5-hydroxymethylcytosine in DNA repair: A new player or a red herring?

Active DNA demethylation performed by ten-eleven translocation (TET) enzymes produces 5-hydroxymethylcytosines, 5-formylcytosines, and 5-carboxylcytosines. Recent observations suggest that 5-hydroxymethylcytosine is a stable epigenetic mark rather than merely an intermediate of DNA demethylation. However, the clear functional role of this new epigenetic player is elusive. The contribution of 5-hydroxymethylation to DNA repair is being discussed currently. Recently, Jiang and colleagues have demonstrated that DNA damage response-activated ATR kinase phosphorylates TET3 in mammalian cells and promotes DNA demethylation and 5-hydroxymethylcytosine accumulation. Moreover, TET3 catalytic activity is important for proper DNA repair and cell survival. Here, we discuss recent studies on the potential role of 5-hydroxymethylation in DNA repair and genome integrity maintenance.     

Red leaves, insects and coevolution: a red herring?

W.D. (Bill) Hamilton proposed that coevolution between plants and herbivorous insects explains the bright autumnal colouration of leaves. Accordingly, plants invest in bright signals to reduce their herbivore load, whereas insects use these bright signals to identify less-defended hosts more efficiently. Archetti and Brown have recently revisited this theory by explaining its basic predictions and providing new research perspectives. Their work presents an important basis to our understanding of non-green leaf colouration, provided that alternative adaptive explanations on the photoprotective and antioxidant role of leaf pigments, or their possible function in crypsis to herbivores are incorporated into future research.     

Estrogen mitogenic action. III. Is phenol red a “red herring”?

The reported estrogenic action of phenol red and/or its lipophilic contaminants has led to the widespread use of indicator-free culture medium to conduct endocrine studies in vitro. Because we have recently developed methods to measure large-magnitude estrogen effects in the tissue culture medium containing phenol red, we concluded that the indicator issue required further evaluation. To do this, we selected nine estrogen receptor positive (ER+) cell lines representing four target tissues and three species. We investigated phenol red using five different experimental protocols. First, 17beta-estradiol (E2) responsive growth of all nine ER+ cells lines was compared in the medium with and without the indicator. Second, using representative lines we asked if phenol red was mitogenic in the indicator-free medium. The dose-response effects of phenol red were compared directly to those of E2. Third, we asked if tamoxifen-inhibited growth equally in phenol red-containing and indicator-free medium. This study was based on a report indicating that antiestrogen effects should be seen only in phenol red-containing medium. Fourth, we asked if phenol red displaced the binding of 3H-E2 using ERK intact human breast cancer cells. Fifth, we compared E2 and phenol red as inducers of the progesterone receptor using a human breast cancer cell line. All the experiments presented in this report support the conclusion that the concentration of phenol red contaminants in a standard culture medium available today is not sufficient to cause estrogenic effects. In brief, our studies indicate that the real issue of how to demonstrate estrogenic effects in culture resides elsewhere than phenol red. We have found that the demonstration of sex steroid hormone-mitogenic effects in culture depends upon conditions that maximize the effects of a serum-borne inhibitor(s). When the effects of the inhibitor are optimized, the presence or absence of phenol red makes no everyday difference to the demonstration of estrogen mitogenic effects with several target cell types from diverse species.     

Are red algae plants?

For 200 years prior to the 1938 publication of H. F. Copeland, all authorities (with one exception) classified red algae (Rhodophyta) within Kingdom Plantae or its equivalent. Copeland's reclassification of red algae within Kingdom Protista or Protoctista drew from an alternative tradition, dating to Cohn in 1867, in which red algae were viewed as the earliest or simplest eukaryotes. Analyses of ribosomal RNA (rRNA) sequence data initially favoured Copeland's reclassification. Many more rRNA gene (rDNA) sequences are now available from the eukaryote lineages most closely related to red algae, and based on these data, the hypothesis that red algae and green plants are sister groups cannot be rejected. An increasing body of sequence, intron-location and functional data from nuclear- and mitochondrially encoded proteins likewise supports a sister-group relationship between red algae and green plants. Submerging Kingdoms Plantae, Animalia and Fungi into Eukarya would provide a more natural framework for the eventual resolution of whether red algae are plants or prorists.     

Overcompensation by plants: Herbivore optimization or red herring?

Summary The increased growth rates, higher total biomass, and increased seed production occasionally found in grazed or clipped plants are more accurately interpreted as the results of growth at one end of a spectrum of normal plant regrowth patterns, rather than as overcompensation, herbivore-stimulated growth, plantherbivore mutualisms, or herbivore enhanced fitness. Plants experience injury from a wide variety of sources besides herbivory, including fire, wind, freezing, heat, and trampling; rapid regrowth may have been selected for by any one of the many types of physical disturbance or extreme conditions that damage plant tissues, or by a combination of all of them. Rapid plant regrowth is more likely to have evolved as a strategy to reduce the negative impacts of all types of damage than as a strategy to increase fitness following herbivory above ungrazed levels. There is no evolutionary justification and little evidence to support the idea that plant-herbivore mutualisms are likely to evolve. Neither life history theory nor recent theoretical models provide plausible explanations for the benefits of herbivory.Several assumptions underlie all discussions of the benefits of herbivory: that plant species are able to evolve a strategy of depending on herbivores to increase their productivity and fitness; that herbivores do not preferentially regraze the overcompensating plants; that resources will be sufficient for regrowth; and that being larger is always better than being smaller. None of these assumptions is necessarily correct.     

Negative density‐dependent dispersal in tsetse (Glossina spp): red flag or red herring?

A deterministic model of the distribution of tsetse flies (Glossina spp) was used to assess the extent to which the efficacy of control operations would be affected by three different modes of density dependence in per capita adult dispersal: (i) density‐independent dispersal which has been commonly adopted in previous models, (ii) positive density‐dependent dispersal which has occasionally been discussed in the tsetse literature, (iii) negative density‐dependent dispersal (NDDD). The last has recently been suggested, from genetic studies, to change the dispersal rate of tsetse by up to 200‐fold, thereby posing a severe risk for the success of tsetse control operations. Modelling outputs showed that NDDD poses no such risk, provided the mean daily dispersal of tsetse is below about 1 km, which is greater than any rate actually recorded in the field or indicated by the genetic studies. NDDD can be problematic only if tsetse disperse at rates that appear highly unlikely, or even impossible, on energetic grounds. Under some circumstances these high rates would help rather than hinder the control officer. NDDD is not necessary to explain the results of control operations, and not sufficient to explain the results of successful control programmes.     

Are carotenoids the blue-light photoreceptor in the photoinduction of protoperithecia in Neurospora crassa?

A triple albino mutant of Neurospora crassa with a measured content of carotenoids absorbing at 470 nm less than 0.5% of that of the wild type (calculated value less than 8·10^-4%) had the same threshold for photoinduction of protoperithecia as the wild type when illuminated with monochromatic light at 471 nm. This is strong evidence against the hypothesis that the bulk of carotenoids are the blue-light photoreceptor for this phenomenon. However, it is impossible to exclude traces of carotenoids acting as the photoreceptor at less than 3·10^-12 M in a very efficient sensory transduction chain.Abbreviations A absorbance - al albino mutant - WT wild type     

Are red leaves photosynthetically active?

At irradiances close to those representing a sunny day, red and green leaves of poinsettia (Euphorbia pulcherrima) showed only minor differences in their photosynthetic capacities despite the strong differences in their pigment composition. However, contrarily to green leaves, red leaves did not show inhibition of photosynthesis at high irradiances, because anthocyanins protected chloroplasts from photoinhibition.     

Are dietary carotenoids beneficial? Reactions of carotenoids with oxy-radicals and singlet oxygen.

Carotenoids play diverse roles in biology and medicine. Both the quenching of singlet oxygen (energy transfer) and interaction with oxy-radicals (electron transfer, H-atom transfer and addition reactions) are key processes in understanding many of these roles. Much previous work in 'simple' solvents is reviewed and new results in cell membrane models are presented. The possible consequences of using carotenoids as dietary supplements are discussed.     

Are morphometric indices accurate indicators of stored energy in herring Clupea harengus?

The accuracy of the morphometric indices Fulton's K, somatic K and relative condition factor, K_n, as measures of individual North Sea herring Clupea harengus muscle fat content was investigated using the Distell Fish Fat meter. The accuracy of fat‐meter readings from an individual fish was validated by comparison with Soxhlet extraction analysis. The studies conducted demonstrated that Fulton's K is not consistently or strongly correlated with individual C. harengus muscle fat content, as defined by the fat‐meter estimates. The study shows that somatic K and K_n may be better indices of individual North Sea C. harengus muscle fat content than Fulton's K. These morphometric indices, however, should only be used after prior validation against a more direct measure of fat content.     

Does titanium in ionic form display a tissue-specific distribution?

Most studies have focused on the biodistribution of titanium(IV) oxide as nanoparticles or crystals in organism. But several reports suggested that titanium is released from implant in ionic form. Therefore, gaining insight into toxicokinetics of Ti ions will give valuable information, which may be useful when assessing the health risks of long-term exposure to titanium alloy implants in patients. A micro synchrotron radiation-induced X-ray fluorescence (µ-SRXRF) was utilized to investigate the titanium distribution in the liver, spleen and kidneys of rats following single intravenous or 30-days oral administration of metal (6 mg Ti/b.w.) in ionic form. Titanium was mainly retained in kidneys after both intravenous and oral dosing, and also its compartmentalization in this organ was observed. Titanium in the liver was non-uniformly distributed—metal accumulated in single aggregates, and some of them were also enriched in calcium. Correlation analysis showed that metal did not displace essential elements, and in liver titanium strongly correlated with calcium. Two-dimensional maps of Ti distribution show that the location of the element is characteristic for the route of administration and time of exposure. We demonstrated that µ-SRXRF can provide information on the distribution of titanium in internal structures of whole organs, which helps in enhancing our understanding of the mechanism of ionic titanium accumulation in the body. This is significant due to the popularity of titanium implants and the potential release of metal ions from them to the organism.     

Costly sexual signals: are carotenoids rare, risky or required?

Theories of animal signalling emphasize the importance of costliness-to be effective, signals must be dependable; to be dependable, signals must carry costs-and carotenoid-based signals are a favoured example. The traditional view that carotenoids are costly because they are scarce still carries weight. However, biomedical research has led to alternative views on costliness, mainly related to beneficial, but also to detrimental, effects of carotenoids. Recent improvements in our understanding of carotenoids suggest that the relative importance of these mechanisms will soon be determined, leading to a fresh outlook on cost-based signalling.