An evolutionary epigenetic clock in plants.

Molecular clocks are the basis for dating the divergence between lineages over macroevolutionary timescales (~105 to 108 years). However, classical DNA-based clocks tick too slowly to inform us about the recent past. Here, we demonstrate that stochastic DNA methylation changes at a subset of cytosines in plant genomes display a clocklike behavior. This "epimutation clock" is orders of magnitude faster than DNA-based clocks and enables phylogenetic explorations on a scale of years to centuries. We show experimentally that epimutation clocks recapitulate known topologies and branching times of intraspecies phylogenetic trees in the self-fertilizing plant Arabidopsis thaliana and the clonal seagrass Zostera marina, which represent two major modes of plant reproduction. This discovery will open new possibilities for high-resolution temporal studies of plant biodiversity.

Deep-sea predator niche segregation revealed by combined cetacean biologging and eDNA analysis of cephalopod prey.

Fundamental insight on predator-prey dynamics in the deep sea is hampered by a lack of combined data on hunting behavior and prey spectra. Deep-sea niche segregation may evolve when predators target specific prey communities, but this hypothesis remains untested. We combined environmental DNA (eDNA) metabarcoding with biologging to assess cephalopod community composition in the deep-sea foraging habitat of two top predator cetaceans. Risso's dolphin and Cuvier's beaked whale selectively targeted distinct epi/meso- and bathypelagic foraging zones, holding eDNA of 39 cephalopod taxa, including 22 known prey. Contrary to expectation, extensive taxonomic overlap in prey spectra between foraging zones indicated that predator niche segregation was not driven by prey community composition alone. Instead, intraspecific prey spectrum differences may drive differentiation for hunting fewer, more calorific, mature cephalopods in deeper waters. The novel combination of methods presented here holds great promise to disclose elusive deep-sea predator-prey systems, aiding in their protection.

Differential gene expression patterns related to lipid metabolism in response to ocean acidification in larvae and juveniles of Atlantic cod.

Elevated environmental carbon dioxide (pCO2) levels have been found to cause organ damage in the early life stages of different commercial fish species, including Atlantic cod (Gadus morhua). To illuminate the underlying mechanisms causing pathologies in the intestines, the kidney, the pancreas and the liver in response to elevated pCO2, we examined related gene expression patterns in Atlantic cod reared for two months under three different pCO2 regimes: 380 µatm (control), 1800 µatm (medium) and 4200 µatm (high). We extracted RNA from whole fish sampled during the larval (32 dph) and early juvenile stage (46 dph) for relative expression analysis of 18 different genes related to essential metabolic pathways. At 32 dph, larvae subjected to the medium treatment displayed an up-regulation of genes mainly associated with fatty acid and glycogen synthesis (GYS2, 6PGL, ACoA, CPTA1, FAS and PPAR1b). Larvae exposed to the high pCO2 treatment upregulated fewer but similar genes (6PGL, ACoA and PPAR1b,). These data suggest stress-induced alterations in the lipid and fatty acid metabolism and a disrupted lipid homeostasis in larvae, providing a mechanistic link to the findings of lipid droplet overload in the liver and organ pathologies. At 46 dph, no significant differences in gene expression were detected, confirming a higher resilience of juveniles in comparison to larvae when exposed to elevated pCO2 up to 4200 µatm.

Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae.

Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a "stealth stress" for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.

Effects of parental acclimation and energy limitation in response to high CO2 exposure in Atlantic cod.

Ocean acidification (OA), the dissolution of excess anthropogenic carbon dioxide in ocean waters, is a potential stressor to many marine fish species. Whether species have the potential to acclimate and adapt to changes in the seawater carbonate chemistry is still largely unanswered. Simulation experiments across several generations are challenging for large commercially exploited species because of their long generation times. For Atlantic cod (Gadus morhua), we present first data on the effects of parental acclimation to elevated aquatic CO2 on larval survival, a fundamental parameter determining population recruitment. The parental generation in this study was exposed to either ambient or elevated aquatic CO2 levels simulating end-of-century OA levels (~1100 µatm CO2) for six weeks prior to spawning. Upon fully reciprocal exposure of the F1 generation, we quantified larval survival, combined with two larval feeding regimes in order to investigate the potential effect of energy limitation. We found a significant reduction in larval survival at elevated CO2 that was partly compensated by parental acclimation to the same CO2 exposure. Such compensation was only observed in the treatment with high food availability. This complex 3-way interaction indicates that surplus metabolic resources need to be available to allow a transgenerational alleviation response to ocean acidification.

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.

Populations distributed across a broad thermal cline are instrumental in addressing adaptation to increasing temperatures under global warming. Using a space-for-time substitution design, we tested for parallel adaptation to warm temperatures along two independent thermal clines in Zostera marina, the most widely distributed seagrass in the temperate Northern Hemisphere. A North-South pair of populations was sampled along the European and North American coasts and exposed to a simulated heatwave in a common-garden mesocosm. Transcriptomic responses under control, heat stress and recovery were recorded in 99 RNAseq libraries with ~13 000 uniquely annotated, expressed genes. We corrected for phylogenetic differentiation among populations to discriminate neutral from adaptive differentiation. The two southern populations recovered faster from heat stress and showed parallel transcriptomic differentiation, as compared with northern populations. Among 2389 differentially expressed genes, 21 exceeded neutral expectations and were likely involved in parallel adaptation to warm temperatures. However, the strongest differentiation following phylogenetic correction was between the three Atlantic populations and the Mediterranean population with 128 of 4711 differentially expressed genes exceeding neutral expectations. Although adaptation to warm temperatures is expected to reduce sensitivity to heatwaves, the continued resistance of seagrass to further anthropogenic stresses may be impaired by heat-induced downregulation of genes related to photosynthesis, pathogen defence and stress tolerance.

Reaction paths of phosphine dissociation on silicon (001).

Using density functional theory and guided by extensive scanning tunneling microscopy (STM) image data, we formulate a detailed mechanism for the dissociation of phosphine (PH3) molecules on the Si(001) surface at room temperature. We distinguish between a main sequence of dissociation that involves PH2+H, PH+2H, and P+3H as observable intermediates, and a secondary sequence that gives rise to PH+H, P+2H, and isolated phosphorus adatoms. The latter sequence arises because PH2 fragments are surprisingly mobile on Si(001) and can diffuse away from the third hydrogen atom that makes up the PH3 stoichiometry. Our calculated activation energies describe the competition between diffusion and dissociation pathways and hence provide a comprehensive model for the numerous adsorbate species observed in STM experiments.

Collective lipid bilayer dynamics excited by surface acoustic waves.

We use standing surface acoustic waves to induce coherent phonons in model lipid multilayers deposited on a piezoelectric surface. Probing the structure by phase-controlled stroboscopic x-ray pulses we find that the internal lipid bilayer electron density profile oscillates in response to the externally driven motion of the lipid film. The structural response to the well-controlled motion is a strong indication that bilayer structure and membrane fluctuations are intrinsically coupled, even though these structural changes are averaged out in equilibrium and time integrating measurements. Here the effects are revealed by a timing scheme with temporal resolution on the picosecond scale in combination with the sub-nm spatial resolution, enabled by high brilliance synchrotron x-ray reflectivity.

Single pulse coherence measurements in the water window at the free-electron laser FLASH.

The spatial coherence of free-electron laser radiation in the water window spectral range was studied, using the third harmonic (λ<(3rd) = 2.66 nm) of DESY's Free-electron LASer in Hamburg (FLASH). Coherent single pulse diffraction patterns of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) multilamellar lipid stacks have been recorded. The intensity histogram of the speckle pattern around the first lamellar Bragg peak, corresponding to the d = 5 nm periodicity of the stack, reveals an average number of transverse modes of M¯ = 3.0 of the 3rd harmonic. Using the lipid stack as a 'monochromator', pulse-to-pulse fluctuations in the third harmonic λ(3rd) have been determined to be 0.033 nm.

Structure and Volta potential of lipid multilayers: effect of X-ray irradiation.

The effect of hard X-ray radiation on the structure and electrostatics of solid-supported lipid multilayer membranes is investigated using a scanning Kelvin probe (SKP) integrated with a high-energy synchrotron beamline to enable in situ measurements of the membranes' local Volta potential (V(p)) during X-ray structural characterization. The undulator radiation employed does not induce any detectable structural damage, but the V(p) of both bare and lipid-modified substrates is found to undergo strong radiation-induced shifts, almost immediately after X-ray exposure. Sample regions that are macroscopically distant (~cm) from the irradiated region experience an exponential V(p) growth with a characteristic time constant of several minutes. The V(p) variations occurring upon periodic on/off X-ray beam switching are fully or partially reversible depending on the location and time-scale of the SKP measurement. The general relevance of these findings for synchrotron-based characterization of biomolecular thin films is critically reviewed.

Nonequilibrium collective dynamics in photoexcited lipid multilayers by time resolved diffuse x-ray scattering.

We study the nonequilibrium shape fluctuations in fluorescence labeled phospholipid multibilayers composed of the model lipid DOPC and the well-known lipid dye Texas red, driven out of equilibrium by short laser pulses. The temporal evolution of the lipid bilayer undulations after excitation was recorded by time resolved x-ray diffraction. Already at moderate peak intensities (Pp≤10(5) W/cm2), pulsed laser illumination leads to significant changes of the undulation modes in a well-defined lateral wavelength band. The observed phenomena evolve on nano- to microsecond time scales after optical excitation, and can be described in terms of a modulation instability in the lipid multilamellar stack.

Ohm's law survives to the atomic scale.

As silicon electronics approaches the atomic scale, interconnects and circuitry become comparable in size to the active device components. Maintaining low electrical resistivity at this scale is challenging because of the presence of confining surfaces and interfaces. We report on the fabrication of wires in silicon--only one atom tall and four atoms wide--with exceptionally low resistivity (~0.3 milliohm-centimeters) and the current-carrying capabilities of copper. By embedding phosphorus atoms within a silicon crystal with an average spacing of less than 1 nanometer, we achieved a diameter-independent resistivity, which demonstrates ohmic scaling to the atomic limit. Atomistic tight-binding calculations confirm the metallicity of these atomic-scale wires, which pave the way for single-atom device architectures for both classical and quantum information processing.

Bateman's principle and immunity in a sex-role reversed pipefish.

In diverse animal species, from insects to mammals, females display a more efficient immune defence than males. Bateman's principle posits that males maximize their fitness by increasing mating frequency whereas females gain fitness benefits by maximizing their lifespan. As a longer lifespan requires a more efficient immune system, these implications of Bateman's principle may explain widespread immune dimorphism among animals. Because in most extant animals, the provisioning of eggs and a higher parental investment are attributes of the female sex, sex-role reversed species provide a unique opportunity to assess whether or not immune dimorphism depends on life history and not on sex per se. In the broad-nosed pipefish Syngnathus typhle, males brood and nourish the eggs in a ventral pouch and thus invest more into reproduction than females. We found males to have a more active immune response both in field data from four populations and also in an experiment under controlled laboratory conditions. This applied to different measures of immunocompetence using innate as well as adaptive immune system traits. We further determined the specificity of immune response initiation after a fully factorial primary and secondary exposure to a common marine pathogen Vibrio spp. Males not only had a more active but also a more specific immune defence than females. Our results thus indeed suggest that the sex that invests more into the offspring has the stronger immune defence.

Influence of cholesterol on the collective dynamics of the phospholipid acyl chains in model membranes.

We have studied the packing and collective dynamics of the phospholipid acyl chains in a model membrane composed of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and cholesterol in varied phase state. After a structural characterization of this two-component model bilayer using X-ray reflectivity, we have carried out coherent inelastic neutron scattering to investigate the chain dynamics. Both DMPC/cholesterol membranes exhibited much sharper and more pronounced low-energy inelastic excitations than a pure DMPC membrane. In the high-energy regime above 10 meV, the insertion of cholesterol into the membrane was found to shift the position of the inelastic excitation towards values otherwise found in the pure lipids gel phase. Thus, the dissipative collective short-range dynamics of the acyl chains is strongly influenced by the presence of cholesterol.

Membrane fusion intermediates and the effect of cholesterol: an in-house X-ray scattering study.

We have developed an X-ray scattering setup which allows to study membrane fusion intermediates or other nonlamellar lipid mesophases by laboratory-scale X-ray sources alone, thus taking advantage of unrestricted beamtime compared to synchrotron sources. We report results of a study of pure lipid bilayers and phospholipid/cholesterol binary mixtures. Stalks, putative intermediate structures occurring during the membrane fusion process, can clearly be identified from reconstructed electron density maps. Phase diagrams of the lyotropic phase behavior of DOPC/cholesterol and DPhPC/cholesterol samples are presented. If cholesterol is present in moderate concentrations, it can substantially promote the formation of stalks at higher degree of hydration. In addition, a possibly new phase in DOPC/cholesterol is found at high cholesterol content in the low humidity range.

Atomic-scale, all epitaxial in-plane gated donor quantum dot in silicon.

Nanoscale control of doping profiles in semiconductor devices is becoming of critical importance as channel length and pitch in metal oxide semiconductor field effect transistors (MOSFETs) continue to shrink toward a few nanometers. Scanning tunneling microscope (STM) directed self-assembly of dopants is currently the only proven method for fabricating atomically precise electronic devices in silicon. To date this technology has realized individual components of a complete device with a major obstacle being the ability to electrically gate devices. Here we demonstrate a fully functional multiterminal quantum dot device with integrated donor based in-plane gates epitaxially assembled on a single atomic plane of a silicon (001) surface. We show that such in-plane regions of highly doped silicon can be used to gate nanostructures resulting in highly stable Coulomb blockade (CB) oscillations in a donor-based quantum dot. In particular, we compare the use of these all epitaxial in-plane gates with conventional surface gates and find superior stability of the former. These results show that in the absence of the randomizing influences of interface and surface defects the electronic stability of dots in silicon can be comparable or better than that of quantum dots defined in other material systems. We anticipate our experiments will open the door for controlled scaling of silicon devices toward the single donor limit.

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.

As ecosystem engineers, seagrasses are angiosperms of paramount ecological importance in shallow shoreline habitats around the globe. Furthermore, the ancestors of independent seagrass lineages have secondarily returned into the sea in separate, independent evolutionary events. Thus, understanding the molecular adaptation of this clade not only makes significant contributions to the field of ecology, but also to principles of parallel evolution as well. With the use of Dr. Zompo, the first interactive seagrass sequence database presented here, new insights into the molecular adaptation of marine environments can be inferred. The database is based on a total of 14 597 ESTs obtained from two seagrass species, Zostera marina and Posidonia oceanica, which have been processed, assembled and comprehensively annotated. Dr. Zompo provides experimentalists with a broad foundation to build experiments and consider challenges associated with the investigation of this class of non-domesticated monocotyledon systems. Our database, based on the Ruby on Rails framework, is rich in features including the retrieval of experimentally determined heat-responsive transcripts, mining for molecular markers (SSRs and SNPs), and weighted key word searches that allow access to annotation gathered on several levels including Pfam domains, GeneOntology and KEGG pathways. Well established plant genome sites such as The Arabidopsis Information Resource (TAIR) and the Rice Genome Annotation Project are interfaced by Dr. Zompo. With this project, we have initialized a valuable resource for plant biologists in general and the seagrass community in particular. The database is expected to grow together with more data to come in the near future, particularly with the recent initiation of the Zostera genome sequencing project.The Dr. Zompo database is available at http://drzompo.uni-muenster.de/

Small effective population sizes in two planktonic freshwater copepod species (Eudiaptomus) with apparently large census sizes.

In small planktonic organisms, large census sizes (N(c)) suggest large effective population sizes (N(e)), but reliable estimates are rare. Here, we present N(e)/N(c) ratios for two freshwater copepod species (Eudiaptomus sp.) using temporal samples of multilocus microsatellite genotypes and a pseudo-likelihood approach. N(e)/N(c) ratios were very small in both Eudiaptomus species (10(-7)-10(-8)). Although we hypothesized that the species producing resting eggs (E. graciloides) had a larger N(e) than the other (E. gracilis), estimates were not statistically different (E. graciloides: N(e) = 672.7, CI: 276-1949; E. gracilis: N(e) = 1027.4, CI: 449-2495), suggesting that the propagule bank of E. graciloides had no detectable influence on N(e).

Single P and As dopants in the Si(001) surface.

Using first-principles density functional theory, we discuss doping of the Si(001) surface by a single substitutional phosphorus or arsenic atom. We show that there are two competing atomic structures for isolated Si-P and Si-As heterodimers, and that the donor electron is delocalized over the surface. We also show that the Si atom dangling bond of one of these heterodimer structures can be progressively charged by additional electrons. It is predicted that surface charge accumulation as a result of tip-induced band bending leads to structural and electronic changes of the Si-P and Si-As heterodimers which could be observed experimentally. Scanning tunneling microscopy (STM) measurements of the Si-P heterodimer on a n-type Si(001) surface reveal structural characteristics and a bias-voltage dependent appearance, consistent with these predictions. STM measurements for the As:Si(001) system are predicted to exhibit similar behavior to P:Si(001).

Individual MHC class I and MHC class IIB diversities are associated with male and female reproductive traits in the three-spined stickleback.

Genes of the major histocompatibility complex (MHC) are indispensable for pathogen defence in vertebrates. With wild-caught three-spined sticklebacks (Gasterosteus aculeatus) we conducted the first study to relate individual reproductive parameters to both MHC class I and II diversities. An optimal MHC class IIB diversity was found for male nest quality. However, male breeding colouration was most intense at a maximal MHC class I diversity. One MHC class I allele was associated with male redness. Similarly, one MHC class IIB allele was associated with continuous rather than early female reproduction, possibly extending the reproductive period. Both alleles occurred more frequently with increasing individual allele diversity. We suggest that if an allele is currently not part of the optimum, it had not been propagated by choosy females. The parasite against which this allele provides resistance is therefore unlikely to have been predominant the previous year - a step to negative frequency-dependent selection.