Sequence plasticity in the antigen-binding site of a therapeutic anti-HER2 antibody

We have examined the plasticity of the antigen-combining site of a high-affinity antibody. In phage-displayed Fab libraries, selected CDR positions and one FR position of the humanized anti-Her2 antibody hu4D5 were substituted with all 20 amino acids. Antigen-binding selections were used to enrich for high-affinity variants, and a large number of sequences were obtained prior to convergence of the selected pool to a small set of clones. As expected, sequence variability of the antigen-binding site is overall diminished compared to known IgG sequences; however, certain positions retain much higher variability than others. The sequence variability map of the hu4D5 binding site is compared with a map derived from previous alanine-scanning of the antibody. Affinities of soluble Fab fragments for antigen confirm that multiple variants were selected with high affinity for antigen, including one variant with a single point mutation that was about threefold improved in affinity compared to the parental hu4D5. Interestingly, this mutation is one of the most radical in terms of changing side-chain chemistry (Trp for Asp) and occurs at the most plastic site as calculated by the Wu-Kabat variability coefficient. Thus variability mapping yields information about the antibody-antigen interaction that is useful and complementary to that obtained by alanine scanning mutagenesis.

Hierarchical organization of modularity in metabolic networks

Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated biochemical networks lacks quantitative support. Here, we show that the metabolic networks of 43 distinct organisms are organized into many small, highly connected topologic modules that combine in a hierarchical manner into larger, less cohesive units, with their number and degree of clustering following a power law. Within Escherichia coli, the uncovered hierarchical modularity closely overlaps with known metabolic functions. The identified network architecture may be generic to system-level cellular organization.

A comparison of efficacy and toxicity between electroporation and adenoviral gene transfer

BACKGROUND

Electroporation of skeletal muscle after injection of naked DNA was shown by others to increase transgene expression. Information regarding tissue damage caused by electroporation is conflicting. It is also not well known how plasmid electroporation compares with transfection by adenoviral vectors. To investigate these questions the most used protocol for muscle electroporation was used, i.e. 8 pulses of 200 V/cm and 20 ms at a frequency of 1 Hz.

RESULTS

Intra-muscular DNA transfer of pLuciferase was increased by 2 logs after electroporation, confirming data described by others. However, the blood levels of the encoded protein were still lower than those obtained after injection of first generation adenoviral vectors. Also, the electroporation procedure, on its own, caused severe muscle damage consisting of rhabdomyolysis and infiltration, whereas the adenoviral vectors caused only a slight infiltration. As damage of targeted tissue may be an advantage in the case of tumour transfection, we also compared the two transfection methods in tumour tissue. In case of poorly permissive tumours, adenoviral vectors cannot transfect more than 2% of the tumour tissue without inducing significant liver damage. In contrast, the electroporation seems to offer a wider therapeutic window since it does not cause any systemic toxicity and still induce's significant transfection.

CONCLUSIONS

Plasmid electroporation of the muscle induce severe local damage and is of no advantage over adenoviral vectors for obtaining high blood levels of a vector encoded protein. In contrast, electroporation of tumours might be safer than adenoviral gene transfer.

Cerebral energetics and spiking frequency: the neurophysiological basis of fMRI

Functional MRI (fMRI) is widely assumed to measure neuronal activity, but no satisfactory mechanism for this linkage has been identified. Here we derived the changes in the energetic component from the blood oxygenation level-dependent (BOLD) fMRI signal and related it to changes in the neuronal spiking frequency in the activated voxels. Extracellular recordings were used to measure changes in cerebral spiking frequency (Deltanu/nu) of a neuronal ensemble during forepaw stimulation in the alpha-chloralose anesthetized rat. Under the same conditions localized changes in brain energy metabolism (DeltaCMR(O2)/CMR(O2)) were obtained from BOLD fMRI data in conjunction with measured changes in cerebral blood flow (DeltaCBF/CBF), cerebral blood volume (DeltaCBV/CBV), and transverse relaxation rates of tissue water (T(2)(*) and T(2)) by MRI methods at 7T. On stimulation from two different depths of anesthesia DeltaCMR(O2)/CMR(O2) approximately Deltanu/nu. Previous (13)C magnetic resonance spectroscopy studies, under similar conditions, had shown that DeltaCMR(O2)/CMR(O2) was proportional to changes in glutamatergic neurotransmitter flux (DeltaV(cyc)/V(cyc)). These combined results show that DeltaCMR(O2)/CMR(O2) approximately DeltaV(cyc)/V(cyc) approximately Deltanu/nu, thereby relating the energetic basis of brain activity to neuronal spiking frequency and neurotransmitter flux. Because DeltaCMR(O2)/CMR(O2) had the same high spatial and temporal resolutions of the fMRI signal, these results show how BOLD imaging, when converted to DeltaCMR(O2)/CMR(O2), responds to localized changes in neuronal spike frequency.

Mechanisms for temporal tuning and filtering by postsynaptic signaling pathways

Networks of signaling pathways perform complex temporal decoding functions in diverse biological systems, including the synapse, development, and bacterial chemotaxis. This paper examines temporal filtering and tuning properties of synaptic signaling pathways as a possible substrate for emergent temporal decoding. A mass action kinetic model of 16 synaptic signaling pathways was used to dissect out the contribution of these pathways in linear cascades and when coupled to form a network. The model predicts two primary mechanisms of temporal tuning of pathways: a weighted summation of responses of pathways with different timings and the presence of biochemical feedback loop(s) with emergent dynamics. Regulatory inputs act differently on these two tuning mechanisms. In the first case, regulators act like a gain-control on pathways with different intrinsic tuning. In the case of feedback loops, the temporal properties of the loop itself are changed. These basic tuning mechanisms may underlie specialized temporal tuning functions in more complex signaling systems in biology.

Passive antibody administration (immediate immunity) as a specific defense against biological weapons

The potential threat of biological warfare with a specific agent is proportional to the susceptibility of the population to that agent. Preventing disease after exposure to a biological agent is partially a function of the immunity of the exposed individual. The only available countermeasure that can provide immediate immunity against a biological agent is passive antibody. Unlike vaccines, which require time to induce protective immunity and depend on the host's ability to mount an immune response, passive antibody can theoretically confer protection regardless of the immune status of the host. Passive antibody therapy has substantial advantages over antimicrobial agents and other measures for postexposure prophylaxis, including low toxicity and high specific activity. Specific antibodies are active against the major agents of bioterrorism, including anthrax, smallpox, botulinum toxin, tularemia, and plague. This article proposes a biological defense initiative based on developing, producing, and stockpiling specific antibody reagents that can be used to protect the population against biological warfare threats.

Simultaneous quantification of cell motility and protein-membrane-association using active contours

We present a new method for the quantification of dynamic changes in fluorescence intensities at the cell membrane of moving cells. It is based on an active contour method for cell-edge detection, which allows tracking of changes in cell shape and position. Fluorescence intensities at specific cortical subregions can be followed in space and time and correlated with cell motility. The translocation of two GFP tagged proteins (CRAC and GRP1) from the cytosol to the membrane in response to stimulation with the chemoattractant cAMP during chemotaxis of Dictyostelium cells and studies of the spatio-temporal dynamics of this process exemplify the method: We show that the translocation can be correlated with motility parameters and that quantitative differences in the rate of association and dissociation from the membrane can be observed for the two PH domain containing proteins. The analysis of periodic CRAC translocation to the leading edge of a cell responding to natural cAMP waves in a mound demonstrates the power of this approach. It is not only capable of tracking the outline of cells within aggregates in front of a noisy background, but furthermore allows the construction of spatio-temporal polar plots, capturing the dynamics of the protein distribution at the cell membrane within the cells' moving co-ordinate system. Compilation of data by means of normalised polar plots is suggested as a future tool, which promises the so-far impossible practicability of extensive statistical studies and automated comparison of complex spatio-temporal protein distribution patterns.

GRGDSP peptide-bound silicone membranes withstand mechanical flexing in vitro and display enhanced fibroblast adhesion

Mechanobiological studies of cardiac tissue require devices that allow forces to be exerted on cells in vitro. Silicone elastomer is often used in these devices because it is flexible and transparent, permitting optical imaging of the cells. However, native untreated silicone is hydrophobic and is unsuitable for cell culture. Peptides covalently bound to silicone surfaces are examined here for the enhancement of cellular adhesion during in vitro dynamic flexing. A procedure is described for the chemical modification of medical grade silicone membranes with covalently bound GRGDSP peptides. The conditions for mechanical studies of cardiac cell cultures are then duplicated and it is demonstrated that the peptide layers survive 48 h of mechanical flexing in vitro. Specifically, mechanical flexing in vitro of the 30 pmol/cm2 peptide-modified silicone membranes has no significant effect on the amount of peptides that remains bound to the surface. Cardiac fibroblasts display enhanced adhesion to these peptide-bound silicone membranes for at least 24 h of growth, compared with native silicone or tissue culture polystyrene. The effects of serum versus serum-free media on fibroblast growth are also examined.

Determination of cellular strains by combined atomic force microscopy and finite element modeling

Many organs adapt to their mechanical environment as a result of physiological change or disease. Cells are both the detectors and effectors of this process. Though many studies have been performed in vitro to investigate the mechanisms of detection and adaptation to mechanical strains, the cellular strains remain unknown and results from different stimulation techniques cannot be compared. By combining experimental determination of cell profiles and elasticities by atomic force microscopy with finite element modeling and computational fluid dynamics, we report the cellular strain distributions exerted by common whole-cell straining techniques and from micromanipulation techniques, hence enabling their comparison. Using data from our own analyses and experiments performed by others, we examine the threshold of activation for different signal transduction processes and the strain components that they may detect. We show that modulating cell elasticity, by increasing the F-actin content of the cytoskeleton, or cellular Poisson ratio are good strategies to resist fluid shear or hydrostatic pressure. We report that stray fluid flow in some substrate-stretch systems elicits significant cellular strains. In conclusion, this technique shows promise in furthering our understanding of the interplay among mechanical forces, strain detection, gene expression, and cellular adaptation in physiology and disease.

The evolution and state of modern technology for prostate cryosurgery

Cryosurgery is the in situ ablation of a target tissue by application of extreme cold temperature. The ability of cryosurgery to ablate tissue is unquestioned. It is the controlled application of a cryoinjury in a manner to minimize morbidity that is problematic. Prostate cryosurgery is complicated by the proximity of the prostate to adjacent structures that are sensitive to a freeze injury, namely the urethra, rectal wall, and neurovascular bundles. Several recent technological advances have led to the development of an effective treatment protocol with acceptable morbidity. These include the advent of real-time transrectal ultrasound, cryomachines with almost instant freeze-thaw control through the use of the Joule-Thompson effect, and warming catheters to effectively preserve the integrity of the urethra and external sphincter. Further, temperature monitoring at the posterior margin of the prostate sometimes combined with an injection of saline solution into Denonvilliers fascia has reduced the occurrence of urethrorectal fistula formation to 0% to 0.5% in modern series. We review the key innovations of prostate cryosurgery that differentiate this state-of-the-art procedure from that used by early investigators to even that of the early 1990s. Potential future innovations, specifically related to image guidance of the procedure, are also addressed.

Understanding muscle coordination of the human leg with dynamical simulations

Muscles coordinate multijoint motion by generating forces that cause reaction forces throughout the body. Thus, a muscle can redistribute existing segmental energy by accelerating some segments and decelerating others. In the process, a muscle may also produce or absorb energy, in which case its summed energetic effect on the segments is positive or negative, respectively. This Borelli Lecture shows how dynamical simulations derived from musculoskeletal models reveal muscle-induced segmental energy redistribution and muscle co-functions and synergies. Synergy occurs when co-excited muscles distribute segmental energy differently to execute the motor task. In maximum height jumping, high vertical velocity at lift-off occurs desirably at full body extension because biarticular leg muscles redistribute the energy produced by the uniarticular leg muscles. In pedaling, synergistic ankle plantarflexor force generation during leg extension allows the high energy produced by the uniarticular hip and knee extensors to be delivered to the crank. An analogous less-powerful flexor synergy exists during leg flexion. Hamstrings reduce crank deceleration during the leg extension-to-flexion transition by not only producing energy but delivering it to the crank through its contribution to the tangential (accelerating) crank force, though this hamstrings function occurs at the opposite (flexion-extension) transition when pedaling backwards. In walking, the eccentric quadriceps activity in early stance not only decelerates the leg but also accelerates the trunk. In mid-stance, the uni- and biarticular plantarflexors, by having opposite segmental energetic effects, act in synergy to support the whole body, so segmental potential and kinetic energy exchange can occur. To conclude, the extraction of unmeasurable variables from dynamical simulations emulating task kinematics, kinetics, and EMGs shows how the production of force and energy by individual muscles contribute to the energy flow among the individual segments during task execution.

Neutrophil chemotaxis in linear and complex gradients of interleukin-8 formed in a microfabricated device

Although a wealth of knowledge about chemotaxis has accumulated in the past 40 years, these studies have been hampered by the inability of researchers to generate simple linear gradients instantaneously and to maintain them at steady state. Here we describe a device microfabricated by soft lithography and consisting of a network of microfluidic channels that can generate spatially and temporally controlled gradients of chemotactic factors. When human neutrophils are positioned within a microchannel, their migration in simple and complex interleukin-8 (IL-8) gradients can be tested. The cells exhibit strong directional migration toward increasing concentrations of IL-8 in linear gradients. Neutrophil migration halts abruptly when cells encounter a sudden drop in the chemoattractant concentration to zero ("cliff" gradient). When neutrophils are challenged with a gradual increase and decrease in chemoattractant ("hill" gradient), however, the cells traverse the crest of maximum concentration and migrate further before reversing direction. The technique described in this paper provides a robust method to investigate migratory cells under a variety of conditions not accessible to study by earlier techniques.

Primer on medical genomics part II: Background principles and methods in molecular genetics

The nucleus of every human cell contains the full complement of the human genome, which consists of approximately 30,000 to 70,000 named and unnamed genes and many intergenic DNA sequences. The double-helical DNA molecule in a human cell, associated with special proteins, is highly compacted into 22 pairs of autosomal chromosomes and an additional pair of sex chromosomes. The entire cellular DNA consists of approximately 3 billion base pairs, of which only 1% is thought to encode a functional protein or a polypeptide. Genetic information is expressed and regulated through a complex system of DNA transcription, RNA processing, RNA translation, and posttranslational and cotranslational modification of proteins. Advances in molecular biology techniques have allowed accurate and rapid characterization of DNA sequences as well as identification and quantification of cellular RNA and protein. Global analytic methods and human genetic mapping are expected to accelerate the process of identification and localization of disease genes. In this second part of an educational series in medical genomics, selected principles and methods in molecular biology are recapped, with the intent to prepare the reader for forthcoming articles with a more direct focus on aspects of the subject matter.

Quantitative 3-d diagnostic ultrasound imaging using a modified transducer array and an automated image tracking technique

An approach for acquiring dimensionally accurate three-dimensional (3-D) ultrasound data from multiple 2-D image planes is presented. This is based on the use of a modified linear-phased array comprising a central imaging array that acquires multiple, essentially parallel, 2-D slices as the transducer is translated over the tissue of interest. Small, perpendicularly oriented, tracking arrays are integrally mounted on each end of the imaging transducer. As the transducer is translated in an elevational direction with respect to the central imaging array, the images obtained by the tracking arrays remain largely coplanar. The motion between successive tracking images is determined using a minimum sum of absolute difference (MSAD) image matching technique with subpixel matching resolution. An initial phantom scanning-based test of a prototype 8 MHz array indicates that linear dimensional accuracy of 4.6% (2 sigma) is achievable. This result compares favorably with those obtained using an assumed average velocity [31.5% (2 sigma) accuracy] and using an approach based on measuring image-to-image decorrelation [8.4% (2 sigma) accuracy]. The prototype array and imaging system were also tested in a clinical environment, and early results suggest that the approach has the potential to enable a low cost, rapid, screening method for detecting carotid artery stenosis. The average time for performing a screening test for carotid stenosis was reduced from an average of 45 minutes using 2-D duplex Doppler to 12 minutes using the new 3-D scanning approach.

Writing with DNA and protein using a nanopipet for controlled delivery

We present a new, general method for the controlled deposition of biological molecules on surfaces, based on a nanopipet operating in ionic solution. The potential applied to the pipet tip controls the flux of biological molecules from the pipet, allowing fine control of the delivery rate. We used the ion current to control the distance of the pipet from the surface of a glass slide and deposited the fluorescently labeled DNA or protein G at a defined location onto the surface. Features of 830 nm size were obtained by depositing the biotinylated DNA onto a streptavidin surface; 1.3 mum size spots were obtained by depositing protein G onto a positively charged glass surface.

Expression of TGF-beta1 and beta3 but not apoptosis factors relates to flow-induced aortic enlargement

BACKGROUND

Cell proliferation and apoptosis are both involved in arterial wall remodeling. Increase in blood flow induces arterial enlargement. The molecular basis of flow-induced remodeling in large elastic arteries is largely unknown.

METHODS

An aortocaval fistula (ACF) model in rats was used to induce enlargement in the abdominal aorta. Aortic gene expression of transforming growth factors beta (TGF-beta) and apoptosis-related factors was assessed at 1 and 3 days and 1, 2, 4, and 8 weeks. Expression levels were determined using a ribonuclease protection assay and western blotting. Cell proliferation and apoptosis were analyzed using BrdU incorporation and TUNEL techniques.

RESULTS

Blood flow increased 5-fold immediately after ACF (P<0.05). Lumen diameter of the aorta was 30% and 75% larger at 2 and 8 weeks respectively than those of controls (P<0.05). mRNA levels of TGF-beta1 and TGF-beta3 increased after ACF, peaked at 3 days (P<0.05) and returned to normal level at 1 week and thereafter. Western blotting showed enhanced expression of TGF-beta1 at 3 days and TGF-beta3 at 1 and 3 days and 1 week (P<0.05). mRNA levels of Bcl-xS initially decreased at 1 day, 3 days and 1 week, followed a return to baseline level at 2 weeks. Cell proliferation was observed at all time points after ACF (P<0.001 vs. controls) with proliferation in endothelial cells more significant than smooth muscle cells. Apoptosis was not significant.

CONCLUSIONS

Gene expression of TGF-beta1 and beta3 precedes arterial enlargement. Expression of apoptosis related factors is little regulated in the early stage of the flow-induced arterial remodeling.

Fifteen minutes of fim: control of type 1 pili expression in E. coli

Pili are used by Escherichia coli to attach to and invade mammalian tissues during host infection and colonization. Expression of type 1 pili, believed to act as virulence factors in urinary tract infections, is under control of the 'firm' genetic network. This network is able to sense the environment and actuate phase variation control. It is a prime exemplar of an integrative regulatory system because of its role in mediating a complex infection process, and because it instantiates a number of regulatory motifs, including DNA inversion and stochastic variation. With the help of a mathematical model, we explore the mechanisms and architecture of the fim network. We explain (1) basic network operation, including the roles of the recombinase and global regulatory protein concentrations, their DNA binding affinities, and their switching rates in observed phase variation behavior; (2) why there are two recombinases when one would seem to suffice; (3) the source of on-to-off switching specificity of FimE; (4) the role of fimE orientational control in switch dynamics; and (5) how temperature tuning of piliation is achieved. In the process, we identify a general regulatory motif that tunes phenotype to an environmental variable, and explain a number of apparent experimental inconsistencies.

Type I shorthorn sculpin antifreeze protein: recombinant synthesis, solution conformation, and ice growth inhibition studies

A number of structurally diverse classes of "antifreeze" proteins that allow fish to survive in sub-zero ice-laden waters have been isolated from the blood plasma of cold water teleosts. However, despite receiving a great deal of attention, the one or more mechanisms through which these proteins act are not fully understood. In this report we have synthesized a type I antifreeze polypeptide (AFP) from the shorthorn sculpin Myoxocephalus scorpius using recombinant methods. Construction of a synthetic gene with optimized codon usage and expression as a glutathione S-transferase fusion protein followed by purification yielded milligram amounts of polypeptide with two extra residues appended to the N terminus. Circular dichroism and NMR experiments, including residual dipolar coupling measurements on a 15N-labeled recombinant polypeptide, show that the polypeptides are alpha-helical with the first four residues being more flexible than the remainder of the sequence. Both the recombinant and synthetic polypeptides modify ice growth, forming facetted crystals just below the freezing point, but display negligible thermal hysteresis. Acetylation of Lys-10, Lys-20, and Lys-21 as well as the N terminus of the recombinant polypeptide gave a derivative that displays both thermal hysteresis (0.4 degrees C at 15 mg/ml) and ice crystal faceting. These results confirm that the N terminus of wild-type polypeptide is functionally important and support our previously proposed mechanism for all type I proteins, in which the hydrophobic face is oriented toward the ice at the ice/water interface.

Nitric oxide as an anterograde neurotransmitter in the trigeminal motor pool

We demonstrate the presence of nitric oxide synthase containing fibers within the guinea pig trigeminal motor nucleus and describe the effects of nitric oxide (NO) on trigeminal motoneurons. Using immunohistochemical techniques, we observed nitrergic fibers displaying varicosities and giving rise to bouton-like structures in apposition to retrogradely labeled motoneuron processes, most of which were dendrites. NO-donors evoked a membrane depolarization (mean 7.5 mV) and a decrease in rheobase (mean 38%). These substances also evoked an apparent increase in an hyperpolarization-activated cationic current (I(H)). These changes were not accompanied by any modification of the motoneurons' input resistance or time constant. The effects were suppressed by blocking the cytosolic guanlyate cyclase. A membrane-permeant cyclic guanosine 3,5'-monophosphate (cGMP) analogue mimicked the effects of NO. There was a considerable increase in synaptic activity following NO-donors or db-cGMP application. Tetrodotoxin supressed the increase in synaptic activity evoked by NO-donors. The histological and electrophysiological evidence, taken together, indicates the existence of a nitrergic system able to modulate trigeminal motoneurons under yet unknown physiological conditions.

Retinal prosthesis for the blind

Most of current concepts for a visual prosthesis are based on neuronal electrical stimulation at different locations along the visual pathways within the central nervous system. The different designs of visual prostheses are named according to their locations (i.e., cortical, optic nerve, subretinal, and epiretinal). Visual loss caused by outer retinal degeneration in diseases such as retinitis pigmentosa or age-related macular degeneration can be reversed by electrical stimulation of the retina or the optic nerve (retinal or optic nerve prostheses, respectively). On the other hand, visual loss caused by inner or whole thickness retinal diseases, eye loss, optic nerve diseases (tumors, ischemia, inflammatory processes etc.), or diseases of the central nervous system (not including diseases of the primary and secondary visual cortices) can be reversed by a cortical visual prosthesis. The intent of this article is to provide an overview of current and future concepts of retinal and optic nerve prostheses. This article will begin with general considerations that are related to all or most of visual prostheses and then concentrate on the retinal and optic nerve designs. The authors believe that the field has grown beyond the scope of a single article so cortical prostheses will be described only because of their direct effect on the concept and technical development of the other prostheses, and this will be done in a more general and historic perspective.

Pyrosequencing technology and the need for versatile solutions in molecular clinical research

An increasing amount of genetic information is rapidly becoming available to the practitioners of medicine and pharmacology. This knowledge promises to revolutionize the determination of diagnoses and prognoses for genetically-based disorders as well as infectious diseases and to enable tailoring of treatment to suit the individual patient. As genomics becomes ripe for clinical implementation, versatile technologies that can handle all the relevant types of analyses will be requested by many clinicians. The recently established Pyrosequencing technology for rapid determination of short DNA sequences has gained widespread acceptance and is being used in a broad range of applications. It can provide a solution for many emerging issues in molecular clinical research and applications, owing to its reliability and high flexibility together with its user-friendly attributes.

Model-predictive control of hyperthermia treatments

A model-predictive controller (MPC) of the thermal dose in hyperthermia cancer treatments has been developed and evaluated using simulations with one-point and one-dimensional models of a tumor. The developed controller is the first effort in: 1) the application of feedback control to pulsed, high-temperature hyperthermia treatments; 2) the direct control of the treatment thermal dose rather than the treatment temperatures; and 3) the application of MPC to hyperthermia treatments. Simulations were performed with different blood flow rates in the tumor and constraints on temperatures in normal tissues. The results demonstrate that 1) thermal dose can be controlled in the presence of plant-model mismatch and 2) constraints on the maximum allowable temperatures in normal tissue and/or the pulsed power magnitude can be directly incorporated into MPC and met while delivering the desired thermal dose to the tumor. For relatively high blood flow rates and low transducer surface intensities--factors that limit the range of temperature variations in the tumor, the linear MPC, obtained by piece-wise linearization of the dose-temperature relationship, provides an adequate performance. For large temperature variations, the development of nonlinear MPC is necessary.

5'-,3'-inverted thymidine-modified antisense oligodeoxynucleotide targeting midkine. Its design and application for cancer therapy

Oligodeoxynucleotides modified at both 5'- and 3'-ends with inverted thymidine (5'-,3'-inverted T) were introduced as new reagents for antisense strategies. These modifications were performed to make the oligodeoxynucleotides resistant to nucleases. The effectiveness of these oligodeoxynucleotides was evaluated in terms of inhibition of synthesis of midkine (MK), a heparin-binding growth factor, and consequent inhibition of growth of CMT-93 mouse rectal carcinoma cells. 5'-,3'-Inverted T antisense MK suppressed synthesis of MK by CMT-93 cells and their growth in culture. Furthermore, 5'-,3'-inverted T oligodeoxynucleotides exhibited less cytotoxicity and better stability than phosphorothioate oligodeoxynucleotides. When 5'-,3'-inverted T antisense MK was mixed with atelocollagen, and injected into CMT-93 tumors pregrown in nude mice, tumor growth was markedly suppressed as compared with tumors injected with sense controls. The suppressive effect of 5'-,3'-inverted T antisense MK on tumor growth was stronger than that of phosphorothioate antisense MK. These findings indicated the usefulness of inverted thymidine-modified antisense oligodeoxynucleotides as a new reagent instead of phosphorothioate-modified oligodeoxynucleotides.

A new optical method for the non-invasive detection of minimal tissue alterations

Histological analysis, which is used to detect and diagnose most tissue alterations, requires an invasive biopsy procedure and a time-consuming tissue treatment, which limit its efficiency in providing rapid, cost-effective diagnosis and hinder the longitudinal study of tissue alteration. To address these limitations, we have developed a novel procedure, using the features of elastic-scattering spectroscopy, for a real-time, non-invasive analysis of tissues. We have tested whether this approach can detect in vivo changes in mouse skin induced by a single exposure to either complete Freund's adjuvant or 12-O-tetradecanoylphorbol-13-acetate, two drugs known to induce discrete alterations of epidermis and dermis, without obvious changes on the skin surface. Here we report that the evaluation of localized absorption and reduced scattering coefficients permitted the detection of changes in skin regions that showed histological alterations, but not in regions which failed to be modified by the drugs. Results show that the optical in vivo analysis of small regions has sufficient specificity and sensitivity to detect minimal alterations of superficial tissues. In view of the prominent involvement of mucosal alterations in most human diseases, including carcinomas, the method provides a useful complement to standard biopsy, notably for the in vivo screening of early in situ epithelial alterations.

Polybrene increases retrovirus gene transfer efficiency by enhancing receptor-independent virus adsorption on target cell membranes

Cationic polymers, such as polybrene and protamine sulfate, are typically used to increase the efficiency of retrovirus-mediated gene transfer, however, the mechanism of their enhancement of transduction has remained unclear. As retrovirus transduction is fundamentally limited by the slow diffusion of virus to the target cell surface, we investigated the ability of polybrene to modulate this initial transport step. We compared the ability of both envelope (gp70) and capsid (p30) protein based assays to quantitate virus adsorption and found that p30 based assays were more reliable due to their ability to distinguish virus binding from free gp70 binding. Using the p30 based assay, we established that polybrene concentrations, which yielded 10-fold increases in transduction also, yielded a significant increase in virus adsorption rates on murine fibroblasts. Surprisingly, this enhancement, and adsorption in general, were receptor and envelope independent, as adsorption occurred equivalently on receptor positive and negative Chinese hamster ovary cells, as well as with envelope positive and negative virus particles. These findings suggest that the currently accepted physical model for early steps in retrovirus transduction may need to be reformulated to accommodate an initial adsorption step whose driving force does not include the retrovirus concentration, and the reclassification of currently designated 'receptor' molecules as fusion triggers. The implication of these findings with respect to the development of targeted retrovirus-mediated gene therapy protocols is discussed.

Analytic chemistry. Everyone's a (future) chemist

The development of small, portable "lab-on-a-chip" devices has the potential to provide individuals with the tools for complex chemical and biochemical analysis. In his Perspective, Burns charts recent progress toward fabricating such devices. He highlights the report by Terray et al., who use latex spheres manipulated by optical traps to pump fluids. The integration of such components into larger, more complex devices will open up applications from airborne contaminant detection to genetic testing and screening.

Dynamic imaging of T cell-dendritic cell interactions in lymph nodes

T cell immune responses begin within organized lymphoid tissues. The pace, topology, and outcomes of the cellular interactions that underlie these responses have, so far, been inferred from static imaging of sectioned tissue or from studies of cultured cells. Here we report dynamic visualization of antigen-specific T cells interacting with dendritic cells within intact explanted lymph nodes. We observed immunological synapse formation and prolonged interactions between these two cell types, followed by the activation, dissociation, and rapid migration of T cells away from the antigenic stimulus. This high-resolution spatiotemporal analysis provides insight into the nature of cell interactions critical to early immune responses within lymphoid structures.

On computational control of flow in airblast atomisers for pulmonary drug delivery

Among different approaches to successful pharmacotherapy the pulmonary drug delivery (PDD) mode plays an increasingly important role. In this paper PDD systems based on air-blast atomisation have been analysed mathematically. In order to allow the bioengineer to estimate the degree of effectiveness of a specific system prototype and to lay the basic principles for design, a conservation-law-based mathematical model is discussed. Key control parameters that allow improvement in the efficiency of the system have been identified and main characteristics of the system have been analysed numerically as functions of these parameters.

The device and algorithm for estimation of the mechanoemisson chaos in blood of patients with gastric cancer

The mechanoemission (ME) of blood is developed as a result of mechanochemical activation of a sample which is layered onto chromatographic paper. This paper describes computer-controlled device, aimed for generation, detection and analysis of ME data in the blood of the persons investigated. The original algorithm for estimation of ME chaos in blood is developed. For gastric cancer patients an increase of ME chaos is observed in comparison with healthy individuals and patients with inflammation of gastric mucosa. The concept of deterministic chaos is biohierarchical for the host of a cancer patient. In the light of this we have calculated that spatial chaos for gastric cancer patients is also increased in the geometrical structure of tumor cells and magnetic resonance imaging of the stomach. The concept of deterministic chaos may find an application in the development of new multi-computer organizations for medical diagnostic equipment.

Engineering cellular microenvironments to improve cell-based drug testing

Recent progress in the biology of cell adhesion is enabling cell culture models to better reproduce in vivo functions. Cues from adhesion to extracellular matrix and neighboring cells are important regulators of cell behaviors. The recent adaptation of semiconductor tools to spatially organize cells and their adhesions has enhanced our ability to engineer cell functions ex vivo. By using these tools to create more in vivo-like cultures, cell-based drug discovery and target validation could be improved. This review explores the biological advances made by these microfabrication tools and discusses how they could enable high-throughput cell-based assays.

Piezoelectrically actuated flextensional micromachined ultrasound droplet ejectors

This paper reports a variation on the design of the flextensional transducer for use in ejecting liquids. The transducer is constructed by depositing a piezoelectric thin film to a thin, edge-clamped, circular annular plate. By placing a fluid behind one face of a vibrating compound plate that has an orifice at its center, we achieve continuous or drop-on-demand ejection of the fluid. We present results of ejection of water and isopropanol. The ejector is harmless to sensitive fluids and can be used to eject fuels as well as chemical and biological samples. Micromachined two-dimensional array piezoelectrically actuated flextensional droplet ejectors were realized using planar silicon micromachining techniques. Typical resonant frequency of the micromachined device ranges from 400 kHz to 4.5 MHz. The ejection of water thru a 5-microm diameter orifice at 3.5 MHz was demonstrated by using the developed micromachined two-dimensional array ejectors.

Model of nitric oxide diffusion in an arteriole: impact of hemoglobin-based blood substitutes

Administration of hemoglobin-based oxygen carriers (HBOCs) frequently results in vasoconstriction that is primarily attributed to the scavenging of endothelium-derived nitric oxide (NO) by cell-free hemoglobin. The ensuing pressor response could be caused by the high NO reactivity of HBOC in the vascular lumen and/or the extravasation of hemoglobin molecules. There is a need for quantitative understanding of the NO interaction with HBOC in the blood vessels. We developed a detailed mathematical model of NO diffusion and reaction in the presence of an HBOC for an arteriolar-size vessel. The HBOC reactivity with NO and degree of extravasation was studied in the range of 2-58 x 10(6) M(-1) x s(-1) and 0-100%, respectively. The model predictions showed that the addition of HBOC reduced the smooth muscle (SM) NO concentration in the activation range (12-28 nM) for soluble guanylate cyclase, a major determinant of SM contraction. The SM NO concentration was significantly reduced when the extravasation of HBOC molecules was considered. The myoglobin present in the parenchymal cells scavenges NO, which reduces the SM NO concentration.

Molecular diagnostics: hurdles for clinical implementation

In the coming years, molecular diagnostics will continue to be of critical importance to public health worldwide. It will facilitate the detection and characterization of disease, as well as monitoring of the drug response, and will assist in the identification of genetic modifiers and disease susceptibility. A wide range of molecular-based tests is available to assess DNA variation and changes in gene expression. However, there are major hurdles to overcome before the implementation of these tests in clinical laboratories, such as which test to employ, the choice of technology and equipment, and issues such as cost-effectiveness, accuracy, reproducibility, personnel training, reimbursement by third-party payers and intellectual property. At present, PCR-based testing predominates; however, alternative technologies aimed at reducing genome complexity without PCR are anticipated to gain momentum in the coming years. Furthermore, development of integrated chip devices ("lab-on-a-chip") should allow point-of-care testing and facilitate genetic readouts from single cells and molecules. Together with proteomic-based testing, these advances will improve molecular diagnostic testing and will present additional challenges for implementing such testing in health care settings.

Erythrocyte consumption of nitric oxide in presence and absence of plasma-based hemoglobin

Experimental measurements have suggested a consumption rate of nitric oxide (NO) by red blood cells (RBCs) that is orders of magnitude smaller than that of an equivalent concentration of free hemoglobin in solution. This difference has been attributed to external diffusion limitations in the transport of NO from the plasma to the surface of the RBC or to resistance in the transport through the erythrocytic membrane. A detailed mathematical model is developed to quantify the resistance to NO transport around a single RBC and to predict the consumption rate in the presence and absence of extracellular hemoglobin. We provide a description for the NO consumption rate as a function of hematocrit, RBC radius, membrane permeability, and extracellular hemoglobin concentration. We predict a first-order rate constant for NO consumption in blood between 7.5 x 10(2) and 6.5 x 10(3) s(-1) at a hematocrit of 45% for membrane permeability values between 0.1 and 40 cm/s. Our results suggest that the difference in NO uptake by RBCs and free hemoglobin is smaller than previously reported and it is hematocrit dependent.

Rapidly recovering hydrogel scaffolds from self-assembling diblock copolypeptide amphiphiles

Protein-based hydrogels are used for many applications, ranging from food and cosmetic thickeners to support matrices for drug delivery and tissue replacement. These materials are usually prepared using proteins extracted from natural sources, which can give rise to inconsistent properties unsuitable for medical applications. Recent developments have utilized recombinant DNA methods to prepare artificial protein hydrogels with specific association mechanisms and responsiveness to various stimuli. Here we synthesize diblock copolypeptide amphiphiles containing charged and hydrophobic segments. Dilute solutions of these copolypeptides would be expected to form micelles; instead, they form hydrogels that retain their mechanical strength up to temperatures of about 90 degrees C and recover rapidly after stress. The use of synthetic materials permits adjustment of copolymer chain length and composition, which we varied to study their effect on hydrogel formation and properties. We find that gelation depends not only on the amphiphilic nature of the polypeptides, but also on chain conformations--alpha-helix, beta-strand or random coil. Indeed, shape-specific supramolecular assembly is integral to the gelation process, and provides a new class of peptide-based hydrogels with potential for applications in biotechnology.

Efficiency of embryoid body formation and hematopoietic development from embryonic stem cells in different culture systems

Embryonic stem (ES) cells have tremendous potential as a cell source for cell-based therapies. Realization of that potential will depend on our ability to understand and manipulate the factors that influence cell fate decisions and to develop scalable methods of cell production. We compared four standard ES cell differentiation culture systems by measuring aspects of embryoid body (EB) formation efficiency and cell proliferation, and by tracking development of a specific differentiated tissue type-blood-using functional (colony-forming cell) and phenotypic (Flk-1 and CD34 expression) assays. We report that individual murine ES cells form EBs with an efficiency of 42 +/- 9%, but this value is rarely obtained because of EB aggregation-a process whereby two or more individual ES cells or EBs fuse to form a single, larger cell aggregate. Regardless of whether EBs were generated from a single ES cell in methylcellulose or liquid suspension culture, or aggregates of ES cells in hanging drop culture, they grew to a similar maximum cell number of 28,000 +/- 9,000 cells per EB. Among the three methods for EB generation in suspension culture there were no differences in the kinetics or frequency of hematopoietic development. Thus, initiating EBs with a single ES cell and preventing EB aggregation should allow for maximum yield of differentiated cells in the EB system. EB differentiation cultures were also compared to attached differentiation culture using the same outputs. Attached colonies were not similarly limited in cell number; however, hematopoietic development in attached culture was impaired. The percentage of early Flk-1 and CD34 expressing cells was dramatically lower than in EBs cultured in suspension, whereas hematopoietic colony formation was almost completely inhibited. These results provide a foundation for development of efficient, scalable bioprocesses for ES cell differentiation, and inform novel methods for the production of hematopoietic tissues.