The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

Background

A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized.

Results

We generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined.

Conclusions

We describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.

[Very preterm births in French Polynesia: update and proposal for follow-up]

INTRODUCTION

The care of premature infants in French Polynesia is complicated by this country's geographic isolation. We undertook an evaluation of the medical care of very premature infants (VPIs) to find local solutions to this problem.

OBJECTIVES

The objectives were to determine the incidence, mortality, and the short- and long-term outcome of very preterm infants in French Polynesia.

METHODS

We retrospectively reviewed the medical charts of all infants born alive at<32 gestational age (GA) and>24 GA from January 2007 to December 2011. Perinatal characteristics and outcomes were examined by univariate and multivariate analysis.

RESULTS

In total, 204 VPIs were born during the 5-year study period, comprising 0.9% of all births. Infants less than 28 GA comprised 0.1% of all births. Sixty-two percent of mothers were of extreme age including 43% less than 25 years old. Prematurity was attributed to spontaneous preterm labor in 63% of cases and preeclampsia in 29%. Spontaneous multiple pregnancies comprised 15% of the cases. Alcohol and tobacco consumption were frequently noted (>8% and 26% mothers, respectively). Seventy-eight percent of VPIs had received prenatal steroids. Intrauterine growth was normal in 89%. Mortality occurred in 9.3% (19 patients). Mortality was higher with lower gestational age (P<0.05) and absence of prenatal steroids (P<0.05) in univariate and multivariate analysis. The primary cause of death was sepsis. Hyaline membrane disease occurred in 44% of patients, 80% of whom received surfactant therapy. In total, 16.2% newborns developed bronchodysplasia, 3.4% necrotizing enterocolitis, 3% cerebral hemorrhage, and 1.5% leukomalacia. Long-term outcome was marked by 52% of the patients lost to follow-up by 2 years of age, mostly because of geographic isolation. For the 72 patients followed-up, four developed asthma and three cerebral palsy; 70% were attending school by 3 years of age.

CONCLUSIONS

The incidence, mortality, and morbidity of very preterm birth in French Polynesia are comparable to reports from metropolitan centers in France. Conversely, nearly one-half of the patients were lost to follow-up, precluding meaningful information on intellectual development and other outcomes. We recommend organizing a long-term follow-up network to detect cognitive sequelae and adapting such a system to the geographical residence of French Polynesian families.

The InterPro protein families database: the classification resource after 15 years

The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and sites. Central to the InterPro database are predictive models, known as signatures, from a range of different protein family databases that have different biological focuses and use different methodological approaches to classify protein families and domains. InterPro integrates these signatures, capitalizing on the respective strengths of the individual databases, to produce a powerful protein classification resource. Here, we report on the status of InterPro as it enters its 15th year of operation, and give an overview of new developments with the database and its associated Web interfaces and software. In particular, the new domain architecture search tool is described and the process of mapping of Gene Ontology terms to InterPro is outlined. We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years. InterPro (version 48.0) contains 36 766 member database signatures integrated into 26 238 InterPro entries, an increase of over 3993 entries (5081 signatures), since 2012.

[Intestinal fistula: an unusual complication of necrotizing enterocolitis in the preterm infant]

Intestinal fistula is a rare complication in necrotizing enterocolitis (NEC) and is typically associated with a colonic stricture. We report the case of a preterm infant with severe NEC, who developed an ileocolic fistula followed by the appearance of a colonic stricture after surgical treatment. This report shows how complex the outcome of NEC can be: a contrast enema should be done in NEC when the clinical or biological outcome is not favorable, in order not to delay the diagnosis of intestinal fistula.

[Revelation of an acute lymphoblastic leukemia in the delivery room]

Acute leukemia is uncommon in neonates and has a much poorer prognosis than in older children. We report on a case of acute lymphoblastic leukemia observed in a neonate who had bleeding and hepatosplenomegaly at birth, which justified intensive care during the first postnatal week. Despite early appropriate treatment, the patient died at 7 months of age. We present here physical and laboratory findings, which indicate a grim prognosis. These criteria should be considered carefully in order to ensure a realistic information for the parents and appropriate decisions.

Ex vivo blood stimulation assay as a translational research tool in the development of the ticilimumab (CP-675,206)

2542

Background: Cytotoxic T Lymphocyte-associated Antigen 4 (CTLA4) is an activation-induced T lymphocyte negative costimulatory receptor which down-regulates cellular immune responses. CTLA4 blockade may break peripheral immunological tolerance, leading to an effective immune response to cancer. Tools for assessing the effects of such a blockade are limited, as CTLA4 is not constitutively expressed on circulating T cells, and because activated lymphocytes are difficult to access in vivo. Therefore, we have employed ex vivo blood stimulation assays to define pharmacodynamic properties of the anti-CTLA4 antibody, ticilimumab. Methods: Ex vivo blood stimulation assays employed staphylococcal enterotoxin A (SEA) to stimulate isolated peripheral blood mononuclear cells (PBMC) or whole blood. Stimulation was monitored by production of interleukin 2 (IL-2). This assay was used preclinically to predict in vivo responses in animal models and in samples from cancer patients, as a batch release assay for production runs of ticilimumab, and clinically as a pharmacodynamic measurement in clinical trials of ticilimumab. Results: Screening experiments using the SEA assay allowed us to identify the lead candidate mAb with optimal CTLA4 blockade activity, ticilimumab. Dose-dependent increases in IL-2 production were observed in PBMC and whole blood samples up to an in vitro concentration of 100 ug/mL of ticilimumab, with 10 ug/mL identified as the minimum predicted efficacious concentration (Ceff). This functional potency assay was adapted for qualification of production lots of ticilimumab. Whole blood taken from cynomolgus monkeys dosed with ticilimumab demonstrated significant enhancement of IL-2 production at the same magnitude observed in in vitro experiments. Additionally, longitudinal samples taken from healthy volunteers and cancer patients suggested that an enhancement of 2.8 fold would be indicative of a pharmacodynamic effect of ticilimumab. Conclusions: The SEA assay provides a functional assessment of ticilimumab activity and can be used to guide the clinical development of this agent. Our data suggest that T cell reactivity is enhanced in the presence of ticilimumab in vitro, in primate models and in humans.

[Table: see text]

Utilisation de l'érythropoïétine recombinante humaine chez l'enfant atteint de cancer

Eighty percent of children with cancer suffer from anemia at the time of diagnosis. The physiopathology of anemia is complex. Although anemia can be life threatening, its consequences on the physical, psychological and social state of the child are often minimized. Blood transfusion is the main treatment of anemia: its efficacy is immediate but shortlasting, and it involves infectious and hemolytic risks. The human recombinant erythropoietin has been used for more than 25-years, and is often prescribed to adults with cancer and anemia. The human recombinant erythropoietin rHuEPO is nowadays used when blood transfusion is contra-indicated because of religious or cultural considerations, although several promising studies have been conducted about rHuEPO and children with cancer since 1996: it might be soon the preferential alternative treatment to anemia in children with cancer.

High density lipoprotein deficiency and foam cell accumulation in mice with targeted disruption of ATP-binding cassette transporter-1

Recently, the human ATP-binding cassette transporter-1 (ABC1) gene has been demonstrated to be mutated in patients with Tangier disease. To investigate the role of the ABC1 protein in an experimental in vivo model, we used gene targeting in DBA-1J embryonic stem cells to produce an ABC1-deficient mouse. Expression of the murine Abc1 gene was ablated by using a nonisogenic targeting construct that deletes six exons coding for the first nucleotide-binding fold. Lipid profiles from Abc1 knockout (-/-) mice revealed an approximately 70% reduction in cholesterol, markedly reduced plasma phospholipids, and an almost complete lack of high density lipoproteins (HDL) when compared with wild-type littermates (+/+). Fractionation of lipoproteins by FPLC demonstrated dramatic alterations in HDL cholesterol (HDL-C), including the near absence of apolipoprotein AI. Low density lipoprotein (LDL) cholesterol (LDL-C) and apolipoprotein B were also significantly reduced in +/- and -/- compared with their littermate controls. The inactivation of the Abc1 gene led to an increase in the absorption of cholesterol in mice fed a chow or a high-fat and -cholesterol diet. Histopathologic examination of Abc1-/- mice at ages 7, 12, and 18 mo demonstrated a striking accumulation of lipid-laden macrophages and type II pneumocytes in the lungs. Taken together, these findings demonstrate that Abc1-/- mice display pathophysiologic hallmarks similar to human Tangier disease and highlight the capacity of ABC1 transporters to participate in the regulation of dietary cholesterol absorption.

Functional and structural diversity of the human Dickkopf gene family

Wnt proteins influence many aspects of embryonic development, and their activity is regulated by several secreted antagonists, including the Xenopus Dickkopf-1 (xDkk-1) protein. xDkk-1 inhibits Wnt activities in Xenopus embryos and may play a role in induction of head structures. Here, we characterize a family of human Dkk-related genes composed of Dkk-1, Dkk-2, Dkk-3, and Dkk-4, together with a unique Dkk-3 related protein termed Soggy (Sgy). hDkks 1-4 contain two distinct cysteine-rich domains in which the positions of 10 cysteine residues are highly conserved between family members. Sgy is a novel secreted protein related to Dkk-3 but which lacks the cysteine-rich domains. Members of the Dkk-related family display unique patterns of mRNA expression in human and mouse tissues, and are secreted when expressed in 293T cells. Furthermore, secreted hDkk-2 and hDkk-4 undergo proteolytic processing which results in cleavage of the second cysteine-rich domain from the full-length protein. Members of the human Dkk-related family differ not only in their structures and expression patterns, but also in their abilities to inhibit Wnt signaling. hDkk-1 and hDkk-4, but not hDkk-2, hDkk-3 or Sgy, suppress Wnt-induced secondary axis induction in Xenopus embryos. hDkk-1 and hDkk-4 do not block axis induction triggered either by Xenopus Dishevelled (Xdsh) or Xenopus Frizzled-8 (Xfz8), both of which function to transduce signals from Wnt ligands. Thus, hDkks 1 and 4 may inhibit Wnt activity by a mechanism upstream of Frizzled. Our findings highlight the structural and functional heterogeneity of human Dkk-related proteins.

Development of a gas chromatography-mass spectrometry method for the analysis of aminoglycoside antibiotics using experimental design for the optimisation of the derivatisation reactions

A packed column GC-electron-capture detection method for the analysis of the aminoglycoside antibiotics kanamycin and gentamicin was adapted to capillary GC-MS. The analytes were derivatised using a two-step procedure involving trimethylsilylation of the hydroxyl groups with trimethylsilylimidazole and acylation of the amino groups with heptafluorobutyrylimidazole. Electron impact mass spectra of the resulting derivatives of kanamycin A and gentamicins C1, C1a and C2 are given and interpreted. The derivatisation procedure was optimised using experimental design. This chemometrical approach considers main effects as well as interactions of the influential parameters, thus conducting a more thorough investigation of the method than the common step-by-step approach. Optimisation using fractional factorial and Box Behnken Designs produced a derivatisation method featuring better yield than previously published methods while in many cases requiring less reagents and shorter reaction times.

Structure-property relationships of trimetazidine derivatives and model compounds as potential antioxidants

Twenty-five compounds (trimetazidine derivatives and other compounds, mostly having a free phenolic group) were examined for their radical scavenging and antioxidant properties. Their reaction with DPPH (2,2-diphenyl-1-picrylhydrazyl) as a measure of radical scavenging capacity was assessed by two parameters, namely EC50 (the concentration of antioxidant decreasing DPPH by 50%), and log Z, a kinetic parameter proposed here and derived from initial second-order rate constants and antioxidant/DPPH ratios. Antioxidant activities were determined by the inhibition of lipid peroxidation and albumin oxidation. The most active compounds were derivatives having a trolox or hydroquinone moiety. Physicochemical and structural properties were determined by molecular modeling as lipophilicity (virtual log P calculations) and H-Surf (solvent-accessible surface of hydroxyl hydrogen) and by quantum mechanical calculations (deltaH(ox) = oxidation enthalpy; deltaH(abs) = enthalpy of hydrogen abstraction). QSAR models were derived to identify molecular mechanisms responsible for the reactivity toward the DPPH radical and for the inhibition of lipid peroxidation. A useful prediction of antioxidant capacity could be achieved from calculated molecular properties and the kinetic parameter developed here.

Curcumin and curcumin derivatives inhibit Tat-mediated transactivation of type 1 human immunodeficiency virus long terminal repeat

The transcription of HIV1 provirus is regulated by both cellular and viral factors. Various evidence suggests that Tat protein secreted by HIV1-infected cells may have additional action in the pathogenesis of AIDS because of its ability to also be taken up by non-infected cells. Curcumin [diferuloylmethane or 1,7-bis-(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione] is the yellow pigment in turmeric Curcuma longa (Linn). It exhibits a variety of pharmacological effects including antiinflammatory and antiretroviral activities. Here, we demonstrated that curcumin used at 10 to 100 nM inhibited Tat transactivation of HIV1-LTR lacZ by 70 to 80% in HeLa cells. In order to develop more efficient curcumin derivatives, we synthesized and tested in the same experimental system the inhibitory activity of reduced curcumin (C1), which lacks the spatial structure of curcumin; allyl-curcumin (C2), which possesses a condensed allyl derivative on curcumin that plays the role of metal chelator; and tocopheryl-curcumin (C3), which enhances the antioxidant activity of the molecule. Results obtained with C1, C2 and C3 curcumin derivatives showed a significant inhibition (70 to 85%) of Tat transactivation. Despite the fact that tocopheryl-curcumin (C3) failed to scavenge O2.-, this curcumin derivative exhibited the most activity; 70% inhibition was obtained at 1 nM, while only 35% inhibition was obtained with the curcumin.

[Efficacy of Triatec in monotherapy and in combination with Lasilix in a French multicenter study]

The 770 subjects enrolled into the French multicenter trial of Triatec (ramipril) presented the usual characteristics of moderate hypertension. After a low rate of response to placebo (9.1 p. 100), over half the active treatment patients responded to Triatec 2.5 mg (57 p. 100). Later on, Triatec 5 mg achieved control of half the remaining patients (55.6 p. 100); lastly, among non-responders to that posology, no difference was noted between monotherapy with 10 mg of Triatec, and the combination of 20 mg of Lasilix (furosemide) and Triatec 5 mg (respectively 44.7 p. 100 and 47.4 p. 10 responders). As a whole, more than 90 p. 100 of the patients responded to the proposed treatment plan.

["Spike focus" during the evolution of febrile convulsion: an electrophysiological and clinical study of 35 patients (author's transl)]

Out of 500 patients with febrile convulsions, 41 were found to have a spike focus on E.E.G., 35 of these were then followed up. The clinical features of the seizure in these 35 children did not differ from the group in general. The initial focus was practically always unilateral, except for one case with an asynchronous bioccipital focus. The most frequent site was occipital (43 p. 100). Migration of the focus was relatively rare. In 35 patients the focus disappeared, in 45 p. 100 within a year and in 88 p. 100 within 3 years. Following the disappearance of the focus, generalised sharp wave activity was seen in 30 p. 100 cases, all 35 children being under treatment. All the seizures with the exception of two children who have become epileptic were benign rendering long term anticonvulsant therapy unnecessary.

Sub-acute toxicity of xylitol in rats; absence of hepatotoxicity

Some workers have suggested that 6 days xylitol administration to rats results in hepatic dysfunction. In our study xylitol was administered to rats by daily gastric intubation for a period of 14 days. Dose levels were 1.25, 2.5, 5 and 10 g/kg. During treatment (2, 5 and 14 days), animals were submitted to careful clinical examinations and to blood serum analysis related to hepatic functions. They were sacrificed after 2, 5, and 14 days treatment. In the 2 and 5 days treatment groups, main organs were submitted to histological study. This examination was only performed on liver in the 14 days treatment group. No evidence of hepatotoxicity was recorded. Serum levels of all parameters measured were within normal limits (including bilirubin and serum alkaline phosphatase (SAP). No anomalies were shown histologically.

[Toxicologic evaluation of irradiated corn starch by long term experimentation with rats]

Maize starch pasteurized by irradiation was fed to OFA rats (Sprague Dawley derived) in an uncooked form (irradiated at 300 krad.) and in a cooked form (irradiated at 300 and 600 krad.) at dietary level of 62%. A six month toxicity trial was performed with uncooked starch and a 24 month trial with cooked starch. At the same time a reproduction study was conducted, over 3 generations with 2 litters per generation, using both uncooked and cooked irradiated starch. The parent generation (Fo) was randomly selected from animals in the feeding study and after the production of the F1a and F1b generations they were returned to that study. Control groups corresponding to each form of starch were established. They were fed the same diet except that the starch was not irradiated. The results of the various investigations conducted during the study (behavior, growth, mortality, haematology, serum biochemistry, histopathology) did not reveal any toxicological effect due to treatment, nor any effect on reproduction. No significant differences were shown between treated and control group.