Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool

Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.

Shotgun proteomics analysis of SARS-CoV-2-infected cells and how it can optimize whole viral particle antigen production for vaccines

Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and is continuing to spread rapidly around the globe. No effective vaccine is currently available to prevent COVID-19, and intense efforts are being invested worldwide into vaccine development. In this context, all technology platforms must overcome several challenges resulting from the use of an incompletely characterized new virus. These include finding the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles. Here, we describe a shotgun tandem mass spectrometry workflow, the data produced can be used to guide optimization of the conditions for viral amplification. In parallel, we analysed the changes occurring in the host cell proteome following SARS-CoV-2 infection to glean information on the biological processes modulated by the virus that could be further explored as potential drug targets to deal with the pandemic.

Direct Meta-Analyses Reveal Unexpected Microbial Life in the Highly Radioactive Water of an Operating Nuclear Reactor Core

The pools of nuclear reactor facilities constitute harsh environments for life, bathed with ionizing radiation, filled with demineralized water and containing toxic radioactive elements. The very few studies published to date have explored water pools used to store spent nuclear fuels. Due to access restrictions and strong handling constraints related to the high radioactivity level, nothing is presently known about life in water pools that directly cool nuclear cores. In this work, we investigated the microbial communities in the cooling pool of the French Osiris nuclear reactor using direct meta-omics approaches, namely, DNA metabarcoding and proteotyping based on 16S ribosomal RNA gene sequencing and on peptide analysis, respectively. We identified 25 genera in the highly radioactive core water supply during operation with radionuclide activity higher than 3 × 109 Bq/m3. The prevailing genera Variovorax and Sphingomonas at operation were supplanted by Methylobacterium, Asanoa, and Streptomyces during shutdown. Variovorax might use dihydrogen produced by water radiolysis as an energy source.

Exposure to low-dose bisphenol A impairs meiosis in the rat seminiferous tubule culture model: a physiotoxicogenomic approach

BACKGROUND

Bisphenol A (BPA) is one of the most widespread chemicals in the world and is suspected of being responsible for male reproductive impairments. Nevertheless, its molecular mode of action on spermatogenesis is unclear. This work combines physiology and toxicogenomics to identify mechanisms by which BPA affects the timing of meiosis and induces germ-cell abnormalities.

METHODS

We used a rat seminiferous tubule culture model mimicking the in vivo adult rat situation. BPA (1 nM and 10 nM) was added to the culture medium. Transcriptomic and meiotic studies were performed on the same cultures at the same exposure times (days 8, 14, and 21). Transcriptomics was performed using pangenomic rat microarrays. Immunocytochemistry was conducted with an anti-SCP3 antibody.

RESULTS

The gene expression analysis showed that the total number of differentially expressed transcripts was time but not dose dependent. We focused on 120 genes directly involved in the first meiotic prophase, sustaining immunocytochemistry. Sixty-two genes were directly involved in pairing and recombination, some of them with high fold changes. Immunocytochemistry indicated alteration of meiotic progression in the presence of BPA, with increased leptotene and decreased diplotene spermatocyte percentages and partial meiotic arrest at the pachytene checkpoint. Morphological abnormalities were observed at all stages of the meiotic prophase. The prevalent abnormalities were total asynapsis and apoptosis. Transcriptomic analysis sustained immunocytological observations.

CONCLUSION

We showed that low doses of BPA alter numerous genes expression, especially those involved in the reproductive system, and severely impair crucial events of the meiotic prophase leading to partial arrest of meiosis in rat seminiferous tubule cultures.

Reply to comment on Fisichella et al. (2012), "Intestinal toxicity evaluation of TiO2 degraded surface-treated nanoparticles: a combined physico-chemical and toxicogenomics approach in Caco-2 cells" by Faust et al

In this response, we discuss the major differences that clearly distinguish our results from those mentioned by Faust et al. In particular, the experiments have been conducted on nanoparticles of different nature, what mainly explains the observed discrepancies.

Alterations in gene expression in cultured human cells after acute exposure to uranium salt: Involvement of a mineralization regulator

The risk of exposure of workers or populations to materials, such as uranium, of nuclear fuel process origins is a major concern worldwide. Our goal is to improve the knowledge of mechanisms ruling its chemical toxicity, and to search for proteins as potential indicator of effect. Such a marker of internal damage remains to be discovered in the case of uranium. This study, based on DNA microarrays, reports a comparative gene expression analysis following acute uranium exposure of several human cell lines taken from kidneys or lungs as representative targets. Among uranium altered genes, no common gene was found between cells originating from lungs and kidney. In contrast, a set of 24 altered genes was common to two kidney cell lines. Transcriptional levels of a subset of renal genes were assessed with qRT-PCR. Furthermore, we highlighted a gene (SPP1) coding for a secreted protein (osteopontin) linked to ectopic mineralization. Immunoblotting assays showed that uranyl ions affect the excretion of osteopontin in a time- and dose-dependent manner. We consider that osteopontin, described as associated with bone resorbtion and kidney mineral stones, is a worthwhile candidate to be tested in vivo as a potential indicator of uranyl mineralization effects.

Primary progressive multiple sclerosis: a comparative study of the diagnostic criteria

We assessed the different sets of diagnostic criteria for primary progressive multiple sclerosis (PPMS), in order to determine their sensitivity when applied to a cohort of 261 PPMS patients. According to the Thompson criteria, 168 patients (64.4%) had definite PPMS, 84 patients (32.2%) had probable PPMS, and nine patients (3.4%) had possible PPMS; according to the McDonald criteria, 180 patients (69%) had PPMS; according to the revised McDonald criteria, 194 patients (74.3%) had PPMS. Our findings indicate that the revised McDonald criteria are more sensitive than the original McDonald criteria, but less sensitive than the Thompson criteria. Multiple Sclerosis 2007; 13: 622-625. http://msj.sagepub.com

Transcriptomic and proteomic responses of human renal HEK293 cells to uranium toxicity

The industrial use of uranium, in particular depleted uranium, has pin-pointed the need to review its chemical impact on human health. Global methodologies, applied to the field of toxicology, have demonstrated their applicability to investigation of fine molecular mechanisms. This report illustrate the power of toxicogenomics to evaluate the involvement of certain genes or proteins in response to uranium. We particularly show that 25% of modulated genes concern signal transduction and trafficking, that the calcium pathway is heavily disturbed and that nephroblastomas-related genes are involved (WIT-1, STMN1, and STMN2). A set of 18 genes was deregulated whatever the concentration of toxicant, which could constitute a signature of uranium exposure. Moreover, a group of downregulated genes, with corresponding disappearing proteins (HSP90, 14-3-3 protein, HMGB1) in two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), are good candidates for use as biomarkers of uranium effects. These results reveal a cross-checking between transcriptomic and proteomic technologies. Moreover, our temporal gene expression profiles suggest the existence of a concentration threshold between adaptive response and severe cell deregulation. Our results confirm the involvement of genes already described and also provide new highlights on cellular response to uranium.

[Prion diseases]

Creutzfeldt-Jakob disease, kuru, Gerstmann Sträussler Scheinker syndrome and fatal familial insomnia in humans, as well as scrapie and bovine spongiform encephalopathy, in animals, are fatal disorders of the central nervous system that are part of the group of transmissible spongiform encephalopathies, (TSE) or prion diseases. Neuronal intracellular spongiosis and the accumulation of abnormal, protease resistant prion protein in the nervous central system characterize TSE. The conformational change of a host protein, prion protein, into a pathological isoform is the key pathogenetic event in TSE. Despite their relative rarity, prion diseases have a great impact on the scientific community and society in general. There are two major reasons: first, the heretical hypothesis of a disease transmitted by an "infectious protein" in the absence of nucleic acid, the basis of the conformational transmissibility concept; second, the panic originated from the appearance of new variant Creutzfeldt-Jakob disease and the evidence linking it to the exposure of humans to bovine spongiform encephalopathy via food contaminated by affected bovine tissue. Novel therapeutic approaches are examined.

Gerstmann-Sträussler-Scheinker disease and the French-Alsatian A117V variant

Gerstmann-Sträussler-Scheinker disease is a rare familial form of prion disease. This autosomal dominant disorder is constantly associated with a point mutation on the PrP gene. Eight mutations affecting respectively codons 102, 105, 117, 145, 202, 212 and 218, have been so far described. Symptoms are variable and include ataxia and dementia. They generally appear between the fourth and sixth decade. Mean duration of the disease (5 years) is on the whole longer than that of other familial forms of prion diseases. Gerstmann-Sträussler-Scheinker disease is neuropathologically characterized by the presence of numerous multicentric or unicentric PrP amyloid deposits widespread throughout the encephalon. Spongiform change is inconstant. Neurofibrillary tangles have been described in some families. Clinicopathological features show considerable variability. Pathogenesis of amyloidosis and associated lesions as well as factors underlying the phenotypic polymorphism of the disease remain only partially known.

Decreased platelet aggregation during pregnancy correlates with gestational age

In vivo platelet aggregation was determined in pregnant women at different gestational ages and nonpregnant women by a modification of a method. A higher platelet count ratio (PCR) was found in pregnant women after a gestational age of 13 weeks. At 16-30 and 31-41 weeks of gestation, in vivo platelet aggregation was significantly decreased. The PCR, meaning the ratio of non-aggregated platelets to all circulating platelets, correlated significantly with gestational age. It is suggested that the decrease in in vivo aggregation measured during pregnancy reflects a summarized effect of different factors during pregnancy connected to placenta and uteroplacental vessels.

[Prion encephalopathies]

Spongiform encephalopathies, also called prion encephalopathies, are characterized, in human as well as in animals, by (1) their clinical picture which indicates strict localisation in central nervous system, (2) their histological aspect: spongiform degeneration and neuronal loss, and (3) their transmissibility in the same animal species but also from man to animal. The nature of the pathogenic agent is still debated. This agent could be one isoform of the prion protein which, probably because of a modification of its tertiary structure, is partially resistant to proteolytic enzymes. Recent description of a bovine spongiform encephalopathy caused by meat flour absorption has raised again the question of the transmissibility of these animal diseases to human.

Gerstmann-Sträussler-Scheinker disease in an Alsatian family: clinical and genetic studies

The clinical progression of Gerstmann-Sträussler-Scheinker disease in a family of Alsatian origin is reported. The age of onset and the duration of evolution were variable. The clinical picture became more complex over the generations: in the first generations, isolated dementia and in later generations a triad of pyramidal, pseudobulbar syndromes and dementia associated with spinal cord and cerebellar features. Prion gene analysis showed that four surviving patients carry double missense changes at codons 117 and 129, identical to those found in one case at necropsy and 10 other healthy members of the family. The missense changes were not found in 100 controls. No member of the family had modification of condons 102, 178, or 200. The lod score suggests linkage between the missense change at codon 117 and Gerstmann-Sträussler-Scheinker disease in this family.

Immunochemical, molecular genetic, and transmission studies on a case of Gerstmann-Sträussler-Scheinker syndrome

Using immunostaining with anti-prion protein (PrP) antiserum, we detected numerous kuru plaques in the brain of a 24-year-old man with Gerstmann-Sträussler-Scheinker syndrome. Immunoreactivity on Western blotting of the protease-resistant PrP fraction from the frozen brain was weak. PrP gene analysis showed substitution of alanine to valine in codon 117 but no substitution in codon 102. As the experimental transmission of the disease to mice was negative, a pathogen of a relatively low infectivity may cause the disease in predisposed family members.

Diagnosis of Chlamydia trachomatis infection--culture versus serology

The diagnostic value of different laboratory methods in detecting Chlamydia trachomatis infections in high risk groups was analysed. The efficiency of a direct specimen test was compared with serology (IgG and IgM ELISA) and culture in L929 cells, stained either with fluorescein conjugated monoclonal antibodies or with iodine. Patients (no. = 1041) with localized genital infections attending a STD clinic, sexual contacts and patients with ascending infections from urological and gynecological clinics were examined. Chlamydia trachomatis was detected in 225 patients: 210 (93.3%) were reactive in the direct test (smears stained with monoclonal antibodies), whereas culture missed only 5 (sensitivity 97.8%) when stained by the same method. Cultures stained with iodine produced the lowest recovery rate (73.8%), but this rate increased to 80.9% when a second passage was performed. In addition the prevalence of Neisseria gonorrhoeae, Mycoplasma hominis, Ureaplasma urealyticum, Candida albicans and Trichomonas vaginalis was investigated. In patients with non-gonococcal urethritis (no. = 331) and cervicitis (no. = 353), Chlamydia trachomatis was isolated in 32.3% and 12.8% respectively. However, this pathogen could be isolated in only 3 (15.8%) out of 19 patients with epididymitis and 15 (14%) out of 107 patients with adnexitis, although 66.7% and 93.3% respectively had specific IgG antibodies. Specific IgM could by detected with a sandwich ELISA in patients with adnexitis (46.7%), epididymitis (33.3%), cervicitis (22.2%), non-gonococcal urethritis (14%) and in the sexual partners of patients with genital infections (35.7%). The direct specimen test with monoclonal antibodies is the method of choice for the diagnosis of a C. trachomatis infection in patients with urethritis and cervicitis.(ABSTRACT TRUNCATED AT 250 WORDS)

[Emboligenic abscess of the aortic ring disclosing gonococcal endocarditis. Value of echocardiography]

Echocardiography has become a valuable diagnostic modality in bacterial endocarditis and of even more importance in following the subsequent course of the infection while on medical therapy. It can play an extremely important role in certain clinical circumstances, even before blood culture results are available or hemodynamic or auscultatory abnormalities appear. Nevertheless, in spite of this usefulness, the limitations of echocardiography should be recognized. The examination lacks absolute specificity and sensitivity which could result in inaccurate or delayed information in diagnosing a lesion or in recognizing local or regional complications. These advantages and limitations are well illustrated in an unusual case due to Neisseria gonorrhoeae, a causative agent whose incidence may increase over the years to come.