Rad52 and Ku bind to different DNA structures produced early in double-strand break repair

DNA double-strand breaks are repaired by one of two main pathways, non-homologous end joining or homologous recombination. A competition for binding to DNA ends by Ku and Rad52, proteins required for non-homologous end joining and homologous recombination, respectively, has been proposed to determine the choice of repair pathway. In order to test this idea directly, we compared Ku and human Rad52 binding to different DNA substrates. How ever, we found no evidence that these proteins would compete for binding to the same broken DNA ends. Ku bound preferentially to DNA with free ends. Under the same conditions, Rad52 did not bind preferentially to DNA ends. Using a series of defined substrates we showed that it is single-stranded DNA and not DNA ends that were preferentially bound by Rad52. In addition, Rad52 aggregated DNA, bringing different single-stranded DNAs in close proximity. This activity was independent of the presence of DNA ends and of the ability of the single-stranded sequences to form extensive base pairs. Based on these DNA binding characteristics it is unlikely that Rad52 and Ku compete as ‘gatekeepers’ of different DNA double-strand break repair pathways. Rather, they interact with different DNA substrates produced early in DNA double-strand break repair.     

Identification of essential genes in the human fungal pathogen Aspergillus fumigatus by transposon mutagenesis

The opportunistic pathogen Aspergillus fumigatus is the most frequent cause of deadly airborne fungal infections in developed countries. In order to identify novel antifungal-drug targets, we investigated the genome of A. fumigatus for genes that are necessary for efficient fungal growth. An artificial A. fumigatus diploid strain with one copy of an engineered impala160 transposon from Fusarium oxysporum integrated into its genome was used to generate a library of diploid strains by random in vivo transposon mutagenesis. Among 2,386 heterozygous diploid strains screened by parasexual genetics, 1.2% had a copy of the transposable element integrated into a locus essential for A. fumigatus growth. Comparison of genomic sequences flanking impala160 in these mutants with that of the genome of A. fumigatus allowed the characterization of 20 previously uncharacterized A. fumigatus genes. Among these, homologues of genes essential for Saccharomyces cerevisiae growth have been identified, as well as genes that do not have homologues in other fungal species. These results confirm that heterologous transposition using the transposable element impala is a powerful tool for functional genomics in ascomycota, and they pave the way for defining the complete set of essential genes in A. fumigatus, the first step toward target-based development of new antifungal drugs.     

Continuous enzymatic regeneration of redox mediators used in biotransformation reactions employing flavoproteins

Oxidoreductases are a group of enzymes that have been regarded uneconomical for industrial processes due to their dependence on cofactors or prosthetic groups for activity and the difficulties of regenerating these. Especially, flavoproteins have long been neglected for biocatalytical applications. The prosthetic group of some of these enzymes, but not all, can be regenerated by oxygen, resulting in hydrogen peroxide formation, which is detrimental to enzyme stability. As a contribution to alleviating this problem, a novel concept for the regeneration of electron acceptors (redox mediators) for flavoenzymes is described. Flavin-containing enzymes such as cellobiose dehydrogenase (CDH) or pyranose oxidase (P2O) are used in conjunction with laccases and a redox mediator. The flavin of the synthetic enzyme is reduced while the oxidized product of interest is formed, in turn, the flavin is reoxidized with the help of an electron acceptor, which then is regenerated using a laccase. Laccases are copper containing phenol oxidases that can transfer four electrons to oxygen, producing two molecules of water. Preliminary screening experiments with different redox mediators, and a coupled enzyme system of CDH and laccase, showed that a wide variety of different substances can efficiently shuttle electrons between these two enzymes. Among them are substituted and unsubstituted ortho- and para-quinones, benzoquinone imines, cation radicals such as 2,2′-azinobis(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS), redox dyes such as phenothiazines or phenoxazines, as well as iron complexes.

Experiments in which CDH completely oxidizes lactose to lactobionic acid and P2O entirely converts glucose to 2-keto-glucose are presented. Catalytic amounts of redox mediators are used and continuously regenerated by a laccase. Specific productivities of up to 19.3 g·(h·kU)⁻¹ and 72 g·(h·kU)⁻¹ for CDH and P2O, respectively, were found. The total turnover numbers (TTNs) for the two enzymes used were in the range of 10⁵–10⁶. Oxygen supply for the laccase is a crucial factor in avoiding rate limitation. Undeniably, this system facilitates the efficient use of a hitherto underexploited group of enzymes for preparative purposes.     

Development of a S. cerevisiae whole cell biocatalyst for in vitro sialylation of oligosaccharides

Absence of sialylation on recombinant glycoproteins compromises their efficacy as therapeutic agents, as it results in rapid clearance from the human bloodstream. To circumvent this, several strategies are followed, including the implementation of a post-secretion glycosylation step. In this paper we describe the engineering of yeast cells expressing active surface exposed Trypanosoma cruzi trans-sialidase (TS) fused to the yeast Aga2 protein, and the use of this yeast in the sialylation of synthetic oligosaccharides. In an attempt to improve overall protein accessibility on the yeast surface, we abolished hyperglycosylation on the yeast cell wall proteins. This was achieved by disrupting the OCH1 gene of the TS surface expressing strain, which resulted in increased enzymatic activity. Using a fluorescence-based activity assay and DSA-FACE structural analysis, we obtained almost complete conversion to a fully sialylated acceptor, whereas in the wild type situation this conversion was only partial. Increasing protein accessibility on the yeast surface by modifying the glycosylation content thus proved to be a valuable approach in increasing the cell wall associated activity of an immobilised enzyme, hence resulting in a more effective biocatalyst system.     

Waste Treatment and Assessment of Long-Term Emissions (8pp)

Goal, Scope and Background The disposal phase of a product’s life cycle in LCA is often neglected or based on coarse indicators like ‘kilogram waste’. The goal of report No. 13 of the ecoinvent project (Doka 2003) is to create detailed Life Cycle Inventories of waste disposal processes. The purpose of this paper is to give an overview of the models behind the waste disposal inventories in ecoinvent, to present exemplary results and to discuss the assessment of long-term emissions. This paper does not present a particular LCA study. Inventories are compiled for many different materials and various disposal technologies. Considered disposal technologies are municipal incineration and different landfill types, including sanitary landfills, hazardous waste incineration, waste deposits in deep salt mines, surface spreading of sludges, municipal wastewater treatment, and building dismantling. The inventoried technologies are largely based on Swiss plants. Inventories can be used for assessment of the disposal of common, generic waste materials like paper, plastics, packaging etc. Inventories are also used within the ecoinvent database itself to inventory the disposal of specific wastes generated during the production phase. Inventories relate as far as possible to the specific chemical composition of the waste material (waste-specific burdens). Certain expenditures are not related to the waste composition and are inventoried with average values (process-specific burdens). Methods The disposal models are based on previous work, partly used in earlier versions of ecoinvent/ETH LCI data. Important improvements were the extension of the number of considered chemical elements to 41 throughout all disposal models and new landfill models based on field data. New inventories are compiled for waste deposits in deep salt mines and building material disposal. Along with the ecoinvent data and the reports, also Excel-based software tools were created, which allow ecoinvent members to calculate waste disposal inventories from arbitrary waste compositions. The modelling of long-term emissions from landfills is a crucial part in any waste disposal process. In ecoinvent long-term emissions are defined as emissions occurring 100 years after present. They are reported in separate emission categories. The landfill inventories include long-term emissions with a time horizon of 60’000 years after present. Results and Discussion As in earlier studies, the landfills prove to be generally relevant disposal processes, as also incineration and wastewater treatment processes produce landfilled wastes. Heavy metals tend to concentrate in landfills and are washed out to a varying degree over time. Long-term emissions usually represent an important burden from landfills. Comparisons between burdens from production of materials and the burdens from their disposal show that disposal has a certain relevance. Conclusion The disposal phase should by default be included in LCA studies. The use of a material not only necessitates its production, but also requires its disposal. The created inventories and user tools facilitate heeding the disposal phase with a similar level of detail as production processes. The risk of LCA-based decisions shifting burdens from the production or use phase to the disposal phase because of data gaps can therefore be diminished. Recommendation and Perspective Future improvements should include the modelling of metal ore refining waste (tailings) which is currently neglected in ecoinvent, but is likely to be relevant for metals production. The disposal technologies considered here are those of developed Western countries. Disposal in other parts of the World can differ distinctly, for logistic, climatic and economic reasons. The cross-examination of landfill models to LCIA soil fate models could be advantageous. Currently only chemical elements, like copper, zinc, nitrogen etc. are heeded by the disposal models. A possible extension could be the modelling of the behaviour of chemical compounds, like dioxins or other hydrocarbons.     

Antigen-driven interactions with dendritic cells and expansion of Foxp3+ regulatory T cells occur in the absence of inflammatory signals

Foxp3+ regulatory T cells (Tregs) play a pivotal role in the maintenance of peripheral T cell tolerance and are thought to interact with dendritic cells (DC) in secondary lymphoid organs. We analyzed here the in vivo requirements for selective expansion of Ag-specific Treg vs CD4+CD25- effector T cells and engagement of Ag-specific Treg-DC interactions in secondary lymphoid organs. Using i.v. Ag delivery in the absence of inflammation, we found that CD4+CD25+Foxp3+ Tregs undergo vigorous expansion and accumulate whereas naive CD4+CD25-Foxp3- T cells undergo abortive activation. Quantifying directly the interactions between Tregs and CD11c+ DC, we found that Tregs establish cognate contacts with endogenous CD11c+ DC in spleen and lymph nodes at an early time point preceding their expansion. Importantly, we observed that as few as 10(3) Tregs selectively expanded by i.v. Ag injection are able to suppress B and T cell immune responses in mouse recipients challenged with the Ag. Our results demonstrate that Tregs are selectively mobilized by Ag recognition in the absence of inflammatory signals, and can induce thereafter potent tolerance to defined Ag targets.     

Synthetic substrate analogues for UDP-GlcNAc: Manα1-6R β(1-2)-N-acetylglucosaminyltransferase II. Substrate specificity and inhibitors for the enzyme

UDP-GlcNAc: Man1-6R (1-2)-N-acetylglucosaminyltransferase II (GlcNAc-T II; EC 2.4.1.143) is a key enzyme in the synthesis of complexN-glycans. We have tested a series of synthetic analogues of the substrate Man1-6(GlcNAc1-2Man1-3)Man-O-octyl as substrates and inhibitors for rat liver GlcNAc-T II. The enzyme attachesN-acetylglucosamine in 1-2 linkage to the 2-OH of the Man1-6 residue. The 2-deoxy analogue is a competitive inhibitor (K _i=0.13mm). The 2-O-methyl compound does not bind to the enzyme presumably due to steric hindrance. The 3-, 4- and 6-OH groups are not essential for binding or catalysis since the 3-, 4- and 6-deoxy and -O-methyl derivatives are all good substrates. Increasing the size of the substituent at the 3-position to pentyl and substituted pentyl groups causes competitive inhibition (K _i=1.0–2.5mm). We have taken advantage of this effect to synthesize two potentially irreversible GlcNAc-T II inhibitors containing a photolabile 3-O-(4,4-azo)pentyl group and a 3-O-(5-iodoacetamido)pentyl group respectively. The data indicate that none of the hydroxyls of the Man1-6 residue are essential for binding although the 2- and 3-OH face the catalytic site of the enzyme. The 4-OH group of the Man-O-octyl residue is not essential for binding or catalysis since the 4-deoxy derivative is a good substrate; the 4-O-methyl derivative does not bind. This contrasts with GlcNAc-T I which cannot bind to the 4-deoxy-Man- substrate analogue. The data are compatible with our previous observations that a bisectingN-acetylglucosamine at the 4-OH position prevents both GlcNAc-T I and GlcNAc-T II catalysis. However, in the case of GlcNAc-T II, the bisectingN-acetylglucosamine prevents binding due to steric hindrance rather than to removal of an essential OH group. The 3-OH of the Man1-3 is an essential group for GlcNAc-T II since the 3-deoxy derivative does not bind to the enzyme. The trisaccharide GlcNAc1-2Man1-3Man-O-octyl is a good inhibitor (K _i=0.9mm). The above data together with previous studies indicate that binding of the GlcNAc1-2Man1-3Man- arm of the branched substrate to the enzyme is essential for catalysis. Abbreviations: GlcNAc-T I, UDP-GlcNAc:Man1-3R (1-2)-N-acetylglucosaminyltransferase I (EC 2.4.1.101); GlcNAc-T II, UDP-GlcNAc:Man1-6R (1-2)-N-acetylglucosaminyltransferase II (EC 2.4.1.143); MES, 2-(N-morpholino)ethane sulfonic acid monohydrate.     

Synthesis of Brunfelsamidine Ribonucleoside and Certain Related Compounds by the Stereospecific Sodium Salt Glycosylation Procedure

Abstract

A synthesis of 2,4-dideazaribavirin ( 2 ), brunfelsamidine ribonucleoside ( 8c ) and certain related derivatives are described for the first time using the stereospecific sodium salt glycosylation procedure. Glycosylation of the sodium salt of pyrrole-3-carbonitrile ( 4 ) with 1-chloro-2, 3-O-t-isopropylidene-5-O-t-butyldimethylsilyl-α-D-ribofuranose ( 5 ) gave exclusively the corresponding blocked nucleoside ( 6 ) with β-anomeric configuration, which on deprotection provided 1-β-D-ribofuranosylpyrrole-3-carbonitrile ( 7 ). Functional group tranformation of 7 gave 2 , 8c and related 3-substituted pyrrole ribonucleosides. These compounds are devoid of any significant antiviral/antitumor activity invitro.     

Circadian Pattern of Wheel‐Running Activity of a South American Subterranean Rodent (Ctenomys cf knightii)

Circadian rhythms are regarded as essentially ubiquitous features of animal behavior and are thought to confer important adaptive advantages. However, although circadian systems of rodents have been among the most extensively studied, most comparative biology is restricted to a few related species. In this study, the circadian organization of locomotor activity was studied in the subterranean, solitary north Argentinean rodent, Ctenomys knightii. The genus, Ctenomys, commonly known as Tuco‐tucos, comprises more than 50 known species over a range that extends from 12°S latitude into Patagonia, and includes at least one social species. The genus, therefore, is ideal for comparative and ecological studies of circadian rhythms. Ctenomys knightii is the first of these to be studied for its circadian behavior. All animals were wild caught but adapted quickly to laboratory conditions, with clear and precise activity‐rest rhythms in a light‐dark (LD) cycle and strongly nocturnal wheel running behavior. In constant dark (DD), the rhythm expression persisted with free‐running periods always longer than 24 h. Upon reinstatement of the LD cycle, rhythms resynchronized rapidly with large phase advances in 7/8 animals. In constant light (LL), six animals had free‐running periods shorter than in DD, and 4/8 showed evidence of “splitting.” We conclude that under laboratory conditions, in wheel‐running cages, this species shows a clear nocturnal rhythmic organization controlled by an endogenous circadian oscillator that is entrained to 24 h LD cycles, predominantly by light‐induced advances, and shows the same interindividual variable responses to constant light as reported in other non‐subterranean species. These data are the first step toward understanding the chronobiology of the largest genus of subterranean rodents.