Immobilization in quartz fiber felt reinforced silica aerogel improves the activity of Candida rugosa lipase in organic solvents

Candida rugosa lipase is a very useful catalyst, but its rapid inactivation by simple alcohols is a drawback. The present study was focussed on the encapsulation of this enzyme in silica aerogels reinforced with quartz fiber felt. The activity of the immobilized lipase in an organic solvent could be significantly improved over that of the free enzyme and of previous immobilization techniques, by evaporating the alcohol formed during a pre-hydrolysis of the silica precursor, before adding the aqueous enzyme solution. The alcohol evaporation technique was previously used by other authors to immobilized enzymes, but applied to xerogels dried by evaporation, while in the present case the wet gels obtained were dried by the CO₂ supercritical method to obtain aerogels. Besides, such silica aerogels were also reinforced by impregnating a commercial ceramic quartz fiber felt of St. Gobain with the silica sol containing the enzyme, before gelation. The ceramic composites heterogeneous biocatalysts obtained could be used for a large number of times without any apparent deterioration.     

Large area micropatterning of cells on polydimethylsiloxane surfaces

Background

Precise spatial control and patterning of cells is an important area of research with numerous applications in tissue engineering, as well as advancing an understanding of fundamental cellular processes. Poly (dimethyl siloxane) (PDMS) has long been used as a flexible, biocompatible substrate for cell culture with tunable mechanical characteristics. However, fabrication of suitable physico-chemical barriers for cells on PDMS substrates over large areas is still a challenge.

Results

Here, we present an improved technique which integrates photolithography and cell culture on PDMS substrates wherein the barriers to cell adhesion are formed using the photo-activated graft polymerization of polyethylene glycol diacrylate (PEG-DA). PDMS substrates with varying stiffness were prepared by varying the base to crosslinker ratio from 5:1 to 20:1. All substrates show controlled cell attachment confined to fibronectin coated PDMS microchannels with a resistance to non-specific adhesion provided by the covalently immobilized, hydrophilic PEG-DA.

Conclusions

Using photolithography, it is possible to form patterns of high resolution stable at 37°C over 2 weeks, and microstructural complexity over large areas of a few cm². As a robust and scalable patterning method, this technique showing homogenous and stable cell adhesion and growth over macroscales can bring microfabrication a step closer to mass production for biomedical applications.

     

Application of network methods for understanding evolutionary dynamics in discrete habitats

In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene‐flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population‐genetics literature; however, these models have usually addressed relatively simple settings of habitable patches and have stopped short of providing general methodologies for addressing nontrivial gene‐flow patterns. In the last decades, network theory – a branch of discrete mathematics concerned with complex interactions between discrete elements – has been applied to address several problems in population genetics by modelling gene flow between habitat patches using networks. Here, we present the idea and concepts of modelling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population‐genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology.     

Facile fabrication of gelatin‐based biopolymeric optical waveguides

The rapid development in optical detection techniques for sensing applications has led to an increased need for biocompatible, biodegradable, and disposable optical components. We present a controllable fabrication technique for an entirely biopolymeric planar optical waveguide via simple spin‐coating. The refractive index difference, thermal responsive properties, and inherent biocompatibility of gelatin and agarose were exploited in the fabrication of thin, stacked films that efficiently guide light in a core layer with higher index of refraction. These planar waveguides were fabricated using a simple spin‐coating technique, which resulted in controllable layer thicknesses and smooth layer interfaces. This technique, therefore, offers a path for routine engineering of biopolymer structures with contrasting refractive indices. The thermal stability of the gelatin core layer was improved using two crosslinkers; glutaraldehyde or microbial Transglutaminase. Light guiding in the core layer of the waveguide was demonstrated using a simple He–Ne laser setup. Guiding efficiency was further illustrated by directly embedding fluorescent markers within the core layer and detecting their spectral signature. Combined with the biopolymers' inherent biocompatibility and biodegradability, our simple strategy to fabricate disposable optical components holds the potential for the development of applications in biological sensing and implantable biomedical devices. Biotechnol. Bioeng. 2009;103: 725–732. © 2009 Wiley Periodicals, Inc.     

Perfluorooctyl bromide dispersions in aqueous media for biomedical applications.

In studying perfluorooctyl bromide (PFOB) dispersions in aqueous media, we have used two types of surfactant: egg yolk phospholipids (EYP) and polyglycerol esters (PGE). Our interest in these dispersions arises from their potential biomedical applications as imaging solutions and oxygen-carrying solutions (i.e., blood substitutes). For EYP systems, we have identified the dispersion structure as consisting of (a) PFOB droplets (250-nm diameter) stabilized by a phospholipid monolayer adsorbed irreversibly at the o/w interface and (b) small empty phospholipid vesicles. With both surfactants commercial preparations yielded stable systems, while purified samples, being non-dispersible, could not be made to act as emulsifiers. In both cases, minor components in the commercial surfactant were found to be necessary for the formation of a stable dispersion, enabling the transport of the pure surfactant to the PFOB/water interface.     

An isothermal method for whole genome amplification of fresh and degraded DNA for comparative genomic hybridization, genotyping and mutation detection.

Molecular genotyping has important biomedical and forensic applications. However, limiting amounts of human biological material often yield genomic DNA (gDNA) in insufficient quantity and of poor quality for a reliable analysis. This motivated the development of an efficient whole genome amplification method with quantitatively unbiased representation usable on fresh and degraded gDNA. Amplification of fresh frozen, formalin-fixed paraffin-embedded (FFPE) and DNase-degraded DNA using degenerate oligonucleotide-primed PCR or primer extension amplification using a short primer sequence bioinformatically optimized for coverage of the human genome was compared with amplification using current primers by chromosome-based and BAC-array comparative genomic hybridization (CGH), genotyping at short tandem repeats (STRs) and single base mutation detection. Compared with current primers, genome amplification using the bioinformatically optimized primer was significantly less biased on CGH in self-self hybridizations, and replicated tumour genome copy number aberrations, even from FFPE tissue. STR genotyping could be performed on degraded gDNA amplified using our technique but failed with multiple displacement amplification. Of the 18 different single base mutations 16 (89.5%) were correctly identified by sequencing gDNA amplified from clinical samples using our technique. This simple and efficient isothermal method should be helpful for genetic research and clinical and forensic applications.     

Transport characteristics of expiratory droplets and droplet nuclei in indoor environments with different ventilation airflow patterns

Expiratory droplets and droplet nuclei can be pathogen carriers for airborne diseases. Their transport characteristics were studied in detail in two idealized floor-supply-type ventilation flow patterns: Unidirectional-upward and single-side-floor, using a multiphase numerical model. The model was validated by running interferometric Mie imaging experiments using test droplets with nonvolatile content, which formed droplet nuclei, ultimately, in a class-100 clean-room chamber. By comparing the droplet dispersion and removal characteristics with data of two other ceiling-supply ventilation systems collected from a previous work, deviations from the perfectly mixed ventilation condition were found to exist in various cases to different extent. The unidirectional-upward system was found to be more efficient in removing the smallest droplet nuclei (formed from 1.5 mum droplets) by air extraction, but it became less effective for larger droplets and droplet nuclei. Instead, the single-side-floor system was shown to be more favorable in removing these large droplets and droplet nuclei. In the single-side-floor system, the lateral overall dispersion coefficients for the small droplets and nuclei (initial size 相似文献   

Using a Search Engine-Based Mutually Reinforcing Approach to Assess the Semantic Relatedness of Biomedical Terms

Background

Determining the semantic relatedness of two biomedical terms is an important task for many text-mining applications in the biomedical field. Previous studies, such as those using ontology-based and corpus-based approaches, measured semantic relatedness by using information from the structure of biomedical literature, but these methods are limited by the small size of training resources. To increase the size of training datasets, the outputs of search engines have been used extensively to analyze the lexical patterns of biomedical terms.

Methodology/Principal Findings

In this work, we propose the Mutually Reinforcing Lexical Pattern Ranking (ReLPR) algorithm for learning and exploring the lexical patterns of synonym pairs in biomedical text. ReLPR employs lexical patterns and their pattern containers to assess the semantic relatedness of biomedical terms. By combining sentence structures and the linking activities between containers and lexical patterns, our algorithm can explore the correlation between two biomedical terms.

Conclusions/Significance

The average correlation coefficient of the ReLPR algorithm was 0.82 for various datasets. The results of the ReLPR algorithm were significantly superior to those of previous methods.     

Advances in biomedical applications of pectin gels

Pectin, due to its simple and cytocompatible gelling mechanism, has been recently exploited for different biomedical applications including drug delivery, gene delivery, wound healing and tissue engineering. Recent studies involving pectin for the biomedical field are reviewed, with the aim to capture the state of art on current research about pectin gels for biomedical applications, moving outside the traditional fields of application such as the food industry or pharmaceutics. Pectin structure, sources and extraction procedures have been discussed focussing on the properties of the polysaccharide that can be tuned to optimize the gels for a desired application and possess a fundamental role in application of pectin in the biomedical field.     

Hydrogel Nanofilaments via Core-Shell Electrospinning

Recent biomedical hydrogels applications require the development of nanostructures with controlled diameter and adjustable mechanical properties. Here we present a technique for the production of flexible nanofilaments to be used as drug carriers or in microfluidics, with deformability and elasticity resembling those of long DNA chains. The fabrication method is based on the core-shell electrospinning technique with core solution polymerisation post electrospinning. Produced from the nanofibers highly deformable hydrogel nanofilaments are characterised by their Brownian motion and bending dynamics. The evaluated mechanical properties are compared with AFM nanoindentation tests.     

Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.     

Membrane orientation of droplets prepared fromChara corallina internodal cells

Summary It is generally accepted that the membrane surrounding droplets from characean cells originates from the tonoplast, but there is some uncertainty regarding droplet membrane sidedness. This issue was addressed directly by combining two different droplet isolation methods and the patch clamp technique. Neutral red accumulation was used to demonstrate the presence of H⁺-transport over the membrane and to predict membrane orientation. Two types of droplet populations with differently oriented membranes could be formed in an iso-osmotic bath solution. Cytoplasmic droplets (cytosolic side of the tonoplast inside) contained cytoplasm, while the second type of droplet population contained vacuolar sap (vacuolar droplets, vacuolar side of the tonoplast inside). Smaller vesicles also appeared inside the droplets, with an apparently inversely oriented membrane. Confocal laser scanning microscopy indirectly demonstrated that, at least with one of the droplet isolation methods, the plasma membrane entirely remains in the internodal cell after intracellular perfusion. Both types of droplet populations allowed the formation of excised patches and single-channel measurements by the patch clamp technique. Properties of anion channels in the tonoplast could be used to prove the predicted membrane orientation, knowing that Ca²⁺ can only activate these channels from the cytosolic side. These results provide useful data for studies addressing ligand-binding, block and modulation, organization and interaction of proteins within the membrane or with other regulatory factors, where it is important to control membrane orientation.     

The use of a fluorescent dye, Nile red, to evaluate the lipid content of single mammalian oocytes

This study aimed to investigate the use of Nile red, a fluorescent dye specific for intracellular lipid droplets, to quantify the lipid content of single mammalian oocytes. It was hypothesized that a higher amount of lipid present in lipid droplets in an oocyte would result in a higher amount of emitted fluorescent light. Following fixation and subsequent staining of denuded oocytes, the fluorescence of the whole oocyte was visualized by fluorescence microscopy and quantified with a photometer and photomultiplier connected to the microscope. The peak of fluorescence was observed in the yellow spectrum (590 nm) and the fluorescence was restricted to the lipid droplets corresponding to apolar lipids. Nile red concentrations ranging from 0.1 to 10 microg/ml yielded similar results. After fixation, a minimum of 2 h staining was necessary to reach maximal fluorescence which remained stable for several hours. The position of the microscopic focus within the oocyte had no influence on the amount of measured fluorescence. Successive measurements of the same oocyte yielded very similar results indicating the repeatability of the method. Finally, the technique was validated by comparing the lipid content of bovine, porcine and murine immature oocytes, which are known to contain different amounts of lipids. After staining, the fluorescence of murine oocytes was 2.8-fold lower than the fluorescence of bovine oocytes which in turn were 2.4 times less fluorescent than porcine oocytes. Based on this study, it can be said that this rather fast and easy technique allows for the relative quantification of the lipid content (present in the lipid droplets) of one single oocyte. The different amounts of emitted fluorescent light in bovine, porcine and murine oocytes correlated with the known lipid contents in these three species. This technique could be used to compare the lipid content of oocytes originating from different donors, from different sized follicles or cultured in various conditions.     

Cell electrospinning: a unique biotechnique for encapsulating living organisms for generating active biological microthreads/scaffolds

Jet-based technologies are increasingly being explored as potential high-throughput and high-resolution methods for the manipulation of biological materials. Previously shown to be of use in generating scaffolds from biocompatible materials, we were interested to explore the possibility of using electrospinning technology for the generation of scaffolds comprised of living cells. For this, it was necessary to identify appropriate parameters under which viable threads containing living cells could be produced. Here, we describe a method of electrospinning that can be used to deposit active biological threads and scaffolds. This has been achieved by use of a coaxial needle arrangement where a concentrated living biosuspension flows through the inner needle and a medical-grade poly(dimethylsiloxane) (PDMS) medium with high viscosity (12,500 mPa s) and low electrical conductivity (10-15 S m-1) flows through the outer needle. Using this technique, we have identified the operational conditions under which the finest cell-bearing composite microthreads are formed. Collected cells that have been cultured, postelectrospinning, have been viable and show no evidence of having incurred any cellular damage during the bionanofabrication process. This study demonstrates the feasibility of using coaxial electrospinning technology for biological and biomedical applications requiring the deposition of living cells as composite microthreads for forming active biological scaffolds.     

Enzyme overproduction: Principle and application

The rapprochement between gene physiology and protein chemistry proffered a wishful manipulation or programming of biological blueprint which we now know as recombinant DNA technology. Its premises are very many and ends are manifold. Until rather recently, the recombinant DNA technique could conceive the idea of engineering enzyme molecules by cloning and selection of the gene in question for enzyme production. At least, in principle, the process is too simple but its underlying mechanism is rather much stringent. Various experimental paradigms have been brought to work for production of enzyme at will by introducing a given gene into a high yielding system of microorganisms. It facilitates overproduction of enzymes of interest which can be implicated in several important industrial, biomedical, and environmental processes at a large scale. Such approaches of enzymes made-to-application have already started asserting tremendously in doing their appropriate jobs at the level of molecular interactions. A rapid progress in this important and interesting area of biocatalytic manipulation will certainly achieve the goal of biocatalysis-made-to-order by altering kinetic and thermodynamic components of enzyme molecules.     

Building bio-assays with magnetic particles on a digital microfluidic platform

Digital microfluidics (DMF) has emerged as a promising liquid handling technology for a variety of applications, demonstrating great potential both in terms of miniaturization and automation. DMF is based on the manipulation of discrete, independently controllable liquid droplets, which makes it highly reconfigurable and reprogrammable. One of its most exclusive advantages, compared to microchannel-based microfluidics, is its ability to precisely handle solid nano- and microsized objects, such as magnetic particles. Magnetic particles have become very popular in the last decade, since their high surface-to-volume ratio and the possibility to magnetically separate them from the matrix make them perfect suitable as a solid support for bio-assay development. The potential of magnetic particles in DMF-based bio-assays has been demonstrated for various applications. In this review we discuss the latest developments of magnetic particle-based DMF bio-assays with the aim to present, identify and analyze the trends in the field. We also discuss the state-of-the art of device integration, current status of commercialization and issues that still need to be addressed. With this paper we intend to stimulate researchers to exploit and unveil the potential of these exciting tools, which will shape the future of modern biochemistry, microbiology and biomedical diagnostics.     

On the relationship between common amplitude surface roughness parameters and surface area: Implications for the study of cell–material interactions

In order to show that surface area is not always a quantity proportional to the surface roughness, we have constructed simple surfaces consisting of boxes of the same height equally spaced, and rms roughness and surface area have been computed. We have shown how we can get examples of surface configurations for which an increment in the surface roughness corresponds to a decrease in the surface area, although this is observed only for surfaces having similar rms roughness. We have also shown that even in the more intuitive situations where an increase in the surface roughness leads to an increase in the surface area, this increase is not necessarily equivalent. Analogous conclusions have been found when roughness was evaluated through the average roughness. These results could be interesting when analyzing interfacial phenomena such as cell adhesion, especially from a microscopic point of view, where the exact contact area between interacting phases governs these phenomena, and an exact-as-possible approximation to its real value is desirable. Also, the results of this paper could be of interest in various biomedical applications where the modulation of material surface-by-surface roughness may play a significant role. It can be concluded that care should be taken when using roughness parameters as estimators or indicators of the contact area between phases, since the relationship is not always simple.     

PepFect 14, a novel cell-penetrating peptide for oligonucleotide delivery in solution and as solid formulation

Numerous human genetic diseases are caused by mutations that give rise to aberrant alternative splicing. Recently, several of these debilitating disorders have been shown to be amenable for splice-correcting oligonucleotides (SCOs) that modify splicing patterns and restore the phenotype in experimental models. However, translational approaches are required to transform SCOs into usable drug products. In this study, we present a new cell-penetrating peptide, PepFect14 (PF14), which efficiently delivers SCOs to different cell models including HeLa pLuc705 and mdx mouse myotubes; a cell culture model of Duchenne's muscular dystrophy (DMD). Non-covalent PF14-SCO nanocomplexes induce splice-correction at rates higher than the commercially available lipid-based vector Lipofectamine 2000 (LF2000) and remain active in the presence of serum. Furthermore, we demonstrate the feasibility of incorporating this delivery system into solid formulations that could be suitable for several therapeutic applications. Solid dispersion technique is utilized and the formed solid formulations are as active as the freshly prepared nanocomplexes in solution even when stored at an elevated temperatures for several weeks. In contrast, LF2000 drastically loses activity after being subjected to same procedure. This shows that using PF14 is a very promising translational approach for the delivery of SCOs in different pharmaceutical forms.     

Unsupervised clustering of fMRI and MRI time series

Unsupervised clustering represents a powerful technique for self-organized segmentation of biomedical image time series data describing groups of pixels exhibiting similar properties of local signal dynamics. The theoretical background is presented in the beginning, followed by several medical applications demonstrating the flexibility and conceptual power of these techniques. These applications range from functional MRI data analysis to dynamic contrast-enhanced perfusion MRI and breast MRI. For fMRI, these methods can be employed to identify and separate time courses of interest, along with their associated spatial patterns. When applied to dynamic perfusion MRI, they identify groups of voxels associated with time courses that are clinically informative and straightforward to interpret. In breast MRI, a segmentation of the lesion is achieved and in addition a subclassification is obtained within the lesion with regard to regions characterized by different MRI signal time courses. In the present paper, we conclude that unsupervised clustering techniques provide a robust method for blind analysis of time series image data in the important and current field of functional and dynamic MRI.     

Phase separation in a sheared gelatin/maltodextrin mixture studied by small-angle light scattering

The influence of shear on the structure of a gelatin/maltodextrin mixture was investigated using small-angle light scattering both during phase separation and after phase separation was allowed to occur quiescently. In all cases, phase separation occurred via spinodal decomposition to form a droplet morphology, and a characteristic length scale was formed in the structure that was prevalent during shear, as well as in quiescent conditions. Below the critical shear rate for droplet breakup, shear accelerated the coarsening rate of the droplets. A transient regime of rapid hydrodynamic coarsening was present when shear was initiated after phase separation and at late times in all cases once the droplets attained a certain size. At the critical shear rate for droplet breakup (1 s(-1)), the rapid repetition of breakup and coarsening was postulated to occur, which enabled a microstructure consisting of elongated droplets with a narrow size distribution to form. When the shear rate enabled droplets to extend to such an extent that a percolated structure could form (10 s(-1)), then the structure was relatively stable and changed very slowly over time. At very high shear rates (100 s(-1)), droplet breakup was suppressed and a highly fibrillar morphology formed that was stable only while the system was under shear. Cessation of shear at high rates led to fiber breakup and the formation of many small droplets. For a given shear rate, the final microstructure appeared to be independent of the time that shear was started when the structure consisted of discrete droplets or fibers. When a percolated structure could form, however, the shear history appeared to be important.