MacroH2A histone variants limit chromatin plasticity through two distinct mechanisms

MacroH2A histone variants suppress tumor progression and act as epigenetic barriers to induced pluripotency. How they impart their influence on chromatin plasticity is not well understood. Here, we analyze how the different domains of macroH2A proteins contribute to chromatin structure and dynamics. By solving the crystal structure of the macrodomain of human macroH2A2 at 1.7 Å, we find that its putative binding pocket exhibits marked structural differences compared with the macroH2A1.1 isoform, rendering macroH2A2 unable to bind ADP‐ribose. Quantitative binding assays show that this specificity is conserved among vertebrate macroH2A isoforms. We further find that macroH2A histones reduce the transient, PARP1‐dependent chromatin relaxation that occurs in living cells upon DNA damage through two distinct mechanisms. First, macroH2A1.1 mediates an isoform‐specific effect through its ability to suppress PARP1 activity. Second, the unstructured linker region exerts an additional repressive effect that is common to all macroH2A proteins. In the absence of DNA damage, the macroH2A linker is also sufficient for rescuing heterochromatin architecture in cells deficient for macroH2A.     

A review of <Emphasis Type="Italic">Solanum mauritianum</Emphasis> biocontrol: prospects,promise and problems: a way forward for South Africa and globally

The invasive tree Solanum mauritianum Scopoli remains one of the world’s most widespread environmental weeds. Despite biocontrol providing one of the few viable long-term solutions to tackling S. mauritianum invasions globally, only South Africa and, more recently, New Zealand, have programmes in place. Ongoing biocontrol efforts against S. mauritianum are reviewed here with particular reference to South Africa. The South African programme has suffered a troubled history, with considerable research efforts culminating in the eventual release and establishment of only two insect agents, Gargaphia decoris Drake and Anthonomus santacruzi Hustache. The difficulties experienced have hindered research into new agents, causing apprehension in using biocontrol internationally. However, recent studies have demonstrated that biocontrol may be deserving of renewed investment, particularly within an integrated management context. In this review, we advocate for the revival of the S. mauritianum biocontrol programme in South Africa, and discuss possible avenues for future research internationally.     

Lipid metabolism of phenol-tolerant <Emphasis Type="Italic">Rhodococcus opacus</Emphasis> strains for lignin bioconversion

Background

Lignin is a recalcitrant aromatic polymer that is a potential feedstock for renewable fuel and chemical production. Rhodococcus opacus PD630 is a promising strain for the biological upgrading of lignin due to its ability to tolerate and utilize lignin-derived aromatic compounds. To enhance its aromatic tolerance, we recently applied adaptive evolution using phenol as a sole carbon source and characterized a phenol-adapted R. opacus strain (evol40) and the wild-type (WT) strain by whole genome and RNA sequencing. While this effort increased our understanding of the aromatic tolerance, the tolerance mechanisms were not completely elucidated.

Results

We hypothesize that the composition of lipids plays an important role in phenol tolerance. To test this hypothesis, we applied high-resolution mass spectrometry analysis to lipid samples obtained from the WT and evol40 strains grown in 1 g/L glucose (glucose), 0.75 g/L phenol (low phenol), or 1.5 g/L phenol (high phenol, evol40 only) as a sole carbon source. This analysis identified?>?100 lipid species of mycolic acids, phosphatidylethanolamines (PEs), phosphatidylinositols (PIs), and triacylglycerols. In both strains, mycolic acids had fewer double bond numbers in phenol conditions than the glucose condition, and evol40 had significantly shorter mycolic acid chain lengths than the WT strain in phenol conditions. These results indicate that phenol adaptation affected mycolic acid membrane composition. In addition, the percentage of unsaturated phospholipids decreased for both strains in phenol conditions compared to the glucose condition. Moreover, the PI content increased for both strains in the low phenol condition compared to the glucose condition, and the PI content increased further for evol40 in the high phenol condition relative to the low phenol condition.

Conclusions

This work represents the first comprehensive lipidomic study on the membrane of R. opacus grown using phenol as a sole carbon source. Our results suggest that the alteration of the mycolic acid and phospholipid membrane composition may be a strategy of R. opacus for phenol tolerance.

     

Subtle variation in size and shape of the whole forewing and the red band among co‐mimics revealed by geometric morphometric analysis in Heliconius butterflies

Heliconius are unpalatable butterflies that exhibit remarkable intra‐ and interspecific variation in wing color pattern, specifically warning coloration. Species that have converged on the same pattern are often clustered in Müllerian mimicry rings. Overall, wing color patterns are nearly identical among co‐mimics. However, fine‐scale differences exist, indicating that factors in addition to natural selection may underlie wing phenotype. Here, we investigate differences in shape and size of the forewing and the red band in the Heliconius postman mimicry ring (H. erato phyllis and the co‐mimics H. besckei, H. melpomene burchelli, and H. melpomene nanna) using a landmark‐based approach. If phenotypic evolution is driven entirely by predation pressure, we expect nonsignificant differences among co‐mimics in terms of wing shape. Also, a reinforcement of wing pattern (i.e., greater similarity) could occur when co‐mimics are in sympatry. We also examined variation in the red forewing band because this trait is critical for both mimicry and sexual communication. Morphometric results revealed significant but small differences among species, particularly in the shape of the forewing of co‐mimics. Although we did not observe greater similarity when co‐mimics were in sympatry, nearly identical patterns provided evidence of convergence for mimicry. In contrast, mimetic pairs could be distinguished based on the shape (but not the size) of the red band, suggesting an “advergence” process. In addition, sexual dimorphism in the red band shape (but not size) was found for all lineages. Thus, we infer that natural selection due to predation by birds might not be the only mechanism responsible for variation in color patterns, and sexual selection could be an important driver of wing phenotypic evolution in this mimicry ring.     

Testing the AC/DC hypothesis: Rock and roll is noise pollution and weakens a trophic cascade

Anthropogenic sound is increasingly considered a major environmental issue, but its effects are relatively unstudied. Organisms may be directly affected by anthropogenic sound in many ways, including interference with their ability to detect mates, predators, or food, and disturbances that directly affect one organism may in turn have indirect effects on others. Thus, to fully appreciate the net effect of anthropogenic sound, it may be important to consider both direct and indirect effects. We report here on a series of experiments to test the hypothesis that anthropogenic sound can generate cascading indirect effects within a community. We used a study system of lady beetles, soybean aphids, and soybean plants, which are a useful model for studying the direct and indirect effects of global change on food webs. For sound treatments, we used several types of music, as well as a mix of urban sounds (e.g., sirens, vehicles, and construction equipment), each at volumes comparable to a busy city street or farm tractor. In 18‐hr feeding trials, rock music and urban sounds caused lady beetles to consume fewer aphids, but other types of music had no effect even at the same volume. We then tested the effect of rock music on the strength of trophic cascades in a 2‐week experiment in plant growth chambers. When exposed to music by AC/DC, who articulated the null hypothesis that “rock and roll ain't noise pollution” in a song of the same name, lady beetles were less effective predators, resulting in higher aphid density and reduced final plant biomass relative to control (no music) treatments. While it is unclear what characteristics of sound generate these effects, our results reject the AC/DC hypothesis and demonstrate that altered interspecific interactions can transmit the indirect effects of anthropogenic noise through a community.     

Sulfur bacteria in sediments of two coastal ecosystems: the Bassin d'Arcachon and the Etang du Prévost, France

Enumeration of the functional groups of sulfur bacteria was performed in the sediments in the Bassin d'Arcachon, a mesotidal lagoon with strong tidal currents and dominant populations of seagrass (Zostera noltii), and in the Etang du Prévost, a shallow lagoon with moderate tidal fluctuations and dominant populations of floating seaweed (Ulva sp.). In addition, data were collected on the distribution of oxygen and sulfide at the water-sediment interface during diel cycles. Bacterial enumeration studies revealed highest numbers in the top two cm of the sediments for three functional groups of sulfur bacteria, these being the sulfate-reducing bacteria (SRB), the colorless sulfur bacteria (CSB), and the phototrophic sulfur bacteria (PSB). In both systems high numbers of SRB were encountered, suggesting ample availability of organic matter. A comparison between different sites in each ecosystem showed that sediments overlain by more stagnant water were dominated by PSB, whereas those overlain by more oxygenated water were dominated by CSB. Important factors are the physical forces induced by tidal currents and the degree of daily exchange of water between the lagoons and the sea. These factors may explain the differences observed between the two systems with regard to the development of anoxic conditions, more so than the level of eutrophication. It appears that rooted plants play an important role in the introduction of oxygen into the sediments, thus enhancing the competitive position of CSB compared to PSB. Mini-electrodes studies revealed high concentrations of free sulfide at the inner site of the Etang du Prévost but very low concentrations at the inner station of the Bassin d'Arcachon, which may be explained by the high iron input of the latter, rather than by differences in the rate of sulfide production.     

p-Chlorophenylalanine Changes Serotonin Transporter mRNA Levels and Expression of the Gene Product

Abstract: After a single intraperitoneal injection of the irreversible tryptophan hydroxylase inhibitor p -chlorophenylalanine (PCPA; 300 mg/kg), there was a rapid down-regulation of serotonin (5-HT) transporter mRNA levels in cell bodies. This change was significant at 1 and 2 days after PCPA administration within the ventromedial but not the dorsomedial portion of the dorsal raphe nucleus. Seven days after PCPA treatment, 5-HT transporter mRNA levels were significantly elevated compared with controls in both regions of the dorsal raphe nucleus. PCPA administration produced no change in the [³H]-citalopram binding and synaptosomal [³H]5-HT uptake in terminal regions at 2 and 7 days after treatment but significantly reduced both these parameters by ∼20% in the hippocampus and in cerebral cortex 14 days after PCPA administration. The striatum showed a lower sensitivity to this effect. No significant changes were observed in the levels of [³H]citalopram binding to 5-HT cell bodies in the dorsal raphe nucleus. In the same animals used for 5-HT transporter mRNA level measurements, levels of tryptophan hydroxylase mRNA in neurons of the ventromedial and dorsomedial portions of the dorsal raphe nucleus were increased 2 days after PCPA administration and fell to control levels 7 days after injection in the ventromedial region but not in the dorsomedial portion of the dorsal raphe nucleus, where they remained significantly higher than controls. Altogether, these results show that changes in 5-HT transporter mRNA are not temporally related to changes in 5-HT transporter protein levels. In addition, our results suggest that the 5-HT transporter and tryptophan hydroxylase genes are regulated by different mechanisms. We also provide further evidence that dorsal raphe 5-HT neurons are differentially regulated by drugs, depending on their location.     

DIDS increases K+ secretion through an I sKchannel in apical membrane of vestibular dark cell epithelium of gerbil

Vestibular dark cell epithelium secretes K⁺ via I _sKchannels in the apical membrane. The previous observation that disulfonic stilbenes increased the equivalent short circuit current (I _sc) suggested that these agents might be useful investigative tools in this tissue. The present experiments were conducted to determine if the increase in I _scwas associated with an increase in K⁺ flux and if the effect was directly on the I _sKchannel or indirectly via a cytosolic intermediary. Measurements of transepithelial K⁺ flux with the K⁺-selective vibrating probe and of changes in net cellular solute flux by measurements of epithelial cell height showed that 4,4-diisothiocyanatostilbene-2,2-disulfonic acid (DIDS) increased K⁺ flux by a factor of 1.96±0.71 and caused net solute efflux. The apical membrane was partitioned with a macropatch pipette and DIDS was applied either to the membrane outside the pipette, inside the pipette or to the entire apical membrane. DIDS inside the pipette increased the current across the patch, the membrane conductance, the slowly-inactivating (I _sK) component of the membrane current and shifted the reversal voltage toward the equilibrium potential for K⁺. DIDS outside the patch decreased the patch current and conductance, consistent with shunting of current away from the membrane patch. These findings strongly support the notion that DIDS increases K⁺ secretion through I _sKchannels in the apical membrane of vestibular dark cell epithelium by acting directly on the channels or on a tightly colocalized membrane component.We thank Dr. Peter J.S. Smith and Alan Shipley of the National Vibrating Probe Facility at the Marine Biological Laboratory at Woods Hole, MA for their support and assistance in the measurements of K⁺ flux. This work was supported by National Institutes of Health grants R01-DC00212, R29-DC1098 and P41-RR01395.     

Notes on the geographic distribution of howling monkeys in the marajó archipelago, pará, Brazil

I review the distribution of genus Alouattain the Marajó Archipelago based on geographic variation of pelage color patterns. Specific differences exist among the labeled specimens at Museu Paraense Emílio Goeldi, which are confirmed via new field information from wild populations. The animals from Marajó, Caviana, and Mexiana Islands possess color patterns of Alouatta belzebul,while Alouatta seniculusis confirmed as the species that inhabits Gurupá Island. The high variability of pelage coloration of the animals from Marajó, Caviana, and Mexiana Islands includes all phenotypes formerly designated as different subspecies. The howler populations from these three islands belong to the same subspecies as those populations that inhabit the region of Tucurui dam reservoir (area 4). Finally, it seems that, as also suggested by chromosome studies, A. belzebulprobably comprises different epiphenotypes without taxonomic validity.     

The effects of pond duration on the life history traits of an ephemeral pond crustacean,Eulimnadia texana

We examined the relationship between pond duration and life history characters of the clam shrimp Eulimnadia texana, a species inhabiting ephemeral ponds in southwestern North America. Since the shrimp live in temporary habitats, we predicted that there should be high selection pressure on life history characteristics associated with rapid development (e.g., fast growth, early maturity, etc.), rather than selection for increased longevity. Pond duration was estimated using a combination of average monthly rainfall and pond size (surface to volume ratio). Shrimp that live in smaller ponds (high surface to volume ratio)in areas with low average rainfall should, on average, experience a shorter total time available for development than those in larger ponds or in areas of higher rainfall. These shrimp should have an earlier age at maturity, reduced longevity, lower fecundity, and faster growth. Five replicate populations of clam shrimp were collected as cysts from five ponds. These shrimp were raised in a common garden experiment in the laboratory. Daily measurements of growth and egg production were taken and ages at maturity and death were recorded. Shrimp from areas with higher average rainfall had slower growth, higher fecundity, greater longevity, and an earlier age at maturity than those from areas with lower average rainfall. If average rainfall is an accurate measure of pond duration, then the first three of these life history traits differ in the directions expected. However, age at maturity varied in a manner opposite to that expected, being earlier in the ponds with longer duration. Surface to volume ratio was not helpful in further resolving differences in these life history characters. This revised version was published online in August 2006 with corrections to the Cover Date.