A web of imprinting in stem cells

Imprinted genes are the prototypical epigenetically regulated genes. On the basis of findings in adult lung stem cells, Zacharek et?al. (2011) suggest in this issue of Cell Stem Cell that epigenetic silencing of imprinted genes is a common requirement for maintaining self-renewal in adult stem cell populations.     

Eyes,More Than Other Facial Features,Enhance Real-World Donation Behavior

Humans often behave more prosocially when being observed in person and even in response to subtle eye cues, purportedly to manage their reputation. Previous research on this phenomenon has employed the “watching eyes paradigm,” in which adults displayed greater prosocial behavior in the presence of images of eyes versus inanimate objects. However, the robustness of the effect of eyes on prosocial behavior has recently been called into question. Therefore, the first goal of the present study was to attempt to replicate this effect. Additionally, it remains unclear whether the watching-eyes effect is driven specifically by reputation management (owing to the monitoring function of the eyes) or whether any cues indexing human presence more generally also have a similar effect. To address these questions, the current study compared prosocial behavior in the presence of eyes versus inanimate objects as well as other human features. The study was conducted as a field experiment at a children’s museum. Each week, the donation signs were changed to show eyes, noses, mouths, or chairs. Total donation amount and number of patrons per week were recorded. Participants donated more when they were exposed to eyes than to inanimate objects (chairs). We thus replicated the previously reported watching-eyes effect. Moreover, more money was donated when individuals were exposed to eyes than to more general cues of human presence (nose and mouth). The current findings suggest that eyes play a special role in promoting cooperation in humans, likely by serving as cues of monitoring and thus eliciting reputation management behavior.     

Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family

Background

It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5''-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.

Results

Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5''-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.

Conclusions

Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5''-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.     

Physical limits on kinesin-5–mediated chromosome congression in the smallest mitotic spindles

A characteristic feature of mitotic spindles is the congression of chromosomes near the spindle equator, a process mediated by dynamic kinetochore microtubules. A major challenge is to understand how precise, submicrometer-scale control of kinetochore micro­tubule dynamics is achieved in the smallest mitotic spindles, where the noisiness of microtubule assembly/disassembly will potentially act to overwhelm the spatial information that controls microtubule plus end–tip positioning to mediate congression. To better understand this fundamental limit, we conducted an integrated live fluorescence, electron microscopy, and modeling analysis of the polymorphic fungal pathogen Candida albicans, which contains one of the smallest known mitotic spindles (<1 μm). Previously, ScCin8p (kinesin-5 in Saccharomyces cerevisiae) was shown to mediate chromosome congression by promoting catastrophe of long kinetochore microtubules (kMTs). Using C. albicans yeast and hyphal kinesin-5 (Kip1p) heterozygotes (KIP1/kip1∆), we found that mutant spindles have longer kMTs than wild-type spindles, consistent with a less-organized spindle. By contrast, kinesin-8 heterozygous mutant (KIP3/kip3∆) spindles exhibited the same spindle organization as wild type. Of interest, spindle organization in the yeast and hyphal states was indistinguishable, even though yeast and hyphal cell lengths differ by two- to fivefold, demonstrating that spindle length regulation and chromosome congression are intrinsic to the spindle and largely independent of cell size. Together these results are consistent with a kinesin-5–mediated, length-dependent depolymerase activity that organizes chromosomes at the spindle equator in C. albicans to overcome fundamental noisiness in microtubule self-assembly. More generally, we define a dimensionless number that sets a fundamental physical limit for maintaining congression in small spindles in the face of assembly noise and find that C. albicans operates very close to this limit, which may explain why it has the smallest known mitotic spindle that still manifests the classic congression architecture.     

The efficiency and effectiveness of different sea urchin removal methods for kelp forest restoration

Sea urchin overgrazing has caused widespread phase shifts from kelp forests to “urchin barrens” on many temperate reefs, reducing habitat complexity, productivity, and biodiversity. Sea urchin removal is increasingly used for kelp restoration; however, few studies have quantified the efficiency and effectiveness of different removal methods, resulting in limited understanding of their practicality. In this study, the efficiency (removal rate) and effectiveness (proportion removed) of four removal methods were evaluated in northeastern New Zealand. We compared culling or collecting sea urchins by either SCUBA or freediving in 128 small-scale plots (25 m²). We also evaluated the efficiency and effectiveness of culling in four large (1.6–2 ha) barren areas, scales relevant for restoration. On average, culling sea urchins was 1.9–4.4 times faster than collecting, and SCUBA was 1.5–3.3 times faster than freediving. Removal rates increased with sea urchin density, especially for culling on SCUBA, while freediving removal rates increased with experience. Effectiveness was lower in large-scale removals (86–93% of sea urchins ≥40 mm removed) compared to small-scale removals (98–99%), but sufficient for restoration objectives. Estimated time per area (using SCUBA culling) was similar across large-scale removals (49–57 hours/ha), despite an almost 2-fold variation in initial sea urchin densities (approximately 4–8 urchins/m²), suggesting area may better predict total removal time than simply number of sea urchins across low-density ranges. While sea urchin removal provides a rapid, feasible, and effective approach to restoring kelp in urchin barrens, restoration plans need to also address the causes of sea urchin overpopulation to ensure long-term benefits.     

Influence of light on plant allelochemicals: A synergistic defense in higher plants

Plant phototoxins are broad-spectrum biocides which adversely affect an array of potential plant enemies, including among others disease-causing pathogens, nematodes, insect herbivores, and competing plant species. Thus far, plants which contain these broad-spectrum allelochemicals have been found to occur in open habitats (i.e., in full sunlight) where a defensive mechanism mediated by light would seem to operate most effectively. The levels of available light in shaded environments, although considerably lower than full sun (1–10% of full sun), are equivalent to the intensities of light used to kill phototoxin-treated insects in laboratory studies. This suggests that phototoxic reactions might mediate important organismal interactions in shaded environments as well. In this study, more than 230 Costa Rican rainforest plants were bioassayed for phototoxic metabolites in an effort to ascertain their prevalence among plants growing in moderate to extreme shade. Microbial bioassays, employing Bacillus cereus (a gram positive bacterium), Escherichia coli (a gram negative bacterium), and Saccharomyces cerevisiae (a yeast) were used to rapidly and sensitively indicate phototoxic action and potential for insecticidal action. Tissue extracts from 12 plant families tested positive for phototoxins. This is the first report of phototoxins occurring in eight of those families (Acanthaceae, Campanulaceae, Gesnariaceae, Loganiaceae, Malpigaceae, Phytolaccaceae, Piperaceae, and Sapotaceae). The presence of phototoxins in rainforest plants suggests that phototoxic plant allelochemicals may function as important defenses in low-light, as well as high-light, environments.     

Changes in ventilation in response to ramp changes in treadmill exercise load

These experiments examined the changes in ventilation during a 40-s ramp increase in exercise load, produced by increasing either the speed of the treadmill or the grade, to equivalent end-points of oxygen uptake. Six subjects underwent five trials each for grade and speed, while ventilation was monitored breath-by-breath. For each subject, ventilation versus time for all five of the speed trials was plotted on a single graph and fitted by linear regression. The data for the grade trials were similarly treated. For all subjects, the slope of the regression line for the speed plots was found to be significantly (P < 0.05) greater than that for the grade plots. We concluded that these experimental results support the hypothesis that the neural drive to ventilation persists as exercise continues and is proportionately related to the frequency of limb movement.