Efficacy of a First Course of Ibuprofen for Patent Ductus Arteriosus Closure in Extremely Preterm Newborns According to Their Gestational Age-Specific Z-Score for Birth Weight

Objective

Therapeutic strategies for patent ductus arteriosus (PDA) in very preterm infants remain controversial. To identify infants likely to benefit from treatment, we analysed the efficacy of a first course of ibuprofen in small-for-gestational age (SGA) newborns.

Study design

This single-centre retrospective study included 185 infants born at 24+0–27+6 weeks of gestation with haemodynamically significant PDA, who were treated by intravenous ibuprofen (Pedea): 10 mg/kg on day one and 5 mg/kg on days two and three. Birth weight and gestational age (GA) were analysed with reference to the standard deviations from the Olsen growth curve to define GA-specific Z-scores for birth weights. The efficacy of treatment was evaluated by echocardiography 48 hours after the last dose of ibuprofen. The primary outcome was failure of the first course of ibuprofen associated in a composite criterion with the most severe outcomes.

Results

The risk of treatment failure increased according to a continuous gradient in SGA neonates. A higher risk was observed on multiple regression analysis (crude OR: 3.8; 95% CI [1.2–12.3] p = 0.02; adjusted OR: 12.8; 95% CI [2.3–70.5] p=0.003).

Conclusion

There is a linear relationship between infant birth weight and PDA treatment: the failure rate of a first course of ibuprofen increases with increasing degree of growth restriction.     

Quality control of microbiota metagenomics by k-mer analysis

Background

The biological and clinical consequences of the tight interactions between host and microbiota are rapidly being unraveled by next generation sequencing technologies and sophisticated bioinformatics, also referred to as microbiota metagenomics. The recent success of metagenomics has created a demand to rapidly apply the technology to large case–control cohort studies and to studies of microbiota from various habitats, including habitats relatively poor in microbes. It is therefore of foremost importance to enable a robust and rapid quality assessment of metagenomic data from samples that challenge present technological limits (sample numbers and size). Here we demonstrate that the distribution of overlapping k-mers of metagenome sequence data predicts sequence quality as defined by gene distribution and efficiency of sequence mapping to a reference gene catalogue.

Results

We used serial dilutions of gut microbiota metagenomic datasets to generate well-defined high to low quality metagenomes. We also analyzed a collection of 52 microbiota-derived metagenomes. We demonstrate that k-mer distributions of metagenomic sequence data identify sequence contaminations, such as sequences derived from “empty” ligation products. Of note, k-mer distributions were also able to predict the frequency of sequences mapping to a reference gene catalogue not only for the well-defined serial dilution datasets, but also for 52 human gut microbiota derived metagenomic datasets.

Conclusions

We propose that k-mer analysis of raw metagenome sequence reads should be implemented as a first quality assessment prior to more extensive bioinformatics analysis, such as sequence filtering and gene mapping. With the rising demand for metagenomic analysis of microbiota it is crucial to provide tools for rapid and efficient decision making. This will eventually lead to a faster turn-around time, improved analytical quality including sample quality metrics and a significant cost reduction. Finally, improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1406-7) contains supplementary material, which is available to authorized users.     

Electron paramagnetic resonance in human fingernails: the sponge model implication

The most significant problem of electron paramagnetic resonance (EPR) fingernail dosimetry is the presence of two signals of non-radiation origin that overlap the radiation-induced signal (RIS), making it almost impossible to perform dose measurements below 5 Gy. Historically, these two non-radiation components were named mechanically induced signal (MIS) and background signal (BKS). In order to investigate them in detail, three different methods of MIS and BKS mutual isolation have been developed and implemented. After applying these methods, it is shown here that fingernail tissue, after cut, can be modeled as a deformed sponge, where the MIS and BKS are associated with the stress from elastic and plastic deformations, respectively. A sponge has a unique mechanism of mechanical stress absorption, which is necessary for fingernails in order to perform its everyday function of protecting the fingertips from hits and trauma. Like a sponge, fingernails are also known to be an effective water absorber. When a sponge is saturated with water, it tends to restore to its original shape, and when it loses water, it becomes deformed again. The same happens to fingernail tissue. It is proposed that the MIS and BKS signals of mechanical origin be named MIS1 and MIS2 for MISs 1 and 2, respectively. Our suggested interpretation of the mechanical deformation in fingernails gives also a way to distinguish between the MIS and RIS. The results obtained show that the MIS in irradiated fingernails can be almost completely eliminated without a significant change to the RIS by soaking the sample for 10 min in water. The proposed method to measure porosity (the fraction of void space in spongy material) of the fingernails gave values of 0.46–0.48 for three of the studied samples. Existing results of fingernail dosimetry have been obtained on mechanically stressed samples and are not related to the “real” in vivo dosimetric properties of fingernails. A preliminary study of these properties of pre-soaked (unstressed) fingernails has demonstrated their significant difference from fingernails stressed by cut. They show a higher stability signal, a less intensive non-radiation component, and a nonlinear dose dependence. The findings in this study set the stage for understanding fingernail EPR dosimetry and doing in vivo measurements in the future.     

The deletion of the pif gene improves the biosafety of the baculovirus-based technologies

Our goal was to improve the biosafety of baculovirus-based technologies by deleting the pif (per os infectivity factor) gene from baculovirus expression vectors. Such a deletion would block transmission in nature without disturbing protein production. A pif deletion mutant of Autographa californica multiplecapsid nucleopolyhedrovirus (AcMNPV) was constructed and its infectivity to two host species was tested by oral or intrahemocoelic inoculation. Virus replication after oral inoculation was monitored using PCR. Oral inoculations with a mixture of the wild type and the pif deletion viruses were carried out. The pif deletion blocked oral infection but it did not hamper infectivity in cell culture. The blockage took place early after inoculation and could not be overcome by mixed inoculations with the wild type. The cat gene was inserted under the control of the polyhedrin promoter in the deletion mutant and the wild type CAT yield was measured in Spodoptera frugiperda insect cells (Sf9) infected with either recombinant. The pif deletion did not hamper CAT production. This deletion significantly improved CAT yields early in the infection. Hence, expression vectors lacking pif may produce higher quality protein. The pif deletion is a simple measure that dramatically reduces the chances of virus spread or gene transfer in nature.     

LXR antagonists induce ABCD2 expression

X-linked adrenoleukodystrophy (X-ALD) is a rare neurodegenerative disorder characterized by the accumulation of very-long-chain fatty acids resulting from a β-oxidation defect. Oxidative stress and inflammation are also key components of the pathogenesis. X-ALD is caused by mutations in the ABCD1 gene, which encodes for a peroxisomal half ABC transporter predicted to participate in the entry of VLCFA-CoA into the peroxisome, the unique site of their β-oxidation. Two homologous peroxisomal ABC transporters, ABCD2 and ABCD3 have been proven to compensate for ABCD1 deficiency when overexpressed. Pharmacological induction of these target genes could therefore represent an alternative therapy for X-ALD patients. Since LXR activation was shown to repress ABCD2 expression, we investigated the effects of LXR antagonists in different cell lines. Cells were treated with GSK(17) (a LXR antagonist recently discovered from the GlaxoSmithKline compound collection), 22(S)-hydroxycholesterol (22S-HC, another LXR antagonist) and 22R-HC (an endogenous LXR agonist). We observed up-regulation of ABCD2, ABCD3 and CTNNB1 (the gene encoding for β-catenin, which was recently demonstrated to induce ABCD2 expression) in human HepG2 hepatoma cells and in X-ALD skin fibroblasts treated with LXR antagonists. Interestingly, induction in X-ALD fibroblasts was concomitant with a decrease in oxidative stress. Rats treated with 22S-HC showed hepatic induction of the 3 genes of interest. In human, we show by multiple tissue expression array that expression of ABCD2 appears to be inversely correlated with NR1H3 (LXRα) expression. Altogether, antagonists of LXR that are currently developed in the context of dyslipidemia may find another indication with X-ALD.     

Q-band electron paramagnetic resonance dosimetry in tooth enamel: biopsy procedure and determination of dose detection limit

High-frequency Q-band (37 GHz) electron paramagnetic resonance (EPR) dosimetry allows to perform fast (i.e., measurement time <15 min) dose measurements using samples obtained from tooth enamel mini-biopsy procedures. We developed and tested a new procedure for taking tooth enamel biopsy for such dose measurements. Recent experience with EPR dose measurements in Q-band using mini-probes of tooth enamel has demonstrated that a small amount of tooth enamel (2–10 mg) can be quickly obtained from victims of a radiation accident. Accurate dose assessments can further be carried out in a very short time to provide important information for medical treatment. Here, the Q-band EPR dose detection limit for 5 and 10 mg samples is estimated to be 367 and 248 mGy, respectively. These values are comparable to the critical parameters determined for conventional X-band EPR in tooth enamel.     

Regulation of the adrenoleukodystrophy-related gene (ABCD2): Focus on oxysterols and LXR antagonists

The regulation of the ABCD2 gene is recognized as a possible therapeutic target for X-linked adrenoleukodystrophy, a rare neurodegenerative disease caused by mutations in the ABCD1 gene. Up-regulation of ABCD2 expression has indeed been demonstrated to compensate for ABCD1 deficiency, restoring peroxisomal β-oxidation of very-long-chain fatty acids. Besides the known inducers of the ABCD2 gene (phenylbutyrate and histone deacetylase inhibitors, fibrates, dehydroepiandrosterone, thyroid hormone and thyromimetics), this review will focus on LXR antagonists and 22S-hydroxycholesterol, recently described as inducers of ABCD2 expression. Several LXR antagonists have been identified and their possible indication for neurodegenerative disorders will be discussed.     

Ex vivo cultures of glioblastoma in three-dimensional hydrogel maintain the original tumor growth behavior and are suitable for preclinical drug and radiation sensitivity screening

Identification of new drugs and predicting drug response are major challenges in oncology, especially for brain tumors, because total surgical resection is difficult and radiation therapy or chemotherapy is often ineffective. With the aim of developing a culture system close to in vivo conditions for testing new drugs, we characterized an ex vivo three-dimensional culture system based on a hyaluronic acid-rich hydrogel and compared it with classical two-dimensional culture conditions. U87-MG glioblastoma cells and seven primary cell cultures of human glioblastomas were subjected to radiation therapy and chemotherapy drugs. It appears that 3D hydrogel preserves the original cancer growth behavior and enables assessment of the sensitivity of malignant gliomas to radiation and drugs with regard to inter-tumoral heterogeneity of therapeutic response. It could be used for preclinical assessment of new therapies.