Bioengineering Center

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

Hundreds of individual human cancer genome sequences are expected to be published in 2010, and thousands per year after that. The International Cancer Genome Consortium (ICGC) was launched with the aim of keeping track of the data relating to large-scale cancer genome studies of all major cancers in adults and children — a total of 50 different cancer types and/or subtypes. In this issue the ICGC team ( http://www.icgc.org ) spells out the policies and planning for the project. The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.

Polyurethanes (PUs) are a class of versatile materials with great potential for use in different applications, especially based on their structure–property relationships.

Following a seeding growth approach, gold nanoparticles of diameters 5−40 nm were prepared with 10−15% standard deviation in diameter from 3.5 ± 0.7 nm gold particle seeds. Particle size can be controlled by varying the ratio of seed to metal salt, and thus any size in the range 5−40 nm can be prepared. The method can also be scaled up to produce 10−100 mg of gold nanoparticles.

Two important goals in stem cell research are to control the cell proliferation without differentiation and to direct the differentiation into a specific cell lineage when desired. Here, we demonstrate such paths by controlling only the nanotopography of culture substrates. Altering the dimensions of nanotubular-shaped titanium oxide surface structures independently allowed either augmented human mesenchymal stem cell (hMSC) adhesion or a specific differentiation of hMSCs into osteoblasts by using only the geometric cues, absent of osteogenic inducing media. hMSC behavior in response to defined nanotube sizes revealed a very dramatic change in hMSC behavior in a relatively narrow range of nanotube dimensions. Small (approximately 30-nm diameter) nanotubes promoted adhesion without noticeable differentiation, whereas larger (approximately 70- to 100-nm diameter) nanotubes elicited a dramatic stem cell elongation (approximately 10-fold increased), which induced cytoskeletal stress and selective differentiation into osteoblast-like cells, offering a promising nanotechnology-based route for unique orthopedics-related hMSC treatments.

A general automatic approach is presented for accommodating local shape variation when mapping a two-dimensional (2-D) or three-dimensional (3-D) template image into alignment with a topologically similar target image. Local shape variability is accommodated by applying a vector-field transformation to the underlying material coordinate system of the template while constraining the transformation to be smooth (globally positive definite Jacobian). Smoothness is guaranteed without specifically penalizing large-magnitude deformations of small subvolumes by constraining the transformation on the basis of a Stokesian limit of the fluid-dynamical Navier-Stokes equations. This differs fundamentally from quadratic penalty methods, such as those based on linearized elasticity or thin-plate splines, in that stress restraining the motion relaxes over time allowing large-magnitude deformations. Kinematic nonlinearities are inherently necessary to maintain continuity of structures during large-magnitude deformations, and are included in all results. After initial global registration, final mappings are obtained by numerically solving a set of nonlinear partial differential equations associated with the constrained optimization problem. Automatic regridding is performed by propagating templates as the nonlinear transformations evaluated on a finite lattice become singular. Application of the method to intersubject registration of neuroanatomical structures illustrates the ability to account for local anatomical variability.

OBJECTIVE: Musculoskeletal models provide a non-invasive means to study human movement and predict the effects of interventions on gait. Our goal was to create an open-source 3-D musculoskeletal model with high-fidelity representations of the lower limb musculature of healthy young individuals that can be used to generate accurate simulations of gait. METHODS: Our model includes bony geometry for the full body, 37 degrees of freedom to define joint kinematics, Hill-type models of 80 muscle-tendon units actuating the lower limbs, and 17 ideal torque actuators driving the upper body. The model's musculotendon parameters are derived from previous anatomical measurements of 21 cadaver specimens and magnetic resonance images of 24 young healthy subjects. We tested the model by evaluating its computational time and accuracy of simulations of healthy walking and running. RESULTS: Generating muscle-driven simulations of normal walking and running took approximately 10 minutes on a typical desktop computer. The differences between our muscle-generated and inverse dynamics joint moments were within 3% (RMSE) of the peak inverse dynamics joint moments in both walking and running, and our simulated muscle activity showed qualitative agreement with salient features from experimental electromyography data. CONCLUSION: These results suggest that our model is suitable for generating muscle-driven simulations of healthy gait. We encourage other researchers to further validate and apply the model to study other motions of the lower extremity. SIGNIFICANCE: The model is implemented in the open-source software platform OpenSim. The model and data used to create and test the simulations are freely available at https://simtk.org/home/full_body/, allowing others to reproduce these results and create their own simulations.

Integrin adhesion receptors play a crucial role in regulating interactions between cells and extracellular matrix (ECM). Integrin activation initiates multiple intracellular signaling pathways and results in regulation of cell functions such as motility, proliferation and differentiation. Two key observations regarding the biophysical nature of integrin-mediated cell-matrix interactions motivated the present study: (1) cell motility can be regulated by modulating the magnitude of cell-substratum adhesion, by varying cell integrin expression level, integrin-ECM binding affinity or substratum ECM surface density; and (2) integrin clustering enables assembly of multiple cytoplasmic regulatory and structural proteins at sites of aggregated integrin cytoplasmic domains, activating certain intracellular signalling pathways. Here, using a minimal integrin adhesion ligand, YGRGD, we test the hypothesis that ligand clustering can affect cell migration in a manner related to its modulation of cell-substratum adhesion. We employ a synthetic polymer-linking method, which allows us to independently and systematically vary both the average surface density and the local (approx. 50 nm scale) spatial distribution of the YGRGD peptide, against a background otherwise inert with respect to cell adhesion. In this system, the ligand was presented in three alternative spatial distributions: singly, in clusters with an average of five ligands per cluster, or in clusters with an average of nine ligands per cluster; for each of these spatial distributions, a range of average ligand densities (1,000-200,000 ligands/micrometer(2)) were examined. Cluster spacing was adjusted in order to present equivalent average ligand densities independently of cluster size. The murine NR6 fibroblast cell line was used as a model because its migration behavior on ECM in the presence and absence of growth factors has been well-characterized and it expresses integrins known to interact with the YGRGD peptide. Using time-lapse videomicroscopy and analysis of individual cell movement paths, we find that NR6 cells can migrate on substrata where adhesion is mediated solely by the YGRGD peptide. As previously observed for migration of NR6 cells on fibronectin, migration speed on YGRGD is a function of the average surface ligand density. Strikingly, clustering of ligand significantly reduced the average ligand density required to support cell migration. In fact, non-clustered integrin ligands support cell attachment but neither full spreading nor haptokinetic or chemokinetic motility. In addition, by quantifying the strength of cell-substratum adhesion, we find that the variation of cell speed with spatial presentation of YGRGD is mediated via its effect on cell adhesion. These effects on motility and adhesion are also observed in the presence of epidermal growth factor (EGF), a known motility-regulating growth factor. Variation in YGRGD presentation also affects the organization of actin filaments within the cell, with a greater number of cells exhibiting stress fibers at higher cluster sizes of YGRGD. Our observations demonstrate that cell motility may be regulated by varying ligand spatial presentation at the nanoscale level, and suggest that integrin clustering is required to support cell locomotion.

Vascular calcification contributes to the high risk of cardiovascular mortality in chronic kidney disease (CKD) patients. Dysregulation of calcium (Ca) and phosphate (P) metabolism is common in CKD patients and drives vascular calcification. In this article, we review the physiological regulatory mechanisms for Ca and P homeostasis and the basis for their dysregulation in CKD. In addition, we highlight recent findings indicating that elevated Ca and P have direct effects on vascular smooth muscle cells (VSMCs) that promote vascular calcification, including stimulation of osteogenic/chondrogenic differentiation, vesicle release, apoptosis, loss of inhibitors, and extracellular matrix degradation. These studies suggest a major role for elevated P in promoting osteogenic/chondrogenic differentiation of VSMC, whereas elevated Ca has a predominant role in promoting VSMC apoptosis and vesicle release. Furthermore, the effects of elevated Ca and P are synergistic, providing a major stimulus for vascular calcification in CKD. Unraveling the complex regulatory pathways that mediate the effects of both Ca and P on VSMCs will ultimately provide novel targets and therapies to limit the destructive effects of vascular calcification in CKD patients.

Microvascular networks support metabolic activity and define microenvironmental conditions within tissues in health and pathology. Recapitulation of functional microvascular structures in vitro could provide a platform for the study of complex vascular phenomena, including angiogenesis and thrombosis. We have engineered living microvascular networks in three-dimensional tissue scaffolds and demonstrated their biofunctionality in vitro. We describe the lithographic technique used to form endothelialized microfluidic vessels within a native collagen matrix; we characterize the morphology, mass transfer processes, and long-term stability of the endothelium; we elucidate the angiogenic activities of the endothelia and differential interactions with perivascular cells seeded in the collagen bulk; and we demonstrate the nonthrombotic nature of the vascular endothelium and its transition to a prothrombotic state during an inflammatory response. The success of these microvascular networks in recapitulating these phenomena points to the broad potential of this platform for the study of cardiovascular biology and pathophysiology.

Adaptations of the critical-incident technique were used to gather reports of anesthesia-related human error and equipment failure. A total of 139 anesthesiologists, residents, and nurse-anesthetists from four hospitals participated as subjects in directed or open-ended interviews, and 48 of them functioned as "trained observers." A total of 1,089 descriptions of preventable "critical incidents" were collected. Of these, 70 represented errors or failures that had contributed in some way to a "substantive negative outcome." From these incidents, ten potential strategies were developed for prevention or detection of incidents. Overall patterns observed in this wider study were similar to those of our earlier report. The incidents most frequently reported included breathing circuit disconnections, drug-syringe swaps, gas-flow control errors and losses of gas supply. Only 4% of the incidents with substantive negative outcomes involved equipment failure, confirming the previous impression that human error is the dominant issue in anesthesia mishaps. Among the broad categories of key strategies for mishap prevention were additional technical training, improved supervision, improved organization, equipment human-factors improvements, and use of additional monitoring instrumentation. The data also suggest that less healthy patients are more likely to be affected adversely by errors. It is suggested that, in future studies of anesthesia mortality and morbidity, untoward events should be classified according to preventive strategy rather than outcome alone as an aid to those who wish to apply the experience of others to lessen the risk in their individual practice.

The various types of cells that comprise the tumor mass all carry molecular markers that are not expressed or are expressed at much lower levels in normal cells. These differentially expressed molecules can be used as docking sites to concentrate drug conjugates and nanoparticles at tumors. Specific markers in tumor vessels are particularly well suited for targeting because molecules at the surface of blood vessels are readily accessible to circulating compounds. The increased concentration of a drug in the site of disease made possible by targeted delivery can be used to increase efficacy, reduce side effects, or achieve some of both. We review the recent advances in this delivery approach with a focus on the use of molecular markers of tumor vasculature as the primary target and nanoparticles as the delivery vehicle.

While nanoparticles occur naturally in the environment and have been intentionally used for centuries, the production and use of engineered nanoparticles has seen a recent spike, which makes environmental release almost certain. Therefore, recent efforts to characterize the toxicity of engineered nanoparticles have focused on the environmental implications, including exploration of toxicity to organisms from wide-ranging parts of the ecosystem food webs. Herein, we summarize the current understanding of toxicity of engineered nanoparticles to representatives of various trophic levels, including bacteria, plants, and multicellular aquatic/terrestrial organisms, to highlight important challenges within the field of econanotoxicity, challenges that analytical chemists are expertly poised to address.

Synthetic materials that are capable of autonomous healing upon damage are being developed at a rapid pace because of their many potential applications. Despite these advancements, achieving self-healing in permanently cross-linked hydrogels has remained elusive because of the presence of water and irreversible cross-links. Here, we demonstrate that permanently cross-linked hydrogels can be engineered to exhibit self-healing in an aqueous environment. We achieve this feature by arming the hydrogel network with flexible-pendant side chains carrying an optimal balance of hydrophilic and hydrophobic moieties that allows the side chains to mediate hydrogen bonds across the hydrogel interfaces with minimal steric hindrance and hydrophobic collapse. The self-healing reported here is rapid, occurring within seconds of the insertion of a crack into the hydrogel or juxtaposition of two separate hydrogel pieces. The healing is reversible and can be switched on and off via changes in pH, allowing external control over the healing process. Moreover, the hydrogels can sustain multiple cycles of healing and separation without compromising their mechanical properties and healing kinetics. Beyond revealing how secondary interactions could be harnessed to introduce new functions to chemically cross-linked polymeric systems, we also demonstrate various potential applications of such easy-to-synthesize, smart, self-healing hydrogels.

This paper reports a new method of applying Deep Eutectic Solvents (DES) for extracting lignin from woody biomass with high yield and high purity.

Skeletal muscle architecture is defined as the arrangement of fibers in a muscle and functionally defines performance capacity. Architectural values are used to model muscle-joint behavior and to make surgical decisions. The two most extensively used human lower extremity data sets consist of five total specimens of unknown size, gender, and age. Therefore, it is critically important to generate a high-fidelity human lower extremity muscle architecture data set. We disassembled 27 muscles from 21 human lower extremities to characterize muscle fiber length and physiologic cross-sectional area, which define the excursion and force-generating capacities of a muscle. Based on their architectural features, the soleus, gluteus medius, and vastus lateralis are the strongest muscles, whereas the sartorius, gracilis, and semitendinosus have the largest excursion. The plantarflexors, knee extensors, and hip adductors are the strongest muscle groups acting at each joint, whereas the hip adductors and hip extensors have the largest excursion. Contrary to previous assertions, two-joint muscles do not necessarily have longer fibers than single-joint muscles as seen by the similarity of knee flexor and extensor fiber lengths. These high-resolution data will facilitate the development of more accurate musculoskeletal models and challenge existing theories of muscle design; we believe they will aid in surgical decision making.

Photoluminescence of graphene quantum-dot can be sensitively tuned by size, edge configurations, shape, chemical functionalities, defects, heteroatom-doping and hybridization states.

We study the problem of building text classifiers using positive and unlabeled examples. The key feature of this problem is that there is no negative example for learning. Recently, a few techniques for solving this problem were proposed in the literature. These techniques are based on the same idea, which builds a classifier in two steps. Each existing technique uses a different method for each step. We first introduce some new methods for the two steps, and perform a comprehensive evaluation of all possible combinations of methods of the two steps. We then propose a more principled approach to solving the problem based on a biased formulation of SVM, and show experimentally that it is more accurate than the existing techniques.

Growth factors, hormones, and other regulatory molecules are traditionally required in tissue engineering studies to direct the differentiation of progenitor cells along specific lineages. We demonstrate that mechanical stimulation in vitro, without ligament-selective exogenous growth and differentiation factors, induces the differentiation of mesenchymal progenitor cells from the bone marrow into a ligament cell lineage in preference to alternative paths (i.e., bone or cartilage cell lineages). A bioreactor was designed to permit the controlled application of ligament-like multidimensional mechanical strains (translational and rotational strain) to the undifferentiated cells embedded in a collagen gel. The application of mechanical stress over a period of 21 days up-regulated ligament fibroblast markers, including collagen types I and III and tenascin-C, fostered statistically significant cell alignment and density and resulted in the formation of oriented collagen fibers, all features characteristic of ligament cells. At the same time, no up-regulation of bone or cartilage-specific cell markers was observed.

Semiconductor quantum dots (QDs) are light-emitting particles on the nanometer scale that have emerged as a new class of fluorescent labels for chemical analysis, molecular imaging, and biomedical diagnostics. Compared with traditional fluorescent probes, QDs have unique optical and electronic properties such as size-tunable light emission, narrow and symmetric emission spectra, and broad absorption spectra that enable the simultaneous excitation of multiple fluorescence colors. QDs are also considerably brighter and more resistant to photobleaching than are organic dyes and fluorescent proteins. These properties are well suited for dynamic imaging at the single-molecule level and for multiplexed biomedical diagnostics at ultrahigh sensitivity. Here, we discuss the fundamental properties of QDs; the development of next-generation QDs; and their applications in bioanalytical chemistry, dynamic cellular imaging, and medical diagnostics. For in vivo and clinical imaging, the potential toxicity of QDs remains a major concern. However, the toxic nature of cadmium-containing QDs is no longer a factor for in vitro diagnostics, so the use of multicolor QDs for molecular diagnostics and pathology is probably the most important and clinically relevant application for semiconductor QDs in the immediate future.