General methods of sequence comparison

Mathematical methods for comparison of nucleic acid sequences are reviewed. There are two major methods of sequence comparison: dynamic programming and a method referred to here as the regions method. The problem types discussed are comparison of two sequences, location of long matching segments, efficient database searches and comparison of several sequences. This work was supported by a grant from the System Development Foundation.     

Interval graphs and maps of DNA

A special class of interval graphs is defined and characterized, and an algorithm is given for their construction. These graphs are motivated by an important representation of DNA called restriction maps by molecular biologists. Circular restriction maps are easily included. Supported by a grant from the System Development Foundation. Supported by an NSF grant and through a grant from the System Development Foundation.     

Behavioral plasticity in aDrosophila mutant,dunce DE276

Summary Drosophila X-linked mutantdunce ^DB276 fails to display learning in an olfactory learning paradigm, in spite of being able to sense odorants and shock (Byers, 1977; Fig. 1). However, conditions exist under which the flies display associative behavior (Table 1, Figs. 3, 5). Memory appears to be short-lived (Table 1, Figs. 3, 5) and labile (Figs. 3, 4). It is suggested that thedunce ^DB276 mutation affects an early memory phase.I thank G. Bicker, D. Byers and W.G. Quinn for valuable comments. This work was supported by a grant from the United States-Israel Binational Science Foundation, Jerusalem. The author is incumbent of the Barecha Foundation Career Development Chair.     

Line geometries for sequence comparisons

Well-known dynamic programming algorithms exist for comparing two finite sequences inO(N ²) time and storage, whereN is the common sequence length. Extensions to the comparison ofM finite sequences requireO((2N) ^M) time and storage, making such algorithms difficult even forM=3. A simple generalization of the sequences makes it possible to obtain some results about the geometry of sequence alignments. These ideas suggest heuristic approaches to problems of comparing several sequences. IfM sequences are known to be related by a binary tree, they can be aligned inO(MN ²) time andO(N ²+NM) storage. This work was supported by a grant from the System Development Foundation.     

Trace feature map: a model of episodic associative memory

An approach to episodic associative memory is presented, which has several desirable properties as a human memory model. The design is based on topological feature map representation of data. An ordinary feature map is a classifier, mapping an input vector onto a topologically meaningful location on the map. A trace feature map, in addition, creates a memory trace on that location. The traces can be stored episodically in a single presentation, and retrieved with a partial cue. Nearby traces overlap, which results in plausible memory interference behavior. Performance degrades gracefully as the memory is overloaded. More recent traces are easier to recall as are traces that are unique in the memory.This research was supported in part by an ITA Foundation grant and by fellowships from the Academy of Finland, the Emil Aaltonen Foundation and the Foundation for the Advancement of Technology (Finland) when the author was at UCLA     

Tutorial on large deviations for the binomial distribution

We present, in an easy to use form, the large deviation theory of the binomial distribution: how to approximate the probability ofk or more successes inn independent trials, each with success probabilityp, when the specified fraction of successes,a≡k/n, satisfies 0<p<a<1. Supported by NIH grant GM 36230 and NSF grant DMS 8601986. Supported by NIH grant GM 36230 and a grant from the System Development Foundation.     

Versatility in computer automation for biofeedback: The Behavioral Assessment and Rehabilitative Training System (BARTS)

User versatility in a system for computer-automated biofeedback training is the degree to which the assessment and training parameters may be altered by the user's employing English language or other simple code, that is, without altering the system's applications software. The Behavioral Assessment and Rehabilitative Training System (BARTS) includes a design and control program that allows for the specification of assessment and training protocols by persons who are entirely lacking in computer programming skills. This paper describes the logic for data acquisition and training that is incorporated in the BARTS, describes the parameters that must be specified in constituting unique assessment or training protocols, and illustrates the system's application in a research-oriented biofeedback clinic.This work was supported by NINCDS Grant 1 R01 N 15796 (C. S. Cleeland and G. K. Montgomery), and by a grant from the Charles E. Culpepper Foundation, Inc., New York.     

Eye movements of monkeys during learning of color and form discrimination problems involving reversal and nonreversal shifts

Eye movements of monkeys were measured during performance on a series of two-choice color and form discriminations which involved reversal and nonreversal shifts. Neither the amount of visual scanning nor the duration of individual fixations was related to the relevant dimension or to the type of shift. However, amount of scanning increased over the series of problems and was linearly related to the time to respond. The last fixation of a trial tended to be on the positive stimulus and a fixation near the end of a trial tended to be longer than one near the beginning.This research was supported by a research grant (GB-18953X) from the National Science Foundation to the first author. Part of the research served as the basis for the second author's doctoral dissertation (Vaughan, 1970).     

On the number of phenotype structures in genetic systems

Phenotype structures in genetic systems are carefully defined in an abstract setting so that a considerable amount of enumerative theory can be brought to bear on the problem of enumerating them. Recent results can be used to simplify the computations, and a natural correspondence is suggested which changes the problem of finding the number of phenotype structures to the problem of determining the numbers of certain graphs with colored points. Work supported in part by a grant from the National Science Foundation. Work supported in part by Grant 73-2502 from the Air Force Scientific Research.     

Caloric requirements of human populations: A model

Currently available models used for predicting human caloric requirements do not reflect the great variability in activity patterns observed among populations, and are insensitive to important anthropometric, demographic, and environmental variables. They are thus inadequate for application to many populations and problems of anthropological interest. We present a model for determining caloric requirements which more accurately accommodates the effects of variation in activity and in anthropometries on individual needs, and which predicts population requirements based on individual needs and demographic parameters. The model is tested on four populations (the Andean community of Nuñoa, Peru, the Dobe !Kung of Botswana, and two New Guinean villages) and is found to provide consistently better estimates of caloric requirements than are generated by the Food and Agriculture/World Health Organization's model. This model should be useful to anthropologists and human ecologists concerned with problems involving human energy consumption, such as the efficiency of subsistence strategies, optimum family composition, or certain consequences of increased labor migration or technological change.This research was supported by a grant from the Research Foundation of the State University of New York. Funds for computer time and materials were provided by the State University of New York at Binghamton and The Pennsylvania State University.     

A parameter identification problem arising from a model of canalicular bile formation

We develop a simple mathematical model for bile formation and analyze some features of the model that suggest the design for future physiological experiments. The mathematical model results in a boundary value problem for a system of functional differential equations depending on several physical parameters. From the observability of the boundary values we can identify, both qualitatively and quantitatively, some of these physical parameters. This identification then suggests physical experiments from which one could infer some of the bile transport phenomena that are not, at present, directly observable. The mathematical parameter identification problem is solved by converting the boundary value problem to a transition time problem for a quadratic system of ordinary differential equations on the plane where we are able to employ some special properties of quadratic systems in order to obtain a solution.The author was supported by the Air Force Office of Scientific Research and the National Science Foundation under the grants AF-AFOSR-89-0078 and DMS-9022621The author was supported by National Institutes of Health under grant number R37 DK-27623     

On lipid droplets in renal interstitial cells

Summary By examining Epon sections of the renal papilla, it is demonstrated that a brief period of salt repletion in salt-depleted rats induces a considerable increase in the number of lipid droplets in the renal interstitial cells. It is supposed that this difference indicates that the lipid droplets contain substances which are physiologically important for the kidneys. Possibly, these substances are prostaglandins, which have been demonstrated previously by other authors in extracts from the renal medulla.This work was supported by a grant from the Danish State Research Foundation.The author wishes to acknowledge the support and inspiration given by E. Bojesen, M.D., and P. Leyssac, M.D., the Institute of Experimental Medicine.     

Resonances of biological cells at audible frequencies

Two theories are discussed to account for the observed resonances of biological cells at sonic frequencies. One theory assumes the cell wall to be a stretched balloon surrounded by, and filled with, an incompressible fluid. The other treats the cell wall as a rigid shell. Both lead to reasonable physical constants for the cell wall. The initial phases of this work were supported by a grant from the Wisconsin Alumni Research Foundation to Professor H. B. Wahlin and were included in the author's theses submitted to the Graduate School of the University of Wisconsin in partial fulfillment of the degree of Doctor of Philosophy, August, 1949. The work is being supported at present by a grant to the Johnson Foundation from the Raytheon Manufacturing Company.     

Highly regenerative tissue cultures from axillary tiller buds of sexually mature oat plants (Avena sativa L.)

Summary Competent tissue cultures were initiated from axillary tiller buds and immature leaves of two cultivars ofAvena sativa L. and cultured on agar nutrient medium containing 2 mg/l of 2,4-dichlorophenoxyacetic acid and 1 mg/l benzyladenine. Using a technique of selective excision and subculturing of the shoot-forming tissues and rejecting the root-froming tissues, we regenerated numerous plants either on hormone-free medium or by allowing the subculture with hormone to age under usual culture-room light conditions. This research was supported in part through a grant to A. W. G. from BARD (Binational Agricultural Research and Development Foundation). N. S. S. is grateful to the Ministry of Education and Culture, Government of India, New Delhi, for the award of a National Scholarship for study abroad 1980–81.     

Membrane function in cystic fibrosis. I. Putrescine transport in normal and cystic fibrosis fibroblasts

Putrescine transport was examined in normal and cystic fibrosis fibroblasts. No differences were observed in accumulation pattern, kinetics of uptake, or efflux between CF and normal cells. In both growing and growth-arrested CF and normal fibroblasts, exogenously supplied putrescine remained unchanged for at least 60 min. Some differences were observed in the response of CF and normal cells to environmental (media) changes.This research was supported by a grant from the Cystic Fibrosis Foundation and by a grant from the National Institutes of Health, Training Grant (GM01316 11 GNC).     

The expected fraction of clonable genomic DNA

Random clone mapping of genomic DNA is a subject of great interest in molecular biology.E. coli has just been mapped and work is progressing on some human chromosomes. In this paper we give estimates of the fraction of genomic DNA which is not clonable by partial digest with a restriction enzyme. Research supported by grants from the National Institutes of Health and the System Development Foundation.     

Photoacoustic spectroscopic analysis of marine phytoplankton

The 500–800 nm spectra of replicata phytoplankton cultures freeze-dried upon glass fiber filters were determined both by photoacoustic spectroscopy (PAS) and by photoelectric absorption spectrophotometry. A number of the features of biological interest are better resolved in the PAS spectra. Further, PAS is sufficiently sensitive that it could be applied in the analysis of readily obtainable field samples.Contribution number 9322 from the Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543. The work at Woods Hole was supported by the Office of Naval Research contract ONR N00014-66-c 0241, National Science Foundation grant GA 002783 and the Tai Ping Foundation. Reprint requests should be addressed to the first author.     

Pyruvate kinase binding to particles in brain

Interaction of pyruvate kinase with membrane fractions of rat brain homogenates was shown to be electrostatic. Ionic compounds readily solubilized the enzyme from membranes, and the enzyme was more readily solubilized at high pH versus low pH. Developmental patterns indicated that the particulate and soluble forms of pyruvate kinase increased nearly in synchrony from birth until maturity.The author is grateful for the technical assistance provided by Dolores Suga. This research was supported by a grant (MA 5447) from the Medical Research Council of Canada.     

Redundant DNA of Neurospora crassa

Approximately 20% of the DNA of Neurospora crassa consists of redundant sequences. This is calculated from the reassociation rate of fragmented, denatured DNA as measured by hydroxyapatite column chromatography. The redundant DNA has a complexity of 10⁵ base pairs and a repetition frequency of up to 60 copies per genome. Its buoyant density in CsCl is 1.720 g/ml and its hypochromicity 20–24%. Base composition determination shows 54% GC content like Neurospora nuclear DNA. DNA-RNA hybridization studies indicate that rRNA and tRNA cistrons make up 2.3 and 1.2%, respectively, of the redundant fraction. Pulse-labeled RNA is shown to hybridize with both redundant and unique DNA fractions, suggesting that both fractions are transcribed.This work is supported by a grant from National Science Foundation (GB 8058) and National Institute of Health Research Career Development Award (K3GM31-238).     

Global stability in a chemostat with multiple nutrients

We study a single species in a chemostat, limited by two nutrients, and separate nutrient uptake from growth. For a broad class of uptake and growth functions it is proved that a nontrivial equilibrium may exist. Moreover, if it exists it is unique and globally stable, generalizing a result in [15]. supported in part by NSF grant DMS 0342153. supported in part by NSF grant DEB-0083566 and the Andrew W. Mellon Foundation. supported in part by USAF grant F49620-01-1-0063 and NSF grant CCR-0206789. Part of this work was carried out when P. De Leenheer was a post-doctoral fellow at DIMACS, Rutgers University, supported in part by NSF grant EIA03-331486 and USAF grant F49620-01-1-0063.