Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and $$ {HO}_2/{O}_2^{-} $$ radicals

Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and \( {HO}_2/{O}_2^{-} \) radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of \( {HO}_2/{O}_2^{-} \) radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton.

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Graphical Abstract Reactivity of vitamin C toward hydroxyl and \( {HO}_2/{O}_2^{-} \) radicals

     

Role for DNA polymerase kappa in the processing of N2-N2-guanine interstrand cross-links

Although there exists compelling genetic evidence for a homologous recombination-independent pathway for repair of interstrand cross-links (ICLs) involving translesion synthesis (TLS), biochemical support for this model is lacking. To identify DNA polymerases that may function in TLS past ICLs, oligodeoxynucleotides were synthesized containing site-specific ICLs in which the linkage was between N(2)-guanines, similar to cross-links formed by mitomycin C and enals. Here, data are presented that mammalian cell replication of DNAs containing these lesions was approximately 97% accurate. Using a series of oligodeoxynucleotides that mimic potential intermediates in ICL repair, we demonstrate that human polymerase (pol) kappa not only catalyzed accurate incorporation opposite the cross-linked guanine but also replicated beyond the lesion, thus providing the first biochemical evidence for TLS past an ICL. The efficiency of TLS was greatly enhanced by truncation of both the 5 ' and 3 ' ends of the nontemplating strand. Further analyses showed that although yeast Rev1 could incorporate a dCTP opposite the cross-linked guanine, no evidence was found for TLS by pol zeta or a pol zeta/Rev1 combination. Because pol kappa was able to bypass these ICLs, biological evidence for a role for pol kappa in tolerating the N(2)-N(2)-guanine ICLs was sought; both cell survival and chromosomal stability were adversely affected in pol kappa-depleted cells following mitomycin C exposure. Thus, biochemical data and cellular studies both suggest a role for pol kappa in the processing of N(2)-N(2)-guanine ICLs.     

Conformational analysis of macrocyclic frankincense (<Emphasis Type="Italic">Boswellia</Emphasis>) diterpenoids

Frankincense oleoresin has been used in traditional medicine for more than 5000 years. The phytochemistry of frankincense (Boswellia spp.) resins includes triterpenoids (including boswellic acids and their derivatives), diterpenoids (cembrenoids and cneorubenoids), and essential oils. The macrocyclic cembrene diterpenoids may play a part in the biological activities of frankincense resin, but neither the biological targets nor the modes of interaction with the targets are currently known. How these macrocycles interact with biological macromolecules likely depends on what conformation(s) are energetically available to them. In this work, a conformational analysis of 15 Boswellia cembrene diterpenoids and 1 verticillane diterpenoid was carried out at the B3LYP/6-31G* and M06-2X/6-31G* levels of theory, including the SM8 aqueous solvation model. The lowest-energy conformations of boscartin B and incensole oxide were the same as the previously reported X-ray crystal structures, while the lowest-energy conformations of boscartins A and C were very similar to the crystal structures. Boscartins D-H and isoincensole oxide showed only one low-energy conformation for each compound and are predicted to be conformationally locked. Incensole, isoincensolol, and serratol are predicted to be conformationally mobile with several low-energy forms. The conformational mobility of Boswellia cembrenoid diterpenoids depends largely on the degree of epoxidation, either oxirane or tetrahydrofuran rings.     

Evidence of multiple introductions and genetic admixture of the Asian brush-clawed shore crab <Emphasis Type="Italic">Hemigrapsus takanoi</Emphasis> (Decapoda: Brachyura: Varunidae) along the Northern European coast

The Asian brush-clawed shore crab Hemigrapsus takanoi is a non-indigenous species along the Northern European coast. Although the history of range expansion of European H. takanoi has been well-documented, little is known about the genetic compositions of either the introduced European populations or the native Asian ones. We therefore collected H. takanoi broadly from their native Asian sites and introduced European ranges, and genotyped them by sequencing the mitochondrial 16S RNA gene and by analyzing nuclear microsatellite loci. Our results revealed that the H. takanoi Bay of Seine (France) populations consisted of a genetic admixture between populations in Japan and those in the Yellow Sea region. These French populations should be carefully monitored in the future, since the genetic admixture of multiple source populations may accelerate range expansion in non-indigenous organisms. Our results also suggested that shipping lines from East Asia were more probable vectors than historical juvenile oyster transportations from Japan for the foundation of present European H. takanoi populations. Interestingly, gene flow between populations in Japan and those in the Yellow Sea region (i.e., domestic invasion) was not observed despite the higher potential for artificial translocations via shipping lines in the native Asian range compared with those from Asia to Europe. The lack of domestic invasions implied that intra-specific priority effects of the resident H. takanoi populations played an important role in preventing the successful colonization of artificially-transferred individuals.     

Assessing the diversity of New Zealand freshwater harpacticoid copepods (Crustacea: Copepoda) using mitochondrial DNA (COI) barcodes

Taxonomic and ecological studies of freshwater harpacticoid copepods are limited globally by the ability to easily and accurately identify specimens. Here, we test the use of the mitochondrial cytochrome c oxidase subunit I (COI) gene locus as a tool for assessing the diversity of freshwater Harpacticoida. We obtained sequences from New Zealand harpacticoid copepods, representing two families, five genera and nine species, including the non-indigenous Elaphoidella sewelli. All species were delineated by the COI gene. However, high intraspecific diversity was evident among populations of Elaphoidella bidens (>12%), and between North and South Island populations of Bryocamptus pygmaeus (>18%), potentially indicating the presence of morphologically cryptic taxa. We suggest that mitochondrial DNA (COI) sequences can provide a useful tool for the routine identification of freshwater harpacticoid copepods. Applications of these data will include assessing species diversity and biogeography as well as assisting with the detection of non-indigenous species.     

Stereochemistry modulates the stability of reduced interstrand cross-links arising from R- and S-alpha-CH3-gamma-OH-1,N2-propano-2'-deoxyguanosine in the 5'-CpG-3' DNA sequence

The solution structures of 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' and 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' interstrand DNA cross-links in the 5'-CpG-3' sequence were determined by NMR spectroscopy. These were utilized as chemically stable surrogates for the corresponding carbinolamine interstrand cross-links arising from the crotonaldehyde- and acetaldehyde-derived R- and S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts. The results provide an explanation for the observation that interstrand cross-link formation in the 5'-CpG-3' sequence by the R- and S-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adducts is dependent upon stereochemistry, favoring the R-alpha-CH3-gamma-OH-1,N2-propanodeoxyguanosine adduct [Kozekov, I. D., Nechev, L. V., Moseley, M. S., Harris, C. M., Rizzo, C. J., Stone, M. P., and Harris, T. M. (2003) J. Am. Chem. Soc. 125, 50-61]. Molecular dynamics calculations, restrained by NOE-based distances and empirical restraints, revealed that both the 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' and 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-links were located in the minor groove and retained Watson-Crick hydrogen bonds at the tandem cross-linked C.G base pairs. However, for the 5'-Cp-N2-dG-3'-R-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the center of the minor groove, whereas for the 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link, the (alpha)-CH3 group was positioned in the 3' direction, showing steric interference with the DNA helix. The 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link exhibited a lower thermal stability as evidenced by NMR spectroscopy as a function of temperature. The two cross-links also exhibited apparent differences in the conformation of the interstrand three-carbon cross-link, which may also contribute to the lower apparent thermodynamic stability of the 5'-Cp-N2-dG-3'-S-(alpha)-CH3-propyl-5'-Cp-N2-dG-3' cross-link.     

Mutagenic potential of DNA-peptide crosslinks mediated by acrolein-derived DNA adducts

Current data suggest that DNA-peptide crosslinks are formed in cellular DNA as likely intermediates in the repair of DNA-protein crosslinks. In addition, a number of naturally occurring peptides are known to efficiently conjugate with DNA, particularly through the formation of Schiff-base complexes at aldehydic DNA adducts and abasic DNA sites. Since the potential role of DNA-peptide crosslinks in promoting mutagenesis is not well elucidated, here we report on the mutagenic properties of Schiff-base-mediated DNA-peptide crosslinks in mammalian cells. Site-specific DNA-peptide crosslinks were generated by covalently trapping a lysine-tryptophan-lysine-lysine peptide to the N(6) position of deoxyadenosine (dA) or the N(2) position of deoxyguanosine (dG) via the aldehydic forms of acrolein-derived DNA adducts (gamma-hydroxypropano-dA or gamma-hydroxypropano-dG, respectively). In order to evaluate the potential of DNA-peptide crosslinks to promote mutagenesis, we inserted the modified oligodeoxynucleotides into a single-stranded pMS2 shuttle vector, replicated these vectors in simian kidney (COS-7) cells and tested the progeny DNAs for mutations. Mutagenic analyses revealed that at the site of modification, the gamma-hydroxypropano-dA-mediated crosslink induced mutations at only approximately 0.4%. In contrast, replication bypass of the gamma-hydroxypropano-dG-mediated crosslink resulted in mutations at the site of modification at an overall frequency of approximately 8.4%. Among the types of mutations observed, single base substitutions were most common, with a prevalence of G to T transversions. Interestingly, while covalent attachment of lysine-tryptophan-lysine-lysine at gamma-hydroxypropano-dG caused an increase in mutation frequencies relative to gamma-hydroxypropano-dG, similar modification of gamma-hydroxypropano-dA resulted in decreased levels of mutations. Thus, certain DNA-peptide crosslinks can be mutagenic, and their potential to cause mutations depends on the site of peptide attachment. We propose that in order to avoid error-prone replication, proteolytic degradation of proteins covalently attached to DNA and subsequent steps of DNA repair should be tightly coordinated.     

Quantifying how acquired interactions with native and invasive insects influence population growth rates of a non-indigenous plant

Non-native species often acquire novel interspecific interactions, which are central to several hypotheses of invasion success, including biotic resistance and invasional meltdown. However, the outcome of these interactions is not often linked with the demographic evidence based on the full life cycle of the species. The Philippine Ground Orchid (Spathoglottis plicata) has invaded Puerto Rico and has acquired both negative and positive interspecific interactions involving the native weevil Stethobaris polita and the invasive red fire ant Solenopsis invicta, respectively. We studied a population in the Rio Abajo Forest, and asked how these interactions affect population demography by using a combination of field, experimental and modelling approaches. Stage-structured matrix population models based on four years of field observations showed that the population of S. plicata is growing at a rate (λ) of 1.05 under natural conditions. When we modified fecundity values based on experimental exclusion of weevils and ants, the control treatment showed a similar λ. Excluding weevils increased λ to 1.20, whereas the exclusion of ants decreased λ to 1.03. When we incorporate demographic and environmental stochasticity in our models, exclusion of invasive red fire ants significantly reduces the orchid abundance over time. Although weevils offer some biotic resistance to S. plicata, these effects do not prevent orchid population growth and expansion. On the other hand, invasive red fire ants have a positive effect on the invasive orchid’s λ, partially supporting the invasional meltdown hypothesis. This study presents a method that allows one to combine opposing mechanisms of species interactions within the same quantitative framework, and the results highlight the importance of considering acquired plant–animal interactions and stochastic processes when evaluating the population growth rates and dynamics of invasive plants.     

The effects of introduced plants on songbird reproductive success

The effects of non-native plants on habitat use are well studied; however, whether introduced plants negatively influence reproductive output of animal populations has received much less attention. We conducted a systematic literature review to evaluate the influence of non-native plants on reproductive performance in songbirds. Our global search resulted in 32 relevant articles, from which we compiled a dataset of 133 songbird responses to nesting in or around non-native vegetation. Reproductive metrics examined included measures of nest survival/mortality, productivity, fledgling survival, adult survival, nestling condition, and brood parasitism. Thirty-five percent of songbird reproductive responses were negative (n = 47), with 31% positive (n = 41) and 34% neutral (n = 45) responses found. Only 15% of responses were statistically significant effects (n = 20), and of these, negative effects were reported three times as often as positive effects. Non-significant trends were more prevalent (51% of responses), and the frequency of negative and positive trends was similar. The probability of finding a negative response (significant effect or non-significant trend) was higher for birds using introduced shrubs and wetland habitats. Mechanisms underlying responses were diverse, though similar drivers, such as differences in vegetation characteristics, predation pressure, and resource availability, were offered to explain both positive and negative effects. We found evidence for non-native plants as ecological traps in 39% of articles that assessed these phenomena (n = 16). This review highlights the sparsity of research targeting reproductive responses to plant invasion and synthesizes existing information to enhance our understanding of how birds respond to non-native plants. Our findings could be used to inform future research priorities in a world increasingly dominated by novel ecosystems.     

Current advances in molecular methods for detection of nitrite-dependent anaerobic methane oxidizing bacteria in natural environments

Nitrite-dependent anaerobic methane oxidation (n-damo) process uniquely links microbial nitrogen and carbon cycles. Research on n-damo bacteria progresses quickly with experimental evidences through enrichment cultures. Polymerase chain reaction (PCR)-based methods for detecting them in various natural ecosystems and engineered systems play a very important role in the discovery of their distribution, abundance, and biodiversity in the ecosystems. Important characteristics of n-damo enrichments were obtained and their key significance in microbial nitrogen and carbon cycles was investigated. The molecular methods currently used in detecting n-damo bacteria were comprehensively reviewed and discussed for their strengths and limitations in applications with a wide range of samples. The pmoA gene-based PCR primers for n-damo bacterial detection were evaluated and, in particular, several incorrectly stated PCR primer nucleotide sequences in the published papers were also pointed out to allow correct applications of the PCR primers in current and future investigations. Furthermore, this review also offers the future perspectives of n-damo bacteria based on current information and methods available for a better acquisition of new knowledge about this group of bacteria.