Genomic insights into rapid speciation within the world's largest tree genus Syzygium.

Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.

Fibroblasts stimulate macrophage migration in interconnected extracellular matrices through tunnel formation and fiber alignment.

In vivo, macrophages and fibroblasts navigate through and remodel the three-dimensional (3D) extra-cellular matrix (ECM). The orientation of fibers, the porosity, and degree of cross-linking can change the interconnectivity of the ECM and affect cell migration. In turn, migrating cells can alter their microenvironment. To study the relationships between ECM interconnectivity and migration of cells, we assembled collagen hydrogels with dense (DCN) or with loosely interconnected networks (LCN). We find that in DCNs, RAW 264.7 macrophages in monocultures were virtually stationary. In DCN co-cultures, Balb/c 3T3 fibroblasts created tunnels that provided conduits for macrophage migration. In LCNs, fibroblasts aligned fibers up to a distance of 100 µm, which provided tracks for macrophages. Intra-cellular and extra-cellular fluorescent fragments of internalized and degraded collagen were detected inside both cell types as well as around their cell peripheries. Macrophages expressed higher levels of urokinase-type plasminogen activator receptor associated protein (uPARAP)/mannose receptor 1 (CD206) compared to α2ß1 indicating that collagen internalization in these cells occurred primarily via integrin-independent mechanisms. Network remodeling indicated by higher Young's modulus was observed in fibroblast monocultures as a result of TGF-ß secretion. This work unveils new roles for fibroblasts in forming tunnels in networked ECM to modulate macrophage migration.

Unified mechanism of local drivers in a percolation model of atrial fibrillation.

The mechanisms of atrial fibrillation (AF) are poorly understood, resulting in disappointing success rates of ablative treatment. Different mechanisms defined largely by different atrial activation patterns have been proposed and, arguably, this dispute has slowed the progress of AF research. Recent clinical evidence suggests a unifying mechanism of local drivers based on sustained reentrant circuits in the complex atrial architecture. Here, we present a percolation inspired computational model showing spontaneous emergence of AF that strongly supports, and gives a theoretical explanation for, the clinically observed diversity of activation. We show that the difference in surface activation patterns is a direct consequence of the thickness of the discrete network of heart muscle cells through which electrical signals percolate to reach the imaged surface. The model naturally follows the clinical spectrum of AF spanning sinus rhythm, paroxysmal AF, and persistent AF as the decoupling of myocardial cells results in the lattice approaching the percolation threshold. This allows the model to make the prediction that, for paroxysmal AF, reentrant circuits emerge near the endocardium, but in persistent AF they emerge deeper in the bulk of the atrial wall. If experimentally verified, this may go towards explaining the lowering ablation success rate as AF becomes more persistent.

Multi-cellular transitional organotypic models to investigate liver fibrosis.

Hepatic fibrosis is the result of wound healing and inflammation resulting in organ dysfunction. Hepatocytes, liver sinusoidal endothelial cells (LSECs), Kupffer cells (KCs), and hepatic stellate cells (HSCs) play critical roles in fibrogenesis. As the liver undergoes fibrosis, there are populations of cells that are healthy, fibrotic as well as those undergoing fibrosis. We investigated how a varying mechanical environment could induce changes in hepatic cells. In this study, a gradient in the mechanical properties of the microenvironment resulted in transitioning phenotypes in hepatic cells. We have designed detachable polyelectrolyte multilayers (PEMs) whose elastic moduli ranged from 21 to 43 kPa to serve as Space of Disse mimics. We assembled novel 3D organotypic liver models comprised of hepatocytes, LSECs, HSCs, KCs, and the Space of Disse mimic. We demonstrate how cells in contact with a mechanical gradient exhibit different properties compared to cells cultured using non-gradient PEMs. Significant differences were observed in HSC and KC proliferation between 3D cultures assembled with gradient and non-gradient PEMs. While HSCs on the stiffer regions of the gradient PEMs expressed both GFAP and α-SMA, cells in cultures assembled with homogeneous 43 kPa multilayers primarily expressed α-SMA. Over an 8-day culture, the elastic modulus in the 21 and 43 kPa regions of the gradient PEMs increased by 1.6 and 3.7-fold, respectively. This was accompanied by a 4-fold increase in hydroxyproline. Such in vitro tissues can be used to investigate the effects of liver fibrosis. STATEMENT OF SIGNIFICANCE: We have assembled a liver model assembled with four major primary hepatic cell types to investigate how a varying mechanical environment induces changes in hepatic cells. In this study, a gradient in the mechanical properties of the microenvironment results in transitioning phenotypes in hepatic cells. Our goal was to investigate the interplay between mechanical properties and a multi-cellular engineered liver tissue. In these models, Kupffer cell proliferation and hepatic stellate cell activation occurred due to mechanical cues and inter-cellular signaling across a distance of 2000 µm. These models are unique, in that, fibrosis was initiated purely through changes to the microenvironment. These models were not exposed to fibrogenic factors nor were the models assembled with cells from fibrotic rats. To the best of our knowledge, these are the first liver models that capture how a gradient microenvironment can result in transitioning cellular phenotypes.

Measuring Cytoplasmic Stiffness of Fibroblasts as a Function of Location and Substrate Rigidity Using Atomic Force Microscopy.

The cytoplasmic stiffness of cells plays a significant role during cell migration. As a cell migrates, differences in cytoplasmic properties occur that subsequently modulate migratory behavior. The properties of the substrate to which cells are adherent also play a role. To accurately measure the cytoplasmic stiffness of cells, we provide detailed instructions on how to assemble hydrogels that exhibit different elastic moduli, culturing cells on these substrates followed by a step-by-step process to measure and analyze the cytoplasmic properties of fibroblasts. In this study, we have measured the elastic moduli of cells at different locations to demonstrate how this property varies as a function of where the measurement is performed. The degree of anisotropy measured by the difference between cytoplasmic stiffness at the two edges of the cell also varied as a function of the elasticity of their underlying substrates. Larger differences in cytoplasmic stiffness between the leading and trailing edges were observed on substrates with a higher elastic modulus. The methods reported in this study can provide information on cellular properties, specifically, how the elastic modulus of cells can be probed and analyzed in vitro.

Extracellular matrix remodeling in 3D: implications in tissue homeostasis and disease progression.

The extracellular matrix (ECM) plays a critical role in regulating cell behavior during tissue homeostasis and in disease progression. Through a combination of adhesion, contraction, alignment of ECM proteins and subsequent degradation, cells change the chemical, mechanical, and physical properties of their surrounding matrix. Other contributing factors to matrix remodeling are the de novo synthesis of ECM proteins, post-translational modifications and receptor-mediated internalization. In this review, we highlight how each of these processes contributes to the maintenance of homeostasis and in disease conditions such as cancer and liver fibrosis. This article is categorized under: Implantable Materials and Surgical Technologies > Nanotechnology in Tissue Repair and Replacement.

The design of antimicrobial LL37-modified collagen-hyaluronic acid detachable multilayers.

UNLABELLED: The design of antimicrobial membranes and thin films are critical for the design of biomaterials that can combat bacterial contamination. Since the long-term use of conventional antibiotics can result in bacterial resistance, there is a critical need to incorporate natural antimicrobial peptides (AMPs) that not only prevent a wide range of pathogens from causing infections but can also promote many beneficial outcomes in wounded tissues. We report the design and antimicrobial properties of detachable collagen (COL)/hyaluronic acid (HA) polyelectrolyte multilayers (PEMs) modified with LL-37, a naturally occurring human AMP. LL-37 was physically adsorbed and chemically immobilized on the surface of PEMs. The antimicrobial and cytotoxic properties of PEMs were tested with Gram-negative Escherichia coli (E. coli, strain DH10B) and primary rat hepatocytes, respectively. The ability to prevent bacterial adhesion and to neutralize an E. coli layer was investigated as a function of LL-37 concentration. An interesting trend was that even unmodified PEMs exhibited a 40% reduction in bacterial adhesion. When LL-37 was physically adsorbed on PEMs, bacterial adhesion was significantly lower on the surface of the films as well as in the surrounding broth. Immobilizing LL-37 resulted in less than 3% bacterial adhesion on the surface due to the presence of the peptide. LL-37 modified PEMs did not result in any cytotoxicity up to input concentrations of 16µM. More importantly, urea and albumin secretion by hepatocytes were unaffected even at high LL-37 concentrations. The COL/HA PEMs can serve as antimicrobial coatings, biological membranes and as in vitro platforms to investigate pathogen-tissue interactions. STATEMENT OF SIGNIFICANCE: Antimicrobial peptides (AMPs) are emerging as an alternative to conventional antibiotics. We report the antimicrobial properties of detachable collagen (COL)/hyaluronic acid (HA) polyelectrolyte multilayers (PEMs) modified with LL-37, a human AMP. The antimicrobial and cytotoxic properties were tested with gram-negative Escherichia coli (E. coli, strain DH10B) and primary rat hepatocytes, respectively. Unmodified PEMs exhibited a 40% reduction in bacterial adhesion. When LL-37 was physically adsorbed on PEMs, the sustained release of the active peptide killed planktonic bacteria. Immobilizing LL-37 resulted in less than 3% bacterial adhesion. LL-37 modified PEMs did not result in cytotoxicity up to input concentrations of 16µM. The COL/HA PEMs can serve as antimicrobial coatings and to investigate pathogen-cell interactions.

The Leaf Essential Oil of Eugenia reinwardtiana Growing in Australia.

The leaf essential oils of the two chemotypes of Eugenia reinwardtiana (Blume) DC growing in Australia have been investigated. Chemotype 1, isolated in 0.2% yield, w/w, dry weight, contained major amounts of α-pinene (10-26%), limonene (1-15%), ß-caryophyllene (0.7-11%), α-humulene (0.9-16%) and bicyclogermacrene (1-23%). The second chemotype, found only on coastal dunes SW of Lockerbie Qld, and isolated in 0.4-0.6% (w/w, dry weight), contained α-pinene (tr-8.5%) ß-caryophyllene (12-27%) and α-humulene (1-17%) as the major terpenes. This chemotype also contained the novel aliphatic diketone, 2-butyl-2,4,4-trimethyl-5-methoxycyclohex-5-en-1,3-dione (18-33%), whose structure determination is reported herein.

Designing a fibrotic microenvironment to investigate changes in human liver sinusoidal endothelial cell function.

The deposition of extracellular matrix (ECM) proteins by hepatic cells during fibrosis leads to the stiffening of the organ and perturbed cellular functions. Changes in the elasticity of liver tissue are manifested by altered phenotype in hepatic cells. We have investigated changes in human liver sinusoidal endothelial cells (hLSECs) that occur as the elastic modulus of their matrix transitions from healthy (6kPa) to fibrotic (36kPa) conditions. We have also investigated the role played by Kupffer cells in the dedifferentiation of hLSECs. We report the complete loss of fenestrae and the expression of CD31 at the surface as a result of increasing elastic moduli. LSECs exhibited a greater number of actin stress fibers and vinculin focal adhesion on the stiffer substrate, as well. A novel finding is that these identical trends can be obtained on soft (6kPa) substrates by introducing an inflamed microenvironment through the addition of Kupffer cells. hLSEC monocultures on 6kPa gels exhibited fenestrae that were 140.7±52.6nm in diameter as well as a lack of surface CD31 expression. Co-culturing hLSECs with rat Kupffer cells (rKCs) on 6kPa substrates, resulted in the complete loss of fenestrae, an increase in CD31 expression and in a well-organized cytoskeleton. These results demonstrate that the increasing stiffness of liver matrices does not solely result in changes in hLSEC phenotype. Even on soft substrates, culturing hLSECs in an inflamed microenvironment can result in their dedifferentiation. Our findings demonstrate the interplay between matrix elasticity and inflammation in the progression of hepatic fibrosis.

Opposing Rigidity-Protein Gradients Reverse Fibroblast Durotaxis.

The migration of cells is a complex and dynamic process that is governed by several stimuli acting simultaneously. In vivo, cells receive and process a wide range of cues that guide their motion and migratory characteristics such as speed and directionality. The design of biomaterials that can recapitulate the combinatorial signaling environment can aid in understanding how migrating cells respond to more than one stimulus and when one cue dominates over the other. We have designed hydrogel substrates that exhibit opposing rigidity-and collagen gradients. Within the boundaries of the interfacial region, the values for substrate modulus decreased in one direction with a concomitant increase in the concentration of surface-bound collagen. The well-known durotactic migration of fibroblasts was first validated on substrates that only exhibit a gradient in modulus while keeping the concentration of surface-bound collagen constant. Upon increasing the collagen concentration on the low-modulus regions by 4- or 7-fold compared to the high-modulus side of the interface, cells exhibited directed migration toward the soft regions of the substrate. This effect was more pronounced when the surface-bound collagen concentration was 7-fold greater. Cell displacements, areas, cytoskeleton and focal adhesions were investigated on the opposing rigidity-immobilized collagen gradients. These features were affected by the elastic modulus of the substrate as well as the change in protein concentration. In the future, incorporating multiple gradients within a single substrate will lead to a deeper and more comprehensive understanding of cells navigate through the complex in vivo microenvironment.

Identifying priority areas for conservation and management in diverse tropical forests.

The high concentration of the world's species in tropical forests endows these systems with particular importance for retaining global biodiversity, yet it also presents significant challenges for ecology and conservation science. The vast number of rare and yet to be discovered species restricts the applicability of species-level modelling for tropical forests, while the capacity of community classification approaches to identify priorities for conservation and management is also limited. Here we assessed the degree to which macroecological modelling can overcome shortfalls in our knowledge of biodiversity in tropical forests and help identify priority areas for their conservation and management. We used 527 plant community survey plots in the Australian Wet Tropics to generate models and predictions of species richness, compositional dissimilarity, and community composition for all the 4,313 vascular plant species recorded across the region (>1.3 million communities (grid cells)). We then applied these predictions to identify areas of tropical forest likely to contain the greatest concentration of species, rare species, endemic species and primitive angiosperm families. Synthesising these alternative attributes of diversity into a single index of conservation value, we identified two areas within the Australian wet tropics that should be a high priority for future conservation actions: the Atherton Tablelands and Daintree rainforest. Our findings demonstrate the value of macroecological modelling in identifying priority areas for conservation and management actions within highly diverse systems, such as tropical forests.

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.

The phylogeny of Celastraceae tribe Euonymeae (≈ 230 species in eight genera in both the Old and New Worlds) was inferred using morphological characters together with plastid (matK, trnL-F) and nuclear (ITS and 26S rDNA) genes. Tribe Euonymeae has been defined as those genera of Celastraceae with generally opposite leaves, isomerous carpels, loculicidally dehiscent capsules, and arillate seeds (except Microtropis). Euonymus is the most diverse (129 species) and widely cultivated genus in the tribe. We infer that tribe Euonymeae consists of at least six separate lineages within Celastraceae and that a revised natural classification of the family is needed. Microtropis and Quetzalia are inferred to be distinct sister groups that together are sister to Zinowiewia. The endangered Monimopetalum chinense is an isolated and early derived lineage of Celastraceae that represents an important component of phylogenetic diversity within the family. Hedraianthera is sister to Brassiantha, and we describe a second species (Brassiantha hedraiantheroides A.J. Ford) that represents the first reported occurrence of this genus in Australia. Euonymus globularis, from eastern Australia, is sister to Menepetalum, which is endemic to New Caledonia, and we erect a new genus (Dinghoua R.H. Archer) for it. The Madagascan species of Euonymus are sister to Pleurostylia and recognized as a distinct genus (Astrocassine ined.). Glyptopetalum, Torralbasia, and Xylonymus are all closely related to Euonymus sensu stricto and are questionably distinct from it. Current intrageneric classifications of Euonymus are not completely natural and require revision.

Leaf chemical and spectral diversity in Australian tropical forests.

Leaf chemical and spectral properties of 162 canopy species were measured at 11 tropical forest sites along a 6024 mm precipitation/yr and 8.7 degrees C climate gradient in Queensland, Australia. We found that variations in foliar nitrogen, phosphorus, chlorophyll a and b, and carotenoid concentrations, as well as specific leaf area (SLA), were expressed more strongly among species within a site than along the entire climate gradient. Integrated chemical signatures consisting of all leaf properties did not aggregate well at the genus or family levels. Leaf chemical diversity was maximal in the lowland tropical forest sites with the highest temperatures and moderate precipitation levels. Cooler and wetter montane tropical forests contained species with measurably lower variation in their chemical signatures. Foliar optical properties measured from 400 to 2500 nm were also highly diverse at the species level, and were well correlated with an ensemble of leaf chemical properties and SLA (r2 = 0.54-0.83). A probabilistic diversity model amplified the leaf chemical differences among species, revealing that lowland tropical forests maintain a chemical diversity per unit richness far greater than that of higher elevation forests in Australia. Modeled patterns in spectral diversity and species richness paralleled those of chemical diversity, demonstrating a linkage between the taxonomic and remotely sensed properties of tropical forest canopies. We conclude that species are the taxonomic unit causing chemical variance in Australian tropical forest canopies, and thus ecological and remote sensing studies should consider the role that species play in defining the functional properties of these forests.

Phylogeny of the Celastreae (Celastraceae) and the relationships of Catha edulis (qat) inferred from morphological characters and nuclear and plastid genes.

The phylogeny of Celastraceae tribe Celastreae, which includes about 350 species of trees and shrubs in 15 genera, was inferred in a simultaneous analysis of morphological characters together with nuclear (ITS and 26S rDNA) and plastid (matK, trnL-F) genes. A strong correlation was found between the geography of the species sampled and their inferred relationships. Species of Maytenus and Gymnosporia from different regions were resolved as polyphyletic groups. Maytenus was resolved in three lineages (New World, African, and Austral-Pacific), while Gymnosporia was resolved in two lineages (New World and Old World). Putterlickia was resolved as nested within the Old World Gymnosporia. Catha edulis (qat, khat) was resolved as sister to the clade of Allocassine, Cassine, Lauridia, and Maurocenia. Gymnosporia cassinoides, which is reportedly chewed as a stimulant in the Canary Islands, was resolved as a derived member of Gymnosporia and is more closely related to Lydenburgia and Putterlickia than it is to Catha. Therefore, all eight of these genera are candidates for containing cathinone- and/or cathine-related alkaloids.