A microcomputer interface for a digital audio processor-based data recording system.

An inexpensive interface is described that performs direct transfer of digitized data from the digital audio processor and video cassette recorder based data acquisition system designed by Bezanilla (1985, Biophys. J., 47:437-441) to an IBM PC/XT microcomputer. The FORTRAN callable software that drives this interface is capable of controlling the video cassette recorder and starting data collection immediately after recognition of a segment of previously collected data. This permits piecewise analysis of long intervals of data that would otherwise exceed the memory capability of the microcomputer.     

Automated analysis of prerecorded evoked electromyographic activity from rat muscle

An automated microprocessor-based data acquisition and analysis system has been developed specifically to quantify electromyographic (EMG) activity induced by the convulsant agent catechol in the anaesthetized rat. The stimulus and EMG response are recorded on magnetic tape. On playback, the stimulus triggers a digital oscilloscope and, via interface circuitry, a BBC B microcomputer. The myoelectric activity is digitized by the oscilloscope before being transferred under computer control via a RS232 link to the microcomputer. This system overcomes the problems of dealing with signals of variable latency and allows quantification of latency, amplitude, area and frequency of occurrence of specific components within the signal. The captured data can be used to generate either signal or superimposed high resolution graphic reproductions of the original waveforms. Although this system has been designed for a specific application, it could easily be modified to allow analysis of any complex waveform.     

Automated proton titrations of pancreatic phospholipase A2

A computer-controlled titration system has been developed, tested, and used for analysis of the proton-titration behavior of pancreatic phospholipase A₂ from ox, horse, and pig. The results revealed an error in the reported amino acid composition of the equine enzyme. A simple interface for the input of digitized data from a pH meter is described together with the software developed for controlling the titration experiments.     

Evolution of digit identity in the three-toed Italian skink Chalcides chalcides: a new case of digit identity frame shift

SUMMARY Digit identity in the avian wing is a classical example of conflicting anatomical and embryological evidence regarding digit homology. Anatomical in conjunction with phylogenetic evidence supports the hypothesis that the three remaining digits in the bird wing are digits 1, 2, and 3. At the same time, various lines of embryological evidence support the notion that these digits develop in positions that normally produce digits 2, 3, and 4. In recent years, gene expression as well as experimental evidence was published that supports the hypothesis that this discrepancy arose from a digit identity shift in the evolution of the bird wing. A similar but less well-known controversy has been ongoing since the late 19th century regarding the identity of the digits of the three-toed Italian skink, Chalcides chalcides . Comparative anatomy identifies these digits as 1, 2, and 3, while embryological evidence suggests their derivation from embryological positions 2, 3, and 4. Here we re-examine this evidence and add gene expression data to determine the identity of the three digits of C. chalcides . The data confirm that the adult and the embryological evidence for digit identity are in conflict, and the expression of Hoxd11 suggests that digits 1, 2, and 3 develop in positions 2, 3, and 4. We conclude that in C. chalcides , and likely in its close relatives, a digit identity frame shift has occurred, similar to the one in avian evolution. This result suggests that changes in of digit identity might be a more frequent consequence of digit reduction than previously assumed.     

Frame-shifts of digit identity in bird evolution and Cyclopamine-treated wings

SUMMARY A highly conserved spatio-temporal pattern of cartilage formation reveals that the digits of the bird wing develop from positions that become digits 2, 3, and 4 in other amniotes. However, the morphology of the digits of early birds like Archaeopteryx corresponds to that of digits 1, 2, and 3 of other archosaurs. A hypothesis is that a homeotic "frame-shift" occurred, such that in the bird wing, digits 1, 2, and 3 develop from the embryological positions of digits 2, 3, and 4. Experimental homeotic transformations of single digits are well-documented, but frame-shifts of more than one digit are not. We investigated the pattern of cartilage formation in the development of Cyclopamine-treated wings. When Cyclopamine was applied between stages 18 and 21, morphologies that normally develop from positions 2 and 3 developed from positions 3 and 4. The serial shift of digit identity toward posterior confirms a mechanistic possibility that was previously inferred from the evolutionary history of birds.     

录象机在生物组织连续切片的计算机三维重建系统中的应用

录象机(Video Tape Recorder)作为输入、输出设备,应用于“生物组织连续切片的计算机三维重建系统”中,其效果是令人满意的.由于研制的“同步再生”单元(Sync RecoveryUnit)有效地消除了静放噪声,从而使Cromemco微型计算机的图象输入接口SDD(Super DazzlerDigitizer)能够稳定地逐帧采集录象机输出的静止图象.录制并编辑计算机三维重建后的生物组织显微结构的空间旋转视图,使其在录象机的监视器上显示得更生动、逼真,更有体视感;还可脱离主机在任何场合演示重建结果.本文还就录象机在生物医学序列图象分析中的应用前景进行了讨论.     

Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees

OBJECTIVES: To describe, implement, and test an efficient algorithm to obtain multipoint identity-by-descent (IBD) probabilities at arbitrary positions among marker loci for general pedigrees. Unlike existing programs, our algorithm can analyze data sets with large numbers of people and markers. The algorithm has been implemented in the SimWalk2 computer package. METHODS: Using a rigorous testing regimen containing five pedigrees of various sizes with realistic marker data, we compared several widely used IBD computation programs: Allegro, Aspex, GeneHunter, MapMaker/Sibs, Mendel, Sage, SimWalk2, and Solar. RESULTS: The testing revealed a few discrepancies, particularly on consanguineous pedigrees, but overall excellent results in the deterministic multipoint packages. SimWalk2 was also found to be in good agreement with the deterministic multipoint programs, usually matching to two decimal places the kinship coefficient that ranges from 0 to 1. However, the packages based on single-point IBD estimation, while consistent with each other, often showed poor results, disagreeing with the multipoint kinship results by as much as 0.5. CONCLUSIONS: Our testing has clearly shown that multipoint IBD estimation is much better than single-point estimation. In addition, our testing has validated our algorithm for estimating IBD probabilities at arbitrary positions on general pedigrees.     

Electrophoretic gel image analysis software for the molecular biology laboratory

We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.     

Effect of salt stress on photosystem Ⅱ heterogeneity in wheat leaves

In order to study the effects of salt stress on photosystem Ⅱ (PSⅡ) heterogeneity, signal from the fluorometer was digitized via a microcomputer interface to record PSⅡ fluorescence induction kinetics. Changes of parameters (Fm, Fp1 and F0) from the fast phase of fluorescence induction curve showed that the percentage of QB-nonreducing PSⅡ reaction centers dropped at first, and then rose with the increase of stress intensity and time. This indicated that the electron transfer from QA to QB is one of the sites where the photochemical and photophysical processes of PSⅡ are damaged by the salt stress.     

Thermal Resistance of Salmonellae and Staphylococci in Foods

The heat-resistant Salmonella senftenberg 775W and two strains of Staphylococcus aureus were tested at temperatures up to 68.3 C (71.1 C for S. senftenberg) in four different media. From the survival data, decimal reduction times (D values) were calculated for each set of conditions, and decimal reduction time curves were constructed for each bacterial strain in each medium. Slopes of decimal reduction time curves (Z(D)) ranged from 4.52 to 6.38 C with a single exception. There was no statistical heterogeneity among the remaining values. Results were in close agreement with published results of similar studies conducted at somewhat lower temperatures and support the practice of using a slope value (Z(D)) of 5.56 C for establishing time-temperature relationships for food processing. It is recommended that such a decimal reduction time curve not be extrapolated to temperatures more than 5.56 C higher than those actually tested.     

The developmental evolution of avian digit homology: An update

The identity of avian digits has been unresolved since the beginning of evolutionary morphology in the mid-19th century, i.e. as soon as questions of phylogenetic homology have been raised. The main source of concern is the persistent discrepancy between anatomical/paleontological and embryological evidence over the identity of avian digits. In this paper, recent evidence pertaining to the question of avian digit homology is reviewed and the various ideas of how to resolve the disagreement among developmental and phylogenetic evidence are evaluated. Paleontological evidence unequivocally supports the hypothesis that the fully formed digits of maniraptoran theropods are digits DI, DII, and DIII, because the phylogenetic position of Herrerasaurus is resolved, even when hand characters are excluded from the analysis. Regarding the developmental origin of the three digits of the avian hand the discovery of an anterior digit condensation in the limb bud of chickens and ostriches conclusively shows that these three digits are developing from condensations CII, CIII, and CIV. The existence of this additional anterior condensation has been confirmed in four different labs, using four different methods: Alcian blue staining, PNA affinity histochemistry, micro-capillary regression and Sox9 expression. Finally, recent evidence shows that the digit developing from condensation CII has a Hox gene expression pattern that is found in digit DI of mice forelimb and chick hind limbs. The sum of these data supports the idea that digit identity has shifted relative to the location of condensations, known as Frame Shift Hypothesis, such that condensation CII develops into digit DI and condensation CIII develops into digit DII, etc. A review of the literature on the digit identity of the Italian Three-toed Skink or Luscengola (Chalcides chalcides), shows that digit identity frame shifts may not be limited to the bird hand but may be characteristic of “adaptive” digit reduction in amniotes (sensu Steiner, H., Anders, G., 1946. Zur Frage der Entstehung von Rudimenten. Die Reduktion der Gliedmassen von Chalcides tridactylus Laur. Rev. Suisse Zool. 53, 537–546) in general. In this mode of evolution two digits are lost, in the course of the adaptation of the three anterior digits to a function that does not require the two posterior digits. This evidence suggests that the evolution of digits in tetrapods can proceed at least on two distinct levels of integration, the level of digit condensations and that of adult digits.     

Manual digital pressures during knuckle‐walking in chimpanzees (Pan troglodytes)

Considerable attention has been given to hand morphology and function associated with knuckle‐walking in the African apes because of the implications they have for the evolution of bipedalism in early hominins. Knuckle‐walking is associated with a unique suite of musculoskeletal features of the wrist and hand, and numerous studies have hypothesized that these anatomical features are associated with the dynamics of load distribution across the digits during knuckle‐walking. We collected dynamic digital pressures on two chimpanzees during terrestrial and simulated arboreal locomotion. Comparisons were made across substrates, limb positions, hand positions, and age categories. Peak digital pressures were similar on the pole and on the ground but were distributed differently across the digits on each substrate. In young animals, pressure was equally high on digits 2–4 on the ground but higher on digits 3 and 4 on the pole. Older animals experience higher pressures on digits 2 and 3 on the ground. Hand posture (palm‐in vs. palm‐back) influenced the distribution and timing of peak pressures. Age‐related increases in body mass also result in higher overall pressures and increased variation across the digital row. In chimpanzees, digit 5 typically bears relatively little load regardless of hand position or substrate. These are the first quantitative data on digital pressures during knuckle‐walking in hominoids, and they afford the opportunity to develop hypotheses about variation among hominoids and biomechanical models of wrist and forearm loading. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

A microprocessor-regulated constant voltage, current, wattage, and temperature electrophoresis power supply

The analog control circuitry typically found in commercial electrophoresis power supplies was replaced by a digital microcomputer. Analog to digital converters were used to monitor the voltage applied to and current passed through an electrophoresis cell. Microcomputer programming was employed to compare converter input values with preselected operating parameters and then calculate a required output voltage. Timing sequences were generated through programming utilizing clocks located on the interface boards. A digital to analog converter was employed to apply a control voltage to a constant voltage power supply. This process was completed at least 20 times each second. BASIC programming subroutines were written to maintain constant voltage, current, power (wattage), and temperature. To these operating procedures, other techniques such as automated endpoint detection of isoelectric focusing and pulsed waveform outputs were easily added. This power supply containing a microcomputer system as the feedback element was shown to have a greater stability and versatility than conventional supplies.     

Sequence specificity in the dimerization of transmembrane alpha-helices.

While several reports have suggested a role for helix-helix interactions in membrane protein oligomerization, there are few direct biochemical data bearing on this subject. Here, using mutational analysis, we show that dimerization of the transmembrane alpha-helix of glycophorin A in a detergent environment is spontaneous and highly specific. Very subtle changes in the side-chain structure at certain sensitive positions disrupt the helix-helix association. These sensitive positions occur at approximately every 3.9 residues along the helix, consistent with their comprising the interface of a closely fit transmembranous supercoil of alpha-helices. By contrast with other reported cases of interactions between transmembrane helices, the set of interfacial residues in this case contains no highly polar groups. Amino acids with aliphatic side chains define much of the interface, indicating that precise packing interactions between the helices may provide much of the energy for association. These data highlight the potential general importance of specific interactions between the hydrophobic anchors of integral membrane proteins.     

A microcomputer (PC 9801/MS mouse) system to record and analyze time-intensity curves of sweetness

The sweetness of sugar, glucose, xylose, saccharin, aspartame,etc. was assessed by magnitude estimation, with sensory intensitiesof 5, 10 and 20 defined as being equivalent to 2.5, 5.0 and10.0% concentrations of sugar in tap water. Sensory magnitudewas determined as being the input through a ‘mouse’to a microcomputer, PC 9801F2, which digitized the time intoseconds, while intensity was expressed in terms of tenths ofthe sensory magnitude 1.0. The two-dimensional information wasregistered on floppy disc memory and retrieved to calculatethe average time-intensity curves for each subject, or the averagefor several subjects. With this technique, it is easy to measure:(i) time of maximum intensity; (ii) height of maximum intensity;(iii) amount of adaptation; (iv) amount of after-taste; or (v)total amplitude (the sum of areas under the curve during andafter stimulation). The subjects were seven male students. Witha little training, they produced highly reliable curves forthe replicates of a sweetener at one concentration. Multidimensionalscaling of these curves did not disclose any clusterings ofnatural versus synthetic sweeteners.     

Collection and analysis of kinetic data from a stopped-flow spectrophotometer using a microcomputer

A method of interfacing an inexpensive microcomputer to a stopped-flow kinetics spectrophotometer is described. It allows software-selectable sampling frequencies between 0.1 ms and 8 s and large numbers of data points to be collected. Machine language routines to use the interface are described and these allow the sampling frequency to be altered during data collection to ensure adequate numbers of points in critical regions of the kinetic profile. BASIC programs for collection and analysis of multicomponent kinetic data using this system are also described. Due to the large number of data points that can be collected and the ability to selectively sample transmittance values in regions where the signal is rapidly changing with time, relatively unsophisticated methods of data analysis can be used. These methods are suitable for use by microcomputers and mean that data analysis and acquisition can be performed on the same microcomputer in real time. To illustrate this, multicomponent analysis of kinetic transients is performed on simulated data and on the dissociation kinetics of the ethidium-DNA complex.     

Autoradiographic quantitation of radiolabeled proteoglycans.

Radiolabeled proteoglycans or glycosaminoglycans were precipitated with the cationic dye safranin O onto a sheet of nitrocellulose filter using a dot-blot apparatus. An autoradiography film was exposed against the nitrocellulose sheet. The developed film and the nitrocellulose sheet were separately digitized in a flat-bed-gray-scale scanner connected to a microcomputer. An image analysis program of the microcomputer was used to quantify the density of the radioactivity dots produced in the film, and the intensity of the dye spots on nitrocellulose. With this procedure, a single sample containing the minimum of about 20 ng uronic acid and 5 dpm of incorporated 35SO4 was quantified for both total glycosaminoglycan content and radioactivity. Unincorporated 35SO4 and low molecular mass radioactivity (e.g. products of glycosaminoglycan degrading enzymes) did not interfere since they were quantitatively washed through the membrane before the assay.     

An optical comparator for measuring two-dimensional polyacrylamide gel electrophoresis records using an on-line microcomputer

A comparator which makes it possible to compare two wet gels or photographic negatives or autoradiograms through a flickering light system has been built. The system consists of two special-purpose projectors which combine the images on a digitizing platform. When the lights are switched On and off out of phase, the positions of the common components remain unchanged, whereas those that are spatially displaced appear to jump from side to side and those present in one image but not the other switch on and off. This produces a flickering image in which differences are readily seen. Commercial camera lenses were used to construct the projectors and the overall specifications for the system are given. The coordinates of both the displaced components, as well as the selected standards from the two images, are digitized and entered automatically into an on-line microcomputer. By using an iterative procedure for collecting records from several superimposable records of the gel, it is possible to compensate for the lack of total reproducibility over the whole gels. These coordinates are then normalized and superimposed on a master map through a television display using a curser to adjust the coordinates. The whole procedure can be repeated for many gels using a common reference gel in the comparator, and the result is a set of normalized coordinates which can be plotted on a single map to provide a final record of the experiments.