Development of phase plates for electron microscopes and their biological application

After slow progress in the efforts to develop phase plates for electron microscopes, functional phase plates with thin carbon films have recently been reported. An electron microscope enhanced with thin-film phase plates has practical advantages. It permits collecting high-contrast images of intact biological specimens without harsh and lengthy sample preparation, such as fixation, dehydration, resin-embedding, staining and thin-sectioning. This report reviews the state of the art for phase plates in biological electron microscopy and focuses upon the conditions required for functional thin-film phase plates. The current disadvantages of thin-film phase plates are also addressed and potential solutions are proposed.     

pH measurement and a rational and practical pH control strategy for high throughput cell culture system

The number of therapeutic proteins produced by cell culture in the pharmaceutical industry continues to increase. During the early stages of manufacturing process development, hundreds of clones and various cell culture conditions are evaluated to develop a robust process to identify and select cell lines with high productivity. It is highly desirable to establish a high throughput system to accelerate process development and reduce cost. Multiwell plates and shake flasks are widely used in the industry as the scale down model for large‐scale bioreactors. However, one of the limitations of these two systems is the inability to measure and control pH in a high throughput manner. As pH is an important process parameter for cell culture, this could limit the applications of these scale down model vessels. An economical, rapid, and robust pH measurement method was developed at Eli Lilly and Company by employing SNARF‐4F 5‐(‐and 6)‐carboxylic acid. The method demonstrated the ability to measure the pH values of cell culture samples in a high throughput manner. Based upon the chemical equilibrium of CO₂, HCO, and the buffer system, i.e., HEPES, we established a mathematical model to regulate pH in multiwell plates and shake flasks. The model calculates the required %CO₂ from the incubator and the amount of sodium bicarbonate to be added to adjust pH to a preset value. The model was validated by experimental data, and pH was accurately regulated by this method. The feasibility of studying the pH effect on cell culture in 96‐well plates and shake flasks was also demonstrated in this study. This work shed light on mini‐bioreactor scale down model construction and paved the way for cell culture process development to improve productivity or product quality using high throughput systems. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Kinetic model of regulation of muscle protein activity.

The widely accepted steric model of calcium regulation of actin-myosin interactions in vertebrate muscles has to be completed to fit the kinetic data. It should be supposed that: (1) the thin filaments consist of functionally independent units, containing seven actin sites regulated by one troponin-tropomyosin complex; (2) actin sites become available for myosin heads only due to fluctuations of tropomyosin position; (3) binding of calcium to troponin results either in the shift of the tropomyosin equilibrium position or in the weakening of its interactions with actin strand so that the probability of effective fluctuations increases; (4) link formation between myosin head and some of the available actin site fixates the tropomyosin in such a position that the other six actin sites of the same functional unit become available for myosin too.The model gives linear kinetic scheme for the transitions of a functional unit between nine states (a “turned off” state, and eight “turned on” ones with different occupancy by myosin heads). The dependences of the apparent rate constants of actomyosin formation and dissociation upon the myosin head and substrate concentrations are obtained from the Lymn-Taylor scheme. The frequency of the actomyosin complexes dissociation is assumed to give the ATPase rate.The model fits the kinetic data on the ATP hydrolysis by myosin subfragment-1 with regulated or unregulated actin as a cofactor under various conditions. It shows a sharp dependence of activation upon the apparent affinity of the actin and myosin sites. Therefore, the model appears to be applicable to myosin controlled systems.     

Ion exchange chromatography of proteins-prediction of elution curves and operating conditions. I. Theoretical considerations

A mathematical model is proposed for the elution of proteins on ion exchange columns by a linear gradient increase and stepwise increase of ionic strength in order to predict relationships between the elution characteristics (the peak position, the peak width, etc.) and the operating conditions (the flow rate, the slope of gradient, etc). This model is in principle based on the continuous-flow plate theory, in which the protein concentration and ionic strength dependent distibution coefficient between proteins and ion exchangers and zone sperading effects are taken into consideration. The advantage of this model is its simplicity since it requires only two parameters: The distribution coefficient and the number of plates. Since the distribution coefficient of proteins depends on both the protein concentration and ionic strength of the elution buffer, the number of plates should vary with time. However, it is extremely difficult to take into consideration the time-dependent number of plates. Therefore, we assume that the number of plates is constant and related to that number derived from a mass balance model which includes longitudinal dispersion and gel phase diffusion. On the basis of these assumptions, a method for determining the number of plates by the moment method is presented. Although the dependencies of the peak position and peak width on the slope of linear gradient are predictable by numerical calculations of the present model, simpler methods for prediction of these dependencies are desirable. A graphical method is proposed for prediction of the peak position. For prediction of the peak width, an asymptotic solution is derived from a quasi-steady-state model.     

Modeling the weak hydrogen bonding of pyrrole and dichloromethane through Raman and DFT study

Raman spectra of neat pyrrole (C(4)H(5)N) and its binary mixtures with dichloromethane (CH(2)Cl(2), DCM) with varying mole fractions of C(4)H(5)N from 0.1 to 0.9 were recorded in order to monitor the influence of molecular interaction on spectral features of selected vibrational bands of pyrrole in the region 600-1600 cm(-1). Only 1369 cm(-1) vibrational band of pyrrole shows a significant change in its peak position in going from neat pyrrole to the complexes. The 1369 cm(-1) band shows (～6 cm(-1)) blue shift upon dilution and the corresponding linewidth shows the maximum shift at C?=?0.5 mole fraction of pyrrole upon dilution which clearly indicates that the concentration fluctuation model plays major role. Quantum chemical calculation using density functional theory (DFT) and ab-initio (MP2 and HF) methods were performed employing high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat pyrrole and its complexes with DCM in gas phase. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. In order to account for the solvent effect on vibrational features and changes in optimized structural parameters of pyrrole, polarizable continuum model (PCM) (bulk solvations) and PCM (specific plus bulk solvations) calculations were performed. Two possible configurations of pyrrole + DCM complex have been predicted by B3LYP and HF methods, whereas the MP2 method gave only single configuration in which H atom of DCM is bonded to π ring of the pyrrole molecule. This affects significantly the ring vibrations of pyrrole molecule, which was also observed in our experimental results.     

A New Self-Loading Locomotion Mechanism for Wall Climbing Robots Employing Biomimetic Adhesives

A versatile locomotion mechanism is introduced and experimentally verified. This mechanism comprises four rectangular wheels (legs) with rotational phase difference which enables the application of pressure to each contacting surface for securing it to the surface using bio-inspired or pressure-sensitive adhesives. In this mechanism, the adhesives are applied to two rigid plates attached to each wheel via hinges incorporating torsional springs. The springs force the plates back to their original position after the contact with the surface is lost in the course of locomotion. The wheels are made of low-modulus elastomers, and the pressure applied during contact is controlled by the elastic modulus, geometry and phase difference of wheels. This reliable adhesion system does not rely upon gravity for adhering to surfaces, and provides the locomotion mechanism with the ability to climb walls and transition from horizontal to vertical surfaces.     

Studies on the action of nerve growth factor. III. Role of RNA and protein synthesis in the process of neurite outgrowth.

Chick embryo dorsal root and sympathetic ganglia cultured on untreated tissue culture plates exhibited a dependence upon both RNA and protein synthesis for the expression of nerve growth factor-mediated neurite outgrowth. Neurite outgrowth was no longer dependent upon RNA synthesis, but remained dependent upon continued protein synthesis when ganglia were cultured in plasma clots, or on either collagen or poly-l-lysine coated plates. Nerve growth factor-induced neurite outgrowth was dependent upon the presence of either microexudates, which may play an important role as functional components of the substratum across which neurites migrate, or exogenous substrata such as collagen, fibrin, or poly-l-lysine.     

Electromyographic evaluation of masseter and anterior temporalis muscles in rest position of edentulous patients with temporomandibular disorders, before and after using complete dentures with sliding plates

Objectives: This study was performed with the purpose of investigating electromyographic (EMG) activity of the anterior temporalis and masseter muscles in edentulous individuals with temporomandibular disorder (TMD), before and after using sliding plates on complete dentures in the mandibular rest position. Background: Edentulous patients may present TMD, which is characterised by pain in temporomandibular joints, masticatory and neck muscles, uncoordinated and limited mandible movements, joint sounds and an altered occlusal relationship. It is imperative to offer treatment in order to re‐establish stomatognathic system structures before submitting the individual to any definitive restorative treatment. Materials and methods: The patients were edentulous for at least 10 years. EMG recordings were made before the insertion of the dentures (0 months) and also after using the sliding plates at the fourth month, 9th month and 12th month, using computerised electromyography K6‐I/ EMG Light Channel Surface. EMG evaluations of the muscles were performed under the following clinical conditions: rest position with dentures (R1), rest position without dentures (R2), rest position with dentures post‐activity (chewing) (R3), rest position without dentures post‐activity (chewing) (R4). Results: All patients obtained remission of muscular fatigue and reduced pain in stomatognathic system structures. Temporalis muscle showed significant increase in EMG activity compared with initial values (p < 0.01). Masseter muscles showed significantly lower mean values (p < 0.01) compared with initial values. Conclusion: The sliding plates allowed the process of neuromuscular deprogramming, contributing to muscular balance of the masticatory system, and are therefore indicated to be used before the fabrication of definitive complete dentures in patients with TMD.     

Adaptation of aequorin functional assay to high throughput screening

AequoScreen, a cellular aequorin-based functional assay, has been optimized for luminescent high-throughput screening (HTS) of G protein-coupled receptor (GPCRs). AequoScreen is a homogeneous assay in which the cells are loaded with the apoaequorin cofactor coelenterazine, diluted in assay buffer, and injected into plates containing the samples to be tested. A flash of light is emitted following the calcium increase resulting from the activation of the GPCR by the sample. Here we have validated a new plate reader, the Hamamatsu Photonics FDSS6000, for HTS in 96- and 384-well plates with CHO-K1 cells stably coexpressing mitochondrial apoaequorin and different GPCRs (AequoScreen cell lines). The acquisition time, plate type, and cell number per well have been optimized to obtain concentration-response curves with 4000 cells/well in 384-well plates and a high signal:background ratio. The FDSS6000 and AequoScreen cell lines allow reading of twenty 96- or 384-well plates in 1 h with Z' values of 0.71 and 0.78, respectively. These results bring new insights to functional assays, and therefore reinforce the interest in aequorin-based assays in a HTS environment.     

Morphology and function of the feeding apparatus of the lungfish, Lepidosiren paradoxa (Dipnoi)

The feeding mechanism of the South American lungfish, Lepidosiren paradoxa retains many primitive teleostome characteristics. In particular, the process of initial prey capture shares four salient functional features with other primitive vertebrates: 1) prey capture by suction feeding, 2) cranial elevation at the cranio-vertebral joint during the mouth opening phase of the strike, 3) the hyoid apparatus plays a major role in mediating expansion of the oral cavity and is one biomechanical pathway involved in depressing the mandible, and 4) peak hyoid excursion occurs after maximum gape is achieved. Lepidosiren also possesses four key morphological and functional specializations of the feeding mechanism: 1) tooth plates, 2) an enlarged cranial rib serving as a site for the origin of muscles depressing the hyoid apparatus, 3) a depressor mandibulae muscle, apparently not homologous to that of amphibians, and 4) a complex sequence of manipulation and chewing of prey in the oral cavity prior to swallowing. The depressor mandibulae is always active during mouth opening, in contrast to some previous suggestions. Chewing cycles include alternating adduction and transport phases. Between each adduction, food may be transported in or out of the buccal cavity to position it between the tooth plates. The depressor mandibulae muscle is active in a double-burst pattern during chewing, with the larger second burst serving to open the mouth during prey transport. Swallowing is characterized by prolonged activity in the hyoid constrictor musculature and the geniothoracicus. Lepidosiren uses hydraulic transport achieved by movements of the hyoid apparatus to position prey within the oral cavity. This function is analogous to that of the tongue in many tetrapods.     

Oriented Immobilization of Anti-Pneumolysin Tagged Recombinant Antibody Fragments

Recombinant antibodies such as Fab and scFv are monovalent and small in size, although their functional affinity can be improved through tag-specific immobilization. In order to find the optimum candidate for oriented immobilization, we generated Fab and scFv fragments derived from an anti-pneumolysin monoclonal antibody PLY-7, with histidine and cysteine residues added in diverse arrangements. Tagged antibody fragments scFv-Cys7-His6, His6-scFv-Cys7, and Fab-Cys7 lost considerable affinity for the antigen; however, Fab-His6, Fab-Cys1, and scFv-His6-Cys1 were able to detect immobilized antigen, revealing that the position and number of histidine and cysteine residues are involved differently in the reactivity of antibody fragments. Random and orientated immobilizations were carried out using conventional polystyrene and commercial surface-pretreated ELISA plates. The best orientation performance was obtained with Fab-Cys1-biotin on streptavidin-coated plates with increased signal levels of 62%, while oriented immobilization of Fab-His6 and scFv-His6-Cys1 on nickel- and maleimide-coated plates failed to improve the ELISA sensitivity.     

Anatomy and function of the ptychoid defensive mechanism in the mite Euphthiracarus cooki (Acari: Oribatida)

Ptychoidy is a defensive adaptation of several groups of oribatid mites in which legs and coxisternum can be fully retracted into the opisthosoma and protected by a ventrally deflected prodorsum, resulting in a seed-like appearance. Using Euphthiracarus cooki as a model, we examined details of exoskeletal and muscular anatomy in combination with studies of live individuals to provide the first functional analysis of ptychoidy. There are two main functional components: the first is a set of exoskeletal and muscular adaptations, mostly of the podosoma and prodorsum, that combine to effect leg withdrawal and prodorsal deflection; the second comprises adaptations of the opisthosoma that allow control of hydrostatic pressure during the large hemocoel volume adjustments associated with ptychoidy. Adaptations important in the closing process (enptychosis) are found in four body regions. Much of the podosomal exoskeleton (especially pleural) is unsclerotized, which facilitates leg retraction and prodorsal deflection during enptychosis. The coxisternum has several flexible furrows along which it folds in order to bring legs into a tightly parallel arrangement. The prodorsum has specialized attachment surfaces (manubrium and inferior retractor process) for retractor muscles and a paired bothridial scale that participates in prodorsal alignment during enptychosis. The subcapitulum has a prominent capitular apodeme on which important retractor muscles insert. The mineralized notogaster has an anterior "collar" that accommodates the retracted prodorsum; it includes paired notches and receptacles that accommodate the bothridial scales, thereby creating a temporary fixed axis for rotation of the prodorsum in a "lazy hinge" mechanism. Specialized muscles form the retractor system; most conspicuous are the large coxisternal retractors and prodorsal retractors, both of which originate on the notogaster. Other components have adjustor roles; among them are muscles of the endosternal system that control retraction of the subcapitulum and assist leg retraction, and the dorsoventral muscles which adjust the folded coxisternum. Hemolymph pressure control is a function of the opisthosoma, where the principle exoskeletal elements form a pleated venter, having a cross-sectional shape like an inverted "W." Paired holoventral plates (each representing fused genital, aggenital, anal, and anal plates) form the inner angle and are flanked by paired plicature plates. The holoventral plates are connected medially in two ways : 1) by three permanent bridges of sclerotized cuticle that include an anterior phragmatal bridge and two widely spaced, hollow apodemes (preanal, postanal); 2) by temporary zipper-like closures of two different types. Lateral compression of the pleats is effected by a series of transversely arranged, lateral compressor muscles that run from plicature to holoventral plate edges, and from holoventral plate edges to the medial apodemes. Compression increases hydrostatic pressure in the opisthosoma and stores energy in both the slightly deformed, mineralized notogaster and in the three holoventral bridges. During normal activity the compressor system is active and the inflated podosomal region provides support for the extended legs. When the mite is irritated, the prodorsum is hydraulically ejected from its active position in the notogastral collar, then relaxation of the compressors causes a fall in hemolymph pressure and return of the notogaster to an undeformed condition. Muscles of the retractor system then act in specific sequence to retract and adjust the coxisternum and prodorsum until they are precisely positioned at the completion of enptychosis. The process takes between 0.5 and 1 sec. When irritation ceases, partial opening allows sensory leg hairs to "test" the environment. Resumption of normal, active posture (ecptychosis) involves activation of the lateral compressor system and hydraulic inflation of the podosoma, through which legs are extended and the prodorsum is reflected.     

Orientation of the valine-1 side chain of the gramicidin transmembrane channel and implications for channel functioning. A 2H NMR study.

The orientation of the valine-1 side chain of gramicidin was determined by solid-state 2H NMR using valine-1-deuterated (d8) gramicidin. The peptide was incorporated into DMPC bilayers that were oriented between glass plates. When the plates were oriented with their normal perpendicular to the magnetic field, four quadrupolar splittings were observed of 106, 68, 9.7, and 2.0 kHz. These resonances were assigned to C alpha D, C beta D, and the deuterons of each of the C gamma D3 methyl groups, respectively. The average orientation of the various C-D bonds was calculated with respect to the helix axis. The angle obtained for the C alpha-D resonance was consistent with a single-stranded beta 6.3-helical model for the backbone but not with double-helical models. The angles of the side chain were then fitted to a model for the right-handed beta 6.3-helix. Rotation of the valine-1 side chain yielded a set of torsion angles that matched the angles as determined from the 2H NMR measurements. The corresponding orientation of the valine-1 side chain (chi 1 = -5 degrees) was found to be quite unusual, but it explains well the importance of a branched side chain at position 1 for channel formation and stability. A van der Waals interaction between valine-1 of one monomer and alanine-5 of the other helps to stabilize the gramicidin dimer.     

Induction of negative signal through CD2 during antigen-specific T cell activation.

We have investigated the role of CD2 molecules in Ag-specific T cell activation by using a mouse model system in which the function of CD2 can be analyzed without the apparent influence of major accessory molecules, such as CD4 or LFA-1. Transfection of the CD2 gene into a CD2- T cell hybridoma confers the enhancement of IL-2 production upon Ag stimulation. Anti-CD2 mAb inhibits the Ag-specific response of the CD2-transfectant, not only to the level of CD2- cells but to the background. B cells, but not MHC class II-transfected L cells, serve as APC to induce the inhibition of Ag response. The complete abrogation of the response is observed only upon the stimulation through TCR with Ag in the presence of APC but not through either TCR-CD3 or other molecules such as Thy-1. Furthermore, the inhibition can also be observed when anti-CD2 mAb is immobilized on culture plates, suggesting that the inhibition of Ag response results from transducing the negative signal through the CD2 molecule. The experiments on cytoplasmic domain-deleted CD2-transfected T cells reveal that the cytoplasmic portion is responsible for the CD2-mediated abrogation of Ag responses. These results imply that CD2 has important roles in T cell responses not only as an activation and adhesion molecule but also as a regulatory molecule of Ag-specific responses through the TCR.     

Highly water-soluble matrix metalloproteinases inhibitors and their effects in a rat adjuvant-induced arthritis model

A new series of succinate-based dual inhibitors against matrix metalloproteinases (MMPs) and tumor necrosis factor alpha converting enzyme (TACE) possessing highly-water solubility was designed, synthesized, and evaluated for enzyme inhibition. Incorporating of acidic or basic functional groups at the P(2)' position afforded sufficient water solubility without significant loss of inhibitory potencies. Compound 18e, which had a guanidino group at the P(2)' position as the basic functional group, exhibited broad inhibition against target enzymes for a relatively long period in rat plasma (beta t(1/2); 2.0h) after sc administration when compared with compounds possessing acidic functional groups (18a and 18b). Consequently, the representative compound 18e together with compound 18b, Marimastat and Trocade were evaluated in the rat adjuvant-induced arthritis model, a model of chronic cartilage destruction. It is concluded that the newly synthesized highly water-soluble compound 18e showed significant activity in suppressing hindpaw swelling and the bone destruction with a minimal administration period (days 3-7).     

Efficiency of a visual system under conditions of uncertainty of the appearance of a moving object

The effect of uncertainty of a moving object appearance in the noise field upon the coefficient efficiency, we studied. At short durations of presentation (40-80 msec) and high level of external noise, this effect was maximal: magnified 100 times. The efficiency coefficient dependence on the duration of a moving object presentation was shown to be characterized by two maximums. The position of minimum situated between these two maximums was found to be independent of either presence or absence of uncertainty of a number of parameters: such as initial position of the object the image, time of its appearance, noise level, velocity and direction of the movement, and has a latency approximately 120 sec. A functional model of the observed phenomena, has been proposed.     

Structural and Biochemical Evidence That a TEM-1 ��-Lactamase N170G Active Site Mutant Acts via Substrate-assisted Catalysis

TEM-1 β-lactamase is the most common plasmid-encoded β-lactamase in Gram-negative bacteria and is a model class A enzyme. The active site of class A β-lactamases share several conserved residues including Ser⁷⁰, Glu¹⁶⁶, and Asn¹⁷⁰ that coordinate a hydrolytic water involved in deacylation. Unlike Ser⁷⁰ and Glu¹⁶⁶, the functional significance of residue Asn¹⁷⁰ is not well understood even though it forms hydrogen bonds with both Glu¹⁶⁶ and the hydrolytic water. The goal of this study was to examine the importance of Asn¹⁷⁰ for catalysis and substrate specificity of β-lactam antibiotic hydrolysis. The codon for position 170 was randomized to create a library containing all 20 possible amino acids. The random library was introduced into Escherichia coli, and functional clones were selected on agar plates containing ampicillin. DNA sequencing of the functional clones revealed that only asparagine (wild type) and glycine at this position are consistent with wild-type function. The determination of kinetic parameters for several substrates revealed that the N170G mutant is very efficient at hydrolyzing substrates that contain a primary amine in the antibiotic R-group that would be close to the Asn¹⁷⁰ side chain in the acyl-intermediate. In addition, the x-ray structure of the N170G enzyme indicated that the position of an active site water important for deacylation is altered compared with the wild-type enzyme. Taken together, the results suggest the N170G TEM-1 enzyme hydrolyzes ampicillin efficiently because of substrate-assisted catalysis where the primary amine of the ampicillin R-group positions the hydrolytic water and allows for efficient deacylation.     

Functionally orthologous viral and cellular microRNAs studied by a novel dual-fluorescent reporter system

Recent research raised the possibility that some viral microRNAs (miRNAs) may function as orthologs of cellular miRNAs. In the present work, to study the functional orthologous relationships of viral and cellular miRNAs, we first constructed a dual-fluorescent protein reporter vector system for the easy determination of miRNA function. By expressing the miRNAs and the indicator and internal control fluorescent proteins individually from a single vector, this simple reporter system can be used for miRNA functional assays that include visualizing miRNA activity in live cells. Sequence alignments indicated that the simian virus 40 (SV40) encoded miRNA sv40-mir-S1-5p contains a seed region identical to that of the human miRNA hsa-miR423-5p. Using the new reporter system, it was found that sv40-mir-S1-5p and hsa-miR423-5p downregulate the expression of common artificial target mRNAs and some predicted biological targets of hsa-miR423-5p, demonstrating that they are functional orthologs. The human immunodeficiency virus 1 (HIV-1) encoded hiv1-miR-N367 also contains a seed sequence identical to that of the human miRNA hsa-miR192. Functional assays showed that hiv1-miR-N367 and hsa-miR192 could downregulate common artificial and predicted biological targets, suggesting that these miRNAs may also act as functional orthologs. Thus, this study presents a simple and universal system for testing miRNA function and identifies two new pairs of functional orthologs, sv40-mir-S1-5p and hsa-miR423-5p as well as hiv-1-miR-N367 and hsa-miR192. These findings also expand upon our current knowledge of functional homology and imply that a more general phenomenon of orthologous relationships exists between viral and cellular miRNAs.