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.     

Pattern recognition in several sequences: Consensus and alignment

The comparison of several sequences is central to many problems of molecular biology. Finding consensus patterns that define genetic control regions or that determine structural or functional themes are examples of these problems. Previously proposed methods, such as dynamic programming, are not adequate for solving problems of realistic size. This paper gives a new and practical solution for finding unknown patterns that occur imperfectly above a preset frequency. Algorithms for finding the patterns are given as well as estimates of statistical significance. This author supported by a grant from the System Development Foundation. This author supported by NSF grant MCS-8301960 and by a grant from the System Development Foundation. This author supported by NIH grant GM19036.     

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.     

A nonlinear ergodic theorem for discrete systems

A theorem concerning the asymptotic behavior of a general class of systems of difference equations is proven. This theorem guarantees the existence of a stable normalized distribution vector, and enables the constructing of a scalar limiting equation for an aggregate variable. This theory is illustrated using an example from population dynamics, a nonlinear size-structured model of competition for a dynamically modeled limiting resource.Supported in the Program in Applied Mathematics at the University of Arizona by the Applied Mathematics and Population Biology/Ecology Divisions of the National Science Foundation under grant No. DMS-8902508. Supported at Cornell University by the US Army Research Office through the Mathematical Sciences Institute, Contract DAAL03-91-C-0027, and by the National Science Foundation through the Biometrics Unit, grant No. DEB-9253570; This work comprises part of the author's dissertation at the University of Arizona, directed by J. M. Cushing     

Exclusion gene mapping utilizing patients with chromosome imbalance: The HL-A system as a prototype

Summary 17 chromosomally unbalanced patients, their siblings and parents were tested for HL-A types and for up to 25 other polymorphic systems to determine whether there was gain or loss of an allele concurrent with the gain or loss of chromosome material. 5 patients had trisomy of part or all of a chromosome; 2 had trisomy of a segment and also deletion of chromosome material. All 7 were due to a familial translocation. The remaining patients had small deletions; 5 had ring chromosomes, 4 had rod deletions and 1 had missing chromosome material due to a heritable translocation. All cases were informative at the HL-A loci because of the high degree of polymorphism of the system whereas only some of the other systems were informative. None of the 17 patients showed unusual inheritance of HL-A or any other of the polymorphic systems examined. These results provide evidence excluding the HL-A and other loci from a number of possible locations in the human genome.Supported by Maternal and Child Health Services 920 and a grant from the Medical Research Foundation of Oregon.Supported by NIH grants AM 13173 and HD-05082 and a Basil O'Connor Starter Research Grant from the National Foundation March of Dimes.Supported by Crippled Children's Division of Oregon Summer Student Funds.Supported by a grant from the National Foundation March of Dimes.     

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.     

Quantitative autoradiographic assessment of 3H-estradiol uptake in immunocytochemically characterized pituitary cells

Summary Dry-mount autoradiography was combined with peroxidase immunocytochemistry to examine estrogen uptake in four pituitary cell types. Quantification by silver grain counts was used to compare ³H-estradiol uptake in nuclei of pituitary cells 60 min after i.v. injection into short-term (control) and long-term ovariectomized and in long-term thyroidectomized rats. Under all three hormonal states, the order of labeling intensity was: gonadotropes > somatotropes > lactotropes > thyrotropes. Long-term ovariectomy caused a significant increase in estrogen uptake of gonadotropes, somatotropes and lactotropes, while uptake in thyrotropes decreased. Long-term thyroidectomy decreased uptake in somatotropes, lactotropes and thyrotropes while gonadotropes remained unchanged.Supported by NICHHD grant HD-03007 to D.A.K., NICHHD grant HD-03110 to the Biological Sciences Research Center of Child Development Research Institute and a grant from the Rockefeller Foundation to the Laboratories for Reproductive Biology.     

Mid-prophase human chromosomes. The attainment of 2000 bands

Summary Human mid-prophase chromosomes exposed to amethopterin, actinomycin D, and bromodeoxyuridine display more than 2000 bands per haploid set and show a remarkable resemblance to the fine chromomeric structures of early pachytene.Supported in part by grant No. 1-568 from the National Foundation and by NIH grant GM26800     

A simplified method for the rapid preparation of peroxidase-anti-peroxidase (PAP) complexes

Summary A modified method is described for the rapid production of peroxidase-antiperoxidase complexes to be used in immunocytochemistry. In this method anti-peroxidase antibodies are precipitated from crude serum with peroxidase at equivalence and subsequently resolubilized at low pH with excess peroxidase. The complexes are isolated from unbound immunoglobulin and peroxidase by gelfiltration. The method combines the advantages of both previously described preparation procedures. The resulting PAP-complex, when tested in indirect immunocytochemistry, is comparable to that obtained in established preparation procedures.Supported by a grant from the Queen Wilhelmina Cancer Foundation (grant no. PA 77/52)     

MAXAMIZE. A DNA sequencing strategy advisor.

The MAXAMIZE advisory system determines from user-provided restriction maps an optimal strategy to do nucleotide sequencing by methods involving end-labeled fragments. The maps may be either simple linear restriction maps of fragments or complex circular maps including restriction sites of a vector. The whole system is interactive and is written in the Genetic English language provided by the GENESIS System, a molecular genetics knowledge representation and manipulation package. In addition, MAXAMIZE provides bookkeeping facilities for sequencing and offers advise on how to verify the newly obtained sequence data.     

Slime a plasmodioid variant ofNeurospora crassa

The slime variant of Neurospora is unique among the higher Fungi in growing on an agar surface by plasmodium-like outflows which are devoid of cell walls, and in which cells from older parts of an agar colony, and those in liquid culture, have very deficient cell walls. Heterocaryon studies indicate that the nucleus determines the slime phenotype. Genetic studies show that three independently inherited characters are essential to but insufficient for the slime phenotype. Some, but not all isolates with all three characteristics give rise to vegetatively derived isolates with stable slime phenotypes.Supported in part by grant G-6174 from the National Science Foundation, and in part by grant GM-06965 from the National Institutes of Health, U.S. Public Health Service.     

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.     

Induced chromosome aberrations in early embryogenesis of mice

Summary A 28-year-old man, whose infant son died of multiple malformations, was shown to have a balanced 13q-/18q+ translocation. He was phenotypically and mentally normal. Studies of the pedigree revealed the presence of bilateral microtia on the side of the spouse of the proband, transmitted in a dominant mode through four generations. Occasional cells from the proband and his mother exhibited an elongated long arm of a chromosome 16.This work was supported by a grant from the National Swiss Foundation for Scientific Research (Credit No. 3.211.69).Supported by Grant 64-411A from the Ford Foundation Population Program.     

Fine structural alterations with age in the fat body of the adult male housefly,Musca domestica

Summary The fat body of the adult housefly is composed of two types of cells, the lipid-and glycogen-rich fat body cells and the oenocytes. A comparison of the fine structure of the abdominal fat body in 4-day old and 31–35 day old male houseflies indicated an increase in lipid and a decrease in glycogen content in the fat body cells of old flies. Oenocytes of old flies exhibit deteriorative alterations with an accumulation of secondary lysosomes. Both fat body cells and oenocytes in senile flies are ingested by hemocytes.Supported by a grant from the National Science Foundation.     

Age of sexual maturity in the stump-tailed macaque (Macaca arctoides): A birth from laboratory born parents

Data are given for sexual maturation in a male (fertile mating at 3.25 years post-natal) and female (fertile mating at 3.0 years post-natal)M. arctoides. Comparisons with data forM. mulatta andM. fuscata suggest that these ages are unusually early for macaques.Supported by a grant from the Nuffield Foundation.     

Glucagon and glicentin immunoreactive cells in human colon

Summary An immunohistochemical study of glucagon and glicentin immunoreactive endocrine cells in the human colon epithelium was performed. Serial sections and qualitative analysis show a cell population containing both immunoreactivities. However, there is another cell population exhibiting only an immunoreactivity with glicentin. The exact distribution of these immunoreactive endocrine cells within the colon crypt segments is also analysed. The significance of these findings concerning the synthesis of glucagon and glicentin and their function is discussed.Supported by a grant of the German Research Foundation and by a research grant AM 17537 from the National Institutes of Health, Bethesda, Maryland (USA) Dr. Colony was the recipient of a stipend for a research project in the Federal Republic of Germany from the Deutscher Akademischer Austauschdienst (DAAD)     

The origin of protein bodies in developing soybean cotyledons: a proposal

Summary The biogenesis of protein bodies is examined in cotyledons of soybean (Glycine max, Merr) at the time when reserve protein is beginning to accumulate in the cotyledons. Reserve protein is deposited in the central vacuoles of parenchyma cells and new protein bodies arise from the central vacuole by pinching-off small masses of reserve protein surrounded by a portion of the tonoplast.Supported by a grant to MJC from the National Science Foundation (Metabolic Biology) and a grant (to BYY) from the National Research Council of Canada.On leave from the Department of Biology, University of New Brunswick, N.B., Canada.     

A note on the diffusion approximation for single neuron firing problems

Summary This paper presents a well-known stochastic model used to describe the firing or discharge pattern of a single neuron in terms of various input processes, and shows how the potential level of the neuron can be given by means of a diffusion equation approximation. There is a discussion of the adequacy of this approximation, and the paper concludes with a brief discussion of first passage time problems.Supported in part by a grant from the Alfred P. Sloan Foundation to the Committee on Mathematical Biology and by a grant of the Statistical Branch, Office of Naval Research to the Department of Statistics, University of Chicago.     

Ultrastructural demonstration of amine granules in the adrenal medullary cells of the rat using acid permanganate fixation

Summary Potassium permanganate fixative is usually employed at pH 7.0. At this pH the amines in the granules of the adrenal medullary cells do not react with permanganate. When the pH was adjusted to 5.0, electron dense precipitates were seen in the amine granules of part of the medullary cells, probably noradrenalin containing cells.Supported by the grant from the Finnish Cultural Foundation     

Immunocytochemistry of a “private” luteinizing-hormone-releasing hormone system in the pituitary

Summary Immunocytochemistry of paraffin sections of Bouin-fixed rat pituitaries with antiserum to luteinizinghormone-releasing hormone (LHRH) revealed two types of cells. Type I cells exhibit granular staining throughout their cytoplasm. The immunoreactivity of type II cells is confined to a much smaller area of the cytoplasm. Type I cells are located in the ventral margin of the pars intermedia, the region between the pars intermedia and the pars distalis, and the pars distalis adjacent to this region. Type II cells have a broader distribution in the pars distalis, but tend to concentrate in the region of the pars distalis near the pars intermedia. Type I cells are distinct from gonadotropes. Type II cells appear to comprise a subgroup of gonadotropes. Staining in type I, but not type II, cells in pituitary explants, maintained in serum-free media for seven days, is as intense as that in normal pituitary tissue. The data suggest that the type I cells are producing an intrinsic LHRH-like material and may be responsible, in part, for the regulation of some gonadotropes.Supported by NIH grants HD12932, NS15843 and NS15809 (LAS), National Science Foundation grant BNS 82-05643 (LAS), and a grant from the Phillippe Foundation (JYL)