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Glycans are an essential structural component of Immunoglobulin G (IgG) that modulate its structure and function. However, regulatory mechanisms behind this complex posttranslational modification are not well known. Previous genome-wide association studies (GWAS) identified 29 genomic regions involved in regulation of IgG glycosylation, but only a few were functionally validated. One of the key functional features of IgG glycosylation is the addition of galactose (galactosylation). We performed GWAS of IgG galactosylation (N=13,705) and identified 16 significantly associated loci, indicating that IgG galactosylation is regulated by a complex network of genes that extends beyond the galactosyltransferase enzyme that adds galactose to IgG glycans. Gene prioritization identified 37 candidate genes. Using a recently developed CRISPR/dCas9 system we manipulated gene expression of candidate genes in thein vitroIgG expression system. Up- and downregulation of three genes,EEF1A1, MANBAandTNFRSF13B, changed the IgG glycome composition, which confirmed that these three genes are involved in IgG galactosylation in thisin vitroexpression system.

Supplementary Table 1. Directly measured glycans and derived glycan traits; Supplementary Table 2. IgG glycome composition in CRC patients and controls; Supplementary Table 3. Pleiotropic effects of top glycan SNPs relevant for fucosylation on CRC.

Purpose: Alternative glycosylation has significant structural and functional consequences on IgG and consequently also on cancer immunosurveillance. Because of technological limitations, the effects of highly heritable individual variations and the differences in the dynamics of changes in IgG glycosylation on colorectal cancer were never investigated before.Experimental Design: Using recently developed high-throughput UPLC technology for IgG glycosylation analysis, we analyzed IgG glycome composition in 760 patients with colorectal cancer and 538 matching controls. Effects of surgery were evaluated in 28 patients sampled before and three times after surgery. A predictive model was built using regularized logistic regression and evaluated using a 10-cross validation procedure. Furthermore, IgG glycome composition was analyzed in 39 plasma samples collected before initial diagnosis of colorectal cancer.Results: We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. Although a model based on age and sex did not show discriminative power (AUC = 0.499), the addition of glycan variables into the model considerably increased the discriminative power of the model (AUC = 0.755). However, none of these differences were significant in the small set of samples collected before the initial diagnosis.Conclusions: Considering the functional relevance of IgG glycosylation for both tumor immunosurveillance and clinical efficacy of therapy with mAbs, individual variation in IgG glycosylation may turn out to be important for prediction of disease course or the choice of therapy, thus warranting further, more detailed studies of IgG glycosylation in colorectal cancer. Clin Cancer Res; 22(12); 3078–86. ©2016 AACR.

Alternative glycosylation of immunoglobulin G (IgG) is functionally important in multiple human physiological and pathological states. Our understanding of molecular mechanisms that regulate IgG glycosylation is vague because of the complexity of this process, which involves hundreds of genes. Several genome-wide association (GWA) studies have revealed a network of genes associated with IgG glycosylation that are pleiotropic for a number of diseases. Here, we report a design of a versatile system for IgG production and gene manipulations that can be used for in vitro functional follow-up of GWA hits or any gene of interest. The system is based on CRISPR-dCas9, extended by a piggyBac integrase compatible vector, and drives IgG production in HEK-293F cells. We validated our systems that stably express VPR-dCas9 and KRAB-dCas9 by manipulation of four glyco-genes with a known role in IgG glycosylation, and then functionally validated three GWAS hits for IgG glycosylation with an as-yet-unknown role in this process.

Many recent epigenetic studies utilize the advantages of CRISPR/dCas9 based tools in linking certain epigenetic modification with gene expression regulation. Various multifactorial diseases often contain changed epigenetic signatures at many loci, so tools for simultaneously targeting different loci would significantly facilitate the understanding of disease pathogenesis. We tested different dCas9 orthologs (dCjCas9, dNmCas9, dSt1Cas9, dFnCas9, dSaCas9 and dSpCas9) in C-terminal fusion with DNMT3A effector domain to find candidates that potentiate effector domain to perform its function at the target site. We demonstrated that nuclear localization signals (NLS) at both termini of fusion constructs is crucial for both proper nuclear import of such large constructs as well as for maximization of targeted DNA methylation activity. We identified SpCas9, SaCas9 and CjCas9 as potential candidates for the fusion constructs. With further optimization of the SaCas9 ortholog, due to less complex PAM requirements in contrast to CjCas9, we showed that N-terminal fusion with DNMT3A (dSaCas9- DNMT3A) is optimal to exert targeted DNA methylation activity comparable to the dSpCas9- DNMT3A construct. N-terminal fusions showed better results for both Cas9 orthologs, SaCas9 and SpCas9, so it can be used as universal approach for linking different effector domains in order to obtain highly active fusions.

Glycosylation of immunoglobulin G (IgG) largely defines function of this antibody and regulates inflammation on multiple levels but the mechanisms and the genes involved in the process of IgG glycosylation are still vaguely understood. Genome wide association studies (GWAS) enabled identification of many genes potentially involved in IgG glycosylation but in the most cases functional validation is missing. Composition of the IgG glycome changes significantly with various diseases and ageing. In women, the most prominent change occurs during the perimenopausal period and a recent intervention study revealed that estrogen regulates IgG glycosylation. The most affected IgG glycome features are galactosylation, sialylation and structures with bisecting GlcNac. Analysis of the Signaling Pathway Projects (SPP) web knowledgebase revealed that E2 affects expression of four genes with yet unknown role in IgG glycosylation with three of them associated with galactosylation (RUNX1, RUNX3 and SPINK4) and one associated with sialylation (ELL2) through previous GWA studies. To map downstream signaling mechanisms responsible for the effect of estrogen on IgG glycome composition we utilized our recently developed in vitro IgG expression system HEK293-FS for targeted CRISPRa/CRISPRi manipulation of candidate loci. This system exploits stably integrated dCas9-VPR or dCas9-KRAB expression cassettes for targeted upregulation or downregulation of genes via transient transfection of FreeStyleTM 293-F cells with specific gRNAs. We successfully upregulated or downregulated RUNX1, RUNX3, SPINK4 and ELL2 but only upregulation of RUNX3 (Runt-related factor 3) and SPINK4 (Serine Peptidase Inhibitor Kazal Type 4) resulted with concomitant change in IgG glycome composition. Upregulation of RUNX3 resulted with significant decrease in galactosylated glycans accompanied with increase in agalactosylated glycans. Upregulation of SPINK4 was also accompanied with decrease in galactosylated glycans but the ratio of agalactosylated glycans remained stable. To further explore the role of SPINK4 and RUNX3 in IgG galactosylation we measured B4GALT1 (beta-1, 4- galactosyltransferase 1) expression after upregulation and observed no significant change in B4GALT1 transcript levels. This suggests that RUNX3 and SPINK4 do not suppress B4GALT1 on transcription level, but through some indirect pathway that should be further investigated. Taken together, the results of this study suggest the molecular mechanism through which E2 could regulate IgG glycosylation, specifically galactosylation.

Pro- or anti-inflammatory activity of immunoglobulin G (IgG) depends largely on differential N- glycosylation of its Fc region. Alternative glycosylation affects binding efficiency of this antibody to antigens, ligands, or different complexes of the immune system, which modulates immune response. While previous genome-wide association studies (GWAS) succeeded to associate functional network of gene loci with IgG glycosylation pleiotropic with inflammatory diseases, it is still unclear whether these genes have a functional importance and if so, how they are involved in this process. For this purpose, we applied already established system based on FreeStyle™ 293-F cells, with stably integrated CRISPR/dCas9 fusions (dCas9-VPR or dCas9-KRAB) for direct regulation of the candidate genes using appropriate sgRNAs. The cell system is designed to secrete IgG molecules, so that glycans can be analyzed as the final phenotype following gene manipulations. The GWA hits were grouped with respect to different glycosylation traits such as galactosylation (KIF3C, NFKB1, MANBA, SLC38A10, TNFRSF13B, EEF1A1, HIVEP2), fucosylation (MYCBP, ACVR1C, KIF11, TBX21, TBKBP1, NFATC2), sialylation (IL6ST, GGA2, SLC17A9, SPPL3) and bisecting GlcNAC (TCF3, SMARCB1, DERL2, RRBP1, KDELR2). Out of seven genes associated with galactysylation only MANBA, NFKB1, TNFRSF13B and EEF1A1 showed change of agalactosylated structures when upregulated using dCas9-VPR. Out of six hits associated with fucosylation, only upregulation of TBX21 and TBKBP1 showed significant changes in galactosylation, but we did not detect any changes in fucosylation. This can suggest that a different cell model might be preferable to validate if these GWA hits are responsible for fucosylation, since glycans on IgG produced from FreeStyle™ 293-F cells possess only core fucose. Out of five loci associated with bisecting GlcNac, only the upregulation of KDELR2 produced an increase in biantennary glycan structures with bisecting GlcNac. The upregulation of DERL2 and RRBP1 resulted in an increase of digalactosylated biantennary glycans. Out of four GWA hits for sialylation, only downregulation of SPPL3 led to hyperglycoslation with the corresponding increase in sialylated and galactosylated structures and decrease in agalactosylated glycans, even though all the genes were successfully up - or downregulated. In conclusion, in our cell model, which produces human plasma-like IgG, we have proven the functional role of several GWA hits which are not glycosyltransferases but are associated with the IgG glycosylation pathway. Ongoing research will unravel the exact role of these genes in an integrated picture of molecular mechanism regulating IgG glycosylation.

Due to the limited therapeutic options after ischemic stroke, gene therapy has emerged as a promising choice, especially with recent advances in viral vector delivery systems. Therefore, we aimed to provide the current state of the art of lentivirus (LV) and adeno-associated virus (AAV) mediated gene interventions in preclinical ischemic stroke models. A systematic analysis including qualitative and quantitative syntheses of studies published until December 2020 was performed. Most of the 87 selected publications used adult male rodents and the preferred stroke model was transient middle cerebral artery occlusion. LV and AAV vectors were equally used for transgene delivery, however loads of AAVs were higher than LVs. Serotypes having broad cell tropism, the use of constitutive promoters, and virus delivery before the stroke induction via stereotaxic injection in the cortex and striatum were preferred in the analyzed studies. The meta-analysis based on infarct volume as the primary outcome confirmed the efficacy of the preclinical interventions. The quality assessment exposed publication bias and setbacks in regard to risks of bias and study relevance. The translational potential could increase by using specific cell targeting, post-stroke interventions, non-invasive systematic delivery, and use of large animals.

Alternative glycosylation of immunoglobulin G (IgG) is functionally important in multiple human physiological and pathological states. One of the best examples is a simple fucosylation that can switch IgG effector function between pro- and anti- inflammatory, which is critical in production of therapeutic antibodies. Several genome-wide association studies revealed a network of genes associated with IgG glycosylation which are pleiotropic for several diseases. To understand the complex molecular mechanisms that regulate IgG glycosylation, we designed a versatile system for IgG production and gene manipulation that can be used for in vitro functional follow-up of GWA hits or any gene of interest. The system is based on CRISPR/dCas9, extended by a piggyBac integrase compatible vector, and drives IgG production in HEK-293F cells, essentially creating derived cell lines with integrated machinery for programmed transcriptional control. Transient transfection of those cells with the second component of the system, a plasmid for monocistronic expression of both IgG chains and co-expression of gRNA molecules, enables the readout of IgG glycan profiles following precisely targeted up- or downregulation of genes of interest. Though the development of the system was complex, its utilization by the end user is simple and straightforward. Transfection of the large dCas9 fusion constructs is quite inefficient and represents a bottleneck in effective experimental design with high throughput. The bipartite nature of the system ensures that only the cells expressing gRNA (with concomitant transcriptional alteration) produce IgG that is analyzed for glycosylation profile. We validated our derived cell lines that stably express VPR-dCas9 and KRAB-dCas9 by manipulation of four glycogenes with a known role in IgG glycosylation. Transcriptional up- and downregulation of B4GALT1, encoding the enzyme that adds galactose to the core glycan structure, had the predictable effect on the abundance of agalactosylated and galactosylated structures, changing the glycosylation profile depending on the transcript level. Similarly, downregulation of FUT8, encoding a fucosyltransferase, decreased the core-fucosylated structures, while upregulation of ST6GAL1 and MGAT3 increased sialylated structures and those with a bisecting GlcNAc, respectively, which was in line with the expected change in enzyme levels. Interestingly, the change in sialylated structures was accompanied by changes in galactosylation, again demonstrating the complexity of the IgG glycosylation network. Our newly developed system for transient expression of can be used for studying the role of genes associated with IgG glycosylation by GWA studies. It can also be easily repurposed to serve as a model for other proteins and their posttranslational modifications, with appropriate targeting via gRNA.

Establishing causal relationship between epigenetic marks and gene transcription requires molecular tools, which can precisely modify specific genomic regions. Here, we present a modular and extensible CRISPR/dCas9-based toolbox for epigenetic editing and direct gene regulation. It features a system for expression of orthogonal dCas9 proteins fused to various effector domains and includes a multi-gRNA system for simultaneous targeting dCas9 orthologs to up to six loci. The C- and N-terminal dCas9 fusions with DNMT3A and TET1 catalytic domains were thoroughly characterized. We demonstrated simultaneous use of the DNMT3A-dSpCas9 and TET1-dSaCas9 fusions within the same cells and showed that imposed cytosine hyper- and hypo-methylation altered level of gene transcription if targeted CpG sites were functionally relevant. Dual epigenetic manipulation of the HNF1A and MGAT3 genes, involved in protein N-glycosylation, resulted in change of the glycan phenotype in BG1 cells. Furthermore, simultaneous targeting of the TET1-dSaCas9 and VPR-dSpCas9 fusions to the HNF1A regulatory region revealed strong and persistent synergistic effect on gene transcription, up to 30 days following cell transfection, suggesting involvement of epigenetic mechanisms in maintenance of the reactivated state. Also, modulation of dCas9 expression effectively reduced off-target effects while maintaining the desired effects on target regions.

Molecular tools for gene regulation and epigenome editing consist of two main parts: the targeting moiety binding a specific genomic locus and the effector domain performing the editing or regulatory function. The advent of CRISPR-Cas9 technology enabled easy and flexible targeting of almost any locus by co-expression of a small sgRNA molecule, which is complementary to the target sequence and forms a complex with Cas9, directing it to that particular target. Here, we review strategies for recruitment of effector domains, used in gene regulation and epigenome editing, to the dCas9 DNA-targeting protein. To date, the most important CRISPR-Cas9 applications in gene regulation are CRISPR activation or interference, while epigenome editing focuses on targeted changes in DNA methylation and histone modifications. Several strategies for signal amplification by recruitment of multiple effector domains deserve special focus. While some approaches rely on altering the sgRNA molecule and extending it with aptamers for effector domain recruitment, others use modifications to the Cas9 protein by direct fusions with effector domains or by addition of an epitope tag, which also has the ability to bind multiple effector domains. A major barrier to the widespread use of CRISPR-Cas9 technology for therapeutic purposes is its off-target effect. We review efforts to enhance CRISPR-Cas9 specificity by selection of Cas9 orthologs from various bacterial species and their further refinement by introduction of beneficial mutations. The molecular tools available today enable a researcher to choose the best balance of targeting flexibility, activity amplification, delivery method and specificity.

Epigenetic studies relied so far on correlations be- tween epigenetic marks and gene expression pat- tern. Technologies developed for epigenome edit- ing now enable direct study of functional relevance of precise epigenetic modifications and gene reg- ulation. The reversible nature of epigenetic modi- fications, including DNA methylation, has been al- ready exploited in cancer therapy for remodeling the aberrant epigenetic landscape. However, this was achieved non-selectively using epigenetic inhibitors. Epigenetic editing at specific loci represents a novel approach that might selectively and heritably alter gene expression. Here, we developed a CRISPR- Cas9-based tool for specific DNA methylation con- sisting of deactivated Cas9 (dCas9) nuclease and cat- alytic domain of the DNA methyltransferase DNMT3A targeted by co–expression of a guide RNA to any 20 bp DNA sequence followed by the NGG trinucleotide. We demonstrated targeted CpG methylation in a ∼35 bp wide region by the fusion protein. We also showed that multiple guide RNAs could target the dCas9- DNMT3A construct to multiple adjacent sites, which enabled methylation of a larger part of the promoter. DNA methylation activity was specific for the tar- geted region and heritable across mitotic divisions. Finally, we demonstrated that directed DNA methy- lation of a wider promoter region of the target loci IL6ST and BACH2 decreased their expression.

Background: Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methylation of candidate genes for inflammatory bowel disease (IBD) have demonstrated significant associations between genetic and epigenetic changes and IBD. Independent GWA studies have identified genetic variants in the BACH2, IL6ST, LAMB1, IKZF1, and MGAT3 loci to be associated with both IBD and immunoglobulin G (IgG) glycosylation. Methods: Using bisulfite pyrosequencing, we analyzed CpG methylation in promoter regions of these five genes from peripheral blood of several hundred IBD patients and healthy controls (HCs) from two independent cohorts, respectively. Results: We found significant differences in the methylation levels in the MGAT3 and BACH2 genes between both Crohn's disease and ulcerative colitis when compared to HC. The same pattern of methylation changes was identified for both genes in CD19 + B cells isolated from the whole blood of a subset of the IBD patients. A correlation analysis was performed between the MGAT3 and BACH2 promoter methylation and individual IgG glycans, measured in the same individuals of the two large cohorts. MGAT3 promoter methylation correlated significantly with galactosylation, sialylation, and bisecting GlcNAc on IgG of the same patients, suggesting that activity of the GnT-III enzyme, encoded by this gene, might be altered in IBD. The correlations between the BACH2 promoter methylation and IgG glycans were less obvious, since BACH2 is not a glycosyltransferase and therefore may affect IgG glycosylation only indirectly. Conclusions: Our results suggest that epigenetic deregulation of key glycosylation genes might lead to an increase in pro-inflammatory properties of IgG in IBD through a decrease in galactosylation and sialylation and an increase of bisecting GlcNAc on digalactosylated glycan structures. Finally, we showed that CpG methylation in the promoter of the MGAT3 gene is altered in CD3 + T cells isolated from inflamed mucosa of patients with ulcerative colitis from a third smaller cohort, for which biopsies were available, suggesting a functional role of this glyco-gene in IBD pathogenesis. The authors would like to thank Stephanie Scott for her organizational and administrational contribution. The study has been funded by the EU FP7 grant European Commission IBD-BIOM (contract # 305479), EU FP7 Regional Potential Grant INTEGRA-Life (contract # 315997), European Structural and Investment Funds grant for the Croatian National Centre of Research Excellence in Personalized Healthcare (contract # KK.01.1.1.01.0010), and Croatian Science Foundation grant EpiGlycoIgG (contract # 3361). Financial support from Portugal (PI: SSP): FEDER—Fundo Europeu de Desenvolvimento Regional funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia/ Ministério da Ciência, Tecnologia e Inovação in the framework of the project (POCI-01/0145-FEDER-016601; PTDC/DTP-PIC/0560/2014) was received. SSP also acknowledges the European Crohn’s and Colitis Organization (ECCO) and the “Broad Medical Research program at Crohn’s and Colitis Foundation of America-CCFA” for funding. SSP acknowledges the Portuguese Group of Study on IBD (GEDII) for funding. A.M.D. [PD/BD/105982/2014] also acknowledges FCT for funding. IBD-BIOM consortium: Daniel Kolarich (Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany), Manfred Wuhrer (Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, the Netherlands), Dermot P. B. McGovern (F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles), Iain K. Pemberton (IP Research Consulting SAS, Paris, France), Daniel IR Spencer (Ludger Ltd., Culham Science Centre, Oxford, UK, Daryl L. Fernandes (Ludger Ltd., Culham Science Centre, Oxford, UK), Rahul Kalla, Kate O’Leary, Alex T Adams, Hazel Drummond, Elaine Nimmo, Ray Boyapati, David C Wilson (Centre for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK), Ray Doran (Ludger Ltd., Culham Science Centre, Oxford, UK), Igor Rudan (all, Centre for Population Health Sciences, University of Edinburgh, Edinburgh, UK), Paolo Lionetti (Paediatric Gastroenterology Unit, AOU Meyer, Viale Pieraccini, Florence, Italy), Natalia Manetti (Department of Medical and Surgical Sciences, Division of Gastroenterology, University Hospital Careggi, Florence, Italy), Fabrizio Bossa (Department of Medical Sciences, Division of Gastroenterology, IRCCS-CSS Hospital, Viale Cappuccini, Rotondo, Italy), Paola Cantoro, Anna Kohn (Division of Gastroenterology, S. Camillo Hospital, Rome, Italy), Giancarlo Sturniolo (Gastrointestinal Unit, University of Padua, Padua, Italy), Silvio Danese (IBD Unit, Humanitas Research Institute, Rozzano, Milan, Italy), Mariek Pierik (Maastricht University Medical Centre (MUMC), Maastricht, the Netherlands), and David C. Wilson (Centre for Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK). This independent research was generously supported by the following grants: EU FP7 research grant IBD-BIOM (contract # 305479) to JS, VA, GL, and VZ; EU FP7 Regional Potential Grant INTEGRA-Life (contract # 315997) to GL and VZ; European Structural and Investment Funds grant for the Croatian National Centre of Research Excellence in Personalized Healthcare (contract # KK.01.1.1.01.0010) to GL and VZ; Croatian Science Foundation grant EpiGlycoIgG (contract # 3361) to VZ; FEDER COMPETE 2020 POCI, Portugal 2020, and Portuguese funds through FCT (contracts # POCI-01/0145-FEDER-016601 and PTDC/DTP-PIC/0560/2014) to SP; and FTC (contract # PD/BD/105982/2014) to AMD.

The incidence of perinatal mortality of Arabian horses in Croatia is in accordance with the high frequency of lethal and sublethal mutations in Arabian horses in other countries. The objective of this study was to investigate the frequency of recessive genes causing lavender foal syndrome (LFS) in three Croatian breeds of Arabian horse and to compare these findings with the literature reports. Pedigree and molecular analyses indicated the existence of three distinct breeds of Arabian horses (Traditional Arabian, Shagya Arab, and Pure Arabian horse) in Croatia. Molecular analyses were performed on 100 blood samples (n = 100) of Arabian horses by analyzing isolated and quality-tested genomic DNA. Polymerase chain reaction-restriction fragment length polymorphism analysis of the MYO5A gene was performed for LFS determination. The proportion of heterozygous carriers and the frequency of the LFS allele were lower in Arabian horse breeds in Croatia than in other reports. The LFS allele was found exclusively in the Pure Arabian breed, supporting the findings of other studies on Egyptian Arabian horses. The results are consistent with the interbreeding of Pure Arabian horses in Croatia with Egyptian Arabian horses. The Traditional Arabian and Shagya Arab breeds showed a lower frequency of the LFS allele. Based on these results, screening of the entire population of Arabian horses in Croatia for mutations responsible for multiple inherited genetic disorders should be included in breeding programs.

Background The RAS association domain family protein 1a (RASSF1A) is a prominent tumor suppressor gene showing altered promoter methylation in testicular germ cell tumors (TGCT). RASSF1A promoter hypermethylation might represent an early event in TGCT tumorigenesis. We investigated whether the RASSF1A promoter methylation in peripheral blood of TGCT patients can be associated with testicular cancer risk. Materials and methods Following a meta-analysis, we performed a cohort study including 32 testicular cancer patients and 32 healthy controls. Promoter methylation of the RASSF1A and O6-methylguanine-DNA-methyltransferase (MGMT) genes was analyzed using bisulfite pyrosequencing of DNA from peripheral blood. Results Meta-analysis showed an odds ratio (OR) of 7.69 for RASSF1A promoter methylation as a risk factor for TGCT. Cohort study found altered methylation of the RASSF1A promoter in blood of TGCT patients. Methylation was higher in TGCT patients before BEP chemotherapy. Conclusion The meta-analysis indicates a role of the RASSF1A promoter hypermethylation from peripheral blood in TCGT. We confirmed that finding in our cohort study, which represents the first report of changed RASSF1A promoter methylation in peripheral blood TGCT.

Background: The RAS association domain family protein 1a (RASSF1A) is a prominent tumor suppressor gene showing altered promoter methylation in testicular germ cell tumors (TGCT). RASSF1A promoter hypermethylation might represent an early event in TGCT tumorigenesis. We investigated whether the RASSF1A promoter methylation in peripheral blood of TGCT patients can be associated with testicular cancer risk. Materials and Methods: Following a meta-analysis, we performed a cohort study including 32 testicular cancer patients and 32 healthy controls. Promoter methylation of the RASSF1A and O6-methylguanine-DNA-methyltransferase (MGMT) genes was analyzed using bisulfite pyrosequencing of DNA from peripheral blood. Results: Meta-analysis showed an odds ratio (OR) of 7.69 for RASSF1A promoter methylation as a risk factor for TGCT. Cohort study found altered methylation of the RASSF1A promoter in blood of TGCT patients. Methylation was higher in TGCT patients before BEP chemotherapy. Conclusion: The meta-analysis indicates a role of the RASSF1A promoter hypermethylation from peripheral blood in TCGT. We confirmed that finding in our cohort study, which represents the first report of changed RASSF1A promoter methylation in peripheral blood TGCT.

Haematological and blood biochemical variables are key elements for routine assessment of animal health status, with implications in animal production and food safety. However, only reliable reference intervals of haematological and biochemical blood variables can provide the basis for accurate interpretation of the obtained blood results. Haematological and biochemical blood values critically dependent on living conditions, region, husbandry, rearing location, and diet. The aim of this study was to determine the reference intervals for selected important and informative haematological and blood biochemical variables for females of the Croatian indigenous sheep breed, Lika pramenka. We used several advanced statistical methods and assessed their applicability for determination of relevant reference intervals under conditions specific to indigenous sheep breeding. The results show that the reference intervals from the available literature are orientational but not adequate for the specific challenges encountered in raising indigenous breeds in their natural habitat. This was illustrated by the large number of clinically healthy animals with blood variable values falling outside the reference intervals given in the sources available previously., Hematološki i biokemijski krvni pokazatelji ključan su element pri rutinskom procjenjivanju zdravstvenog statusa životinja, produktivnosti životinja te sigurnosti hrane. Međutim, samo pouzdani referentni intervali hematoloških i biokemijskih pokazatelja u krvi mogu pružiti osnovu za precizno tumačenje dobivenih rezultata. Hematološke i biokemijske vrijednosti u krvi uvelike ovise o uvjetima držanja, regiji u kojoj se životinje drže, načinu uzgoja, mjestu uzgoja te hranidbi životinja. Cilj ovog istraživanja bio je utvrditi pouzdane referentne intervale za odabrane važne i informativne hematološke i biokemijske pokazatelje u krvi ženskih životinja hrvatske izvorne pasmine ličke pramenke. U istraživanju su korištene napredne statističke metode te je procijenjena njihova primjenjivost za određivanje relevantnih referentnih intervala u specifičnim uvjetima ovčarstva izvornim pasminama. Rezultati pokazuju da su referentni intervali iz dostupne literature orijentacijski, ali ne i dovoljni pri specifičnim izazovima u uzgoju izvornih pasmina u njihovom prirodnom staništu. To je ilustrirano velikim brojem klinički zdravih životinja čije se vrijednosti krvnih pokazatelja nalaze izvan referentnih intervala danim u prijašnjim istraživanjima.

Hepatitis E is a viral zoonotic disease infecting swine worldwide. Since pigs represent a likely animal reservoir for the hepatitis E virus, the epidemiology of naturally occurring hepatitis E was investigated in Croatian swine herds. Nearly all tested animals were seropositive for antibodies against the hepatitis E virus (55/60, 91.7%). Active infection was detected in all age groups by RT-PCR of viral RNA in serum (8/60, 13.3%) and bile samples (3/37, 8.1%), which was further confirmed by histopathological findings of characteristic lesions in the livers of the infected animals. Three new strains of hepatitis E virus were isolated from Croatian pig herds. Phylogenetic analysis using median-joining networks clustered those Croatian strains with isolates from various parts of the world, indicating their likely origin in international trade. Similarity to human isolates implies a zoonotic potential of Croatian strains, which raises a public health concern, especially in the light of the high prevalence of hepatitis E in the herds studied.

Changes in N-glycosylation of plasma proteins are observed in many types of cancer, nevertheless, few studies suggest the exact mechanism involved in aberrant protein glycosylation. Here we studied the impact of DNA methylation on the N-glycome in the secretome of the HepG2 cell line derived from hepatocellular carcinoma (HCC). Since the majority of plasma glycoproteins originate from the liver, the HepG2 cells represent a good model for glycosylation changes in HCC that are detectable in blood, which is an easily accessible analytic material in a clinical setting. Two different concentrations of 5-aza-2′-deoxycytidine (5-aza-2dC) differentially affected global genome methylation and induced different glycan changes. Around twenty percent of 84 glyco-genes analysed changed expression level after the 5-aza-2dC treatment as a result of global genome hypomethylation. A correlation study between the changes in glyco-gene expression and the HepG2 glycosylation profile suggests that the MGAT3 gene might be responsible for the glycan changes consistently induced by both doses of 5-aza-2dC. Core-fucosylated tetra-antennary structures were decreased in quantity likely as a result of hypomethylated MGAT3 gene promoter followed by increased expression of this gene.

Purpose: Alternative glycosylation has significant structural and functional consequences on IgG and consequently also on cancer immunosurveillance. Because of technological limitations, the effects of highly heritable individual variations and the differences in the dynamics of changes in IgG glycosylation on colorectal cancer were never investigated before. Experimental Design: Using recently developed high-throughput UPLC technology for IgG glycosylation analysis, we analyzed IgG glycome composition in 760 patients with colorectal cancer and 538 matching controls. Effects of surgery were evaluated in 28 patients sampled before and three times after surgery. A predictive model was built using regularized logistic regression and evaluated using a 10-cross validation procedure. Furthermore, IgG glycome composition was analyzed in 39 plasma samples collected before initial diagnosis of colorectal cancer. Results: We have found that colorectal cancer associates with decrease in IgG galactosylation, IgG sialylation and increase in core-fucosylation of neutral glycans with concurrent decrease of core-fucosylation of sialylated glycans. Although a model based on age and sex did not show discriminative power (AUC = 0.499), the addition of glycan variables into the model considerably increased the discriminative power of the model (AUC = 0.755). However, none of these differences were significant in the small set of samples collected before the initial diagnosis. Conclusions: Considering the functional relevance of IgG glycosylation for both tumor immunosurveillance and clinical efficacy of therapy with mAbs, individual variation in IgG glycosylation may turn out to be important for prediction of disease course or the choice of therapy, thus warranting further, more detailed studies of IgG glycosylation in colorectal cancer. Clin Cancer Res; 22(12); 3078–86. ©2016 AACR.

Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data shows that IBD-associated hypermethylation within the TXK promoter region negatively correlates with gene expression in whole-blood and CD8+ T cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression., Epigenetic perturbations may be an important factor in diseases where both genes and environment play a role. Here, Ventham and colleagues show that DNA methylation changes in inflammatory bowel disease are related to the underlying genotype, and are associated with cell-specific changes to gene expression.

Background Most eukaryotic proteins are modified by covalent addition of glycan molecules that considerably influence their function. Aberrant glycosylation is profoundly involved in malignant transformation, tumor progression and metastasis. Some glycan structures are tumor-specific and reflect disturbed glycan biosynthesis pathways. Methods We analyzed DNA methylation and expression of 86 glyco-genes in melanoma, hepatocellular, breast and cervical cancers using data from publicly available databases. We also analyzed methylation datasets without the available matching expression data for glyco-genes in lung cancer, and progression of melanoma into lymph node and brain metastases. Results Ten glyco-genes (GALNT3, GALNT6, GALNT7, GALNT14, MGAT3, MAN1A1, MAN1C1, ST3GAL2, ST6GAL1, ST8SIA3) showing changes in both methylation and expression in the same type of cancer belong to GalNAc transferases, GlcNAc transferases, mannosidases and sialyltransferases, which is in line with changes in glycan structures already reported in the same type of tumors. Some of those genes were additionally identified as potentially valuable for disease prognosis. The MGAT5B gene, so far identified as specifically expressed in brain, emerged as a novel candidate gene that is epigenetically dysregulated in different cancers other than brain cancer. We also report for the first time aberrant expression of the GALNT and MAN genes in cancer by aberrant promoter methylation. Conclusions Aberrant expression of glyco-genes due to aberrant promoter methylation could be a way leading to characteristic glycosylation profiles commonly described in cancer. General significance Methylation status in promoters of candidate glyco-genes might serve as prognostic markers for specific tumors and point to potential novel targets for epigenetic drugs. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.

Genome editing tools, such as TALEN (transcription activator-like effector nuclease) or CRISPR-Cas9 (CRISPR-associated protein-9 nuclease) systems, enable functional studies by targeted gene knockout. They introduce double-stranded breaks (DSBs) into a DNA molecule in a sequence-specific manner, thereby stimulating the error-prone non-homologous end joining repair mechanism, leading to probable gene inactivation when the coding sequence is targeted. Vectors for expression of TALEN and Cas9-based constructs targeting the human IL6ST and HNF1A genes were assembled and tested for their ability to introduce DSBs when transfected into cultured cells using the luciferase assay. The Cas9-based construct targeting the IL6ST gene was shown to be active, while the two TALEN-based constructs did not introduce DSBs above background level. Both the TALEN and the CRISPR-Cas9 constructs targeting the HNF1A gene were found to be active, with the TALEN showing higher activity in a dose-dependent manner. The constructed genome-editing tools can be used for functional analysis of the putative role of HNF1A and IL6ST genes in IgG glycosylation, as shown previously by genome wide association studies. This work is licensed under a Creative Commons Attribution 4.0 International License.

Newcastle disease (ND) is one of the most important diseases of poultry and other avian species. The usual mean to control ND is specific immunoprophylaxis. Although chickens are routinely vaccinated against ND, vaccination of ostriches is less well understood. We investigated the effect of vaccination against Newcastle disease via different routes on specific antibody titer in 24 adult ostriches, divided into three experimental and one control group. The vaccine was administered in drinking water to the first, by spraying to the second, and oculo-nasally to the third group. The results have indicated antibody production with titers sufficient for humoral immunity in all experimental groups. The strongest immune response was determined in the group vaccinated by spraying. .

Voltage-dependent anion channels (VDACs) are porin-type betta-barrel diffusion pores. They are prominent in the outer membrane of mitochondria and facilitate metabolite exchange between the organelle and the cytosol. Here we studied the subcellular distribution of a plant VDAC-like protein between plastids and mitochondria in green and non-green tissue. Using in vitro studies of dual-import into mitochondria and chloroplasts as well as transient expression of fluorescence-labeled polypeptides, it could be clearly demonstrated that this VDAC isoform targets exclusively to mitochondria and not to plastids. Our results support the idea that plastids evolved a concept of solute exchange with the cytosol different from that of mitochondria.

The Toc core complex consists of the pore-forming Toc75 and the GTPases Toc159 and Toc34. We confirm that the receptor form of Toc159 is integrated into the membrane. The association of Toc34 to Toc75/Toc159 is GTP dependent and enhanced by preprotein interaction. The N-terminal half of the pSSU transit peptide interacts with high affinity with Toc159, whereas the C-terminal part stimulates its GTP hydrolysis. The phosphorylated C-terminal peptide of pSSU interacts strongly with Toc34 and therefore inhibits binding and translocation of pSSU into Toc proteoliposomes. In contrast, Toc159 recognises only the dephosphorylated forms. The N-terminal part of the pSSU presequence does not influence binding to the Toc complex, but is able to block import into proteoliposomes through its interaction with Toc159. We developed a model of differential presequence recognition by Toc34 and Toc159.

Adaptive response to stress is a fundamental property of living systems. At the cellular level, many different types of stress elicit an essentially limited repertoire of adaptive responses. Epigenetic changes are the main mechanism for medium- to long-term adaptation to accumulated (intense, long-term, or repeated) stress. We propose the adaptive deregulation of the epigenome in response to stress (ADERS) hypothesis which assumes that the unspecific adaptive stress response grows stronger with the increasing stress level, epigenetically activating response gene clusters while progressively deregulating other cellular processes. The balance between the unspecific adaptive response and the general epigenetic deregulation is critical because a strong response can lead to pathology, particularly to malignant transformation. The main idea of our hypothesis is the continuum traversed by a cell subjected to accumulated stress, which lies between an unspecific adaptive response and pathological deregulation—the two extremes sharing the same underlying cause, which is a manifestation of a unified epigenetically mediated adaptive response to stress. The evolutionary potential of epigenetic regulation in multigenerational adaptation is speculatively discussed in the light of neo-Lamarckism. Finally, an approach to testing the proposed hypothesis is presented, relying on either the publicly available datasets or on conducting new experiments.

a b s t r a c t Hematological and biochemical tests are widely used for assessment of health status and diagnosis of disease in domestic animals. They are almost indispensible in health man- agement of organic flocks, but environmental conditions and food supply can be highly variable in organic farming, which may cause levels of many analytes to lie outside the published reference intervals. We investigated key hematological and biochemical param- eters in organically raised sheep in Croatia. Different (mostly indigenous) breeds raised in various geographic regions were evaluated throughout the year. We identified key param- eters that varied under different conditions using classification based on machine learning. Our findings suggest that location (which determines climate and food availability) has a profound effect on hematological and biochemical values in organically raised sheep. The effect of location was more pronounced than that of breed and season. The results clearly show the merit of establishing specific reference intervals for each flock, especially in organic farming. We demonstrate feasibility of this approach by successful calculation of reference intervals from a small sample (30 individuals) using robust statistical methods. © 2012 Elsevier B.V. All rights reserved.

Background Most proteins are glycosylated, with glycans being integral structural and functional components of a glycoprotein. In contrast to polypeptides, which are fully encoded by the corresponding gene, glycans result from a dynamic interaction between the environment and a network of hundreds of genes. Scope of review Recent developments in glycomics, genomics and epigenomics are discussed in the context of an evolutionary advantage for higher eukaryotes over microorganisms, conferred by the complexity and adaptability which glycosylation adds to their proteome. Major conclusions Inter-individual variation of glycome composition in human population is large; glycome composition is affected by both genes and environment; epigenetic regulation of “glyco-genes” has been demonstrated; and several mechanisms for transgenerational inheritance of epigenetic marks have been documented. General significance Epigenetic recording of acquired characteristics and their transgenerational inheritance could be important mechanisms used by higher organisms to compete or collaborate with microorganisms.

Monitoring of animal health status in organic farming relies in part on the availability of exact reference intervals for key hematological and biochemical blood parameters. Once determined, these intervals provide a baseline for interpreting routine laboratory blood tests in order to assess nutritional status, stress or disease. In this study, reference intervals for hematological and blood biochemical parameters were determined for Dalmatian pramenka, an indigenous Croatian sheep breed. A recently developed nonparametric method based on bootstrap resampling was used for calculation of reference intervals, and its performance was compared with that of a conventional nonparametric method. Hematological and blood biochemical profi les from 114 organically reared Dalmatian pramenka sheep were constructed and used for calculation of reference intervals using the new approach. The new method enabled convenient and reliable determination of reference intervals from a relatively small sample size, without the need for transformation or fi ltering of the raw data. Separate reference ranges for male and female sheep were found to be unnecessary for most of the investigated parameters., Praćenje zdravstvenog statusa u ekološkom uzgoju dijelom se temelji na raspoloživosti preciznih referentnih raspona za ključne hematološke i biokemijske pokazatelje. Jednom utvrđeni, ovi rasponi služe kao polazište za interpretaciju rutinskih laboratorijskih pretraga krvi, dajući informacije o hranidbenom statusu životinje te izloženosti stresu ili bolesti. Ovim istraživanjem utvrđeni su referentni rasponi za ključne hematološke i biokemijske pokazatelje ovaca izvorne hrvatske pasmine dalmatinska pramenka. Pri tome je korištena razmjerno nova neparametrijska metoda temeljena na ponovljenom uzorkovanju s ponavljanjem (bootstrap), a njeni rezultati su uspoređeni s rezultatima odabrane konvencionalne neparametrijske metode. Hematološki i biokemijski profi li 114 ekološki uzgajanih ovaca pasmine dalmatinska pramenka poslužili su za računanje referentnih raspona novom metodom, koja se pokazala jednostavnom i pouzdanom čak i na malom uzorku, bez potrebe za transformacijom ili filtriranjem izvornih podataka. Određivanje zasebnih intervala za muške i ženske životinje se pokazalo nepotrebnim kod većine istraživanih parametara.

Chloroplasts originated in an endosymbiotic event more than 1.2 billion years ago (Butterfield, 2000), when a photosynthetic cyanobacterium was taken up by a heterotrophic cell. This event was followed by a massive transfer of genetic material to the host nucleus (Martin, 2003), which led to a problem for the newly established endosymbiotic relationship: proteins encoded by the transferred genes were now being synthesized in the cytosol of the host cell, and had to be transferred back to their place of action, the newly acquired chloroplast. Here, the chloroplast outer envelope is the first barrier for the cytosol-synthesized proteins. For a long time, the prevailing opinion was that the outer envelope of chloroplasts is like a molecular sieve – full of holes and leaky, with maybe a limited selectivity (Flügge, 2000). However, a significant body of recently accumulated evidence points to a tightly controlled regulation of the traffic across the outer envelope, previous picture of a molecular sieve being attributed to artifacts of at that time widely used patch-clamping technique (Soll et al., 2000). One of the molecular gates controlling the entry of molecules into chloroplasts is the protein translocon, responsible for selection and import of protein molecules. The first task of this complex is the recognition and binding of chloroplastic precursor proteins which have to be imported. Most of such proteins are synthesized with a cleavable Nterminal transit sequence, which is both necessary and sufficient to target them for chloroplast import (Sveshnikova et al, 2000 ; Bruce, 2001). The transit sequence consists of 20 to 150 amino acids, has an overall positive charge and is rich with hydroxylated amino acids (Soll and Schleiff, 2004). Its variable length and divergent primary structure suggest that it is not a specific sequence motif, but rather a certain structural characteristic, which is recognized by the receptors. For a long time it was believed that only outer envelope proteins lack an Nterminal transit sequence and some authors suggest that they might have an internal signal instead (Bruce et al., 2001 ; Schleiff and Klösgen, 2001). However, recent proteomic approaches identified many plastid proteins without an obvious signal with the above outlined characteristics within the coding region (Kleffmann et al., 2004). Therefore, the characteristics of the targeting signal and translocation events will be revisited for these proteins in future. The first hint for an alternative route in Arabidopsis thaliana came from the observed endoplasmic reticulum intermediate of α – carbonic anhydrase before its translocation into plastids (Villarejo et al., 2005).

Background: Since testicular cancer shows different disease progress depending on etiology and the neoplastic tissue profile, with epigenetic changes being a likely underlying mechanism, we investigated CpG methylation of MGMT and RASSF1, which had been identified as promising candidate biomarkers for disease progression, chemotherapy success and prognosis. Methods: Genomic DNA was isolated from blood of 32 healthy individuals and 32 patients with testicular cancer before and after the chemotherapy: etoposide, cisplatin, bleomycin (BEP). Eighteen samples were seminomas and 14 were nonseminomas. For quantitative measurement of DNA methylation levels in MGMT and RASSF1A, bisulfite-converted DNA was amplified by PCR and then sequenced using a pyrosequencing technology. Results: Methylation levels were not significantly different for MGMT before and after chemotherapy ; however, methylation of the tested CpG sites in RASSF1 was significantly higher in patients before treatment compared with controls at 5 of 9 sites, two sites remaining significant even after the Bonferroni correction. Methylation of RASSF1 approached that of the controls after treatment. In addition, we found indications that additional stratification by histopathological profile might add value to MGMT and RASSF1 methylation as a prognostic marker. The methylation of LINE1 elements was similar in patients before and after chemotherapy. Conclusions: Increasing statistical power by studying larger cohorts has a potential to further confirm RASSF1 methylation as a chemotherapy success biomarker, while additional stratification by histopahological characteristics could give further insight leading to more accurate prognosis using both RASSF1 and MGMT, thereby enabling better risk- adapted management of testicular cancer.

beta-Barrel-shaped channels of the Omp85 family are involved in the translocation or assembly of proteins of bacterial, mitochondrial, and plastidic outer membranes. We have compared these proteins to understand the evolutionary development of the translocators. We have demonstrated that the proteins from proteobacteria and mitochondria have a pore diameter that is at least five times smaller than found for the Omp85 in cyanobacteria and plastids. This finding can explain why Omp85 from cyanobacteria (but not the homologous protein from proteobacteria) was remodeled to become the protein translocation pore after endosymbiosis. Further, the pore-forming region of the Omp85 proteins is restricted to the C terminus. Based on a phylogenetic analysis we have shown that the pore-forming domain displays a different evolutionary relationship than the N-terminal domain. In line with this, the affinity of the N-terminal domain to the C-terminal region of the Omp85 from plastids and cyanobacteria differs, even though the N-terminal domain is involved in gating of the pore in both groups. We have further shown that the N-terminal domain of nOmp85 takes part in homo-oligomerization. Thereby, the differences in the phylogeny of the two domains are explained by different functional constraints acting on the regions. The pore-forming domain, however, is further divided into two functional regions, where the distal C terminus itself forms a dimeric pore. Based on functional and phylogenetic analysis, we suggest an evolutionary scenario that explains the origin of the contemporary translocon.

Reconstitution of proteins into liposomes is a widespread approach to analyzing their biological function. Many protocols exist for this procedure and for the subsequent analysis of proteins. Here, we establish a procedure for preparation and analysis of liposomes with a lipid composition reflecting the outer envelope of chloroplasts. First, the stability of the liposomes in different buffer systems was investigated to provide information for the storage of the reconstituted system. Then, the size of the liposomes created by filtration through a polycarbonate filter dependent on the lipid composition was analyzed. Subsequently, solubilization of the liposomes composed of lipids with the outer envelope composition by dodecylmaltoside and octylglucoside as a preceding step of reconstitution was studied. Finally, we developed a straightforward method to determine the size of liposomes by absorption spectroscopy. The described setup allows the construction of reconstitution protocols, including the final determination of the liposome size.

Around 2200 copies of genes encoding ribosomal RNA (rRNA) in pedunculate oak, Quercus robur, are organized into two rDNA loci, the major (NOR-1) and the minor (NOR-2) locus. We present the first cytogenetic evidence indicating that the NOR-1 represents the active nucleolar organizer responsible for rRNA synthesis, while the NOR-2 probably stays transcriptionally silent and does not participate in the formation of the nucleolus in Q. robur, which is a situation resembling the well-known phenomenon of nucleolar dominance. rDNA chromatin topology analyses in cycling root tip cells by light and electron microscopy revealed the minor locus to be highly condensed and located away from the nucleolus, while the major locus was consistently associated with the nucleolus and often exhibited different levels of condensation. In addition, silver precipitation was confined exclusively to the NOR-1 locus. Also, NOR-2 was highly methylated at cytosines and rDNA chromatin was marked with histone modifications characteristic for repressive state. After treatment of the root cells with the methylation inhibitor 5-aza-2′- deoxycytidine, we observed an increase in the total level of rRNA transcripts and a decrease in DNA methylation level at the NOR-2 locus. Also, NOR-2 sites relocalized with respect to the nuclear periphery/nucleolus, however, the relocation did not affect the contribution of this locus to nucleolar formation, nor did it affect rDNA chromatin decondensation, strongly suggesting that NOR-2 has lost the function of rRNA synthesis and nucleolar organization.

The aim of this study was to detect HEV by immunohistochemistry (IHC) and to determine infected organs and cell types. The samples of lung, liver, spleen, intestines, kidney and lymph nodes were collected from 3 fattening pigs previously found HEV-positive by nested RT-PCR. For IHC detection a mouse anti-HEV Mab (USBiological*) is used. HEV antigen was detected in liver of all 3 pigs in periportal inflammatory cells and in hepatocytes in centrolobar degeneration process and in mesenterial lymph nodes.

The aim of our study was to clarify the presence of HEV and described histopathological lesions in pigs in Croatia. A 37 fatteners were completely postmortem examined and samples of bile were colected and tested by nested PCR for presence of HEV. The liver tissue was collected for histological examination. HEV RNA was detected in 3 (8, 1%) of total 37 pigs. A moderate inflammatory reaction was present in periportal spaces as well as centrolobar necrosis and degeneration of hepatocytes with lymphoplasmacytic hepatitis was detected in 3 pigs. The study confirmed presence of HEV infection in Croatian large pig production units.

This study presents the first molecular data on the basis and the origin of Huntington disease in Croatia and is the first such analysis performed among a Slavic population. We analyzed three trinucleotide polymorphisms in the HD gene: CAG, CCG and GAG Delta2642 (E2642del) triplets. Analysis of the CAG repeat size among 44 Huntington patients (39-66 CAGs) and 51 normal individuals (9-34 CAGs) showed that the range of the repeats was similar to previous findings. The frequency of the CCG and Delta2642 polymorphic alleles on N and HD chromosomes was found to correlate well with earlier reports for Western European populations. We found significance for both the CCG7 allele (p=0.004) and the Delta2642 allele (p

Epigenetic variation in natural populations with contrasting habitats might be an important element, in addition to the genetic variation, in plant adaptation to environmental stress. Here, we assessed genetic, epigenetic, and cytogenetic structure of the three Lilium bosniacum populations growing on distinct habitats. One population was growing under habitual ecological conditions for this species and the other two were growing under stress associated with high altitude and serpentine soil. Amplified fragment length polymorphism and methylation-sensitive amplification polymorphism analyses revealed that the three populations did not differentiate genetically, but were clearly separated in three distinct clusters according to DNA methylation profiles. Principal coordinate analysis showed that overall epigenetic variation was closely related to habitat conditions. A new methylation-sensitive amplification polymorphism scoring approach allowed identification of mainly unmethylated (φST = 0.190) and fully CpG methylated (φST = 0.118) subepiloci playing a role in overall population differentiation, in comparison with hemimethylated sites (φST = 0.073). In addition, unusual rDNA repatterning and the presence of B chromosomes bearing 5S rDNA loci were recorded in the population growing on serpentine soil, suggesting dynamic chromosome rearrangements probably linked to global genome demethylation, which might have reactivated some mobile elements. We discuss our results considering our earlier data on morphology and leaf anatomy of several L. bosniacum populations, and suggest a possible role of epigenetics as a key element in population differentiation associated with environmental stress in these particular lily populations.

The precursor protein receptor at the chloroplast outer membrane atToc33 is a GTPase, which can be inactivated by phosphorylation in vitro, being arrested in the GDP loaded state. To assess the physiological function of phosphorylation, attoc33 knock out mutants were complemented with a mutated construct mimicking the constitutively phosphorylated state. Our data suggest that the reduced functionality of the mutant protein can be compensated by its upregulation. Chloroplast biogenesis and photosynthetic activity are impaired in the mutants during the early developmental stage, which is consistent with the requirement of atToc33 in young photosynthetic tissues.

BACKGROUND AND AIMS: Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn's disease (CD) and ulcerative colitis (UC), are sometimes hard to distinguish. Glycosylation of IgG has been associated with CD and UC. IgG Fc-glycosylation affects IgG effector functions. We evaluated changes in IgG Fc- glycosylation associated with UC and CD, as well as with disease characteristics in different patient groups. METHODS: We analyzed 3441 plasma samples obtained from 2 independent cohorts of patients with CD (874 patients from Italy and 391 from the United States) or UC (1056 from Italy and 253 from the US and healthy individuals [controls] ; 427 in Italy and 440 from the United States). IgG Fc-glycosylation (tryptic glycopeptides) was analyzed by liquid chromatography coupled to mass spectrometry. We analyzed associations between disease status (UC vs controls, CD vs controls, and UC vs CD) and glycopeptide traits, and associations between clinical characteristics and glycopeptide traits, using a logistic regression model with age and sex included as covariates. RESULTS: Patients with CD or UC had lower levels of IgG galactosylation than controls. For example, the odds ratio (OR) for IgG1 galactosylation in patients with CD was 0.59 (95% confidence interval [CI], 0.51-0.69) and for patients with UC was 0.81 (95% CI, 0.71-0.92). Fucosylation of IgG was increased in patients with CD vs controls (for IgG1: OR, 1.27 ; 95% CI, 1.12-1.44), but decreased in patients with UC vs controls (for IgG23: OR, 0.72 ; 95% CI, 0.63-0.82). Decreased galactosylation associated with more severe CD or UC, including the need for surgery in patients with UC vs controls (for IgG1: OR, 0.69 ; 95% CI, 0.54-0.89) and in patients with CD vs controls (for IgG23: OR, 0.78 ; 95% CI, 0.66-0.91). CONCLUSIONS: In a retrospective analysis of plasma samples from patients with CD or UC, we associated levels of IgG Fc-glycosylation with disease (compared to controls) and its clinical features. These findings could increase our understanding of mechanisms of CD and UC pathogenesis and be used to develop diagnostics or guide treatment.