Development of real-time PCR and hybridization methods for detection and identification of thermophilic Campylobacter spp. in pig faecal samples

Aims: To develop a real-time (rt) PCR for species differentiation of thermophilic Campylobacter and to develop a method for assessing co-colonization of pigs by Campylobacter spp. Methods and results: The specificity of a developed 5’nuclease rt-PCR for species-specific identification of C. jejuni, C. coli, C. lari, C. upsaliensis and of a hipO gene nucleotide probe for detection of C. jejuni by colony-blot hybridization were determined by testing a total of 75 reference strains of Campylobacter spp. and related organisms. The rt-PCR method allowed species-specific detection of Campylobacter spp. in naturally infected pig faecal samples after an enrichment step, whereas the hybridization approach enhanced the specific isolation of C. jejuni (present in minority to C. coli) from pigs. Conclusions: The rt-PCR was specific for Campylobacter jejuni, C. coli, C. lari, and C. upsaliensis and the colony-blot hybridization approach provided an effective tool for isolation of C. jejuni from pig faecal samples typically dominated by C. coli. Significance and impact of study: Species differentiation between thermophilic Campylobacter is difficult by phenotypic methods and the developed rt-PCR provides an easy and fast method for such differentiation. Detection of C. jejuni by colony hybridization may increase the isolation rate of this species from pig feces

Increase in concentration of soluble HLA-G in high-quality embryos after intracytoplasmic sperm injection

Non-invasive methods are normally preferred to conventional invasive methods when selecting suitable embryos to improve pregnancy rates after assisted reproduction techniques. One of the most recognized non-invasive methods is to examine the supernatants of embryo culture media. Soluble human leukocyte antigen, class I, G (sHLA-G) antigen is a non-classical class I molecule that has been widely considered as a marker of pregnancy failure or implantation success. In the current study of some Iranian patients, we examined the concentration of sHLA-G at different time points after intracytoplasmic sperm injection and compared the rates to the morphology and quality of the selected embryos. We showed that the concentration of sHLA-G increases over time in high-quality embryos. We conclude that there is a positive relationship between morphology, quality, and sHLA-G concentration. We suggest that this relationship can be used to increase the chance of a successful pregnancy

An overview of chromatin modifications

The last 15 years have witnessed tremendous progress in elucidating the roles of chromatin modifications in transcription regulation, DNA repair, replication, recombination, and other genomic processes. In this issue of Biopolymers, a series of reviews will summarize recent advances in our understanding of chromatin modifying enzymes and explore unresolved questions with respect to their regulation and functions in gene expression and other nuclear processes. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 95–97, 2013.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94507/1/22158_ftp.pd

Spiral arm kinematics for Milky Way stellar populations

We present a new theoretical population synthesis model (the Galaxy model) to examine and deal with large amounts of data from surveys of the Milky Way and to decipher the present and past structure and history of our own Galaxy. We assume the Galaxy to consist of a superposition of many composite stellar populations belonging to the thin and thick discs, the stellar halo and the bulge, and to be surrounded by a single dark matter halo component. A global model for the Milky Way's gravitational potential is built up self-consistently with the density profiles from the Poisson equation. In turn, these density profiles are used to generate synthetic probability distribution functions (PDFs) for the distribution of stars in colour- magnitude diagrams (CMDs). Finally, the gravitational potential is used to constrain the stellar kinematics by means of the moment method on a (perturbed)-distribution function. Spiral arms perturb the axisymmetric disc distribution functions in the linear response framework of density-wave theory where we present an analytical formula of the so-called 'reduction factor' using hypergeometric functions. Finally, we consider an analytical non-axisymmetric model of extinction and an algorithm based on the concept of probability distribution function to handle CMDs with a large number of stars. A genetic algorithm is presented to investigate both the photometric and kinematic parameter space. This galaxy model represents the natural framework to reconstruct the structure of the Milky Way from the heterogeneous data set of surveys such as Gaia-ESO, SEGUE, APOGEE2, RAVE and the Gaia mission

Integrative mixture of experts to combine clinical factors and gene markers

Motivation: Microarrays are being increasingly used in cancer research to better characterize and classify tumors by selecting marker genes. However, as very few of these genes have been validated as predictive biomarkers so far, it is mostly conventional clinical and pathological factors that are being used as prognostic indicators of clinical course. Combining clinical data with gene expression data may add valuable information, but it is a challenging task due to their categorical versus continuous characteristics. We have further developed the mixture of experts (ME) methodology, a promising approach to tackle complex non-linear problems. Several variants are proposed in integrative ME as well as the inclusion of various gene selection methods to select a hybrid signature

Rim lesions are demonstrated in early relapsing–remitting multiple sclerosis using 3 T-based susceptibility-weighted imaging in a multi-institutional setting

PURPOSE: Rim lesions, characterised by a paramagnetic rim on susceptibility-based MRI, have been suggested to reflect chronic inflammatory demyelination in multiple sclerosis (MS) patients. Here, we assess, through susceptibility-weighted imaging (SWI), the prevalence, longitudinal volume evolution and clinical associations of rim lesions in subjects with early relapsing–remitting MS (RRMS). METHODS: Subjects (n = 44) with recently diagnosed RRMS underwent 3 T MRI at baseline (M0) and 1 year (M12) as part of a multi-centre study. SWI was acquired at M12 using a 3D segmented gradient-echo echo-planar imaging sequence. Rim lesions identified on SWI were manually segmented on FLAIR images at both time points for volumetric analysis. RESULTS: Twelve subjects (27%) had at least one rim lesion at M12. A linear mixed-effects model, with ‘subject’ as a random factor, revealed mixed evidence for the difference in longitudinal volume change between rim lesions and non-rim lesions (p = 0.0350 and p = 0.0556 for subjects with and without rim lesions, respectively). All 25 rim lesions identified showed T1-weighted hypointense signal. Subjects with and without rim lesions did not differ significantly with respect to age, disease duration or clinical measures of disability (p > 0.05). CONCLUSION: We demonstrate that rim lesions are detectable in early-stage RRMS on 3 T MRI across multiple centres, although their relationship to lesion enlargement is equivocal in this small cohort. Identification of SWI rims was subjective. Agreed criteria for defining rim lesions and their further validation as a biomarker of chronic inflammation are required for translation of SWI into routine MS clinical practice. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00234-021-02768-x

IL-33-dependent Type 2 inflammation during rhinovirus-induced asthma exacerbations in vivo

Rationale: Rhinoviruses are the major cause of asthma exacerbations; however, its underlying mechanisms are poorly understood. We hypothesized that the epithelial cell–derived cytokine IL-33 plays a central role in exacerbation pathogenesis through augmentation of type 2 inflammation. Objectives: To assess whether rhinovirus induces a type 2 inflammatory response in asthma in vivo and to define a role for IL-33 in this pathway. Methods: We used a human experimental model of rhinovirus infection and novel airway sampling techniques to measure IL-4, IL-5, IL-13, and IL-33 levels in the asthmatic and healthy airways during a rhinovirus infection. Additionally, we cultured human T cells and type 2 innate lymphoid cells (ILC2s) with the supernatants of rhinovirusinfected bronchial epithelial cells (BECs) to assess type 2 cytokine production in the presence or absence of IL-33 receptor blockade. Measurements and Main Results: IL-4, IL-5, IL-13, and IL-33 are all induced by rhinovirus in the asthmatic airway in vivo and relate to exacerbation severity. Further, induction of IL-33 correlates with viral load and IL-5 and IL-13 levels. Rhinovirus infection of human primary BECs induced IL-33, and culture of human T cells and ILC2s with supernatants of rhinovirus-infected BECs strongly induced type 2 cytokines. This induction was entirely dependent on IL-33. Conclusions: IL-33 and type 2 cytokines are induced during a rhinovirus-induced asthma exacerbation in vivo. Virus-induced IL-33 and IL-33–responsive T cells and ILC2s are key mechanistic links between viral infection and exacerbation of asthma. IL-33 inhibition is a novel therapeutic approach for asthma exacerbation

Negative phenotypic and genetic associations between copulation duration and longevity in male seed beetles

Reproduction can be costly and is predicted to trade-off against other characters. However, while these trade-offs are well documented for females, there has been less focus on aspects of male reproduction. Furthermore, those studies that have looked at males typically only investigate phenotypic associations, with the underlying genetics often ignored. Here, we report on phenotypic and genetic trade-offs in male reproductive effort in the seed beetle, Callosobruchus maculatus. We find that the duration of a male's first copulation is negatively associated with subsequent male survival, phenotypically and genetically. Our results are consistent with life-history theory and suggest that like females, males trade-off reproductive effort against longevity

Raman vibrational dynamics of hydrated ions in the low-frequency spectral region

The hydration structure of ions in aqueous environments can have a significant influence on their chemical and biological properties. Due to its inherent dynamical character, determination of the hydration shell around dissolved ions has proved challenging, mainly so for cations such as sodium and potassium which form diffuse and dynamic hydrating structures. The low frequency polarized Raman spectrum, as retrieved by time resolved isotropic optical Kerr effect measurements, is sensitive to structural fluctuations and can reveal information about ion-water interactions through their Raman active vibrational modes. Here we study a series of mixtures of sodium, potassium and lithium hydroxide solutions by changing cation concentration pairwise (namely, sodium/potassium or sodium/lithium) while keeping constant the hydroxide concentration. The hydroxide-water hydrogen bond vibration, which produces a well-defined isotropic Raman mode, appears at higher frequencies from the cation-water Raman active vibrations. In addition to previously reported lithium-water low frequency vibrations, clear spectral features could be resolved from the concentration studies and assigned to sodium-water hydration shell vibrations. However, potassium related low frequency spectral features remain elusive. The same method was applied to mixtures of the same cations with a halide anion (chloride) in order to rule out any specific features related to the dissolved hydroxide anion. Comparison between halide and hydroxide measurements confirmed the presence of the cation modes and further revealed a low frequency spectral feature related to hydroxide induced changes in water polarizability

Structure of the planetary boundary layer over southeast England: modeling and measurements

The Weather Research and Forecasting model was applied to analyze variations in the planetary boundary layer (PBL) structure over Southeast England including central and suburban London. The parameterizations and predictive skills of two nonlocal mixing PBL schemes, YSU and ACM2, and two local mixing PBL schemes, MYJ and MYNN2, were evaluated over a variety of stability conditions, with model predictions at a 3 km grid spacing. The PBL height predictions, which are critical for scaling turbulence and diffusion in meteorological and air quality models, show significant intra-scheme variance (> 20%), and the reasons are presented. ACM2 diagnoses the PBL height thermodynamically using the bulk Richardson number method, which leads to a good agreement with the lidar data for both unstable and stable conditions. The modeled vertical profiles in the PBL, such as wind speed, turbulent kinetic energy (TKE), and heat flux, exhibit large spreads across the PBL schemes. The TKE predicted by MYJ were found to be too small and show much less diurnal variation as compared with observations over London. MYNN2 produces better TKE predictions at low levels than MYJ, but its turbulent length scale increases with height in the upper part of the strongly convective PBL, where it should decrease. The local PBL schemes considerably underestimate the entrainment heat fluxes for convective cases. The nonlocal PBL schemes exhibit stronger mixing in the mean wind fields under convective conditions than the local PBL schemes and agree better with large-eddy simulation (LES) studies