DNA replication stress: Causes,resolution and disease

DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.     

Eye ontogeny in Pleurodema bufoninum: A comparison with Pleurodema somuncurense (Anura,Leptodactylidae)

Vision is one of the main sensory systems in amphibians, and the eye structure is highly associated with habitat conditions. The ontogeny, as well as the adult structure, of the eye has been studied in only a few species. The life change after metamorphosis is accompanied by changes in the visual environment. The aim of this work is to describe the eye ontogeny of Pleurodema bufoninum and to compare it with that of Pleurodema somuncurense . Specimens of both Pleurodema species were processed for histology analysis at different stages of development, including the tadpole, postmetamorphic, and adult forms. Eyes in both Pleurodema species are composed of the 3 tunics, tunica fibrosa , tunica vasculosa , and tunica interna , and the lens. Additionally, in both, the iris presents a projection on its dorsal and ventral free ends that screens the cornea. This structure has been reported in the eye of several anuran species and is called the umbraculum, meniscus or pupillary nodule. Our results show that the structures related to light capture (retina and lens) appear early in larval life, while the components of the terrestrial‐life eye (scleral cartilage, specialized cornea, eyelids, nictitating membrane, and Harderian's gland) do not develop until the metamorphic climax, when the tadpole leaves the water. The adult eyes of P. bufoninum and P. somuncurense are very similar in structure and development.     

Endoplasmic reticulum stress in insulin resistance and diabetes

The endoplasmic reticulum is the main intracellular Ca²⁺ store for Ca²⁺ release during cell signaling. There are different strategies to avoid ER Ca²⁺ depletion. Release channels utilize first Ca²⁺-bound to proteins and this minimizes the reduction of the free luminal [Ca²⁺]. However, if release channels stay open after exhaustion of Ca²⁺-bound to proteins, then the reduction of the free luminal ER [Ca²⁺] (via STIM proteins) activates Ca²⁺ entry at the plasma membrane to restore the ER Ca²⁺ load, which will work provided that SERCA pump is active. Nevertheless, there are several noxious conditions that result in decreased activity of the SERCA pump such as oxidative stress, inflammatory cytokines, and saturated fatty acids, among others. These conditions result in a deficient restoration of the ER [Ca²⁺] and lead to the ER stress response that should facilitate recovery of the ER. However, if the stressful condition persists then ER stress ends up triggering cell death and the ensuing degenerative process leads to diverse pathologies; particularly insulin resistance, diabetes and several of the complications associated with diabetes. This scenario suggests that limiting ER stress should decrease the incidence of diabetes and the mobility and mortality associated with this illness.     

How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation

Oxygen radical formation in mitochondria is an incompletely understood attribute of eukaryotic cells. Recently, a kinetic model was proposed, in which the ratio between electrons entering the respiratory chain via FADH₂ or NADH determines radical formation. During glucose breakdown, the ratio is low; during fatty acid breakdown, the ratio is high (the ratio increasing—asymptotically—with fatty acid length to 0.5, when compared with 0.2 for glucose). Thus, fatty acid oxidation would generate higher levels of radical formation. As a result, breakdown of fatty acids, performed without generation of extra FADH₂ in mitochondria, could be beneficial for the cell, especially in the case of long and very long chained ones. This possibly has been a major factor in the evolution of peroxisomes. Increased radical formation, as proposed by the model, can also shed light on the lack of neuronal fatty acid oxidation and tells us about hurdles during early eukaryotic evolution. We specifically focus on extending and discussing the model in light of recent publications and findings.     

Kinetic parameters of nitrate uptake by different catch crop species: effects of low temperatures or previous nitrate starvation

The pollution of aquifers by NO^?₃ in temperate environments is aggravated by farming practices that leave the ground bare during winter. The use of catch crops during this time may decrease nitrate loss from the soil. Nitrate uptake by several catch crop species (Brassica napus L., Sinapis alba L., Brassica rapa L., Raphanus sativus L., Trifolium alexandrinum L., Trifolium incarnatum L., Phacelia tanacetifolia Benth., Lolium perenne L., Lolium multiflorum Lam. and Secale cereale L.) was here studied in relation to transpiration rate and low temperatures applied to the whole plant or to roots only. The Michaelis constant (K_m), maximum uptake rate (V_max), time of induction and contributions of inducible and constitutive mechanisms were estimated from measurements of NO^?₃ depletion in the uptake medium. There were large differences between species, with K_m (μM) values ranging between 5.12 ± 0.64 (Trifolium incarnatum) and 36.4 ± 1.97 (Lolium perenne). Maximum NO^?₃ uptake rates expressed per unit root weight were influenced by ageing, temperature and previous NO^?₃ nutrition. They were also closely correlated with water flow through the roots and with shoot/root ratio of these species. The combined results from all species and treatments showed that V_max increased with shoot/root ratio, suggesting a regulatory role for the shoots in NO^?₃ uptake. Overall, the results showed a great diversity in NO^?₃ uptake characteristics between species in terms of kinetic parameters, contribution of the constitutive system (100% of total uptake in ryegrass, nil in Fabaceae) and time of induction.     

Assessing population genetic structure and variability with RAPD data: Application to Vaccinium macrocarpon (American Cranberry)

A method for estimating and comparing population genetic variation using random amplified polymorphic DNA (RAPD) profiling is presented. An analysis of molecular variance (AMOVA) is extended to accomodate phenotypic molecular data in diploid populations in Hardy-Weinberg equilibrium or with an assumed degree of selfing. We present a two step strategy: 1) Estimate RAPD site frequencies without preliminary assumptions on the unknown population structure, then perform significance testing for population substructuring. 2) If population structure is evident from the first step, use this data to calculate better estimates for RAPD site frequencies and sub-population variance components. A nonparametric test for the homogeneity of molecular variance (HOMOVA) is also presented. This test was designed to statistically test for differences in intrapopulational molecular variances (heteroscedasticity among populations). These theoretical developments are applied to a RAPD data set in Vaccinium macrocarpon (American cranberry) using small sample sizes, where a gradient of molecular diversity is found between central and marginal populations. The AMOVA and HOMOVA methods provide flexible population analysis tools when using data from RAPD or other DNA methods that provide many polymorphic markers with or without direct allelic data.     

Site-Specific Structural Variations Accompanying Tubular Assembly of the HIV-1 Capsid Protein

The 231-residue capsid (CA) protein of human immunodeficiency virus type 1 (HIV-1) spontaneously self-assembles into tubes with a hexagonal lattice that is believed to mimic the surface lattice of conical capsid cores within intact virions. We report the results of solid-state nuclear magnetic resonance (NMR) measurements on HIV-1 CA tubes that provide new information regarding changes in molecular structure that accompany CA self-assembly, local dynamics within CA tubes, and possible mechanisms for the generation of lattice curvature. This information is contained in site-specific assignments of signals in two- and three-dimensional solid-state NMR spectra, conformation-dependent ¹⁵N and ¹³C NMR chemical shifts, detection of highly dynamic residues under solution NMR conditions, measurements of local variations in transverse spin relaxation rates of amide ¹H nuclei, and quantitative measurements of site-specific ¹⁵N–¹⁵N dipole–dipole couplings. Our data show that most of the CA sequence is conformationally ordered and relatively rigid in tubular assemblies and that structures of the N-terminal domain (NTD) and the C-terminal domain (CTD) observed in solution are largely retained. However, specific segments, including the N-terminal β-hairpin, the cyclophilin A binding loop, the inter-domain linker, segments involved in intermolecular NTD–CTD interactions, and the C-terminal tail, have substantial static or dynamical disorder in tubular assemblies. Other segments, including the 3₁₀-helical segment in CTD, undergo clear conformational changes. Structural variations associated with curvature of the CA lattice appear to be localized in the inter-domain linker and intermolecular NTD–CTD interface, while structural variations within NTD hexamers, around local 3-fold symmetry axes, and in CTD–CTD dimerization interfaces are less significant.     

Novel Interaction of the Z-DNA Binding Domain of Human ADAR1 with the Oncogenic c-Myc Promoter G-Quadruplex

Both G-quadruplex and Z-DNA can be formed in G-rich and repetitive sequences on genome, and their formation and biological functions are controlled by specific proteins. Z-DNA binding proteins, such as human ADAR1, have a highly conserved Z-DNA binding domain having selective affinity to Z-DNA. Here, our study identifies the Z-DNA binding domain of human ADAR1 (hZα_ADAR1) as a novel G-quadruplex binding protein that recognizes c-myc promoter G-quadruplex formed in NHEIII₁ region and represses the gene expression. An electrophoretic migration shift assay shows the binding of hZα_ADAR1 to the intramolecular c-myc promoter G-quadruplex-forming DNA oligomer. To corroborate the binding of hZα_ADAR1 to the G-quadruplex, we conducted CD and NMR chemical shift perturbation analyses. CD results indicate that hZα_ADAR1 stabilizes the parallel-stranded conformation of the c-myc G-quadruplex. The NMR chemical shift perturbation data reveal that the G-quadruplex binding region in hZα_ADAR1 was almost identical with the Z-DNA binding region. Finally, promoter assay and Western blot analysis show that hZα_ADAR1 suppresses the c-myc expression promoted by NHEIII₁ region containing the G-quadruplex-forming sequence. This finding suggests a novel function of Z-DNA binding protein as a regulator of G-quadruplex-mediated gene expression.     

Diel fragrance pattern correlates with olfactory preferences of diurnal and nocturnal flower visitors in Salix caprea (Salicaceae)

Floral scent, often a complex mixture of several volatile organic compounds (VOCs), has generally been interpreted as an adaptation to attract pollinators. However, not many studies have analysed which VOCs are functionally relevant for the reproductive success of a plant. Here, we show that, in Salix caprea (Salicaceae), temporal changes in floral scent emission during the day and night attract two different types of flower visitor: bees during the day and moths during the evening and night. We analysed the contribution of the two flower visitor groups to the reproductive success of the plant. The differences in scent emitted during the peak activity times of flower visitors (day versus night) were quantified and the response of 13 diurnal/nocturnal pollinator taxa to the floral scents was tested using gas chromatographic and electroantennographic techniques. Many of the c. 40 identified scent compounds were physiologically active, and bees and moths responded to nearly identical sets of compounds, although the response strengths differed. In bioassays, bees preferred the most abundant 1,4‐dimethoxybenzene over lilac aldehyde, a compound with increased emission at night, whereas moths preferred lilac aldehyde over 1,4‐dimethoxybenzene. Pollination by wind plus nocturnal pollinators (mainly moths) or by wind alone contributed less to seed set than pollination by wind plus diurnal pollinators (mainly bees). This suggests that the emission of scent during the night and attracting moths have no significant effect on reproductive success. It is possible that the emission of lilac aldehydes and other compounds at night is s result of phylogenetic constraints. Future studies should investigate whether moths may produce a marginal fitness gain in some years and/or some populations. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 624–640.