Conditions Of Low Oxygen Tension Research Articles

Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion.

Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.

Coronavirus disease 2019 (COVID-19) in special groups: A single-center experience in sickle cell disease patients in Saudi Arabia.

BACKGROUND:Sickle cell disease (SCD) is a group of hereditary diseases, inherited as autosomal recessive disorder, which causes mutation in the β-globin gene. As a result, there is a change in the sixth amino acid from glutamic acid to valine. The affected red blood cell is then prone to polymerization and sickling crisis under conditions of low oxygen tension. One of the major causes of mortality in SCD is acute chest syndrome (ACS). On the other hand, coronavirus disease 2019 (COVID-19) is a pandemic disease that carries significant mortality and morbidity worldwide with unknown outcomes in the affected SCD population. This study was created for that reason.MATERIALS AND METHODS:We report a case series of ten SCD patients who were affected by COVID-19 and required admission between May 1, 2020, and October 30, 2020, at a tertiary care hospital in Dhahran, eastern region of Saudi Arabia. Historical data were obtained retrospectively from electronic records. MS Excel was used for data entry, and SPSS version 23 was used for data analysis.RESULTS:The mean age of the patients involved in the study was 32 years, and the mean duration of symptoms was 5.7 days. None required critical care admission, and there was no mortality. All patients were discharged from hospital in good condition with no requirement of home oxygen.CONCLUSION:Although we expected a fatal outcome of SCD patients affected by COVID-19 infection, our limited case series showed favorable disease behavior and outcome, with a suspicion of underlying unclear protective mechanism from serious complications. However, further studies are required to better understand COVID-19 behavior in SCD patients.

Connectivity Map Analysis Indicates PI3K/Akt/mTOR Inhibitors as Potential Anti-Hypoxia Drugs in Neuroblastoma

Simple SummaryA large percentage of patients with neuroblastoma relapse and die, despite treatment, thus demanding new personalized strategies and therapeutic targets. Hypoxia, a condition of reduced oxygenation in several solid tumors, has profound effects on the neuroblastoma (NB) tumor biology and patient prognosis. Establishing new connections between hypoxia and pharmacological compounds may provide novel treatment strategies for NB patients. In the present study, we successfully identified 19 compounds mainly belonging to the class of PI3K/Akt/mTOR inhibitors, whose anti-hypoxia effect was shown on the gene expression profile of nine distinct cell lines using connectivity map software. We independently confirmed these findings on NB cells cultured under hypoxia conditions and treated with the mTORC inhibitor PP242. PI3K/Akt/mTOR inhibitors represent a potential effective class of compounds targeting hypoxia in neuroblastoma. PI3K/Akt/mTOR inhibitors may thus find future applicability as a new adjuvant therapy in randomized clinical trials involving neuroblastoma patients with hypoxic tumors.Neuroblastoma (NB) is one of the deadliest pediatric cancers, accounting for 15% of deaths in childhood. Hypoxia is a condition of low oxygen tension occurring in solid tumors and has an unfavorable prognostic factor for NB. In the present study, we aimed to identify novel promising drugs for NB treatment. Connectivity Map (CMap), an online resource for drug repurposing, was used to identify connections between hypoxia-modulated genes in NB tumors and compounds. Two sets of 34 and 21 genes up- and down-regulated between hypoxic and normoxic primary NB tumors, respectively, were analyzed with CMap. The analysis reported a significant negative connectivity score across nine cell lines for 19 compounds mainly belonging to the class of PI3K/Akt/mTOR inhibitors. The gene expression profiles of NB cells cultured under hypoxic conditions and treated with the mTORC complex inhibitor PP242, referred to as the Mohlin dataset, was used to validate the CMap findings. A heat map representation of hypoxia-modulated genes in the Mohlin dataset and the gene set enrichment analysis (GSEA) showed an opposite regulation of these genes in the set of NB cells treated with the mTORC inhibitor PP242. In conclusion, our analysis identified inhibitors of the PI3K/Akt/mTOR signaling pathway as novel candidate compounds to treat NB patients with hypoxic tumors and a poor prognosis.

Osteomyelitis in Children with Sickle Cell Disease: A Challenging Diagnosis: Case Report from Cameroon

Introduction: Sickle Cell Disease (SCD) is the most prevalent genetic disease in the world predominantly in the African population with Sickle Cell Anaemia (SCA) being its dominant form. One of the most frequent complications of SCD is osteomyelitis. SCA is due to a point mutation in the beta globin chain of haemoglobin. This is responsible for the sickled shape of RBCs under low oxygen tension conditions leading to obstruction in the microcirculation. This leads to vaso-occlusive crises (VOC) which has a similar clinical presentation to that of osteomyelitis, another complication of SCD. Case Presentation: We present the case of a three-year-old girl with SCA who presented with an inability to bear weight in a febrile context. A diagnosis of VOC was initially made, which was later on changed to both a left chronic tibial and right distal femoral osteomyelitis following a series of biological, and imaging investigations. Surgical debridement and drainage were performed, resulting 9 weeks later in the involution of fever and leg pain. Conclusion: Osteomyelitis when associated with SCD is a dreadful and deathly disease in low income countries as it also presents like VOC therefore higher suspicion index is recommended. It is therefore important to take this into consideration at an early stage in patients with homozygous sickle cell disease so as to rapidly initiate multidisciplinary care. Appropriate investigations, appropriate antibiotic therapy, and timely surgical intervention would help to greatly reduce morbidity and mortality.

The Importance of Hypoxia-Inducible Factors (HIF-1 and HIF-2) for the Pathophysiology of Inflammatory Bowel Disease.

(1) Background: Hypoxia is a common feature of inflammation when hypoxia inducible factors (HIFs) adapt cells to conditions of low oxygen tension and inflammation. We studied the role of HIF-1 and HIF-2 in cells of the myeloid lineage in a mouse model of acute colitis. (2) Methods: Mice with and without a conditional knockout for either Hif-1a or Hif-2a or Hif-1a and Hif-2a in cells of the myeloid lineage were treated with 2.5% dextran sodium sulfate (DSS) for 6 days to induce an acute colitis. We analyzed the course of inflammation with respect to macroscopic (disease activity index) and microscopic (histology score and immunohistochemical staining of immune cells) parameters and quantified the mRNA expression of cytokines and chemokines in the colon and the mesenteric lymph nodes. (3) Results: A conditional knockout of myeloid Hif-1a ameliorated whereas the knockout of Hif-2a aggravated murine DSS colitis by increased recruitment of neutrophils to deeper layers of the colon. This led to higher expression of Il6, Ifng, Cd11c, Cd4, and Cd8 in the colon but also induced anti-inflammatory mediators such as Foxp3 and Il10. A conditional knockout of Hif-1a and Hif-2a did not show any differences compared to wildtype mice. (4) Conclusions: Myeloid HIF-1α and HIF-2α play opposing roles in acute DSS colitis. Thus, not only a cell type specific, but also the isoform specific modulation of HIFs needs to be addressed in attempts to modify HIF for therapeutic purposes.

Hypoxia Predicts Poor Prognosis in Neuroblastoma Patients and Associates with Biological Mechanisms Involved in Telomerase Activation and Tumor Microenvironment Reprogramming

The biological and clinical heterogeneity of neuroblastoma (NB) demands novel biomarkers and therapeutic targets in order to drive the most appropriate treatment for each patient. Hypoxia is a condition of low-oxygen tension occurring in poorly vascularized tumor tissues. In this study, we aimed to assess the role of hypoxia in the pathogenesis of NB and at developing a new clinically relevant hypoxia-based predictor of outcome. We analyzed the gene expression profiles of 1882 untreated NB primary tumors collected at diagnosis and belonging to four existing data sets. Analyses took advantage of machine learning methods. We identified NB-hop, a seven-gene hypoxia biomarker, as a predictor of NB patient prognosis, which is able to discriminate between two populations of patients with unfavorable or favorable outcome on a molecular basis. NB-hop retained its prognostic value in a multivariate model adjusted for established risk factors and was able to additionally stratify clinically relevant groups of patients. Tumors with an unfavorable NB-hop expression showed a significant association with telomerase activation and a hypoxic, immunosuppressive, poorly differentiated, and apoptosis-resistant tumor microenvironment. NB-hop defines a new population of NB patients with hypoxic tumors and unfavorable prognosis and it represents a critical factor for the stratification and treatment of NB patients.

Thiazolyl-pyrazole derivatives as potential antimycobacterial agents

Mycobacterium tuberculosis (Mtb) is an obligate aerobe that is capable of long-term persistence under conditions of low oxygen tension. A series of thiazolyl-pyrazole derivatives (6a–f, 7a–f, 8c, 8e) were screened for antimycobacterial activity against dormant M. tuberculosis H37Ra (D-MTB) and M. bovis BCG (D-BCG). Nine thiazolyl-pyrazole analogs, 6c, 6e, 7a, 7b, 7c, 7e, 7f, 8c and 8e exhibited promissing minimum inhibitory concentration (MIC) values (0.20–28.25 µg/mL) against D-MTB and D-BCG strains of Mtb. Importantly, six compounds (7a, 7b, 7e, 7f, 8c and 8e) exhibited excellent antimycobacterial activity and low cytotoxicity at the maximum evaluated concentration of >250 µg/mL. Finally, the promising antimycobacterial activity and lower cytotoxicity profile suggested that, these compounds could be further subjected for optimization and development as a lead, which could have the potential to treat tuberculosis.

A discrete role for alternative oxidase under hypoxia to increase nitric oxide and drive energy production

Alternative oxidase (AOX) is an integral part of the mitochondrial electron transport and can prevent reactive oxygen species (ROS) and nitric oxide (NO) production under non-stressed, normoxic conditions. Here we assessed the roles of AOX by imposing stress under normoxia in comparison to hypoxic conditions using AOX over expressing (AOX OE) and anti-sense (AOX AS) transgenic Arabidopsis seedlings and roots. Under normoxic conditions stress was induced with the defence elicitor flagellin (flg22). AOX OE reduced NO production whilst this was increased in AOX AS. Moreover AOX AS also exhibited an increase in superoxide and therefore peroxynitrite, tyrosine nitration suggesting that scavenging of NO by AOX can prevent toxic peroxynitrite formation under normoxia. In contrast, during hypoxia interestingly we found that AOX is a generator of NO. Thus, the NO produced during hypoxia, was enhanced in AOX OE and suppressed in AOX AS. Additionally, treatment of WT or AOX OE with the AOX inhibitor SHAM inhibited hypoxic NO production. The enhanced levels of NO correlated with expression of non-symbiotic haemoglobin, increased NR activity and ATP production. The ATP generation was suppressed in nia1,2 mutant and non symbiotic haemoglobin antisense line treated with SHAM. Taken together these results suggest that hypoxic NO generation mediated by AOX has a discrete role by feeding into the haemoglobin-NO cycle to drive energy efficiency under conditions of low oxygen tension.

The Atypical Response Regulator AtvR Is a New Player in Pseudomonas aeruginosa Response to Hypoxia and Virulence.

Two-component systems are widespread in bacteria, allowing adaptation to environmental changes. The classical pathway is composed of a histidine kinase that phosphorylates an aspartate residue in the cognate response regulator (RR). RRs lacking the phosphorylatable aspartate also occur, but their function and contribution during host-pathogen interactions are poorly characterized. AtvR (PA14_26570) is the only atypical response regulator with a DNA-binding domain in the opportunistic pathogen Pseudomonas aeruginosa Macrophage infection with the atvR mutant strain resulted in higher levels of tumor necrosis factor alpha secretion as well as increased bacterial clearance compared to those for macrophages infected with the wild-type strain. In an acute pneumonia model, mice infected with the atvR mutant presented increased amounts of proinflammatory cytokines, increased neutrophil recruitment to the lungs, reductions in bacterial burdens, and higher survival rates in comparison with the findings for mice infected with the wild-type strain. Further, several genes involved in hypoxia/anoxia adaptation were upregulated upon atvR overexpression, as seen by high-throughput transcriptome sequencing (RNA-Seq) analysis. In addition, atvR was more expressed in hypoxia in the presence of nitrate and required for full expression of nitrate reductase genes, promoting bacterial growth under this condition. Thus, AtvR would be crucial for successful infection, aiding P. aeruginosa survival under conditions of low oxygen tension in the host. Taken together, our data demonstrate that the atypical response regulator AtvR is part of the repertoire of transcriptional regulators involved in the lifestyle switch from aerobic to anaerobic conditions. This finding increases the complexity of regulation of one of the central metabolic pathways that contributes to Pseudomonas ubiquity and versatility.

Artificial neural network classifier predicts neuroblastoma patients’ outcome

BackgroundMore than fifty percent of neuroblastoma (NB) patients with adverse prognosis do not benefit from treatment making the identification of new potential targets mandatory. Hypoxia is a condition of low oxygen tension, occurring in poorly vascularized tissues, which activates specific genes and contributes to the acquisition of the tumor aggressive phenotype. We defined a gene expression signature (NB-hypo), which measures the hypoxic status of the neuroblastoma tumor. We aimed at developing a classifier predicting neuroblastoma patients’ outcome based on the assessment of the adverse effects of tumor hypoxia on the progression of the disease.MethodsMulti-layer perceptron (MLP) was trained on the expression values of the 62 probe sets constituting NB-hypo signature to develop a predictive model for neuroblastoma patients’ outcome. We utilized the expression data of 100 tumors in a leave-one-out analysis to select and construct the classifier and the expression data of the remaining 82 tumors to test the classifier performance in an external dataset. We utilized the Gene set enrichment analysis (GSEA) to evaluate the enrichment of hypoxia related gene sets in patients predicted with “Poor” or “Good” outcome.ResultsWe utilized the expression of the 62 probe sets of the NB-Hypo signature in 182 neuroblastoma tumors to develop a MLP classifier predicting patients’ outcome (NB-hypo classifier). We trained and validated the classifier in a leave-one-out cross-validation analysis on 100 tumor gene expression profiles. We externally tested the resulting NB-hypo classifier on an independent 82 tumors’ set. The NB-hypo classifier predicted the patients’ outcome with the remarkable accuracy of 87 %. NB-hypo classifier prediction resulted in 2 % classification error when applied to clinically defined low-intermediate risk neuroblastoma patients. The prediction was 100 % accurate in assessing the death of five low/intermediated risk patients. GSEA of tumor gene expression profile demonstrated the hypoxic status of the tumor in patients with poor prognosis.ConclusionsWe developed a robust classifier predicting neuroblastoma patients’ outcome with a very low error rate and we provided independent evidence that the poor outcome patients had hypoxic tumors, supporting the potential of using hypoxia as target for neuroblastoma treatment.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1194-3) contains supplementary material, which is available to authorized users.

The ETS Factor Myeloid Elf-1-Like Factor (MEF)/Elf4 Is Transcriptionally and Functionally Activated by Hypoxia.

Hypoxia-inducible factor (HIF)-1α is a transcription factor belonging to the HIF family that is activated in mammalian cells during conditions of low oxygen tension or hypoxia to induce an adaptive response and promote cell survival. Some of the genes targeted by HIF-1α are important for angiogenesis and proliferation. Here, we found that the E26 transformation-specific (ETS) transcription factor myeloid elf-1-like factor (MEF)/Elf4 is activated by HIF-1α. MEF induces genes such as human beta-defensin 2 (HβD2) and perforin (PRF1), and is known to affect the cell cycle. Treatment with hypoxia mimetic CoCl2 or low O2 incubation up-regulated MEF mRNA and protein levels in various cell lines. HIF-1α overexpression in HEK293 cells also increased MEF mRNA and protein levels. In contrast, HIF-1α knockdown by small interfering RNA (siRNA) suppressed the induction of MEF in response to hypoxia. HIF-1α binds to the hypoxia response element in the MEF promoter region (-200 bp) and activates MEF promoter under hypoxia condition. The induction of MEF by hypoxia/HIF-1α correlated with the increase of MEF target genes HβD2 and PRF1. Intriguingly, the hypoxia-induced expression of HIF-1α target gene vascular endothelial growth factor (VEGF) was enhanced by the exogenous addition of MEF. Overall, these data indicate that hypoxia or HIF-1α positively regulates MEF expression and function.

Snapshots of Conformational Changes Shed Light into the NtrX Receiver Domain Signal Transduction Mechanism

Brucella abortus is an important pathogenic bacterium that has to overcome oxygen deficiency in order to achieve a successful infection. Previously, we proved that a two-component system formed by the histidine kinase NtrY and the response regulator NtrX is essential to achieve an adaptive response to low oxygen tension conditions. Even though the relevance of this signaling pathway has already been demonstrated in other microorganisms, its molecular activation mechanism has not yet been described in detail. In this article, we report the first crystal structures from different conformations of the NtrX receiver domain from B. abortus, and we propose a sequence of events to explain the structural rearrangements along the activation process. The analysis of the structures obtained in the presence of the phosphoryl group analog beryllofluoride led us to postulate that changes in the interface formed by the α4 helix and the β5 strand are important for the activation, producing a reorientation of the α5 helix. Also, a biochemical characterization of the NtrX receiver domain enzymatic activities was performed, describing its autophosphorylation and autodephosphorylation kinetics. Finally, the role of H85, an important residue, was addressed by site-directed mutagenesis. Overall, these results provide significant structural basis for understanding the response regulator activation in this bacterial two-component system.

Evaluation of the simulated physiological oocyte maturation system for improving bovine in vitro embryo production

The aim of this study was to test the simulated physiological oocyte maturation (SPOM)-adapted system during bovine oocyte maturation to improve embryo development. Oocytes were obtained from follicles of 3 to 8 mm in diameter that were aspirated from ovaries obtained from a slaughterhouse. To verify the effect of the maturation system on in vitro embryo production, the cleavage, blastocyst rates on Days 7 and 8, embryo size, and total cell number were evaluated. The resulting data on embryo development were analyzed by the chi-square test, whereas data on embryo size and total cell number were analyzed by the Kruskal-Wallis test. First, the SPOM system principle was tested in our IVM system, in which 0.01 IU/mL of purified FSH and 10% of fetal calf serum were used during maturation. However, the cleavage and blastocyst rates on Days 7 and 8 were drastically reduced compared with those of the control group (P < 0.05). Increasing the dose of purified FSH to 0.1 IU/mL in the SPOM-adapted system did not affect (P > 0.05) embryo production, which remained lower than that of the control group. When less competent oocytes obtained from 1 to 3 mm follicles were used, the SPOM-adapted system was also unable to improve embryo production. To make the adapted system as similar as possible to the reported system, recombinant FSH was associated with BSA during maturation and embryo culture was performed under low oxygen tension conditions. Nevertheless, a reduction (P < 0.05) in the blastocyst rates was also observed, whereas the size and total cell number were similar to those of the control group (P > 0.05). It can be concluded that an SPOM-adapted system used under different culture conditions does not improve in vitro embryo development.

PRODUCTION, PURIFICATION, AND CHEMICAL STABILITY OF RECOMBINANT HUMAN INTERFERON-γ IN LOW OXYGEN TENSION CONDITION: A FORMULATION APPROACH

The low stability of recombinant human interferon-γ (rhIFN-γ) therapeutic protein imposes some restrictions in its medical applications. In the current study, the effect of oxygen tension on the stability of purified rhIFN-γ was investigated. The rhIFN-γ was purified (>99%) by a two-step chromatographic process. Storage vials were filled by purified formulated product under normal atmospheric oxygen and low oxygen tension conditions. At different time intervals, the amounts of rhIFN-γ covalent dimers and deamidated forms were analyzed using analytical high-performance liquid chromatography (HPLC; size exclusion and cation exchange) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) methods. To determine the biological activity of purified rhIFN-γ, an antiviral activity assay against vesicular stomatitis virus (VSV) was performed. Upon rhIFN-γ long-term storage in a low oxygen tension condition, the amounts of rhIFN-γ covalent dimers and deamidated forms and also the biological activity of rhIFN-γ changed a little. In contrast, by 9 months of storage of rhIFN-γ preparations under normal atmospheric condition, the amount of covalent dimers and deamidated forms increased with time and reached to approximately 3.5% and 11.5% of the initial amount, respectively. The antiviral specific activity of 9-month-old rhIFN-γ preparations decreased to 41% of the initial amount at normal storage condition, while no significant reduction was seen at the low oxygen tension condition. In conclusion, oxygen tension during storage could have a significant impact on rhIFN-γ stability and finally on the quality of pharmaceutical rhIFN-γ product.

Logic Learning Machine creates explicit and stable rules stratifying neuroblastoma patients

BackgroundNeuroblastoma is the most common pediatric solid tumor. About fifty percent of high risk patients die despite treatment making the exploration of new and more effective strategies for improving stratification mandatory. Hypoxia is a condition of low oxygen tension occurring in poorly vascularized areas of the tumor associated with poor prognosis. We had previously defined a robust gene expression signature measuring the hypoxic component of neuroblastoma tumors (NB-hypo) which is a molecular risk factor. We wanted to develop a prognostic classifier of neuroblastoma patients' outcome blending existing knowledge on clinical and molecular risk factors with the prognostic NB-hypo signature. Furthermore, we were interested in classifiers outputting explicit rules that could be easily translated into the clinical setting.ResultsShadow Clustering (SC) technique, which leads to final models called Logic Learning Machine (LLM), exhibits a good accuracy and promises to fulfill the aims of the work. We utilized this algorithm to classify NB-patients on the bases of the following risk factors: Age at diagnosis, INSS stage, MYCN amplification and NB-hypo. The algorithm generated explicit classification rules in good agreement with existing clinical knowledge. Through an iterative procedure we identified and removed from the dataset those examples which caused instability in the rules. This workflow generated a stable classifier very accurate in predicting good and poor outcome patients. The good performance of the classifier was validated in an independent dataset. NB-hypo was an important component of the rules with a strength similar to that of tumor staging.ConclusionsThe novelty of our work is to identify stability, explicit rules and blending of molecular and clinical risk factors as the key features to generate classification rules for NB patients to be conveyed to the clinic and to be used to design new therapies. We derived, through LLM, a set of four stable rules identifying a new class of poor outcome patients that could benefit from new therapies potentially targeting tumor hypoxia or its consequences.

Generation of explicit rules predicting neuroblastoma patients’ outcome

Generation of explicit rules predicting neuroblastoma patients’ outcome

Translation of a Robust, Biology-Driven, Prognostic Classifier of Cancer Patients' Outcome into Clinically Relevant Rules

Motivations. Cancer patient's outcome is written in part in the gene expression profile of the tumor. Clinical bioinformatic is instrumental in extracting the relevant gene clusters (signatures), the prediction models and the rules for patients stratification and clinical decision making. Hypoxia, a condition of low oxygen tension occurring in poorly vascularized tissues, has a profound effects on tumor growth and resistance to therapy. We utilized a novel biology driven approach coupled with appropriate feature selection [1] to identify the signature of hypoxic neuroblastoma cells (NB-Hypo) that stratifies neuroblastoma patients in good and poor outcome [2]. In the present work, we develop and validate a robust classifier to predict neuroblastoma patients' outcome on the bases of tumor hypoxia and we identify the most informative clinically relevant rules that combine classical risk factors and NB-hypo prognostic signature. Methods. Gene expression profiles of 182 neuroblastoma tumors were used to develop and validate our prediction models. Validation was performed either by leave one out cross validation or 66% split of the dataset in training and testing. We utilized a Multi Layer Perceptron (MLP), a feedforward Artificial Neural Network classifier, to predict patients' outcome (alive or dead 5 years after diagnosis). Integrated analysis of classical risk factors and prognostic NB-hypo signature utilized either C4.5, an efficient algorithm used to generate decision tree or Rulex 2.0, a software suite capable of building Intelligible Learning Machines (ILM) through Shadow Clustering (SC) [3]. The classifiers were trained and tested on the expression values of the 62 probsets constituting NB-hypo signature. Furthermore, in some instances NB-hypo was condensed into a single binary attribute by means of an unsupervised k-means clustering of the patients' cohort based on the NB-hypo, 62 probsets expression values. Results. The NB-hypo classifier based on MLP predicted the outcome with an accuracy of 87% and was able to correctly predict poor outcome of all patients in the low-intermediate risk classes. The accuracy increased when NB-hypo classifier predicted the hypoxic state of neuroblastoma tumors even when it was not associated with poor outcome. Thus, NB-hypo classifier, while probing the hypoxic status of the tumor, is a new and robust predictor of neuroblastoma patient's outcome with very low error rate that decreases to negligible levels in localized tumors. Clinicians utilize established risk factors ( tumor stage, amplification of the MYCN oncogene or age at diagnosis) for prognosis and treatment choice. We investigated whether NB-hypo could be successfully added to the classical decision process improving risk definition and whether the relevant rules could be expressed in a clinically applicable form. We choose to utilize decision tree and ILM algorithms to facilitate the extraction of clinically applicable rules. Decision tree analysis revealed interesting relationships among risk factors and pointed to NB-hypo as the key element in identifying poor prognosis patients in stage 3 neuroblastoma. However, the divide and conquer approach employed by decision tree was unsatisfactory for a global study of these variables because of the excessive fragmentation of the database into small, poorly indicative groups of patients. In contrast, the covering algorithm adopted by SC identified a set of 11 rules each with a coverage greater than 30% and with less than 0.1% error. NB-hypo was integral part of these rules either as representative probsets or as a single binary attribute. Interestingly, the algorithm divided the expression values of individual probsets in broad (generally two), statistically different, categories corresponding to clearly identifiable low and high expression levels. This conversion was critical for counteracting the variability microarray experiment data. The importance of NB-hypo for outcome prediction of low risk neuroblastoma patients was confirmed. Moreover, we established rules for outcome prediction of stage 4 neuroblastoma patients that are very heterogeneous and difficult to stratify. In summary, we found that biology-based gene expression signatures and machine learning lead to patients outcome prediction and that appropriate clinical bioinformatic approaches can extract relevant rules translatable to the clinical setting. This approach was developed for neuroblastoma tumors but the rationale and methodology can be applied successfully to other types of cancer.

Oxygen sensing is impaired in ATM-defective cells

The transcription factor hypoxia-inducible factor 1α (HIF-1α) is a master regulator of cell adaptation to decreasing oxygen levels. High oxygen tension promotes proteosomal degradation of HIF-1α via a pathway that requires hydroxylation of prolines 402 and 564. Low oxygen tension, hypoxia, inactivates the hydroxylases responsible for these modifications through a mechanism that is not fully understood but appears to require mitochondrial respiration and production of reactive oxygen species, ROS. Cells from individuals affected by ataxia telangiectasia syndrome have an impaired mitochondrial activity and a constitutive oxidative stress. Here we show that, in these cells, HIF-1α is efficiently degraded even in condition of low oxygen tension. Mechanistically this depends from a blunted increase in intracellular concentration of ROS in response to hypoxia which in turn is due to an increased cellular capacity of buffering ROS. We suggest that regulation of HIF-1α stability may depend on fold change of ROS relative to the basal level more than on their absolute value. Since elevated oxidative stress is a hallmark of many human disorders our finding may be relevant to different pathologies.

Salmonella spp. survival strategies within the host gastrointestinal tract

Human salmonellosis infections are usually acquired via the food chain as a result of the ability of Salmonella serovars to colonize and persist within the gastrointestinal tract of their hosts. In addition, after food ingestion and in order to cause foodborne disease in humans, Salmonella must be able to resist several deleterious stress conditions which are part of the host defence against infections. This review gives an overview of the main defensive mechanisms involved in the Salmonella response to the extreme acid conditions of the stomach, and the elevated concentrations of bile salts, osmolytes and commensal bacterial metabolites, and the low oxygen tension conditions of the mammalian and avian gastrointestinal tracts.

Implications of the Inability of Listeria monocytogenes EGD-e To Grow Anaerobically Due to a Deletion in the Class III NrdD Ribonucleotide Reductase for Its Use as a Model Laboratory Strain

Listeria monocytogenes is a Gram-positive facultative intracellular bacterium that causes life-threatening diseases in humans. It grows and survives in environments of low oxygen tension and under conditions of strict anaerobiosis. Oxygen-limiting conditions may be an important factor in determining its pathogenicity. L. monocytogenes serovar 1/2a strain EGD-e has been employed intensively to elucidate the mechanisms of intracellular multiplication and virulence. Listeria possesses genes encoding class I aerobic and class III anaerobic ribonucleotide reductases (RNRs). The class III RNR consists of a catalytic subunit NrdD and an activase NrdG. Surprisingly, L. monocytogenes EGD-e, but not other L. monocytogenes strains or other listerial species, is unable to grow under strict anaerobic conditions. Inspection of listerial NrdD amino acid sequences revealed a six-amino acid deletion in the C-terminal portion of the EGD-e protein, next to the essential glycyl radical domain. Nevertheless, L. monocytogenes EGD-e can grow under microaerophilic conditions due to the recruitment of residual class Ia RNR activity. A three-dimensional (3D) model based on the structure of bacteriophage T4 NrdD identified the location of the deletion, which appears in a highly conserved part of the NrdD RNR structure, in the α/β barrel domain near the glycyl radical domain. The deleted KITPFE region is essential either for interactions with the NrdG activase or, indirectly, for the stability of the glycyl radical loop. Given that L. monocytogenes EGD-e lacks a functional anaerobic RNR, the present findings are relevant to the interpretation of studies of pathogenesis with this strain specifically, in particular under conditions of low oxygen tension.