Efficient computation of the inverse of gametic relationship matrix for a marked QTL

Best linear unbiased prediction of genetic merits for a marked quantitative trait locus (QTL) using mixed model methodology includes the inverse of conditional gametic relationship matrix (G^-1) for a marked QTL. When accounting for inbreeding, the conditional gametic relationships between two parents of individuals for a marked QTL are necessary to build G^-1 directly. Up to now, the tabular method and its adaptations have been used to compute these relationships. In the present paper, an indirect method was implemented at the gametic level to compute these few relationships. Simulation results showed that the indirect method can perform faster with significantly less storage requirements than adaptation of the tabular method. The efficiency of the indirect method was mainly due to the use of the sparseness of G^-1. The indirect method can also be applied to construct an approximate G^-1 for populations with incomplete marker data, providing approximate probabilities of descent for QTL alleles for individuals with incomplete marker data.     

Tissue engineering a blood vessel: Regulation of vascular biology by mechanical stresses

Important to the tissue engineeping of a substitute blood vessel is an understanding of those faators which regulat vascular biology. A major factor in the mechanical environment imposed by the hemodynamics of the vascular system. In this the vascular endothelium play a critical role, and mver the past two deaades much has been learned about the influence of hemodynamics on vascular endothelial biology, to a large degree using cell culture to study the effects of flow and cyclic stretch. In our laboratory, such studies ape low being extended through the development of a model of the arterial wall involving the co-culture of endothelial cells and smomth muscle cells. The development of such a model and its use in the study of endothelial cells and smmooth muscle the evolution of approaaheq to tissue engileeping a blood vessel.     

Acoustic characterisation of thoracic body tissues in the audible frequency range

A previous study by Jones and Thomas [2] suggests that data relating to the physiological condition within the thoracic cavity may be obtainable utilising low frequency acoustic signals applied to the mouth and detected on the chest wall. In order to evaluate the contribution to the mouth to chest wall frequency response of the separate elements within the thorax, and to estimate the effect on this response when the lung physiology changes, an acoustic model of the thorax is required. To aid the development of this model, experiments have been carried out in order to establish the frequency dependence of the acoustic attenuation and speed of propagation through thoracic tissue samples in the audible frequency range 20–500 Hz. Samples from the porcine family were used due to their physical similarity to those of humans and their being obtainable within a short time of death.The results of this work can be utilised in the development of an acoustic model of the human thorax, this in turn enabling simulation and analysis of low frequency acoustic transmission from the trachea to the chest wall.     

Optimised two-dimensional electrophoresis procedures for the protein characterisation of structural tissues

The protein analysis of structural tissues is typically highly problematic. Amniotic membrane displays unique wound healing and anti-scarring properties; however, little is known concerning its active protein content. The structural nature of amniotic membrane necessitated development and extensive optimisation of the entire two-dimensional (2-D) workflow. Proteins were extracted using powerful solubilisation buffers and analysis carried out using 2-D electrophoresis followed by mass spectrometry (MS) identification. Preservation and processing resulted in prefractionation of soluble from structural and membrane-associated proteins. Enhanced protein solubility was achieved by cysteine blocking using both N,N-dimethylacrylamide (DMA) alkylation and bis(2-hydroxyethyl) disulphide (HED); an alternative procedure for the effective application of HED is demonstrated. The benefits of precipitation and cup-loading versus in-gel rehydration were also assessed, with procedures for the employment of HED with the latter described. Following optimisation, a representative sample 21 proteins were identified from amniotic membrane using MS verify procedures were MS-compatible. Our results demonstrate that techniques for the reproducible separation of proteins from a proteinaceous structural tissue have been optimised. Briefly, proteins are extracted using a thiourea/urea extraction buffer containing carrier ampholytes, dithiothreitol (DTT), and 3-(cyclohexylamino)-1-propanesulfonic acid (CHAPS). After DMA alkylation, proteins were precipitated (using the 2-D clean-up kit from Amersham Biosciences) and resolubilised in extraction buffer containing a lower concentration of DTT. Samples were either cup-loaded onto rehydrated HED-containing strips or rebuffered into HED-containing buffer followed by in-gel rehydration.     

Estimation of the physiological mechanical conditioning in vascular tissue engineering by a predictive fluid-structure interaction approach

The in vitro replication of physiological mechanical conditioning through bioreactors plays a crucial role in the development of functional Small-Caliber Tissue-Engineered Blood Vessels. An in silico scaffold-specific model under pulsatile perfusion provided by a bioreactor was implemented using a fluid-structure interaction (FSI) approach for viscoelastic tubular scaffolds (e.g. decellularized swine arteries, DSA). Results of working pressures, circumferential deformations, and wall shear stress on DSA fell within the desired physiological range and indicated the ability of this model to correctly predict the mechanical conditioning acting on the cells-scaffold system. Consequently, the FSI model allowed us to a priori define the stimulation pattern, driving in vitro physiological maturation of scaffolds, especially with viscoelastic properties.     

Climate‐driven elevational variation in range sizes of vascular plants in the central Himalayas: A supporting case for Rapoport's rule

A fundamental yet controversial topic in biogeography is how and why species range sizes vary along spatial gradients. To advance our understanding of these questions and to provide insights into biological conservation, we assessed elevational variations in the range sizes of vascular plants with different life forms and biogeographical affinities and explored the main drivers underlying these variations in the longest valley in China''s Himalayas, the Gyirong Valley. Elevational range sizes of vascular plants were documented in 96 sampling plots along an elevational gradient ranging from 1,800 to 5,400 m above sea level. We assessed the elevational variations in range size by averaging the range sizes of all recorded species within each sampling plot. We then related the range size to climate, disturbance, and the mid‐domain effect and explored the relative importance of these factors in explaining the range size variations using the Random Forest model. A total of 545 vascular plants were recorded in the sampling plots along the elevational gradient. Of these, 158, 387, 337, and 112 were woody, herbaceous, temperate, and tropical species, respectively. The range size of each group of vascular plants exhibited uniform increasing trends along the elevational gradient, which was consistent with the prediction of Rapoport''s rule. Climate was the main driver of the increasing trends of vascular plant range sizes in the Gyirong Valley. The climate variability hypothesis and mean climate condition hypothesis could both explain the elevation–range size relationships. Our results reinforce the previous notion that Rapoport''s rule applies to regions where the influence of climate is the most pronounced, and call for close attention to the impact of climate change to prevent species range contraction and even extinction due to global warming.     

Lineage depletion of stromal vascular fractions isolated from human adipose tissue: a novel approach towards cell enrichment technology

The therapeutic rationale for tissue repair and regeneration using stem cells is at its infancy and needs advancement in understanding the role of individual component’s innate capability. As stem cells of adipose tissue reside in a more heterogeneous population of stromal vascular fractions, cell separation or sorting becomes an eminent step towards revealing their unique properties. This study elucidates the comparative efficacy of lineage depleted adipose derived stromal vascular fraction (SVF) and their innate ability using magnetic activated cell sorter (MACS). To this end, isolated SVF from human adipose tissue was lineage depleted according to the manufacturer’s instructions using specific antibody cocktail through MACS. The enriched lineage negative (lin−) and lineage positive (lin+) cell fractions were cultured, phenotypically characterized for the panel of cell surface markers using flowcytometry and subjected to osteoblastic and adipogenic differentiation. The expression profile obtained for lin− cells was CD34−/CD45−/HLADR−/CD49d−/CD140b−/CD31−/CD90+/CD105+/CD73+/CD54+/CD166+/CD117− when compared to Lin+ cells expressing CD34+/CD45+/HLADR−/CD49d−/CD140b+/CD31−/CD90+/CD105+/CD73+/CD54+/CD166+/CD117+ (CD—cluster of differentiation). These results, thus, advances our understanding on the inherent property of the individual cell population. Furthermore, both the fractions exhibited mesodermal lineage differentiation capacity. To conclude, this research pursuit rationalized the regenerative therapeutic applicability of both lin− and lin+ cultures of human adipose tissue for disorders of mesodermal, haematological and vascular origin.     

An intelligent bioreactor system for the cultivation of a bioartificial vascular graft

Cardiovascular disease is the most common cause of death, accounting for 31% of deaths worldwide. As purely synthetic grafts implicate concomitant anticoagulation and autologous veins are rare, tissue‐engineered vascular grafts are urgently needed. For successful in vitro cultivation of a bioartificial vascular graft, the suitable bioreactor should provide conditions comparable to vasculogenesis in the body. Such a system has been developed and characterized under continuous and pulsatile flow, and a variety of sensors has been integrated into the bioreactor to control parameters such as temperature, pressure up to 500 mbar, glucose up to 4.5 g/L, lactate, oxygen up to 150 mbar, and flow rate. Wireless data transfer (using the ZigBee specification based on the IEEE 802.15.4 standard) and multiple corresponding sensor signal processing platforms have been implemented as well. Ultrasound is used for touchless monitoring of the growing vascular structure as a quality control before implantation (maximally achieved ultrasound resolution 65 μm at 15 MHz). To withstand the harsh conditions of steam sterilization (120°C for 20 min), all electronics were encapsulated. With such a comprehensive physiologically conditioning, sensing, and imaging bioreactor system, all the requirements for a successful cultivation of vascular grafts are available now.     

The influence of fiber dispersion on the mechanical response of aortic tissues in health and disease: a computational study

Changes in the structural components of aortic tissues have been shown to play a significant role in the pathogenesis of aortic degeneration. Therefore, reliable stress analyses require a suitable and meaningful constitutive model that captures micro-structural changes. As recent data show, in-plane and out-of-plane collagen fiber dispersions vary significantly between healthy and aneurysmatic aortic walls. The aim of this study is to computationally investigate the influence of fiber dispersion on the mechanical response of aortic tissues in health and disease. In particular, the influence of three different fiber dispersions is studied: (i) non-rotationally symmetric dispersion, the most realistic assumption for aortic tissues; (ii) transversely isotropic dispersion, a special case; (iii) perfectly aligned fibers (no dispersion in either plane), another special case. Explicit expressions for the stress and elasticity tensors as needed for the implementation in a finite element code are provided. Three representative numerical examples are studied: planar biaxial extension, inflation of residually stressed and pre-stretched aortic segments and inflation of an idealized abdominal aortic aneurysm (AAA) geometry. For the AAA geometry the case of isotropic dispersion is additionally analyzed. Documented structural and mechanical parameters are taken from human aortas (healthy media/adventitia and AAA). The influence of fiber dispersions upon magnitudes and distributions of stresses and deformations are presented and analyzed. Stresses vary significantly, especially in the AAA case, where material stiffening is significantly influenced by fiber dispersion. The results highlight the need to incorporate the structural differences into finite element simulations to obtain more accurate stress predictions. Additionally, results show the capability of one constitutive model to represent different scenarios of aortic micro-structures allowing future studies of collagen reorientation during disease progression.     

Modelling the fracture-healing process as a moving-interface problem using an interface-capturing approach

We present a novel numerical model of the fracture-healing process using interface-capturing techniques, a well-known approach from fields like fluid dynamics, to describe tissue growth. One advantage of this method is its direct connection to experimentally observable parameters, including tissue-growth velocities. In our model, osteogenesis, chondrogenesis and revascularisation are triggered by mechanical stimuli via mechano-transduction based on previously established hypothesis of Claes and Heigele. After experimentally verifying the convergence of the numerical method, we compare the predictions of our model with those of the already established Ulm bone-healing model, which serves as a benchmark, and corroborate our results with existing animal experiments. We demonstrate that the new model can predict the history of the interfragmentary movement and forecast a tissue evolution that appears similar to the experimental results. Furthermore, we compare the relative tissue concentration in the healing domain with outcomes of animal experiments. Finally, we discuss the possible application of the model to new fields, where numerical simulations could also prove beneficial.     

Extracting the time-dependent transmission rate from infection data via solution of an inverse ODE problem

The transmission rate of many acute infectious diseases varies significantly in time, but the underlying mechanisms are usually uncertain. They may include seasonal changes in the environment, contact rate, immune system response, etc. The transmission rate has been thought difficult to measure directly. We present a new algorithm to compute the time-dependent transmission rate directly from prevalence data, which makes no assumptions about the number of susceptible or vital rates. The algorithm follows our complete and explicit solution of a mathematical inverse problem for SIR-type transmission models. We prove that almost any infection profile can be perfectly fitted by an SIR model with variable transmission rate. This clearly shows a serious danger of overfitting such transmission models. We illustrate the algorithm with historic UK measles data and our observations support the common belief that measles transmission was predominantly driven by school contacts.     

Rotating versus perfusion bioreactor for the culture of engineered vascular constructs based on hyaluronic acid

It is generally accepted that dynamic culture conditions are required for vascular tissue engineering. We compared the effects of two dynamic culture systems, a perfusion and a rotating bioreactor, using tubular constructs based on hyaluronic acid seeded with porcine aortic smooth muscle cells (SMC), that we recently showed to be adequate for the generation of vascular tissue. In perfused constructs mechanical stimulation importantly affected cell morphology, increased the incidence of cell proliferation and reduced apoptosis. However, extracellular matrix deposition, cytoskeletal organization and mechanical properties were poor. In rotated constructs cell proliferation was also higher and apoptosis lower than in static controls. Rotated constructs showed the highest ultimate stress and the lowest elastic modulus. Our data indicate that the rotating bioreactor is more efficient than the perfusion bioreactor and we then suggest that this method can be considered a valid alternative to complex bioreactor systems described in the literature.     

Modeling,simulations, and optimization of smooth muscle cell tissue engineering for the production of vascular grafts

The paper presents a transient, continuum, two-phase model of the tissue engineering in fibrous scaffolds, including transport equations for the flowing culture medium, nutrient and cell concentration with transverse and in-plane diffusion and cell migration, a novel feature of local in-plane transport across a phenomenological pore and innovative layer-by-layer cell filling approach. The model is successfully validated for the smooth muscle cell tissue engineering of a vascular graft using crosslinked, electrospun gelatin fiber scaffolds for both static and dynamic cell culture, the latter in a dynamic bioreactor with a rotating shaft on which the tubular scaffold is attached. Parametric studies evaluate the impact of the scaffold microstructure, cell dynamics, oxygen transport, and static or dynamic conditions on the rate and extent of cell proliferation and depth of oxygen accessibility. An optimized scaffold of 75% dry porosity is proposed that can be tissue engineered into a viable and still fully oxygenated graft of the tunica media of the coronary artery within 2 days in the dynamic bioreactor. Such scaffold also matches the mechanical properties of the tunica media of the human coronary artery and the suture retention strength of a saphenous vein, often used as a coronary artery graft.     

基于粒度反推法的景观生态安全格局优化——以海口市秀英区为例

景观生态安全格局优化是改善生态环境、促进人与自然和谐发展的有效途径。为给海口市秀英区生态环境建设提供科学依据和景观生态安全格局优化方法改进提供参考,提出了粒度反推法和生态阻力面综合构建法,结合GIS技术和最小耗费距离模型探讨了海口市秀英区景观生态安全格局优化途径。结果表明:(1)400m粒度生态景观组分是秀英区生态源地选取的合适参照,秀英区有生态源地18块、生态廊道17条、生态节点11个,新增生态源地建设的参考规模为38.5hm2,生态源地的生态服务极限距离为800m,需将现有的11块非生态景观类型斑块转换为生态景观类型,总面积20.26 hm2。(2)粒度反推法能为生态源地选取提供客观参考,在生态源地选择方面比传统方法具有更强的理论基础和客观性,解决了客观选取生态源地的问题。(3)综合生态阻力面能对生态阻力的实际情况进行较好地模拟。显、隐性生态阻力面之间存在显著差异,能反映生态系统中潜在的生态薄弱点,这些生态薄弱点往往是容易被忽略而又需要重点建设的区域。     

Explant culture: An advantageous method for isolation of mesenchymal stem cells from human tissues

Mesenchymal stem cell (MSC) research progressively moves towards clinical phases. Accordingly, a wide range of different procedures were presented in the literature for MSC isolation from human tissues; however, there is not yet any close focus on the details to offer precise information for best method selection. Choosing a proper isolation method is a critical step in obtaining cells with optimal quality and yield in companion with clinical and economical considerations. In this concern, current review widely discusses advantages of omitting proteolysis step in isolation process and presence of tissue pieces in primary culture of MSCs, including removal of lytic stress on cells, reduction of in vivo to in vitro transition stress for migrated/isolated cells, reduction of price, processing time and labour, removal of viral contamination risk, and addition of supporting functions of extracellular matrix and released growth factors from tissue explant. In next sections, it provides an overall report of technical highlights and molecular events of explant culture method for isolation of MSCs from human tissues including adipose tissue, bone marrow, dental pulp, hair follicle, cornea, umbilical cord and placenta. Focusing on informative collection of molecular and methodological data about explant methods can make it easy for researchers to choose an optimal method for their experiments/clinical studies and also stimulate them to investigate and optimize more efficient procedures according to clinical and economical benefits.     

Windows of operation for bioreactor design for the controlled formation of tissue‐engineered arteries

The availability of large numbers of units of artificial arteries would offer significant benefits to the clinical management of bypass surgery. Tissue engineering offers the potential of providing vessels that can mimic the morphology, function, and physiological environment of native vessels. Ideally this would involve culturing stem cells in vitro within a biodegradable tubular scaffold so as to construct tissue for implantation. Essential to establishing a robust process for the production of tissue‐engineered arteries is the understanding of the impact of changes in the operating conditions and bioreactor design on the construct formation. In this article, models of transport phenomena were developed to predict the critical flow rates and mass transfer requirements of a prototype bioreactor for the formation of tissue‐engineered arteries. The impact of the cell concentration, tube geometry, oxygen effective diffusivity in alginate, substrate and metabolite concentration levels, feed rate, and recycle rate on the design of the bioreactor was visualized using windows of operation and contour plots. The result of this analysis determined the best configuration of the bioreactor that meets the cellular transport requirements as well as being reliable in performance while seeking to reduce the amount of nutrients to be used. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Selective chromogenic and fluorogenic peptide substrates for the assay of cysteine peptidases in complex mixtures

This study describes the design, synthesis, and use of selective peptide substrates for cysteine peptidases of the C1 papain family, important in many biological processes. The structure of the newly synthesized substrates is Glp-Xaa-Ala-Y (where Glp = pyroglutamyl; Xaa = Phe or Val; and Y = pNA [p-nitroanilide], AMC [4-amino-7-methylcoumaride], or AFC [4-amino-7-trifluoromethyl-coumaride]). Substrates were synthesized enzymatically to guarantee selectivity of the reaction and optical purity of the target compounds, simplifying the scheme of synthesis and isolation of products. The hydrolysis of the synthesized substrates was evaluated by C1 cysteine peptidases from different organisms and with different functions, including plant enzymes papain, bromelain, ficin, and mammalian lysosomal cathepsins B and L. The new substrates were selective for C1 cysteine peptidases and were not hydrolyzed by serine, aspartic, or metallo peptidases. We demonstrated an application of the selectivity of the synthesized substrates during the chromatographic separation of a multicomponent set of digestive peptidases from a beetle, Tenebrio molitor. Used in combination with the cysteine peptidase inhibitor E-64, these substrates were able to differentiate cysteine peptidases from peptidases of other classes in midgut extracts from T. molitor larvae and larvae of the genus Tribolium; thus, they are useful in the analysis of complex mixtures containing peptidases from different classes.