Lysine 27 dimethylation of Drosophila linker histone dH1 contributes to heterochromatin organization independently of H3K9 methylation

Post-translational modifications (PTMs) of core histones are important epigenetic determinants that correlate with functional chromatin states. However, despite multiple linker histone H1s PTMs have been identified, little is known about their genomic distribution and contribution to the epigenetic regulation of chromatin. Here, we address this question in Drosophila that encodes a single somatic linker histone, dH1. We previously reported that dH1 is dimethylated at K27 (dH1K27me2). Here, we show that dH1K27me2 is a major PTM of Drosophila heterochromatin. At mitosis, dH1K27me2 accumulates at pericentromeric heterochromatin, while, in interphase, it is also detected at intercalary heterochromatin. ChIPseq experiments show that >98% of dH1K27me2 enriched regions map to heterochromatic repetitive DNA elements, including transposable elements, simple DNA repeats and satellite DNAs. Moreover, expression of a mutated dH1K27A form, which impairs dH1K27me2, alters heterochromatin organization, upregulates expression of heterochromatic transposable elements and results in the accumulation of RNA:DNA hybrids (R-loops) in heterochromatin, without affecting H3K9 methylation and HP1a binding. The pattern of dH1K27me2 is H3K9 methylation independent, as it is equally detected in flies carrying a H3K9R mutation, and is not affected by depletion of Su(var)3–9, HP1a or Su(var)4–20. Altogether these results suggest that dH1K27me2 contributes to heterochromatin organization independently of H3K9 methylation.     

Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function

The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5′ leader Ψ elements plus poorly defined additional features. We previously defined minimal 5′ leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5′ leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5′ leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination.     

Testing the Generality of a Trophic-cascade Model for Plague

Climate may affect the dynamics of infectious diseases by shifting pathogen, vector, or host species abundance, population dynamics, or community interactions. Black-tailed prairie dogs (Cynomys ludovicianus) are highly susceptible to plague, yet little is known about factors that influence the dynamics of plague epizootics in prairie dogs. We investigated temporal patterns of plague occurrence in black-tailed prairie dogs to assess the generality of links between climate and plague occurrence found in previous analyses of human plague cases. We examined long-term data on climate and plague occurrence in prairie dog colonies within two study areas. Multiple regression analyses revealed that plague occurrence in prairie dogs was not associated with climatic variables in our Colorado study area. In contrast, plague occurrence was strongly associated with climatic variables in our Montana study area. The models with most support included a positive association with precipitation in April–July of the previous year, in addition to a positive association with the number of “warm” days and a negative association with the number of “hot” days in the same year as reported plague events. We conclude that the timing and magnitude of precipitation and temperature may affect plague occurrence in some geographic areas. The best climatic predictors of plague occurrence in prairie dogs within our Montana study area are quite similar to the best climatic predictors of human plague cases in the southwestern United States. This correspondence across regions and species suggests support for a (temperature-modulated) trophic-cascade model for plague, including climatic effects on rodent abundance, flea abundance, and pathogen transmission, at least in regions that experience strong climatic signals.     

Alzheimer's disease and Down's syndrome: Sharing of a unique cerebrovascular amyloid fibril protein

The cerebrovascular amyloid protein from a case of adult Down's syndrome was isolated and purified. Amino acid sequence analysis showed it to be homologous to that of the β protein of Alzheimer's disease. This is the first chemical evidence of a relationship between Down's syndrome and Alzheimer's disease. It suggests that Down's syndrome may be a predictable model for Alzheimer's disease. Assuming the β protein is a human gene product, it also suggests that the genetic defect in Alzheimer's disease is localized on chromosome 21.     

Within-Crop Air Temperature and Humidity Outcomes on Spatio-Temporal Distribution of the Key Rose Pest Frankliniella occidentalis

Frankliniella occidentalis (Pergande) is a key pest of various crops worldwide. In this study, we analyse the dependence of the infestation of this pest on spatially distributed micro climatic factors in a rose greenhouse. Despite the importance of this subject, the few existing studies have been realized in laboratory rather than in greenhouse conditions. However, recent progress on greenhouse microclimate characterisation has highlighted the strong indoor climate heterogeneity that may influence the within-crop pest distribution. In this study, both microclimate (air temperature and humidity) and thrips distribution were simultaneously mapped in a rose greenhouse. The measurements were sensed in a horizontal plane situated at mid-height of the rose crop inside the greenhouse. Simultaneously, thrips population dynamics were assessed after an artificial and homogeneous infestation of the rose crop. The spatio-temporal distribution of climate and thrips within the greenhouse were compared, and links between thrips infestation and climatic conditions were investigated. A statistical model was used to define the favourable climate conditions for thrips adults and larvae. Our results showed that (i) the air temperature and air humidity were very heterogeneously distributed within the crop, (ii) pest populations aggregated in the most favourable climatic areas and (iii) the highest population density of thrips adults and larvae were recorded at 27°C and 22°C for temperature and 63% and 86% for humidity, respectively. These findings confirm, in real rose cropping conditions, previous laboratory studies on the F. occidentalis climatic optimum and provide a solid scientific support for climatic-based control methods against this pest.     

Impacts of predator-mediated interactions along a climatic gradient on the population dynamics of an alpine bird

According to classic theory, species'' population dynamics and distributions are less influenced by species interactions under harsh climatic conditions compared to under more benign climatic conditions. In alpine and boreal ecosystems in Fennoscandia, the cyclic dynamics of rodents strongly affect many other species, including ground-nesting birds such as ptarmigan. According to the ‘alternative prey hypothesis’ (APH), the densities of ground-nesting birds and rodents are positively associated due to predator–prey dynamics and prey-switching. However, it remains unclear how the strength of these predator-mediated interactions change along a climatic harshness gradient in comparison with the effects of climatic variation. We built a hierarchical Bayesian model to estimate the sensitivity of ptarmigan populations to interannual variation in climate and rodent occurrence across Norway during 2007–2017. Ptarmigan abundance was positively linked with rodent occurrence, consistent with the APH. Moreover, we found that the link between ptarmigan abundance and rodent dynamics was strongest in colder regions. Our study highlights how species interactions play an important role in population dynamics of species at high latitudes and suggests that they can become even more important in the most climatically harsh regions.     

Seasonal climatic niche and migration movements of Double‐crested Cormorants

Avian migrants are challenged by seasonal adverse climatic conditions and energetic costs of long‐distance flying. Migratory birds may track or switch seasonal climatic niche between the breeding and non‐breeding grounds. Satellite tracking enables avian ecologists to investigate seasonal climatic niche and circannual movement patterns of migratory birds. The Double‐crested Cormorant (Nannopterum auritum, hereafter cormorant) wintering in the Gulf of Mexico (GOM) migrates to the Northern Great Plains and Great Lakes and is of economic importance because of its impacts on aquaculture. We tested the climatic niche switching hypothesis that cormorants would switch climatic niche between summer and winter because of substantial differences in climate between the non‐breeding grounds in the subtropical region and breeding grounds in the northern temperate region. The ordination analysis of climatic niche overlap indicated that cormorants had separate seasonal climatic niche consisting of seasonal mean monthly minimum and maximum temperature, seasonal mean monthly precipitation, and seasonal mean wind speed. Despite non‐overlapping summer and winter climatic niches, cormorants appeared to be subjected to similar wind speed between winter and summer habitats and were consistent with similar hourly flying speed between winter and summer. Therefore, substantial differences in temperature and precipitation may lead to the climatic niche switching of fish‐eating cormorants, a dietary specialist, between the breeding and non‐breeding grounds.     

The interactions between nucleic acids and polyamines: I. High resolution carbon-13 and hydrogen-1 nuclear magnetic resonance studies of spermidine and 5'-AMP

In 0.5 M solution at pH 7.6, interaction of spermidine and 5'-AMP is demonstrated by downfield proton NMR shifts. Shifts of ribose and adenine protons support a model in which triprotonated spermidine engages the phosphate, anion with the C-3 diamine segment in a conformation to maximize interaction and the C-4 ammo segment extended to interact with adenine N-7 (base anti, 2'endo, g'g' and gg nucleoside conformation). Changes in carbon-13 chemical shifts for ribose C-5' (downfield), C-2' C-3', and C-4' (upfield) and for adenine C-6 and C-8 (upfield) support this model. In 0.006 M solution no significant changes in proton shifts and therefore no evidence for interaction was found. Spermidine and 5'-UMP (0.006 M) showed interaction at pH 10.5 (small upfield shifts in the proton nmr) interpreted as changing conformation by solvent interaction. In 0.006 M 3'-UMP at pH 10.5 small downfield proton shifts induced by spennidine are attributed to interactions with phosphate anion.     

Respiration Rate of Steinernema feltiae Infective Juveniles at Several Constant Temperatures

Respiration was measured in dauer stages of the insect-parasitic nematode Steinernema feltiae (= Neoaplectana carpocapsae) at 7, 17, and 27 C. Respiration, Q₁₀, and nematode viability were temperature dependent. Mean O₂ consumption for 5 × 10⁵ nematodes the first 24 hours was 0.27 ml at 7 C, 0.83 ml at 17 C, and 2.68 ml at 27 C. The Q₁₀ was 3.10 for 7-17 C and 3.24 for 17-27 C. Some nematodes died during 2, 14, and 21 days at 27, 17, and 7 C, respectively. The respiratory quotient was below 1 at all temperatures tested. A standard asymptotic model is expressed as oxygen consumed = 2.77 * {1 - exponent[-time * exponent(-B + C * temperature)]}; where 2.77 is the maximum response at 27 C. This model estimates nematode O₂ consumption and viability at storage temperatures between 7 and 27 C. The nematodes died when the O₂ concentration reached 0.5 ml/5 × 10⁵ nematodes. This model may be used to predict O₂ requirements of S. feltiae infective juveniles when stored as a waterless concentrate.     

Prophage lambda at unusual chromosomal locations: III. The components of the secondary attachment sites

The integration of phage λ occurs by a reciprocal genetic exchange, promoted by the product of phage int gene, at specific sites on the phage and bacterial genomes (att's). Lysogenic bacteria thus contain two att's which bracket the inserted prophage. Genetically, the phage, bacterial and prophage att's differ from each other, indicating that each site has specific elements which segregate during recombination.In hosts that lack the bacterial att, phage integration occurs at about 0.5% the normal frequency. It results from Int-promoted recombination between the phage att and any one of many secondary sites in the bacterial genome. To analyze these sites, we measured Int-promoted recombination at the secondary prophage att's. We found that they differed from the normal prophage att's and from the phage att. The secondary sites, therefore, do not appear to carry any of the specific elements of the phage or bacterial att's.The transducing phage isolated from secondary site lysogens integrate at two loci. In the absence of helper, they insert via homology with the bacterial DNA. Co-infection with helper results in their integration at the normal bacterial att.     

Climate-Based Models for Pulsed Resources Improve Predictability of Consumer Population Dynamics: Outbreaks of House Mice in Forest Ecosystems

Accurate predictions of the timing and magnitude of consumer responses to episodic seeding events (masts) are important for understanding ecosystem dynamics and for managing outbreaks of invasive species generated by masts. While models relating consumer populations to resource fluctuations have been developed successfully for a range of natural and modified ecosystems, a critical gap that needs addressing is better prediction of resource pulses. A recent model used change in summer temperature from one year to the next (ΔT) for predicting masts for forest and grassland plants in New Zealand. We extend this climate-based method in the framework of a model for consumer–resource dynamics to predict invasive house mouse (Mus musculus) outbreaks in forest ecosystems. Compared with previous mast models based on absolute temperature, the ΔT method for predicting masts resulted in an improved model for mouse population dynamics. There was also a threshold effect of ΔT on the likelihood of an outbreak occurring. The improved climate-based method for predicting resource pulses and consumer responses provides a straightforward rule of thumb for determining, with one year’s advance warning, whether management intervention might be required in invaded ecosystems. The approach could be applied to consumer–resource systems worldwide where climatic variables are used to model the size and duration of resource pulses, and may have particular relevance for ecosystems where global change scenarios predict increased variability in climatic events.     

Thermal Tolerance of the Coffee Berry Borer Hypothenemus hampei: Predictions of Climate Change Impact on a Tropical Insect Pest

Coffee is predicted to be severely affected by climate change. We determined the thermal tolerance of the coffee berry borer , Hypothenemus hampei, the most devastating pest of coffee worldwide, and make inferences on the possible effects of climate change using climatic data from Colombia, Kenya, Tanzania, and Ethiopia. For this, the effect of eight temperature regimes (15, 20, 23, 25, 27, 30, 33 and 35°C) on the bionomics of H. hampei was studied. Successful egg to adult development occurred between 20–30°C. Using linear regression and a modified Logan model, the lower and upper thresholds for development were estimated at 14.9 and 32°C, respectively. In Kenya and Colombia, the number of pest generations per year was considerably and positively correlated with the warming tolerance. Analysing 32 years of climatic data from Jimma (Ethiopia) revealed that before 1984 it was too cold for H. hampei to complete even one generation per year, but thereafter, because of rising temperatures in the area, 1–2 generations per year/coffee season could be completed. Calculated data on warming tolerance and thermal safety margins of H. hampei for the three East African locations showed considerably high variability compared to the Colombian site. The model indicates that for every 1°C rise in thermal optimum (T_opt.), the maximum intrinsic rate of increase (r _max) will increase by an average of 8.5%. The effects of climate change on the further range of H. hampei distribution and possible adaption strategies are discussed. Abstracts in Spanish and French are provided as supplementary material Abstract S1 and Abstract S2.     

Climate influences on female survival in a declining population of southern elephant seals (Mirounga leonina)

The Southern Ocean has been disproportionately affected by climate change and is therefore an ideal place to study the influence of changing environmental conditions on ecosystems. Changes in the demography of predator populations are indicators of broader shifts in food web structure, but long‐term data are required to study these effects. Southern elephant seals (Mirounga leonina) from Macquarie Island have consistently decreased in population size while all other major populations across the Southern Ocean have recently stabilized or are increasing. Two long‐term mark‐recapture studies (1956–1967 and 1993–2009) have monitored this population, which provides an opportunity to investigate demographic performance over a range of climatic conditions. Using a 9‐state matrix population model, we estimated climate influences on female survival by incorporating two major climatic indices into our model: The Southern Annular Mode (SAM) and the Southern Oscillation Index (SOI). Our best model included a 1 year lagged effect of SAM and an unlagged SOI as covariates. A positive relationship with SAM1 (lagged) related the previous year''s SAM with juvenile survival, potentially due to changes in local prey availability surrounding Macquarie Island. The unlagged SOI had a negative effect on both juvenile and adult seals, indicating that sea ice dynamics and access to foraging grounds on the East Antarctic continental shelf could explain the different contributions of ENSO events on the survival of females in this population.     

Climatic factors influencing triatomine occurrence in Central-West Brazil

We estimated the geographic distributions of triatomine species in Central-West Region of Brazil (CW) and analysed the climatic factors influencing their occurrence. A total of 3,396 records of 27 triatomine species were analysed. Using the maximum entropy method, ecological niche models were produced for eight species occurring in at least 20 municipalities based on 13 climatic variables and elevation. Triatoma sordida and Rhodnius neglectus were the species with the broadest geographic distributions in CW Brazil. The Cerrado areas in the state of Goiás were found to be more suitable for the occurrence of synanthropic triatomines than the Amazon forest areas in the northern part of the state of Mato Grosso. The variable that best explains the evaluated models is temperature seasonality. The results indicate that almost the entire region presents climatic conditions that are appropriate for at least one triatomine species. Therefore, it is recommended that entomological surveillance be reinforced in CW Brazil.     

Altitude‐mediated soil properties,not geography or climatic distance,explain the distribution of a tropical endemic herb

Understanding the ecological processes that govern species'' range margins is a fundamental question in ecology with practical implications in conservation biology. The center‐periphery hypothesis predicts that organisms have higher abundance at the center of their geographic range. However, most tests of this hypothesis often used raster data, assuming that climatic conditions are consistent across one square km. This assumption is not always justified, particularly for mountainous species for which climatic conditions can vary widely across a small spatial scale. Previous studies rarely evenly sample occurrence data across the species'' distribution. In this study, we sampled an endemic perennial herb, Thunbergia atacorensis (Acanthanceae), throughout its range in West Africa using 54 plots and collected data on (a)biotic variables, the species density, leaf mass per area, and basal diameter. We built a structural equation model to test the direct and indirect effects of distance from geographic and climatic niche centers, and altitude on Thunbergia density as mediated by abiotic and biotic factors, population demographic structure, and individual size. Contrary to the prediction of the center‐periphery hypothesis, we found no significant effect of distance from geographic or climatic niche centers on plant density. This indicates that even the climatic center does not necessarily have optimal ecological conditions. In contrast, plant density varied with altitudinal gradient, but this was mediated by the effect of soil nitrogen and potassium which had positive effect on plant size. Surprisingly, we found no direct or mediating effect of interspecific competition on plant density. Altogether, our results highlight the role of geography, climatic, and ecological mismatch in predicting species distribution. Our study highlights that where altitudinal gradient is strong local‐scale heterogeneity in abiotic factors can play important role in shaping species range limits.     

Biotic and Climatic Velocity Identify Contrasting Areas of Vulnerability to Climate Change

Metrics that synthesize the complex effects of climate change are essential tools for mapping future threats to biodiversity and predicting which species are likely to adapt in place to new climatic conditions, disperse and establish in areas with newly suitable climate, or face the prospect of extirpation. The most commonly used of such metrics is the velocity of climate change, which estimates the speed at which species must migrate over the earth’s surface to maintain constant climatic conditions. However, “analog-based” velocities, which represent the actual distance to where analogous climates will be found in the future, may provide contrasting results to the more common form of velocity based on local climate gradients. Additionally, whereas climatic velocity reflects the exposure of organisms to climate change, resultant biotic effects are dependent on the sensitivity of individual species as reflected in part by their climatic niche width. This has motivated development of biotic velocity, a metric which uses data on projected species range shifts to estimate the velocity at which species must move to track their climatic niche. We calculated climatic and biotic velocity for the Western Hemisphere for 1961–2100, and applied the results to example ecological and conservation planning questions, to demonstrate the potential of such analog-based metrics to provide information on broad-scale patterns of exposure and sensitivity. Geographic patterns of biotic velocity for 2954 species of birds, mammals, and amphibians differed from climatic velocity in north temperate and boreal regions. However, both biotic and climatic velocities were greatest at low latitudes, implying that threats to equatorial species arise from both the future magnitude of climatic velocities and the narrow climatic tolerances of species in these regions, which currently experience low seasonal and interannual climatic variability. Biotic and climatic velocity, by approximating lower and upper bounds on migration rates, can inform conservation of species and locally-adapted populations, respectively, and in combination with backward velocity, a function of distance to a source of colonizers adapted to a site’s future climate, can facilitate conservation of diversity at multiple scales in the face of climate change.     

How does the reliability of a model affect children's choice to learn socially or individually?

The effect of model reliability on children's choices to learn socially versus individually is pertinent to theories addressing cultural evolution and theories of selective trust. Here the effect of a reliable versus unreliable model on children's preferences to learn socially or individually was examined, as well as their subsequent imitation on a puzzle box task. Experiment One (N = 156) found children were more likely to ask to learn socially when presented with a novel task, after witnessing an unreliable rather than a reliable model. Experiment Two (N = 40) found children select a new unknown model, over the previously unreliable model, suggesting a preference to learn socially was created, although not specifically from the unreliable model. Experiment Three (N = 48) replicated children's learning preference in Experiment One with a new task, and showed children's attention is drawn towards other sources of social information (another adult model) when viewing an unreliable model, and also found a reliable model caused more fidelity of imitation. Together these results suggest that model unreliability causes greater social learning requests and attention to other, even novel, models when they are available. These findings evidence human children's strong propensity to learn socially compared with non-human animals; and suggest there is a more complicated relationship between learning preference, model reliability and selective trust than has been captured in previous research.     

Does climatic warming increase the risk of frost damage in northern trees?

Abstract. The effect of climatic warming on the timing of bud burst and the subsequent risk of frost damage on trees in central Finland was assessed with the aid of a computer model, 73 years of temperature data and a climatic scenario corresponding to doubled level of atmospheric CO₂. In general, climatic warming hastened bud burst, due to ontogenetic development during warm spells in autumn, winter and spring. During the years with the warmest winters in the scenario conditions: (a) bud burst took place during mid-winter; and (2) depending on the year, the trees were subsequently exposed to temperatures between −27 and −10°C. This finding suggests that the risk of frost damage to trees will be increased if the predicted climatic warming occurs. Because of the assumptions used in the model, the results are not conclusive, but they do point out the importance of further experimental studies on genetic and environmental regulation of timing of bud burst in trees.