A human protein atlas for normal and cancer tissues based on antibody proteomics

Antibody-based proteomics provides a powerful approach for the functional study of the human proteome involving the systematic generation of protein-specific affinity reagents. We used this strategy to construct a comprehensive, antibody-based protein atlas for expression and localization profiles in 48 normal human tissues and 20 different cancers. Here we report a new publicly available database containing, in the first version, approximately 400,000 high resolution images corresponding to more than 700 antibodies toward human proteins. Each image has been annotated by a certified pathologist to provide a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues. Our results suggest it should be possible to extend this analysis to the majority of all human proteins thus providing a valuable tool for medical and biological research.     

SNaPshot Assay for the Detection of the Most Common CFTR Mutations in Infertile Men

Congenital bilateral absence of vas deferens (CBAVD) is the most common CFTR-related disorder (CFTR-RD) that explains about 1–2% of the male infertility cases. Controversial data have been published regarding the involvement of CFTR mutations in infertile men with non-obstructive azoospermia and oligozoospermia. Here, we describe single base extension (SNaPshot) assay for detection of 11 common CFTR mutations: F508del, G542X, N1303K, 621+1G->T, G551D, R553X, R1162X, W1282X, R117H, 2184insA and 1717-1G->A and IVS8polyT variants. The assay was validated on 50 previously genotyped samples and was used to screen a total of 369 infertile men with different impairment of spermatogenesis and 136 fertile controls. Our results show that double heterozygosity of cystic fibrosis (CF) and CFTR-related disorder (CFTR-RD) mutations are found in a high percentage (22.7%) of infertile men with obstructive azoospermia, but not in other studied groups of infertile men. The SNaPshot assay described here is an inexpensive, fast and robust method for primary screening of the most common CFTR mutations both in patients with classical CF and CFTR-RD. It can contribute to better understanding of the role of CFTR mutations in impaired spermatogenesis, ultimately leading to improved management of infertile men.     

Neuroimmunomodulative properties of dipeptidyl peptidase IV/CD26 in a TNBS-induced model of colitis in mice

Causal connections between dipeptidyl peptidase IV, also known as CD26 molecule (DPP IV/CD26) and inflammatory bowel disease (IBD) have been shown, but mechanisms of these interactions are unclear. Our hypothesis was that DPP IV/CD26 could affect the neuroimmune response during inflammatory events. Therefore, we aimed to evaluate its possible role and the relevance of the gut-brain axis in a model of IBD in mice. Trinitrobenzenesulfonic acid-induced (TNBS) colitis was induced in CD26-deficient (CD26(-/-) ) and wild-type (C57BL/6) mice. Pathohistological and histomorphometrical measurements were done. Concentrations and protein expressions of DPP IV/CD26 substrates neuropeptide Y (NPY) and vasoactive intestinal peptide (VIP) were determined. Concentrations of IL-6 and IL-10 were evaluated. Investigations were conducted at systemic and local levels. Acute inflammation induced increased serum NPY concentrations in both mice strains, more enhanced in CD26(-/-) mice. Increased NPY concentrations were found in colon and brain of C57BL/6 mice, while in CD26(-/-) animals only in colon. VIP and IL-6 serum and tissue concentrations were increased in both mice strains in acute inflammation, more pronouncedly in CD26(-/-) mice. IL-10 concentrations, after a decrease in serum of both mice strains, increased promptly in CD26(-/-) mice. Decreased IL-10 concentration was found in brain of C57BL/6 mice, while it was increased in colon of CD26(-/-) mice in acute inflammation. DPP IV/CD26 deficiency affects the neuroimmune response at systemic and local levels during colitis development and resolution in mice. Inflammatory changes in the colon reflected on investigated parameters in the brain, suggesting an important role of the gut-brain axis in IBD pathogenesis.     

TMBIM5 is the Ca2+/H+ antiporter of mammalian mitochondria

Mitochondrial Ca²⁺ ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca²⁺ content and cytosolic Ca²⁺ homeostasis strictly depend on Ca²⁺ transporters. In recent decades, the major players responsible for mitochondrial Ca²⁺ uptake and release have been identified, except the mitochondrial Ca²⁺/H⁺ exchanger (CHE). Originally identified as the mitochondrial K⁺/H⁺ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cell‐based and cell‐free biochemical assays demonstrate the absence or greatly reduced Na⁺‐independent mitochondrial Ca²⁺ release in TMBIM5 knockout or pH‐sensing site mutants, respectively, and pH‐dependent Ca²⁺ transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the long‐sought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca²⁺ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca²⁺ exchange.     

Quantitative determination of secoiridoid and xanthone glycosides of Gentiana dinarica Beck cultured in vitro

Gentiana dinarica Beck, native to the Balkan Dinaric Mountains, was established in vitro from axillary shoot buds. It was maintained in the form of shoot cultures on MS medium supplemented with 1.0 mg l^?1 6-benzyladenine (BA) and 0.1 mg l^?1 α-naphthaleneacetic acid and excised root cultures were maintained on ½ MS medium with 0.5 mg l^?1 indole-3-butyric acid (IBA). Shoot cultures, adventitious roots and excised root cultures were analysed by HPLC techniques for the presence of secoiridoids and xanthones. Gentiopicrin and swertiamarin, the dominant components of shoot cultures, could not be detected in root cultures. Xanthones were present in both shoot and root cultures with norswertianin-1-O-primeveroside as the dominant metabolite. The secoiridoid and xanthone content, although characteristic for certain plant organs, was dependent on the concentration of plant growth regulators (BA and IBA) added to the medium. BA in the shoot multiplication stage strongly increased the secondary metabolite (SEM) content of shoot cultures. IBA had little effect on SEM accumulation in shoots during rooting, while it moderately stimulated SEM accumulation in excised root cultures.     

Influence of carbohydrate source on xanthone content in root cultures of Gentiana dinarica Beck

The effects of different types and concentrations of sugars on root growth and xanthone production in root culture of Gentiana dinarica were investigated. The results showed that sucrose, glucose and fructose all supported root growth, and sucrose was superior in terms of growth index, dry mass and fresh/dry mass ratio then fructose or glucose at the same concentrations. However, considering equimolar concentration of sugars, their contribution to the root growth was similar. The HPLC analysis of roots indicated the presence of xanthone compounds, and the contents of norswertianin-1-O-primeveroside (1), norswertianin-1-O-glucoside (2), gentioside (3) and norswertianin (4) were evaluated. In all samples, norswertianin-1-O-primeveroside (1) was present in highest concentration, followed by norswertianin-1-O-glucoside (2), whereas gentioside (3) and norswertianin (4) were present in lower amounts. The production of xanthones was affected by both type and concentration of sugar. In general, roots growing in media supplemented with sucrose contained higher levels of xanthones. The amounts of xanthone primeveroses (1) and (3) increased with the increase of concentrations of all types of sugars, whereas higher sugar concentrations resulted in reduction of the contents of norswertianin-1-O-glucoside (2) and aglycone norswertianin (4). The roots were also evaluated regarding the content of total phenolics and higher accumulation of total phenolic compounds was observed in roots grown in fructose-containing medium. Antioxidant activity was determined by 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay, and high correlation between total phenolic content and antiradical activity was observed (r = ?0.83).     

Xanthone compounds in shoot cultures of <Emphasis Type="Italic">Gentianella bulgarica</Emphasis>

Shoot cultures of Gentianella bulgarica established from seedling epicotyls were maintained on MS medium supplemented with BA 0.2 mg l⁻¹ + NAA 0.1 mg l⁻¹. Cultures were prone to precocious flowering requiring the use of small shoot buds for multiplication purposes. The contents of three xanthone compounds identified as DGL, BGL, and DMB, in different plant material were determined by HPLC. The analysis revealed that the production of xanthones was affected by different concentrations of BA in medium. Shoot cultures grown at higher BA concentrations contained more DGL than material grown in nature. The concentrations of other two xanthones were lower in shoot cultures than in plants from nature. The radical scavenging activity of plant extracts and xanthones was investigated by DPPH test. Samples from plants grown in nature showed the highest activity (IC₅₀ = 0.26 mg ml⁻¹), while the extracts of shoot cultures grown in media with higher concentrations of BA showed moderate activities (IC₅₀ from 1.6 to 4.4 mg ml⁻¹).     

Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions

XRCC4 (X-ray cross-complementation group 4) and XLF (XRCC4-like factor) are two essential interacting proteins in the human NHEJ (non-homologous end-joining) pathway that repairs DNA DSBs (double-strand breaks). The individual crystal structures show that the dimeric proteins are homologues with protomers containing head domains and helical coiled-coil tails related by approximate two-fold symmetry. Biochemical, mutagenesis, biophysical and structural studies have identified the regions of interaction between the two proteins and suggested models for the XLF-XRCC4 complex. An 8.5 ? (1 ? = 0.1 nm) resolution crystal structure of XLF-XRCC4 solved by molecular replacement, together with gel filtration and nano-ESI (nano-electrospray ionization)-MS results, demonstrates that XLF and XRCC4 dimers interact through their head domains and form an alternating left-handed helical structure with polypeptide coiled coils and pseudo-dyads of individual XLF and XRCC4 dimers at right angles to the helical axis.     

Polycyclic aromatic hydrocarbons and heavy metals in Kostrena coastal area

The aim of this study was to determine pollution by polycyclic aromatic hydrocarbons (PAH) and heavy metals in seawater and sediment in Kostrena coastal area, as well as their toxicity using bioluminescence based tests. Total PAH concentration in seawater ranged 1.7-155.3 ng/L. The share of carcinogenetic PAH was relatively high, ranging 22-48.3%. Nickel concentrations in seawater were beyond detection limits (< 0.1 microg/L), vanadium concentrations ranged 0.66-1.96 microg/L, chrome concentrations were beyond detection limits, and copper concentrations were also beyond detection limits or extremely low (up to 0.32 microg/L). EC50 values in seawater ranged 23.80-90.90 ng/L. Correlation between total PAH concentration and toxicity of seawater showed strong connection between them (r = 0.9579). Total PAH concentration in marine sediment ranged 58.02-1116 microg/kg dry weight (d.w.). The share of carcinogenetic PAH was extremely high ranging 10-53%. Nickel concentrations in marine sediment ranged 8-24 mg/kg d.w., vanadium concentrations ranged 24-42 mg/kg d.w., chrome concentrations ranged 11-19 mg/kg d.w., and copper concentrations ranged 7-25 mg/kg d.w. EC50 values in marine sediment ranged 818-4596 microg/kg d.w. Correlation between total PAH concentration and toxicity of marine sediment showed weak connection between them (r = 0.2590). Previous studies of seawater samples from areas of the Adriatic sea under the direct influence of oil industry did not include concentrations of heavy metals, which makes our study the first to present such comprehensive results. Our results point out the need for further evaluations and following of marine environment pollution and its consequences on living organisms and marine ecosystem in whole.