In Situ Liquid Cell TEM Reveals Bridge-Induced Contact and Fusion of Au Nanocrystals in Aqueous Solution

During nanoparticle coalescence in aqueous solution, dehydration and initial contact of particles are critically important but poorly understood processes. In this work, we used in situ liquid-cell transmission electron microscopy to directly visualize the coalescence process of Au nanocrystals. It is found that the Au atomic nanobridge forms between adjacent nanocrystals that are separated by a ∼0.5 nm hydration layer. The nanobridge structure first induces initial contact of Au nanocrystals over their hydration layers and then surface diffusion and grain boundary migration to rearrange into a single nanocrystal. Classical density functional theory calculations and ab initio molecular dynamics simulations suggest that the formation of the nanobridge can be attributed to the accumulation of auric ions and a higher local supersaturation in the gap, which can promote dehydration, contact, and fusion of Au nanocrystals. The discovery of this multistep process advances our understanding of the nanoparticle coalescence mechanism in aqueous solutions.

Symmetric coalescence of two hydraulic fractures

The formation of a fracture network is a key process for many geophysical and industrial practices from energy resource recovery to induced seismic management. We focus on the initial stage of a fracture network formation using experiments on the symmetric coalescence of two equal coplanar, fluid-driven, penny-shaped fractures in a brittle elastic medium. Initially, the fractures propagate independently of each other. The fractures then begin to interact and coalesce, forming a bridge between them. Within an intermediate period after the initial contact, most of the fracture growth is localized along this bridge, perpendicular to the line connecting the injection sources. Using light attenuation and particle image velocimetry to measure both the fracture aperture and velocity field, we characterize the growth of this bridge. We model this behavior using a geometric volume conservation argument dependent on the symmetry of the interaction, with a 2D approximation for the bridge. We also verify experimentally the scaling for the bridge growth and the shape of the thickness profile along the bridge. The influence of elasticity and toughness of the solid, injection rate of the fluid, and initial location of the fractures are captured by our scaling.

Reconstructing the phylogeny of new world monkeys (platyrrhini): evidence from multiple non-coding loci

Among mammalian phylogenies, those characterized by rapid radiations are particularly problematic. The New World monkeys (NWMs, Platyrrhini) comprise 3 families and 7 subfamilies, which radiated within a relatively short time period. Accordingly, their phylogenetic relationships are still largely disputed. In the present study, 56 nuclear non-coding loci, including 33 introns (INs) and 23 intergenic regions (IGs), from 20 NWM individuals representing 18 species were used to investigate phylogenetic relationships among families and subfamilies. Of the 56 loci, 43 have not been used in previous NWM phylogenetics. We applied concatenation and coalescence tree-inference methods, and a recently proposed question-specific approach to address NWM phylogeny. Our results indicate incongruence between concatenation and coalescence methods for the IN and IG datasets. However, a consensus was reached with a single tree topology from all analyses of combined INs and IGs as well as all analyses of question-specific loci using both concatenation and coalescence methods, albeit with varying degrees of statistical support. In detail, our results indicated the sister-group relationships between the families Atelidae and Pitheciidae, and between the subfamilies Aotinae and Callithrichinae among Cebidae. Our study provides insights into the disputed phylogenetic relationships among NWM families and subfamilies from the perspective of multiple non-coding loci and various tree-inference approaches. However, the present phylogenetic framework needs further evaluation by adding more independent sequence data and a deeper taxonomic sampling. Overall, our work has important implications for phylogenetic studies dealing with rapid radiations.

A combined three-dimensional in vitro-in silico approach to modelling bubble dynamics in decompression sickness

The growth of bubbles within the body is widely believed to be the cause of decompression sickness (DCS). Dive computer algorithms that aim to prevent DCS by mathematically modelling bubble dynamics and tissue gas kinetics are challenging to validate. This is due to lack of understanding regarding the mechanism(s) leading from bubble formation to DCS. In this work, a biomimetic in vitro tissue phantom and a three-dimensional computational model, comprising a hyperelastic strain-energy density function to model tissue elasticity, were combined to investigate key areas of bubble dynamics. A sensitivity analysis indicated that the diffusion coefficient was the most influential material parameter. Comparison of computational and experimental data revealed the bubble surface's diffusion coefficient to be 30 times smaller than that in the bulk tissue and dependent on the bubble's surface area. The initial size, size distribution and proximity of bubbles within the tissue phantom were also shown to influence their subsequent dynamics highlighting the importance of modelling bubble nucleation and bubble-bubble interactions in order to develop more accurate dive algorithms.

Effect of Emulsifier Concentration and Physical State on the In Vitro Digestion Behavior of Oil-in-Water Emulsions

The influence of emulsifier physical state and concentration on the in vitro digestion of oil-in-water (O/W) emulsions was investigated. Two citrated monoacylglycerols, glyceryl stearate citrate (GSC, bulk mp of 55-65 °C) and glyceryl oleate citrate (GOC, bulk mp of 0-10 °C), were used at 0.5 or 5 wt % of the emulsions to generate 20 wt % soybean oil O/W emulsions. Oil droplet lipolysis was slower in emulsions with 0.5 wt % emulsifier versus in those with 5 wt % emulsifier, resulting from the reduced surface-to-volume ratio in emulsions at 0.5 wt % emulsifier and the increased concentration of hydrolyzable groups at 5 wt % emulsifier. When excluding gastric digestion, all emulsions were similarly digested, confirming that emulsion intestinal digestion was highly dependent on gastric preprocessing. Finally, at a given emulsifier concentration, GSC-based emulsions with an interfacial crystalline shell experienced a decreased rate of intestinal lipid digestion compared with their GOC-based counterparts, confirming that emulsifier physical state played a role in lipid digestion.

Multi-locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes

PREMISE OF THE STUDY

Both incomplete lineage sorting and reticulation have been proposed as causes of phylogenetic incongruence. Disentangling these factors may be most difficult in long-lived, wind-pollinated plants with large population sizes and weak reproductive barriers.

METHODS

We used solution hybridization for targeted enrichment and massive parallel sequencing to characterize low-copy-number nuclear genes and high-copy-number plastomes (Hyb-Seq) in 74 individuals of Pinus subsection Australes, a group of ~30 New World pine species of exceptional ecological and economic importance. We inferred relationships using methods that account for both incomplete lineage sorting and reticulation.

KEY RESULTS

Concatenation- and coalescent-based trees inferred from nuclear genes mainly agreed with one another, but they contradicted the plastid DNA tree in recovering the Attenuatae (the California closed-cone pines) and Oocarpae (the egg-cone pines of Mexico and Central America) as monophyletic and the Australes sensu stricto (the southern yellow pines) as paraphyletic to the Oocarpae. The plastid tree featured some relationships that were discordant with morphological and geographic evidence and species limits. Incorporating gene flow into the coalescent analyses better fit the data, but evidence supporting the hypothesis that hybridization explains the non-monophyly of the Attenuatae in the plastid tree was equivocal.

CONCLUSIONS

Our analyses document cytonuclear discordance in Pinus subsection Australes. We attribute this discordance to ancient and recent introgression and present a phylogenetic hypothesis in which mostly hierarchical relationships are overlain by gene flow.

A matter of phylogenetic scale: Distinguishing incomplete lineage sorting from lateral gene transfer as the cause of gene tree discord in recent versus deep diversification histories

PREMISE OF THE STUDY

Discordant gene trees are commonly encountered when sequences from thousands of loci are applied to estimate phylogenetic relationships. Several processes contribute to this discord. Yet, we have no methods that jointly model different sources of conflict when estimating phylogenies. An alternative to analyzing entire genomes or all the sequenced loci is to identify a subset of loci for phylogenetic analysis. If we can identify data partitions that are most likely to reflect descent from a common ancestor (i.e., discordant loci that indeed reflect incomplete lineage sorting [ILS], as opposed to some other process, such as lateral gene transfer [LGT]), we can analyze this subset using powerful coalescent-based species-tree approaches.

METHODS

Test data sets were simulated where discord among loci could arise from ILS and LGT. Data sets where analyzed using the newly developed program CLASSIPHY (Huang et al., ) to assess whether our ability to distinguish the cause of discord among loci varied when ILS and LGT occurred in the recent versus deep past and whether the accuracy of these inferences were affected by the mutational process.

KEY RESULTS

We show that accuracy of probabilistic classification of individual loci by the cause of discord differed when ILS and LGT events occurred more recently compared with the distant past and that the signal-to-noise ratio arising from the mutational process contributes to difficulties in inferring LGT data partitions.

CONCLUSIONS

We discuss our findings in terms of the promise and limitations of identifying subsets of loci for species-tree inference that will not violate the underlying coalescent model (i.e., data partitions in which ILS, and not LGT, contributes to discord). We also discuss the empirical implications of our work given the many recalcitrant nodes in the tree of life (e.g., origins of angiosperms, amniotes, or Neoaves), and recent arguments for concatenating loci.

Temperature-induced Coalescence of Droplets Manipulated by Optical Trapping in an Oil-in-Water Emulsion

Coalescence of oil droplets in an oil-in-water (O/W) emulsion was achieved with heating and optical trapping. Three types of O/W emulsions were prepared by adding a mixture of butanol and n-decane to an aqueous solution containing a cationic surfactant (cetyltrimethylammonium bromide, CTAB), an anionic surfactant (sodium dodecyl sulfate, SDS), or a neutral hydrophilic polymer (polyethylene glycol, PEG) as an emulsifier. Two oil droplets in the emulsions were randomly trapped in a square capillary tube by two laser beams in order to induce coalescence. Coalescence of the droplets could not be achieved at room temperature (25°C) regardless of the type of emulsifier. Conversely, the droplets prepared with PEG coalesced at a temperature higher than 30°C, although the droplets with ionic surfactants CTAB and SDS did not coalesce even at the elevated temperature due to their electrostatic repulsion. The size of the resultant coalesced droplet was consistent with that calculated from the size of the two droplets of oil, which indicated successful coalescence of the two droplets. We also found that the time required for the coalescence could be correlated with the temperature using an Arrhenius plot.

Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

BACKGROUND AND AIMS

Bee orchids (Ophrys) have become the most popular model system for studying reproduction via insect-mediated pseudo-copulation and for exploring the consequent, putatively adaptive, evolutionary radiations. However, despite intensive past research, both the phylogenetic structure and species diversity within the genus remain highly contentious. Here, we integrate next-generation sequencing and morphological cladistic techniques to clarify the phylogeny of the genus.

METHODS

At least two accessions of each of the ten species groups previously circumscribed from large-scale cloned nuclear ribosomal internal transcibed spacer (nrITS) sequencing were subjected to restriction site-associated sequencing (RAD-seq). The resulting matrix of 4159 single nucleotide polymorphisms (SNPs) for 34 accessions was used to construct an unrooted network and a rooted maximum likelihood phylogeny. A parallel morphological cladistic matrix of 43 characters generated both polymorphic and non-polymorphic sets of parsimony trees before being mapped across the RAD-seq topology.

KEY RESULTS

RAD-seq data strongly support the monophyly of nine out of ten groups previously circumscribed using nrITS and resolve three major clades; in contrast, supposed microspecies are barely distinguishable. Strong incongruence separated the RAD-seq trees from both the morphological trees and traditional classifications; mapping of the morphological characters across the RAD-seq topology rendered them far more homoplastic.

CONCLUSIONS

The comparatively high level of morphological homoplasy reflects extensive convergence, whereas the derived placement of the fusca group is attributed to paedomorphic simplification. The phenotype of the most recent common ancestor of the extant lineages is inferred, but it post-dates the majority of the character-state changes that typify the genus. RAD-seq may represent the high-water mark of the contribution of molecular phylogenetics to understanding evolution within Ophrys; further progress will require large-scale population-level studies that integrate phenotypic and genotypic data in a cogent conceptual framework.

Reorganizing Polymer Chains with Cyclodextrins

During the past several years, we have been utilizing cyclodextrins (CDs) to nanostructure polymers into bulk samples whose chain organizations, properties, and behaviors are quite distinct from neat bulk samples obtained from their solutions and melts. We first form non-covalently bonded inclusion complexes (ICs) between CD hosts and guest polymers, where the guest chains are highly extended and separately occupy the narrow channels (~0.5⁻1.0 nm in diameter) formed by the columnar arrangement of CDs in the IC crystals. Careful removal of the host crystalline CD lattice from the polymer-CD-IC crystals leads to coalescence of the guest polymer chains into bulk samples, which we have repeatedly observed to behave distinctly from those produced from their solutions or melts. While amorphous polymers coalesced from their CD-ICs evidence significantly higher glass-transition temperatures, Tgs, polymers that crystallize generally show higher melting and crystallization temperatures (Tms, Tcs), and some-times different crystalline polymorphs, when they are coalesced from their CD-ICs. Formation of CD-ICs containing two or more guest homopolymers or with block copolymers can result in coalesced samples which exhibit intimate mixing between their common homopolymer chains or between the blocks of the copolymer. On a more practically relevant level, the distinct organizations and behaviors observed for polymer samples coalesced from their CD-ICs are found to be stable to extended annealing at temperatures above their Tgs and Tms. We believe this is a consequence of the structural organization of the crystalline polymer-CD-ICs, where the guest polymer chains included in host-IC crystals are separated and confined to occupy the narrow channels formed by the host CDs during IC crystallization. Substantial degrees of the extended and un-entangled natures of the IC-included chains are apparently retained upon coalescence, and are resistant to high temperature annealing. Following the careful removal of the host CD lattice from each randomly oriented IC crystal, the guest polymer chains now occupying a much-reduced volume may be somewhat "nematically" oriented, resulting in a collection of randomly oriented "nematic" regions of largely extended and un-entangled coalesced guest chains. The suggested randomly oriented nematic domain organization of guest polymers might explain why even at high temperatures their transformation to randomly-coiling, interpenetrated, and entangled melts might be difficult. In addition, the behaviors and uses of polymers coalesced from their CD-ICs are briefly described and summarized here, and we attempted to draw conclusions from and relationships between their behaviors and the unique chain organizations and conformations achieved upon coalescence.

Hybrid asexuality as a primary postzygotic barrier between nascent species: On the interconnection between asexuality, hybridization and speciation

Although sexual reproduction is ubiquitous throughout nature, the molecular machinery behind it has been repeatedly disrupted during evolution, leading to the emergence of asexual lineages in all eukaryotic phyla. Despite intensive research, little is known about what causes the switch from sexual reproduction to asexuality. Interspecific hybridization is one of the candidate explanations, but the reasons for the apparent association between hybridization and asexuality remain unclear. In this study, we combined cross-breeding experiments with population genetic and phylogenomic approaches to reveal the history of speciation and asexuality evolution in European spined loaches (Cobitis). Contemporary species readily hybridize in hybrid zones, but produce infertile males and fertile but clonally reproducing females that cannot mediate introgressions. However, our analysis of exome data indicates that intensive gene flow between species has occurred in the past. Crossings among species with various genetic distances showed that, while distantly related species produced asexual females and sterile males, closely related species produce sexually reproducing hybrids of both sexes. Our results suggest that hybridization leads to sexual hybrids at the initial stages of speciation, but as the species diverge further, the gradual accumulation of reproductive incompatibilities between species could distort their gametogenesis towards asexuality. Interestingly, comparative analysis of published data revealed that hybrid asexuality generally evolves at lower genetic divergences than hybrid sterility or inviability. Given that hybrid asexuality effectively restricts gene flow, it may establish a primary reproductive barrier earlier during diversification than other "classical" forms of postzygotic incompatibilities. Hybrid asexuality may thus indirectly contribute to the speciation process.

Coalescence Processes of Droplets and Liquid Marbles

The coalescence process of droplets and, more recently, of liquid marbles, has become one of the most essential manipulation schemes in digital microfluidics. This process is indispensable for realising microfluidic functions such as mixing and reactions at microscale. This paper reviews previous studies on droplet coalescence, paying particular attention to the coalescence of liquid marbles. Four coalescence systems have been reviewed, namely, the coalescence of two droplets freely suspended in a fluid; the coalescence of two sessile droplets on a solid substrate; the coalescence of a falling droplet and a sessile droplet on a solid substrate; and liquid marble coalescence. The review is presented according to the dynamic behaviors, physical mechanisms and experimental parameters of the coalescence process. It also provides a systematic overview of how the coalescence process of droplets and liquid marbles could be induced and manipulated using external energy. In addition, the practical applications of liquid marble coalescence as a novel microreactor are highlighted. Finally, future perspectives on the investigation of the coalescence process of liquid marbles are proposed. This review aims to facilitate better understanding of the coalescence of droplets and of liquid marbles as well as to shed new insight on future studies.

Coalescence-Induced Self-Propulsion of Droplets on Superomniphobic Surfaces

We utilized superomniphobic surfaces to systematically investigate the different regimes of coalescence-induced self-propulsion of liquid droplets with a wide range of droplet radii, viscosities, and surface tensions. Our results indicate that the nondimensional jumping velocity V_j^* is nearly constant (V_j^* ≈ 0.2) in the inertial-capillary regime and decreases in the visco-capillary regime as the Ohnesorge number Oh increases, in agreement with prior work. Within the visco-capillary regime, decreasing the droplet radius R₀ results in a more rapid decrease in the nondimensional jumping velocity V_j^* compared to increasing the viscosity μ. This is because decreasing the droplet radius R₀ increases the inertial-capillary velocity V_ic in addition to increasing the Ohnesorge number Oh.

Tuning Superhydrophobic Nanostructures To Enhance Jumping-Droplet Condensation

It was recently discovered that condensation growing on a nanostructured superhydrophobic surface can spontaneously jump off the surface, triggered by naturally occurring coalescence events. Many reports have observed that droplets must grow to a size of order 10 μm before jumping is enabled upon coalescence; however, it remains unknown how the critical jumping size relates to the topography of the underlying nanostructure. Here, we characterize the dynamic behavior of condensation growing on six different superhydrophobic nanostructures, where the topography of the nanopillars was systematically varied. The critical jumping diameter was observed to be highly dependent upon the height, diameter, and pitch of the nanopillars: tall and slender nanopillars promoted 2 μm jumping droplets, whereas short and stout nanopillars increased the critical size to over 20 μm. The topology of each surface is successfully correlated to the critical jumping diameter by constructing an energetic model that predicts how large a nucleating embryo needs to grow before it can inflate into the air with an apparent contact angle large enough for jumping. By extending our model to consider any possible surface, it is revealed that properly designed nanostructures should enable nanometric jumping droplets, which would further enhance jumping-droplet condensers for heat transfer, antifogging, and antifrosting applications.

Preparation of Porous Stainless Steel Hollow-Fibers through Multi-Modal Particle Size Sintering towards Pore Engineering

The sintering of metal powders is an efficient and versatile technique to fabricate porous metal elements such as filters, diffusers, and membranes. Neck formation between particles is, however, critical to tune the porosity and optimize mass transfer in order to minimize the densification process. In this work, macro-porous stainless steel (SS) hollow-fibers (HFs) were fabricated by the extrusion and sintering of a dope comprised, for the first time, of a bimodal mixture of SS powders. The SS particles of different sizes and shapes were mixed to increase the neck formation between the particles and control the densification process of the structure during sintering. The sintered HFs from particles of two different sizes were shown to be more mechanically stable at lower sintering temperature due to the increased neck area of the small particles sintered to the large ones. In addition, the sintered HFs made from particles of 10 and 44 μm showed a smaller average pore size (<1 μm) as compared to the micron-size pores of sintered HFs made from particles of 10 μm only and those of 10 and 20 μm. The novel HFs could be used in a range of applications, from filtration modules to electrochemical membrane reactors.

Selective Laser Sintering of Nano Al₂O₃ Infused Polyamide

Nano Al₂O₃ polyamide composites are evaluated for processing by selective laser sintering. A thermal characterization of the polymer composite powders allowed us to establish the possible initial settings. Initial experiments are conducted to identify the most suitable combinations of process parameters. Based on the results of the initial trials, more promising ranges of different process parameters could be identified. The post sintering characterization showed evidence of sufficient inter-particle sintering and intra-layer coalescence. While the inter-particle coalescence gradually improved, the porosity levels slightly decreased with increasing laser power. The nano-filler particles tend to agglomerate around the beads along the solid tracks, possibly due to Van der Walls forces. The tensile stress results showed an almost linear increase with increasing nano-filler content.

Minimal-assumption inference from population-genomic data

Samples of multiple complete genome sequences contain vast amounts of information about the evolutionary history of populations, much of it in the associations among polymorphisms at different loci. We introduce a method, Minimal-Assumption Genomic Inference of Coalescence (MAGIC), that reconstructs key features of the evolutionary history, including the distribution of coalescence times, by integrating information across genomic length scales without using an explicit model of coalescence or recombination, allowing it to analyze arbitrarily large samples without phasing while making no assumptions about ancestral structure, linked selection, or gene conversion. Using simulated data, we show that the performance of MAGIC is comparable to that of PSMC' even on single diploid samples generated with standard coalescent and recombination models. Applying MAGIC to a sample of human genomes reveals evidence of non-demographic factors driving coalescence.

Evolution of Rosaceae Fruit Types Based on Nuclear Phylogeny in the Context of Geological Times and Genome Duplication

Fruits are the defining feature of angiosperms, likely have contributed to angiosperm successes by protecting and dispersing seeds, and provide foods to humans and other animals, with many morphological types and important ecological and agricultural implications. Rosaceae is a family with ∼3000 species and an extraordinary spectrum of distinct fruits, including fleshy peach, apple, and strawberry prized by their consumers, as well as dry achenetum and follicetum with features facilitating seed dispersal, excellent for studying fruit evolution. To address Rosaceae fruit evolution and other questions, we generated 125 new transcriptomic and genomic datasets and identified hundreds of nuclear genes to reconstruct a well-resolved Rosaceae phylogeny with highly supported monophyly of all subfamilies and tribes. Molecular clock analysis revealed an estimated age of ∼101.6 Ma for crown Rosaceae and divergence times of tribes and genera, providing a geological and climate context for fruit evolution. Phylogenomic analysis yielded strong evidence for numerous whole genome duplications (WGDs), supporting the hypothesis that the apple tribe had a WGD and revealing another one shared by fleshy fruit-bearing members of this tribe, with moderate support for WGDs in the peach tribe and other groups. Ancestral character reconstruction for fruit types supports independent origins of fleshy fruits from dry-fruit ancestors, including the evolution of drupes (e.g., peach) and pomes (e.g., apple) from follicetum, and drupetum (raspberry and blackberry) from achenetum. We propose that WGDs and environmental factors, including animals, contributed to the evolution of the many fruits in Rosaceae, which provide a foundation for understanding fruit evolution.

INFERRING PHYLOGENIES FROM mtDNA VARIATION: MITOCHONDRIAL-GENE TREES VERSUS NUCLEAR-GENE TREES

An accurately resolved gene tree may not be congruent with the species tree because of lineage sorting of ancestral polymorphisms. DNA sequences from the mitochondrially encoded genes (mtDNA) are attractive sources of characters for estimating the phylogenies of recently evolved taxa because mtDNA evolves rapidly, but its utility is limited because the mitochondrial genes are inherited as a single linkage group (haplotype) and provide only one independent estimate of the species tree. In contrast, a set of nuclear genes can be selected from distinct chromosomes, such that each gene tree provides an independent estimate of the species tree. Another aspect of the gene-tree versus species-tree problem, however, favors the use of mtDNA for inferring species trees. For a three-species segment of a phylogeny, the branching order of a gene tree will correspond to that of the species tree if coalescence of the alleles or haplotypes occurred in the internode between the first and second bifurcation. From neutral theory, it is apparent that the probability of coalescence increases as effective population size decreases. Because the mitochondrial genome is maternally inherited and effectively haploid, its effective population size is one-fourth that of a nuclear-autosomal gene. Thus, the mitochondrial-haplotype tree has a substantially higher probability of accurately tracking a short internode than does a nuclear-autosomal-gene tree. When an internode is sufficiently long that the probability that the mitochondrial-haplotype tree will be congruent with the species tree is 0.95, the probability that a nuclear-autosomalgene tree will be congruent is only 0.62. If each of k independently sampled nuclear-gene trees has a probability of congruence with the species tree of 0.62, then a sample of 16 such trees would be required to be as confident of the inference based on the mitochondrial-haplotype tree. A survey of mtDNA-haplotype diversity in 34 species of birds indicates that coalescence is generally very recent, which suggests that coalescence times are typically much shorter than internodal branch lengths of the species tree, and that sorting of mtDNA lineages is not likely to confound the species tree. Hybridization resulting in transfer of mtDNA haplotypes among branches could also result in a haplotype tree that is incongruent with the species tree; if undetected, this could confound the species tree. However, hybridization is usually easy to detect and should be incorporated in the historical narrative of the group, because reticulation, as well as cladistic events, contributed to the evolution of the group.

Pressure compression of CdSe nanoparticles into luminescent nanowires

Oriented attachment (OA) of synthetic nanocrystals is emerging as an effective means of fabricating low-dimensional nanoscale materials. However, OA relies on energetically favorable nanocrystal facets to grow nanostructured materials. Consequently, nanostructures synthesized through OA are generally limited to a specific crystal facet in their final morphology. We report our discovery that high-pressure compression can induce consolidation of spherical CdSe nanocrystal arrays, leading to unexpected one-dimensional semiconductor nanowires that do not exhibit the typical crystal facet. In particular, in situ high-pressure synchrotron x-ray scattering, optical spectroscopy, and high-resolution transmission electron microscopy characterizations indicate that by manipulating the coupling between nanocrystals through external pressure, a reversible change in nanocrystal assemblies and properties can be achieved at modest pressure. When pressure is increased above a threshold, these nanocrystals begin to contact one another and consolidate, irreversibly forming one-dimensional luminescent nanowires. High-fidelity molecular dynamics (MD) methods were used to calculate surface energies and simulate compression and coalescence mechanisms of CdSe nanocrystals. The MD results provide new insight into nanowire assembly dynamics and phase stability of nanocrystalline structures.

Correction: Synthesis, dynamic NMR characterization and XRD studies of novel N,N'-substituted piperazines for bioorthogonal labeling

[This corrects the article DOI: 10.3762/bjoc.12.242.].

Bran-induced effects on the evolution of bubbles and rheological properties in bread dough

Evolution of bubbles is the key to volume development in bread dough. The influence of wheat bran on bubble growth in bread dough through the mixing, fermentation, and proofing stages is described as a function of its level of addition. Confocal laser scanning microscopy in combination with image processing tools was used to obtain the bubble size and shape parameters. The relationship between bubble behavior and dough rheology was mapped using biaxial extension and dynamic oscillatory rheometry studies. With increase in level of bran addition, mean bubble size decreased corresponding to each stage and showed an inverse relationship with dough overpressure and elastic modulus. Addition of wheat bran was observed to suppress the bubble coarsening phenomenon in dough. Experimental observations indicated the plausibility of coalescence-mediated bubble growth in bread dough during the latter stages of fermentation and proofing, which was hindered in the presence of bran particles.

PRACTICAL APPLICATION

The results of this work provide an insight to the underlying mechanism by which wheat bran addition impacts the volume development in bread dough. The inferences presented in this research work can be used as a basis to study bubble dynamics in an opaque food system such as bread dough. This information would be of interest to industrial researchers working on the new product development of aerated bakery products with functional fibrous ingredients.

The evolution of the competition-dispersal trade-off affects α- and β-diversity in a heterogeneous metacommunity

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities.

Coalescing red algae exhibit noninvasive, reversible chimerism

Chimerism is produced by the somatic fusion of two or more genetically distinct conspecific individuals. In animals, the main cost of fusion is competition between genetically different cell lineages and the probability of original cell line replacement by more competitive invasive lines, which limits its natural frequency (3%-5%). In red and brown seaweeds, chimerism is widespread (27%-53%), seemingly without the negative outcomes described for animals. The rigidity of cell walls in macroalgae prevents cell motility and invasions. In addition, in moving waters, most somatic fusions involve the holdfast. Histological observations in laboratory-built bicolor macroalgal chimeras indicated that upright axes emerge from the base of plants by proliferation and vertical growth of discrete cell groups that include one or just a few of the cell lineages occurring in the holdfasts. Laboratory experiments showed growth competition between cell lineages, thus explaining lineage segregation during growth along originally chimeric erect axes. Genotyping of the axes showed more heterogeneous tissues basally, but apically more homogeneous ones, generating a vertical gradient of allele abundance and diversity. The few chimeric primary branches produced, eventually became homogenous after repeated branching. Therefore, coalescing macroagae exhibit a unique pattern of post-fusion growth, with the capacity to reverse chimerism. This pattern is significantly different from those in animals and land plants, suggesting chimerism is a biologically heterogeneous concept.

Anchored phylogenomics improves the resolution of evolutionary relationships in the rapid radiation of Protea L

PREMISE OF THE STUDY

Estimating phylogenetic relationships in relatively recent evolutionary radiations is challenging, especially if short branches associated with recent divergence result in multiple gene tree histories. We combine anchored enrichment next-generation sequencing with species tree analyses to produce a robust estimate of phylogenetic relationships in the genus Protea (Proteaceae), an iconic radiation in South Africa.

METHODS

We sampled multiple individuals within 59 out of 112 species of Protea and 6 outgroup species for a total of 163 individuals, and obtained sequences for 498 low-copy, orthologous nuclear loci using anchored phylogenomics. We compare several approaches for building species trees, and explore gene tree-species tree discrepancies to determine whether poor phylogenetic resolution reflects a lack of informative sites, incomplete lineage sorting, or hybridization.

KEY RESULTS

Phylogenetic estimates from species tree approaches are similar to one another and recover previously well-supported clades within Protea, in addition to providing well-supported phylogenetic hypotheses for previously poorly resolved intrageneric relationships. Individual gene trees are markedly different from one another and from species trees. Nonetheless, analyses indicate that differences among gene trees occur primarily concerning clades supported by short branches.

CONCLUSIONS

Species tree methods using hundreds of nuclear loci provided strong support for many previously unresolved relationships in the radiation of the genus Protea. In cases where support for particular relationships remains low, these appear to arise from few informative sites and lack of information rather than strongly supported disagreement among gene trees.