Identification of stable QTLs for vegetative and reproductive traits in the microvine (Vitis vinifera L.) using the 18 K Infinium chip

BACKGROUND

The increasing temperature associated with climate change impacts grapevine phenology and development with critical effects on grape yield and composition. Plant breeding has the potential to deliver new cultivars with stable yield and quality under warmer climate conditions, but this requires the identification of stable genetic determinants. This study tested the potentialities of the microvine to boost genetics in grapevine. A mapping population of 129 microvines derived from Picovine x Ugni Blanc flb, was genotyped with the Illumina® 18 K SNP (Single Nucleotide Polymorphism) chip. Forty-three vegetative and reproductive traits were phenotyped outdoors over four cropping cycles, and a subset of 22 traits over two cropping cycles in growth rooms with two contrasted temperatures, in order to map stable QTLs (Quantitative Trait Loci).

RESULTS

Ten stable QTLs for berry development and quality or leaf area were identified on the parental maps. A new major QTL explaining up to 44 % of total variance of berry weight was identified on chromosome 7 in Ugni Blanc flb, and co-localized with QTLs for seed number (up to 76 % total variance), major berry acids at green lag phase (up to 35 %), and other yield components (up to 25 %). In addition, a minor QTL for leaf area was found on chromosome 4 of the same parent. In contrast, only minor QTLs for berry acidity and leaf area could be found as moderately stable in Picovine. None of the transporters recently identified as mutated in low acidity apples or Cucurbits were included in the several hundreds of candidate genes underlying the above berry QTLs, which could be reduced to a few dozen candidate genes when a priori pertinent biological functions and organ specific expression were considered.

CONCLUSIONS

This study combining the use of microvine and a high throughput genotyping technology was innovative for grapevine genetics. It allowed the identification of 10 stable QTLs, including the first berry acidity QTLs reported so far in a Vitis vinifera intra-specific cross. Robustness of a set of QTLs was assessed with respect to temperature variation.

Bone mineral density in patients with symptoms suggestive of spondyloarthritis

Patients with axial spondyloarthritis (axSpA) have an increased risk of osteoporosis related to inflammation. We evaluate the performance of low bone mineral density (BMD) in diagnosis of axSpA for patients with symptoms suggestive of the disease. A low BMD (T ≤ -2) could be an additional tool for the diagnosis of axSpA.

INTRODUCTION

Diagnosis of axial spondyloarthritis (axSpA) can be challenging, especially in the absence of radiographic abnormalities. Patients with axSpA have an increased risk of osteoporosis related to inflammation. This study evaluated the performance of low bone mineral density (BMD) in diagnosis of axSpA for patients with symptoms suggestive of the disease.

METHODS

Medical files of patients that visited a tertiary centre for symptoms suggestive of axSpA were reviewed. Two hundred and sixty-seven patients were classified in confirmed axSpA or unconfirmed axSpA according to the diagnosis of a senior rheumatologist. BMD measurements results and percentage of patients with a low BMD (T ≤ -2) at either spine or hip were compared between the two groups. Diagnostic performances of low BMD (specificity, sensitivity, positive, negative predictive values and positive likelihood ratio (LR+)) were assessed.

RESULTS

Compared to patients with unconfirmed axSpA (n = 74), patients with confirmed axSpA (n = 193) had similar age, were more frequently male, with positive HLA B27, higher disease duration and higher C-reactive protein (CRP). Low BMD was more frequent at spine and hip, in patients with confirmed (40.3%) than unconfirmed axSpA (24.6%, p = 0.021). The LR+ of low BMD for an axSpA diagnosis was 2.60 and 3.12 at the spine and hip. In the subgroup of patients without any radiographic abnormalities (n = 128), the LR+ of low BMD for an axSpA diagnosis was 2.90 and 2.54 at the spine and hip.

CONCLUSION

In patients with symptoms suggestive of axSpA, a low BMD (T ≤ -2) could be an additional tool for the diagnosis of axSpA.

Ontology-guided distortion control for robust-lossless database watermarking: application to inpatient hospital stay records

In this paper, we propose a new semantic distortion control method for database watermarking. It is based on the identification of the semantic links that exist in-between attribute's values in tuples by means of an ontology. Such a database distortion control provides the capability for any watermarking scheme to avoid incoherent records and consequently ensures: i) the normal interpretation of watermarked data, i.e. introducing a watermark semantically imperceptible; ii) prevent the identification by an attacker of watermarked tuples. The solution we present herein successfully combines this semantic distortion control method with a robust lossless watermarking scheme. Experimental results conducted on a medical database of more than one half million of inpatient hospital stay records also show a non-negligible gain of performance in terms of robustness and database distortion.

162 CAN CHLAMYDIA ABORTUS BE TRANSMITTED BY EMBRYO TRANSFER IN GOATS?

Chlamydia abortus is a gram-negative obligate intracellular bacterium. Its lifecycle includes a resistant infectious form and a metabolically active non-infectious form. Chlamydia abortus infection results in abortion in goats; in nonpregnant animals the infection is usually subclinical. Chlamydia abortus presents a major zoonotic risk for pregnant women. The aim of this study was to investigate whether the embryonic zona pellucida (ZP) protects early embryo cells from infection and to test the efficacy of the washing protocol recommended by the IETS for bovine embryos. The study was performed in triple replicate: 14 donor goats, certified negative by ELISA and PCR to C. abortus, were synchronized, superovulated, and subsequently inseminated by males controlled negative for C. abortus. Fifty-two ZP-intact embryos (8–16 cells) were collected 4 days later, by laparotomy. The embryos were randomly divided into 12 batches. Nine batches of 5 embryos were incubated in a medium containing 4 × 107 Chlamydia mL–1, AB7 strain. After incubation for 18 h at 37°C in an atmosphere of 5% CO2, the embryos were washed in batches in 10 successive baths of PBS and 5% FCS solution in accordance with IETS guidelines for bovine embryos. In parallel, 3 batches of ZP-intact embryos (2, 2, and 3 embryos in the first, second, and third batches, respectively) were used as controls by being subjected to similar procedures, but without exposure to C. abortus. The 10 wash baths were collected separately and centrifuged for 1 h at 13 000 × g. The washed embryos and the pellets of the 10 centrifuged wash baths were frozen at –20°C before examination for evidence of C. abortus using RT-PCR. Chlamydia abortus DNA was found in all batches of infected ZP-intact embryos (9/9) after 10 successive washes. It was also detected in the tenth wash fluid for 4 batches (4/9) of infected embryos. As expected, none of the embryos or their washing fluids in the control batches were DNA positive. These results demonstrate that C. abortus adheres to and/or penetrates the ZP of in vivo caprine embryos after in vitro infection, and that the standard washing protocol recommended by the IETS for bovine embryos failed to remove it. The persistence of these bacteria after washing makes the embryo a potential means of transmission of the bacterium during embryo transfer from infected donor goat to healthy recipients and/or their offspring. Further studies are required to investigate whether enzymatic and/or antibiotic treatment of infected caprine embryos can eliminate C. abortus from the ZP.

The importance of intraoperative transesophageal echocardiography in the surgical decision in cardiac surgery

OBJECTIVE

To determine the importance of intraoperative transesophageal echocardiography (IOTEE) in the surgical decision in patients undergoing cardiac surgery.

PATIENTS AND METHOD

Prospective observational study of patients undergoing cardiac surgery from January 2009 to May 2012, which was monitored with IOTEE by the anesthesiologist in charge. The data collected were: 1) type of surgery; 2) preoperative echocardiographic diagnosis (baseline ECHO); 3) echocardiographic diagnosis before entering cardiopulmonary bypass (CPB) (pre-CPB IOTEE); 4) any differences between the baseline ECHO and the pre-CPB IOTEE (new pre-CPB finding) and whether these differences modified the planned surgery, and 5) echocardiographic diagnosis after disconnection of CPB (unexpected post-CPB finding) and whether these post-CPB echocardiographic findings led to reinstating it. The software program SPSS(®) was used for data analysis.

RESULTS

The total number of patients studied was 1,273. Monitoring with IOTEE showed "new pre-CPB" findings in 98 patients (7.7%), and 43.8% of these led to a change in the scheduled surgery. Of these findings, the most frequent were abnormalities of the mitral valve that had not been diagnosed, and which led to a replacement or repair that had not been scheduled. The incidence of "unexpected post-CPB findings" was 6.2% (79 patients), and 46.8% of those required reinstating the CPB and modifying the surgery performed. The failed valve repairs and dysfunctional valve prostheses were the main causes that led to re-entry into CPB. In the remaining 42 patients, with "unexpected post-CPB findings", there were no changes in the surgical procedure as the echocardiographic findings were not considered to be significant enough to re-establish CPB and revise or change the surgical procedure.

CONCLUSION

Intraoperative monitoring with IOTEE by the anesthesiologist during surgery provides important information before and after the CPB that resulted in modifying surgical management.

Burden of proximal humerus fractures in the French National Hospital Database

OBJECTIVE

To describe the characteristics of patients hospitalized for osteoporotic proximal humerus fracture in 2009 in France, in-patient mortality, and further hospitalizations for hip fracture.

METHODS

Data were extracted from the French Hospital National Database. We selected patients aged 40 years and over hospitalized for proximal humerus fracture in 2009, without cancer. Based on their unique identification number, we described the next hospitalizations occurring in 2009-2011 whatever the causes. Incidence, in-patient mortality, and hospital costs were calculated.

RESULTS

We numbered 10,874 patients (77% of women, mean age 72.5 years). The incidence per million was 477 and 163 in women and men, respectively. This incidence increased with age and was higher in women (i.e. 1374 and 320 in women and men aged over 74 years, respectively). Surgical treatment was applied in 56% of patients; median hospital stay was 5 days. Rehabilitation unit was necessary in 26% of cases. In-patient mortality was 1.1%. The overall hospital costs was €34 millions. Rehospitalizations occurred for 61% of the patients and had more co-morbidities than others. Near 8% of the rehospitalized patients were for hip fractures occurring in a median of 353 days after hospitalization for proximal humerus fracture. The hospital costs for these rehospitalizations was €52 millions.

CONCLUSION

Proximal humerus fractures incidence increases with aging, especially in women. These fractures are associated with a significant in-patient mortality and health care resources utilization. Patients with such fracture must receive high priority for optimal post fracture treatment.

Both sunitinib and sorafenib are effective treatments for pheochromocytoma in a xenograft model

Pheochromocytomas and paragangliomas are rare neuroendocrine tumors which develop from chromaffin cells of the adrenal medulla and extra-adrenal sites, leading to excess catecholamine release and hypertension. Many of the tumors are characterized by a high vascularity, suggesting the possible implementation of anti-angiogenic therapies for patients. Here, the efficacy of the tyrosine kinase inhibitors sunitinib and sorafenib was investigated in vivo and in vitro. Oral treatment with either sunitinib or sorafenib (40mg/kg/day) for 14days induced a marked reduction in the volume and weight of PC12 pheochromocytoma cell tumor xenografts in mice. Assessment of tumoral neo-angiogenesis, assessed by morphometric analysis of the vascular network after CD31 immunolabeling, showed that both sunitinib and sorafenib reduced the microvessel area (-85% and -80%, respectively) and length (-80% and -78%, respectively) in treated compared to control tumors. In addition, the number of vessel nodes was significantly lower in treated tumors (-95% and -84%, respectively). Furthermore, cleaved caspase 3 immunolabeling revealed a marked increase in the number of apoptotic cells in tumors from treated animals. Sunitinib and sorafenib could exert a direct effect on PC12 cell viability in vitro. While sunitinib induced a rapid (4h) and pronounced (5-fold) increase in caspase-3/7-dependent apoptosis, sorafenib seems to exert its cytotoxic activity through a different mechanism. Altogether, our data demonstrate that sunitinib and sorafenib have the ability to impair pheochromocytoma development by inhibiting angiogenesis and reducing tumor cell viability. These results strongly suggest that both sunitinib and sorafenib could represent valuable therapeutic tools for pheochromocytoma.

Ketamine alters cortical integration of GABAergic interneurons and induces long-term sex-dependent impairments in transgenic Gad67-GFP mice

Ketamine, a non-competitive N-methyl-D-aspartate (NMDA) antagonist, widely used as an anesthetic in neonatal pediatrics, is also an illicit drug named Super K or KitKat consumed by teens and young adults. In the immature brain, despite several studies indicating that NMDA antagonists are neuroprotective against excitotoxic injuries, there is more and more evidence indicating that these molecules exert a deleterious effect by suppressing a trophic function of glutamate. In the present study, we show using Gad67-GFP mice that prenatal exposure to ketamine during a time-window in which GABAergic precursors are migrating results in (i) strong apoptotic death in the ganglionic eminences and along the migratory routes of GABAergic interneurons; (ii) long-term deficits in interneuron density, dendrite numbers and spine morphology; (iii) a sex-dependent deregulation of γ-aminobutyric acid (GABA) levels and GABA transporter expression; (iv) sex-dependent changes in the response to glutamate-induced calcium mobilization; and (v) the long-term sex-dependent behavioral impairment of locomotor activity. In conclusion, using a preclinical approach, the present study shows that ketamine exposure during cortical maturation durably affects the integration of GABAergic interneurons by reducing their survival and differentiation. The resulting molecular, morphological and functional modifications are associated with sex-specific behavioral deficits in adults. In light of the present data, it appears that in humans, ketamine could be deleterious for the development of the brain of preterm neonates and fetuses of addicted pregnant women.

Denosumab significantly increases bone mineral density and reduces bone turnover compared with monthly oral ibandronate and risedronate in postmenopausal women who remained at higher risk for fracture despite previous suboptimal treatment with an oral bisphosphonate

Managing osteoporotic patients suboptimally adherent to bisphosphonates (BPs) is difficult. Such patients who remained at higher risk for fracture (≥1 risk factor) were transitioned to denosumab or a monthly oral BP. Denosumab-treated subjects had significantly greater increases in bone mineral density and decreases in bone turnover in this 12-month study.

INTRODUCTION

A clinical need exists to manage patients who are suboptimally adherent to oral BPs and remain at higher risk for fracture. Here, we compare the effects on bone mineral density (BMD) and bone turnover of transitioning such patients to denosumab or monthly oral BP (ibandronate or risedronate).

METHODS

In two previous multicenter, open-label studies, postmenopausal women ≥55 years previously treated with, though suboptimally adherent to, a daily or weekly BP were randomized to denosumab 60 mg subcutaneously every 6 months (N = 852) or oral BP 150 mg monthly (N = 851) for 12 months. In this combined post-hoc analysis, a subset of higher risk subjects was identified, and the percentage changes from baseline in BMD and serum C-telopeptide of type I collagen (sCTX-1) were assessed.

RESULTS

In the overall population, denosumab was associated with greater gains in BMD at 12 months than monthly oral BP at the total hip, femoral neck, and lumbar spine (p < 0.0001 for all). In higher risk subjects, denosumab led to greater gains in BMD than oral BPs at the total hip (2.2 vs 0.8 %), femoral neck (1.8 vs 0.3 %), and lumbar spine (3.7 vs 1.4 %) (p < 0.0001 for all). Denosumab also led to greater decreases in sCTX-1 in the overall population and higher risk subjects at months 1 and 6 (p < 0.0001 for both). Adverse events and serious adverse events were generally similar between treatment groups.

CONCLUSIONS

Transitioning to denosumab was well tolerated and more effective in increasing BMD and reducing bone turnover than cycling to a monthly oral BP treatment in subjects who remained at higher fracture risk despite suboptimal BP treatment.

Can we continue to neglect genomic variation in introgression rates when inferring the history of speciation? A case study in a Mytilus hybrid zone

The use of molecular data to reconstruct the history of divergence and gene flow between populations of closely related taxa represents a challenging problem. It has been proposed that the long-standing debate about the geography of speciation can be resolved by comparing the likelihoods of a model of isolation with migration and a model of secondary contact. However, data are commonly only fit to a model of isolation with migration and rarely tested against the secondary contact alternative. Furthermore, most demographic inference methods have neglected variation in introgression rates and assume that the gene flow parameter (Nm) is similar among loci. Here, we show that neglecting this source of variation can give misleading results. We analysed DNA sequences sampled from populations of the marine mussels, Mytilus edulis and M. galloprovincialis, across a well-studied mosaic hybrid zone in Europe and evaluated various scenarios of speciation, with or without variation in introgression rates, using an Approximate Bayesian Computation (ABC) approach. Models with heterogeneous gene flow across loci always outperformed models assuming equal migration rates irrespective of the history of gene flow being considered. By incorporating this heterogeneity, the best-supported scenario was a long period of allopatric isolation during the first three-quarters of the time since divergence followed by secondary contact and introgression during the last quarter. By contrast, constraining migration to be homogeneous failed to discriminate among any of the different models of gene flow tested. Our simulations thus provide statistical support for the secondary contact scenario in the European Mytilus hybrid zone that the standard coalescent approach failed to confirm. Our results demonstrate that genomic variation in introgression rates can have profound impacts on the biological conclusions drawn from inference methods and needs to be incorporated in future studies.