Antilisterial Properties of Selected Strains from the Autochthonous Microbiota of a Swiss Artisan Soft Smear Cheese.

High incidences of the foodborne pathogen have been reported on smear cheeses, and despite increased hygiene efforts, this incidence has remained stable in recent years. Applying antilisterial strains may increase the safety of smear cheeses. To find and test antilisterial strains, we inoculated fresh soft cheeses from nine dairies with the surrogate species and assessed its growth under standardized ripening conditions.

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

Background: As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need.

Results: OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses.

High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.

Background: Next-generation sequencing (NGS) methods and especially 16S rRNA gene amplicon sequencing have become indispensable tools in microbial ecology. While they have opened up new possibilities for studying microbial communities, they also have one drawback, namely providing only relative abundances and thus compositional data. Quantitative PCR (qPCR) has been used for years for the quantification of bacteria.

Antimicrobial Susceptibility of subsp. from Milk Products and Other Habitats.

As components of many cheese starter cultures, strains of subsp. () must be tested for their antimicrobial susceptibility to avoid the potential horizontal transfer of antibiotic resistance (ABR) determinants in the human body or in the environment. To this end, a phenotypic test, as well as a screening for antibiotic resistance genes (ARGs) in genome sequences, is commonly performed.

Development of a High-Throughput Microfluidic qPCR System for the Quantitative Determination of Quality-Relevant Bacteria in Cheese.

The composition of the cheese microbiome has an important impact on the sensorial quality and safety of cheese. Therefore, much effort has been made to investigate the microbial community composition of cheese. Quantitative real-time polymerase chain reaction (qPCR) is a well-established method for detecting and quantifying bacteria.

Evaluation of a new culture medium for the enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese.

Enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese is challenging, due to the relatively high number of species it may host. We describe medium SPY9.

Antibiotic Susceptibility Profiles of Pediococcus pentosaceus from Various Origins and Their Implications for the Safety Assessment of Strains with Food-Technology Applications.

Abstract: In the fight against the spread of antibiotic resistance, authorities usually require that strains "intentionally added into the food chain" be tested for their antibiotic susceptibility. This applies to strains used in starter or adjunct cultures for the production of fermented foods, such as many strains of Pediococcus pentosaceus. The European Food Safety Authority recommends testing strains for their antibiotic susceptibility based on both genomic and phenotypic approaches.

SpeciesPrimer: a bioinformatics pipeline dedicated to the design of qPCR primers for the quantification of bacterial species.

Background: Quantitative real-time PCR (qPCR) is a well-established method for detecting and quantifying bacteria, and it is progressively replacing culture-based diagnostic methods in food microbiology. High-throughput qPCR using microfluidics brings further advantages by providing faster results, decreasing the costs per sample and reducing errors due to automatic distribution of samples and reagents. In order to develop a high-throughput qPCR approach for the rapid and cost-efficient quantification of microbial species in complex systems such as fermented foods (for instance, cheese), the preliminary setup of qPCR assays working efficiently under identical PCR conditions is required.

Toxicology and Pharmacokinetic Studies in Mice and Nonhuman Primates of the Nontoxic, Efficient, Targeted Hexameric FasL: CTLA4-FasL.

Cytotoxic T-lymphocyte antigen 4 (CTLA4)-FasL, a homo-hexameric signal converter protein, is capable of inducing robust apoptosis in malignant cells of the B-cell lineage expressing its cognate B7 and Fas targets, while sparing nonmalignant ones. This fusion protein's striking proapoptotic efficacy stems from its complementary abilities to coordinately activate apoptotic signals and abrogate antiapoptotic ones. A limiting factor in translating FasL or Fas receptor agonists into the clinic has been lethal hepatotoxicity.

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.

Background: Reads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics.

Update on Tetracycline Susceptibility of Pediococcus acidilactici Based on Strains Isolated from Swiss Cheese and Whey.

Bacterial strains used as starter cultures in the production of fermented foods may act as reservoirs for antibiotic resistance (AbR) genes. To avoid the introduction of such genes into the food chain, the presence of acquired AbR in bacterial strains added to food must be tested. Standard protocols and microbiological cut-off values have been defined to provide practitioners with a basis for evaluating whether their bacterial isolates harbor an acquired resistance to a given antibiotic.

Fn14·TRAIL fusion protein is oligomerized by TWEAK into a superefficient TRAIL analog.

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) demonstrates specific anti-cancer activity, but insufficient efficacy in patients. A fusion protein Fn14·TRAIL, that combines soluble TRAIL molecule with a specific TWEAK receptor Fn14, is a better apoptosis-inducer for hepatocellular carcinomas than soluble TRAIL. However, Fn14·TRAIL does not effectively induce apoptosis in tumors of the lymphoid origin.

Highly efficient, in-vivo Fas-mediated apoptosis of B-cell lymphoma by hexameric CTLA4-FasL.

Non-Hodgkin lymphomas (NHLs) account for 4% of all malignancies. 5-year survival rate increased to 50% with new treatment modalities, however there is need for new effective treatment for the more aggressive, relapsing forms. Recently, CTLA4-FasL, that can bind to B7 and Fas receptor (Fas), was shown to induce robust apoptosis of cell lines originating from B cell lymphomas expressing both B7 and Fas, by activating pro-apoptotic signals in parallel to abrogating anti-apoptotic ones.

Linking bacterial population dynamics and nutrient removal in the granular sludge biofilm ecosystem engineered for wastewater treatment.

Intensive nutrient removal from wastewater in anaerobic-aerobic systems using granular sludge should rely on optimal balances at biofilm and microbial ecology levels. This study targets the impacts of reactor characteristics and fluctuations in operation conditions on nutrient removal and bacterial community structures by means of microbial and numerical ecology methods. The dynamics of both predominant and accompanying populations were investigated with high resolution on temporal and phylogenetic scales in two reactors operated during 5 months with synthetic wastewater.

Fn14•TRAIL effectively inhibits hepatocellular carcinoma growth.

Background: New strategies for the treatment of hepatocellular carcinoma (HCC) are needed, given that currently available chemotherapeutics are inefficient. Since tumor growth reflects the net balance between pro-proliferative and death signaling, agents shifting the equilibrium toward the latter are of considerable interest. The TWEAK:Fn14 signaling axis promotes tumor cell proliferation and tumor angiogenesis, while TRAIL:TRAIL-receptor (TRAIL-R) interactions selectively induce apoptosis in malignant cells.

Correlations between environmental variables and bacterial community structures suggest Fe(III) and vinyl chloride reduction as antagonistic terminal electron-accepting processes.

Natural attenuation of anaerobic aquifers contaminated with tetrachloroethene (PCE) often results in the accumulation of the intermediates cis-dichloroethene and vinyl chloride (VC) which are even more toxic than the parent compound. Reasons for this accumulation were investigated in a PCE-contaminated aquifer in which VC accumulation has previously been shown to occur using stable isotope techniques. Multifactorial analysis of bacterial community structure data and environmental variables showed that in general terminal electron-accepting processes were shaping the bacterial community structures.

PyroTRF-ID: a novel bioinformatics methodology for the affiliation of terminal-restriction fragments using 16S rRNA gene pyrosequencing data.

Background: In molecular microbial ecology, massive sequencing is gradually replacing classical fingerprinting techniques such as terminal-restriction fragment length polymorphism (T-RFLP) combined with cloning-sequencing for the characterization of microbiomes. Here, a bioinformatics methodology for pyrosequencing-based T-RF identification (PyroTRF-ID) was developed to combine pyrosequencing and T-RFLP approaches for the description of microbial communities. The strength of this methodology relies on the identification of T-RFs by comparison of experimental and digital T-RFLP profiles obtained from the same samples.

Ecology and biogeography of bacterial communities associated with chloroethene-contaminated aquifers.

Massive usage, along with careless handling, storage, spills, and leakages made chloroethenes (CEs) one of the most abundant classes of groundwater contaminants. Anaerobic organohalide respiring bacteria (OHRB) can couple reductive dechlorination of CEs with energy conservation, a central microbial process in (enhanced) natural attenuation of CE-contaminated aquifers. Spatial variability of OHRB guild members present in contaminated sites has not yet been investigated in detail and it is not known whether the spatial localization of contaminated sites could impact differentially remediation capacities.

CD40·FasL and CTLA-4·FasL fusion proteins induce apoptosis in malignant cell lines by dual signaling.

Evolution of apoptosis resistance in both lymphoma and leukemia cells is well documented, and induction of apoptosis in malignant cells is a major goal of cancer therapy. Up-regulation of anti-apoptotic signals is one of the mechanisms whereby resistance to apoptosis emerges. We have previously described the fusion proteins CD40·FasL and CTLA-4·FasL, which are formed from two functional membrane proteins and induce apoptosis of activated T cells.

Ex vivo transduction of human dermal tissue structures for autologous implantation production and delivery of therapeutic proteins.

Systemic delivery of therapeutic proteins through gene transfer approaches has been carried out mostly by ex vivo transduction of single cells or by direct in vivo injection of an expression vector. In this work an intact miniature biopsy of human dermis (microdermis) is harvested and transduced ex vivo by a viral vector encoding a gene for the therapeutic protein. The microdermis preserves its three-dimensional structure and viability during the ex vivo manipulations.

Human erythropoietin gene therapy for patients with chronic renal failure.

Gene therapy holds a major promise. However, until now, this promise was fulfilled only in few cases, in rare genetic diseases. One very common clinical condition is anemia.