A Mechanobiology-based Algorithm to Optimize the Microstructure Geometry of Bone Tissue Scaffolds

Complexity of scaffold geometries and biological mechanisms involved in the bone generation process make the design of scaffolds a quite challenging task. The most common approaches utilized in bone tissue engineering require costly protocols and time-consuming experiments. In this study we present an algorithm that, combining parametric finite element models of scaffolds with numerical optimization methods and a computational mechano-regulation model, is able to predict the optimal scaffold microstructure. The scaffold geometrical parameters are perturbed until the best geometry that allows the largest amounts of bone to be generated, is reached. We study the effects of the following factors: (1) the shape of the pores; (2) their spatial distribution; (3) the number of pores per unit area. The optimal dimensions of the pores have been determined for different values of scaffold Young''s modulus and compression loading acting on the scaffold upper surface.Pores with rectangular section were predicted to lead to the formation of larger amounts of bone compared to square section pores; similarly, elliptic pores were predicted to allow the generation of greater amounts of bone compared to circular pores. The number of pores per unit area appears to have rather negligible effects on the bone regeneration process. Finally, the algorithm predicts that for increasing loads, increasing values of the scaffold Young''s modulus are preferable.The results shown in the article represent a proof-of-principle demonstration of the possibility to optimize the scaffold microstructure geometry based on mechanobiological criteria.     

Identification of quantitative trait loci associated with bone traits and body weight in an F2 resource population of chickens*

Bone fractures at the end of lay are a significant problem in egg-laying strains of hens. The objective of the current study was to identify quantitative trait loci (QTL) associated with bone mineralization and strength in a chicken resource population. Layer (White Leghorn hens) and broiler (Cobb-Cobb roosters) lines were crossed to generate an F2 population of 508 hens over seven hatches, and 26 traits related to bone integrity, including bone mineral density (BMD) and content (BMC), were measured. Genotypes of 120 microsatellite markers on 28 autosomal groups were determined, and interval mapping was conducted to identify QTL regions. Twenty-three tests representing three chromosomal regions (chromosomes 4, 10 and 27) contained significant QTL that surpassed the 5% genome-wise threshold, and 47 tests representing 15 chromosomes identified suggestive QTL that surpassed the 5% chromosome-wise threshold. Although no significant QTL influencing BMD and BMC were detected after adjusting for variation in body weight and egg production, multiple suggestive QTL were found. These results support previous experiments demonstrating an important genetic regulation of bone strength in chickens, but suggest the regulation may be due to the effects of multiple genes that each account for relatively small amounts of variation in bone strength.     

Influence of functionally graded pores on bone ingrowth in cementless hip prosthesis: a finite element study using mechano-regulatory algorithm

Cementless hip prostheses with porous outer coating are commonly used to repair the proximally damaged femurs. It has been demonstrated that stability of prosthesis is also highly dependent on the bone ingrowth into the porous texture. Bone ingrowth is influenced by the mechanical environment produced in the callus. In this study, bone ingrowth into the porous structure was predicted by using a mechano-regulatory model. Homogenously distributed pores (200 and 800 \(\upmu \)m in diameter) and functionally graded pores along the length of the prosthesis were introduced as a porous coating. Bone ingrowth was simulated using 25 and 12 \(\upmu \)m micromovements. Load control simulations were carried out instead of traditionally used displacement control. Spatial and temporal distributions of tissues were predicted in all cases. Functionally graded pore decreasing models gave the most homogenous bone distribution, the highest bone ingrowth (98%) with highest average Young’s modulus of all tissue phenotypes approximately 4.1 GPa. Besides this, the volume of the initial callus increased to 8.33% in functionally graded pores as compared to the 200 \(\upmu \)m pore size models which increased the bone volume. These findings indicate that functionally graded porous surface promote bone ingrowth efficiently which can be considered to design of surface texture of hip prosthesis.     

Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

Screening large numbers of target regions in multiple DNA samples for sequence variation is an important application of next-generation sequencing but an efficient method to enrich the samples in parallel has yet to be reported. We describe an advanced method that combines DNA samples using indexes or barcodes prior to target enrichment to facilitate this type of experiment. Sequencing libraries for multiple individual DNA samples, each incorporating a unique 6-bp index, are combined in equal quantities, enriched using a single in-solution target enrichment assay and sequenced in a single reaction. Sequence reads are parsed based on the index, allowing sequence analysis of individual samples. We show that the use of indexed samples does not impact on the efficiency of the enrichment reaction. For three- and nine-indexed HapMap DNA samples, the method was found to be highly accurate for SNP identification. Even with sequence coverage as low as 8x, 99% of sequence SNP calls were concordant with known genotypes. Within a single experiment, this method can sequence the exonic regions of hundreds of genes in tens of samples for sequence and structural variation using as little as 1 μg of input DNA per sample.     

Cinnabar mineralization in fossil small mammal remains as a consequence of diagenetic processes

The peculiar red colour of fossil small mammal remains from a late Miocene section in southern Spain suggests an unusual diagenetic alteration. These remains have been studied by means of environmental scanning electron microscope equipped with different detectors, energy dispersive X‐ray spectroscopy and an inductively coupled plasma optical emission spectrometer. The red colour is caused by the presence of cinnabar (HgS) in the pores of the fossil bones and teeth, filling the dentinal and bone tubules and other cavities that at life were filled by organic matter. A nearby cinnabar outcrop in the metamorphic materials of Sierra Nevada is interpreted as the source of mercury. This element was mobilized by meteoric diagenesis and incorporated as cinnabar in a palustrine environment, occupying pores and cavities of mammal remains shortly after the degradation of the organic matter (post‐mortem enrichment), during the early diagenesis.     

Gaps in structurally similar proteins: towards improvement of multiple sequence alignment

An algorithm was developed to locally optimize gaps from the FSSP database. Over 2 million gaps were identified from all versus all FSSP structure comparisons, and datasets of non-identical gaps and flanking regions comprising between 90,000 and 135,000 sequence fragments were extracted for statistical analysis. Relative to background frequencies, gaps were enriched in residue types with small side chains and high turn propensity (D, G, N, P, S), and were depleted in residue types with hydrophobic side chains (C, F, I, L, V, W, Y). In contrast, regions flanking a gap exhibited opposite trends in amino acid frequencies, i.e., enrichment in hydrophobic residues and a high degree of secondary structure. Log-odds scores of residue type as a function of position in or around a gap were derived from the statistics. Three simple experiments demonstrated that these scores contained significant predictive information. First, regions where gaps were observed in single sequences taken from HOMSTRAD structure-based multiple sequence alignments generally scored higher than regions where gaps were not observed. Second, given the correct pairwise-aligned cores, the actual positions of gaps could be reproduced from sequence more accurately using the structurally-derived statistics than by using random pairwise alignments. Finally, revision of the Clustal-W residue-specific gap opening parameters with this new information improved the agreement of Clustal-W alignments with the structure-based alignments. At least three applications for these results are envisioned: improvement of gap penalties in pairwise (or multiple) sequence alignment, prediction of regions of single sequences likely (or unlikely) to contain indels, and more accurate placement of gaps in automated pairwise structure alignment.     

Broad activation of the glomerular layer enhances subsequent olfactory responses

Early olfactory experience with a specific odorant enhances the subsequent response of the glomerular layer of the rat olfactory bulb to that same odorant. Because different odorants activate different glomerular layer regions, it seemed plausible that experience with a large number of odorants might result in enhanced glomerular activation during subsequent exposure to both the previously experienced odorants and the novel odorants evoking activity in regions that overlapped with those previously stimulated by different odorants. To this end, 7 odorants were selected using our glomerular response data archive that together stimulated much of the glomerular layer (alpha-phellandrene, benzaldehyde, L-carvone, decanal, pentanol, santalol, and valeric acid). Young rats were exposed to a different odorant each day for 7 days, and this cycle was repeated 3 times from postnatal days 1-21. The [(14)C]2-deoxyglucose technique was used to measure neural activity in response to both previously experienced and novel odorants. The 2 novel odorants (alpha-ionone and L-menthone) activate regions of the glomerular layer that overlap with those stimulated by the 7 enrichment odorants. Our results indicate that early experience with multiple odorants results in increased responsiveness both to previously experienced odorants and to novel odorants that stimulate previously activated regions of the bulb.     

Effects of endotoxemia on the sheep lung microvascular membrane: a two-pore theory

We analyzed the effects of Escherichia coli endotoxin infusion on pulmonary microvessels in sheep by using a two-pore mathematical model of the microvascular barrier. Five sheep were prepared with lung lymph fistulas and instrumented to measure pulmonary arterial and left atrial pressures. Multiple indicator-dilution curves (with 125I-labeled albumin, 51Cr-labeled erythrocytes, [14C]urea, and 3H2O) were measured at base line and during phases 1 and 2 of the endotoxin response. Alterations in the membrane integrity in response to endotoxin infusion were quantified by using a two-pore theory of the microvascular barrier that incorporated lymph, protein, pressure, and multiple indicator measurements. The modeling results showed a slight change in the size of the pores during phase 1 but a 56% decrease in the number of small pores and a twofold increase in the number of large pores with respect to base-line values. During phase 2 the large pore size increased by 40%, and the total number of pores returned to base-line values. The analysis showed that endotoxin effects on fluid and protein exchange in the lung cannot be explained by hemodynamic and surface area changes alone. An apparent increase in lung microvascular permeability occurs during phases 1 and 2 of the endotoxin reaction, with a substantial decrease in perfused microvascular surface area during phase 1.     

Determination of the heterogeneous anisotropic elastic properties of human femoral bone: From nanoscopic to organ scale

Cortical bone is a multiscale composite material. Its elastic properties are anisotropic and heterogeneous across its cross-section, due to endosteal bone resorption which might affect bone strength. The aim of this paper was to describe a homogenization method leading to the estimation of the variation of the elastic coefficients across the bone cross-section and along the bone longitudinal axis. The method uses the spatial variations of bone porosity and of the degree of mineralization of the bone matrix (DMB) obtained from the analysis of 3-D synchrotron micro-computed tomography images. For all three scales considered (the foam (100 nm), the ultrastructure (5 μm) and the mesoscale (500 μm)), the elastic coefficients were determined using the Eshelby’s inclusion problem. DMB values were used at the scale of the foam. Collagen was introduced at the scale of the ultrastructure and bone porosity was introduced at the mesoscale. The pores were considered as parallel cylinders oriented along the bone axis. Each elastic coefficient was computed for different regions of interest, allowing an estimation of its variations across the bone cross-section and along the bone longitudinal axis. The method was applied to a human femoral neck bone specimen, which is a site of osteoporotic fracture. The computed elastic coefficients for cortical bone were in good agreement with experimental results, but some discrepancies were obtained in the endosteal part (trabecular bone). These results highlight the importance of accounting for the heterogeneity of cortical bone properties across bone cross-section and along bone longitudinal axis.     

Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules

The defining step in most chromatin immunoprecipitation (ChIP) assays is the use of an antibody to enrich for a particular protein or histone modification state associated with segments of chromatin. The specificity of the antibody is critical to the interpretation of the experiment, yet this property is rarely reported. Here, we present a quantitative method using mass spectrometry to characterize the specificity of key histone H3 modification-targeting antibodies that have previously been used to characterize the "histone code." We further extend the use of these antibody reagents to the observation of long range correlations among disparate histone modifications. Using purified human histones representing the mixture of chromatin states present in living cells, we were able to quantify the degree of target enrichment and the specificity of several commonly used, commercially available ChIP grade antibodies. We found significant differences in enrichment efficiency among various reagents directed against four frequently studied chromatin marks: H3K4me2, H3K4me3, H3K9me3, and H3K27me3. For some antibodies, we also detected significant off target enrichment of alternate modifications at the same site (i.e., enrichment of H3K4me2 by an antibody directed against H3K4me3). Through cluster analysis, we were able to recognize patterns of co-enrichment of marks at different sites on the same histone protein. Surprisingly, these co-enrichments corresponded well to "canonical" chromatin states that are exemplary of activated and repressed regions of chromatin. Altogether, our findings suggest that 1) the results of ChIP experiments need to be evaluated with caution given the potential for cross-reactivity of the commonly used histone modification recognizing antibodies, 2) multiple marks with consistent biological interpretation exist on the same histone protein molecule, and 3) some components of the histone code may be transduced on single proteins in living cells.     

Enrichment of the Murine Natural Killer (NK) and Mitogen Induced Cellular Cytotoxicity (MICC) Cells Using Preparative Free-Flow High Voltage Electrophoresis

A procedure using preparative free-flow high voltage electrophoresis is described for the fractionation of murine spleen and bone marrow cells so as to obtain cell subpopulations that are either enriched in or depleted of “natural killer” (NK) cells and “mitogen-induced cellular cytotoxicity” (MICC) effector cells. A nearly three fold enrichment in the NK and MICC activities of spleen cells was achieved. The enrichment in these cells could be further increased if the phagocytic cells were removed prior to electrophoresis. When bone marrow cells were fractionated a two and a half fold increase of NK activity, and a one and a half fold enrichment of MICC activity was achieved. In both cases, other fractions were nearly devoid of NK and MICC activity. The cell recovery after electrophoresis averages 70% of the cells applied, and at least 90% of these cells were viable. MICC and NK effector cells could not be separated to a useful extent electro-phoretically but were found to be separable using Sephadex G-10 gel filtration columns. The MICC but not the NK cells were retained on these columns.     

Enrichment of the murine natural killer (NK) and mitogen induced cellular cytotoxicity (MICC) cells using preparative free-flow high voltage electrophoresis.

A procedure using preparative free-flow high voltage electrophoresis is described for the fractionation of murine spleen and bone marrow cells so as to obtain cell subpopulations that are either enriched in or depleted of "natural killer" (NK) cells and "mitogen-induced cellular cytotoxicity" (MICC) effector cells. A nearly three fold enrichment in the NK and MICC activities of spleen cells was achieved. The enrichment in these cells could be further increased if the phagocytic cells were removed prior to electrophoresis. When bone marrow cells were fractionated a two and a half fold increase of NK activity, and a one and a half fold enrichment of MICC activity was achieved. In both cases, other fractions were nearly devoid of NK and MICC activity. The cell recovery after electrophoresis averages 70% of the cells applied, and at least 90% of these cells were viable. MICC and NK effector cells could not be separated to a useful extent electrophoretically but were found to be separable using Sephadex C-10 gel filtration columns. The MICC but not the NK cells were retained on these columns.     

Natural variation and differential diagnosis of skeletal changes in tuberculosis

Twenty-six documented cases (17 blacks, 9 whites) of skeletal tuberculosis from the Hamann-Todd Osteological Collection, Cleveland Museum of Natural History, were analyzed for lesion variability and patterns of multiple site involvement. In addition, several documented cases of pathologic conditions (osteomyelitis, vertebral fractures, and malignant bone tumors) that resemble skeletal tuberculosis were photographed and described for use in differential diagnosis. The range of variation of tuberculous lesions was found to be considerable. Thirty-eight percent (10/26) of the cases display skeletal lesions in two or more regions concomitantly. The average number of vertebrae affected, as well as the incidence of multiple bone involvement, were found to be higher in blacks. Certain combinations of skeletal lesions (e. g., spine-rib, spine-rib-sternum, and spine-hip) may be useful in the diagnosis of tuberculosis in dry bone material.     

Nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large RNAs

The highly conserved peptidyl transferase center (PTC) of the ribosome contains an RNA pore that serves as the entrance to the exit tunnel. Analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rRNA) RNAs. These typically have dimensions of 1–2 nm, with a total area of ∼100 Ų or more, and most are associated with one or more ribosomal proteins. The PTC example and the other rRNA pores result from the packing of helices. However, in the non-PTC cases the nitrogenous bases do not protrude into the pore, thereby limiting the potential for hydrogen bonding within the pore. Instead, it is the RNA backbone that largely defines the pore likely resulting in a negatively charged environment. In many but not all cases, ribosomal proteins are associated with the pores to a greater or lesser extent. With the exception of the PTC case, the large subunit pores are not found in what are thought to be the evolutionarily oldest regions of the 23S rRNA. The unusual nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs early in evolution rather than simple folding of a single RNA. An initial survey of nonribosomal RNA crystal structures revealed additional pores, thereby showing that they are likely a general feature of RNA tertiary structure.     

用于高通量测序的基因组靶序列捕获方法的建立

文章旨在建立一种基因组目标靶序列捕捉文库的方法,并结合第二代测序技术,以实现候选基因区段的深度测序。利用Agilent公司的eArray在线平台,对1250个基因的11824个外显子共2414977bp的基因组序列进行120个碱基长度的捕捉探针(钓饵)设计,并制备成SureSelect液相靶序列捕获试剂。选用2例人基因组DNA,超声打断后末端补平并磷酸化,连接SOLiD接头,回收150bp～200bp的DNA片段,与靶序列探针杂交捕获目标序列,油包水微乳滴PCR扩增后,磁珠分离富集,上SOLiD测序系统通过工作流程分析(WFA)进行文库质量的评价,或正式测序反应。结果显示对所包含的11147个基因外显子片段设计出并合成了46509个捕捉探针,制备成SureSelect试剂盒。探针可有效地捕捉并富集基因组DNA的目标靶片段,定量PCR显示富集效率可达29倍。WFA分析表明文库可以在SOLiD仪器进行正式测序。测序结果显示靶序列区域的测序数占有效总测序数的比例达到70%,覆盖率均在200×以上。结果表明本研究所建立的SureSelect基因组靶序列捕捉、富集建立测序文库的技术路线可行,可直接用于SOLiD测序仪的测序。     

Prediction of cortical bone elastic constants by a two-level micromechanical model using a generalized self-consistent method

A two-level micromechanical model of cortical bone based on a generalized self-consistent method was developed to take into consideration the transversely isotropic elasticity of many microstructural features in cortical bone, including Haversian canals, resorption cavities, and osteonal and interstitial lamellae. In the first level, a single osteon was modeled as a two-phase composite such that Haversian canals were represented by elongated pores while the surrounding osteonal lamellae were considered as matrix. In the second level, osteons and resorption cavities were modeled as multiple inclusions while interstitial lamellae were regarded as matrix. The predictions of cortical bone elasticity from this two-level micromechanical model were mostly in agreement with experimental data for the dependence of transversely isotropic elasticity of human femoral cortical bone on porosity. However, variation in cortical bone elastic constants was greater in experimental data than in model predictions. This could be attributed to variations in the elastic properties of microstructural features in cortical bone. The present micromechanical model of cortical bone will be useful in understanding the contribution of cortical bone porosity to femoral neck fractures.     

Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions

The search for feature enrichment is a widely used method to characterize a set of genes. While several tools have been designed for nominal features such as Gene Ontology annotations or KEGG Pathways, very little has been proposed to tackle numerical features such as the chromosomal positions of genes. For instance, microarray studies typically generate gene lists that are differentially expressed in the sample subgroups under investigation, and when studying diseases caused by genome alterations, it is of great interest to delineate the chromosomal regions that are significantly enriched in these lists. In this article, we present a positional gene enrichment analysis method (PGE) for the identification of chromosomal regions that are significantly enriched in a given set of genes. The strength of our method relies on an original query optimization approach that allows to virtually consider all the possible chromosomal regions for enrichment, and on the multiple testing correction which discriminates truly enriched regions versus those that can occur by chance. We have developed a Web tool implementing this method applied to the human genome (http://www.esat.kuleuven.be/~bioiuser/pge). We validated PGE on published lists of differentially expressed genes. These analyses showed significant overrepresentation of known aberrant chromosomal regions.     

Enhancing the identification of phosphopeptides from putative basophilic kinase substrates using Ti (IV) based IMAC enrichment

Metal and metal oxide chelating-based phosphopeptide enrichment technologies provide powerful tools for the in-depth profiling of phosphoproteomes. One weakness inherent to current enrichment strategies is poor binding of phosphopeptides containing multiple basic residues. The problem is exacerbated when strong cation exchange (SCX) is used for pre-fractionation, as under low pH SCX conditions phosphorylated peptides with multiple basic residues elute with the bulk of the tryptic digest and therefore require more stringent enrichment. Here, we report a systematic evaluation of the characteristics of a novel phosphopeptide enrichment approach based on a combination of low pH SCX and Ti(4+)-immobilized metal ion affinity chromatography (IMAC) comparing it one-to-one with the well established low pH SCX-TiO(2) enrichment method. We also examined the effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFP), trifluoroacetic acid (TFA), or 2,5-dihydroxybenzoic acid (DHB) in the loading buffer, as it has been hypothesized that high levels of TFA and the perfluorinated solvent HFP improve the enrichment of phosphopeptides containing multiple basic residues. We found that Ti(4+)-IMAC in combination with TFA in the loading buffer, outperformed all other methods tested, enabling the identification of around 5000 unique phosphopeptides containing multiple basic residues from 400 μg of a HeLa cell lysate digest. In comparison, ～ 2000 unique phosphopeptides could be identified by Ti(4+)-IMAC with HFP and close to 3000 by TiO(2). We confirmed, by motif analysis, the basic phosphopeptides enrich the number of putative basophilic kinases substrates. In addition, we performed an experiment using the SCX/Ti(4+)-IMAC methodology alongside the use of collision-induced dissociation (CID), higher energy collision induced dissociation (HCD) and electron transfer dissociation with supplementary activation (ETD) on considerably more complex sample, consisting of a total of 400 μg of triple dimethyl labeled MCF-7 digest. This analysis led to the identification of over 9,000 unique phosphorylation sites. The use of three peptide activation methods confirmed that ETD is best capable of sequencing multiply charged peptides. Collectively, our data show that the combination of SCX and Ti(4+)-IMAC is particularly advantageous for phosphopeptides with multiple basic residues.     

Selective staining of immature hemopoietic cells with merocyanine 540 in flow cytometry

Merocyanine 540 (MC540) has been reported to bind hemopoietic cells specifically. In this study, MC540 was used as a probe for the cytofluorometric discrimination of hemopoietic cells. In PHA-stimulated lymphocytes or HL-60 cells induced to differentiate with DMSO, MC540 binding was increased in actively proliferating cells and undifferentiated cells as compared with the more differentiated cells of the same lineage. Mononuclear bone marrow cells exhibited a discrete distribution of MC fluorescence. Sorting a population with high MC540 fluorescence (MC+ population) produced a 9-14-fold enrichment of granulocyte-macrophage progenitors (CFU-GM), and a recovery of all S-G2M phase cells (BrdUrd/DNA analysis). Cytological examination of the sorted MC+ population confirmed the enrichment in immature cells from all lineages. Double-labeling experiments using MC540 and Hoechst 33342 on total bone marrow or peripheral blood cells confirmed that the MC+ population included all the cycling cells. The proportion of S-G2M phase cells in this MC+ population was 29.3 +/- 7.8 for 15 bone marrow samples and 16.3 +/- 6.8 for 10 blood samples. MC540 could therefore be used as a marker for human hemopoietic cells, and it represents a useful tool for investigation of hemopoiesis in normal or leukemic bone marrow.     

Phylogenetic analysis of aerobic freshwater and marine enrichment cultures efficient in hydrocarbon degradation: effect of profiling method

Aerobically grown enrichment cultures derived from hydrocarbon-contaminated seawater and freshwater sediments were generated by growth on crude oil as sole carbon source. Both cultures displayed a high rate of degradation for a wide range of hydrocarbon compounds. The bacterial species composition of these cultures was investigated by PCR of the 16S rDNA gene using multiple primer combinations. Near full-length 16S rDNA clone libraries were generated and screened by restriction analysis prior to sequence analysis. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) was carried out using two other PCR primer sets targeting either the V3 or V6-V8 regions, and sequences derived from prominent DGGE bands were compared to sequences obtained via cloning. All data sets suggested that the seawater culture was dominated by alpha-subgroup proteobacteria, whereas the freshwater culture was dominated by members of the beta- and gamma-proteobacteria. However, the V6-V8 primer pair was deficient in the recovery of Sphingomonas-like 16S rDNA due to a 3' terminal mismatch with the reverse primer. Most 16S rDNA sequences recovered from the marine enrichment were not closely related to genera containing known oil-degrading organisms, although some were detected. All methods suggested that the freshwater enrichment was dominated by genera containing known hydrocarbon-degrading species.