Jon K. Laerdahl

Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.

Primary sclerosing cholangitis (PSC) is a chronic bile duct disease affecting 2.4–7.5% of individuals with inflammatory bowel disease. We performed a genome-wide association analysis of 2,466,182 SNPs in 715 individuals with PSC and 2,962 controls, followed by replication in 1,025 PSC cases and 2,174 controls. We detected non-HLA associations at rs3197999 in MST1 and rs6720394 near BCL2L11 (combined P = 1.1 × 10−16 and P = 4.1 × 10−8, respectively).

Gas phase nucleophilic substitution

Abstract The literature on gas phase nucleophilic substitution reactions at aliphatic carbon has been reviewed. The emphasis has been on journal articles published in the period 1990–2001. The present review outlines our current understanding of concepts such as potential energy surfaces, structure–energy relationships, microsolvation, and dynamical and mechanistic details based on both experimental and theoretical evidence. The accuracy of various theoretical schemes for calculating potential energy surfaces has been assessed. A critical account on mechanistic concepts used in the literature is given.

Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci

BACKGROUND & AIMS A limited number of genetic risk factors have been reported in primary sclerosing cholangitis (PSC). To discover further genetic susceptibility factors for PSC, we followed up on a second tier of single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS). METHODS We analyzed 45 SNPs in 1221 PSC cases and 3508 controls. The association results from the replication analysis and the original GWAS (715 PSC cases and 2962 controls) were combined in a meta-analysis comprising 1936 PSC cases and 6470 controls. We performed an analysis of bile microbial community composition in 39 PSC patients by 16S rRNA sequencing. RESULTS Seventeen SNPs representing 12 distinct genetic loci achieved nominal significance (p(replication) <0.05) in the replication. The most robust novel association was detected at chromosome 1p36 (rs3748816; p(combined)=2.1 × 10(-8)) where the MMEL1 and TNFRSF14 genes represent potential disease genes. Eight additional novel loci showed suggestive evidence of association (p(repl) <0.05). FUT2 at chromosome 19q13 (rs602662; p(comb)=1.9 × 10(-6), rs281377; p(comb)=2.1 × 10(-6) and rs601338; p(comb)=2.7 × 10(-6)) is notable due to its implication in altered susceptibility to infectious agents. We found that FUT2 secretor status and genotype defined by rs601338 significantly influence biliary microbial community composition in PSC patients. CONCLUSIONS We identify multiple new PSC risk loci by extended analysis of a PSC GWAS. FUT2 genotype needs to be taken into account when assessing the influence of microbiota on biliary pathology in PSC.

DNA base repair – recognition and initiation of catalysis

Endogenous DNA damage induced by hydrolysis, reactive oxygen species and alkylation modifies DNA bases and the structure of the DNA duplex. Numerous mechanisms have evolved to protect cells from these deleterious effects. Base excision repair is the major pathway for removing base lesions. However, several mechanisms of direct base damage reversal, involving enzymes such as transferases, photolyases and oxidative demethylases, are specialized to remove certain types of photoproducts and alkylated bases. Mismatch excision repair corrects for misincorporation of bases by replicative DNA polymerases. The determination of the 3D structure and visualization of DNA repair proteins and their interactions with damaged DNA have considerably aided our understanding of the molecular basis for DNA base lesion repair and genome stability. Here, we review the structural biochemistry of base lesion recognition and initiation of one-step direct reversal (DR) of damage as well as the multistep pathways of base excision repair (BER), nucleotide incision repair (NIR) and mismatch repair (MMR).

Genome-Wide Association Analysis in Primary Sclerosing Cholangitis and Ulcerative Colitis Identifies Risk Loci at GPR35 and TCF4

Approximately 60%‐80% of patients with primary sclerosing cholangitis (PSC) have concurrent ulcerative colitis (UC). Previous genome‐wide association studies (GWAS) in PSC have detected a number of susceptibility loci that also show associations in UC and other immune‐mediated diseases. We aimed to systematically compare genetic associations in PSC with genotype data in UC patients with the aim of detecting new susceptibility loci for PSC. We performed combined analyses of GWAS for PSC and UC comprising 392 PSC cases, 987 UC cases, and 2,977 controls and followed up top association signals in an additional 1,012 PSC cases, 4,444 UC cases, and 11,659 controls. We discovered novel genome‐wide significant associations with PSC at 2q37 [rs3749171 at G‐protein‐coupled receptor 35 (GPR35); P = 3.0 × 10−9 in the overall study population, combined odds ratio [OR] and 95% confidence interval [CI] of 1.39 (1.24‐1.55)] and at 18q21 [rs1452787 at transcription factor 4 (TCF4); P = 2.61 × 10−8, OR (95% CI) = 0.75 (0.68‐0.83)]. In addition, several suggestive PSC associations were detected. The GPR35 rs3749171 is a missense single nucleotide polymorphism resulting in a shift from threonine to methionine. Structural modeling showed that rs3749171 is located in the third transmembrane helix of GPR35 and could possibly alter efficiency of signaling through the GPR35 receptor. Conclusion: By refining the analysis of a PSC GWAS by parallel assessments in a UC GWAS, we were able to detect two novel risk loci at genome‐wide significance levels. GPR35 shows associations in both UC and PSC, whereas TCF4 represents a PSC risk locus not associated with UC. Both loci may represent previously unexplored aspects of PSC pathogenesis. (HEPATOLOGY 2013;58:1074–1083)

D- or L-alanine : That is the question

The question is reopened, whether L- or D-alanine is more stable. Calculated parity-violating energy shifts for the 13 stable conformers of gaseous alanine (the picture shows the global minima) indicate that the stabilization of a certain enantiomer is strongly dependent on its conformation. Naturally occurring L-alanine is preferred for only seven of the investigated structures, which allows no definite conclusion on the relative stability of the two chiral forms to explain the origin of homochirality in living organisms.

Characterization of novel mutations in the catalytic domain of the PCSK9 gene

Objectives.  To expand our understanding of the structure and function of proprotein convertase subtilisin/kexin type 9 (PCSK9) by studying how naturally occurring mutations in PCSK9 disrupt the function of PCSK9.

The accuracy of the pseudopotential approximation. III. A comparison between pseudopotential and all-electron methods for Au and AuH

The quality of the pseudopotential approximation has been tested thoroughly by calculating spectroscopic properties of the gold atom and ground state AuH for eight different effective core potentials using Hartree–Fock, second-order Mo/ller–Plesset and coupled cluster methods. The pseudopotential valence basis set {φ}v for Au was chosen to be identical for all pseudopotentials, a subset of the all-electron basis set {φ}v⊂{φ}AE, and the condition was applied that all sets are of near basis set limit quality. The pseudopotential results are compared with data obtained from nonrelativistic, scalar relativistic Douglas–Kroll and fully relativistic four-component all-electron calculations. The variation between the results obtained for all valence electron small-core pseudopotentials and all electron Douglas–Kroll calculations is found to be small (for the Stuttgart pseudopotential Δre=0.001 A, ΔDe=0.03 eV, Δωe=9 cm−1, Δμe=0.04 D). Sizable differences to all electron results are only found for the 11 valence e...

Annotated Expressed Sequence Tags (ESTs) from pre-smolt Atlantic salmon (Salmo salar) in a searchable data resource

BackgroundTo identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service.DescriptionTwenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component.ConclusionWe describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches.

Early-onset Crohn’s disease and autoimmunity associated with a variant in CTLA-4

Objective IBD is a group of complex, systemic disorders associated with intestinal inflammation and extraintestinal manifestations. Recent studies revealed Mendelian forms of IBD, which contributed significantly to our understanding of disease pathogenesis and the heritability of IBD. Design We performed exome sequencing in a family with Crohn’s disease (CD) and severe autoimmunity, analysed immune cell phenotype and function in affected and non-affected individuals, and performed in silico and in vitro analyses of cytotoxic T lymphocyte-associated protein 4 (CTLA-4) structure and function. Results A novel missense variant was identified in CTLA4 encoding CTLA-4, a coinhibitory protein expressed by T cells and required for regulation of T cell activation. The residue affected by the mutation, CTLA-4 Tyr60, is evolutionarily highly conserved, and the identified Y60C variant is predicted to affect protein folding and structural stability and demonstrated to cause impaired CTLA-4 dimerisation and CD80 binding. Intestinal inflammation and autoimmunity in carriers of CTLA-4 Y60C exhibit incomplete penetrance with a spectrum of clinical presentations ranging from asymptomatic carrier status to fatal autoimmunity and intestinal inflammation. In a clinically affected CTLA-4 Y60C carrier, T cell proliferation was increased in vitro and associated with an increased ratio of memory to naive T cells in vivo, consistent with impaired regulation of T cell activation. Conclusions Our results support the concept that variants in CTLA4 provide the basis for a novel Mendelian form of early-onset CD associated with systemic autoimmunity. Incomplete penetrance of autoimmunity further indicates the presence of other genetic and/or environmental modifiers.