Homozygosity Haplotype and Whole-Exome Sequencing Analysis to Identify Potentially Functional Rare Variants Involved in Multiple Sclerosis among Sardinian Families

Multiple Sclerosis (MS) is a complex multifactorial autoimmune disease, whose sex- and age-adjusted prevalence in Sardinia (Italy) is among the highest worldwide. To date, 233 loci were associated with MS and almost 20% of risk heritability is attributable to common genetic variants, but many low-frequency and rare variants remain to be discovered. Here, we aimed to contribute to the understanding of the genetic basis of MS by investigating potentially functional rare variants. To this end, we analyzed thirteen multiplex Sardinian families with Immunochip genotyping data. For five families, Whole Exome Sequencing (WES) data were also available. Firstly, we performed a non-parametric Homozygosity Haplotype analysis for identifying the Region from Common Ancestor (RCA). Then, on these potential disease-linked RCA, we searched for the presence of rare variants shared by the affected individuals by analyzing WES data. We found: (i) a variant (43181034 T > G) in the splicing region on exon 27 of CUL9; (ii) a variant (50245517 A > C) in the splicing region on exon 16 of ATP9A; (iii) a non-synonymous variant (43223539 A > C), on exon 9 of TTBK1; (iv) a non-synonymous variant (42976917 A > C) on exon 9 of PPP2R5D; and v) a variant (109859349-109859354) in 3′UTR of MYO16.     

Hafnia alvei lipopolysaccharides: Isolation, sugar composition and SDS-PAGE analysis

Abstract Lipopolysaccharides (LPS) of 33 strains of Hafnia alvei were isolated and purified. LPS content of the dry bacterial mass ranged from 1.2 to 4.5%. All examined lipopolysaccharides contained glucose, glucosamine, heptose, 3-deoxy-octulosonic acid and often galactose. Rhamnose, mannose, galactosamine, mannosamine and unidentified amino sugars were found in some H. alvei strains. Sialic acid was present in LPS of one strain. d -3-Hydroxybutyryl groups also were identified in lipopolysaccharides of 5 strains of this genus.
SDS-PAGE of the lipopolysaccharides was presented in the paper. According to these results two core types exist in H. alvei .     

Phylogenetic and biochemical characterization of acidophilic bacteria

Abstract: In the course of our studies to determine appropriate conditions to transform Thiobacillus ferrooxidans , we have adopted a tetrathionate-containing medium. A number of different, apparently stable colony morphologies have arisen from cultures presumed to be pure while grown on iron-containing medium. In an effort to assess whether these different morphologies are indicative of previously undetected contamination, or simply manifestations of physiological variability within a strain, we have applied a number of biochemical and genetic techniques, including cellular fatty acid analysis and 16S rRNA sequence determination. These data should allow us to unequivocally characterize and compare the organisms present in our cultures.     

THE FUNCTION OF HEAT-SHOCK PROTEINS IN STRESS TOLERANCE

We earlier demonstrated that hsp68 is deficiently induced upon stress in the glucocorticoid-resistant, dedifferentiated Reuber rat hepatoma clone 2 cells, but is strongly activated in the differentiated, glucocorticoid-sensitive Faza 967 cells from which clone 2 was derived. We used the two cell types to address the questions whether hsp68 is specifically involved in the development of thermotolerance and/or thermoresistance or drug resistance. Our experiments show that clone 2 cells were not protected from the killing effect of heat by pretreatment with sodium arsenite, whereas Faza 967 cells were. These results strongly suggest a role of hsp68 in the development of thermotolerance in hepatoma cells. Stable heat-resistant variants of clone 2 cells were also isolated, where an increased basal expression of several hsps was observed together with the (at least partial) restoration of the heat-inducibility of hsp68. These results suggest that several hsps are needed to protect the critical biological processes at high temperature. The heat-resistant hepatoma cells also became resistant to several anticancer drugs. The multidrug resistance of the hepatoma variants correlates with the overexpression of the plasma membrane P-glycoprotein. Our results showing that severely stressed hepatoma cells overexpressed the mdr gene(s) raise the possibility that the P-gp may participate in protection against environmental stress such as heat.     

Galectin-9 recognizes and exhibits antimicrobial activity toward microbes expressing blood group–like antigens

While adaptive immunity recognizes a nearly infinite range of antigenic determinants, immune tolerance renders adaptive immunity vulnerable to microbes decorated in self-like antigens. Recent studies suggest that sugar-binding proteins galectin-4 and galectin-8 bind microbes expressing blood group antigens. However, the binding profile and potential antimicrobial activity of other galectins, particularly galectin-9 (Gal-9), has remained incompletely defined. Here, we demonstrate that while Gal-9 possesses strong binding preference for ABO(H) blood group antigens, each domain exhibits distinct binding patterns, with the C-terminal domain (Gal-9C) exhibiting higher binding to blood group B than the N-terminal domain (Gal-9N). Despite this binding preference, Gal-9 readily killed blood group B–positive Escherichia coli, whereas Gal-9N displayed higher killing activity against this microbe than Gal-9C. Utilization of microarrays populated with blood group O antigens from a diverse array of microbes revealed that Gal-9 can bind various microbial glycans, whereas Gal-9N and Gal-9C displayed distinct and overlapping binding preferences. Flow cytometric examination of intact microbes corroborated the microbial glycan microarray findings, demonstrating that Gal-9, Gal-9N, and Gal-9C also possess the capacity to recognize distinct strains of Providencia alcalifaciens and Klebsiella pneumoniae that express mammalian blood group–like antigens while failing to bind related strains that do not express mammalian-like glycans. In each case of microbial binding, Gal-9, Gal-9N, and Gal-9C induced microbial death. In contrast, while Gal-9, Gal-9N, and Gal-9C engaged red blood cells, each failed to induce hemolysis. These data suggest that Gal-9 recognition of distinct microbial strains may provide antimicrobial activity against molecular mimicry.     

Early endocytotic steps in elicited macrophages: omega-shaped plasma membrane vesicles at their cell surface.

Fluid-phase and receptor-mediated endocytosis were studied in Freund's adjuvant elicited macrophages. These cells were found to bind and internalize significantly larger amounts of peroxidase-antiperoxidase (PAP) immune complex than resident macrophages. Similarly the rate of the fluid-phase uptake was higher in elicited cells. When studying the early steps of endocytotic processes, omega-shaped plasma membrane pits (d～90 nm) were found at the macrophage cell surface. Although occurring occasionally in resident cells, their number was highly increased after elicitation in 30% of the macrophage cell population. The different morphology of these cells coincided with a lower endocytotic activity and a very strong ecto Ca²⁺-ATPase reaction. The present findings indicate that the elicited macrophage population is heterogenous and consists of different subclasses.     

Diel phytoplankton periodicity in Mikołajskie lake,Poland, as determined by different methods in parallel

Photosynthetic rates as measured by the oxygen light and dark bottle method were highly correlated with estimates using the ¹⁴C technique. The high O₂/¹⁴C ratios found are explained by algal respiration and extracellular release which are included in photosynthetic measurements by the oxygen technique, while the ¹⁴C method yields values close to net photosynthesis. Separation of net- and nannoplankton using a 50 μm plankton net for filtration was not comparable to distinctions made by microscopic examination. Separation of both by filtration caused a significant decrease in the photosynthetic activity of nannoplankton in 24-hour incubations, but had no detectable effect after 4 hours of exposure. “Bottle effects” in 24-hour measurements of photosynthesis were similar using both methods. Asymmetric photosynthetic time-curves as well as vertical phytoplankton migrations were the main reasons for errors in estimates of daily photosynthetic rates from part-day incubations which were extrapolated to the entire day.     

Effect of Thermal Effluents and Retention Time on Lake Functioning and Ecological Efficiencies in Plankton Communities

The following changes were observed in three lakes as a result of their heating and decrease of retention time (data for summer periods): increase of mixing rate, active bottom area, and nutrients (P_inorg., N_inorg.) concentrations; significant changes in gross primary production, phytoplankton biomass and production of filtering cladocerans. These changes seem to indicate the higher efficiency of utilization of autochthonous trophic resources and energy transfer in plankton.     

The case for the hybrid capital approach for the measurement of the welfare and sustainability

This paper provides an overview of the plethora of approaches that are available to measure welfare and sustainable development. Many methods exist but there is no consensus on the ‘correct’ approach. Furthermore, we also show that the wide variety of sustainable development indictor (SDI) sets which have been adopted also show significant differences. We argue that this is mostly because many of these studies do not use a theoretical approach. We argue that the ‘capital approach’, which is used in the sustainability debate, is the most promising method to enhance international harmonization. Support is mounting in the scientific, policy and statistical communities for this approach in which economic capital, human capital, natural capital and social capital are distinguished. Many applications of this method express these capital stocks in monetary units (the ‘monetary capital approach’). This paper argues that the ‘hybrid capital approach’, in which the capital stocks can also be measured in non-monetary units, is probably more likely to achieve consensus over a large number of countries and institutes. Also a number of challenges remain for the capital approach. We argue that ideally the indicators should be based on satellite accounts of the national accounting framework. Also the capital approach could be further expanded to current welfare, progress of societies, inequality, and the international dimension of sustainability. We conclude that if the hybrid capital approach is adopted it may become easier to make consistent, theoretically sound and policy relevant comparisons between countries.