Mouse centric and pericentric satellite repeats form distinct functional heterochromatin

Heterochromatin is thought to play a critical role for centromeric function. However, the respective contributions of the distinct repetitive sequences found in these regions, such as minor and major satellites in the mouse, have remained largely unsolved. We show that these centric and pericentric repeats on the chromosomes have distinct heterochromatic characteristics in the nucleus. Major satellites from different chromosomes form clusters associated with heterochromatin protein 1alpha, whereas minor satellites are individual entities associated with centromeric proteins. Both regions contain methylated histone H3 (Me-K9 H3) but show different micrococcal nuclease sensitivities. A dinucleosome repeating unit is found specifically associated with major satellites. These domains replicate asynchronously, and chromatid cohesion is sustained for a longer time in major satellites compared with minor satellites. Such prolonged cohesion in major satellites is lost in the absence of Suv39h histone methyltransferases. Thus, we define functionally independent centromeric subdomains, which spatio-temporal isolation is proposed to be important for centromeric cohesion and dissociation during chromosome segregation.     

The dehaloperoxidase paradox

The dual functions of the dehaloperoxidase-hemoglobin of Amphitrite ornata leads to a paradox. Peroxidase and hemoglobin functions require ferric and ferrous resting states, respectively. Assuming that hemoglobin function is the dominant function, the starting point for peroxidase activation would be the oxyferrous state. Activation of that state leads to the ferryl intermediate, followed by one-electron oxidation of the substrate, which results in the ferric state. Since no exogenous reductant is known, there is no return to the ferrous form or hemoglobin function. The observation that an internal binding site for 4-bromophenol leads to inhibition leads to a further paradox that the enzyme would be inhibited immediately upon activation under ambient conditions in benthic ecosystems where the inhibitor, 4-bromophenol is present in greater concentration than the substrate, 2,4,6-tribromophenol. In this review, we explore the unresolved aspects of the reaction scheme that leads to the apparent paradox. Recent data showing activation of the oxyferrous state, an extremely high reduction potential and exogenous reduction by the 2,6-dibromoquinone product present a potential resolution of the paradox. These aspects are discussed in the context of control of reactivity radical pathways and reactivity by the motion of the distal histidine, H55, which in turn is coupled to the binding of substrate and inhibitor.     

The dehaloperoxidase paradox

The dual functions of the dehaloperoxidase-hemoglobin of Amphitrite ornata leads to a paradox. Peroxidase and hemoglobin functions require ferric and ferrous resting states, respectively. Assuming that hemoglobin function is the dominant function, the starting point for peroxidase activation would be the oxyferrous state. Activation of that state leads to the ferryl intermediate, followed by one-electron oxidation of the substrate, which results in the ferric state. Since no exogenous reductant is known, there is no return to the ferrous form or hemoglobin function. The observation that an internal binding site for 4-bromophenol leads to inhibition leads to a further paradox that the enzyme would be inhibited immediately upon activation under ambient conditions in benthic ecosystems where the inhibitor, 4-bromophenol is present in greater concentration than the substrate, 2,4,6-tribromophenol. In this review, we explore the unresolved aspects of the reaction scheme that leads to the apparent paradox. Recent data showing activation of the oxyferrous state, an extremely high reduction potential and exogenous reduction by the 2,6-dibromoquinone product present a potential resolution of the paradox. These aspects are discussed in the context of control of reactivity radical pathways and reactivity by the motion of the distal histidine, H55, which in turn is coupled to the binding of substrate and inhibitor.     

The memory paradox

Declarative and emotional memories are key to quality of life and day-to-day functioning. The absence of memory or the inability to recall memories properly in an emotional context leads to dysfunction but, paradoxically, memories that generate too much emotion can be equally disabling.     

The paradox of invasion

It is paradoxical that exotic species invade and displace native species that are well adapted to local environments. Yet, even those exotics that eventually become abundant and widespread, often do so only after having failed to establish following multiple earlier introductions. The first pattern, while not generally discussed in this context, is usually explained by exotic species pre‐adaptations for human‐altered environments and by a release from enemies. It can be understood further by examining the superior quality of colonists from large species‐rich regions and the historical contingency of evolution. The second pattern is generally explained by invoking demographic and environmental stochasticity; however, it can be understood further by examining the role of environmental variation over space and by metapopulation dynamics. These processes provide a context in which these patterns of invasion are not paradoxical, but instead, expected.     

The origin of heterochromatin in eukaryotes

This study is an attempt to reconstruct the stages of the evolution of heterochromatin in eukaryotes. According to the hypothesis put forward in the work, the origin of satellite DNAs (stDNAs) was directly related to certain functional characteristics of DNA polymerases, and stDNAs themselves are products of accidental slippage at replication initiation sites. Even at the moment when the stDNAs precursors (protosatellites) appeared, they had properties of selfish DNA. Therefore, specific complex mechanisms of genetic control of their replication and recombination have developed in evolution to restrict the spread of these DNAs over the genome. The host control over protosatellites has led to the appearance of the main heterochromatic characteristics in them, such as late replication, decreased recombination, and denser chromatin packing compared to euchromatin. The next stage of heterochromatin evolution led to the union of protosatellite clusters and ordinary genes if late replication was necessary for these genes or if gene complexes already formed required protection from the destructure effect of crossing over. The known cases of location of certain genes in heterochromatic blocks in Drosophila melanogaster, the eukaryote that has been best studied genetically, confirm this hypothesis.     

The many hues of plant heterochromatin

Recent sequence and cytogenetic analyses of heterochromatin in Arabidopsis, together with other results from Arabidopsis and maize, indicate that plant heterochromatin can have very different origins, compositions and dynamics. Shared features that must determine and/or be a result of its unique biological properties are also revealed.     

The ascorbic acid paradox

Ascorbic acid (AA) is a common culture medium and dietary supplement. While AA is most commonly known for its antioxidant properties, it is also known to function as a pro-oxidant under select conditions. However, the complexity and often unknown composition of biological culture systems makes prediction of AA behaviour in supplemented cultures challenging. The frequent observation of outcomes inconsistent with antioxidant behaviour suggests that AA may be playing a pro-oxidant role more often than appreciated. In this work we explored the intracellular and extracellular impact of AA supplementation on KG1a myeloid leukaemia cells over a 24-h culture period following the addition of the AA supplement. At 24 h we found that supplementation of AA up to 250 μM resulted in intracellular antioxidant behaviour. However, when these same cultures were evaluated at 2 or 4 h we observed pro-oxidant activity at the higher AA concentrations indicating that the outcome was very much time and dose dependent. In contrast, pro-oxidant activity was never observed in the extracellular medium. Paradoxically, and to our knowledge not previously reported, we observed that intracellular pro-oxidant activity and extracellular antioxidant activity could occur simultaneously. These results indicate that the precise activity of AA supplementation varies as a function of dose, time and cellular location. Further, these results demonstrate how in the absence of careful culture characterization the true impact of AA on cultures could be underappreciated.     

The minimal genome paradox

The concept of a 'minimal genome' has appeared as an attempt to answer the question what the minimum number of genes or minimum amount of DNA to support life is. Since bacteria are cells bearing the smallest genomes, it has been generally accepted that the minimal genome must belong to a bacterial species. Currently the most popular chromosome in studies on a minimal genome belongs to Mycoplasma genitalium, a parasite bacterium whose total genetic material is as small as approximately 580 kb. However, the problem is how we define life, and thus also a minimal genome. M. genitalium is a parasite and requires substances provided by its host. Therefore, if a genome of a parasite can be considered as a minimal genome, why not to consider genomes of bacteriophages? Going further, bacterial plasmids could be considered as minimal genomes. The smallest known DNA region playing the function of the origin of replication, which is sufficient for plasmid survival in natural habitats, is as short as 32 base pairs. However, such a small DNA molecule could not form a circular form and be replicated by cellular enzymes. These facts may lead to an ostensibly paradoxical conclusion that the size of a minimal genome is restricted by the physical size of a DNA molecule able to replicate rather, than by the amount of genetic information.     

The early crying paradox

In contemporary Western societies, infants in the first 3 months cry more than at any other time during their life. Although this crying is believed to function to assure nutrition, protection, and mother-infant interaction thought to be essential for later attachment, it also predisposes to complaints of excessive crying (“colic”), discontinuing breast-feeding, and, in the extreme case, child abuse. A resolution of this apparent paradox is proposed based on evidence that elements of caregiving are important determinants of some aspects of early crying. It is argued that early human crying under caretaking conditions typical in Western societies is characterized by prolonged crying bouts, that it is specifically the length of crying bouts (rather than frequency or pattern) that is affected by caregiving practice, and that prolonged crying bouts are probably not characteristic with caretaking practices typical in non-Western societies and possibly in our evolutionary past. It is suggested that caregiving behaviors may recruit normal physiological functions that potentiate cry bout duration in Western caregiving contexts, but reduce it in others. Frequent, short bouts are sufficient, and probably better suited than long bouts, to promote all the positive and presumably adaptive functions claimed for infant crying. Furthermore, they may have provided a mechanism by which infants could enhance their own fitness.     

The paradox of cooperation benefits

It seems obvious that as the benefits of cooperation increase, the share of cooperators in the population should also increase. It is well known that positive assortment between cooperative types, for instance in spatially structured populations, provide better conditions for the evolution of cooperation than complete mixing. This study demonstrates that, assuming positive assortment, under most conditions higher cooperation benefits also increase the share of cooperators. On the other hand, under a specified range of payoff values, when at least two payoff parameters are modified, the reverse is true. The conditions for this paradox are determined for two-person social dilemmas: the Prisoner's Dilemma, the Hawks and Doves game, and the Stag Hunt game, assuming global selection and positive assortment.     

The mitral paradox of choice

Netherlands Heart Journal -