Tumor-specific gene expression patterns with gene expression profiles

Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, "RFE_Relief algorithm" was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.     

The Novel Mechanical Property of Tongue of a Woodpecker

Biomaterials such as bone,teeth,nacre and silk are known to have superior mechanical properties due to their specificnanocomposite structures.Here we report that the woodpecker’s tongue exhibits a novel strength and flexibility due to its specialcomposite micro/nanostructure.The tongue consists of a flexible cartilage-and-bone skeleton covered with a thin layer tissue ofhigh strength and elasticity.At the interface between the cartilage-and-bone skeleton and the tissue layer,there is a hierarchicalfiber-typed connection.It is this special design of the tongue that makes the woodpeckers efficient in catching the insects insidetrees.The special micro/nanostructures of the woodpecker’s tongue show us a potential method to enhance the interfacialconnection between soft and hard material layers for bio-inspired composite system designs.     

Technological Parameters and Design of Bionic Integrated Honeycomb Plates

We investigated an integrated manufacturing method to develop lightweight composite materials. To design the preparation process for the integrated honeycomb plates, the shear and compressive mechanical properties of the corresponding composite materials were also investigated. The results indicate that these composite materials, with two types of resins reinforced by short basalt fibers, exhibit obvious toughness, particularly in their compressive properties. The Epoxy Resin （ER） is denser and has better bonding at the fiber and matrix interface than the vinyl ester resin matrix. Therefore, the ER exhibits better shear and compressive strengths than the vinyl ester resin matrix, thereby providing a design technology of the preparation process of the integrated honeycomb plate. The matrix material of this plate is composed of an epoxy （E51 ）, a curing agent （593）, and a thinner （501） at a ratio of 10：3：1; short basalt fibers are added as a reinforcing material at a 30% volume fraction. By increasing the curing temperature and other experimental conditions, we obtained an expected integrated honeycomb plate. This integrated honeycomb plate possesses properties such as a high fiber content, good shear and compressive performance, and high proc- essing efficiency.     

Crystal structure determination of basic phospholipase A_2 from venom of Agkistrodon halys pallas by molecular replacement method

Basic phospholipase A2 (BPLA2) from the venom of Agkistrodon halys pallas has a strong ability to hemolyze erythrocytes. The asymmetrical unit of P212121 crystal of BPLA2 contains two molecules. Self-rotation function was used to study the orientation relationship of these two molecules. Cross-rotation and translation functions were then used to determine the orientations and positions of the two molecules in the unit cell. The model building and preliminary structure refinement were carried out. The result shows that the two molecules in the asymmetrical unit of orthorhombic crystal are related by a non-crystallographic 2-fold symmetry axis.     

Biomimetic CoUagen/Hydroxyapatite Composite Scaffolds： Fabrication and Characterizations

Biomimetic collagen/hydroxyapatite scaffolds have been prepared by microwave assisted co-titration of phosphorous acid-containing collagen solution and calcium hydroxide-containing solution. The resultant scaffolds have been characterised with respect to their mechanical properties, composition and microstructures. It was observed that the in situ precipitation process could combine collagen fibril formation and hydroxyapatite （HAp） formation in one process step. Collagen fibrils guided hydroxyapatite precipitation to form bone-mimic collagen/hydroxyapatite composite containing both intrafibrillar and interfibrillar hydroxyapatites. The mineral phase was determined as low crystalline calcium-deficient hydroxyapatite with calcium to phosphorus ratio （Ca/P） of 1.4. The obtained 1% （collagen/HAp = 75/25） scaffold has a porosity of 72% and a mean pore size of 69.4 ~tm. The incorporation of hydroxyapatite into collagen matrix improved the mechanical modulus of the scaffold significantly. This could be attributed to hydroxyapatite crystallites in collagen fibrils which restricted the deformation of the collagen fibril network, and the load transfer of the collagen to the higher modulus mineral component of the composite.     

Matrix metalloproteinases and their expression in mammary gland

The matrix metalloproteinases (MMPs) are a family of zine-dependent endopeptidases that play a key role in both normal and pathological processes involving tissue remodeling events.The expression of these proteolytic enzymes is highly regulated by a balance between extracellular matrix (ECM) deposition and its degradation,and is controlled by growth factors,cytokines,hormones,as well as interactions with the ECM macromolecules.Furthermore,the activity of the MMPs is regulated by their natural endogenous inhibitors,which are members of the tissue inhibitor of metalloproteinases (TIMP) family.In the normal mammary gland,MMPs are expressed during ductal development,lobulo-alveolar development in pregnancy and involution after lactation.Under pathological conditions,such as tumorigenesis,the dysregulated expression of MMPs play a role in tumor initiation,progression and malignant conversion as well as facilitating invasion and metastasis of malignant cells through degradation of the ECM and basement membranes.     

Vascularization and osteogenesis in ectopically implanted bone tissue-engineered constructs with endothelial and osteogenic differentiated adipose-derived stem cells

BACKGROUND A major problem in the healing of bone defects is insufficient or absent blood supply within the defect.To overcome this challenging problem,a plethora of approaches within bone tissue engineering have been developed recently.Bearing in mind that the interplay of various diffusible factors released by endothelial cells(ECs)and osteoblasts(OBs)have a pivotal role in bone growth and regeneration and that adjacent ECs and OBs also communicate directly through gap junctions,we set the focus on the simultaneous application of these cell types together with platelet-rich plasma(PRP)as a growth factor reservoir within ectopic bone tissue engineering constructs.AIM To vascularize and examine osteogenesis in bone tissue engineering constructs enriched with PRP and adipose-derived stem cells(ASCs)induced into ECs and OBs.METHODS ASCs isolated from adipose tissue,induced in vitro into ECs,OBs or just expanded were used for implant construction as followed:BPEO,endothelial and osteogenic differentiated ASCs with PRP and bone mineral matrix;BPUI,uninduced ASCs with PRP and bone mineral matrix;BC(control),only bone mineral matrix.At 1,2,4 and 8 wk after subcutaneous implantation in mice,implants were extracted and endothelial-related and bone-related gene expression were analyzed,while histological analyses were performed after 2 and 8 wk.RESULTS The percentage of vascularization was significantly higher in BC compared to BPUI and BPEO constructs 2 and 8 wk after implantation.BC had the lowest endothelial-related gene expression,weaker osteocalcin immunoexpression and Spp1 expression compared to BPUI and BPEO.Endothelial-related gene expression and osteocalcin immunoexpression were higher in BPUI compared to BC and BPEO.BPEO had a higher percentage of vascularization compared to BPUI and the highest CD31 immunoexpression among examined constructs.Except Vwf,endothelial-related gene expression in BPEO had a later onset and was upregulated and well-balanced during in vivo incubation that induced late onset of Spp1 expression and pronounced osteocalcin immunoexpression at 2 and 8 wk.Tissue regression was noticed in BPEO constructs after 8 wk.CONCLUSION Ectopically implanted BPEO constructs had a favorable impact on vascularization and osteogenesis,but tissue regression imposed the need for discovering a more optimal EC/OB ratio prior to considerations for clinical applications.     

Human adult pluripotency: Facts and questions

Cellular reprogramming and induced pluripotent stem cell(IPSC) technology demonstrated the plasticity of adult cell fate, opening a new era of cellular modelling and introducing a versatile therapeutic tool for regenerative medicine.While IPSCs are already involved in clinical trials for various regenerative purposes, critical questions concerning their medium-and long-term genetic and epigenetic stability still need to be answered. Pluripotent stem cells have been described in the last decades in various mammalian and human tissues(such as bone marrow, blood and adipose tissue). We briefly describe the characteristics of human-derived adult stem cells displaying in vitro and/or in vivo pluripotency while highlighting that the common denominators of their isolation or occurrence within tissue are represented by extreme cellular stress. Spontaneous cellular reprogramming as a survival mechanism favoured by senescence and cellular scarcity could represent an adaptative mechanism. Reprogrammed cells could initiate tissue regeneration or tumour formation dependent on the microenvironment characteristics. Systems biology approaches and lineage tracing within living tissues can be used to clarify the origin of adult pluripotent stem cells and their significance for regeneration and disease.     

Insight into generation of induced mesenchymal stem cells from induced pluripotent cells

Mesenchymal stem cells(MSCs)have the potential for use in cell-based regenerative therapies.Currently,hundreds of clinical trials are using MSCs for the treatment of various diseases.However,MSCs are low in number in adult tissues;they show heterogeneity depending upon the cell source and exhibit limited proliferative potential and early senescence in in vitro cultures.These factors negatively impact the regenerative potential of MSCs and therefore restrict their use for clinical applications.As a result,novel methods to generate induced MSCs(iMSCs)from induced pluripotent stem cells have been explored.The development and optimization of protocols for generation of iMSCs from induced pluripotent stem cells is necessary to evaluate their regenerative potential in vivo and in vitro.In addition,it is important to compare iMSCs with primary MSCs(isolated from adult tissues)in terms of their safety and efficacy.Careful investigation of the properties of iMSCs in vitro and their long term behavior in animals is important for their translation from bench to bedside.     

Buzz-pollination in Neotropical bees:genus-dependent frequencies and lack of optimal frequency for pollen release

Over 50 genera of bees release pollen from flower anthers using thoracic vibrations,a phenomenon known as buzz-pollination.The efficiency of this process is directly affected by the mechanical properties of the buzzes,namely the duration,amplitude,and frequency.Nonetheless,although the effects of the former two properties are well described,the role of buzz frequency on pollen release remains unclear.Furthermore,nearly all of the existing studies describing vibrational properties of natural buzz-pollination are limited to bumblebees(Bombus)and carpenter bees(Xvlocopa)constraining our current understanding of this behavior and its evolution.Therefore,we attempted to minimize this shortcoming by testing whether flower anthers exhibit optimal frequency for pollen release and whether bees tune their buzzes to match these(optimal)frequencies.If true,certain frequencies will trigger more pollen release and lighter bees will reach buzz frequencies closer to this optimum to compensate their smaller buzz amplitudes.Two strategies were used to test these hypotheses:(i)the use of(artificial)vibrational playbacks in a broad range of buzz frequencies and amplitudes to assess pollen release by tomato plants(Solarium Ivcopersicum L.)and(ii)the recording of natural buzzes of Neotropical bees visiting tomato plants during pollination.The playback experiment indicates that although buzz frequency does affect pollen release,no optimal frequency exists for that.In addition,the recorded results of natural buzz-pollination reveal that buzz frequencies vary with bee genera and are not correlated with body size.Therefore,neither bees nor plants are tuned to optimal pollen release frequencies.Bee frequency of buzz-pollination is a likely consequence of the insect flight machinery adapted to reach higher accelerations,while flower plant response to buzz-pollination is the likely result of its pollen granular properties.     

Tensile behavior of cortical bone: dependence of organic matrix material properties on bone mineral content

A porous composite model is developed to analyze the tensile mechanical properties of cortical bone. The effects of microporosity (volksman's canals, osteocyte lacunae) on the mechanical properties of bone tissue are taken into account. A simple shear lag theory, wherein tensile loads are transferred between overlapped mineral platelets by shearing of the organic matrix, is used to model the reinforcement provided by mineral platelets. It is assumed that the organic matrix is elastic in tension and elastic-perfectly plastic in shear until it fails. When organic matrix shear stresses at the ends of mineral platelets reach their yield values, the stress-strain curve of bone tissue starts to deviate from linear behavior. This is referred as the microscopic yield point. At the point where the stress-strain behavior of bone shows a sharp curvature, the organic phase reaches its shear yield stress value over the entire platelet. This is referred as the macroscopic yield point. It is assumed that after macroscopic yield, mineral platelets cannot contribute to the load bearing capacity of bone and that the mechanical behavior of cortical bone tissue is determined by the organic phase only. Bone fails when the principal stress of the organic matrix is reached. By assuming that mechanical properties of the organic matrix are dependent on bone mineral content below the macroscopic yield point, the model is used to predict the entire tensile mechanical behavior of cortical bone for different mineral contents. It is found that decreased shear yield stresses and organic matrix elastic moduli are required to explain the mechanical behavior of bones with lowered mineral contents. Under these conditions, the predicted values (elastic modulus, 0.002 yield stress and strain, and ultimate stress and strain) are within 15% of experimental data.     

Effect of bone mineral content on the tensile properties of cortical bone: experiments and theory

The effect of mineral volume fraction on the tensile mechanical properties of cortical bone tissue is investigated by theoretical and experimental means. The mineral content of plexiform, bovine bone was lowered by 18% and 29% by immersion in fluoride solutions for 3 days and 12 days, respectively. The elastic modulus, yield strength and ultimate strength of bone tissue decreased, while the ultimate strain increased with a decrease in mineral content. The mechanical behavior of bone tissue was modeled by using a micromechanical shear lag theory consisting of overlapped mineral platelets reinforcing the organic matrix. The decrease in yield stress, by the 0.002 offset method, of the fluoride treated bones were matched in the theoretical curves by lowering the shear yield stress of the organic matrix. The failure criterion used was based on failure stresses determined from a failure envelope (Mohr's circle), which was constructed using experimental data. It was found that the model predictions of elastic modulus got worse with a decrease in mineral content (being 7.9%, 17.2% and 33.0% higher for the control, 3-day and 12-day fluoride-treated bones). As a result, the developed theory could not fully predict the yield strain of bones with lowered mineral content, being 12.9% and 21.7% lower than the experimental values. The predicted ultimate stresses of the bone tissues with lower mineral contents were within +/- 10% of the experimental values while the ultimate strains were 12.7% and 26.3% lower than the experimental values. Although the model developed in this study did not take into account the presence of hierarchical structures, voids, orientation of collagen molecules and micro cracks, it still indicated that the mechanical properties of the organic matrix depend on bone mineral content.     

Micro-Mechanical Characterization of Lung Tissue Using Atomic Force Microscopy

Matrix stiffness strongly influences growth, differentiation and function of adherent cells^1-3. On the macro scale the stiffness of tissues and organs within the human body span several orders of magnitude⁴. Much less is known about how stiffness varies spatially within tissues, and what the scope and spatial scale of stiffness changes are in disease processes that result in tissue remodeling. To better understand how changes in matrix stiffness contribute to cellular physiology in health and disease, measurements of tissue stiffness obtained at a spatial scale relevant to resident cells are needed. This is particularly true for the lung, a highly compliant and elastic tissue in which matrix remodeling is a prominent feature in diseases such as asthma, emphysema, hypertension and fibrosis. To characterize the local mechanical environment of lung parenchyma at a spatial scale relevant to resident cells, we have developed methods to directly measure the local elastic properties of fresh murine lung tissue using atomic force microscopy (AFM) microindentation. With appropriate choice of AFM indentor, cantilever, and indentation depth, these methods allow measurements of local tissue shear modulus in parallel with phase contrast and fluorescence imaging of the region of interest. Systematic sampling of tissue strips provides maps of tissue mechanical properties that reveal local spatial variations in shear modulus. Correlations between mechanical properties and underlying anatomical and pathological features illustrate how stiffness varies with matrix deposition in fibrosis. These methods can be extended to other soft tissues and disease processes to reveal how local tissue mechanical properties vary across space and disease progression.     

Organic matrixlike macromolecules associated with the mineral phase of sea urchin skeletal plates and teeth

The skeletal plates and teeth of the echinoid Paracentrotus lividus contain a heterogeneous assemblage of macromolecules that are not part of the connective tissue, but are presumably intimately associated with the mineral phase. Upon dissolution of the Mg-calcite mineral phase, some of these molecules are insoluble. The insoluble fractions of the teeth and skeletal plates are quite different, the former being predominantly protein and the latter, primarily some unknown nonproteinaceous material. The soluble constituents are similar in both tissues. These hydrophilic macromolecules have been partially separated and characterized. In both hard parts, two distinct classes of macromolecules are present, as indicated by the amino acid compositions of their protein constituents. These two classes of macromolecules are also present in the shells of a foraminifer and in various mollusks, both of which are formed by the "organic matrix-mediated" biomineralization process. The locations of these macromolecules in the teeth and skeletal plates are not known, nor whether they form coherent structures. It is therefore premature to conclude that these macromolecules do function as an organic matrix, although the results presented are in agreement with such an interpretation.     

Matrix macromolecules in hard tissues control the nucleation and hierarchical assembly of hydroxyapatite

Biogenic minerals found in teeth and bones are synthesized by precise cell-mediated mechanisms. They have superior mechanical properties due to their complex architecture. Control over biomineral properties can be accomplished by regulation of particle size, shape, crystal orientation, and polymorphic structure. In many organisms, biogenic minerals are assembled using a transient amorphous mineral phase. Here we report that organic constituents of bones and teeth, namely type I collagen and dentin matrix protein 1 (DMP1), are effective crystal modulators. They control nucleation of calcium phosphate polymorphs and the assembly of hierarchically ordered crystalline composite material. Both full-length recombinant DMP1 and post-translationally modified native DMP1 were able to nucleate hydroxyapatite (HAP) in the presence of type I collagen. However, the N-terminal domain of DMP1 (amino acid residues 1-334) inhibited HAP formation and stabilized the amorphous phase that was formed. During the nucleation and growth process, the initially formed metastable amorphous calcium phosphate phase transformed into thermodynamically stable crystalline hydroxyapatite in a precisely controlled manner. The organic matrix-mediated controlled transformation of amorphous calcium phosphate into crystalline HAP was confirmed by x-ray diffraction, selected area electron diffraction pattern, Raman spectroscopy, and elemental analysis. The mechanical properties of the protein-mediated HAP crystals were also determined as they reflect the material structure. Such understanding of biomolecule controls on biomineralization promises new insights into the controlled synthesis of crystalline structures.     

Skeletal biology: Where matrix meets mineral

The skeleton is unique from all other tissues in the body because of its ability to mineralize. The incorporation of mineral into bones and teeth is essential to give them strength and structure for body support and function. For years, researchers have wondered how mineralized tissues form and repair. A major focus in this context has been on the role of the extracellular matrix, which harbors key regulators of the mineralization process. In this introductory minireview, we will review some key concepts of matrix biology as it related to mineralized tissues. Concurrently, we will highlight the subject of this special issue covering many aspects of mineralized tissues, including bones and teeth and their associated structures cartilage and tendon. Areas of emphasis are on the generation and analysis of new animal models with permutations of matrix components as well as the development of new approaches for tissue engineering for repair of damaged hard tissue. In assembling key topics on mineralized tissues written by leaders in our field, we hope the reader will get a broad view of the topic and all of its fascinating complexities.     

Altering biomineralization by protein design

To create a bioceramic with unique materials properties, biomineralization exploits cells to create a tissue-specific protein matrix to control the crystal habit, timing, and position of the mineral phase. The biomineralized covering of vertebrate teeth is enamel, a distinctive tissue of ectodermal origin that is collagen-free. In forming enamel, amelogenin is the abundant protein that undergoes self-assembly to contribute to a matrix that guides its own replacement by mineral. Conserved domains in amelogenin suggest their importance to biomineralization. We used gene targeting in mice to replace native amelogenin with one of two engineered amelogenins. Replacement changed enamel organization by altering protein-to-crystallite interactions and crystallite stacking while diminishing the ability of the ameloblast to interact with the matrix. These data demonstrate that ameloblasts must continuously interact with the developing matrix to provide amelogenin-specific protein to protein, protein to mineral, and protein to membrane interactions critical to biomineralization and enamel architecture while suggesting that mutations within conserved amelogenin domains could account for enamel variations preserved in the fossil record.     

Cell mechanics studied by a reconstituted model tissue

Tissue models reconstituted from cells and extracellular matrix (ECM) simulate natural tissues. Cytoskeletal and matrix proteins govern the force exerted by a tissue and its stiffness. Cells regulate cytoskeletal structure and remodel ECM to produce mechanical changes during tissue development and wound healing. Characterization and control of mechanical properties of reconstituted tissues are essential for tissue engineering applications. We have quantitatively characterized mechanical properties of connective tissue models, fibroblast-populated matrices (FPMs), via uniaxial stretch measurements. FPMs resemble natural tissues in their exponential dependence of stress on strain and linear dependence of stiffness on force at a given strain. Activating cellular contractile forces by calf serum and disrupting F-actin by cytochalasin D yield "active" and "passive" components, which respectively emphasize cellular and matrix mechanical contributions. The strain-dependent stress and elastic modulus of the active component were independent of cell density above a threshold density. The same quantities for the passive component increased with cell number due to compression and reorganization of the matrix by the cells.     

Biomineralization: a structural perspective

Biomineralization is an inherently structural subject; the structure of the mineral phase, the structure of the matrix composed of macromolecules and especially the structure of the interphase zone between them. Studies of the dynamics of mineral formation have revealed that a widespread strategy used by many organisms is to first form a disordered mineral phase. Only when it is in place and has adopted its appropriate shape, is it induced to crystallize. Matrix studies have highlighted the importance of a unique group of proteins that are rich in aspartic acid. These are involved in controlling mineral formation. Relating structure to function in mineralized tissues, often involves an understanding of mechanical properties in terms of not only the hierarchical structure of the tissue, but also the graded structure that varies from one location to another. Structure is thus in many respects the foundation upon which the field of biomineralization rests.     

Nanoindentation of lemur enamel: an ecological investigation of mechanical property variations within and between sympatric species

The common morphological metrics of size, shape, and enamel thickness of teeth are believed to reflect the functional requirements of a primate's diet. However, the mechanical and material properties of enamel also contribute to tooth function, yet are rarely studied. Substantial wear and tooth loss previously documented in Lemur catta at the Beza Mahafaly Special Reserve suggests that their dental morphology, structure, and possibly their enamel are not adapted for their current fallback food (the mechanically challenging tamarind fruit). In this study, we investigate the nanomechanical properties, mineralization, and microstructure of the enamel of three sympatric lemur species to provide insight into their dietary functional adaptations. Mechanical properties measured by nanoindentation were compared to measurements of mineral content, prism orientation, prism size, and enamel thickness using electron microscopy. Mechanical properties of all species were similar near the enamel dentin junction and variations correlated with changes in microstructure (e.g., prism size) and mineral content. Severe wear and microcracking within L. catta's enamel were associated with up to a 43% reduction in nanomechanical properties in regions of cracking versus intact enamel. The mechanical and material properties of L. catta's enamel are similar to those of sympatric folivores and suggest that they are not uniquely mechanically adapted to consume the physically challenging tamarind fruit. An understanding of the material and mechanical properties of enamel is required to fully elucidate the functional and ecological adaptations of primate teeth.