Submillisecond Elastic Recoil Reveals Molecular Origins of Fibrin Fiber Mechanics

Fibrin fibers form the structural scaffold of blood clots. Thus, their mechanical properties are of central importance to understanding hemostasis and thrombotic disease. Recent studies have revealed that fibrin fibers are elastomeric despite their high degree of molecular ordering. These results have inspired a variety of molecular models for fibrin’s elasticity, ranging from reversible protein unfolding to rubber-like elasticity. An important property that has not been explored is the timescale of elastic recoil, a parameter that is critical for fibrin’s mechanical function and places a temporal constraint on molecular models of fiber elasticity. Using high-frame-rate imaging and atomic force microscopy-based nanomanipulation, we measured the recoil dynamics of individual fibrin fibers and found that the recoil was orders of magnitude faster than anticipated from models involving protein refolding. We also performed steered discrete molecular-dynamics simulations to investigate the molecular origins of the observed recoil. Our results point to the unstructured αC regions of the otherwise structured fibrin molecule as being responsible for the elastic recoil of the fibers.     

Recoil after Severing Reveals Stress Fiber Contraction Mechanisms

Stress fibers are cellular contractile actomyosin machines central to wound healing, shear stress response, and other processes. Contraction mechanisms have been difficult to establish because stress fibers in cultured cells typically exert isometric tension and present little kinetic activity. In a recent study, living cell stress fibers were severed with laser nanoscissors and recoiled several μm over ∼5 s. We developed a quantitative model of stress fibers based on known components and available structural information suggesting periodic sarcomeric organization similar to striated muscle. The model was applied to the severing assay and compared to the observed recoil. We conclude that the sarcomere force-length relation is similar to that of muscle with two distinct regions on the ascending limb and that substantial external drag forces act on the recoiling fiber corresponding to effective cytosolic viscosity ∼10⁴ times that of water. This may originate from both nonspecific and specific interactions. The model predicts highly nonuniform contraction with caps of collapsed sarcomeres growing at the severed ends. A directly measurable signature of external drag is that cap length and recoil distance increase at intermediate times as t^1/2. The severing data is consistent with this prediction.     

Genomics Reveals the Origins of Historical Specimens

Centuries of zoological studies have amassed billions of specimens in collections worldwide. Genomics of these specimens promises to reinvigorate biodiversity research. However, because DNA degrades with age in historical specimens, it is a challenge to obtain genomic data for them and analyze degraded genomes. We developed experimental and computational protocols to overcome these challenges and applied our methods to resolve a series of long-standing controversies involving a group of butterflies. We deduced the geographical origins of several historical specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old specimens that serve as irreplaceable embodiments of species concepts cannot be confidently assigned to extant species or population due to the lack of diagnostic morphological features and clear documentation of the collection locality. The ability to determine where they were collected will resolve many on-going disputes. More broadly, we show the utility of applying genomics to historical museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.     

Molecular Aspects of Fibrin Clot Solubilization

THE human plasma protein, fibrinogen, is a disulphide bonded¹ dimer², each unit containing an Aα, Bβ and 8 chain^*, interconnected by disulphide bridges³. Thrombin (E.C.3.4.4.-13) releases fibrinopeptides A and B from the Aα and Bβ chains respectively⁴ to form fibrin monomer (α₂β₂γ₂) ? which polymerizes to form fibrin polymer or clotted fibrin. This polymer, following factor XIII (plasma transglutaminase, fibrin stabilizing factor) mediated crosslinking among the α chains and among the γ chains⁵, is one of the major and initiating constituents of a thrombus. Fibrinolytic activators, for example, streptokinase (SK) and urokinase (UK), are of thrombolytic value as they convert the thrombus plasminogen to plasmin (E.C.3.4.4.14) which by fibrinolytic action dissolves the thrombus. Whereas the interaction of fibrinogen and plasmin has been well studied^6–9, little is known concerning the mechanism of plasmin mediated fibrin clot lysis. I report here on the mechanism of non-cross-linked fibrin clot solubilization in near physiological conditions.     

Molecular Views of Human Origins

Over the last half century, comparative genomics has increasingly contributed to the definition, resolution and interpretation of human evolution. Early comparisons demonstrated that African apes and humans were more closely related and diverged later than commonly thought. However, it was difficult to determine the branching between humans, chimpanzees and gorillas. By the 1990s, sufficient biomolecular data had accumulated to demonstrate that chimpanzees and humans shared a common ancestor after the divergence of the gorilla. Current reconstructions place the divergence of humans and chimpanzees at 6–8 million years. Comparative genomics from complete genome sequencing to chromosome painting provide a scenario for the origin of the human genome. Starting form the ancestral mammalian karyotype, we can determine the major steps over the last 90 million years leading to the formation of each human chromosome. Despite considerable technical problems, studies of ancient DNA now provide a direct genetic witness of human evolution and add a temporal dimension to reconstructions of our evolutionary history and phylogeny. Ancient DNA has shown that Neanderthals probably did not interbreed with anatomically modern humans and did not make a significant contribution to the gene pool of our species. Ancient DNA has also contributed to the studies of the colonization of the Americas and the Pacific Island, and the domestication of plants and animals. Understanding the genetic basis of the physical and behavioral traits that distinguish humans from other primates presents one of the great future challenges of science.     

Metabolomics Reveals the Origins of Antimicrobial Plant Resins Collected by Honey Bees

The deposition of antimicrobial plant resins in honey bee, Apis mellifera, nests has important physiological benefits. Resin foraging is difficult to approach experimentally because resin composition is highly variable among and between plant families, the environmental and plant-genotypic effects on resins are unknown, and resin foragers are relatively rare and often forage in unobservable tree canopies. Subsequently, little is known about the botanical origins of resins in many regions or the benefits of specific resins to bees. We used metabolomic methods as a type of environmental forensics to track individual resin forager behavior through comparisons of global resin metabolite patterns. The resin from the corbiculae of a single bee was sufficient to identify that resin''s botanical source without prior knowledge of resin composition. Bees from our apiary discriminately foraged for resin from eastern cottonwood (Populus deltoides), and balsam poplar (P. balsamifera) among many available, even closely related, resinous plants. Cottonwood and balsam poplar resin composition did not show significant seasonal or regional changes in composition. Metabolomic analysis of resin from 6 North American Populus spp. and 5 hybrids revealed peaks characteristic to taxonomic nodes within Populus, while antimicrobial analysis revealed that resin from different species varied in inhibition of the bee bacterial pathogen, Paenibacillus larvae. We conclude that honey bees make discrete choices among many resinous plant species, even among closely related species. Bees also maintained fidelity to a single source during a foraging trip. Furthermore, the differential inhibition of P. larvae by Populus spp., thought to be preferential for resin collection in temperate regions, suggests that resins from closely related plant species many have different benefits to bees.     

Defining Elastic Fiber Interactions by Molecular Fishing: AN AFFINITY PURIFICATION AND MASS SPECTROMETRY APPROACH*

Deciphering interacting networks of the extracellular matrix is a major challenge. We describe an affinity purification and mass spectrometry strategy that has provided new insights into the molecular interactions of elastic fibers, essential extracellular assemblies that provide elastic recoil in dynamic tissues. Using cell culture models, we defined primary and secondary elastic fiber interaction networks by identifying molecular interactions with the elastic fiber molecules fibrillin-1, MAGP-1, fibulin-5, and lysyl oxidase. The sensitivity and validity of our method was confirmed by identification of known interactions with the bait proteins. Our study revealed novel extracellular protein interactions with elastic fiber molecules and delineated secondary interacting networks with fibronectin and heparan sulfate-associated molecules. This strategy is a novel approach to define the macromolecular interactions that sustain complex extracellular matrix assemblies and to gain insights into how they are integrated into their surrounding matrix.Mass spectrometry is emerging as a powerful approach to identify protein interaction partners in molecular complexes. We have developed an affinity purification and mass spectrometry strategy that is applicable to the analysis of molecular interactions of extracellular matrix complexes. The extracellular matrix provides structural support to tissues and profoundly influences cell survival, proliferation, migration, and phenotypic state. It is a complex multimolecular and three-dimensional milieu that comprises assembled networks of tissue-specific combinations of structural and cell-adhesive glycoproteins, proteoglycans, and cross-linking enzymes. The matrix also sequesters numerous growth factors and cytokines, thereby controlling their bioavailability. Delineating the molecular nature of the fundamental interacting networks within complex extracellular matrices is a challenging task. Here, mass spectrometry has given new insights into elastic fiber interactions.Elastic fibers are essential structural elements of the extracellular matrix of dynamic connective tissues such as blood vessels, lungs, skin, and ligaments, endowing these tissues with elastic recoil (1, 2). Their importance is emphasized by elastic fiber defects that cause severe acquired diseases such as aortic aneurysms and pulmonary emphysema and life-threatening heritable disorders such as Marfan syndrome, supravalvular stenosis, and cutis laxa. These fibers are extensive multimolecular assemblies that adopt intricate tissue-specific architectural arrangements. At the morphological level, the fibers comprise a cross-linked elastin core and an outer mantle of fibrillin microfibrils. It has proved challenging to define the composition of tissue elastic fibers biochemically. Cross-linked elastin is highly insoluble and its isolation from tissues requires extreme conditions of hot alkali, which destroys other proteins (2). The efficient extraction of tissue microfibrils requires collagenase and other proteolytic activities that may destroy associated molecules (3). Despite these difficulties, a number of associated proteins, including MAGP-1,1 βigH3, fibulins, and lysyl oxidases (LOX and LOXL (also known as LOXL1)), as well as latent TGFβ-binding proteins (LTBPs), collagen VIII, and emilin-1 have been identified in biochemical and/or colocalization studies (1).Fibrillins are very large glycoproteins (350 kDa) containing 43 calcium-binding epidermal growth factor-like domains and seven TGFβ-binding protein-like (8-cysteine) domains (4). Fibrillin-1 is the more abundant isoform; fibrillin-2 is mainly expressed during development (5, 6). Tropoelastin, the secreted soluble form of elastin, comprises alternating hydrophobic and lysine-rich cross-linking domains. LOX and LOXL are copper-dependent amine oxidases that cross-link elastin through the oxidative deamination of specific lysines (7–9). Elastin is mainly expressed and deposited early in life and undergoes very little turnover in healthy tissues (2). MAGP-1 is a microfibril-associated glycoprotein that binds fibrillin-1 and elastin (10, 11) but is not essential for elastic fiber formation (12). βigH3 was originally identified as a matrix protein, MP78/70, in tissue extracts that solubilized elastin-associated microfibrils (13, 14). Fibulin-4 and -5 play essential roles in elastic fiber formation (15, 16), most likely by regulating elastin deposition onto microfibrils (17, 18). Fibulin-2 interacts with fibrillin-1 (19) but is not essential for elastic fiber formation (20). Fibulin-1-null mice, among other symptoms, display anomalies of aortic arch arteries and hemorrhagic blood vessels, suggesting some involvement in elastic fiber biology (21). Fibulin-3 (also known as Efemp1)-deficient mice exhibit early aging and herniation associated with reduced elastic fiber integrity (22). Collagen VIII and emilin-1 also colocalize to elastic fibers (23, 24).The assembly of microfibrils and elastic fibers remains incompletely understood. We and others recently showed that assembly of the microfibril component is orchestrated by the cell surface through interactions with fibronectin and integrin receptors (25, 26). Heparan sulfate, an abundant pericellular glycosaminoglycan chain attached to syndecan and glypican proteoglycan receptors, also critically influences microfibril formation (27–29). Elastin deposition and stabilization on microfibrils require fibulins and the cross-linking enzymes LOX and/or LOXL.To obtain new insights into the molecular interactions of elastic fibers and how they are integrated into their surrounding matrix, we conducted a detailed affinity capture LC-MS/MS analysis of molecules that interact in culture specifically with four His₆-tagged recombinant human elastic fiber molecules (fibrillin-1, MAGP-1, fibulin-5, and LOX). Tropoelastin was not used as bait because of its highly adhesive nature. Our protocol proved to be an effective strategy for defining specific interactions of elastic fiber molecules in the extracellular matrix. Efficacy was demonstrated through confirmation of known interactions and validation of novel extracellular matrix protein-protein interactions. This approach further allowed us to predict secondary elastic fiber interactions, giving powerful insights into the molecular networks that sustain elastic fibers within higher order extracellular matrices.     

Complex Intramolecular Mechanics of G-actin — An Elastic Network Study

Systematic numerical investigations of conformational motions in single actin molecules were performed by employing a simple elastic-network (EN) model of this protein. Similar to previous investigations for myosin, we found that G-actin essentially behaves as a strain sensor, responding by well-defined domain motions to mechanical perturbations. Several sensitive residues within the nucleotide-binding pocket (NBP) could be identified, such that the perturbation of any of them can induce characteristic flattening of actin molecules and closing of the cleft between their two mobile domains. Extending the EN model by introduction of a set of breakable links which become effective only when two domains approach one another, it was observed that G-actin can possess a metastable state corresponding to a closed conformation and that a transition to this state can be induced by appropriate perturbations in the NBP region. The ligands were roughly modeled as a single particle (ADP) or a dimer (ATP), which were placed inside the NBP and connected by elastic links to the neighbors. Our approximate analysis suggests that, when ATP is present, it stabilizes the closed conformation of actin. This may play an important role in the explanation why, in the presence of ATP, the polymerization process is highly accelerated.     

A Comprehensive Molecular Phylogeny of Dalytyphloplanida (Platyhelminthes: Rhabdocoela) Reveals Multiple Escapes from the Marine Environment and Origins of Symbiotic Relationships

In this study we elaborate the phylogeny of Dalytyphloplanida based on complete 18S rDNA (156 sequences) and partial 28S rDNA (125 sequences), using a Maximum Likelihood and a Bayesian Inference approach, in order to investigate the origin of a limnic or limnoterrestrial and of a symbiotic lifestyle in this large group of rhabditophoran flatworms. The results of our phylogenetic analyses and ancestral state reconstructions indicate that dalytyphloplanids have their origin in the marine environment and that there was one highly successful invasion of the freshwater environment, leading to a large radiation of limnic and limnoterrestrial dalytyphloplanids. This monophyletic freshwater clade, Limnotyphloplanida, comprises the taxa Dalyelliidae, Temnocephalida, and most Typhloplanidae. Temnocephalida can be considered ectosymbiotic Dalyelliidae as they are embedded within this group. Secondary returns to brackish water and marine environments occurred relatively frequently in several dalyeliid and typhloplanid taxa. Our phylogenies also show that, apart from the Limnotyphloplanida, there have been only few independent invasions of the limnic environment, and apparently these were not followed by spectacular speciation events. The distinct phylogenetic positions of the symbiotic taxa also suggest multiple origins of commensal and parasitic life strategies within Dalytyphloplanida. The previously established higher-level dalytyphloplanid clades are confirmed in our topologies, but many of the traditional families are not monophyletic. Alternative hypothesis testing constraining the monophyly of these families in the topologies and using the approximately unbiased test, also statistically rejects their monophyly.     

Computational Modeling Reveals Dendritic Origins of GABAA-Mediated Excitation in CA1 Pyramidal Neurons

GABA is the key inhibitory neurotransmitter in the adult central nervous system, but in some circumstances can lead to a paradoxical excitation that has been causally implicated in diverse pathologies from endocrine stress responses to diseases of excitability including neuropathic pain and temporal lobe epilepsy. We undertook a computational modeling approach to determine plausible ionic mechanisms of GABA_A-dependent excitation in isolated post-synaptic CA1 hippocampal neurons because it may constitute a trigger for pathological synchronous epileptiform discharge. In particular, the interplay intracellular chloride accumulation via the GABA_A receptor and extracellular potassium accumulation via the K/Cl co-transporter KCC2 in promoting GABA_A-mediated excitation is complex. Experimentally it is difficult to determine the ionic mechanisms of depolarizing current since potassium transients are challenging to isolate pharmacologically and much GABA signaling occurs in small, difficult to measure, dendritic compartments. To address this problem and determine plausible ionic mechanisms of GABA_A-mediated excitation, we built a detailed biophysically realistic model of the CA1 pyramidal neuron that includes processes critical for ion homeostasis. Our results suggest that in dendritic compartments, but not in the somatic compartments, chloride buildup is sufficient to cause dramatic depolarization of the GABA_A reversal potential and dominating bicarbonate currents that provide a substantial current source to drive whole-cell depolarization. The model simulations predict that extracellular K⁺ transients can augment GABA_A-mediated excitation, but not cause it. Our model also suggests the potential for GABA_A-mediated excitation to promote network synchrony depending on interneuron synapse location - excitatory positive-feedback can occur when interneurons synapse onto distal dendritic compartments, while interneurons projecting to the perisomatic region will cause inhibition.     

The Molecular Mechanics of Quantized Valence Bonds

A new force field, Quantized Valence Bonds′ Molecular Mechanics (QVBMM) has been included in the molecular modeling program STR3DI.EXE. The QVBMM force field successfully embraces and implements all of the pivotal concepts in VSEPR theory and uniquely integrates lone pairs into molecular mechanics. QVBMM facilitates a detailed analysis of the stereo-electronic effects that contribute to the structural and conformational preferences of organic molecules in their ground states, including those molecules that possess the common heteroatoms. The design, parameterization and application of the force field to a few representative molecules is discussed. The anomeric effect is also briefly examined.     

Proteomic Profiling Reveals the Molecular Control of Oocyte Maturation

Meiotic maturation is an intricate and precisely regulated process orchestrated by various pathways and numerous proteins. However, little is known about the proteome landscape during oocytes maturation. Here, we obtained the temporal proteomic profiles of mouse oocytes during in vivo maturation. We successfully quantified 4694 proteins from 4500 oocytes in three key stages (germinal vesicle, germinal vesicle breakdown, and metaphase II). In particular, we discovered the novel proteomic features during oocyte maturation, such as the active Skp1–Cullin–Fbox pathway and an increase in mRNA decay–related proteins. Using functional approaches, we further identified the key factors controlling the histone acetylation state in oocytes and the vital proteins modulating meiotic cell cycle. Taken together, our data serve as a broad resource on the dynamics occurring in oocyte proteome and provide important knowledge to better understand the molecular mechanisms during germ cell development.     

Measurement of Elastic Modulus of Collagen Type I Single Fiber

Collagen fibers are the main components of the extra cellular matrix and the primary contributors to the mechanical properties of tissues. Here we report a novel approach to measure the longitudinal component of the elastic moduli of biological fibers under conditions close to those found in vivo and apply it to type I collagen from rat tail tendon. This approach combines optical tweezers, atomic force microscopy, and exploits Euler-Bernoulli elasticity theory for data analysis. This approach also avoids drying for measurements or visualization, since samples are freshly extracted. Importantly, strains are kept below 0.5%, which appear consistent with the linear elastic regime. We find, surprisingly, that the longitudinal elastic modulus of type I collagen cannot be represented by a single quantity but rather is a distribution that is broader than the uncertainty of our experimental technique. The longitudinal component of the single-fiber elastic modulus is between 100 MPa and 360 MPa for samples extracted from different rats and/or different parts of a single tail. Variations are also observed in the fibril-bundle / fibril diameter with an average of 325±40 nm. Since bending forces depend on the diameter to the fourth power, this variation in diameter is important for estimating the range of elastic moduli. The remaining variations in the modulus may be due to differences in composition of the fibril-bundles, or the extent of the proteoglycans constituting fibril-bundles, or that some single fibrils may be of fibril-bundle size.     

An Interspecies Analysis Reveals Molecular Construction Principles of Interleukin 27

Interleukin 27 (IL-27) is a cytokine that regulates inflammatory responses. It is composed of an α subunit (IL-27α) and a β subunit (EBI3), which together form heterodimeric IL-27. Despite this general principle, IL-27 from different species shows distinct characteristics: Human IL-27α is not secreted autonomously while EBI3 is. In mice, the subunits show a reciprocal behavior. The molecular basis and the evolutionary conservation of these differences have remained unclear. They are biologically important, however, since secreted IL-27 subunits can act as cytokines on their own.Here, we show that formation of a single disulfide bond is an evolutionary conserved trait, which determines secretion-competency of IL-27α. Furthermore, combining cell-biological with computational approaches, we provide detailed structural insights into IL-27 heterodimerization and find that it relies on a conserved interface. Lastly, our study reveals a hitherto unknown construction principle of IL-27: one secretion-competent subunit generally pairs with one that depends on the other to induce its secretion.Taken together, these findings significantly extend our understanding of IL-27 biogenesis as a key cytokine and highlight how protein assembly can influence immunoregulation.     

Molecular Characterization of Cryptosporidium molnari Reveals a Distinct Piscine Clade

Multilocus phylogenetic analysis of small-subunit (SSU) rRNA and actin from Cryptosporidium molnari clustered this species with the C. molnari-like genotype of an isolate from the guppy, although the two fish isolates seem to be distinct species. The analysis of available piscine genotypes provides some support for cladistic congruence of the genus Piscicryptosporidium, but additional piscine genotypes are needed.Recent reviews accept more than 20 valid cryptosporidium species (7, 20), and characterization of additional isolates is expanding this list rapidly (http://www.vetsci.usyd.edu.au/staff/JanSlapeta/icrypto/index.htm). In addition, numerous morphotypes or genotypes have been proposed whose taxonomic affiliation is unsettled due to incomplete characterization according to minimum consensus standards (5, 7, 24). Five species have been proposed for fish isolates (15), but only Cryptosporidium molnari and Cryptosporidium scophthalmi (2, 4) stand as valid species (20), although not without discussion (7). Fish cryptosporidia present some unique features, which have even led to the genus Piscicryptosporidium being proposed (13). However, lack of genetic support keeps this genus and several fish morphotypes as incertae sedis (12, 15, 24). Detailed biological data on C. molnari and C. scophthalmi have been previously presented (3, 18, 19), but no molecular characterization has yet been conducted, thus hampering species identification of other fish isolates (7, 24) and evaluation of their relationships within the genus (15). Ribosomal and actin gene data on an isolate from guppy fish (Poecilia reticulata) have been obtained, and preliminary analyses of these sequences indicated a basal position in the cryptosporidial tree (17). Although it was regarded as C. molnari-like, biological characterization of this isolate was limited. The purpose of this work was to provide the necessary C. molnari comparative genetic data and to clarify the relationship of available fish isolates in a phylogenetic context.     

In Vivo Time-Resolved Microtomography Reveals the Mechanics of the Blowfly Flight Motor

Dipteran flies are amongst the smallest and most agile of flying animals. Their wings are driven indirectly by large power muscles, which cause cyclical deformations of the thorax that are amplified through the intricate wing hinge. Asymmetric flight manoeuvres are controlled by 13 pairs of steering muscles acting directly on the wing articulations. Collectively the steering muscles account for <3% of total flight muscle mass, raising the question of how they can modulate the vastly greater output of the power muscles during manoeuvres. Here we present the results of a synchrotron-based study performing micrometre-resolution, time-resolved microtomography on the 145 Hz wingbeat of blowflies. These data represent the first four-dimensional visualizations of an organism''s internal movements on sub-millisecond and micrometre scales. This technique allows us to visualize and measure the three-dimensional movements of five of the largest steering muscles, and to place these in the context of the deforming thoracic mechanism that the muscles actuate. Our visualizations show that the steering muscles operate through a diverse range of nonlinear mechanisms, revealing several unexpected features that could not have been identified using any other technique. The tendons of some steering muscles buckle on every wingbeat to accommodate high amplitude movements of the wing hinge. Other steering muscles absorb kinetic energy from an oscillating control linkage, which rotates at low wingbeat amplitude but translates at high wingbeat amplitude. Kinetic energy is distributed differently in these two modes of oscillation, which may play a role in asymmetric power management during flight control. Structural flexibility is known to be important to the aerodynamic efficiency of insect wings, and to the function of their indirect power muscles. We show that it is integral also to the operation of the steering muscles, and so to the functional flexibility of the insect flight motor.