St\"{a}ckel representations of stationary KdV systems

In this article we study St\"{a}ckel representations of stationary KdV systems. Using Lax formalism we prove that these systems have two different representations as separable St\"{a}ckel systems of Benenti type, related with different foliations of the stationary manifold. We do it by constructing an explicit transformation between the jet coordinates of stationary KdV systems and separation variables of the corresponding Benenti systems for arbitrary number of degrees of freedom. Moreover, on the stationary manifold, we present the explicit form of Miura map between both representations of stationary KdV systems, which also yields their bi-Hamiltonian formulation.Comment: 18 pagage

Step by step optimization of luminescence thermometry in MgTiO3:Cr3+, Nd3+@SiO2 nanoparticles towards bioapplications

The increasing popularity of luminescent nanothermometry in recent years can be attributed to its application potential in biomedicine. In response to this need, we describe a biocompatible bimodal luminescent thermometer that operates in ratiometric and luminescence lifetime modes based on particles of MgTiO3:Cr3+,Nd3+@SiO2. The introduction of Cr3+ and Nd3+ dopants enabled the luminescence of Ti3+ ions to be observed, and the difference in the thermal quenching rates of Cr3+ (4T2→4A2), Ti3+ (2T2→2E) and Nd3+ (4F3/2 → 4I11/2) ions enabled the ratiometric thermometers. The highest sensitivity reaching SR = 1.00%K−1 was obtained for MgTiO3:0.1 % Cr3+, 0.1 % Nd3+ at 203 K. The shortening of the lifetime of the 4T2 level of Cr3+ ions associated with its thermal depopulation allows to develop a lifetime-based thermometer with a relative sensitivity reaching 0.85–1.18%K−1 in the physiological temperature range. The deposition of a SiO2 shell on a MgTiO3:Cr3+,Nd3+ did not introduce significant changes in the shape of the emission spectrum and slightly elongates the lifetime by reducing the probability of surface-related nonradiative processes. More importantly, the thermometric performance of this luminescence thermometer was preserved. The low cytotoxicity of the obtained materials underlines their potential in bioapplications of the described luminescent thermometers

Draft Genome Sequences of Mycobacterium kansasii Strains 1010001454, 1010001458, 1010001468, 1010001493, 1010001495, and 1010001469, Isolated from Environmental Sources

Mycobacterium kansasii belongs to the nontuberculous mycobacteria (NTM) and causes opportunistic infections with both pulmonary and extrapulmonary manifestations. Here, we report the draft genome sequences of six environmental M. kansasii strains, designated 1010001495 (type I), 1010001469 (type II), 1010001468 (type III), 1010001458 (type IV), 1010001454 (type V), and 1010001493 (type V), originally isolated in five different European countries.The study was financed by the National Centre for Research and Development: “LIDER” Program (contract no. LIDER/044/457/L-4/12/NCBR/2013)

rs67047829 genotypes of ERV3-1/ZNF117 are associated with lower body mass index in the Polish population

There is now substantial evidence that zinc-finger proteins are implicated in adiposity. Aims were to datamine for high-frequency (near-neutral selection) pretermination-codon (PTC) single-nucleotide polymorphisms (SNPs; n = 141) from a database with > 550,000 variants and analyze possible association with body mass index in a large Polish sample (n = 5757). BMI was regressed (males/females together or separately) against genetic models. Regression for rs67047829 uncovered an interaction-independent association with BMI with both sexes together: mean ± standard deviation, kg/m2: [G];[G], 25.4 ± 4.59 (n = 3650); [G](;)[A], 25.0 ± 4.28 (n = 731); [A];[A], 23.4 ± 3.60 (n = 44); additive model adjusted for age and sex: p = 4.08 × 10–5; beta: − 0.0458, 95% confidence interval (CI) − 0.0732 : − 0.0183; surviving Bonferroni correction; for males: [G];[G], 24.8 ± 4.94 (n = 1878); [G](;)[A], 24.2 ± 4.31 (n = 386); [A];[A], 22.4 ± 3.69 (n = 23); p = 4.20 × 10–4; beta: − 0.0573, CI − 0.0947 : − 0.0199. For average-height males the difference between [G];[G] and [A];[A] genotypes would correspond to ~ 6 kg, suggesting considerable protection against increased BMI. rs67047829 gives a pretermination codon in ERV3-1 which shares an exonic region and possibly promoter with ZNF117, previously associated with adiposity and type-2 diabetes. As this result occurs in a near-neutral Mendelian setting, a drug targetting ERV3-1/ZNF117 might potentially provide considerable benefits with minimal side-effects. This result needs to be replicated, followed by analyses of splice-variant mRNAs and protein expression.The POPULOUS database was the outcome of the project TESTOPLEK which was funded by the Innovative Economy Operational Programme provided by the European Regional Development Fund 2007–2013. This source had no involvement in the study other than funding for the database

The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions

Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention

The genetic basis of endometriosis and comorbidity with other pain and inflammatory conditions

Endometriosis is a common condition associated with debilitating pelvic pain and infertility. A genome-wide association study meta-analysis, including 60,674 cases and 701,926 controls of European and East Asian descent, identified 42 genome-wide significant loci comprising 49 distinct association signals. Effect sizes were largest for stage 3/4 disease, driven by ovarian endometriosis. Identified signals explained up to 5.01% of disease variance and regulated expression or methylation of genes in endometrium and blood, many of which were associated with pain perception/maintenance (SRP14/BMF, GDAP1, MLLT10, BSN and NGF). We observed significant genetic correlations between endometriosis and 11 pain conditions, including migraine, back and multisite chronic pain (MCP), as well as inflammatory conditions, including asthma and osteoarthritis. Multitrait genetic analyses identified substantial sharing of variants associated with endometriosis and MCP/migraine. Targeted investigations of genetically regulated mechanisms shared between endometriosis and other pain conditions are needed to aid the development of new treatments and facilitate early symptomatic intervention

Anonimizacja w dobie wielkich danych – sytuacja biobanków w kontekście RODO

Technological development increased abilities of data analysis collecting gathering and obtaining from wide range of sources including national health registries. Aim of, entering into force on May 2018, General Data Protection Regulation (GDPR) is to regulate analysis of wide range of personal data from profiling to healthy issues. New regulations may hamper the implementation of research, or realization of projects under Horizon 2020 or Digital Poland, that based on data sharing. In order not to waste the opportunities and benefits for humanity that modern technology and „open data” can bring, appropriate measures must be taken to protect the privacy of individuals. But then there is next trap. The more data is protected in the context of privacy protection, the less useful they are for scientific purposes. The key point is to find right balance between security and usability

In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

Introduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors

Genomic insights into the Mycobacterium kansasii complex : an update

Only very recently, has it been proposed that the hitherto existing Mycobacteriumkansasii subtypes (I–VI) should be elevated, each, to a species rank. Consequently, the former M. kansasii subtypes have been denominated as Mycobacterium kansasii (former type I), Mycobacterium persicum (II), Mycobacterium pseudokansasii (III), Mycobacterium innocens (V), and Mycobacterium attenuatum (VI). The present work extends the recently published findings by using a three-pronged computational strategy, based on the alignment fraction-average nucleotide identity, genome-to-genome distance, and core-genome phylogeny, yet essentially independent and much larger sample, and thus delivers a more refined and complete picture of the M. kansasii complex. Furthermore, five canonical taxonomic markers were used, i.e., 16S rRNA, hsp65, rpoB, and tuf genes, as well as the 16S-23S rRNA intergenic spacer region (ITS). The three major methods produced highly concordant results, corroborating the view that each M. kansasii subtype does represent a distinct species. This work not only consolidates the position of five of the currently erected species, but also provides a description of the sixth one, i.e., Mycobacterium ostraviense sp. nov. to replace the former subtype IV. By showing a close genetic relatedness, amonophyletic origin, and overlapping phenotypes, our findings support the recognition of the M. kansasii complex (MKC), accommodating all M. kansasii-derived species and Mycobacterium gastri. None of the most commonly used taxonomic markers was shown to accurately distinguish all the MKC species. Likewise, no species-specific phenotypic characteristics were found allowing for species differentiation within the complex, except the non-photochromogenicity of M. gastri. To distinguish, most reliably, between the MKC species, and between M. kansasii and M. persicum in particular, whole-genome-based approaches should be applied. In the absence of clear differences in the distribution of the virulence-associated region of difference 1 genes among the M. kansasii-derived species, the pathogenic potential of each of these species can only be speculatively assessed based on their prevalence among the clinically relevant population. Large-scale molecular epidemiological studies are needed to provide a better understanding of the clinical significance and pathobiology of the MKC species. The results of the in vitro drug susceptibility profiling emphasize the priority of rifampicin administration in the treatment of MKC-induced infections, while undermining the use of ethambutol, due to a high resistance to this drug