1-Methyl-3-nitropyridine: An Efficient Oxidant of NADH in Non-enzymatic and Enzyme-mediated Processes

It is shown that NADH can be effectively oxidized by 1-methyl-3-nitropyridine in non-enzymatic and enzyme-mediated processes. Mechanistic issues of these reactions are discussed. These processes seem to contribute to the observed cytotoxicity of 1-methyl-3-nitropyridine. A key role of 1-methyl-3-nitropyridinyl radical formed in the enzyme-mediated processes is emphasized.     

Mechanisms behind positive diversity effects on ecosystem functioning: testing the facilitation and interference hypotheses

Little is known about the mechanisms behind positive effects of species richness on ecosystem functioning. In a previous study that showed a positive effect of aquatic detritivore species richness on leaf litter breakdown (process) rates, we proposed that facilitation and release from intra-specific interference were the two most likely mechanisms. To test the interference hypothesis, we performed an experiment using three densities of each of three detritivore species and found varying effects on leaf breakdown rates across species: one species showed no effect, one a positive, marginally insignificant, effect, and a third species showed a significant, positive effect of decreasing density. The density (interference) effect thus partly explained the results from our previous study. The facilitation hypothesis was tested by sequentially introducing and removing two species. We predicted that, if this hypothesis were true, facilitation would be expressed in higher process rates than when replacing with individuals of the same species. We found that process rate per unit biomass did increase when one species was introduced after the other species, while the opposite sequence did not show any increase. Hence, this result was also confirmative of our previous results. Therefore, we conclude that both intra-specific interference and inter-specific facilitation may explain the positive effect of species richness observed in our system. Since many species exhibit intra-specific interference that inhibits foraging efficiency, this may be a general mechanism generating effects of species richness per se. If facilitation is unidirectional, or if it involves few species, it is more likely to be species specific with species identities being more important than species richness per se. We conclude that species loss may be expected to have negative consequences on ecosystem functioning if anyspecies is lost, with additional effects in the event of losing "facilitator" species.     

Structural insights and biomedical potential of IgNAR scaffolds from sharks

In addition to antibodies with the classical composition of heavy and light chains, the adaptive immune repertoire of sharks also includes a heavy-chain only isotype, where antigen binding is mediated exclusively by a small and highly stable domain, referred to as vNAR. In recent years, due to their high affinity and specificity combined with their small size, high physicochemical stability and low-cost of production, vNAR fragments have evolved as promising target-binding scaffolds that can be tailor-made for applications in medicine and biotechnology. This review highlights the structural features of vNAR molecules, addresses aspects of their generation using immunization or in vitro high throughput screening methods and provides examples of therapeutic, diagnostic and other biotechnological applications.     

Therapeutic antibody engineering by high efficiency cell screening

In recent years, several cell-based screening technologies for the isolation of antibodies with prescribed properties emerged. They rely on the multi-copy display of antibodies or antibody fragments on a cell surface in functional form followed by high through put screening and isolation of cell clones that carry an antibody variant with the desired affinity, specificity, and stability. Particularly yeast surface display in combination with high-throughput fluorescence-activated cell sorting has proven successful in the last fifteen years as a very powerful technology that has some advantages over classical generation of monoclonals using the hybridoma technology or bacteriophage-based antibody display and screening. Cell-based screening harbours the benefit of single-cell online and real-time analysis and characterisation of individual library candidates. Moreover, when using eukaryotic expression hosts, intrinsic quality control machineries for proper protein folding and stability exist that allow for co-selection of high-level expression and stability simultaneously to the binding functionality. Recently, promising technologies emerged that directly rely on antibody display on higher eukaryotic cell lines using lentiviral transfection or direct screening on B-cells. The combination of immunisation, B-cell screening and next generation sequencing may open new avenues for the isolation of therapeutic antibodies with prescribed physicochemical and functional characteristics.     

Multiple restrictions of human immunodeficiency virus type 1 in feline cells

The productive replication of human immunodeficiency virus type 1 (HIV-1) occurs exclusively in defined cells of human or chimpanzee origin, explaining why heterologous animal models for HIV replication, pathogenesis, vaccination, and therapy are not available. This lack of an animal model for HIV-1 studies prompted us to examine the susceptibility of feline cells in order to evaluate the cat (Felis catus) as an animal model for studying HIV-1. Here, we report that feline cell lines harbor multiple restrictions with respect to HIV-1 replication. The feline CD4 receptor does not permit virus infection. Feline T-cell lines MYA-1 and FeT-1C showed postentry restrictions resulting in low HIV-1 luciferase reporter activity and low expression of viral Gag-Pol proteins when pseudotyped vectors were used. Feline fibroblastic CrFK and KE-R cells, expressing human CD4 and CCR5, were very permissive for viral entry and HIV-long terminal repeat-driven expression but failed to support spreading infection. KE-R cells displayed a profound block with respect to release of HIV-1 particles. In contrast, CrFK cells allowed very efficient particle production; however, the CrFK cell-derived HIV-1 particles had low specific infectivity. We subsequently identified feline apolipoprotein B-editing catalytic polypeptide 3 (feAPOBEC3) proteins as active inhibitors of HIV-1 particle infectivity. CrFK cells express at least three different APOBEC3s: APOBEC3C, APOBEC3H, and APOBEC3CH. While the feAPOBEC3C did not significantly inhibit HIV-1, the feAPOBEC3H and feAPOBEC3CH induced G to A hypermutations of the viral cDNA and reduced the infectivity approximately 10- to approximately 40-fold.     

Resolving the phylogenetic relationships and evolutionary history of the Drosophila virilis group using multilocus data

The Drosophila virilis group is one of the major lineages of Drosophila previously recognised and it has been used as a model for different types of studies. It comprises 13 species whose phylogenetic relationships are not well resolved. In the present study, six nuclear genes (Adh, fused, Gpdh, NonA, CG9631 and CG7219) and the mitochondrial ribosomal RNA genes (12S-16S) have been used to estimate the evolutionary tree of the group using different methods of phylogenetic reconstruction. Different competing evolutionary hypotheses have also been compared using the Approximately Unbiased test to further evaluate the robustness of the inferred trees. Results are, in general, consistent with previous studies in recovering the four major lineages of the group (D. virilis phylad, Drosophila montana subphylad, Drosophila kanekoi subphylad and Drosophila littoralis subphylad), although D. kanekoi, D. littoralis and Drosophila ezoana are here inferred to be more closely related to the D. virilis phylad than to the D. montana subphylad. The age of the crown group, estimated with a Bayesian method that assumes a relaxed molecular clock, is placed in the late Miocene (～ 10 Mya). The oldest lineages also appeared during this period (～ 7.5 to ～ 8.9 Mya), while the ages of the basal nodes of the montana subphylad and the virilis phylad are located in the early Pliocene (～ 4.9 and ～ 4.1 Mya). Major cladogenesis events correlate to geological and palaeoclimatic occurrences that most likely affected the freshwater and deciduous forests where these species are found. The inferred biogeographical history of the group, based on the statistical dispersal-vicariance analysis, indicates that the last common ancestor of the group had a Holarctic distribution from which the North American and the Eurasian lineages evolved as a result of a vicariant event.     

Drosophila genes that affect meiosis duration are among the meiosis related genes that are more often found duplicated

Using a phylogenetic approach, the examination of 33 meiosis/meiosis-related genes in 12 Drosophila species, revealed nine independent gene duplications, involving the genes cav, mre11, meiS332, polo and mtrm. Evidence is provided that at least eight out of the nine gene duplicates are functional. Therefore, the rate at which Drosophila meiosis/meiosis-related genes are duplicated and retained is estimated to be 0.0012 per gene per million years, a value that is similar to the average for all Drosophila genes. It should be noted that by using a phylogenetic approach the confounding effect of concerted evolution, that is known to lead to overestimation of the duplication and retention rate, is avoided. This is an important issue, since even in our moderate size sample, evidence for long-term concerted evolution (lasting for more than 30 million years) was found for the meiS332 gene pair in species of the Drosophila subgenus. Most striking, in contrast to theoretical expectations, is the finding that genes that encode proteins that must follow a close stoichiometric balance, such as polo, mtrm and meiS332 have been found duplicated. The duplicated genes may be examples of gene neofunctionalization. It is speculated that meiosis duration may be a trait that is under selection in Drosophila and that it has different optimal values in different species.     

New insights into the mechanism of imposex induction in the dogwhelk Nucella lapillus

In an attempt to clarify the mechanism(s) of tributyltin-mediated imposex induction in females of the neogastropod Nucella lapillus, dogwhelks collected in an almost imposex free population were exposed to several treatments for a 3 month-period, and the effects on imposex induction and testosterone/estradiol levels were evaluated. As a positive control, tributyltin (50 ng TBT Sn/L) clearly induced imposex and led to a significant increase in the severity of the phenomenon. In contrast, although a selective P450 aromatase inhibitor (formestane at 0.3 mg/L) was capable of imposex induction, it failed to increase its severity. A vertebrate androgen receptor (AR) antagonist (cyproterone acetate at 1.25 mg/L) in combination with TBT completely blocked the imposex induction capacity of TBT. On the other hand, an estrogen receptor antagonist (tamoxifen at 0.3 mg/L) rendered no effect. The determination of steroid levels in female specimens revealed that TBT induces an elevation of free testosterone (but not the total amount, free+esterified), while the co-administration of the anti-androgen and TBT was able to rescue the increase of free testosterone levels. Despite a minor decrease in the amount of testosterone-fatty acid esters in the TBT group, significant differences in esterified testosterone were not found among treatments. On the contrary, free estradiol levels were elevated in the TBT, anti-androgens and TBT plus anti-androgens groups. These results indicate that free estradiol biosynthesis in TBT-exposed females does not seem to be affected. Overall, our results demonstrate that a selective aromatase inhibitor can induce imposex in N. lapillus but not to a similar extent of TBT, which may suggest the involvement of other mechanism in imposex induction, besides aromatase inhibition. Additionally, the study points to the involvement of AR receptors in imposex induction.     

The confounding effects of light, sonication, and Mn(III)TBAP on quantitation of superoxide using hydroethidine

Previously, we showed that hydroethidine (HE) reacts with intracellular superoxide radical anion (O2-*) to form a unique fluorescent marker product, 2-hydroxyethidium cation (2-OH-E+), that was not formed from HE reaction with other biologically relevant oxidants (H. Zhao et al. Proc. Natl. Acad. Sci. USA102:5727-5732; 2005). Here we rigorously assessed the confounding effects of light, sonication, and Mn(III)TBAP on 2-OH-E+, the HE/O2-* reaction product. Results indicate that continuous exposure to visible light induced photo-oxidation of HE to ethidium cation (E+) by a 2-OH-E+ -dependent mechanism. Treatment of HE with ultrasound, a frequently used technique to lyse cell membranes, induced 2-OH-E+ from in situ generation of O2-*. Mn(III)TBAP, a cell-permeable metal-porphyrin complex used as a catalytic antioxidant, reacts with HE to form E+. This finding provides an alternative interpretation for Mn(III)TBAP effects during the HE/O2-* reaction. In order to correctly interpret the HE reaction with O2-* in cells, it is therefore imperative that HE and HE-derived products be measured by HPLC. A new and improved HPLC-electrochemical (HPLC-EC) detection has been developed for analysis of intracellular O2-*. The HPLC-EC method is at least 10 times more sensitive than the HPLC-fluorescence technique for detecting O2-* in cells.