Real-time PCR in the microbiology laboratory

Use of PCR in the field of molecular diagnostics has increased to the point where it is now accepted as the standard method for detecting nucleic acids from a number of sample and microbial types. However, conventional PCR was already an essential tool in the research laboratory. Real-time PCR has catalysed wider acceptance of PCR because it is more rapid, sensitive and reproducible, while the risk of carryover contamination is minimised. There is an increasing number of chemistries which are used to detect PCR products as they accumulate within a closed reaction vessel during real-time PCR. These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail. It is not only the technology that has changed with the introduction of real-time PCR. Accompanying changes have occurred in the traditional terminology of PCR, and these changes will be highlighted as they occur. Factors that have restricted the development of multiplex real-time PCR, as well as the role of real-time PCR in the quantitation and genotyping of the microbial causes of infectious disease, will also be discussed. Because the amplification hardware and the fluorogenic detection chemistries have evolved rapidly, this review aims to update the scientist on the current state of the art. Additionally, the advantages, limitations and general background of real-time PCR technology will be reviewed in the context of the microbiology laboratory.

Protecting the Australian citrus industry from HLB (greening) disease

Protecting the Australian citrus industry from HLB (greening) disease.

Human herpesvirus-6 infection in liver transplantation

Rejection and infections are the two most common complications after liver transplantation. Human herpesvirus-6 (HHV-6) belongs to the betaherpesviruses, together with its close relatives cytomegalovirus (CMV) and human herpesvirus-7 (HHV-7). The impact of CMV in liver transplantation is well characterized, but the roles of the other two betaherpesviruses have been acknowledged only recently. Although, HHV-6 reactivation after transplantation is usually asymptomatic, the virus may infect the liver transplant, cause an intragraft lymphocyte dominated inflammatory reaction and graft dysfunction. HHV-6 is also suggested to be associated with liver allograft rejection but the mechanisms are unclear. The aim of this study was to investigate the intragraft immunological processes associated with HHV-6, the involvement of HHV-6 in acute liver failure (ALF) and the hepatic HHV-6 infection of the same patients after transplantation. In addition, the occurrence of HHV-6 and HHV-7 was investigated in liver transplant patients with symptomatic CMV infection. HHV-6 infection of the liver graft was associated with portal lymphocyte infiltration and with a significant increase of adhesion molecules (ICAM-1 and VCAM-1) and the number of cells expressing their ligand molecules (LFA-1, VLA-4) and class II antigens. HHV-6 infection was associated with significant immunological changes, but the immune response was limited to lymphocyte infiltration and the adhesion molecule level. However, one third of these patients developed chronic rejection during the follow-up. Of the patients with ALF of unknown origin, most patients demonstrated HHV-6 antigens in the liver, whereas the opposite was seen in ALF patients with a known disease. After transplantation, HHV-6 recurrence was found in the liver transplant in half of these patients with pre-transplant HHV-6 infection of the liver, whereas no post-transplant HHV-6 infection of the liver was seen in patients without pre-transplant HHV-6. Our studies further demonstrated that both HHV-6 and HHV-7 antigenemia often appeared in association with CMV disease in liver transplant patients. The time-related occurrence of the viruses differed, as HHV-6 appeared early after transplantation and regularly preceded CMV whereas HHV-7 often appeared concurrently with CMV. In conclusion, these results indicate that all three betaherpesviruses are common after liver transplantation, often associated with each other. The immunological events caused by HHV-6 in the liver transplant may be involved in, or trigger mechanisms of allograft rejection. In addition, HHV-6 could be one of the causes of ALF, and pre-transplant HHV-6 infection in ALF patients is a risk factor for post-transplant HHV-6 infection of the graft. These results strongly support the clinical significance of HHV-6 in liver transplantation. Even though the reactivation is usually asymptomatic, in some individuals HHV-6 infection may lead to severe manifestations, such as liver failure or in transplant patients, graft dysfunction and rejection.

Design considerations for a micro aerial vehicle aerodynamic characterization facility at the University of Florida research and engineering education facility

This paper describes the design considerations for a proposed aerodynamic characterization facility (ACF) for micro aerial vehicles (MAVs). This is a collaborative effort between the Air Force Research Laboratory Munitions Directorate (AFRL/MN) and the University of Florida Research and Engineering Education Facility (UF/REEF). The ACF is expected to provide a capability for the characterization of the aerodynamic performance of future MAVs. This includes the ability to gather the data necessary to devise control strategies as well as the potential to investigate aerodynamic 'problem areas' or specific failings. Since it is likely that future MAVs will incorporate advanced control strategies, the facility must enable researchers to critically assess such novel methods. Furthermore, the aerodynamic issues should not be seen (and tested) in isolation, but rather the facility should be able to also provide information on structural responses (such as aeroelasticity) as well as integration issues (say, thrust integration or sensor integration). Therefore the mission for the proposed facility ranges form fairly basic investigations of individual technical issues encountered by MAVs (for example an evaluation of wing shapes or control effectiveness) all the way to testing a fully integrated vehicle in a flight configuration for performance evaluation throughout the mission envelope.

Extreme ultraviolet emission lines of Ca XV in solar and laboratory spectra

New R-matrix calculations of electron impact excitation rates in Ca XV are used to derive theoretical electron density diagnostic emission line intensity ratios involving 2s(2)2p(2)- 2s2p(3) transitions, specifically R-1 = I(208.70 Angstrom)/I(200.98 Angstrom), R-2 = I(181.91 Angstrom)/I(200.98 Angstrom), and R-3 = I(215.38 Angstrom)/I(200.98 Angstrom), for a range of electron temperatures (T-e = 10(6.4)-10(6.8) K) and densities (Ne = 10(9)-10(13) cm(-3)) appropriate to solar coronal plasmas. Electron densities deduced from the observed values of R-1, R-2, and R-3 for several solar flares, measured from spectra obtained with the Naval Research Laboratory's S082A spectrograph on board Skylab, are found to be consistent. In addition, the derived electron densities are in excellent agreement with those determined from line ratios in Ca XVI, which is formed at a similar electron temperature to Ca XV. These results provide some experimental verification for the accuracy of the line ratio calculations, and hence the atomic data on which they are based. A set of eight theoretical Ca XV line ratios involving 2s(2)2p(2)-2s2p(3) transitions in the wavelength range similar to140-216 Angstrom are also found to be in good agreement with those measured from spectra of the TEXT tokamak plasma, for which the electron temperature and density have been independently determined. This provides additional support for the accuracy of the theoretical line ratios and atomic data.

Genome-wide association study of Alzheimer's disease with psychotic symptoms

Psychotic symptoms occur in ~40% of subjects with Alzheimer's disease (AD) and are associated with more rapid cognitive decline and increased functional deficits. They show heritability up to 61% and have been proposed as a marker for a disease subtype suitable for gene mapping efforts. We undertook a combined analysis of three genome-wide association studies (GWASs) to identify loci that (1) increase susceptibility to an AD and subsequent psychotic symptoms; or (2) modify risk of psychotic symptoms in the presence of neurodegeneration caused by AD. In all, 1299 AD cases with psychosis (AD+P), 735 AD cases without psychosis (AD-P) and 5659 controls were drawn from Genetic and Environmental Risk in AD Consortium 1 (GERAD1), the National Institute on Aging Late-Onset Alzheimer's Disease (NIA-LOAD) family study and the University of Pittsburgh Alzheimer Disease Research Center (ADRC) GWASs. Unobserved genotypes were imputed to provide data on >1.8 million single-nucleotide polymorphisms (SNPs). Analyses in each data set were completed comparing (1) AD+P to AD-P cases, and (2) AD+P cases with controls (GERAD1, ADRC only). Aside from the apolipoprotein E (APOE) locus, the strongest evidence for association was observed in an intergenic region on chromosome 4 (rs753129; 'AD+PvAD-P' P=2.85 × 10(-7); 'AD+PvControls' P=1.11 × 10(-4)). SNPs upstream of SLC2A9 (rs6834555, P=3.0 × 10(-7)) and within VSNL1 (rs4038131, P=5.9 × 10(-7)) showed strongest evidence for association with AD+P when compared with controls. These findings warrant further investigation in larger, appropriately powered samples in which the presence of psychotic symptoms in AD has been well characterized.Molecular Psychiatry advance online publication, 18 October 2011; doi:10.1038/mp.2011.125.

Lipoproteins and diabetic microvascular complications

Risk factors for the microvascular complications (nephropathy and retinopathy) of Type 1 and Type 2 diabetes mellitus and the associated accelerated atherosclerosis include: age, diabetes duration, genetic factors, hyperglycaemia, hypertension, smoking, inflammation, glycation and oxidative stress and dyslipoproteinaemia. Hypertriglyceridaemia, low HDL and small dense LDL are common features of Type 2 diabetes and Type 1 diabetes with poor glycaemic control or renal complications. With the expansion of knowledge and of clinical and research laboratory tools, a broader definition of 'lipid' abnormalities in diabetes is appropriate. Dyslipoproteinaemia encompasses alterations in lipid levels, lipoprotein subclass distribution, composition (including modifications such as non-enzymatic glycation and oxidative damage), lipoprotein-related enzymes, and receptor interactions and subsequent cell signaling. Alterations occur in all lipoprotein classes; chylomicrons, VLDL, LDL, HDL, and Lp(a). There is also emerging evidence implicating lipoprotein related genotypes in the development of diabetic nephropathy and retinopathy. Lipoprotein related mechanisms associated with damage to the cardiovascular system may also be relevant to damage to the renal and ocular microvasculature. Adverse tissue effects are mediated by both alterations in lipoprotein function and adverse cellular responses. Recognition and treatment of lipoprotein-related risk factors, supported by an increasing array of assays and therapeutic agents, may facilitate early recognition and treatment of high complication risk diabetic patients. Further clinical and basic research, including intervention trials, is warranted to guide clinical practice. Optimal lipoprotein management, as part of a multi-faceted approach to diabetes care, may reduce the excessive personal and economic burden of microvascular complications and the related accelerated atherosclerosis.

Diferencias en costo efectividad del cuidado paliativo domiciliario frente a la atención convencional hospitalaria para el manejo de enfermedades crónicas en fase terminal

En Colombia la dinámica poblacional ha experimentado cambios a través de los años; lo cual modifica las características epidemiológicas y los perfiles de morbimortalidad de la población, aumentando la incidencia y prevalencia de enfermedades crónicas de difícil pronóstico dentro de la población; siendo estos grupos etarios hacía quienes deben destinarse nuevas modalidades de atención y soporte paliativo. Se realizó una revisión sistemática de diversos artículos, clasificados con niveles de evidencia I y II; cuyas variables de análisis fueron: El lugar de fallecimiento del paciente, alivio de la sintomatología, nivel de satisfacción del paciente y sus cuidadores con los servicios recibidos, número de ingresos hospitalarios independientemente de la causa y días promedio de estancia hospitalaria. El 88% de los pacientes que fueron vinculados a la atención domiciliaria falleció en su hogar; el 68% refirió haber experimentado disminución en la intensidad de al menos 2 síntomas como resultado de la atención en casa. El nivel de satisfacción para el cuidado en casa puntuó 19 puntos porcentuales por encima de la calificación que obtuvo el manejo hospitalario. El 23% de los pacientes tratados en su hogar, requirió al menos una hospitalización durante el manejo; mostrando una disminución en el tiempo de estancia hospitalaria de 3.4 días promedio. El manejo paliativo domiciliario de pacientes crónicos en fase terminal, no sólo es una alternativa en la reducción de costos para el sistema de salud, sino que es un factor protector de tipo emocional que refleja también una importante disminución de los riesgos de la hospitalización.

All Hands on Deck: Transdisciplinary Approaches to Emerging Infectious Disease

The increasing burden of emerging infectious diseases worldwide confronts us with numerous challenges, including the imperative to design research and responses that are commensurate to understanding the complex social and ecological contexts in which infectious diseases occur. A diverse group of scientists met in Hawaii in March 2005 to discuss the linked social and ecological contexts in which infectious diseases emerge. A subset of the meeting was a group that focused on ‘‘transdisciplinary approaches’’ to integrating knowledge across and beyond academic disciplines in order to improve prevention and control of emerging infections. This article is based on the discussions of that group. Here, we outline the epidemiological legacy that has dominated infectious disease research and control up until now, and introduce the role of new, transdisciplinary and systems-based approaches to emerging infectious diseases.Wedescribe four cases of transboundary health issues and use them to discuss the potential benefits, as well as the inherent difficulties, in understanding the social–ecological contexts in which infectious diseases occur and of using transdisciplinary approaches to deal with them.

Urinary Mutagenicity in Chemical Laboratory Workers Exposed to Solvents

Solvents represent an important group of environmental pollutants to which people are exposed daily in the workplace. The physico chemical properties of solvents may result in disturbances to cellular structures, including damage to DNA. However, the effects of mixtures of solvents are not well known. Mutations caused by environmental agents are related to cancer development and other degenerative diseases. The work in a research laboratory that uses several types of solvents is equally predisposed to these hazards. In this study, we evaluated the mutagenicity of urine from 29 subjects exposed occupationally to solvents in a chemistry research laboratory and 29 subjects without occupational exposure (controls). Urine samples were collected in polyethylene containers at the end of the work shift. For the concentration and extraction of urine samples the XAD-2 resin was used with acetone as an eluting agent. Several strains of Salmonella typhimurium (TA100, TA98, TA97a, TA1535, YG1024) should be used to assess mutagenic susceptibilities among workers exposed to organic solvents. Different doses of extract (1.5; 3.0; 6.0 and 12.0 m/ equivalents of urine per plate) were tested on S. typhimurium strains TA100 and YG 1024, with and without metabolic activation. The mutagenic activity, measured in Salmonella typhimurium YGI1024 with S9 mix, was significantly greater in urine from workers than from controls (p <= 0.05). These results indicate the relevance of using biomarkers to assess the risk of occupational exposure to organic solvents.

Análise da mutagenecidade urinária e susceptibilidade genética no monitoramento de indivíduos expostos a solventes orgânicos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Uric acid biorhythm, a feature of long-term variation in a clinical laboratory database

Background: The biorhythm of serum uric acid was evaluated in a large sample of a clinical laboratory database by spectral analysis and the influence of the gender and age on uric acid variability. Methods: Serum uric acid values were extracted from a large database of a clinical laboratory from May 2000 to August 2006. Outlier values were excluded from the analysis and the remaining data (n = 73,925) were grouped by gender and age ranges. Rhythm components were obtained by the Lomb Scargle method and Cosinor analysis. Results: Serum uric acid was higher in men than in women older than 13 years (p<0.05). Compared with 0-12 year group, uric acid increased in men but not in women older than 13 years (p<0.05). Circannual (12 months) and transyear (17 months) rhythm components were detected, but they were significant only in adult individuals (>26 years, p<0.05). Cosinor analysis showed that midline estimating statistic of rhythm (MESOR) values were higher in men (range: 353-368 mu mol/L) than in women (range: 240-278 mu mol/L; p<0.05), independent of the age and rhythm component. The extent of predictable change within a cycle, approximated by the double amplitude, represented up to 20% of the corresponding MESOR. Conclusions: Serum uric acid biorhythm is dependent on gender and age and it may have relevant influence on preanalytical variability of clinical laboratory results.

Adaptive immunity is related to coronary artery disease severity after acute coronary syndrome in subjects with metabolic syndrome

Metabolic syndrome (MetS) is an inflammatory state associated with high coronary disease risk. Inflammation and adaptive immunity modulate atherosclerosis and plaque instability. We examined early changes in anti-oxidized lowdensity lipoprotein (LDL) (anti-oxLDL) autoantibodies (Abs) in patients with MetS after an acute coronary syndrome (ACS). Patients of both genders (n=116) with MetS were prospectively included after an acute yocardial infarction (MI) or hospitalization due to unstable angina. Anti-oxLDL Abs (IgG class) were assayed at baseline, three and six weeks after ACS. The severity of coronary disease was evaluated by the Gensini score. We observed a decrease in anti-oxLDL Abs titers (p<0.002 vs. baseline), mainly in males (p=0.01), in those under 65 y (p=0.03), and in subjects with Gensini score above median (p=0.04). In conclusion, early decrease in circulating anti-oxLDL Abs is associated with coronary disease severity among subjects with MetS.