Prescribed fire selects for a pyrophilous soil sub-community in a northern California mixed conifer forest.

Prescribed fire is a critical strategy for mitigating the effects of catastrophic wildfires. While the above-ground response to fire has been well-documented, fewer studies have addressed the effect of prescribed fire on soil microorganisms. To understand how soil microbial communities respond to prescribed fire, we sampled four plots at a high temporal resolution (two burned, two controls), for 17 months, in a mixed conifer forest in northern California, USA.

Deciphering the Impact of Early-Life Exposures to Highly Variable Environmental Factors on Foetal and Child Health: Design of SEPAGES Couple-Child Cohort.

In humans, studies based on Developmental Origins of Health and Disease (DOHaD) concept and targeting short half-lived chemicals, including many endocrine disruptors, generally assessed exposures from spot biospecimens. Effects of early-life exposure to atmospheric pollutants were reported, based on outdoor air pollution levels. For both exposure families, exposure misclassification is expected from these designs: for non-persistent chemicals, because a spot biospecimen is unlikely to capture exposure over windows longer than a few days; for air pollutants, because indoor levels are ignored.

Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.

The worldwide incidence of pulmonary carcinoids is increasing, but little is known about their molecular characteristics. Through machine learning and multi-omics factor analysis, we compare and contrast the genomic profiles of 116 pulmonary carcinoids (including 35 atypical), 75 large-cell neuroendocrine carcinomas (LCNEC), and 66 small-cell lung cancers. Here we report that the integrative analyses on 257 lung neuroendocrine neoplasms stratify atypical carcinoids into two prognostic groups with a 10-year overall survival of 88% and 27%, respectively.

Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA.

Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability.

Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer.

Small-cell lung cancer (SCLC) is an aggressive lung tumor subtype with poor prognosis. We sequenced 29 SCLC exomes, 2 genomes and 15 transcriptomes and found an extremely high mutation rate of 7.4±1 protein-changing mutations per million base pairs.

Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer.

Unlabelled: While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines.

Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer.

Lung cancer remains one of the leading causes of cancer-related death in developed countries. Although lung adenocarcinomas with EGFR mutations or EML4-ALK fusions respond to treatment by epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) inhibition, respectively, squamous cell lung cancer currently lacks therapeutically exploitable genetic alterations. We conducted a systematic search in a set of 232 lung cancer specimens for genetic alterations that were therapeutically amenable and then performed high-resolution gene copy number analyses.

Preparative laser capture microdissection and single-pot cell wall material preparation: a novel method for tissue-specific analysis.

In adaptation to their function the walls of plant cell display tissue-specific variations of composition according to their developmental stage, cell type and stress of various origin. It is therefore important to obtain a precise analytical data describing the cell wall composition with respect to these different factors. In the present work, laser capture microdissection (LCM) was used for isolating different tissues from the stem of Urtica dioica L.

Telomere shortening and telomerase reverse transcriptase expression in preinvasive bronchial lesions.

Purpose: Telomerase, a ribonucleoprotein complex whose activity is related to the expression of its catalytic subunit human telomerase reverse transcriptase (hTERT), restores telomere length in tumor cells and enables immortality after p53/Rb inactivation has been achieved. To determine the timing of hTERT derepression during bronchial carcinogenesis and its relationship with telomere shortening and the p53/Rb pathway alterations, we did an immunohistochemical and in situ hybridization study in preinvasive and invasive bronchial lesions.

Experimental Design: hTERT, P53, P16, cyclin D1, Bax-to-Bcl2 ratio, and Ki67 immunostainings were done in 106 preneoplastic lesions and in paired lung carcinoma and normal bronchial mucosae.

Differential expression of telomerase reverse transcriptase (hTERT) in lung tumours.

Human telomerase reverse transcriptase is a ribonucleoprotein that synthesises telomeric sequences, which decrease at each cell division. In cancer cells, its activity is linked to telomere maintenance leading to unlimited cellular proliferation and immortality. To evaluate the prognostic value of the catalytic subunit telomerase reverse transcriptase (hTERT), we analysed its expression by immunohistochemistry in 122 formalin-fixed lung tumours including 42 squamous cell carcinoma (SCC), 43 adenocarcinoma (ADC), 19 basaloid carcinoma (BC) and 18 small-cell lung carcinoma (SCLC) in comparison with detection of hTERT mRNA by in situ hybridisation and relative telomerase activity by TRAP assay in a subset of tumours.

A simplified cytomegalovirus pp65 antigenemia assay procedure.

A simplified cytomegalovirus (CMV) pp65 antigenemia assay using a one-step erythrocyte lysis, fixation and permeabilization process was compared with a standard protocol, the CMV CINAkit (Argene Biosoft) assay. The results were comparable, both quantitatively and qualitatively. The new method saves time.

Importance of DNA fragmentation in apoptosis with regard to TUNEL specificity.

In the absence of a universal specific molecular tracer of apoptosis, structural DNA alterations provide the basis of labeling systems: double-strand fragmentation for TUNEL (terminal transferase-mediated dUTP nick end-labeling), denaturation for poly (A) in situ hybridization, immunogenicity of single strand DNA, all methods which imply limited specificity due to the unavoidable presence of DNA breaks in virtually all cells. Thus, TUNEL application has been restrained to a narrow spectrum of sample conditions which has limited, in particular, retrospective surveys and apoptotic nuclei-protein double labelings. In the apoptotic nucleus two main obstacles intervene between TUNEL reagents and their targets: DNA hypercondensation and proteins around DNA.

TUNEL apoptotic cell detection in tissue sections: critical evaluation and improvement.

TUNEL, i.e., terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling, has become a widely used staining method to assist in detection of apoptotic cells in tissue sections.

In situ apoptotic cell labeling by the TUNEL method: improvement and evaluation on cell preparations.

TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling) is a method of choice for rapid identification and quantification of the apoptotic cell fraction in cultured cell preparations. However, TUNEL application has been restricted to a narrow spectrum of sample conditions, and only detergents have been proposed as labeling enhancers. This study was aimed at extending TUNEL to variously fixed cells and improving TUNEL sensitivity by optimized pretreatments, the specificity being assessed by reference to the apoptotic morphology.

Comparison of 35S and chemiluminescence for HPV in situ hybridization in carcinoma cell lines and on human cervical intraepithelial neoplasia.

For in situ hybridization (ISH), development of sensitive, nontoxic alternatives to the use of radioactivity is a constant concern. In this trend, and close to chromogenes and fluorophores, chemiluminescence appears an attractive method. A first positive experience in immunocytochemistry and in ISH, by using the enhanced luminol as luminogene substrate for horseradish peroxidase (HRP) led us to compare the sensitivity of 35S autoradiography and chemiluminescence.

Comparison of seven bio- and chemiluminescent reagents for in situ detection of antigens and nucleic acids.

Bio- and chemiluminescence have proved sensitive enough to compete with chromogenic and radioisotopic tracers for in situ detection. However, they must also provide a discriminant morphological analysis of the specific signal. We have tested seven bio- or chemiluminescent reagents for tissue antigen and nucleic acid detection by immunocytochemistry (ICC) or in situ hybridization (ISH).

F(ab) secondary antibodies: a general method for double immunolabeling with primary antisera from the same species. Efficiency control by chemiluminescence.

We propose a general solution to the problem of using antibodies originating in the same species for double immunohistochemical labeling. It relies on the use of a two-step protocol in which a secondary polyclonal monovalent F(ab) antibody present in the first step blocks access in the second of the secondary antibody to the primary antibody, which is continuously present from the first step. The monovalence of the F(ab) fragment eliminates the possibility of its linking the primary antibody from the second step.

Enhanced chemiluminescence: a high-sensitivity detection system for in situ hybridization and immunohistochemistry.

The breakthrough of chemiluminescence in the field of solution immunoassays and transfer membranes prompted us to explore whether a light-based detection system could provide a gain in sensitivity over chromogenic and FITC markers for nucleic acid and protein detection on histological preparations. A Hamamatsu device and an enhanced chemiluminescence (ECL) luminol substrate of the peroxidase were used to detect epithelial and endothelial components by immunohistochemistry (IHC) and for in situ hybridization (ISH) of papilloma virus DNA. The accuracy of the signal was compared to that obtained with DAB-peroxidase, silver-enhanced DAB-peroxidase, NBT-BCIP-alkaline phosphatase, and FITC.

Ultrastructural localization of the major components of the extracellular matrix in normal rat nerve.

In this study we determined the ultrastructural distribution of the various components of the extracellular matrix (laminin, fibronectin, Type I, III, and IV collagens) of the normal peripheral nerve in adult rat. The localization of these macromolecules was investigated in basement membranes as well as in different areas of epi-, peri-, and endoneurium, by use of a pre-embedding immunoperoxidase method.

[Hyperventilation syndrome: current advances].

The hyperventilation syndrome has been described for half a century but clearly remains underdiagnosed. Its acute manifestation is easily diagnosed ("the tip of the iceberg") but its recognition in numerous subtle forms requires a particular degree of alertness on the part of the clinician ("the hidden part of the iceberg"). The incidence of this syndrome in the general population varies according to different authors as between 6-11% and may mimic diverse organic disorders.

[Contribution of polysomnography in the assessment of patients with chronic obstructive bronchopneumopathy].

15 COPD patients underwent a polysomnographic study demonstrating poor quality of sleep, a mean of SAO2 of 88.8 +/- 3.9% and a apneic-hypopnea index (AHI) of 5.

Quantitative image analysis with densitometry for immunohistochemistry and autoradiography of receptor binding sites--methodological considerations.

Major technical progress in the development of computer-based image analysis has made possible the entry of autoradiography and immunohistochemistry into a new era where quantification by densitometry has become easily accessible. Autoradiography could become quantitative and displayed adequate reproducibility with the help of emulsion-coated films and the use of scales of standards of known radioactivity exposed and analyzed in parallel to the tissue sections. Immunohistochemistry after revelation by a color-based enzymatic technique can also become quantitative, providing that standardization of the crucial steps of the procedure and calibration through a parallel treatment of a scale of antigen standards can be ensured.

[Value of monitoring of tracheal respiratory sounds in the diagnosis of nocturnal respiratory dysrhythmias].

Twenty-six patients underwent a polysomnigraphic study allowing sleep staging and respiratory events scoring with the use of the oronasal flow, abdominal, thoracic and total displacement (Respitracet), and ear oximetry. Moreover the patients were also equipped with a tracheal microphone giving a power rectified envelope (sonospirogram). Eleven patients showed abnormal respiratory events that were scored by visual lecture using all respiratory parameters (excluding the sonospirogram) and were classified as obstructive central and mixed apneas-hypopneas.

A human monoclonal IgM with autoantibody activities against heparan sulphate and the mitotic spindle.

A monoclonal IgM kappa from a patient with Waldenström's macroglobulinaemia (IgM-Rod) was found to react at temperatures below 28 degrees C with all tissue basement membranes and the cell coat of non-haematopoietic cells. IgM-Rod antibody was directed against heparan sulphate side chains of heparan sulphate proteoglycans as shown by binding in a solid-phase ELISA to heparan sulphate glycosaminoglycans but not to other purified subcomponents of the extracellular matrix; and by specific inhibition of the observed reactivity by heparitinase treatment. IgM-Rod showed cross-reactivity by indirect immunofluorescence with an as yet unidentified structure expressed in the nucleus during cell division and becoming associated with the mitotic spindle apparatus.