Genomic aberrations associated with outcome in anaplastic oligodendroglial tumors treated within the EORTC phase III trial 26951

Despite similar morphological aspects, anaplastic oligodendroglial tumors (AOTs) form a heterogeneous clinical subgroup of gliomas. The chromosome arms 1p/19q codeletion has been shown to be a relevant biomarker in AOTs and to be perfectly exclusive from EGFR amplification in gliomas. To identify new genomic regions associated with prognosis, 60 AOTs from the EORTC trial 26951 were analyzed retrospectively using BAC-array-based comparative genomic hybridization. The data were processed using a binary tree method. Thirty-three BACs with prognostic value were identified distinguishing four genomic subgroups of AOTs with different prognosis (p < 0.0001). Type I tumors (25%) were characterized by: (1) an EGFR amplification, (2) a poor prognosis, (3) a higher rate of necrosis, and (4) an older age of patients. Type II tumors (21.7%) had: (1) loss of prognostic BACs located on 1p tightly associated with 19q deletion, (2) a longer survival, (3) an oligodendroglioma phenotype, and (4) a frontal location in brain. Type III AOTs (11.7%) exhibited: (1) a deletion of prognostic BACs located on 21q, and (2) a short survival. Finally, type IV tumors (41.7%) had different genomic patterns and prognosis than type I, II and III AOTs. Multivariate analysis showed that genomic type provides additional prognostic data to clinical, imaging and pathological features. Similar results were obtained in the cohort of 45 centrally reviewed?Cvalidated cases of AOTs. Whole genome analysis appears useful to screen the numerous genomic abnormalities observed in AOTs and to propose new biomarkers particularly in the non-1p/19q codeleted AOTs.     

In Silico Analyses of the Role of Codon Usage at the Hemagglutinin Cleavage Site in Highly Pathogenic Avian Influenza Genesis

A vast diversity of 16 influenza hemagglutinin (HA) subtypes are found in birds. Interestingly, viruses from only two subtypes, H5 and H7, have so far evolved into highly pathogenic avian influenza viruses (HPAIVs) following insertions or substitutions at the HA cleavage site by the viral polymerase. The mechanisms underlying this striking subtype specificity are still unknown. Here, we compiled a comprehensive dataset of 20,488 avian influenza virus HA sequences to investigate differences in nucleotide and amino acid usage at the HA cleavage site between subtypes and how these might impact the genesis of HPAIVs by polymerase stuttering and realignment. We found that sequences of the H5 and H7 subtypes stand out by their high purine content at the HA cleavage site. In addition, fewer substitutions were necessary in H5 and H7 HAs than in HAs from other subtypes to acquire an insertion-prone HA cleavage site sequence, as defined based on in vitro and in vivo data from the literature. Codon usage was more favorable for HPAIV genesis in sequences of viruses isolated from species or geographical regions in which HPAIV genesis is more frequently observed in nature. The results of the present analyses suggest that the subtype restriction of HPAIV genesis to H5 and H7 influenza viruses might be due to the particular codon usage at the HA cleavage site in these subtypes.     

FtsEX-independent control of RipA-mediated cell separation in Corynebacteriales

The bacterial cell wall is a multi-layered mesh, whose major component is peptidoglycan (PG), a sugar polymer cross-linked by short peptide stems. During cell division, a careful balance of PG synthesis and degradation, precisely coordinated both in time and space, is necessary to prevent uncontrolled destruction of the cell wall. In Corynebacteriales, the D,L endopeptidase RipA has emerged as a major PG hydrolase for cell separation, and RipA defaults have major implications for virulence of the human pathogens Mycobacterium tuberculosis and Corynebacterium diphtheriae. However, the precise mechanisms by which RipA mediates cell separation remain elusive. Here we report phylogenetic, biochemical, and structural analysis of the Corynebacterium glutamicum homologue of RipA, Cg1735. The crystal structures of full-length Cg1735 in two different crystal forms revealed the C-terminal NlpC/P60 catalytic domain obtruded by its N-terminal conserved coiled-coil domain, which locks the enzyme in an autoinhibited state. We show that this autoinhibition is relieved by the extracellular core domain of the transmembrane septal protein Cg1604. The crystal structure of Cg1604 revealed a (β/α) protein with an overall topology similar to that of receiver domains from response regulator proteins. The atomic model of the Cg1735–Cg1604 complex, based on bioinformatical and mutational analysis, indicates that a conserved, distal-membrane helical insertion in Cg1604 is responsible for Cg1735 activation. The reported data provide important insights into how intracellular cell division signal(s), yet to be identified, control PG hydrolysis during RipA-mediated cell separation in Corynebacteriales.

The Corynebacteriales order of bacteria includes many significant human pathogens, such as Mycobacterium tuberculosis (Mtb) and Corynebacterium diphtheriae. These organisms, often referred to as mycolates, display an atypical cell envelope architecture. Their peptidoglycan (PG) cell wall matrix is uniquely decorated with arabinogalactan polymers that covalently anchor an outer surface layer—the mycomembrane—primarily made up of mycolic acids (1). Long viewed as a relatively inert barrier to osmotic lysis, the PG sacculus is now known to form a dynamic structure that undergoes constant growth, remodeling, and partitioning during the cell cycle (2). Despite extensive biochemical and genetic characterization of the enzymes responsible for the synthesis and degradation of PG (3–5), the mechanisms by which these enzymes coordinate their activities and synchronize them with the cell cycle status remain poorly defined. During cytokinesis, the PG layer is synthesized continuously at the septal junction (6) and needs to be hydrolyzed at precisely the right time and place to allow daughter cell separation (V-snapping). The PG hydrolases essential for this process must be tightly regulated to avoid toxicity (7), since lack of activation leads to multi-septate elongated cells (8) and conversely their dysregulation can be lethal to bacteria (9).PG hydrolase genes usually show high redundancy, and many of these enzymes form multi-protein complexes in which divisome proteins control the hydrolytic activity through proteolysis, protein–protein interactions, or allosteric regulation (10–12). Despite their importance, limited information is available on the PG hydrolases essential for cell division in Corynebacteriales. In Mtb, possibly one of the best studied organisms in this respect, the major PG hydrolase involved in cell separation is Rv1477, a member of the NlpC/P60 superfamily that is also called RipA (for Rpf-interacting protein A) (13, 14). RipA depletion results in the formation of elongated multi-septated cells in vitro, both in Mtb and Mycobacterium smegmatis (14, 15), and leads to reduced Mtb replication in macrophages and to clearance of Mtb in infected mice (15). In Corynebacterium glutamicum (Cglu), another NlpC/P60 superfamily member, Cg1735, was found to fulfill a similar role. Disruption of cg1735 resulted in elongated cells with multiple septa (16, 17), a morphological phenotype that was not observed upon disruption of any of the three other genes (cg0784, cg2401, or cg2402) coding for NlpC/P60 proteins in the genome (16). A similar defect in cell separation involving the formation of chains of bacteria was observed in C. diphtheriae upon disruption of the Cg1735 homolog DIP1281 (18) and in M. marinum upon disruption of IipA (19). Here we show that all these NlpC/P60 hydrolases essential for cell separation are indeed part of a single family in Corynebacteriales containing Mtb RipA. We describe the full-length crystal structure of one of them, Cglu Cg1735, which reveals a striking arrangement of the N-terminal coiled-coil domain tightly associated to the C-terminal NlpC/P60 catalytic domain (CD). We demonstrate that this autoinhibition is released by the membrane-bound periplasmic protein Cg1604 and map the site of interaction. Together with phylogenetic analysis, biochemical, and biophysical characterization, this structural study provides new important insights into the mode of action of the RipA family of endopeptidases on cell separation in Corynebacteriales.     

When Broca experiences the Janus syndrome: an ER-fMRI study comparing sentence comprehension and cognitive sequence processing

The determining of brain regions that exhibit specific activity during sentence comprehension compared to other non-linguistic cognitive tasks constitutes one of the important challenges in the domain of functional neuroimaging of the faculty of language. In the current paper we report an event-related functional magnetic resonance imaging (ER-fMRI) experiment, in which we directly compared the cerebral basis of sentence comprehension on the one hand, and of abstract sequence processing on the other hand. Previous experimental work done in our group, as well as different observations from recent behavioural, neurophysiological and functional neuroimaging experiments led us to propose the hypothesis that both of these tasks would share certain computational properties. Thus, this experiment was designed to show which brain regions would be implicated in both tasks and compare them to brain regions that would be specifically engaged in sentence comprehension. Results from this experiment suggest that distinct sub-regions in the left prefrontal cortex, potentially including Broca's area show distinct activation patterns during both of these tasks. Results are discussed in the context of a construction-based model of sentence processing (see Dominey and Hoen, 2006, this issue) that is based on a dual-path processing mechanism separating function and content information processing. We propose and discuss the hypothesis that subparts of Broca's area BA 44 and BA 45 would respectively be implicated in two different aspects of sentence comprehension: i) a general structure mapping capability and ii) the online integration of semantic representations onto structural constraints.     

Papanicolaou's nebular cells are related to HPV infection and HSIL

Metaplastic cells with nebular cytoplasmic changes in the cervical smear are classified in the Dutch coding system for cervical screening as KOPAC O8 cells. Since these nebulated cells are already documented by Papanicolaou, we refer to these cells as Papanicolaou's nebular cells. We examined the simultaneous presence of these characteristic metaplastic cells and high-grade squamous intraepithelial lesion (HSIL) in a population-based data base from January 1991 and December 1996. The odds ratio (OR) of nebular cells concurring with HSIL increases with age. For the age cohort 30 years, the OR was 7.8 with a 95% confidence interval (CI) of 4.4-13.9. For the age cohort 60 years, the OR was 35.3 with a 95% CI of 7.8-159.2. Aiming to determine the nature of these nebular metaplastic cells, we performed Chlamydia and HPV PCR on 587 and 1,483 smears, respectively. With an OR of 0.9 [0.3-2.4] it is unlikely that Chlamydia plays a role in the appearance of these nebular cells in the smear. This study shows that with an OR of 5.9 [1.7-21.3] HPV is not only related to large koilocytosis but also to a nebular change of small metaplastic cells. This study reports that nebular changes of small metaplastic cells are related to cervical cancer and to HPV infection.     

Affording what's free and paying for choice: comparing the cost of public and private hospitalizations in urban Kerala

OBJECTIVE: To assess the cost of public and private hospitalizations in urban Kerala and discuss policy implications of social disparities in the economic burden of hospital care. METHODS: The NSSO survey on health care (1995-1996) for urban Kerala was analysed with regards to expenditure incurred by hospital episodes. Multilevel linear models were built to assess factors associated with levels of health expenditure. FINDINGS: Hospital care involves paying admission fees in 68% of cases of hospitalizations (98% in private and 20% in public sector) in urban Kerala. Poor households and those headed by casual workers show significantly lower levels of health expenditure and a higher proportion of health-related loss of income than other social groups. Although there is significant expenditure in both sectors for these groups, hospitalization on free public wards is associated with lower expenditure than other options. Factors linked with higher expenditure are: duration of stay; hospitalizations on paying public wards and in the private sector; hospitalizations for above poverty line households and hospitalizations for chronic illnesses. Expenditure for services bought from outside the hospital is important in the public sector. CONCLUSION: Hospitalization incurs significant expenditure in urban Kerala. Greater availability of free medical services in the public sector and financial protection against the cost of hospitalization are warranted.     

Beneficial Effects of High Intensity Interval Training and/or Linseed Oil Supplementation to Limit Obesity-Induced Oxidative Stress in High Fat Diet-Fed Rats

High-intensity interval training (HIIT) and linseed oil (LO) supplementation are effective strategies to reduce obesity-induced oxidative stress. Our aim was to determine whether the HIIT + LO combination prevents obesity-induced oxidative stress in high fat diet (HFD)-fed rats. HFD-fed 8-week-old, male, Wistar rats were subdivided in four groups: HFD, LO (2% of sunflower oil replaced with 2% of LO in the HFD), HIIT (4 days/week for 12 weeks), and HIIT + LO. Wistar rats fed a low-fat diet (LFD) were used as controls. Epididymal and subcutaneous adipose tissue, gastrocnemius muscle, liver, and plasma samples were collected to measure oxidative stress markers (AOPP, oxLDL), antioxidant (SOD, CAT, and GPx activities) and pro-oxidant (NOx and XO) enzyme activities. Compared with the LFD, the HFD altered the pro/antioxidant status in different tissues (increase of AOPP, oxLDL, SOD and catalase activities in plasma, and SOD activity increase in liver and decrease in adipose tissues) but not in gastrocnemius. LO upregulated CAT activity and decreased NOx in liver. HIIT alleviated HFD negative effects in liver by reducing SOD and NOx activities. Moreover, the HIIT + LO combination potentiated SOD activity upregulation in subcutaneous tissue. HIIT and LO supplementation have independent beneficial effects on the pro/antioxidant balance. Their association promotes SOD activity in subcutaneous adipose tissue.     

Determination of Synthetic Musks in Surface Sediment from the Bizerte Lagoon by QuEChERS Extraction Followed by GC-MS

A new analytical method for the simultaneous determination of eight synthetic musks compounds (SMs) including five polycyclic musks (PCMs) and three nitro musks (NMs) was validated for sediment samples based on a simple QuEChERS (Quick, Easy, Cheap, Effective, Rugged and Safe) sample preparation procedure followed by gas chromatography–mass spectrometry (GC–MS). Good analytical performances were obtained for all the target compounds. For the validation of the method, internal calibration (IC) and internal calibration with QuEChERS (ICQ) were compared. Good linearity was obtained for both calibration methods with determination coefficients (R²) ranging between 0.990 for Musk Xylene (MX) and 0.999 for Tonalide (AHTN) with IC and between 0.991 for Musk Ketone (MK) and 0.999 for Traseolide (ATII) with ICQ. The repeatability ranges were 0.1?%–1.9?% with the IC and 0.1?%–2.6?% with the ICQ. The apparent recoveries obtained for SMs in the standard reference sediment (SRM1944) varied in the range of 70?%–98?% and 75?%–103?% in the sediment from the Bizerte Lagoon (Tunisia). The absolute recoveries ranged between 61?% and 92?% for the SRM1944 and between 61?% and 89?% in the sediment from the Bizerte Lagoon. The limits of detection (LOD) calculated for the two main compounds, Galaxolide (HHCB) and Tonalide (AHTN) were 0.3 and 0.1 ng g^?1 respectively. The LODs obtained for ADBI (Celestolide), AHMI (Phantolide), ATII (Traseolide), MM (Muks mosken), MK (Musk Ketone) and MX (Musk Xylene) were 0.08, 0.12, 0.03, 0.34, 0.11, 0.08, 0.10 and 0.15 ng g^?1 respectively. The levels of ∑SMs in surface sediments from the Bizerte Lagoon ranged from 1.4 to 4.5 ng g^?1, which are 1000 times lower that the predicted no effect concentration (PNEC) for marine organisms.