Finite element formulation for the analysis of interfaces, nonlinear and large displacement problems in geotechnical engineering

Ph.D.R. D. Barksdal

Njáls Saga Stemmas, Old And New

Despite its fame as the pre-eminent medieval Icelandic saga, Njáls saga lacks a stemma comprehending all the saga’s manuscripts: only the vellum manuscripts have been surveyed in detail. As part of the Variance of Njáls saga (Breytileki Njáls sögu) project, we produced a stemma of all witnesses to chapter 86 (forty-nine out of the total sixty or so surviving manuscripts and fragments), supplemented with targeted samples from chapter 142 (32 manuscripts). This affords the first systematic insight into the post-medieval manuscript transmission of the saga. The present article focuses on two aspects of the post-medieval transmission which turn out to be of particular interest: the huge popularity of the lost medieval manuscript *Gullskinna in the post-medieval scribal tradition, and a revision of the branch of the Njáls saga stemma labelled as *Y by Einar Ólafur (noted for being represented by Oddabók, AM 466 4to)

A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report

A male patient, born to unrelated Belgian parents, presented at 4 months with epistaxis, haematemesis and haematochezia. On physical examination he presented petechiae and haematomas, and a slightly enlarged liver. Serum transaminases were elevated to 5-10 times upper limit of normal, alkaline phosphatases were 1685 U/L (<720), total bilirubin was 2.53 mg/dl (<1.0), ammonaemia 69 μM (<32), prothrombin time less than 10%, thromboplastin time >180 s (<60) and alpha-fetoprotein 29723 μg/L (<186). Plasma tyrosine (651 μM) and methionine (1032 μM) were strongly increased. In urine, tyrosine metabolites and 4-oxo-6-hydroxyheptanoic acid were increased, but succinylacetone and succinylacetoacetate - pathognomonic for tyrosinemia type I - were repeatedly undetectable. Delta-aminolevulinic acid was normal, which is consistent with the absence of succinylacetone. Abdominal ultrasound and brain CT were normal

COG Complex Complexities : Detailed Characterization of a Complete Set of HEK293T Cells Lacking Individual COG Subunits

The Conserved Oligomeric Golgi complex is an evolutionarily conserved multisubunit tethering complex (MTC) that is crucial for intracellular membrane trafficking and Golgi homeostasis. The COG complex interacts with core vesicle docking and fusion machinery at the Golgi; however, its exact mechanism of action is still an enigma. Previous studies of COG complex were limited to the use of CDGII (Congenital disorders of glycosylation type II)-COG patient fibroblasts, siRNA mediated knockdowns, or protein relocalization approaches. In this study we have used the CRISPR approach to generate HEK293T knock-out (KO) cell lines missing individual COG subunits. These cell lines were characterized for glycosylation and trafficking defects, cell proliferation rates, stability of COG subunits, localization of Golgi markers, changes in Golgi structure, and N-glycan profiling. We found that all KO cell lines were uniformly deficient in cis/medial-Golgi glycosylation and each had nearly abolished binding of Cholera toxin. In addition, all cell lines showed defects in Golgi morphology, retrograde trafficking and sorting, sialylation and fucosylation, but severities varied according to the affected subunit. Lobe A and Cog6 subunit KOs displayed a more severely distorted Golgi structure, while Cog2, 3, 4, 5, and 7 knock outs had the most hypo glycosylated form of Lamp2. These results led us to conclude that every subunit is essential for COG complex function in Golgi trafficking, though to varying extents. We believe that this study and further analyses of these cells will help further elucidate the roles of individual COG subunits and bring a greater understanding to the class of MTCs as a whole

Golgi function and dysfunction in the first COG4-deficient CDG type II patient

The conserved oligomeric Golgi (COG) complex is a hetero-octameric complex essential for normal glycosylation and intra-Golgi transport. An increasing number of congenital disorder of glycosylation type II (CDG-II) mutations are found in COG subunits indicating its importance in glycosylation. We report a new CDG-II patient harbouring a p.R729W missense mutation in COG4 combined with a submicroscopical deletion. The resulting downregulation of COG4 expression additionally affects expression or stability of other lobe A subunits. Despite this, full complex formation was maintained albeit to a lower extent as shown by glycerol gradient centrifugation. Moreover, our data indicate that subunits are present in a cytosolic pool and full complex formation assists tethering preceding membrane fusion. By extending this study to four other known COG-deficient patients, we now present the first comparative analysis on defects in transport, glycosylation and Golgi ultrastructure in these patients. The observed structural and biochemical abnormalities correlate with the severity of the mutation, with the COG4 mutant being the mildest. All together our results indicate that intact COG complexes are required to maintain Golgi dynamics and its associated functions. According to the current CDG nomenclature, this newly identified deficiency is designated CDG-IIj

The COG complex interacts directly with Syntaxin 6 and positively regulates endosome-to-TGN retrograde transport

The conserved oligomeric Golgi (COG) complex interacts with the t-SNARE Syntaxin 6 and promotes endosome-to-TGN retrograde trafficking

Modeling Glycan Processing Reveals Golgi-Enzyme Homeostasis upon Trafficking Defects and Cellular Differentiation

The decoration of proteins by carbohydrates is essential for eukaryotic life yet heterogeneous due to a lack of biosynthetic templates. This complex carbohydrate mixture-the glycan profile-is generated in the compartmentalized Golgi, in which level and localization of glycosylation enzymes are key determinants. Here, we develop and validate a computational model for glycan biosynthesis to probe how the biosynthetic machinery creates different glycan profiles. We combined stochastic modeling with Bayesian fitting that enables rigorous comparison to experimental data despite starting with uncertain initial parameters. This is an important development in the field of glycan modeling, which revealed biological insights about the glycosylation machinery in altered cellular states. We experimentally validated changes in N-linked glycan-modifying enzymes in cells with perturbed intra-Golgi-enzyme sorting and the predicted glycan-branching activity during osteogenesis. Our model can provide detailed information on altered biosynthetic paths, with potential for advancing treatments for glycosylation-related diseases and glyco-engineering of cells

Advances in Congenital Disorders of Glycosylation type II

Congenital Disorders of Glycosylation (CDG) are a group of hereditary, m ostly multisystem, disorders caused by defects in the biosynthesis of th e sugar moiety of glycoproteins and glycolipids. This sugar moiety plays a role in e.g. stability, secretion and interactions of glycoproteins. Since the description of the first two patients with CDG by Jaeken et al . in 1980, multiple defects in N- and O-glycosylation have been describe d. N-glycosylation defects can be divided into two main groups, CDG-I an d CDG-II. CDG-I are defects in the assembly of a precursor, consisting o f 14 oligosaccharides, on the lipid carrier dolichol or in the transfer of this precursor from dolichol to the NH2 group of an asparagine of a n ascent protein. CDG-II comprises defects in the processing of this precu rsor into a complex type N-glycan. During this processing, monosaccharid es are sequentially removed and added by specific enzymes. Isoelectrofocusing (IEF) of serum transferrin shows a so-called type 1 p attern in CDG-I, and in CDG-II often a type 2 pattern. Additional analysis of the glycan structure by MALDI-TOF mass spectromet ry of serum transferrin and/or total serum distinguishes defects in bran ching, demannosylation, galactosylation, sialylation and fucosylation. B ased on the glycan structure, a hypothesis can be made on the possible d efect. O-glycosylation can be checked by IEF of apoC-III, an O-glycosylated pro tein. In contrast to N-glycosylation, O-glycosylation consists only of a n assembly phase which mostly takes place in the Golgi. The O-glycan is linked to the OH group of a serine or threonine of a protein. In 2004, the first patients with a defect in one of the subunits of the Conserved Oligomeric Golgi (COG) complex were described. This protein co mplex is linked to the cytoplasmic side of the Golgi membrane and consis ts of 8 subunits organised in two lobes, lobe A (Cog1-4) and lobe B (Cog 5-8). N- and O-glycosylation were disturbed in these patients. A defect in the COG complex seems to disturb the retrograde vesicular trafficking from Golgi to endoplasmic reticulum and between Golgi cisternae. This l eads to mislocalization and/or degradation of proteins involved in glyco sylation. The defect in retrograde vesicular transport can be demonstrat ed by treatment of fibroblasts with BFA. This normally causes a collapse of the Golgi and redistribution of its membranes to the endoplasmic ret iculum, but in patients with COG defects parts of the Golgi remain. The aims of the study are the detection of basis defects in patients wit h CDG-II. This is important for the patient and his family regarding gen etic counselling and prenatal diagnosis, but also to gain new insights i n the pathogenesis of glycosylation disorders which might lead to therap eutic options in the future. We identified in the course of this research three patients with the sam e mutation in COG7. This mutation was already described by Wu et al. in 2004 in two siblings. Together with a new patient described by Ng et al. in 2007, this brings the total of patients with the c.169+4A>C mutation to 6. The phenotype of all these patients is similar, with early death before the age of 9 months, intrauterine growth retardation, microcephal y, failure to thrive, dysmorphic features including a typical facial ge stalt and finger anomalies, episodes of hyperthermia and variable invol vement of other organs like heart (ASD, VSD), liver (cholestasis), gastr ointestinal system (pseudo-obstruction) and kidneys (obstructive uropath y). One of our three patients was selected for further investigations ba sed on her phenotype which is an argument for the recognisability of the syndrome linked with this COG7 mutation. The patients originated from N orth African countries. We were able to find the same haplotype within 3 different families pointing to an ancestral mutation. We also identified two children with new mutations in the COG complex. The patient with a new mutation in COG1, c.1070+5 G>A, had a peculiar ph enotype which can be described as a costocerebromandibular syndrome incl uding anomalies of ribs and vertebrae, cerebellar atrophy and a Pierre-R obin sequence. He presented also with short stature, microcephaly and at ypical haemolytic uremic syndrome and needed a kidney transplantation be cause of renal insufficiency. The mutation is located in the intron betw een exon 6 and exon 7 and disturbs correct splicing which leads to skipp ing of exon 6, a frameshift and premature stopcodon. Only a small percentage of the transcript is spliced correctly. In this patient a defect in N- and O-glycosylation was observed by means of IEF and mass spectrometry showed a defect mainly in sialylation. A defect in retrograde vesicular transport was shown by BFA treatment of fibroblast s. Although the clinical presentation and mutation are rather severe, th e amount of Cog proteins on western blot was conserved, except for a sma ll decrease in Cog8 protein. This is in contrast to the earlier describe d patient with a truncating COG1 mutation who has a mild presentation an d severely reduced Cog proteins of lobe A and Cog8 on western blot. The patient with a new mutation in COG7 (c.170-7A>G) presented with simi lar characteristics as other COG/COG7 deficient patients, including grow th retardation, microcephaly, hyperthermia and early death. This mutatio n is situated in the same intron as the c.169+4A>C mutation, but affects the splice acceptor instead of the splice donor. The mutation creates a new splice acceptor and this causes aberrant splicing with 6 new base p airs added between exon 1 and exon 2. The resulting protein has two extr a amino acids, alanine and threonine, but is otherwise not altered. In t his patient, a defect in N-and O-glycosylation was observed by means of IEF, and mass spectrometry showed a defect mainly in sialylation. The am ount of Cog7 protein on western blot was only slightly decreased, togeth er with the Cog proteins of lobe B. The fibroblasts of this patient also showed a defect in retrograde vesicular transport after treatment with BFA. We think that the two extra amino acids disturb the function of the COG complex. After exclusion of defects in the COG complex, we searched for new candi date genes for CDG-II. Because CDG is mainly an autosomal recessive diso rder, we used linkage and homozygosity mapping in a Jewish family with 2 affected siblings and 2 unaffected siblings. By SNP array we were able to identify in this family two homozygous regions on chromosome 4 and 13 containing about 200 genes. To reduce the number of genes to check, we compared the expression of the genes between the two affected siblings o n the one hand and their parents and an unaffected sibling on the other hand. A homozygous mutation, IVS4+182G>A, was identified in, a gene with unkno wn function. This mutation is located in the intron between exon 4 and e xon 5 and disrupts splicing leading to two transcripts: a normal one and one where a part of the intron is spliced into the transcript. A frames hift and premature stopcodon at position 204 lead to a truncated protein . We identified this mutation also in another Jewish boy, originating fr om the same region (in Georgia) as the first two patients and presenting with similar features including growth retardation, macrocephaly, failu re to thrive, hepatomegaly, muscle weakness, joint laxity, skeletal dysp lasia and elevated serum creatine kinase. Two of the three children pres ented also with hyperthermia. In a group of unsolved CDG-II patients we found also other mutations in the gene. We found a Turkish boy with a homozygous mutation R to H and a n American girl with compound heterozygous mutations R to C and G to R. The Turkish boy presented with hypotonia, failure to thrive, atypical ha emolytic uremic syndrome and elevated serum CK. The American girl had sk eletal dysplasia in common with the Jewish patients. Apart from a defect in N- and O-glycosylation, demonstrated on IEF, we found evidence for a defect in galactosylation and secondary hyposialylation on mass spectro metry. We searched in fibroblasts for features which would normalize by introdu cing the wild type gene. We found a slightly increased staining with the SBA lectin and a mild delay in retrograde trafficking with BFA. Introdu ction of the wild type gene by means of viral transduction lead to a hig her expression of the abnormal transcript. Either the viral particle or the wild type gene must have affected transcription of the endogenous ge ne. Amaxa nucleofection was a second method to introduce the wild type g ene with high efficiency into patient cells. The difference in lectin st aining appeared decreased and also the delay in retrograde trafficking w as not significantly different in nucleofected cells with introduction o f the wild type gene and without introduction of the wild type gene. Wha t we did see was the protein encoded by gene X localized into perinuclea r swollen vesicles. This suggests an endosomal/lysosomal localization, b ut it might not be physiological. We tried to make antibodies against the protein X to use in functional a ssays. We did not succeed and also Eurogentec did not. Although a band o f the predicted size was identified on western blot, there was no differ ence between this band in fibroblasts of patient and control, either in HeLa cells, HeLa s overexpressing gene X or HeLa s were gene X expressio n was knocked down. Recombinant protein made in E. coli was not visualiz ed by either antibody. Little is known about the function of gene X. We suggest a major role in bone, both because of the clinical presentations of patients with gene X mutations and because of the high expression level we found in murine bone. The predicted structure of gene X with 6 or 7 transmembrane domain s and the repeated motif with two negatively charged amino acids, sugges t that the protein encoded by gene X is a transporter of cations. A prot ein with similar structure is bacteriorhodopsin, a proton pump in archea . If protein X is also a proton pump, it might act to remove protons pro duced during glycosylation in order to keep the Golgi pH constant. A def ect in gene X would then lead to a disturbed (Golgi) pH and secondary di sturbance of glycosylation, but also a disturbed calciumhomeostasis coul d explain disturbed glycosylation by disturbing intra-Golgi transport. It seems that both defects in the COG complex and in gene X disturb the trans-Golgi structure and/or function which lead to defects in galactosy lation and/or sialylation. COG defects do disturb this by an alteration of retrograde vesicular tra fficking, although it is not completely understood how.status: publishe