Immunoglobulin G (IgG) is a major effector molecule of the human immune response, and aberrations in IgG glycosylation are linked to various diseases. However, the molecular mechanisms underlying ...protein glycosylation are still poorly understood. We present a data-driven approach to infer reactions in the IgG glycosylation pathway using large-scale mass-spectrometry measurements. Gaussian graphical models are used to construct association networks from four cohorts. We find that glycan pairs with high partial correlations represent enzymatic reactions in the known glycosylation pathway, and then predict new biochemical reactions using a rule-based approach. Validation is performed using data from a GWAS and results from three in vitro experiments. We show that one predicted reaction is enzymatically feasible and that one rejected reaction does not occur in vitro. Moreover, in contrast to previous knowledge, enzymes involved in our predictions colocalize in the Golgi of two cell lines, further confirming the in silico predictions.
Glycosylation is among the most common post-translational protein modifications. Glycans are complex carbohydrates attached to the surface of many proteins, but are rarely extensively studied in a ...high-throughput manner. However, there is an increasing evidence of their involvement in various physiological processes and diseases. Glycosylation of Immunglobulin G was shown to be important in adaptive immunity, where it can act as a "safety switch" for different types of the immune response. Although the main enzymes of the glycosylation pathway are known, little is understood about how this template-independent process is regulated to result in a faithful synthesis of a specific glycoform. This question was previously addressed using genome-wide association studies (GWAS) and 9 loci were identified as being significantly associated with IgG N-glycosylation. Only 4 of these loci were the known glycosylation enzymes. An additional five loci were discovered by applying a newly developed multivariate GWAS method on the same dataset. Here, by performing a GWAS on 77 IgG N-glycan traits measured by ultra-performance liquid chromatography in more than 8000 samples from four European cohorts the number of genome-wide significant (p? ≤ 2.4 x 10−9) loci increased to 27, 15 of which are novel, with 6 additional loci being suggestively associated (p? ≤ 2.4 x 10−8). To assess which of the genes from the associated loci are more likely to be regulating IgG glycosylation, different gene prioritising strategies were employed. For 7 loci evidence of a non-synonymous amino acid change was found, two of which were predicted to be deleterious. Evidence of regulation through changes in gene expression levels in B-cells, the cell lineage responsible for production of IgG, was found for 4 genes, with an additional 11 genes exhibiting the same evidence with expression in peripheral blood or other immune cells. For the remaining loci the most likely candidate gene was proposed based on co-expression with genes from the enriched gene-sets or based on a physical proximity to the variant with the strongest association. To narrow down the most important loci for a functional follow-up, the omics nature of this data was used to compare glycome-wide SNP effects and suggest how newly discovered loci form a functional network that regulates the established members of the glycosylation pathway. The potential role of IgG glycosylation in various complex traits and diseases was explored by assessing the pleiotropy of the associated SNPs. The inflation of SNPs related to autoimmune, digestive and neurological diseases was observed in glycosylation SNPs. To assess whether IgG N-glycosylation is likely to share the same causal variant as the identified pleiotropic traits and diseases, regional association patterns were compared using summary data based Mendelian Randomisation analyses. This work demonstrates that an increased sample size empowered the identification of novel loci, enabling further insights into the molecular mechanisms underlying protein glycosylation and its relationship with complex human diseases. It also shows that such analyses of omic traits can assist in creating a functional network of the identified loci, prioritising the most important genes and allowing a more focused approach to future experimental functional follow-up.
Cellulose, the main constituent of paper-made objects of cultural heritage (CH), is a favorable substrate for fungal growth. Gamma irradiation is a well-established low-cost treatment convenient for ...decontamination of such objects. Since side-effects to paper-based CH are always a concern the aim of this work was to investigate if a synergism of microbiological contamination and gamma irradiation effects exists and if it induces changes in paper's appearance and structure. The dose rate plays an important yet generally neglected role in the efficacy of the radiation treatment so another goal was to assert its influence on decontamination efficiency and paper properties.
Irradiation conditions for treating the highly resistant secondary colonizer Cladosporium sphaerospermum, as well as the naturally occurring mycobiota were evaluated. Untreated and inoculated samples of paper were irradiated with doses commonly applied to CH objects, as well as to significantly higher doses, at two dose rates that differ for two orders of magnitude. Microbiological analysis of irradiated samples was conducted. Colorimetric analysis, UV-vis and FTIR measurements were performed after short lived reaction species have decayed.
The results have shown that in the case of high contaminations (104 CFU/g) the applied dose needs to be adjusted and that the corresponding dose rate needs to be high enough. While at the dose rate of 31 kGy/h the irradiation dose of 7 kGy seems to be effective to obtain proper reduction of mycobita, at the dose rate that was two orders of magnitude lower the required dose increased approximately ten times. Thus the reevaluation of the recommended dose of 8 ± 2 kGy is needed. Considering the side effects of radiation treatment the dose rate effect has also been observed. At the higher of the investigated dose rates the irradiation doses needed for decontamination did not alter the appearance of paper, while at the lower one the changes were hardly perceptible. The main species showing their contribution to color change were the carbonate anion-radicals that were formed on the CaCO3 paper filler. No oxidation or change in crystallinity of cellulose was detected. Overall changes were too insignificant to make any conclusion on the contribution of mycobiota to the irradiation side-effects on the paper under the studied conditions.
•Dose rate determines radiation treatment efficiency and appearance of side effects.•Reevaluation of recommended 8 ± 2 kGy taking into account the dose rate is needed.•Electron beam treatment of paper-based cultural heritage may be encouraged.•Observable changes occurred at larger doses than needed for cultural heritage.•For samples irradiated to high doses carbonate radical anion absorption appeared.
Azoospermia is a form of male infertility characterized by a complete lack of spermatozoa in the ejaculate. Sertoli cell-only syndrome (SCOS) is the most severe form of azoospermia, where no germ ...cells are found in the tubules. Recently, FANCM gene variants were reported as novel genetic causes of spermatogenic failure. At the same time, FANCM variants are known to be associated with cancer predisposition. We performed whole-exome sequencing on a male patient diagnosed with SCOS and a healthy father. Two compound heterozygous missense mutations in the FANCM gene were found in the patient, both being inherited from his parents. After the infertility assessment, the patient was diagnosed with diffuse astrocytoma. Immunohistochemical analyses in the testicular and tumor tissues of the patient and adequate controls showed, for the first time, not only the existence of a cytoplasmic and not nuclear pattern of FANCM in astrocytoma but also in non-mitotic neurons. In the testicular tissue of the SCOS patient, cytoplasmic anti-FANCM staining intensity appeared lower than in the control. Our case report raises a novel possibility that the infertile carriers of FANCM gene missense variants could also be prone to cancer development.
Prikazani su nova metodologija i rezultati hidrografskih istraživanja na projektu HIDROLAB – Integrirani hidrografski sustav za održivi razvoj morskog ekosustava. U ovom se članku pregledno prikazuje ...eksperimentalni razvoj sustava za prikupljanje prostornih podataka primjenom suvremenih metoda daljinskih istraživanja te analize raspršenja povratnog akustičkog signala u cijelom vodenom stupcu sa svrhom detaljnog i učinkovitog kartiranja podvodnih i priobalnih staništa. Postojeće metode nisu se pokazale dovoljno učinkovitima za dopunu karte podvodnih i priobalnih staništa hrvatskog dijela Jadranskog mora, što je propisano Direktivom 2014/89/EU. Pokrivenost teritorijalnog mora Republike Hrvatske evidentiranim prostiranjem položaja staništa iznosi oko 2%, a tu je evidenciju Republika Hrvatska sukladno Direktivi 92/43/EEZ dužna dovršiti kao osnovu za procjenu ribljeg fonda i određivanje kvota na razini Europske unije. Dosad prikupljeni podaci o staništima morskog dijela različite su preciznosti, različitih formata te su prikupljani različitim metodama (npr. direktnim mjerenjima i indirektnim modeliranjem) zbog čega su nepouzdani i informativnog karaktera. S druge strane primijenjena je nova metodologija kojom se – uz upotrebu višesnopnog ultrazvučnog dubinomjera – morsko dno i morska staništa kartiraju nekoliko desetaka puta brže, točnije i jeftinije.
Sertoli cell-only syndrome (SCOS) is a condition of male infertility characterized by a total absence of spermatogenic cells in nearly all seminiferous tubules. Apart from well-established genetic ...changes such as Klinefelter syndrome, CFTR variants, and Y-chromosome microdeletions, several hundred candidate genes were reported as associated with male infertility. We selected 92 evidence-based genes associated with infertility and investigated data from whole-exome sequencing in 6 individuals with clinically diagnosed SCOS. Eight heterozygous variants passed our filtering criteria, including population frequency ≤ 0.1% and high functional impact indicated by Sift, Polyphen, and CADD scores. Out of them, we considered only variants with putative autosomal dominant effects on infertility that were subsequently validated by Sanger sequencing. This filtering pipeline has led to the final likely causative variants detected in CHD7 and SCYP3 genes that potentially explain SCOS in two of our patients. Our discoveries suggest that gene panel testing of patients with SCOS could improve the diagnostic outcome; however, assembling a gene panel consisting of only genuine causative genes is crucial.
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