Environmental sources along natural cave ripening shape the microbiome and metabolome of artisanal blue-veined cheeses

Abstract Microorganisms colonising processing environments can significantly impact food quality and safety. Here we describe a detailed longitudinal study assessing the impact of cave ripening on the microbial succession and quality markers across different producers of blue-veined cheese. Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome and metabolome. The cheese microbiome was significantly determined by the microbiome of caves, which were a source of Brevibacterium, Corynebacterium, Staphylococcus, Tetragenococcus and Yaniella, among others, as demonstrated through source tracking and the characterization of 613 metagenome assembled genomes. Tetragenococcus koreensis and T. halophilus were detected at high abundance in cheese for the first time, associated with the occurrence of various metabolites, and showed high levels of horizontal gene transfer with other members of the cheese microbiome. Overall, we demonstrated that processing environments can be a source of non-starter microorganisms of relevance to ripening of artisanal fermented foods.

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The Influence of Bisphenol A (BPA) on Neuregulin 1-Like Immunoreactive Nerve Fibers in the Wall of Porcine Uterus

International Journal of Molecular Sciences ◽

10.3390/ijms19102962 ◽

2018 ◽

Vol 19 (10) ◽

pp. 2962 ◽

Cited By ~ 7

Author(s):

Liliana Rytel

Keyword(s):

Bisphenol A ◽

Nerve Fibers ◽

Double Immunofluorescence ◽

Negative Effects ◽

Protective Mechanisms ◽

Neuregulin 1 ◽

Small Doses ◽

The Impact ◽

First Time

Bisphenol A (BPA), a substance commonly used in the manufacture of plastics, shows multidirectional negative effects on humans and animals. Due to similarities to estrogens, BPA initially leads to disorders in the reproductive system. On the other hand, it is known that neuregulin 1 (NRG-1) is an active substance which enhances the survivability of cells, inhibits apoptosis, and protects tissues against damaging factors. Because the influence of BPA on the nervous system has also been described, the aim of the present study was to investigate for the first time the influence of various doses of BPA on neuregulin 1-like immunoreactive (NRG-1-LI) nerves located in the porcine uterus using the routine single- and double-immunofluorescence technique. The obtained results have shown that BPA increases the number and affects the neurochemical characterization of NRG-1-LI in the uterus, and changes are visible even under the impact of small doses of this toxin. The character of observed changes depended on the dose of BPA and the part of the uterus studied. These observations suggest that NRG-1 in nerves supplying the uterus may play roles in adaptive and protective mechanisms under the impact of BPA.

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The Okur-Chung Neurodevelopmental Syndrome (OCNDS) mutation CK2K198R leads to a rewiring of kinase specificity

10.1101/2021.04.05.438522 ◽

2021 ◽

Author(s):

Danielle M Caefer ◽

Nhat Q Phan ◽

Jennifer C Liddle ◽

Jeremy L Balsbaugh ◽

Joseph P O’Shea ◽

...

Keyword(s):

High Resolution ◽

Substrate Specificity ◽

Tyrosine Phosphorylation ◽

Initial Step ◽

Loss Of Function ◽

Scoring Method ◽

Disease Condition ◽

The Impact ◽

First Time

AbstractOkur-Chung Neurodevelopmental Syndrome (OCNDS) is caused by heterozygous mutations to the CSNK2A1 gene, which encodes the alpha subunit of casein kinase II (CK2). The most frequently occurring mutation is lysine 198 to arginine (K198R). To investigate the impact of this mutation, we first generated a high-resolution phosphorylation motif of CK2WT, including the first characterization of specificity for tyrosine phosphorylation activity. A second high resolution motif representing CK2K198R substrate specificity was also generated. Here we report for the first time the impact of the OCNDS associated CK2K198R mutation. Contrary to prior speculation, the mutation does not result in a loss of function, but rather shifts the substrate specificity of the kinase. Broadly speaking the mutation leads to 1) a decreased preference for acidic residues in the +1 position, 2) a decreased preference for threonine phosphorylation, 3) an increased preference for tyrosine phosphorylation, and 4) an alteration of the tyrosine phosphorylation specificity motif. To further investigate the result of this mutation we have developed a probability-based scoring method, allowing us to predict shifts in phosphorylation in the K198R mutant relative to the wild type kinase. As an initial step we have applied the methodology to the set of axonally localized ion channels in an effort to uncover potential alterations of the phosphoproteome associated with the OCNDS disease condition.

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Characterization of transport mechanisms and determinants critical for Na+-dependent Pisymport of the PiT family paralogs human PiT1 and PiT2

AJP Cell Physiology ◽

10.1152/ajpcell.00015.2006 ◽

2006 ◽

Vol 291 (6) ◽

pp. C1377-C1387 ◽

Cited By ~ 34

Author(s):

Pernille Bøttger ◽

Susanne E. Hede ◽

Morten Grunnet ◽

Boy Høyer ◽

Dan A. Klærke ◽

...

Keyword(s):

Mammalian Cells ◽

Divalent Cations ◽

Maximal Activity ◽

Xenopus Laevis Oocytes ◽

Transport Function ◽

Knockout Mutant ◽

Uptake Medium ◽

The Impact ◽

First Time

The general phosphate need in mammalian cells is accommodated by members of the Pitransport (PiT) family ( SLC20), which use either Na+or H+to mediate inorganic phosphate (Pi) symport. The mammalian PiT paralogs PiT1 and PiT2 are Na+-dependent Pi(NaPi) transporters and are exploited by a group of retroviruses for cell entry. Human PiT1 and PiT2 were characterized by expression in Xenopus laevis oocytes with32Pias a traceable Pisource. For PiT1, the Michaelis-Menten constant for Piwas determined as 322.5 ± 124.5 μM. PiT2 was analyzed for the first time and showed positive cooperativity in Piuptake with a half-maximal activity constant for Piof 163.5 ± 39.8 μM. PiT1- and PiT2-mediated Na+-dependent Piuptake functions were not significantly affected by acidic and alkaline pH and displayed similar Na+dependency patterns. However, only PiT2 was capable of Na+-independent Pitransport at acidic pH. Study of the impact of divalent cations Ca2+and Mg2+revealed that Ca2+was important, but not critical, for NaPitransport function of PiT proteins. To gain insight into the NaPicotransport function, we analyzed PiT2 and a PiT2 Pitransport knockout mutant using22Na+as a traceable Na+source. Na+was transported by PiT2 even without Piin the uptake medium and also when Pitransport function was knocked out. This is the first time decoupling of Pifrom Na+transport has been demonstrated for a PiT family member. Moreover, the results imply that putative transmembrane amino acids E55and E575are responsible for linking Piimport to Na+transport in PiT2.

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Multi-Steps Registration Protocol for Multimodal MR Images of Hip Skeletal Muscles in a Longitudinal Study

Applied Sciences ◽

10.3390/app10217823 ◽

2020 ◽

Vol 10 (21) ◽

pp. 7823

Author(s):

Lucia Fontana ◽

Alfonso Mastropietro ◽

Elisa Scalco ◽

Denis Peruzzo ◽

Elena Beretta ◽

...

Keyword(s):

Longitudinal Study ◽

Image Registration ◽

Mr Images ◽

Learning Rates ◽

Speed Up ◽

Muscle Magnetic Resonance Imaging ◽

Magnetic Resonance Imaging Mri ◽

First Time ◽

Tesla Scanner

Image registration is crucial in multimodal longitudinal skeletal muscle Magnetic Resonance Imaging (MRI) studies to extract reliable parameters that can be used as indicators for physio/pathological characterization of muscle tissue and for assessing the effectiveness of treatments. This paper aims at proposing a reliable registration protocol and evaluating its accuracy in a longitudinal study. The hips of 6 subjects were scanned, in a multimodal protocol, at 2 different time points by a 3 Tesla scanner; the proposed multi-step registration pipeline is based on rigid and elastic transformations implemented in SimpleITK using a multi-resolution technique. The effects of different image pre-processing (muscle masks, isotropic voxels) and different parameters’ values (learning rates and mesh sizes) were quantitatively assessed using standard accuracy indexes. Rigid registration alone does not provide satisfactory accuracy for inter-sessions alignment and a further elastic step is needed. The use of isotropic voxels, combined with the muscle masking, provides the best result in terms of accuracy. Learning rates can be increased to speed up the process without affecting the final results. The protocol described in this paper, complemented by open-source software, can be a useful guide for researchers that approach for the first time the issues related to the muscle MR image registration.

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Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population

10.1101/419598 ◽

2018 ◽

Cited By ~ 1

Author(s):

Maria Batool ◽

Syed Baqir Ali ◽

Ali Jaan ◽

Kehkishan Khalid ◽

Syeda Aba Ali ◽

...

Keyword(s):

Gut Microbiota ◽

Dietary Habits ◽

Daily Intake ◽

Early Career ◽

International Standards ◽

Rrna Gene ◽

Oral Microbiota ◽

Fermented Foods ◽

The Impact

ABSTRACTWe describe the characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults representing seven major geographies and six ethnicities in the country. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were early-career students or professionals belonging to 25 major cities of the country. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. Using the crude measure of percentage overlap or similarity between the gut microbiota profile of Pakistani and uBiome dataset as proxy for health, our sequencing indicated that the Pakistani gut microbiota was moderately healthy relative to the uBiome dataset and Pakistani women appeared healthier relative to men. The Pakistani gut microbiome seemed susceptible to obesity and weight gain, levels of probiotics was very high likely due to the popularity of milk-based and fermented foods in the Pakistani diet, and bacteria that metabolize starch and carbohydrates (typically seen in the gut microbiota of honey bee) were abnormally enriched in the gut of Pakistani men. Our investigations reveal serious issues with the dietary habits and lifestyle of Pakistani individuals of consuming food enriched in high carbohydrates and fats, overcooked in oil and spices, following a sedentary lifestyle, little or no daily intake of fresh fruits, over-consumption of antibiotics from a very early age, and health and hygiene standards that do not meet international standards. Our sequencing is the first step towards generating a country-wide understanding of the impact of the local diet and lifestyle on Pakistani gut microbiota and can help understand its overall association with health and wellness.

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Comparison of the In Vitro and Ex Vivo Permeation of Existing Topical Formulations Used in the Treatment of Facial Angiofibroma and Characterization of the Variations Observed

Pharmaceutics ◽

10.3390/pharmaceutics12111060 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1060

Author(s):

Guillaume Le Guyader ◽

Bernard Do ◽

Victoire Vieillard ◽

Karine Andrieux ◽

Muriel Paul

Keyword(s):

Ex Vivo ◽

Thermodynamic Activity ◽

Physico Chemical ◽

Ex Vivo Permeation ◽

Franz Cells ◽

Great Heterogeneity ◽

The Impact ◽

First Time

Rapamycin has been used topically to treat facial angiofibromas associated with tuberous sclerosis for more than a decade. In the absence of a commercial form, a large number of formulations have been clinically tested. However, given the great heterogeneity of these studies, particularly with regard to the response criteria, it was difficult to know the impact and thus to compare the relevance of the formulations used. The objective of this work was therefore to evaluate the link between the diffusion of rapamycin and the physico-chemical characteristics of these different formulations on Strat-M® membranes as well as on human skin using Franz cells. Our results underline the importance of the type of vehicle used (hydrogel > cream > lipophilic ointment), the soluble state of rapamycin and its concentration close to saturation to ensure maximum thermodynamic activity. Thus, this is the first time that a comparative study of the different rapamycin formulations identified in the literature for the management of facial angiofibromas has been carried out using a pharmaceutical and biopharmaceutical approach. It highlights the important parameters to be considered in the development and optimization of topical rapamycin formulations with regard to cutaneous absorption for clinical efficacy.

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Biofilms in Food Processing Environments: Challenges and Opportunities

Annual Review of Food Science and Technology ◽

10.1146/annurev-food-032818-121805 ◽

2019 ◽

Vol 10 (1) ◽

pp. 173-195 ◽

Cited By ~ 23

Author(s):

Avelino Alvarez-Ordóñez ◽

Laura M. Coughlan ◽

Romain Briandet ◽

Paul D. Cotter

Keyword(s):

Food Processing ◽

Biofilm Formation ◽

In Situ Monitoring ◽

Fermented Foods ◽

Microbial Biofilms ◽

Challenges And Opportunities ◽

Intraspecies Variability ◽

The Impact

This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.

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Application of a HACCP–QMRA approach for managing the impact of climate change on food quality and safety

Food Research International ◽

10.1016/j.foodres.2010.01.025 ◽

2010 ◽

Vol 43 (7) ◽

pp. 1915-1924 ◽

Cited By ~ 16

Author(s):

Daniela Popov Janevska ◽

Radovan Gospavic ◽

Ewa Pacholewicz ◽

Viktor Popov

Keyword(s):

Climate Change ◽

Food Quality ◽

Quality And Safety ◽

Impact Of Climate Change ◽

Food Quality And Safety ◽

The Impact

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The impact of functional genomics on microbiological food quality and safety

International Journal of Food Microbiology ◽

10.1016/j.ijfoodmicro.2006.04.014 ◽

2006 ◽

Vol 112 (3) ◽

pp. 195-199 ◽

Cited By ~ 19

Author(s):

S. Brul ◽

F. Schuren ◽

R. Montijn ◽

B.J.F. Keijser ◽

H. van der Spek ◽

...

Keyword(s):

Functional Genomics ◽

Food Quality ◽

Quality And Safety ◽

Food Quality And Safety ◽

The Impact

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Molecular Interaction Characterization Strategies for the Development of New Biotherapeutic Antibody Modalities

Antibodies ◽

10.3390/antib9020007 ◽

2020 ◽

Vol 9 (2) ◽

pp. 7

Author(s):

Xiangdan Wang ◽

Minh Michael Phan ◽

Ji Li ◽

Herman Gill ◽

Simon Williams ◽

...

Keyword(s):

Molecular Interaction ◽

Binding Kinetics ◽

Therapeutic Development ◽

Dosing Regimens ◽

Fit For Purpose ◽

Target Binding ◽

The Impact ◽

First Time

The characterization of target binding interactions is critical at each stage of antibody therapeutic development. During early development, it is important to design fit-for-purpose in vitro molecular interaction characterization (MIC) assays that accurately determine the binding kinetics and the affinity of therapeutic antibodies for their targets. Such information enables PK/PD (pharmacokinetics/pharmacodynamics) modeling, estimation of dosing regimens, and assessment of potency. While binding kinetics and affinities seem to be readily obtained, there is little discussion in the literature on how the information should be generated and used in a systematic manner along with other approaches to enable key drug development decisions. The introduction of new antibody modalities poses unique challenges to the development of MIC assays and further increases the need to discuss the impact of developing context-appropriate MIC assays to enable key decision making for these programs. In this paper, we discuss for the first time the challenges encountered when developing MIC assays supporting new antibody modalities. Additionally, through the presentation of several real case studies, we provide strategies to overcome these challenges to enable investigational new drug (IND) filings.

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