Effect of Isoxanthopterin on the Activity of Transforming DNA in <Emphasis Type="Italic">Bacillus subtilis</Emphasis>

WHEN an aqueous solution of the pteridine, isoxanthopterin, is incubated with salmon sperm DNA, an unstable association of the pteridine with the DNA can be demonstrated by chromatography on “Sephadex”¹. One interesting property of the complex is that the fluorescence of isoxanthopterin is enhanced ten-fold, a phenomenon which has been ascribed, in other cases, to intercalation of a planar heterocycle between base pairs in the DNA double helix². If such an intimate positioning occurred, it might be possible to disrupt the structure of DNA by using radiant energy of a wavelength (345 nm) which would be absorbed by the pteridine but not by the DNA. In a living organism the result would be expressed as a mutational event, or in the extreme case, cell death. We have tested this hypothesis using a sensitive biological indicator—bacterial transformation—to observe effects at specific gene loci. For experimental convenience, changes in DNA were detected by changes in transforming ability of wild type DNA.     

Hybridization ddRAD‐sequencing for population genomics of nonmodel plants using highly degraded historical specimen DNA

Species’ responses at the genetic level are key to understanding the long‐term consequences of anthropogenic global change. Herbaria document such responses, and, with contemporary sampling, provide high‐resolution time‐series of plant evolutionary change. Characterizing genetic diversity is straightforward for model species with small genomes and a reference sequence. For nonmodel species—with small or large genomes—diversity is traditionally assessed using restriction‐enzyme‐based sequencing. However, age‐related DNA damage and fragmentation preclude the use of this approach for ancient herbarium DNA. Here, we combine reduced‐representation sequencing and hybridization‐capture to overcome this challenge and efficiently compare contemporary and historical specimens. Specifically, we describe how homemade DNA baits can be produced from reduced‐representation libraries of fresh samples, and used to efficiently enrich historical libraries for the same fraction of the genome to produce compatible sets of sequence data from both types of material. Applying this approach to both Arabidopsis thaliana and the nonmodel plant Cardamine bulbifera, we discovered polymorphisms de novo in an unbiased, reference‐free manner. We show that the recovered genetic variation recapitulates known genetic diversity in A. thaliana, and recovers geographical origin in both species and over time, independent of bait diversity. Hence, our method enables fast, cost‐efficient, large‐scale integration of contemporary and historical specimens for assessment of genome‐wide genetic trends over time, independent of genome size and presence of a reference genome.     

Detecting host–parasitoid interactions in an invasive Lepidopteran using nested tagging DNA metabarcoding

Determining the host–parasitoid interactions and parasitism rates for invasive species entering novel environments is an important first step in assessing potential routes for biocontrol and integrated pest management. Conventional insect rearing techniques followed by taxonomic identification are widely used to obtain such data, but this can be time‐consuming and prone to biases. Here, we present a next‐generation sequencing approach for use in ecological studies which allows for individual‐level metadata tracking of large numbers of invertebrate samples through the use of hierarchically organised molecular identification tags. We demonstrate its utility using a sample data set examining both species identity and levels of parasitism in late larval stages of the oak processionary moth (Thaumetopoea processionea—Linn. 1758), an invasive species recently established in the United Kingdom. Overall, we find that there are two main species exploiting the late larval stages of oak processionary moth in the United Kingdom with the main parasitoid (Carcelia iliaca—Ratzeburg, 1840) parasitising 45.7% of caterpillars, while a rare secondary parasitoid (Compsilura concinnata—Meigen, 1824) was also detected in 0.4% of caterpillars. Using this approach on all life stages of the oak processionary moth may demonstrate additional parasitoid diversity. We discuss the wider potential of nested tagging DNA metabarcoding for constructing large, highly resolved species interaction networks.     

DNA damage signaling triggers the cytoplasm-to-vacuole pathway of autophagy to regulate cell cycle progression

Budding yeast cells suffering a single unrepaired DNA double-strand break (DSB) trigger the ATR (Mec1)-dependent DNA damage checkpoint and arrest prior to anaphase for 12–15 h, following which they adapt and resume cell division. When the DNA lesion can be repaired, the checkpoint is extinguished and cells “recover” and resume mitosis. In this autophagic punctum, we report that hyperactivation of autophagy—specifically via the cytoplasm-to-vacuole targeting (Cvt) pathway—prevents both adaptation to, and recovery from, DNA damage, resulting in the permanent arrest of cells in G₂/M. We show that Saccharomyces cerevisiae deleted for genes encoding the Golgi-associated retrograde protein transport (GARP) complex are both adaptation- and recovery-defective. GARP mutants such as vps51Δ exhibit mislocalization of the key mitotic regulator, securin (Pds1), and its degradation by the vacuolar protease Prb1. In addition, separase (Esp1), is excluded from the nucleus, accounting for pre-anaphase arrest. Pds1 is degraded via the Cvt pathway. Many of the same defects seen by deleting GARP genes can be mimicked by hyperactivation of the Cvt pathway by overexpressing an unphosphorylatable form of ATG13 or by adding the TORC1 inhibitor rapamycin. These results suggest that nuclear events such as DNA damage can have profound effects on cytoplasmic processes and further expand the burgeoning connections between DNA damage and autophagy.     

Anonymous single‐copy nuclear DNA (scnDNA) markers for two endemic log‐dwelling beetles: Apasis puncticeps and Adelium calosomoides (Tenebrionidae: Lagriinae: Adeliini)

Three approaches — microsatellite library screening, consensus primer PCR (polymerase chain reaction) and sequencing with arbitrary primer pairs (SWAPP) — were used to develop single‐copy nuclear DNA (scnDNA) markers for log‐dwelling beetles Apasis puncticeps and Adelium calosomoides. We are unaware of other nuclear markers for Adeliini. We tested > 70 primer pairs per species, but despite exhaustive optimization, we obtained only five polymorphic markers. Nonetheless, the markers are valuable in detection of effects of habitat fragmentation.     

Involvement of autophagy and mitochondrial dynamics in determining the fate and effects of irreparable mitochondrial DNA damage

Mitochondrial DNA (mtDNA) is different in many ways from nuclear DNA. A key difference is that certain types of DNA damage are not repaired in the mitochondrial genome. What, then, is the fate of such damage? What are the effects? Both questions are important from a health perspective because irreparable mtDNA damage is caused by many common environmental stressors including ultraviolet C radiation (UVC). We found that UVC-induced mtDNA damage is removed slowly in the nematode Caenorhabditis elegans via a mechanism dependent on mitochondrial fusion, fission, and autophagy. However, knockdown or knockout of genes involved in these processes—many of which have homologs involved in human mitochondrial diseases—had very different effects on the organismal response to UVC. Reduced mitochondrial fission and autophagy caused no or small effects, while reduced mitochondrial fusion had dramatic effects.     

Conformational features of 2′-O-methyl-adenosylyl-adenosine

In order to obtain information about the conformational features of a 2′-O-methylated polyribonucleotide at the nearest neighbor level, a detailed nuclear magnetic resonance study of AmpA was undertaken. AmpA was isolated from alkali hydrolysates of yeast RNA, and proton spectra were recorded at 100 MHz in the Fourier transform mode in D₂O solutions, 0.01 M, pH 5.4 and 1.5 at 25°C. ³¹P spectra were recorded at 40.48 MHz. Complete, accurate sets of nmr parameters derived for each nucleotidyl unit by simulation iteration methods. The nmr data were translated into conformational parameters for all the bonds using procedures developed in earlier studies from these laboratories. It is shown that AmpA exists in aqueous solution with a flexible molecular framework, which shows preferences for certain orientations. The ribose rings exist as a ²E ? ³E equilibrium with the —pA ribose showing a bias for the ³E pucker. The C(4′)—C(5′) bonds of both nucleotidyl units show significant preference (75–80%) to exist in gg conformation. The dominant conformer (80%) about C(5′)—O(5′) of the 5′-nucleotidyl unit is g′g′. Even though an unambiguous determination of the orientation of the 3′-phosphate group cannot be made, tentative evidence shows that it preferentially occupies g⁺ domains [O(3′)—P trans to C(3′)—C(2′)] in which the H(3′) —C(3′)—O(3′)—P(3′) dihedral angle is about 31°. There is reasonable evidence that the 2′-O-methyl preferentially occupies the domain in which the O(2′)—CH₃ bond is trans to C(2′)—C(1′). Lowering of pH to 1.5, which results in protonation of both the adenine moieties, causes destacking of AmpA. Such destacking is accompanied by small, but real, perturbations in the conformations about most of the bonds in the backbone. A detailed comparison of the solution conformations of ApA and AmpA clearly shows that 2′-O-methylation strongly influences the conformational preference about the C(3′)—O(3′) bond of the 3′-nucleotidyl unit, in addition to inducing small changes in the overall ribophosphate backbone conformational equilibria. The effect of 2′-O-methylation is such that the C(3′)—O(3′) is forced to occupy preferentially the g⁺ domain rather than the normally preferred g^? domain [O(3′)—P trans to C(3′)—C(4′)] in ApA. The data on ApA and AmpA further reveal that the extent of stacking interaction is less in AmpA compared to ApA. It is suggested that stacked species of AmpA exist as right-handed stacks where the magnitude of ω and ω′ about O(5′)—P and P—O(3′) is about 290°. The reason for the lesser degree of stacking in AmpA compared to ApA is intramolecular interaction between 2′-O-methyl and the flexible O(3′)—P—O(5′) bridge, the interaction causing some perturbation in the magnitudes of ω/ω′, causing destacking. The destacking will lead to an increase in _χCN by a few degrees, causing an increase in ²E populations; the latter in turn will shift the 3′ phosphate group from g^? to g⁺ domains. In short, a coupled series of conformational events is envisioned at the onset of destacking, made feasible by the interaction between the 2′-O-methyl group and the swivel O(3′)—P—O(5′) bridge.     

Toll‐like receptors hit calcium

Mitochondrial Ca²⁺ uptake is a multifarious signal that controls both the activity of matrix dehydrogenases and the sensitivity to apoptotic and necrotic challenges. Recent evidence indicates that mitochondria also play a role in triggering inflammation, as mitochondrial DNA, when released by the cell, is an important damage‐associated molecular pattern (DAMP). Now, Toll‐like receptors (TLRs) are shown to close the loop, by affecting in turn mitochondrial activity. Two studies by Shintani and colleagues, one in this issue of EMBO reports 1 2 , identify a new TLR transduction mechanism that impinges directly on mitochondrial function. Upon binding of CpG oligodeoxynucleotides, TLR9—which in non‐immune cells is retained in the ER—inhibits SERCA2, thus reducing Ca²⁺ transfer to the mitochondria and aerobic metabolism.     

Decline of nucleotide excision repair capacity in aging <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Background  

Caenorhabditis elegans is an important model for the study of DNA damage and repair related processes such as aging, neurodegeneration, and carcinogenesis. However, DNA repair is poorly characterized in this organism. We adapted a quantitative polymerase chain reaction assay to characterize repair of DNA damage induced by ultraviolet type C (UVC) radiation in C. elegans, and then tested whether DNA repair rates were affected by age in adults.     

Efficient species identification of pine marten (<Emphasis Type="Italic">Martes martes</Emphasis>) and red fox (<Emphasis Type="Italic">Vulpes vulpes</Emphasis>) scats using a 5′ nuclease real-time PCR assay

Monitoring wildlife species by DNA identification of samples collected non-invasively is an important tool in conservation management. DNA identification of species from faecal (scat) samples is problematic due to the small quantities and poor quality of the DNA isolated from such samples. This study demonstrates the use of real-time PCR technology in the identification of red fox (Vulpes vulpes) and pine marten (Martes martes). It is shown that real-time PCR can be used to identify fox and pine marten by either melting curve analysis (Tm determination) with SYBR Green 1 detection or by the use of species specific fluorogenic probes. The technique is shown to work efficiently with scat DNA.     

A minimalist barcode can identify a specimen whose DNA is degraded

A DNA barcode based on 650 bp of mitochondrial gene cytochrome c oxidase I is proving to be highly functional in species identification for various animal groups. However, DNA degradation complicates the recovery of a full‐length barcode from many museum specimens. Here we explore the use of shorter barcode sequences for identification of such specimens. We recovered short sequences — i.e. ～100 bp — with a single PCR pass from more than 90% of the specimens in assemblages of moth and wasp museum specimens from which full barcode recovery was only 50%, and the latter were usually less than 8 years old. Short barcodes were effective in identifying specimens, confirming their utility in circumstances where full barcodes are too expensive to obtain and the identification comparisons are within a confined taxonomic group.     

A generation‐time effect on the rate of molecular evolution in bacteria

Molecular evolutionary rate varies significantly among species and a strict global molecular clock has been rejected across the tree of life. Generation time is one primary life‐history trait that influences the molecular evolutionary rate. Theory predicts that organisms with shorter generation times evolve faster because of the accumulation of more DNA replication errors per unit time. Although the generation‐time effect has been demonstrated consistently in plants and animals, the evidence of its existence in bacteria is lacking. The bacterial phylum Firmicutes offers an excellent system for testing generation‐time effect because some of its members can enter a dormant, nonreproductive endospore state in response to harsh environmental conditions. It follows that spore‐forming bacteria would—with their longer generation times—evolve more slowly than their nonspore‐forming relatives. It is therefore surprising that a previous study found no generation‐time effect in Firmicutes. Using a phylogenetic comparative approach and leveraging on a large number of Firmicutes genomes, we found sporulation significantly reduces the genome‐wide spontaneous DNA mutation rate and protein evolutionary rate. Contrary to the previous study, our results provide strong evidence that the evolutionary rates of bacteria, like those of plants and animals, are influenced by generation time.     

Recognition of Pyrimidine Dimers in DNA by the Incision Enzyme from <Emphasis Type="Italic">Micrococcus lysodeikticus</Emphasis>

A SIGNIFICANT proportion of the number of pyrimidine dimers induced in DNA by ultraviolet light is repaired by means of excision-resynthesis^1–3. Two enzymes that excise pyrimidine dimers from DNA have been purified from cells of a highly ultraviolet-resistant microorganism—Micrococcus lysodeikticus^4,5. One of these—an endonuclease—seems to recognize dimers and splits a phosphodiester bond near the dimers in DNA. The mechanism of recognition is not known; in particular, whether the incision enzyme recognizes either a local melting of DNA double helix or a specific chemical modification of one of DNA strands. If the former is correct, the incision enzyme should break the strand opposite to the dimer⁶ and the incision step in repair may lead to mutations⁶ or chromosome aberrations⁷.     

Immunomodulatory efficacy of nisin—a bacterial lantibiotic peptide

Nisin is a peptide bacteriocin, grouped under the category of lantibiotics. It is naturally produced by Lactococcus lactis to eliminate other competing gram‐positive bacteria from its vicinity. Moreover under certain conditions it is reported to be effective against a broad range of gram‐negative bacteria as well. Thus, it has been widely used as a safe food preservative especially in the dairy industry. Because of its wide‐scale consumption, its effect on eukaryotic cells should be of great concern. Here we examine the immunomodulatory efficacy of nisin in vitro. MTT‐based cytotoxicity assay demonstrated nisin's cytotoxicity on human T‐cell lymphoma Jurkat cells, Molt‐4 cells and freshly cultured human lymphocytes at over 200 µM concentration (IC₅₀225 µM ). The cell death mechanism induced by nisin in all these lymphocyte types was independent of oligonucleosomal DNA fragmentation, as analyzed by agarose gel electrophoresis and comet assay. Additionally, scanning electron microscope and fluorescence microscopy demonstrated the ability of nisin to activate human PMNs in vitro. Nisin‐activated neutrophils extruded intact nuclear chromatin to form NETs, well known for neutralization of virulence factors and extermination of bacterial pathogens. Nisin's presence also elevated neutrophil intracellular superoxide levels, normally produced by activated NADPH oxidase and prerequisite to NET formation. These nisin‐induced responses in cellular representatives of two separate branches of human immune system—adaptive and innate—although leading to cell death, did not include DNA fragmentation. From these findings, we propose that nisin might trigger similar AICD mechanisms in lymphocytes and neutrophils, different from conventional apoptosis which involves DNA fragmentation. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Forensic DNA confirms intraguild killing of a chuditch (<Emphasis Type="Italic">Dasyurus geoffroii</Emphasis>) by a feral cat (<Emphasis Type="Italic">Felis catus</Emphasis>)

Because animals killed by predators are often found partially consumed or decomposed, identification of the predator is often unachievable by post mortem examination. Forensic DNA offers an alternative in such situations. Using a novel method to analyse DNA from bite wounds on a freshly-killed chuditch Dasyurus geoffroii, we describe the first confirmed instance in this species of intraguild killing by a feral cat. Unlike post mortem examination, our method of DNA melt curve analysis is highly accurate and requires less time and expense than DNA sequencing.