial effusion and tamponade. A dilated right ventricle with normal contractility and severe tricuspid regurgitation with increase in the right atrial size diagnosed later remains under close surveillance.

Assessing the risks of exposures to multiple chemicals with a common mechanism of toxicity: how to cumulate?

The Food Quality Protection Act (FQPA) of 1996 requires the U.S. EPA to consider the "cumulative effects" of pesticides and other substances that have a "common mechanism of toxicity." Several different methods for combining the exposures to estimate the risk of groups of common mechanism chemicals with different potencies and exposure characteristics are critically evaluated. These are the hazard index (HI), toxicity equivalence factor (TEF), and combined margin of exposure (MOE(T)) procedures as well as the point of departure index (PODI) and cumulative risk index (CRI) methods that are the reciprocals of the HI and MOE(T) approaches, respectively. Each of these methods ideally requires, at a minimum, the availability of in vivo toxicology data for the same toxicological endpoint in the same animal species. Furthermore, all assume that the effects of the individual components in the mixture are independent in nature (i.e., are additive rather than synergistic or antagonistic) and that the dose-response functions for all compounds have a similar slope. The point of departure (POD), preferably the dose corresponding to a given effect level (e.g., the ED(10)), can be used as a measure of the relative potency of the different chemicals in the group. If appropriate exposure and toxicology data are available, and the chemicals in the group have a common uncertainty factor (UF), all the procedures yield a numerically identical result. The fact that different chemicals in the group often have different UFs raises issues for all summation procedures and, in the case of the TEF approach, the UF of the index chemical selected dictates the final result of the assessment. A major distinction between the different methods for addition is the point in the process at which uncertainty is considered. The HI and CRI approaches are problematic because they require application of policy-driven UFs (in the form of RfDs) at that stage of the process where exposure should be expressed in terms of potency. In contrast, the PODI and MOE(T) approaches require application of a single group UF(G) at the end of the risk assessment process although they will also accommodate the application of data-based adjustments earlier in the analysis. Importantly, both the PODI and the MOE(T) approaches allow policy- and data-driven UFs to be separated and thus make the process more transparent; these should be considered the methods of choice for cumulative risk assessment. Assignment of a single group UF is somewhat different from developing an UF for a single chemical and the total weight of evidence available in the group database can be used to advantage to reduce the UFs that need to be applied to the group. This larger database can also be used to refine the PODs for individual members of the group. It is important to emphasize that there remains a great deal of scientific uncertainty about how to proceed with cumulative risk assessment as described in the FQPA. The serious difficulties associated with defining "common mechanism of toxicity" and "concurrent exposure" combined with the current paucity of data and methodology required to conduct cumulative risk assessment suggest that the procedure is not yet ready for use in pesticide regulation.

Global distribution of Pu isotopes and 237Np.

Inventories and compositions of Pu isotopes and 237Np in archived soil samples collected in the 1970s from 54 locations around the world were determined to provide regional baselines for recognizing possible future environmental inputs of non-fallout Pu and Np. As sample sizes used in this work were small (typically 1 g), inhomogeneities in Pu and Np concentrations were easily recognizable and, as a result, we were able to determine that atypical debris in South America, from French testing in the South Pacific, is more widely and uniformly distributed than previously supposed. From our results we conclude that fallout 237Np/239Pu atom ratios are generally lower in the Southern Hemisphere (approximately 0.35) than in the Northern Hemisphere (approximately 0.47.) Moreover, 237Np/239Pu atom ratios are more device-dependent, hence more variable, than counterpart 240Pu/239Pu atom ratios. Given predictable trends caused by sample inhomogeneities, with only two exceptions, the Pu results of this work are entirely consistent with (and in several instances improve on) results previously reported for these same samples. However, unlike earlier interpretations used to explain these results, we recommend that fallout isotopic signatures be represented by mixing lines, rather than averages, to better reflect regional variations of stratospheric fallout inventories relative to tropospheric fallout inventories, and provide the theoretical basis for doing so. Finally, the Np results of this work constitute one of the largest single compilations of such data reported to date.

High throughput direct end sequencing of BAC clones.

Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large genomic regions. For this strategy to be effective, high throughput methods for BAC end sequencing of all the clones in deep coverage BAC libraries needed to be developed. Here we describe a low cost, efficient, 96 well procedure for BAC end sequencing. These methods allow us to generate BAC end sequences from human and Arabidoposis libraries with an average read length of >450 bases and with a single pass sequencing average accuracy of >98%. Application of BAC end sequences in genomic sequen-cing is discussed.

The complete genome sequence of the gastric pathogen Helicobacter pylori.

Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified, underscoring the potential complexity of host-pathogen interaction. Based on the large number of sequence-related genes encoding outer membrane proteins and the presence of homopolymeric tracts and dinucleotide repeats in coding sequences, H. pylori, like several other mucosal pathogens, probably uses recombination and slipped-strand mispairing within repeats as mechanisms for antigenic variation and adaptive evolution. Consistent with its restricted niche, H. pylori has a few regulatory networks, and a limited metabolic repertoire and biosynthetic capacity. Its survival in acid conditions depends, in part, on its ability to establish a positive inside-membrane potential in low pH.

The minimal gene complement of Mycoplasma genitalium.

The complete nucleotide sequence (580,070 base pairs) of the Mycoplasma genitalium genome, the smallest known genome of any free-living organism, has been determined by whole-genome random sequencing and assembly. A total of only 470 predicted coding regions were identified that include genes required for DNA replication, transcription and translation, DNA repair, cellular transport, and energy metabolism. Comparison of this genome to that of Haemophilus influenzae suggests that differences in genome content are reflected as profound differences in physiology and metabolic capacity between these two organisms.

Optimization of Applied Biosystems 373 sequencer stretch modification.

We have optimized the conditions for using the Stretch modification for the Applied Biosystems 373 Automated DNA Sequencers for sequencing double-stranded DNA using 34-cm well-to-read and 48-cm well-to-read configurations. With the manufacturer's recommended settings, uneven spacing within the first 100 bases was observed, which led to miscalls, insertions and deletions in the analyzed data. A significant decrease in accuracy for reads greater than 400 bases was also observed. Various gel concentrations were tested to improve the base spacing for the first 100 bases while maintaining accuracy and usable length of data. A longer average usable length and better resolution of smaller fragments were achieved by increased acrylamide concentration coupled with increased wattage. Using the Applied Biosystems CATALYST 800 Molecular Biology LabStation, Taq dye primer cycle sequencing reactions were optimized for -21 M13 and M13RP1 primers to produce a more even distribution of dye-labeled fragments that increased the overall signal strengths and decreased background signal. These reaction products, run on the Stretch sequencers using the new gel conditions, provided longer reads with increased reliability and accuracy of the data.