Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding

INTRODUCTION

Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent.

OBJECTIVE

To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA.

METHODOLOGY

Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification.

RESULTS

In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols.

CONCLUSION

Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue.

Pepino mosaic virus and Tomato torrado virus: two emerging viruses affecting tomato crops in the Mediterranean basin

The molecular biology, epidemiology, and evolutionary dynamics of Pepino mosaic virus (PepMV) are much better understood than those of Tomato torrado virus (ToTV). The earliest descriptions of PepMV suggest a recent jump from nontomato species (e.g., pepino; Solanum muricatum) to tomato (Solanum lycopersicum). Its stability in contaminated plant tissues, its transmission through seeds, and the global trade of tomato seeds and fruits may have facilitated the global spread of PepMV. Stability and seed transmission also probably account for the devastating epidemics caused by already-established PepMV strains, although additional contributing factors may include the efficient transmission of PepMV by contact and the often-inconspicuous symptoms in vegetative tomato tissues. The genetic variability of PepMV is likely to have promoted the first phase of emergence (i.e., the species jump) and it continues to play an important role as the virus becomes more pervasive, progressing from regional outbreaks to pandemics. In contrast, the long-term progression of ToTV outbreaks is not yet clear and this may reflect factors such as the limited accumulation of the virus in infected plants, which has been shown to be approximately two orders of magnitude less than PepMV. The efficient dispersion of ToTV may therefore depend on dense populations of its principal vectors, Bemisia tabaci and Trialeurodes vaporariorum, as has been proposed for the necrogenic satellite RNA of Cucumber mosaic virus.

Acanthosis nigricans as an indicator of insulin resistance in Chilean adult population

BACKGROUND

Insulin resistance (IR) is associated with a higher risk of multiple diseases and its early detection would allow to minimize the associated risk; the presence of acanthosis nigricans (AN) it's associated to the presence of IR.

OBJECTIVE

To evaluate the sensibility and specificity of AN to diagnose IR in a group of Chilean patients.

METHODS

We designed a cross-sectional study and it was included subjects that were attended at the Center for the Attention of Metabolic Diseases at the Faculty of Medicine, University of Chile. Sixty subjects (18-60 years age) were included. It was determined BMI and diagnosed AN and skin phototype; blood samples were taken and calculated the HOMA-IR. The normality of the variables where analyzed by Kolmogorov-Smirnov test. There were used χ² and the diagnostic concordance between AN and IR was determined using the Kappa index and Pearson's correlation. Sensibility, specificity, positive and negative predictive value were calculated and accepted p<0.05.

RESULTS

The IR diagnose was 67% and AN was 43%. The major proportion of subjects diagnosed as positive for IR were also positive for AN (84.6%). The sensibility of AN to find IR was an 84% and specificity was 100%. Positive and negative predictive values were 100% and 89% respectively. It was observed a positive association between BMI and HOMA-IR (r=0.674; r²=0.454; p<0.001).

CONCLUSION

To detect acanthosis nigricans in Chilean population may be effective for the early diagnose of insulin resistance and, therefore, reduce the associated cost of the late treatment of glucose metabolic disturbances.

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

Background

Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species.

The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL).

Results

We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.

Conclusion

Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most of these markers are located in the coding regions of genes involved in different physiological processes. The platform will also be useful for future mapping and diversity studies, and will be essential in order to accelerate the process of breeding new and better-adapted squash varieties.

[Quality indicators in an intensive care unit: a two-year healthcare-associated infection surveillance program]

OBJECTIVE

To estimate quality healthcare indicators in an intensive care unit (ICU).

METHODS

A prospective observational study was conducted on all patients referred to the medical ICU of Ramón y Cajal hospital (Madrid) for more than 48 hours, from January 1 2008 to December 31 2009.

RESULTS

A total of 503 patients were included, of whom 7.4% developed a healthcare-associated infection (HAI) attributable to their stay in the ICU. The median length of stay was 5 days. A ventilator-associated pneumonia (VAP) was observed in 1.9% of patients, with a VAP rate of 3.8 per 1,000 ventilator-days. A catheter-associated urinary tract infection (CAUTI) was found in 3.6% of the patients, with a CAUTI rate of 4.5 per 1,000 catheter-days. The cumulative incidence of central line-associated bloodstream infection (CLABSI) was 1.8%, with a CLABSI rate of 2.2 per 1,000 central line-days.

CONCLUSIONS

Our results are similar to those of other studies using the same methodology. An HAI surveillance system is a key factor for implementing a healthcare quality improvement system. The obtained indicators allow intra-comparison over time and with other similar hospitals, the monitoring of infection control measures, and thus an effective improvement in healthcare quality and patient safety.

Differential partitioning and speciation of Hg in wet FGD facilities of two Spanish PCC power plants

This paper evaluates the speciation and partitioning of mercury in two Spanish pulverised coal combustion power plants (PP1 and PP2), equipped with wet limestone-based flue gas desulphurisation facilities (FGD) operating with forced oxidation and re-circulation of FGD water streams. These plants are fed with coal (PP1) and coal/pet-coke blends (PP2) with different mercury contents. The behaviour, partitioning and speciation of Hg were found to be similar during the combustion processes but different in the FGD systems of the two power plants. A high proportion (86-88%) of Hg escaped the electrostatic precipitator in gaseous form, Hg2+ being the predominant mercury species (68-86%) to enter the FGD. At this point, a relatively high total Hg retention (72% and 65%) was achieved in the PP1 and PP2 (2007) FGD facilities respectively. However, during the second sampling campaign for PP2 (2008), the mercury removal achieved by the FGD was much lower (26%). Lab-scale tests point to liquid/gas ratio as the main parameter affecting oxidised mercury capture in the scrubber. The partitioning of the gaseous mercury reaching the FGD system in the wastes and by-products differed. In the low mercury input power plant (PP1) most of the mercury (67%) was associated with the FGD gypsum. Moreover in PP2 a significant proportion of the gaseous mercury reaching the FGD system remained in the aqueous phase (45%) in the 2007 sampling campaign while most of it escaped in 2008 (74%). This may be attributed to the scrubber operating conditions and the different composition and chemistry of the scrubber solution probably due to the use of an additive.

Intermediate dose of imatinib in combination with chemotherapy followed by allogeneic stem cell transplantation improves early outcome in paediatric Philadelphia chromosome-positive acute lymphoblastic leukaemia (ALL): results of the Spanish Cooperative Group SHOP studies ALL-94, ALL-99 and ALL-2005

Philadelphia-chromosome acute lymphoblastic leukaemia (Ph+ ALL) is a subgroup of ALL with very high risk of treatment failure. We report here the results of the Sociedad Española de Hematología y Oncología Pediátricas (SEHOP/SHOP) in paediatric Ph+ ALL treated with intermediate-dose imatinib concurrent with intensive chemotherapy. The toxicities and outcome of these patients were compared with historical controls not receiving imatinib. Patients with Ph+ ALL aged 1-18years were enrolled in three consecutive ALL/SHOP trials (SHOP-94/SHOP-99/SHOP-2005). In the SHOP-2005 trial, imatinib (260mg/m(2) per day) was given on day-15 of induction. Allogeneic haematopoietic stem-cell transplantation (HSCT) from a matched related or unrelated donor was scheduled in first complete remission (CR1). Forty-three patients were evaluable (22 boys, median age 6·8years, range, 1·2-15). Sixteen received imatinib whereas 27 received similar chemotherapy without imatinib. Seventeen of 27 and 15 of 16 patients in the non-imatinib and imatinib cohort, respectively, underwent HSCT in CR1. With a median follow-up of 109 and 39months for the non-imatinib and imatinib cohorts, the 3-year event-free survival (EFS) was 29·6% and 78·7%, respectively (P=0·01). These results show that, compared to historical controls, intermediate dose of imatinib given concomitantly with chemotherapy and followed by allogeneic HSCT markedly improved early EFS in paediatric Ph+ ALL.

Selection of reference genes for gene expression studies in zucchini (Cucurbita pepo) using qPCR

The zucchini (Cucurbita pepo) is an important food crop, the transcriptomics of which are a fundamental tool to accelerate the development of new varieties by breeders. However, the suitability of reference genes for data normalization in zucchini has not yet been studied. The aim of this study was to assess the suitability of 13 genes for their potential use as reference genes in quantitative real-time PCR. Assays were performed on 34 cDNA samples representing plants under different stresses and at different developmental stages. The application of geNorm and NormFinder software revealed that the use of a combination of UFP, EF-1A, RPL36aA, PP2A, and CAC genes for the different experimental sets was the best strategy for reliable normalization. In contrast, 18S rRNA and TUA were less stable and unsuitable for use as internal controls. These results provide the possibility to allow more accurate use of qPCR in this horticultural crop.

Bacteria-phage antagonistic coevolution in soil

Bacteria and their viruses (phages) undergo rapid coevolution in test tubes, but the relevance to natural environments is unclear. By using a "mark-recapture" approach, we showed rapid coevolution of bacteria and phages in a soil community. Unlike coevolution in vitro, which is characterized by increases in infectivity and resistance through time (arms race dynamics), coevolution in soil resulted in hosts more resistant to their contemporary than past and future parasites (fluctuating selection dynamics). Fluctuating selection dynamics, which can potentially continue indefinitely, can be explained by fitness costs constraining the evolution of high levels of resistance in soil. These results suggest that rapid coevolution between bacteria and phage is likely to play a key role in structuring natural microbial communities.

Origin, functional role, and clinical impact of Fanconi anemia FANCA mutations

Fanconi anemia is characterized by congenital abnormalities, bone marrow failure, and cancer predisposition. To investigate the origin, functional role, and clinical impact of FANCA mutations, we determined a FANCA mutational spectrum with 130 pathogenic alleles. Some of these mutations were further characterized for their distribution in populations, mode of emergence, or functional consequences at cellular and clinical level. The world most frequent FANCA mutation is not the result of a mutational "hot-spot" but results from worldwide dissemination of an ancestral Indo-European mutation. We provide molecular evidence that total absence of FANCA in humans does not reduce embryonic viability, as the observed frequency of mutation carriers in the Gypsy population equals the expected by Hardy-Weinberg equilibrium. We also prove that long distance Alu-Alu recombination can cause Fanconi anemia by originating large interstitial deletions involving FANCA and 2 adjacent genes. Finally, we show that all missense mutations studied lead to an altered FANCA protein that is unable to relocate to the nucleus and activate the FA/BRCA pathway. This may explain the observed lack of correlation between type of FANCA mutation and cellular phenotype or clinical severity in terms of age of onset of hematologic disease or number of malformations.

Development of expression vectors based on pepino mosaic virus

BACKGROUND

Plant viruses are useful expression vectors because they can mount systemic infections allowing large amounts of recombinant protein to be produced rapidly in differentiated plant tissues. Pepino mosaic virus (PepMV) (genus Potexvirus, family Flexiviridae), a widespread plant virus, is a promising candidate expression vector for plants because of its high level of accumulation in its hosts and the absence of severe infection symptoms. We report here the construction of a stable and efficient expression vector for plants based on PepMV.

RESULTS

Agroinfectious clones were produced from two different PepMV genotypes (European and Chilean), and these were able to initiate typical PepMV infections. We explored several strategies for vector development including coat protein (CP) replacement, duplication of the CP subgenomic promoter (SGP) and the creation of a fusion protein using the foot-and-mouth disease virus (FMDV) 2A catalytic peptide. We found that CP replacement vectors were unable to move systemically and that vectors with duplicated SGPs (even heterologous SGPs) suffered from significant transgene instability. The fusion protein incorporating the FMDV 2A catalytic peptide gave by far the best results, maintaining stability through serial passages and allowing the accumulation of GFP to 0.2-0.4 g per kg of leaf tissue. The possible use of PepMV as a virus-induced gene silencing vector to study gene function was also demonstrated. Protocols for the use of this vector are described.

CONCLUSIONS

A stable PepMV vector was generated by expressing the transgene as a CP fusion using the sequence encoding the foot-and-mouth disease virus (FMDV) 2A catalytic peptide to separate them. We have generated a novel tool for the expression of recombinant proteins in plants and for the functional analysis of virus and plant genes. Our experiments have also highlighted virus requirements for replication in single cells as well as intercellular and long-distance movement.

Chromosome fragility in patients with Fanconi anaemia: diagnostic implications and clinical impact

BACKGROUND

Fanconi anaemia (FA) is a rare syndrome characterized by bone marrow failure, malformations and cancer predisposition. Chromosome fragility induced by DNA interstrand crosslink (ICL)-inducing agents such as diepoxybutane (DEB) or mitomycin C (MMC) is the 'gold standard' test for the diagnosis of FA.

OBJECTIVE

To study the variability, the diagnostic implications and the clinical impact of chromosome fragility in FA.

METHODS

Data are presented from 198 DEB-induced chromosome fragility tests in patients with and without FA where information on genetic subtype, cell sensitivity to MMC and clinical data were available.

RESULTS

This large series allowed quantification of the variability and the level of overlap in ICL sensitivity among patients with FA and the normal population. A new chromosome fragility index is proposed that provides a cut-off diagnostic level to unambiguously distinguish patients with FA, including mosaics, from non-FA individuals. Spontaneous chromosome fragility and its correlation with DEB-induced fragility was also analysed, indicating that although both variables are correlated, 54% of patients with FA do not have spontaneous fragility. The data reveal a correlation between malformations and sensitivity to ICL-inducing agents. This correlation was also statistically significant when the analysis was restricted to patients from the FA-A complementation group. Finally, chromosome fragility does not correlate with the age of onset of haematological disease.

CONCLUSIONS

This study proposes a new chromosome fragility index and suggests that genome instability during embryo development may be related to malformations in FA, while DEB-induced chromosome breaks in T cells have no prognostic value for the haematological disease.

Kinetics of electro-oxidation of ammonia-N, nitrites and COD from a recirculating aquaculture saline water system using BDD anodes

The viability of the electro-oxidation technology provided with boron doped diamond (BDD) electrodes for the treatment and reuse of the seawater used in a Recirculating Aquaculture System (RAS) was evaluated in this work. The influence of the applied current density (5-50 A m(-2)) in the removal of Total Ammonia Nitrogen (TAN), nitrite and chemical oxygen demand (COD) was analyzed observing that complete TAN removal together with important reductions of the other considered contaminants could be achieved, thus meeting the requirements for reuse of seawater in RAS systems. TAN removal, mainly due to an indirect oxidation mechanism was described by a second order kinetics while COD and nitrite removal followed zero-th order kinetics. The values of the kinetic constants for the anodic oxidation of each compound were obtained as a function of the applied current density (k(TAN) = 7.86 × 10(-5) · exp(6.30 × 10(-2) J); kNO2 = 3.43 × 10(-2) J; k(COD) = 1.35 × 10(-2) J). The formation of free chlorine and oxidation by-products, i.e., trihalomethanes (THMs) was followed along the electro-oxidation process. Although a maximum concentration of 1.7 mg l(-1) of total trihalomethanes was detected an integrated process combining electrochemical oxidation in order to eliminate TAN, nitrite and COD and adsorption onto activated carbon to remove the residual chlorine and THMs is proposed, as an efficient alternative to treat and reuse the seawater in fish culture systems. Finally, the energy consumption of the treatment has been evaluated.

Catalytic wet air oxidation with Ni- and Fe-doped mixed oxides derived from hydrotalcites

Catalytic wet air oxidation of Basic Yellow 11 (BY11), a basic dye, was studied in a batch reactor. Layered double hydroxides with the hydrotalcite-like structure containing nickel or iron cations have been prepared by coprecipitation and subsequently calcined leading to Ni- and Fe-doped mixed oxides, respectively. Compared with the results in the wet air oxidation of BY11, these catalysts showed high activity for total organic carbon (TOC), toxicity and dye removal at 120 degrees C and 50 bars after 120 min. It has been demonstrated that the activity depended strongly on the presence of catalyst. The results show that catalysts containing nickel provide a higher extent of oxidation of the dye whereas the reaction carried out with the iron catalyst is faster. The Ni and Fe dispersion determined from the TPR results was higher for the catalysts with a lower Ni or Fe content and decreased for higher Ni or Fe contents. On the basis of activity and selectivity, the Ni containing catalyst with the medium (3%) Ni content was found to be the best catalyst. Finally, a relationship between metal content of the catalyst and reaction rate has been established.

[Transversal study on the prevalence of Metabolic Bone Disease (MBD) and Home Parenteral Nutrition (HPN) in Spain: data from NADYA group]

Patients with intestinal failure who receive HPN are at high risk of developing MBD. The origin of this bone alteration is multifactorial and depends greatly on the underlying disease for which the nutritional support is required. Data on the prevalence of this disease in our environment is lacking, so NADYA-SEMPE group has sponsored this transversal study with the aim of knowing the actual MBD prevalence.

MATERIAL AND METHODS

Retrospective data from 51 patients from 13 hospitals were collected. The questionnaire included demographic data as well as the most clinically relevant for MBD data. Laboratory data (calciuria, PTH, 25 -OH -vitamin D) and the results from the first and last bone densitometry were also registered.

RESULTS

Bone mineral density had only been assessed by densitometry in 21 patients at the moment HPN was started. Bone quality is already altered before HPN in a significant percentage of cases (52%). After a mean follow up of 6 years, this percentage increases up to 81%. Due to retrospective nature of the study and the low number of subjects included it has not been possible to determine the role that HPN plays in MBD etiology. Only 35% of patients have vitamin D levels above the recommended limits and the majority of them is not on specific supplementation.

CONCLUSIONS

HPN is associated with very high risk of MBD, therefore, management protocols that can lead to early detection of the problem as well as guiding for follow up and treatment of these patients are needed.