Computer tools for the analysis of schooling

Synopsis Quantification of fish school structure is difficult because of: (1) the large amount of positional data that must be recorded, (2) the fact that schools are moving, and (3) the fact that schools are threedimensional. Computer tools for addressing these problems include x,y digitizing devices interfaced to computers and interactive computer graphics systems. General computer algorithms now exist for 3-D reconstruction of schools given any two 2-D views such as photographs.Our computerized film analyzer, the Galatea system, is described in detail. This system allows for rapid, accurate input of multiple points which can be followed through each frame in a film sequence. Its software packages perform 3-D reconstructions, analyze undulatory motion, and do extensive statistical tests.     

Graphical analysis of mass and anisotropy changes observed by plasmon-waveguide resonance spectroscopy can provide useful insights into membrane protein function

Plasmon-waveguide resonance spectroscopy is a recently developed optical method that allows characterization of mass and structural changes in two-dimensionally ordered thin films (e.g., proteolipid membranes) deposited onto a sensor surface. Full analysis of these systems involves fitting theoretical curves (obtained using Maxwell's equations) to experimental spectra measured using s- and p-polarized excitation. This allows values to be obtained for refractive indices and optical extinction coefficients in these two directions, as well as a value for film thickness, thereby providing information about mass density and anisotropy changes. This is a time-consuming process that works well for simple systems in which only a single conformational event occurs, but cannot distinguish between events involving multiple conformations that proceed either sequentially or in a parallel series of events. This article describes a graphical method that can distinguish between mass density and anisotropy changes in a simpler, more rapid procedure, even for processes that proceed via multiple conformational events. This involves measurement of plasmon-waveguide resonance spectral shifts obtained upon molecular interactions occurring in deposited films with both s- and p-polarized excitation, and transforming these from an (s-p) coordinate system into a (mass-structure) coordinate system. This procedure is illustrated by data obtained upon the binding of a small peptide, penetratin, to solid-supported lipid bilayer membranes.     

Surface activity in situ, in vivo, and in the captive bubble surfactometer

For studies of the mechanical effects of lung surfactants, the captive bubble surfactometer (CBS) combines the advantages of the continuous film of Pattle's bubbles with the feasibility of the Langmuir-Wilhelmy balance to produce surface tension-area hysteresis loops. The CBS allows the compression of films to very low and stable surface tensions of 1-2 mN/m. Such low and stable surface tensions are in line with results obtained from pressure-volume studies on excised lungs. In addition, the CBS is useful to test other essential physical properties of the surfactant system, including: (1) rapid film formation (within seconds) through adsorption from the hypophase; (2) low film compressibility with a fall in surface tension to very low (<2 mN/m) values during surface compression; and (3) effective replenishment of the surface film on expansion by the incorporation of surfactant material from material associated with the surface (the surface associated surfactant reservoir). Morphological observations of films fixed in situ or in vitro reveal frequently their multilayered structure, which is consistent with the concept of the surface reservoir. The deviation of the bubbles from a Laplacian shape at very low surface tension and the morphological observations suggest that the surfactant film cannot be considered a simple monolayer.     

Chitosan film as rhBMP2 carrier: delivery properties for bone tissue application

Tissue engineering approaches need biomaterials with suitable properties to provide an appropriate environment for cell attachment and growth. The performance of these biomaterials can be greatly enhanced through the incorporation of bioactive agents. For this reason, we developed chitosan films with cell-attachment ability, rhBMP-2 carrier capacity, and good in vivo performance, and we employ them as covering for implantable materials. In this work, we have tried to explain how the rh-BMP2 is delivered to the surroundings from the development chitosan films. Protein diffusion from film, film stability versus in vitro dissolution, and biodegradation were evaluated to study rhBMP-2 delivery. Our results show that chitosan film has sufficiently good features to be used as an rhBMP-2 carrier. A low diffusion rate was observed, which was sufficient to quickly induce an in vitro differentiation stimulus, although heavily activated films retain more than 80-85% of the protein on the film. On the other hand, we estimated that chitosan film dissolution due to initial acidification in the wound environment is no more than 15-20%. We also estimated chitosan film response to lysozyme and concluded that degradation via this process proceeded at a slow kinetic rate. In addition, rhBMP-2 in vitro activity after film processing, as well as in vivo film behavior, were studied. We confirm that rhBMP-2 remains active on the film and after release, both in vitro and in vivo. These results support the conclusion that the developed chitosan film allows sustained release of the rhBMP-2 osteoinductive protein and could be used as an activated coat for implant and surgical prosthesis.     

Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships

The rapid growth in protein structural data and the emergence of structural genomics projects have increased the need for automatic structure analysis and tools for function prediction. Small molecule recognition is critical to the function of many proteins; therefore, determination of ligand binding site similarity is important for understanding ligand interactions and may allow their functional classification. Here, we present a binding sites database (SitesBase) that given a known protein-ligand binding site allows rapid retrieval of other binding sites with similar structure independent of overall sequence or fold similarity. However, each match is also annotated with sequence similarity and fold information to aid interpretation of structure and functional similarity. Similarity in ligand binding sites can indicate common binding modes and recognition of similar molecules, allowing potential inference of function for an uncharacterised protein or providing additional evidence of common function where sequence or fold similarity is already known. Alternatively, the resource can provide valuable information for detailed studies of molecular recognition including structure-based ligand design and in understanding ligand cross-reactivity. Here, we show examples of atomic similarity between superfamily or more distant fold relatives as well as between seemingly unrelated proteins. Assignment of unclassified proteins to structural superfamiles is also undertaken and in most cases substantiates assignments made using sequence similarity. Correct assignment is also possible where sequence similarity fails to find significant matches, illustrating the potential use of binding site comparisons for newly determined proteins.     

Description, validation, and performance characteristics of a new computer-automated sperm motility analysis system

A computer-automated sperm motility assay (CASMA) system has been developed that provides a rapid and accurate analysis of multiple sperm movement parameters and a new measure of linearity, the linear deviation angle. CASMA provides objective, unbiased sampling and accurate quantitation of the movement characteristics of 200 sperm cells in 20 min. It consists of a microscope-mounted video camera, a high-resolution video disk recorder, a video digitizer/memory board mounted in an IBM 9000 microcomputer, and newly developed software. After manual recording, at 60 frames/s, of the video sequences (takes) of sperm suspensions, each take is automatically played back frame by frame, digitized, and stored in video memory. The software searches each frame, recognizes sperm cells, randomly selects a preset number for analysis, and traces each cell through the sequence to generate sperm "tracks" that are then stored in disk memory. This process is repeated for each take. Analysis of the stored tracks of each take yields the mean +/- SEM of the standard sperm motility parameters: percent motile (%M), curvilinear velocity (VC), net velocity (Vn), position-averaged velocity (Va), linear index (Vn/Va), progressiveness ration (Vn/Vc), and curvilinear progressiveness ratio (Va/Vc). Additionally, CASMA allows measurement of the linear deviation angle, a more direct measure of the linearity of sperm movement. For statistical comparisons, multiple takes can be considered either as replicates or separate experimental determinations. Finally, for more detailed analysis, each individually stored track, with its associated parameters, or histogram distributions of all sperm for each parameter can be displayed and printed. The performance of CASMA was evaluated by comparison of CASMA-determined movement parameters with manually determined values derived from the same sperm cells in the same video sequence and by comparison with published values determined using microcinematographic techniques. In each case, the CASMA values were essentially identical to those determined by manual measurements. Finally, CASMA accurately quantitates the linearity of sperm movement, a characteristic previously determined only by much more time-consuming methods. CASMA is a rapid and accurate system for measuring washed bull sperm motility and has reliably analyzed monkey and elephant sperm. The system has the potential to quantitate motility equally well with sperm from any species that have similar sperm head size.     

A spreading technique for forming film in a captive bubble.

Mechanisms underlying the surface properties of lung surfactant are extensively studied in in vitro systems such as the captive-bubble surfactometer (CBS), the pulsating-bubble surfactometer, and the Wilhelmy balance. Among these systems, the CBS is advantageous when a leakproof system and high cycling rates are required. However, widespread application of the CBS to mechanistic studies of dynamic surfactant protein-phospholipid interactions of spread film and to comparative studies between spread and adsorbed film is hampered because spreading of film is difficult. In addition, when film is formed by adsorption, the amount of material required is fairly large. We have developed an easy spreading technique that allows routine formation of film by spreading of small amounts of surfactant components at the air-water interface of an air bubble in a CBS. The technique is reliable, precise, and accurate, and the biophysical activity of film formed by spreading is similar to that of film formed by adsorption. This method will be useful for mechanistic studies of surfactant components under dynamic conditions and for comparative studies of spread films and adsorbed films.     

The glucocorticoid receptor resource.

The glucocorticoid receptor resource focuses on the structure-function relationships of the glucocorticoid receptor. As well as links to sequence and bibliographic databases via the World Wide Web, the database contains sequence comparisons of receptors from different species and source information for glucocorticoid receptor clones, probes, cell lines and antibodies. The resource allows the electronic publication of essays, unpublished data and reviews on steroid receptors. These publications will not be reviewed or edited and should allow the rapid dissemination of information to the scientific community. The resource can be reached at: http://biochem1.basic- sci.georgetown.edu/grr/grr.html.     

Sensitive detection and typing of human papillomavirus DNA in gynecological cell scrapings by slot-blot hybridization

A rapid and sensitive method for detecting and typing human papillomaviruses (HPVs) in cell scrapings is presented. DNA from scrapings is extracted and bound to nitrocellulose filters (Slot-Blot). By DNA-DNA hybridization with specific 32P-labelled HPV-probes (types 6/11 or 16/18) the patient's DNA is then analyzed for the presence of, and for the type of, HPV DNA sequences. A parallel hybridization with a human repetitive element (Alu sequence) allows quantitation of the different hybridization results. Experiments with HeLa cell DNA show that as little as 10(4) HPV sequences can be detected and typed specifically with this test. Evaluation of this test is completed within 6 to 7 days after cell collection. This Slot-Blot method was used to analyse 1330 specimens taken at the Bernese Dysplasia Outpatient Clinic. The results reveal a very high percentage (90%) of HPV-positive cases in the patient group examined.     

Myoblast adhesion and proliferation on biodegradable polymer films with femtosecond laser‐fabricated micro through‐holes

Controlling cell adhesion and cell differentiation is necessary to fabricate a tissue with arbitrary properties for tissue engineering applications. A substrate with a porous structure as a cell scaffold allows the diffusion of the cell culture medium through the scaffold. In this work, we show that the femtosecond laser fabricated micro through‐holes in biodegradable polymer films, enhance myoblast adhesion, and accelerates proliferation and differentiation. ChR2‐C2C12 and UT‐C2C12 cells were seeded on the films with micro through‐holes each fabricated by a single femtosecond laser pulse. Cell adhesion was enhanced on films with holes fabricated by laser irradiation. In addition, cell proliferation was accelerated on films with micro through‐holes that penetrate the film, compared to on films with micro craters that do not penetrate the film. On films with arrays consisting of micro through‐holes, cells aligned along the arrays and cell fusion was enhanced, indicating the acceleration of cell differentiation.     

Measuring and Overcoming Limits of the Saffman-Delbrück Model for Soap Film Viscosities

We observe tracer particles diffusing in soap films to measure the two-dimensional (2D) viscous properties of the films. Saffman-Delbrück type models relate the single-particle diffusivity to parameters of the film (such as thickness h) for thin films, but the relation breaks down for thicker films. Notably, the diffusivity is faster than expected for thicker films, with the crossover at h/d = 5.2 ± 0.9 using the tracer particle diameter d. This indicates a crossover from purely 2D diffusion to diffusion that is more three-dimensional. We demonstrate that measuring the correlations of particle pairs as a function of their separation overcomes the limitations of the Saffman-Delbrück model and allows one to measure the viscosity of a soap film for any thickness.     

Compilation of tRNA sequences.

This compilation presents in a small space the tRNA sequences so far published in order to enable rapid orientation and comparison. The numbering of tRNAPhe from yeast is used as has been done earlier (1) but following the rules proposed by the participants of the Cold Spring Harbor Meeting on tRNA 1978 (2) (Fig. 1). This numbering allows comparisons with the three dimensional structure of tRNAPhe, the only structure known from X-ray analysis. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguously analyzed. Rare nucleosides are named according to the IUPAC-IUB rules (for some more complicated rare nucleosides and their identification see Table 1); those with lengthy names are given with the prefix x and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information the reader is referred either to the original literature or to other tRNA sequence compilations (3--7). Mutant tRNAs are dealt with in a separate compilation prepared by J. Celis (see below). The compilers would welcome any information by the readers regarding missing material or erroneous presentation. On the basis of this numbering system computer printed compilations of tRNA sequences in a linear form and in cloverleaf form are in preparation.     

Field methodology for lateral cranial radiography of nonhuman primates.

The historical lack of field-based radiographic studies of nonhuman primates within the field of anthropology is likely due to the perceived difficulty of transporting and operating X-ray equipment. Here we present a method for taking lateral cranial radiographs of nonhuman primates in the field that is simple to employ, and that produces exposed films suitable for collection of measurement data useful for growth and development studies, as well as for investigating bone and soft-tissue pathology. Several different X-ray units, film types, and portable power sources were used, all producing suitable images of similar quality, indicating that this methodology is likely not overly sensitive to these important parameters.     

Rapid Layer‐Specific Annealing Enabled by Ultraviolet LED with Estimation of Crystallization Energy for High‐Performance Perovskite Solar Cells

A rapid layer‐specific annealing on perovskite active layer enabled by ultraviolet (UV) light‐emitting diode (LED) is demonstrated and efficiency close to 19% is achieved in a simple planar inverted structure ITO/PEDOT:PSS/MAPbI₃/PC₇₁BM/Al without any device engineering. These results demonstrate that if the UV dosage is well managed, UV light is capable of annealing perovskite into high‐quality film rather than simply damaging it. Different in principle from other photonic treatment techniques that can heat up and damage underlying films, the UV‐LED‐annealing method enables layer‐specific annealing because LED light source is able to provide a specific UV wavelength for maximum light absorption of target film. Moreover, the layer‐specific photonic treatment allows accurate estimation of the crystallization energy required to form perovskite film at device quality level.     

AmpliBASE MT: a Mycobacterium tuberculosis diversity knowledgebase

AmpliBASE MT is an online databank of high-resolution DNA fingerprints representing fluorescent amplified fragment length polymorphism (FAFLP) profiles or amplitypes developed for the Mycobacterium tuberculosis complex strains from 48 different countries. AmpliBASE MT is based on a relational database management system that is hyperlinked to visualize genotyping results in the form of DNA fingerprint images for individual strains. A flexible search system based on systematic comparisons of fragment sizes in base pairs allows inter-laboratory comparison of FAFLP profiles. Besides this, the database also displays previously published data on IS6110 profiles, spoligotypes, MIRU-VNTRs and large sequence polymorphisms along with the FAFLP records that will give the overall comparisons. Being the first of its kind, AmpliBASE MT is expected to be a very helpful tool in strengthening the concept of 'geographic genomics' and will be very helpful to molecular epidemiologists and those interested in diagnostic development for tuberculosis.     

Molecular mechanisms of colicin evolution

This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the origin and diversification of colicin clusters. Such mechanisms include movement of colicin plasmids between strains of E. coli and subsequent plasmid cointegration, transposition- and recombination-mediated transfer of colicin and related sequences, and rapid diversification of colicin and immunity proteins through the action of positive selection. The wealth of information contained in colicin sequence comparisons makes this an ideal system with which to explore molecular mechanisms of evolutionary change.      

Expert agreement confirms that negative changes in hand and foot radiographs are a surrogate for repair in patients with rheumatoid arthritis

The objective of the present study was to test the hypothesis that experts recognize repair of erosions and, if so, to determine which, if any, morphologic features permitted them to recognize the repair. We also tested whether scoring by a standard method detected repair. Seven experienced readers of radiographs in rheumatoid arthritis were presented with 64 sets of single joints-of-interest at two time points, randomized and blinded for the correct sequence. The readers assessed which joint was better, and recorded whether any of six specific features were seen. Two independent readers, experienced in scoring by the van der Heijde-modified Sharp method who were not on the expert panel, then scored the complete films that included the joint-of-interest. The panel agreed very well on which of two joints was better, and, even though they did not know the true sequence, the panel accurately assigned a sequence slightly better than chance alone (58%) but worse than their agreement on which image was 'better or worse' (78%). The readers therefore indirectly assigned repair by choosing the second film as the best. Putative repair features were seen in cases of both repair and progression, and were not discriminatory. Similar results were obtained when the experts were presented with the entire hand or foot containing the joint-of-interest. In the third repair exercise, two independent readers who scored whole hands and feet using a standard method found a mean negative score in 22/60 joints-of-interest. All 22 joints were also scored as repair by the panel. Repair was detected reliably by a majority of the panel on viewing paired images based on a better/worse decision and assigning sequence in a set of images that were blinded for sequence by an independent project manager. In this test set of images, repair was manifested by a reduction in the size of erosion in many cases. Size was one feature that aided the experts to detect repair but cannot be the only one; the experts had to find other features to determine whether a smaller erosion was the first in a sequence of radiographs in a patient with progressive damage or was the second film in a patient exhibiting repair. The change in size of erosion was also picked up by independent readers applying the van der Heijde-modified Sharp scoring method and was reflected in their scores.     

Interactions of ovalbumin and of its putative signal sequence with phospholipid monolayers. Possible importance of differing lateral stabilities in protein translocation.

Surface properties of ovalbumin and of its putative signal sequence, and their interactions with phospholipids at an air-water interface, have been studied. The mature protein can form an interfacial film spontaneously from its bulk solution, whereas the signal sequence cannot. Mature ovalbumin also penetrates phospholipid monolayers from the subphase (independently of the type of phospholipid present), whereas its signal sequence does not. The surface stability of a spread film of the signal sequence is, however, higher than that of a film of mature ovalbumin. Above specific threshold concentrations of signal peptide and of mature ovalbumin in mixed films with phospholipids, two separate phases are formed. In such immiscible films, the signal sequence peptide is also able to support a higher lateral surface pressure than mature ovalbumin, at corresponding areas of peptide and mature protein in the mixed monolayers. It is suggested that the differing lateral stabilities of ovalbumin and of its putative signal sequence may be relevant to the translocation of ovalbumin across the membrane of the endoplasmic reticulum, and a scheme for its translocation is proposed that is based on these properties.