Relevance of Secondary Enrichment in the Detection of Salmonella spp. in Food Samples by qPCR According to DIN 10135.

BACKGROUND: When detecting Salmonella spp. in food samples, unlike with culture-based procedures where there are solid standards, PCR techniques are generally dominated by commercial solutions, often backed by the conformity of reference organizations, and based on rigorous validation studies. The few independent standards that exist are not subject to revision and improvement to the same extent as the manufacturer's methods. Moreover, since commercial networks do not promote them, they are implemented less in everyday practice. The German standard DIN 10135 is an example of this. In this method, before PCR detection, a primary enrichment (16-20 h) followed by a secondary selective enrichment of at least 6 h is needed. Nevertheless, it allows the possibility of only applying the first step if evidence of their correct operation is provided. OBJECTIVE: To evaluate how necessary is the secondary enrichment for DIN 10135 standard. METHODS: Short and complete enrichment steps were compared in the context of the evaluation of the limit of detection for 11 types of food. Additionally, a blind assay was performed with 75 food samples. RESULTS: The data show that a simple primary enrichment may be sufficient and that the second selective enrichment with the tested matrixes would not be strictly essential. The blind study obtained a 98.6% of trueness and precision of 100%. CONCLUSIONS: At least for the end consumer products, a secondary enrichment of 6 h is not necessary for all the products tested. HIGHLIGHTS: In the context of the DIN 10135 standard, the primary enrichment (16-20 h, 37 ± 1°C) can be enough for detecting Salmonella spp.

Duplicación 10q23q24, un rearreglo cromosómico asociado a anomalías congénitas múltiples

La duplicación en el brazo largo del cromosoma 10 (10q) es una cromosomopatía poco frecuente caracterizada clínicamente por retraso en el crecimiento prenatal y postnatal asociado a hipotonía, retraso en el desarrollo y hallazgos faciales específicos; que representa un reto diagnóstico en el ámbito clínico. Se presenta el caso de una recién nacida remitida para valoración multidisciplinara al Hospital Universitario San Ignacio en Bogotá, Colombia; en quien se documentó al momento del nacimiento fisura de labio y paladar, hipertelorismo, pabellón auricular con implantación baja e hipertrofia de labios menores. Se realizó resonancia magnética cerebral, la cual reportó pequeños quistes connatales adyacentes a las astas frontales de los ventrículos laterales, sin significado patológico, aparente malrotación de ambos hipocampos, hipertelorismo y queilopalatosquisis bilateral. El reporte del cariotipo con bandeo G confirmó complemento cromosómico 46,XX,dup(10)(q23q24); siendo el primer caso reportado en Colombia.

Duplication on the long arm of chromosome 10 (10q) is a rare chromosomopathy characterized clinically by delayed prenatal and postnatal growth associated with hypotonia, delayed development, and specific facial findings, which represents a diagnostic challenge in the clinical setting. We present the case of a newborn referred for multidisciplinary evaluation at the Hospital Universitario San Ignacio in Bogotá, Colombia; in whom cleft lip and palate, hypertelorism, low-set auricle and hypertrophy of the labia minora were documented at birth. Magnetic resonance imaging of the brain was performed, which reported small connatal cysts adjacent to the frontal horns of the lateral ventricles, without pathological significance, apparent malrotation of both hippocampi, hypertelorism, and bilateral cheilopalatoschisis. The G-band karyotype report confirmed chromosomal complement 46, XX, dup (10) (q23q24); being the first reported case in Colombia.

Aproximación diagnóstica de los errores innatos del metabolismo en la unidad de cuidado intensivo neonatal: acidosis metabólica, hiperamonemia e hipoglicemia / Diagnostic approach of inborn metabolism errors in the neonatal intensive care unit: metabolic acidosis, hyperammonemia and hypoglycemia

RESUMEN Los errores innatos del metabolismo del neonato son enfermedades que requieren una intervención temprana, dado que el manejo oportuno permite la prevención de secuelas severas o desenlaces fatales. Sin embargo, su diagnóstico se dificulta debido a las múltiples manifestaciones clínicas inespecíficas que lo acompañan y a las diversas alteraciones metabólicas que afectan la lectura de los estudios paraclínicos de rutina; sin embargo, una aproximación sistemática que tenga en cuenta las variaciones del metabolismo intermedio, interpretadas a través de pruebas básicas de laboratorio, permite alcanzar en la mayoría de los casos, un diagnóstico certero. La aproximación aquí propuesta se basa en la interpretación de tres estados metabólicos: acidosis metabólica, hiperamonemia e hipoglicemia, y su relación con los resultados de tests de laboratorio que están a la mano en la mayoría de unidades de neonatología. Se plantean diversas recomendaciones en relación a valores normales, flujogramas diagnósticos y recomendaciones sobre toma y conservación de muestras.

ABSTRACT Inborn metabolism errors of newborn babies are diseases that require early intervention since timely management allows the prevention of severe or fatal consequences. However, its diagnosis is difficult due to multiple non-specific clinical manifestations that accompany it and to various metabolic alterations that affect the reading of routine clinical laboratory studies. However, a systematic approach that takes into account the variations of the intermediate metabolism interpreted through basic laboratory tests allows reaching, in most cases, a correct diagnosis. The approach proposed here is based on the interpretation of three metabolic states: metabolic acidosis, hyperammonemia, and hypoglycemia and their relation to the results of laboratory tests that are available in most neonatal units. Various recommendations are presented regarding normal values, diagnostic flowcharts, and recommendations on taking and conservation of the samples.

The short-term response of yeast to potassium starvation.

Potassium is the major intracellular cation in most living cells, including yeasts. Although K(+) has been demonstrated to be necessary for diverse cellular functions, such as enzyme activation, additional, still uncharacterized cellular targets may exist. We show here that in Saccharomyces cerevisiae short-term potassium deprivation impacts in the mRNA level of over one thousand genes. Lack of potassium drastically alters sulfur metabolism (mainly Met and Cys metabolism), triggers an oxidative stress response and activates the retrograde pathway, possibly due to the ammonium accumulation that occurs through the Trk1 potassium transporter. We also observe a remarkable halt in the expression of genes required for ribosome biogenesis and translation, a decrease in expression of diverse components (cyclins, protein kinases) required for progression through the cell cycle and a blockage in septins assembly. Only specific subsets of these changes were observed in a strain deleted for the TRK1 and TRK2 genes growing in the presence of sufficient potassium (50 mM). Therefore, a shortage of potassium in the environment triggers an acute transcriptional response, which covers different aspects of the cell biology so far unexplored, and whose investigation will likely reveal novel functional roles for this cation.

Potassium starvation in yeast: mechanisms of homeostasis revealed by mathematical modeling.

The intrinsic ability of cells to adapt to a wide range of environmental conditions is a fundamental process required for survival. Potassium is the most abundant cation in living cells and is required for essential cellular processes, including the regulation of cell volume, pH and protein synthesis. Yeast cells can grow from low micromolar to molar potassium concentrations and utilize sophisticated control mechanisms to keep the internal potassium concentration in a viable range. We developed a mathematical model for Saccharomyces cerevisiae to explore the complex interplay between biophysical forces and molecular regulation facilitating potassium homeostasis. By using a novel inference method ("the reverse tracking algorithm") we predicted and then verified experimentally that the main regulators under conditions of potassium starvation are proton fluxes responding to changes of potassium concentrations. In contrast to the prevailing view, we show that regulation of the main potassium transport systems (Trk1,2 and Nha1) in the plasma membrane is not sufficient to achieve homeostasis.

Modulation of yeast alkaline cation tolerance by Ypi1 requires calcineurin.

Ypi1 was discovered as an essential protein able to act as a regulatory subunit of the Saccharomyces cerevisiae type 1 protein phosphatase Glc7 and play a key role in mitosis. We show here that partial depletion of Ypi1 causes lithium sensitivity and that high levels of this protein confer a lithium-tolerant phenotype to yeast cells. Remarkably, this phenotype was independent of the role of Ypi1 as a Glc7 regulatory subunit. Lithium tolerance in cells overexpressing Ypi1 was caused by a combination of increased efflux of lithium, mediated by augmented expression of the alkaline cation ATPase ENA1, and decreased lithium influx through the Trk1,2 high-affinity potassium transporters. Deletion of CNB1, encoding the regulatory subunit of the calcineurin phosphatase, blocked Ypi1-induced expression of ENA1, normalized Li(+) fluxes, and abolished the Li(+) hypertolerant phenotype of Ypi1-overexpressing cells. These results point to a complex role of Ypi1 on the regulation of cation homeostasis, largely mediated by the calcineurin phosphatase.

A genomewide screen for tolerance to cationic drugs reveals genes important for potassium homeostasis in Saccharomyces cerevisiae.

Potassium homeostasis is crucial for living cells. In the yeast Saccharomyces cerevisiae, the uptake of potassium is driven by the electrochemical gradient generated by the Pma1 H(+)-ATPase, and this process represents a major consumer of the gradient. We considered that any mutation resulting in an alteration of the electrochemical gradient could give rise to anomalous sensitivity to any cationic drug independently of its toxicity mechanism. Here, we describe a genomewide screen for mutants that present altered tolerance to hygromycin B, spermine, and tetramethylammonium. Two hundred twenty-six mutant strains displayed altered tolerance to all three drugs (202 hypersensitive and 24 hypertolerant), and more than 50% presented a strong or moderate growth defect at a limiting potassium concentration (1 mM). Functional groups such as protein kinases and phosphatases, intracellular trafficking, transcription, or cell cycle and DNA processing were enriched. Essentially, our screen has identified a substantial number of genes that were not previously described to play a direct or indirect role in potassium homeostasis. A subset of 27 representative mutants were selected and subjected to diverse biochemical tests that, in some cases, allowed us to postulate the basis for the observed phenotypes.

Lack of DNA helicase Pif1 disrupts zinc and iron homoeostasis in yeast.

The Saccharomyces cerevisiae gene PIF1 encodes a conserved eukaryotic DNA helicase required for both mitochondrial and nuclear DNA integrity. Our previous work revealed that a pif1Δ strain is tolerant to zinc overload. In the present study we demonstrate that this effect is independent of the Pif1 helicase activity and is only observed when the protein is absent from the mitochondria. pif1Δ cells accumulate abnormal amounts of mitochondrial zinc and iron. Transcriptional profiling reveals that pif1Δ cells under standard growth conditions overexpress aconitase-related genes. When exposed to zinc, pif1Δ cells show lower induction of genes encoding iron (siderophores) transporters and higher expression of genes related to oxidative stress responses than wild-type cells. Coincidently, pif1Δ mutants are less prone to zinc-induced oxidative stress and display a higher reduced/oxidized glutathione ratio. Strikingly, although pif1Δ cells contain normal amounts of the Aco1 (yeast aconitase) protein, they completely lack aconitase activity. Loss of Aco1 activity is also observed when the cell expresses a non-mitochondrially targeted form of Pif1. We postulate that lack of Pif1 forces aconitase to play its DNA protective role as a nucleoid protein and that this triggers a domino effect on iron homoeostasis resulting in increased zinc tolerance.

Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects yeast performance in both potassium-sufficient and potassium-limiting conditions.

A new YNB medium containing very low concentrations of alkali metal cations has been developed to carry out experiments to study potassium homoeostasis. Physiological characterization of Saccharomyces cerevisiae BY4741 strain and the corresponding mutant lacking the main potassium uptake systems (trk1 trk2) under potassium nonlimiting and limiting concentrations was performed, and novel important differences between both strains were found. At nonlimiting concentrations of KCl, the two strains had a comparable cell size and potassium content. Nevertheless, mutants were hyperpolarized, had lower pH and extruded fewer protons compared with the BY4741 strain. Upon transfer to K(+)-limiting conditions, cells of both strains became hyperpolarized and their cell volume and K(+) content diminished; however, the decrease was more relevant in BY4741. In low potassium, trk1 trk2 cells were not able to accomplish the cell cycle to the same extent as in BY4741. Moreover, K(+) limitation triggered a high-affinity K(+)/Rb(+) uptake process only in BY4741, with the highest affinity being reached as soon as 30 min after transfer to potassium-limiting conditions. By establishing basic cellular parameters under standard growth conditions, this work aims to establish a basis for the investigation of potassium homoeostasis at the system level.

Ref2, a regulatory subunit of the yeast protein phosphatase 1, is a novel component of cation homoeostasis.

Maintenance of cation homoeostasis is a key process for any living organism. Specific mutations in Glc7, the essential catalytic subunit of yeast protein phosphatase 1, result in salt and alkaline pH sensitivity, suggesting a role for this protein in cation homoeostasis. We screened a collection of Glc7 regulatory subunit mutants for altered tolerance to diverse cations (sodium, lithium and calcium) and alkaline pH. Among 18 candidates, only deletion of REF2 (RNA end formation 2) yielded increased sensitivity to these conditions, as well as to diverse organic toxic cations. The Ref2F374A mutation, which renders it unable to bind Glc7, did not rescue the salt-related phenotypes of the ref2 strain, suggesting that Ref2 function in cation homoeostasis is mediated by Glc7. The ref2 deletion mutant displays a marked decrease in lithium efflux, which can be explained by the inability of these cells to fully induce the Na+-ATPase ENA1 gene. The effect of lack of Ref2 is additive to that of blockage of the calcineurin pathway and might disrupt multiple mechanisms controlling ENA1 expression. ref2 cells display a striking defect in vacuolar morphogenesis, which probably accounts for the increased calcium levels observed under standard growth conditions and the strong calcium sensitivity of this mutant. Remarkably, the evidence collected indicates that the role of Ref2 in cation homoeostasis may be unrelated to its previously identified function in the formation of mRNA via the APT (for associated with Pta1) complex.

A peroxisomal glutathione transferase of Saccharomyces cerevisiae is functionally related to sulfur amino acid metabolism.

Saccharomyces cerevisiae cells contain three omega-class glutathione transferases with glutaredoxin activity (Gto1, Gto2, and Gto3), in addition to two glutathione transferases (Gtt1 and Gtt2) not classifiable into standard classes. Gto1 is located at the peroxisomes, where it is targeted through a PTS1-type sequence, whereas Gto2 and Gto3 are in the cytosol. Among the GTO genes, GTO2 shows the strongest induction of expression by agents such as diamide, 1-chloro-2,4-dinitrobenzene, tert-butyl hydroperoxide or cadmium, in a manner that is dependent on transcriptional factors Yap1 and/or Msn2/4. Diamide and 1-chloro-2,4-dinitrobenzene (causing depletion of reduced glutathione) also induce expression of GTO1 over basal levels. Phenotypic analyses with single and multiple mutants in the S. cerevisiae glutathione transferase genes show that, in the absence of Gto1 and the two Gtt proteins, cells display increased sensitivity to cadmium. A gto1-null mutant also shows growth defects on oleic acid-based medium, which is indicative of abnormal peroxisomal functions, and altered expression of genes related to sulfur amino acid metabolism. As a consequence, growth of the gto1 mutant is delayed in growth medium without lysine, serine, or threonine, and the mutant cells have low levels of reduced glutathione. The role of Gto1 at the S. cerevisiae peroxisomes could be related to the redox regulation of the Str3 cystathionine beta-lyase protein. This protein is also located at the peroxisomes in S. cerevisiae, where it is involved in transulfuration of cysteine into homocysteine, and requires a conserved cysteine residue for its biological activity.

Saccharomyces cerevisiae cells have three Omega class glutathione S-transferases acting as 1-Cys thiol transferases.

The Saccharomyces cerevisiae genome encodes three proteins that display similarities with human GSTOs (Omega class glutathione S-transferases) hGSTO1-1 and hGSTO2-2. The three yeast proteins have been named Gto1, Gto2 and Gto3, and their purified recombinant forms are active as thiol transferases (glutaredoxins) against HED (beta-hydroxyethyl disulphide), as dehydroascorbate reductases and as dimethylarsinic acid reductases, while they are not active against the standard GST substrate CDNB (1-chloro-2,4-dinitrobenzene). Their glutaredoxin activity is also detectable in yeast cell extracts. The enzyme activity characteristics of the Gto proteins contrast with those of another yeast GST, Gtt1. The latter is active against CDNB and also displays glutathione peroxidase activity against organic hydroperoxides such as cumene hydroperoxide, but is not active as a thiol transferase. Analysis of point mutants derived from wild-type Gto2 indicates that, among the three cysteine residues of the molecule, only the residue at position 46 is required for the glutaredoxin activity. This indicates that the thiol transferase acts through a monothiol mechanism. Replacing the active site of the yeast monothiol glutaredoxin Grx5 with the proposed Gto2 active site containing Cys46 allows Grx5 to retain some activity against HED. Therefore the residues adjacent to the respective active cysteine residues in Gto2 and Grx5 are important determinants for the thiol transferase activity against small disulphide-containing molecules.