Quantification of various phosphatidylcholines in liposomes by enzymatic assay

The purpose of this research was to adapt a colorimetric, phospholipase D-based serum-phospholipid assay for the quantification of phosphatidylcholine (PC) in liposomes using a microtitre plate reader. PC from natural egg PC liposomes was quantified reliably. In contrast, poor sensitivity was found for liposomes composed of saturated PCs (dipalmitoyl-phosphatidylcholine [DPPC], hydrogenated egg PC). Triton X-100 was then added to the liposomes followed by heating above the phase transition temperature. This modified sample preparation resulted in recoveries of 102.6%±1.0%, 104.4%±7.6%, and 109.4%±3.2% for E80, E80-3/cholesterol, and DPPC liposomes, respectively. Absolute quantification of unknown PCs against a choline chloride standard is feasible, but relative measurements against the very same PC are recommended wheneve possible. Validation experiments revealed an absolute quantification limit of 1.25 μg per assay, a good linearity in the range of 25 to 1000μg/mL PC (r²≥0.9990) and a quite high accuracy (99.8%–101.4% of theory) and precision (relative standard deviation ≤3.2%) for all 3 PCs studied. The method is thus regarded as suitable for sensitive, rapid, and reliable routine quantification of PCs in liposomes.     

<Superscript>1</Superscript>H NMR-based metabolic profiling and target analysis: a combined approach for the quality control of <Emphasis Type="Italic">Thymus vulgaris</Emphasis>

The characterization of T. vulgaris plant material for quality control purposes was performed by NMR-based methods. Direct extraction of 141 T. vulgaris samples with DMSO-d ₆ enabled the obtainment of crude extracts with a representative composition in terms of both volatile and non-volatile constituents. The acquisition of 600 MHz ¹H NMR spectra resulted in a dataset which was analyzed by a combination of metabolic profiling and target analysis approaches. Preliminary analysis of the ¹H NMR spectra was performed by principal component analysis, which revealed sample discrimination on a chemotype basis (thymol, carvacrol and linalool chemotypes). Further minor discriminative constituents were identified as p-cymene, γ-terpinene, rosmarinic acid, and 3,4,3′,4′-tetrahydroxy-5,5′-diisopropyl-2,2′-dimethylbiphenyl. Metabolite identification was accomplished by 1D and 2D NMR techniques and supported by spiking experiments. Fast dereplication of constituents not available as reference compounds was performed by HPLC–SPE–NMR experiments. A targeted approach based on qHNMR was validated for quantification of the identified secondary metabolites. Validation was performed in terms of precision (intra-day RSD ≤ 4.51%, inter-day RSD ≤ 4.18%), repeatability (RSD ≤ 2.30%), accuracy (recovery rates within 93.4 and 103.4%), linearity (correlation coefficients ≥ 0.9990), robustness, and stability. The amount of the dominant monoterpene in thymol, carvacrol, and linalool chemotypes was respectively found to be within 0.4–2.6, 0.7–2.3, and 1.1–3.6% (w/w). Variable amounts of the precursors p-cymene and γ-terpinene were found in thymol and carvacrol chemotypes. The highest amount of rosmarinic acid and 3,4,3′,4′-tetrahydroxy-5,5′-diisopropyl-2,2′-dimethylbiphenyl in the analyzed samples was respectively 4.6 and 0.4% (w/w). Since quantification is performed on a weight basis, the essential oil content can be estimated based on the sum of the quantified monoterpenes. The NMR-based analysis of T. vulgaris represents a more comprehensive approach in comparison to traditional chromatographic methods such as GC and LC, respectively employed for the analysis of volatile and non-volatile constituents. Further advantages lie in the simple sample preparation, rapidity and reproducibility of the NMR analysis.     

Long-time variations in leaf mass and area of Mediterranean evergreen broad-leaf and narrow-leaf maquis species

Morphological (dry mass, DM; surface area, LA; leaf mass per area, LMA), anatomical (leaf thickness, L), phenological (leaf life span, LL), and physiological (net photosynthetic rate, P _N) leaf traits of the evergreen species co-occurring in the Mediterranean maquis developing at Castelporziano (Rome) were tested. The correlation analysis indicated that LMA variation was tightly associated with LL variations: Cistus incanus and Arbutus unedo had a short LL (4±1, summer leaves, and 11±1 months, respectively) and low LMA (153±19 g m⁻²) values, Quercus ilex, Phillyrea latifolia, and Pistacia lentiscus high LMA (204±7 g m⁻²) and long LL (22±3 months), Erica arborea, Erica multiflora, and Rosmarinus officinalis a short LL (9±2 months) and an either high (213±29 g m⁻², R. officinalis and E. multiflora) or low (115±17 g m⁻², E. arborea) LMA. LMA values were significantly (p≤0.05) correlated with P _N (r≥0.68). In the tested species, LMA increased in response to the decrease of the total rainfall during the leaf expansion period. LMA variation was due to the unequal variation of DM and LA in the considered species. LMA is thus a good indicator of evergreen maquis species capability to respond to climate change, in particular to total rainfall decrease in the Mediterranean basin.     

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

Verification of candidate biomarkers requires specific assays to selectively detect and quantify target proteins in accessible biofluids. The primary objective of verification is to screen potential biomarkers to ensure that only the highest quality candidates from the discovery phase are taken forward into preclinical validation. Because antibody reagents for a clinical grade immunoassay often exist for a small number of candidates, alternative methodologies are required to credential new and unproven candidates in a statistically viable number of serum or plasma samples. Using multiple reaction monitoring coupled with stable isotope dilution MS, we developed quantitative, multiplexed assays in plasma for six proteins of clinical relevance to cardiac injury. The process described does not require antibodies for immunoaffinity enrichment of either proteins or peptides. Limits of detection and quantitation for each signature peptide used as surrogates for the target proteins were determined by the method of standard addition using synthetic peptides and plasma from a healthy donor. Limits of quantitation ranged from 2 to 15 ng/ml for most of the target proteins. Quantitative measurements were obtained for one to two signature peptides derived from each target protein, including low abundance protein markers of cardiac injury in the nanogram/milliliter range such as the cardiac troponins. Intra- and interassay coefficients of variation were predominantly <10 and 25%, respectively. The configured multiplex assay was then used to measure levels of these proteins across three time points in six patients undergoing alcohol septal ablation for hypertrophic obstructive cardiomyopathy. These results are the first demonstration of a multiplexed, MS-based assay for detection and quantification of changes in concentration of proteins associated with cardiac injury in the low nanogram/milliliter range. Our results also demonstrate that these assays retain the necessary precision, reproducibility, and sensitivity to be applied to novel and uncharacterized candidate biomarkers for verification of proteins in blood.Discovery of disease-specific biomarkers with diagnostic and prognostic utility has become an important challenge in clinical proteomics. In general, unbiased discovery experiments often result in the confident identification of thousands of proteins, hundreds of which may vary significantly between case and control samples in small discovery studies. However, because of the stochastic sampling of proteomes in discovery “omics” experiments, a large fraction of the protein biomarkers “discovered” in these experiments are false positives arising from biological or technical variability. Clearly discovery omics experiments do not lead to biomarkers of immediate clinical utility but rather produce candidates that must be qualified and verified in larger sample sets than were used for discovery (1).Traditional, clinical validation of biomarkers has relied primarily on immunoassays because of their specificity and sensitivity for the target analyte and high throughput capability. However, antibody reagents for a clinical grade immunoassay often only exist for a short list of candidates. The development of a reliable sandwich immunoassay for one target protein is expensive, has a long development time, and is dependent upon the generation of high quality protein antibodies. For the large majority of new, unproven candidate biomarkers, an intermediate verification technology is required that has shorter assay development time lines, lower assay cost, and effective multiplexing of dozens of candidates in low sample volumes. Ideally the approach should be capable of analyzing hundreds of samples of serum or plasma with good precision. The desired outcome of verification is a small number of highly credentialed candidates suitable for traditional preclinical and clinical validation studies.Multiple reaction monitoring (MRM)¹ coupled with stable isotope dilution (SID) MS has recently been shown to be well suited for direct quantification of proteins in plasma (2–4) and has emerged as the core technology for candidate biomarker verification. MRM assays can be highly multiplexed such that a moderate number of candidate proteins (in the range of 10–50) can be simultaneously targeted and measured in the statistically viable number of patient samples required for verification (hundreds of serum samples). However, sensitivity for unambiguous detection and quantification of proteins by MS-based assays is often constrained by sample complexity, particularly when the measurements are being made in complex fluids such as plasma.Many biomarkers of current clinical importance, such as prostate-specific antigen and the cardiac troponins, reside in the low nanogram/milliliter range in plasma and, until recently, have been inaccessible by non-antibody approaches. Our laboratory has recently shown for the first time that a combination of abundant protein depletion with limited fractionation at the peptide level prior to SID-MRM-MS provides robust limits of quantitation (LOQs) in the 1–20 ng/ml range with coefficient of variation (CV) of 10–20% at the LOQ for proteins in plasma (3).Here we demonstrate that this work flow can be extended to configure assays for a number of known markers of cardiovascular disease and, more importantly, can be deployed to measure their concentrations in clinical samples. We modeled a verification study comprising six patients undergoing alcohol septal ablation treatment for hypertrophic obstructive cardiomyopathy, a human model of “planned” myocardial infarction (PMI), and obtained targeted, quantitative measurements for moderate to low concentrations of cardiac biomarkers in plasma. This work provides additional evidence that MS-based assays can be configured and applied to verification of new protein targets for which high quality antibody reagents are not available.     

Analytical Performance of ELISA Assays in Urine: One More Bottleneck towards Biomarker Validation and Clinical Implementation

ELISA is the main approach for the sensitive quantification of protein biomarkers in body fluids and is currently employed in clinical laboratories for the measurement of clinical markers. As such, it also constitutes the main methodological approach for biomarker validation and further qualification. For the latter, specific assay performance requirements have to be met, as described in respective guidelines of regulatory agencies. Even though many clinical ELISA assays in serum are regularly used, ELISA clinical applications in urine are significantly less. The scope of our study was to evaluate ELISA assay analytical performance in urine for a series of potential biomarkers for bladder cancer, as a first step towards their large scale clinical validation. Seven biomarkers (Secreted protein acidic and rich in cysteine, Survivin, Slit homolog 2 protein, NRC-Interacting Factor 1, Histone 2B, Proteinase-3 and Profilin-1) previously described in the literature as having differential expression in bladder cancer were included in the study. A total of 11 commercially available ELISA tests for these markers were tested by standard curve analysis, assay reproducibility, linearity and spiking experiments. The results show disappointing performance with coefficients of variation>20% for the vast majority of the tests performed. Only 3 assays (for Secreted protein acidic and rich in cysteine, Survivin and Slit homolog 2 protein) passed the accuracy thresholds and were found suitable for further application in marker quantification. These results collectively reflect the difficulties in developing urine-based ELISA assays of sufficient analytical performance for clinical application, presumably attributed to the urine matrix itself and/or presence of markers in various isoforms.     

Development of reverse phase protein microarrays for the validation of clusterin, a mid-abundant blood biomarker

Background  

Many putative disease blood biomarkers discovered in genomic and proteomic studies await validation in large clinically annotated cohorts of patient samples. ELISA assays require large quantities of precious blood samples and are not high-throughput. The reverse phase protein microarray platform has been developed for the high-throughput quantification of protein levels in small amounts of clinical samples.     

The indirect effects of multiplicity of infection on baculovirus expressed proteins in insect cells: secreted and non-secreted products

The baculovirus expression vector system was employed to produce human apolipoprotein E and β-galactosidase in order to study the effect of multiplicity of infection on secreted and non-secreted recombinant protein production. Prior knowledge of the influence of other cell culture and infection parameters, such as the cell density at time of infection and the time of harvest, allowed determination of the direct and indirect influences of multiplicity of infection on recombinant protein synthesis and degradation in insect cells. Under non-limited, controlled conditions, the direct effect of multiplicity of infection (10⁻¹−10 pfu/cell) on specific recombinant product yields of non-secreted β-galactosidase was found to be insignificant. Instead, the observed increased in accumulated product was directly correlated to the total number of infected cells during the production period and therefore ultimately dependent on an adequate supply of nutrients. Only the timing of recombinant virus and protein production was influenced by, and dependent on the multiplicity of infection. Evidence is presented in this study that indicates the extremely limited predictability of post-infection cell growth at very low multiplicities of infection of less than 0.1 pfu/cell. Due to the inaccuracy of the current virus quantification techniques, combined with the sensitivity of post-infection cell growth at low MOI, the possibility of excessive post-infection cell growth and subsequent nutrient limitation was found to be significantly increased. Finally, as an example, the degree of product stability and cellular and viral protein contamination at low multiplicity of infection is investigated for a secreted recombinant form of human apolipoprotein E. Comparison of human apolipoprotein E production and secretion at multiplicities of infection of 10⁻⁴−10 pfu/cell revealed increased product degradation and contamination with intracellular proteins at low multiplicities of infection. This revised version was published online in July 2006 with corrections to the Cover Date.     

Integrated protein network and microarray analysis to identify potential biomarkers after myocardial infarction

A significant proportion of patients develop left ventricular (LV) dysfunction and heart failure (HF) after acute myocardial infarction (MI). Existing biomarkers of HF provide limited information after MI. To identify new prognostic biomarkers in MI patients, we designed an approach combining protein interaction networks and microarray analysis of blood cells. Blood samples for RNA and protein analysis were taken from 127 acute MI patients. Echocardiography was performed at one month. Assuming that angiogenesis is related to cardiac repair after MI, a protein-protein interaction network of angiogenesis was constructed and analyzed. Among the 556 proteins and 686 interactions of this network, a cluster of 53 proteins highly specialized in regulation of cell growth was identified. Of these 53 proteins, 38 were found differentially expressed by microarrays between low (≤ 40%) and high (>40%) LV ejection fraction (EF) patients (n = 32). Among these 38 genes, prediction analysis identified a set of three genes able to predict significant LV dysfunction (EF ≤ 40%) with an area under the receiver operating characteristic curve (AUC) of 0.82. These three genes—vascular endothelial growth factor B, thrombospondin-1 and placental growth factor—had a stronger predictive value than brain natriuretic peptide and troponin T (AUC of 0.63). Independent validations on protein expression and quantitative PCR datasets confirmed the results. In conclusion, a new strategy is described that allows identifying new potential biomarkers. The three specific biomarkers described here remain to be validated in a larger patient population.     

Isotope-labeled protein standards: toward absolute quantitative proteomics

Diagnostic development and public health surveillance require technologies that provide specific identification and absolute quantification of protein biomarkers. Beside immunologically related techniques (e.g. enzyme-linked immunosorbent assay), MS is gaining increasing interest due to its high sensitivity and specificity. Furthermore, MS-based analyses are extremely accurate quantitatively, provided that suitable reference standards are available. Recently, the use of chemically synthesized isotope-labeled marker peptides for MS-based absolute quantification of proteins has led to major advances. However, we show here that the use of such peptides can lead to severe biases. In this work, we present an innovative strategy (Protein Standard Absolute Quantification) that uses in vitro-synthesized isotope-labeled full-length proteins as standards for absolute quantification. As those protein standards perfectly match the biochemical properties of the target proteins, they can be directly added into the samples to be analyzed, allowing a highly accurate quantification of proteins even in prefractionated complex samples. The power of our Protein Standard Absolute Quantification methodology for accurate absolute quantification of biomarkers was demonstrated both on water and urine samples contaminated with Staphylococcus aureus superantigenic toxins as typical biomarkers of public health interest.     

Reproducibility of serum cytokines and growth factors

Background: In most studies, circulating biomarkers are usually assessed from a single sample, assuming that this single measurement represents the long-term biomarker status of the individual. Such an assumption is rarely tested although it may not be valid for all biomarkers. The objective of this study was to investigate the temporal reproducibility of a panel of cytokines and growth factors. Methods: Thirty-five postmenopausal women with two annual visits and 30 premenopausal women with three annual visits were randomly selected from the participants in an existing prospective cohort. A total of 23 serum cytokines, nine growth factors and C-reactive protein (CRP) were measured using the Luminex xMap? technology. In addition, for eight biomarkers, regular and high sensitivity (hs) assays were compared. Results: The biomarkers with adequate (>60%) detection rates and acceptable (?0.55) intra-class correlation coefficients (ICCs) were: hsIL-1β, IL-1RA, hsIL-2, hsIL-4, hsIL-5, hsIL-6, hsIL-10, IL-12p40, hsIL-12p70, hsTNF-α, TNF-R1, TNF-R2, CRP, HGF, NGF, and EGFR. The remaining biomarkers either had low temporal reproducibility or were undetectable in more than 40% of samples. Conclusions: The results suggest that 16 of the 41 biomarkers measured with Luminex technology showed sufficient sensitivity and temporal reproducibility in sera.     

The repetitive use of samples to measure multiple cytokines: the sequential ELISA

The inexpensive and highly effective enzyme-linked immunosorbant assay (ELISA) is widely used for the quantification of biomarkers in a variety of biological samples. The applicability of the standard ELISA is difficult when experiments yield low volume samples. In such studies, the capacity of sample collection system does not meet the sample volume requirements to measure multiple different cytokines by the traditional ELISA protocol. In the modified methodology of the sequential ELISA, samples are re-used in multiple successive cycles, dramatically increasing the number of biomarkers which may be measured. Although the protocols presented to date were developed for quantification of cytokines in either blood plasma or cerebrospinal fluid, the sequential ELISA protocol has wide potential for further uses. When only limited quantities of samples are available for analysis, the sequential ELISA technique based on commercially available antibody pairs can be an attractive alternative to more advanced, costly multiplex methods. Additionally, any laboratory that currently runs traditional ELISAs has all the necessary equipment and reagents to perform the sequential ELISA.     

Effect of fungal infection on reproductive potential and survival time of <Emphasis Type="Italic">Tetranychus urticae</Emphasis> (Acari: Tetranychidae)

The effect of fungal infection on the reproductive potential of two-spotted spider mite, Tetranychus urticae, was evaluated as part of the full biocontrol potential of three entomopathogenic fungi by modeling of fecundity probability. Female mites (≤2-day-old) on leaves were exposed to the sprays of Beauveria bassiana, Paecilomyces fumosoroseus and Metarhizium anisopliae at the concentrations of 1.13 × 10³, 1.55 × 10³ and 0.95 × 10³ deposited conidia mm⁻² and then individually reared at 25°C and 12:12 L:D for oviposition. Mite mortalities 10 days after spraying were 73.1, 75.4 and 67.9% in the fungal treatments versus 15.5% in control. On average, females infected by the three fungal species survived 5.8, 6.2 and 6.3 days, and laid 3.1, 4.0 and 4.0 eggs per capita, respectively. These were 3–4 fold lower than the control fecundity at 12.3. The cumulative probabilities [P(m ≤ N)] for the counts of infected and non-infected (control) females laying m eggs per capita (m ≤ N) during 10 days fit very well the equation P(m ≤ N) = 1/[1 + exp(a + bm)] (r ² ≥ 0.98), yielding a solution to the probability for the female mites to achieve a specific fecundity {P(m ≤ N)−P[m ≤ (N − 1)]}. Consequently, the infected mites had 71–78% chance to lay ≤5 eggs per capita but only 5–8% to deposit >10 eggs despite some variation among the tested fungi. In contrast, the chances for the non-infected mites to achieve the low and high fecundities were 23 and 55%. The fitted probabilities provide a full coverage of the fecundity potential of infected versus non-infected mites and are more informative than the mean fecundities.     

Direct electrochemical immunoassay based on a silica nanoparticles/sol–gel composite architecture for encapsulation of immunoconjugate

A highly hydrophobic and non-toxic colloidal silica nanoparticle/polyvinyl butyral sol–gel composite membrane was prepared on a platinum wire electrode. With diphtheria-toxoid (D-Ag) as a model antigen and encapsulation of diphtheria antibody (D-Ab) in the composite architecture, this membrane could be used for reagentless electrochemical immunoassay. It displayed a porous and homogeneous composite architecture without the aggregation of the immobilized protein molecules. The formation of immunoconjugate by a simple one-step immunoreaction between D-Ag in sample solution and the immobilized D-Ab introduced the change in the potential. Under optimal conditions, the D-Ag analyte could be determined in the linear ranges from 10 to 800 ng ml⁻¹ with a relatively low detection limit of 2.3 ng ml⁻¹ at 3δ. The D-Ag immunosensor exhibited good precision, high sensitivity, acceptable stability, accuracy, and reproducibility. This composite membrane could be used efficiently for the entrapment of different biomarkers and clinical applications.     

Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer

The current study analyzed reverse phase protein arrays (RPPA) as a means to experimentally validate biomarkers in blood samples. One microliter samples of sera (n = 71), and plasma (n = 78) were serially diluted and printed on NC-coated slides. CA19-9 levels from RPPA results were compared with identical patient samples as measured by ELISA. There was a strong correlation between RPPA and ELISA (r = 0.87) as determined by scatter plots. Sample reproducibility of CA19-9 levels was excellent (interslide correlation r = 0.88; intraslide correlation r = 0.83). The ability of RPPA to accurately distinguish CA19-9 levels between cancer and noncancer samples were determined using receiver operating characteristic curves and compared with ELISA. The AUC for RPPA and ELISA was comparable (0.87 and 0.86, respectively). When the mean CA19-9 levels of normal samples was used as a cutoff for RPPA and compared with the standard clinical ELISA cutoff, comparable specificities (71% for both) were observed. Notably, RPPA samples normalized to albumin showed increased sensitivity compared to ELISA (90% vs. 75%). As RPPA is a high-throughput method that shows results comparable to that of ELISA, we propose that RPPA is a viable technique for rapid experimental screening and validation of candidate biomarkers in blood samples.     

Metabolomic analysis of cancer cachexia reveals distinct lipid and glucose alterations

Cancer cachexia remains a challenging clinical problem with complex pathophysiology and unreliable diagnostic tools. A blood test to detect this metabolic derangement would aid in early treatment of these patients. A ¹H NMR-based metabolomics approach was used to determine the unique metabolic fingerprint of cachexia and to search for biomarkers in serum samples taken from an established murine model of cancer cachexia. Male CD2F1 mice received a subcutaneous flank injection of C26 adenocarcinoma cells to induce experimental cancer-related cachexia. Two molecular markers of muscle atrophy, upregulation of the E3 ubiquitin ligase Muscle Ring Finger 1 (MuRF1) and aberrant glycosylation of β-dystroglycan (β-DG), were used to confirm muscle wasting in the tumor-bearing mice. Serum samples were collected for metabolomic analysis during the development of the cachexia: at baseline, when the tumor was palpable, and when the mice demonstrated cachexia. The unsupervised statistical analysis demonstrated a distinct metabolic profile with the onset of cachexia. The critical metabolic changes associated with cachexia included increased levels of very low density lipoprotein (VLDL) and low density lipoprotein (LDL), with decreased serum glucose levels. Regression analysis demonstrated a very high correlation of the presence of aberrant glycosylation of β-DG with the unique metabolic profile of cachexia. This study demonstrates for the first time that metabolomics has potential as a diagnostic tool in cancer cachexia, and in further elucidating simultaneous metabolic pathway alterations due to this syndrome. In addition, variations in VLDL and LDL deserve more investigation as surrogate serum biomarkers for cancer cachexia.     

Influence of ultraviolet-C on structure and function of <Emphasis Type="Italic">Synechococcus</Emphasis> sp. PCC 7942 photolyase

In this work, an over-expressed cyclobutane pyrimidine dimer (CPD) photolyase of Synechococcus sp. PCC 7942 was used to investigate UV-C (ultraviolet irradiation of C-region) influence on photoreactivation. In vivo photoreactivation experiments indicated that the survival rate decreased from 100 to 2.6% when the UV-C flux was increased from 1.1 to 68.5 μW/cm². It seemed that the photolyase was easily inactivated at UV-C intensities ≥25.5 μW/cm². Spectrometric analysis indicated that tertiary structure of the photolyase changed evidently when the UV-C fluxes were ≥25.5 μW/cm², while the secondary structure was almost unchanged even at 170 μW/cm². Band shift assay indicated that catalytic activity of the photolyase was impaired at fluxes ≥25.5 μW/cm², but no significant influence on DNA-binding activity was observed. These results suggest that photoreactivation is efficient at UV-C fluxes ≤25.5 μW/cm², but would be impaired by intense UV-C irradiation due to structure changes of the photolyase. Published in Russian in Biokhimiya, 2007, Vol. 72, No. 5, pp. 668–673.     

Comparison of <Emphasis Type="Italic">mecA</Emphasis> Polymerase Chain Reaction With Phenotypic Methods for the Detection of Methicillin-Resistant <Emphasis Type="Italic">Staphylococcus aureus</Emphasis>

In the present study, several conventional methods to detect methicillin-resistant Staphylococcus aureus (MRSA) were compared with polymerase chain reaction (PCR) detection of mecA gene–positive isolates. Cefoxitin E-test was also evaluated as a possible phenotypic method of MRSA detection. Oxacillin agar screen and PBP2′ latex agglutination methods were found to be more sensitive than oxacillin and cefoxitin disk-diffusion methods. Cefoxitin disk diffusion was found to be the most specific. A combination of oxacillin agar screening with cefoxitin disk diffusion, or oxacillin disk diffusion with PBP2′, improved sensitivity and specificity. Cefoxitin E-test with the current break points had low sensitivity and specificity (33.3% and 75%, respectively) for the detection of MRSA. However, changing the break points to ≤ 4 μg/ml and to ≥ 6 μg/ml for sensitive and resistant, respectively, greatly improved both. Changing the 30-μg cefoxitin disk-diffusion break points to ≤ 21 mm for resistant slightly improved sensitivity but had no effect on specificity. It was therefore concluded that the use of more than one screening method is necessary to detect all MRSA isolates in clinical settings.     

Definitions and Epidemiology of Candida Species not Susceptible to Echinocandins

Antifungal susceptibility testing of Candida against the echinocandin antifungal agents (anidulafungin [ANF], caspofungin [CSF], micafungin [MCF]) has been standardized by the Clinical and Laboratory Standards Institute (CLSI) Subcommittee on Antifungal Testing. The CLSI proposed a single set of clinical breakpoints (CBPs) for all three echinocandins and all species of Candida: susceptible, minimum inhibitory concentration (MIC) ≤ 2 μg/mL; nonsusceptible, MIC > 2 μg/mL. Subsequently, these CBPs have been shown to lack sensitivity in detecting strains of Candida with acquired resistance mechanisms associated with treatment failure. Studies using the CLSI method have defined wild-type (WT) MIC distributions and epidemiologic cutoff values (ECVs) for each echinocandin and the common species of Candida. The ECVs serve as a sensitive means of discriminating WT strains from those with acquired resistance mechanisms. WT MIC distributions revealed ECV ranges of 0.03 to 0.25 μg/mL for all major species except C. parapsilosis (1–4 μg/mL) and C. guilliermondii (4–16 μg/mL). These ECVs reliably differentiate WT strains of each species from non-WT strains containing fks mutations. These data, coupled with additional biochemical, clinical, pharmacokinetic, and pharmacodynamic considerations, have resulted in new CBPs of ≤0.25 μg/mL (susceptible), 0.5 μg/mL (intermediate), and ≥1 μg/mL (resistant) for ANF, CSF, and MCF for C. albicans, C. tropicalis, and C. krusei. For these agents and C. parapsilosis, the new CBPs are ≤2 μg/mL (susceptible), 4 μg/mL (intermediate), and ≥8 μg/mL (resistant). For C. glabrata, the CBPs for ANF and CSF are ≤0.12 μg/mL (susceptible), 0.25 μg/mL (intermediate), and ≥0.5 μg/mL (resistant), whereas those for MCF are ≤0.06 μg/mL, 0.12 μg/mL, and ≥0.25 μg/mL, respectively. Application of both ECVs and the lower species-specific CBPs for the echinocandins has proven useful in both resistance surveillance and clinical care and will serve as an important step in international harmonization of in vitro susceptibility testing of this important antifungal class.     

Comparison of phenotypic and molecular distances to predict heterosis and F1 performance in Ethiopian mustard (Brassica carinata A. Braun)

Predicting heterosis and F₁ performance from the parental generation could largely enhance the efficiency of breeding hybrid or synthetic cultivars. This study was undertaken to determine the relationship between parental distances estimated from phenotypic traits or molecular markers with heterosis, F₁ performance and general combining ability (GCA) in Ethiopian mustard (Brassica carinata). Nine inbred lines representing seven different geographic regions of Ethiopia were crossed in half-diallel. The nine parents along with their 36 F₁s were evaluated in a replicated field trail at three locations in Ethiopia. Distances among the parents were calculated from 14 phenotypic traits (Euclidean distance, ED) and 182 random amplified polymorphic DNA (RAPD) markers (Jaccard’s distances, JD), and correlated with heterosis, F₁ performance and GCA sum of parents (GCA_sum). The correlation between phenotypic and molecular distances was low (r=0.34, P≤0.05). Parents with low molecular distance also had low phenotypic distance, but parents with high molecular distance had either high, intermediate or low phenotypic distance. Phenotypic distance was highly significantly correlated with mid-parent heterosis (r=0.53), F₁ performance (r=0.61) and GCA (r=0.79) for seed yield. Phenotypic distance was also positively correlated with (1) heterosis, F₁ performance and GCA for plant height and seeds plant⁻¹, (2) heterosis for number of pods plant⁻¹, and (3) F₁ performance for 1,000 seed weight. Molecular distance was correlated with GCA_sum (r=0.36, P≤0.05) but not significantly with heterosis and F₁ performance for seed yield. For each parent a mean distance was calculated by averaging the distances to the eight other parents. Likewise, mean heterosis was estimated by averaging the heterosis obtained when each parent is crossed with the other eight. For seed yield, both mean ED and JD were significantly correlated with GCA (r=0.90, P≤0.01 for ED and r=0.68, P≤0.05 for JD) and mean heterosis (r=0.79, P≤0.05 for ED and r=0.77, P≤0.05 for JD). In conclusion, parental distances estimated from phenotypic traits better predicted heterosis, F₁ performance and GCA than distances estimated from RAPD markers. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Quantification of arbuscular mycorrhizal fungi activity by the glomalin concentration on hyphal traps

 Strips of horticultural film (16–32 cm²) were used to trap extraradical hyphae emanating from roots of sudangrass [Sorghum sudanense (Piper) Staph] enclosed in 40-μm mesh bags and colonized by Gigaspora rosea FL 224-1, Glomus intraradices EY 113/114, or Glomus caledonium UK 301-1. Strips of film were placed at opposite sides of 17–21 replicate sand culture pots for each isolate and were removed after 12–14 weeks of plant growth. To extract glomalin, a strip was cut into small pieces and submerged in 2 ml of 20 mM citrate, pH 7.0 and then autoclaved for 60 min. A quantitative enzyme-linked immunosorbent assay (ELISA) detected 0.005–0.04 μg glomalin in the volume of extract tested. The Bradford protein assay detected 1.25–5 μg of protein in the volume of extract tested. Both assays gave results ranging from 5–40 μg glomalin/cm² of film. Protein assay values were correlated with ELISA values (r=0.6091, P≤0.001, n=118). Analysis of variance indicated that isolates differed in Bradford protein values (P=0.001), but not ELISA values (P=0.154). Spatial variability of glomalin deposition ca. 7 cm from roots on opposite sides of pots was indicated by significant paired T tests (P<0.05) for protein values for each of the three isolates and ELISA for two isolates. These results indicate that hyphal traps, Bradford protein assay and ELISA are useful to assess hyphal activity over a growing season. Accepted: 11 October 1998