AP endonuclease 1 prevents trinucleotide repeat expansion via a novel mechanism during base excision repair

Base excision repair (BER) of an oxidized base within a trinucleotide repeat (TNR) tract can lead to TNR expansions that are associated with over 40 human neurodegenerative diseases. This occurs as a result of DNA secondary structures such as hairpins formed during repair. We have previously shown that BER in a TNR hairpin loop can lead to removal of the hairpin, attenuating or preventing TNR expansions. Here, we further provide the first evidence that AP endonuclease 1 (APE1) prevented TNR expansions via its 3′-5′ exonuclease activity and stimulatory effect on DNA ligation during BER in a hairpin loop. Coordinating with flap endonuclease 1, the APE1 3′-5′ exonuclease activity cleaves the annealed upstream 3′-flap of a double-flap intermediate resulting from 5′-incision of an abasic site in the hairpin loop. Furthermore, APE1 stimulated DNA ligase I to resolve a long double-flap intermediate, thereby promoting hairpin removal and preventing TNR expansions.     

FepA- and TonB-dependent bacteriophage H8: receptor binding and genomic sequence

H8 is derived from a collection of Salmonella enterica serotype Enteritidis bacteriophage. Its morphology and genomic structure closely resemble those of bacteriophage T5 in the family Siphoviridae. H8 infected S. enterica serotypes Enteritidis and Typhimurium and Escherichia coli by initial adsorption to the outer membrane protein FepA. Ferric enterobactin inhibited H8 binding to E. coli FepA (50% inhibition concentration, 98 nM), and other ferric catecholate receptors (Fiu, Cir, and IroN) did not participate in phage adsorption. H8 infection was TonB dependent, but exbB mutations in Salmonella or E. coli did not prevent infection; only exbB tolQ or exbB tolR double mutants were resistant to H8. Experiments with deletion and substitution mutants showed that the receptor-phage interaction first involves residues distributed over the protein's outer surface and then narrows to the same charged (R316) or aromatic (Y260) residues that participate in the binding and transport of ferric enterobactin and colicins B and D. These data rationalize the multifunctionality of FepA: toxic ligands like bacteriocins and phage penetrate the outer membrane by parasitizing residues in FepA that are adapted to the transport of the natural ligand, ferric enterobactin. DNA sequence determinations revealed the complete H8 genome of 104.4 kb. A total of 120 of its 143 predicted open reading frames (ORFS) were homologous to ORFS in T5, at a level of 84% identity and 89% similarity. As in T5, the H8 structural genes clustered on the chromosome according to their function in the phage life cycle. The T5 genome contains a large section of DNA that can be deleted and that is absent in H8: compared to T5, H8 contains a 9,000-bp deletion in the early region of its chromosome, and nine potentially unique gene products. Sequence analyses of the tail proteins of phages in the same family showed that relative to pb5 (Oad) of T5 and Hrs of BF23, the FepA-binding protein (Rbp) of H8 contains unique acidic and aromatic residues. These side chains may promote binding to basic and aromatic residues in FepA that normally function in the adsorption of ferric enterobactin. Furthermore, a predicted H8 tail protein showed extensive identity and similarity to pb2 of T5, suggesting that it also functions in pore formation through the cell envelope. The variable region of this protein contains a potential TonB box, intimating that it participates in the TonB-dependent stage of the phage infection process.     

A Vaccine Approach for the Prevention of Infections by Multidrug-resistant Enterococcus faecium

The incidence of multidrug-resistant Enterococcus faecium hospital infections has been steadily increasing. With the goal of discovering new vaccine antigens, we systematically fractionated and purified four distinct surface carbohydrates from E. faecium endocarditis isolate Tx16, shown previously to be resistant to phagocytosis in the presence of human serum. The two most abundant polysaccharides consist of novel branched heteroglycan repeating units that include signature sugars altruronic acid and legionaminic acid, respectively. A minor high molecular weight polysaccharide component was recognized as the fructose homopolymer levan, and a glucosylated lipoteichoic acid (LTA) was identified in a micellar fraction. The polysaccharides were conjugated to the CRM₁₉₇ carrier protein, and the resulting glycoconjugates were used to immunize rabbits. Rabbit immune sera were evaluated for their ability to kill Tx16 in opsonophagocytic assays and in a mouse passive protection infection model. Although antibodies raised against levan failed to mediate opsonophagocytic killing, the other glycoconjugates induced effective opsonic antibodies, with the altruronic acid-containing polysaccharide antisera showing the greatest opsonophagocytic assay activity. Antibodies directed against either novel heteroglycan or the LTA reduced bacterial load in mouse liver or kidney tissue. To assess antigen prevalence, we screened a diverse collection of blood isolates (n = 101) with antibodies to the polysaccharides. LTA was detected on the surface of 80% of the strains, and antigens recognized by antibodies to the two major heteroglycans were co-expressed on 63% of these clinical isolates. Collectively, these results represent the first steps toward identifying components of a glycoconjugate vaccine to prevent E. faecium infection.     

Rapid prototyping of scaphoid and lunate bones

In this study, a novel rapid prototyping technology was used to fabricate scaphoid and lunate bone prostheses, two carpal bones that are prone to avascular necrosis. Carpal prostheses were fabricated with an Envisiontec Perfactory® SXGA stereolithography system using Envisiontec eShell 200 photocurable polymer. Fabrication was guided using 3-D models, which were generated using Mimics software (Materialise NV, Leuven, Belgium) from patient computer tomography data. The prostheses were fabricated in a layer-by-layer manner; ∼ 50-μm thick layers were observed in the prostheses. Hardness and Young's modulus values of polymerized eShell 200 material were 93.8 ± 7.25 MPa and 3050 ± 90 MPa, respectively. The minimum compressive force required for fracture was 1360 N for the scaphoid prosthesis and 1248 N for the lunate prosthesis. Polymerized Envisiontec eShell material exhibited high human neonatal epidermal keratinocyte cell viability rate in an MTT assay. The results of this study indicate that small bone prostheses fabricated by stereolithography using eShell 200 polymer may have suitable geometry, mechanical properties, and cytocompatibility properties for in vivo use.     

Using niche‐based GIS modeling to test geographic predictions of competitive exclusion and competitive release in South American pocket mice

Geographic studies addressing the role of competition in determining species’ macrodistributions have been limited by only simple or subjective means of identifying regions of suitable habitat. Now, ecological‐niche models of species’ potential distributions present a possible approach to testing for the geographic patterns predicted under competitive exclusion and competitive release. Previously, we modeled the potential distributions of two spiny pocket mice (Heteromys australis and H. anomalus) in northwestern South America using specimen localities, environmental data, and the Genetic Algorithm for Rule‐Set Prediction (GARP). Here we superimpose the models to examine known distributional records in areas of potential sympatry between the two species, thus testing the geographic predictions of competitive exclusion. In addition, we examine environmental characteristics of known localities, testing for data consistent with competitive release. Areas of potential sympatry are minimal, lying in regions of intermediate water balance. Only records of H. australis are known from areas of potential sympatry in regions where the species’ ranges meet, consistent with exclusion of H. anomalus by H. australis. Heteromys anomalus inhabits areas ecologically suitable for both species only in the isolated Sierra Nevada de Santa Marta, in which H. australis is not present (most likely for historical reasons). Furthermore, environmental characteristics of localities of H. anomalus in biogeographic regions where H. australis is absent fit the pattern predicted under competitive release. In contrast, localities of H. australis show no indication of competitive release. Although the results of present analyses do not conclusively demonstrate competitive exclusion or release, they provide directional hypotheses that can now be tested in experimental field and laboratory studies.