Performance of a novel melting curve-based qPCR assay for malaria parasites in routine clinical practice in non-endemic setting.

BACKGROUND: High-quality malaria diagnosis is essential for effective treatment and clinical disease management. Microscopy and rapid diagnostic tests are the conventional methods performed as first-line malaria diagnostics in non-endemic countries. However, these methods lack the characteristic to detect very low parasitaemia, and accurate identification of the Plasmodium species can be difficult. This study evaluated the performance of the MC004 melting curve-based qPCR for the diagnosis of malaria in routine clinical practice in non-endemic setting. METHODS AND RESULTS: Whole blood samples were collected from 304 patients with clinical suspicion of malaria and analysed by both the MC004 assay and conventional diagnostics. Two discrepancies were found between the MC004 assay and microscopy. Repeated microscopic analysis confirmed the qPCR results. Comparison of the parasitaemia of nineteen Plasmodium falciparum samples determined by both microscopy and qPCR showed the potential of the MC004 assay to estimate the parasite load of P. falciparum. Eight Plasmodium infected patients were followed after anti-malarial treatment by the MC004 assay and microscopy. The MC004 assay still detected Plasmodium DNA although no parasites were seen with microscopy in post-treatment samples. The rapid decline in Plasmodium DNA showed the potential for therapy-monitoring. CONCLUSION: Implementation of the MC004 assay in non-endemic clinical setting improved the diagnosis of malaria. The MC004 assay demonstrated superior Plasmodium species identification, the ability to indicate the Plasmodium parasite load, and can potentially detect submicroscopic Plasmodium infections.

Evaluation of a novel real-time PCR assay for the detection, identification and quantification of Plasmodium species causing malaria in humans.

BACKGROUND: The entry of PCR-based techniques into malaria diagnostics has improved the sensitivity and specificity of the detection of Plasmodium infections. It has been shown that humans are regularly infected by at least six different Plasmodium species. The MC004 real-time PCR assay for malaria diagnosis is a novel single-tube assay that has been developed for the purpose of simultaneously detecting all Plasmodium species known to infect humans, and discrimination between Plasmodium falciparum, Plasmodium vivax, Plasmodium malariae, Plasmodium ovale wallikeri, Plasmodium ovale curtisi, Plasmodium knowlesi (including differentiation of three strains) and Plasmodium cynomolgi (including differentiation of three strains). Detection and identification of Plasmodium species relies on molecular beacon probe-based melting curve analysis. In addition, this assay might be used to quantify the parasitaemia of at least P. falciparum by calculating the level of parasitaemia directly from the Cq-value. METHODS: The samples used in this study comprised reference samples, patient samples, and synthetic controls. The following analytical performance characteristics of the MC004 assay were determined: analytical specificity, limit of detection, the ability to detect mixed infections, and the potential to determine the level of parasitaemia of P. falciparum, including assessment of within-run and between-run precisions. RESULTS: No false positive or false negative results were observed. The limit of detection of P. falciparum was 1 × 10-3 IU/mL (WHO standard). Mixed infections with P. falciparum and non-falciparum species were correctly identified. A calibration curve could be established to quantify the parasitaemia of at least P. falciparum. The within-run and between-run precisions were less than 20% CV at the tested parasitaemia levels of 0.09%, 0.16%, 2.15% and 27.27%. CONCLUSION: Based upon the analytical performance characteristics that were determined, the MC004 assay showed performance suitable for use in clinical settings, as well as epidemiological studies.

Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures.

Higher plant species diverged extensively with regard to the moment (flowering time) and position (inflorescence architecture) at which flowers are formed. This seems largely caused by variation in the expression patterns of conserved genes that specify floral meristem identity (FMI), rather than changes in the encoded proteins. Here, we report a functional comparison of the promoters of homologous FMI genes from Arabidopsis, petunia, tomato and Antirrhinum. Analysis of promoter-reporter constructs in petunia and Arabidopsis, as well as complementation experiments, showed that the divergent expression of leafy (LFY) and the petunia homolog aberrant leaf and flower (ALF) results from alterations in the upstream regulatory network rather than cis-regulatory changes. The divergent expression of unusual floral organs (UFO) from Arabidopsis, and the petunia homolog double top (DOT), however, is caused by the loss or gain of cis-regulatory promoter elements, which respond to trans-acting factors that are expressed in similar patterns in both species. Introduction of pUFO:UFO causes no obvious defects in Arabidopsis, but in petunia it causes the precocious and ectopic formation of flowers. This provides an example of how a change in a cis-regulatory region can account for a change in the plant body plan.

Prevalence of potential underlying aetiology of macrocytic anaemia in Dutch general practice.

BACKGROUND: Macrocytic anaemia (MCV ≥ 100 fL) is a relatively common finding in general practice. However, literature on the prevalence of the different causes in this population is limited. The prevalence of macrocytic anaemia and its underlying aetiology were analysed in a general practice population. The potential effect of the different aetiology on survival was also evaluated. METHODS: Between the 1st of February 2007 and the 1st of February 2015, patients aged 50 years or older and presenting to their general practitioner with a newly diagnosed anaemia, were included in the study. Anaemia was defined as haemoglobin level below 13.7 g/dL in men and below 12.1 g/dL in women. A broad range of laboratory tests was performed for each patient. The causes of anaemia were consequently determined by two independent observers based on the laboratory results. RESULTS: Of the 3324 included patients, 249 (7.5 %) displayed a macrocytic anaemia and were subsequently analysed. An underlying explanation could be established in 204 patients (81.9 %) with 27 patients (13.2 %) displaying multiple causes. Classic aetiology (i.e. alcohol abuse, vitamin B12/folic acid deficiency, haemolysis and possible bone marrow disease) was found in 115 patients. Alternative causes (i.e. anaemia of chronic disease, iron deficiency, renal anaemia and other causes) were encountered in 101 patients. In addition, a notable finding was the median gamma GT of 277 U/L in patients diagnosed with alcohol abuse (N = 24, IQR 118.0-925.5) and 23 U/L in the remaining cohort (N = 138, IQR 14.0-61.0). The distribution of gamma GT values was statistically different (P < 0.001). Five year survival rates were determined for six categories of causes, ranging from 39.9 % (95 % CI 12.9-66.9) for renal anaemia to 76.2 % (95 % CI 49.4-103.0) for the category multiple causes. CONCLUSION: In addition to classic explanations for macrocytosis, alternative causes are frequently encountered in patients with macrocytic anaemia in general practice.

Testing for lactase non-persistence in a Dutch population: Genotyping versus the hydrogen breath test.

BACKGROUND: Lactose intolerance is defined as the presence of gastrointestinal symptoms, such as bloating, abdominal pain or diarrhoea, after consumption of lactose in individuals with lactose malabsorption. Most cases involve primary lactose intolerance, caused by a loss of activity of the enzyme lactase, needed for digestion of lactose. A traditional method of establishing lactose intolerance is the hydrogen breath test (HBT), accompanied by a questionnaire to document complaints experienced by the patient during the test. Due to knowledge on lactase-persistent alleles, DNA genotyping has become available for the diagnostic work-up for lactose intolerance. Both methods are currently in use. The aim of this study is to provide a definite diagnostic approach for patients suspected of lactose intolerance in a Dutch population. METHODS: In this retrospective, observational study, patients aged 15 years or older were included after presenting to their treating physician with symptoms suggestive of lactose intolerance. HBT, including a questionnaire to document complaints and DNA genotyping of LCT-13,910 C/T was performed for each patient as part of a routine diagnostic work-up. RESULTS: 1101 patients were included (29% men). Positive and negative predictive value, sensitivity and specificity of HBT versus DNA genotyping were 80% (CI 75-84), 97% (CI 96-98), 89% (CI 84-92) and 94% (92-96) respectively. The use of the questionnaire added little diagnostic value. CONCLUSIONS: In a population with a high prevalence of lactase-persistent alleles, we advise to exclude HBT from the diagnostic route for suspected lactose intolerance, and replace it with genotyping of lactase-persistent alleles.

The transferrin/log(ferritin) ratio: a new tool for the diagnosis of iron deficiency anemia.

BACKGROUND: Serum ferritin is the best single laboratory test to diagnose iron deficiency anemia (IDA). Ferritin levels <20 µg/L are highly specific for IDA, and ferritin levels >100 µg/L usually exclude IDA. However, ferritin concentrations between 20 and 100 µg/L are often inconclusive. The objective of this study was to improve the diagnosis of IDA when ferritin levels are inconclusive. METHODS: We evaluated the predictive performance of classic (ferritin, mean corpuscular volume, transferrin and serum iron) and modern [reticulocyte hemoglobin content, serum transferrin receptor and soluble transferrin receptor (sTfR)/log(ferr)] iron status parameters to diagnose IDA in 2084 anemic, non-hospitalized patients. The results were validated in an independent cohort of 274 anemic patients. RESULTS: In our study population, 29% (595 patients) of the patients had a ferritin level between 20 and 100 µg/L, hampering diagnosis of IDA. None of the classic or modern parameters was capable of completely separating the IDA population from the non-IDA population. However, using a new parameter, the transferrin/log(ferritin) ratio, the IDA and non-IDA populations can be completely separated. At a cut-off value of 1.70, the transferrin/log(ferritin) ratio indicates IDA in 29% of the patients with inconclusive ferritin levels. CONCLUSIONS: The transferrin/log(ferritin) ratio is a practical new tool that improves diagnosis of iron deficiency when ferritin levels are inconclusive.

DPYD*7 as a Predictor of Severe Fluoropyrimidine-Related Adverse Events.

PURPOSE: Around 20%-30% of patients treated with fluoropyrimidines develop severe treatment-related adverse events (AEs). These are mainly caused by deficiency of dihydropyrimidine dehydrogenase, its main metabolizing enzyme. The DPYD*7 variant allele contains a frameshift mutation that leads to absence of dihydropyrimidine dehydrogenase. Clinical studies on this variant in patients treated with fluoropyrimidines are lacking because of its low minor allelic frequency. However, the DPYD*7 minor allelic frequency is 56-times higher in the Dutch compared with the global population. This allowed us to evaluate fluoropyrimidine tolerability in DPYD*7 variant allele carriers. MATERIALS AND METHODS: Patients treated with standard-of-care fluoropyrimidine who were pretreatment DPYD genotyped for DPYD*2A, *13, 2846A>T, and 1236G>A single-nucleotide polymorphisms were included for analyses. Patients were additionally screened for the DPYD*7 allele (rs72549309, 295-298delTCAT). AEs were graded if they worsened from baseline, according to Common Terminology Criteria for Adverse Events version 5.0. AEs ≥ grade 3 were considered severe. RESULTS: From 3,748 patients, we found 13 patients carrying heterozygous DPYD*7. Relevant clinical data were available for 11 patients. All patients developed fluoropyrimidine-related AEs, of which five patients developed severe AEs (46%). From these five patients, three patients were started with 65% or 50% of standard dose, but apparently still developed severe toxicity. Because of severe AEs, three patients discontinued treatment prematurely (one patient already started with 50% of standard dose) and one patient who started with 50% of standard dose was further reduced to 35% of standard dose. CONCLUSION: In this study, the clinical consequences of carrying the DPYD*7 variant allele were confirmed as 46% of the patients developed severe AEs, even in the presence of initial dose reductions. This underlines the need for prospective studies investigating the required fluoropyrimidine dose for DPYD*7 carriers.

MYC-Positive Diffuse Large B-Cell Lymphoma in Leukemic Phase at Presentation: A Diagnostic and Therapeutic Challenge.

Diffuse large B-cell lymphoma (DLBCL) in leukemic phase at presentation is a rare condition, and it can be challenging to differentiate from acute leukemia or other types of non-Hodgkin lymphoma. To obtain an accurate diagnosis immunophenotyping and cytogenetic analyses should be performed. Herein, we report a 54-year-old woman who experienced loss of consciousness and fever. Laboratory test results revealed leukocytosis, anemia, thrombopenia and hypercalcemia. Morphology of blood smear revealed two abnormal cell populations. However a specific diagnosis could not be made. Immunophenotyping showed two different populations, which was consistent with non-Hodgkin lymphoma. A fluorescence in situ hybridization (FISH) showed MYC and BCL2 rearrangements. Finally a leukemic DLBCL was diagnosed and immediately treatment with rituximab cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) was started. Due to MYC-positivity, lenalidomide was added to the therapy regimen. After treatment the patient achieved complete remission without any clinical sequelae, which is still ongoing after 4 years. Lenalidomide is an oral immunomodulatory drug that downregulates MYC gene and is commonly used in patients with multiple myeloma. Moreover, it can also be a promising therapeutic option for patients with MYC-positivity DLBCL presenting in leukemic phase.

Inflorescence development in petunia: through the maze of botanical terminology.

Flowering plants have developed many ways to arrange their flowers. A flower-bearing branch or system of branches is called an inflorescence. The number of flowers that an inflorescence contains ranges from a single flower to endless flower-clusters. Over the past centuries, botanists have classified inflorescences based on their morphology, which has led to an unfortunate maze of complex botanical terminology. With the rise of molecular developmental biology, research has become increasingly focused on how inflorescences develop, rather than on their morphology. It is the decisions taken by groups of stem cells at the growing tips of shoots, called meristems, on when and where to produce a flower or a shoot that specify the course of inflorescence development. Modelling is a helpful aid to follow the consequences of these decisions for inflorescence development. The so-called transient model can produce the broad inflorescence types: cyme, raceme, and panicle, into which most inflorescences found in nature can be classified. The analysis of several inflorescence branching mutants has led to a solid understanding of cymose inflorescence development in petunia (Petunia hybrida). The cyme of petunia is a distinct body plan compared with the well-studied racemes of Arabidopsis and Antirrhinum, which provides an excellent opportunity to study evolutionary developmental biology (evo-devo) related questions. However, thus far, limited use has been made of this opportunity, which may, at least in part, be due to researchers getting lost in the terminology. Some general issues are discussed here, while focusing on inflorescence development in petunia.

cDNA microarray-based identification of genes and pathways associated with oxaliplatin resistance.

In order to identify genes whose expression is associated with resistance to the chemotherapeutic agent oxaliplatin, transcripts differentially expressed between an oxaliplatin sensitive and a stably resistant subline were compared in six independent replicates using Stanford cDNA microarrays for five cell lines. "Significance analysis of microarrays" (SAM) was used to identify genes whose expression was statistically significantly different in the sensitive versus resistant members of each cell line pair. The biochemical pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database were searched to identify those pathways in which the number of SAM-identified genes exceeded the number expected. This identified four pathways in which upregulated genes were significantly associated with resistance in two of the cell line pairs, and two pathways in which the association was found in three cell line pairs. The search also identified 12 pathways in which downregulated genes were associated with resistance in two cell line pairs and one pathway in which the association reached statistical significance in three cell line pairs. Pathways identified included the ribosome pathway, the Huntington's disease pathway that includes caspase 8, and the ATP synthesis pathways. Determination of the chromosomal location of each SAM-identified gene revealed several locales within which genes lay in close proximity, including three genes (APACD, IF-2, and REV1L) located on chromosome 2 that lie immediately adjacent to each other and were significantly upregulated in three of five cell line pairs. Biochemical pathway and chromosomal mapping of genes identified by SAM as differentially expressed in related cell line pairs points to mechanisms and chromosomal sites not previously suspected of association with the oxaliplatin-resistant phenotype.

Extreme elevation of serum angiotensin-converting enzyme (ACE) activity: always consider familial ACE hyperactivity.

Measurement of serum angiotensin-converting enzyme (ACE) activity can be helpful in the diagnosis and disease monitoring of sarcoidosis. Elevated serum ACE activity is found in 60-70% of sarcoidosis patients. Usually, the ACE activity is mildly increased (<3-fold the upper limit of the reference range) in sarcoidosis patients. Extremely elevated ACE activity is suggestive of the benign condition known as 'familial hyperactivity of ACE'. Familial hyperactivity of ACE is a relatively rare condition and can be confirmed by genetic testing. Considering a genetic cause of strongly elevated serum ACE activity is important to prevent possible overdiagnostics. Here, we highlight the factors that may complicate the interpretation of serum ACE activity measurements, and we present two cases that illustrate the importance of interdisciplinary consultation when extremely elevated serum ACE activity is measured.

Role of EVERGREEN in the development of the cymose petunia inflorescence.

Plants species diverge with regard to the time and place where they make flowers. Flowers can develop from apical meristems, lateral meristems, or both, resulting in three major inflorescence types known as racemes, cymes, and panicles, respectively. The mechanisms that determine a racemose architecture have been uncovered in Arabidopsis and Antirrhinum. To understand how cymes are specified, we studied mutations that alter the petunia inflorescence. Here we show that EVERGREEN (EVG) encodes a WOX homeodomain protein, which is exclusively expressed in incipient lateral inflorescence meristems (IMs), promoting their separation from the apical floral meristem (FM). This is essential for activation of DOUBLE TOP and specification of floral identity. Mutations that change the cymose petunia inflorescence into a solitary flower fully suppress the evg phenotype. Our data suggest a key role for EVG in the diversification of inflorescence architectures and reveal an unanticipated link between the proliferation and identity of meristems.