Analysis of uni and bi-parental markers in mixture samples: Lessons from the 22nd GHEP-ISFG Intercomparison Exercise.

Since 1992, the Spanish and Portuguese-Speaking Working Group of the ISFG (GHEP-ISFG) has been organizing annual Intercomparison Exercises (IEs) coordinated by the Quality Service at the National Institute of Toxicology and Forensic Sciences (INTCF) from Madrid, aiming to provide proficiency tests for forensic DNA laboratories. Each annual exercise comprises a Basic (recently accredited under ISO/IEC 17043: 2010) and an Advanced Level, both including a kinship and a forensic module. Here, we show the results for both autosomal and sex-chromosomal STRs, and for mitochondrial DNA (mtDNA) in two samples included in the forensic modules, namely a mixture 2:1 (v/v) saliva/blood (M4) and a mixture 4:1 (v/v) saliva/semen (M8) out of the five items provided in the 2014 GHEP-ISFG IE. Discrepancies, other than typos or nomenclature errors (over the total allele calls), represented 6.5% (M4) and 4.7% (M8) for autosomal STRs, 15.4% (M4) and 7.8% (M8) for X-STRs, and 1.2% (M4) and 0.0% (M8) for Y-STRs. Drop-out and drop-in alleles were the main cause of errors, with laboratories using different criteria regarding inclusion of minor peaks and stutter bands. Commonly used commercial kits yielded different results for a micro-variant detected at locus D12S391. In addition, the analysis of electropherograms revealed that the proportions of the contributors detected in the mixtures varied among the participants. In regards to mtDNA analysis, besides important discrepancies in reporting heteroplasmies, there was no agreement for the results of sample M4. Thus, while some laboratories documented a single control region haplotype, a few reported unexpected profiles (suggesting contamination problems). For M8, most laboratories detected only the haplotype corresponding to the saliva. Although the GHEP-ISFG has already a large experience in IEs, the present multi-centric study revealed challenges that still exist related to DNA mixtures interpretation. Overall, the results emphasize the need for further research and training actions in order to improve the analysis of mixtures among the forensic practitioners.

The amphiphilic character of glycogenin.

This study describes for the first time the amphiphilicity of the protein moiety of proteoglycogen. Glycogenin but not proteoglycogen associates to phospholipid vesicles and forms by itself stable Gibbs and Langmuir monolayers at the air-buffer interface. The adsorption free energy (-6.7 kcal/mol) and the glycogenin collapse pressure (47 mN/m) are indicative of its high surface activity which can thermodynamically drive and retain the protein at the membrane interface to a maximum equilibrium adsorption surface pressure of 21 mN/m. The marked surface activity of glycogenin is further enhanced by its thermodynamically favorable penetration into zwitterionic and anionic phospholipids with a high cut-off surface pressure point above 30 mN/m. The strong association to phospholipid vesicles and the marked surface activity of glycogenin correspond to a high amphiphilic character which supports its spontaneous association to membrane interfaces, in which the de novo biosynthesis of glycogen was proposed to initiate.

Rotavirus NSP5 phosphorylation is up-regulated by interaction with NSP2.

We have previously shown that a number of isoforms of the non-structural rotavirus protein NSP5 are found in virus-infected cells. These isoforms differ in their level of phosphorylation which, at least in part, appears to occur through autophosphorylation. NSP5 co-localizes with another non-structural protein, NSP2, in the viroplasms of infected cells where virus replication takes place. We now show that NSP5 can be chemically cross-linked in living cells with the viral polymerase VP1 and NSP2. Interaction of NSP5 with NSP2 was also demonstrated by co-immunoprecipitation of NSP2 and NSP5 from extracts of UV-treated rotavirus-infected cells. In addition, in transient transfection assays, NSP5 phosphorylation in vivo was enhanced by co-expression of NSP2. An NSP5 C-terminal domain deletion mutant, was completely unable to be phosphorylated either in the presence or absence of NSP2. However, a 33 aa N-terminal deletion mutant of NSP5 was shown to become hyperphosphorylated in vivo and to be insensitive to NSP2 activation, suggesting a regulatory role for this domain in NSP5 phosphorylation and making it a candidate for the interaction with NSP2. These mutants also allow a preliminary mapping of NSP5 autophosphorylation activity.

Biosynthesis of proteoglycogen: modulation of glycogenin expression in the developing chicken.

Glycogenin, the autoglucosyltransferase that primes the biosynthesis of proteoglycogen, is found in the polysaccharide linked proteoglycogen form in mammals and chicken. Glycogenin was released from proteoglycogen and its activity was measured, together with that of glycogen synthase as well as glycogen content, in muscle, liver, and brain during chicken development. The specific activity of glycogenin, expressed per protein, increased with development only in muscle and was higher than the specific activities measured in liver and brain at any time. Concomitant with the rise in activity, an enhanced expression of the protein was observed with Western blot. The specific activity of glycogen synthase increased with development in muscle and liver, while glycogen accumulation was noticeable only in liver. The results indicate that the molar concentration of proteoglycogen is higher in muscle than in liver. The high glycogen content of liver may indicate that the size of the polysaccharide moiety of proteoglycogen is larger in liver than in muscle. This is the first report of developmental modulation of de novo biosynthesis of glycogen at the level of the primer that initiates glucose polymerization.

Purification of rabbit skeletal muscle proteoglycogen: studies on the glucosyltransferase activity of polysaccharide-free and -bound glycogenin.

Proteoglycogen is the end product in the process of glycogen biogenesis. We have purified rabbit muscle proteoglycogen and studied the glucosyltransferase reactions catalyzed by its protein moiety, glycogenin, free or bound to the polysaccharide. The purification strategy involved dissolution of proteoglycogen and cosedimenting membrane vesicles in a Triton X-114/Triton X-45 mixture followed by partition in the aqueous phase, potassium iodide precipitation of accompanying proteins, and washing by high-speed centrifugation. Glycogenin or a proteoglycogen species of an average molecular mass of 200 kDa was isolated by ion-exchange chromatography after the purified proteoglycogen had been subjected to long or short amylolytic digestion, respectively. Besides autoglucosylation from UDP-glucose, glycogenin was capable of autogalactosylation from UDP-galactose. The autoglucosylation reaction was not inhibited by the simultaneous glucosylation of the exogenous acceptors N-(maltosyl-alpha-1-4-(1-deoxiglucitol))-peptide or n-dodecyl-beta-D-maltoside. The polysaccharide-bound glycogenin species of 200 kDa showed to be active for the glucosylation of exogenous acceptor and represented the isolated proteoglycogen of higher size having glucosyl transferase activity. This is the first description of the isolation of native proteoglycogen and a proteoglycogen species having glucosyltransferase activity.

Cellular and subcellular localization of glycogenin in chicken retina.

We investigated the cellular and subcellular localization of glycogenin in chicken retina using a polyclonal antibody raised against chicken muscle glycogenin. The antiserum recognized both free and glycogen-bound glycogenin on dot blots. Immunocytochemistry revealed an uniform staining of all the retina layers except for the outer segments and ganglion cells layers that were very weakly stained and for the inner segments layer and a zone between the inner nuclear and inner plexiform layers that were heavily stained. Electron microscopy of neuronal cells showed immunoreactivity localized in the cytoplasm and nucleus. This is the first description of the cellular and subcellular localization of glycogenin. Our results suggest that the biosynthesis of glycogen could begin in both, the cytoplasm and nucleus of the neurone.

Phosphorylation generates different forms of rotavirus NSP5.

NSP5 (non-structural protein 5) is one of two proteins encoded by genome segment 11 of group A rotaviruses. In virus-infected cells NSP5 accumulates in the virosomes and is found as two polypeptides with molecular masses of 26 and 28 kDa (26K and 28K proteins). NSP5 has been previously shown to be post-translationally modified by the addition of O-linked monosaccharide residues of N-acetylglucosamine and also by phosphorylation. We have now found that, as a consequence of phosphorylation, a complex modification process gives rise to previously unidentified forms of NSP5, with molecular masses of up to 34 kDa. Treatment with phosphatases of NSP5 obtained from virus-infected cells produced a single band of 26 kDa. NSP5 could be phosphorylated in vitro by incubation of immunoprecipitates with [gamma-32P]ATP, producing mainly phosphorylated products of 28 and 32-34 kDa (32-34K). In both in vivo and in vitro phosphorylated NSP5, phosphates were only found attached via serine and threonine residues. The in vitro translated NSP5 precursor polypeptide, molecular mass 25 kDa (25K), could also be phosphorylated and transformed into a 28K protein by incubation with extracts obtained from virus-infected cells, but not from non-infected cells. In addition, NSP5 labelled in vivo with [1,6-3H]glucosamine showed mainly the presence of the 26K and 28K proteins (converted to 26K by protein phosphatase treatment) suggesting that the type of protein produced is regulated according to the level of phosphorylation and/or O-glycosylation. The results also suggest that NSP5 is autophosphorylated.

Glycogen-bound protein in lower eukaryote and prokaryote.

The proteoglycogen fraction of Neurospora crassa was purified and subjected to radioiodination with [125I]iodide. Amylolysis of the polysaccharide moiety led to the isolation of a labelled 31 kDa-protein. The NH2-terminal amino acid sequence of 10 residues of the 31 kDa-protein was determined. A 31 kDa-protein was also bound to glycogen in Escherichia coli. Proteoglycogen has not been heretofore found in any primitive unicellular organism.

A glycogen precursor associated with membrane in retina.

The incorporation of [14C]glucose from UDP-[14C]glucose into proteoglycogen fractions of a retinal microsomal preparation was studied. From the rate of labelling of acid-insoluble and -soluble proteoglycogen at different sugar-donor concentrations, and from the conversion of the labelled acid-insoluble into an acid-soluble form measured by a 'chase' with unlabelled UDP-glucose, it was concluded that acid-insoluble 42 kDa protein (p42)-bound glycogen of weight-average Mr 4.7 x 10(5) and acid-soluble p42-bound glycogen of weight-average Mr 7.0 x 10(5) [Miozzo, Lacoste & Curtino (1989) Biochem. J. 260, 287-289] are related as precursor and product respectively. About one-third of the acid-insoluble proteoglycogen was excluded from a Sephacryl S-500 column and was associated with large membrane vesicles. Proteoglycogen was not dissociated from the membranes by treatment with saline solutions or with SDS at a low detergent-to-protein ratio. It was dissociated by treatment with detergents under conditions which were shown to solubilize integral membrane sialoglycoconjugates of retina. These results lead us to postulate that the biogenesis of retina glycogen starts on membrane-associated p42 to form acid-insoluble proteoglycogen, which is then dissociated from membranes and converted into acid-soluble proteoglycogen by the 'growth' of its polysaccharide moiety.

Characterization of the proteoglycogen fraction non-extractable from retina by trichloroacetic acid.

The trichloroacetic acid-insoluble 1,4-alpha-glucan fraction from bovine retina was purified and characterized. It is a proteoglycogen fraction containing a 42 kDa protein moiety similar in size to the protein moiety of the trichloroacetic acid-soluble proteoglycogen fraction. The apparent weight-average Mr of acid-insoluble and acid-soluble proteoglycogens are 4.7 x 10(5) and 7.0 x 10(5) respectively. The present results support suggestions from earlier studies indicating that acid-insoluble proteoglycogen is the precursor of the acid-soluble form.