Macromolecular marionettes

Computer graphics can provide useful tools for molecular biology because pictorial displays are the most efficient way for computers to communicate the details of a complex molecular structure to human beings. The development of suitable hardware has led to the establishment of a number of computer graphics installations devoted to the investigation of molecular structure.We describe here the Evans and Sutherland $\text{LDS-1}\text{PDP-10}$ system of the Princeton University Computer Graphics Laboratory, and the program systems that we have developed for applications to the study of protein and nucleic acid structure and interaction. The hardware can generate displays of complicated three-dimensional line drawings. It allows interactive analysis and modification of a display by a human observer, as well as computational analysis of structural data by a powerful general-purpose digital computer, the PDP-10.We have developed programs for the study and analysis of proteins and nucleic acids of known structure, and for construction and experimentation with models of general polypeptides and polynucleotides. These model-building programs permit the generation of displays of polypeptides and polynucleotides of arbitrary sequence and conformation. It is possible to adjust all conformational angles interactively, or with the assistance of supportive software that can carry out a variety of structural manipulations, such as the folding of a selected region into a helical conformation.Although the purely computational problems encountered in this work are relatively straight-forward—a tribute to the power of the equipment—subtle problems arise in defining the role of a human being as a partner in the execution of an interactive program. Our attempts to achieve the most effective combination of human and computers depend on the recognition of the strengths and limitations of each, and of the efficiencies of the channels of communication between them.     

A model for protein transport across the endothelial membrane.

A mathematical model for convective and diffusive transport of protein across the capillary membrane is developed for a radioisotope-labeled species, the protein ¹¹³In-transferrin. Body tissue is modeled as a two-compartment porous medium with liquid and solid phases.In normal human subjects, labeled autologous blood is reinfused as an intravenous bolus, and blood samples are drawn periodically during the study. Gamma emissions detected in a well counter are fed automatically to a $\text{PDP}\text{-}\text{11}\text{10}$ computer for collection and analysis, and a transport parameter, r, which represents the ratio of convective to diffusive protein fluxes, is calculated for each subject. The range of r is 0.20–0.46 with an average ratio of 0.287. The results suggest that diffusion plays a dominant role in systemwide protein transport in the body.     

ATS in exposition

ATS (A Tutorial System) is written in $\text{APL}\text{360}$. It contains an author interrogation program that interviews the author in English and formats his tutorial for him, and a tutorial supervisor program that interfaces with the students. The supervisor program contains many features of machine intelligence (a knowledge of the rules of human discourse) which operate in every tutorial without intervention by the author, and provide the discourse with an aura of intelligent behavior. Certain aspects of both programs are illustrated by terminal examples.     

Digital archiving of biomedical recordings for off-line computer analysis

This article describes a new procedure for archiving biomedical recordings on industry standard digital magnetic tape. Familiar computer methodology is employed for data-banking heartbeat patterns in a format which has been optimized for later analysis. Recordings are made through an encoder-controller unit coupled to a four channel FM cassette data recorder. This unit produces FM analog magnetic tape with square wave identification and calibration code preceding each sample of biomedical data. Code bits and data sample are timed out sequentially in repetitive standardized format. Digital images of these specially formatted analog tape cassettes are then processed by an edit program on an IBM $\text{370}\text{145}$. Here, the identifiers are decoded and data sections located. Identification, calibration, and biomedical recordings are then archived on a directory tape which may be efficiently and repeatedly accessed for future computations.     

Pocket calculator program: Welch's v statistic

A program written for the Hewlett-Packard HP $\text{29}\text{19}\text{C}$ programmable calculator is presented which will calculate the Welch's v statistic for use in comparing means from normally distributed data with unequal sample sizes and variances.     

The influence of varying inspired fractions of O₂ and CO₂ on the development of involuntary breathing movements during maximal apnoea

The growing urge to breathe that occurs during breath-holding results in development of involuntary breathing movements (IBMs). The present study determined whether IBMs are initiated at critical levels of hypercapnia and/or hypoxia during maximal apnoea. Arterial blood gasses at the onset of IBM were monitored during maximal voluntary breath-holds. Eleven healthy men performed breath holds after breathing air, hyperoxic–normocapnia, hypoxic–normocapnia, and normoxic–hypercapnia. Pre-breathing of the gas mixtures facilitated the IBM onset, reducing the time-to-onset for ∼46% (hyperoxic condition) and for ∼80% (hypoxic condition) compared to the normoxic air breathing time. A strong correlation (R = 0.83, P = 0.002) between arterial partial pressure of CO₂ (Pa_CO2${\text{Pa}}_{{\text{CO}}_2}$) at IBM onset after pre-breathing hyperoxic and hypercapnic gas mixtures was observed, suggesting the existence of a possible IBM Pa_CO2${\text{Pa}}_{{\text{CO}}_2}$ threshold level of ∼6.5 ± 0.5 kPa. No clear “threshold” was observed for partial pressure of arterial O₂ (Pa_O2${\text{Pa}}_{{\text{O}}_2}$). However, we observed that IBM onset was influenced, in part, by an interaction between Pa_O2${\text{Pa}}_{{\text{O}}_2}$ and Pa_CO2${\text{Pa}}_{{\text{CO}}_2}$ levels during maximal apnoea. This study demonstrated the complex interaction between arterial blood-gases and the physiological response to maximal breath holding.     

An on-line system for acquisition and processing of cerebral blood flow data

Regional cerebral blood flow is measured by monitoring the clearance from the brain of the gamma emitting radioisotope ¹³³Xe following an intracarotid artery bolus injection. On-line data analysis, which is performed on a PDP $\text{12}\text{30}$ digital computer, involves exponential stripping to isolate grey and white matter flows and integration of the clearance curves to infinity to enable the mean flow to be calculated. The data is displayed in real time and stored on the PDP 12 Linc tapes as a permanent record.     

Effects of two-hour light-dark cycles on feeding, drinking and motor activity of the rat

The effect of two-hour light-dark cycles on feeding, drinking and motor activity in the rat was compared with behavior under the usual $\text{12}\text{12}$ hour cycle. The two-hour cycles consisted of $\text{60}\text{60}$ min, $\text{80}\text{40}$ min and $\text{40}\text{80}$ min light-dark schedules which were maintained each for 7 days. Water intake, frequency of feeding, and motor activity were still significantly higher during dark than during light, although their occurrence during dark was reduced as compared to the $\text{12}\text{12}$ hour control schedule. A free-running circadian rhythm of consummatory behavior with a period length exceeding 24 hours was present throughout the experimental period. The amplitude of the circadian feeding rhythm gradually decreased over time, whereas the percentage of feeding during dark increased. During the circadian phase of minimal food intake, illumination changes affected feeding behavior more strongly than during the phase of maximal food intake. After restoration of the orginal $\text{12}\text{12}$ hour cycle, the amplitude of the nocturnal feeding rhythm increased gradually over several days, whereas the amplitude of the drinking rhythm showed a more rapid recovery. The experiments show that even short cycles of illumination may exert control over the rat's consummatory and motor activity. Short light-dark schedules provide a way for studying separately effects of illumination and of circadian rhythms.     

Soluble peptidoglycan fragments stimulate antibacterial protein synthesis by fat body from larvae of Manduca sexta

Both hemocytes and fat body from larvae of $\text{Manduca}$$\text{sexta}$, which have been injected with inducers of antibacterial protein synthesis, contain immunoreactive lysozyme. However, fat body is a richer source and has been demonstrated to synthesize and release lysozyme and cecropin-like peptides (bactericidins) $\text{in}$$\text{vitro}$. Fat body secretion of lysozyme and bactericidins is stimulated by addition of soluble peptidoglycan fragments to culture medium. The rate of lysozyme secretion by fat body varies as a function of peptidoglycan inducer concentration. These data are consistent with the hypothesis that, $\text{in}$$\text{vivo}$, bacteria must be phagocytized and partially degraded (processed) by hemocytes to generate a signal (peptidoglycan) that subsequently induces antibacterial protein synthesis by fat body.     

Thyroid and thymus morphology in rats following sudden DRL reinforcement schedule changes

The possibility that sudden and maintained changes in an operant reinforcement schedule could induce discernable alterations in tissue morphology was explored. Numbers of thyroid follicles, thyroid (perifollicular) mast cells and thymus mast cells were counted from rats that had been adjusted to 80% free-feed weight and either shifted and maintained upon a DRL 12 sec schedule for 1 to 7 days after two weeks of DRL 6 sec training (DRL $\text{6}\text{12}$ sec group) or maintained on the DRL 6 sec condition (DRL 6 sec controls). Except for a marginal (p=0.06) decrease in thyroid mast cell numbers for the DRL $\text{6}\text{12}$ sec group, relative to the DRL 6 sec controls, these usually responsive morphological measures did not demonstrate statistically significant alterations.     

Influence of temperature on the immune response of juvenile summer flounder,Paralichthysdentatus, and its role in the elimination of Trypanoplasmabullocki infections

Two groups of juvenile summer flounder maintained at 5°C were experimentally infected with the hemoflagellate $\text{Trypanoplasma}$$\text{bullocki}$. Another group maintained at 5°C was not infected. The water temperature of one infected group was raised stepwise to 12°C, 18°C, and 24°C for 2 to 3 weeks at each level. The other infected group was maintained at 5°C for 12 weeks, the duration of the experiment. In addition, juvenile flounder were collected over a temperature range of 6°C to 22°C from February to June, 1982, to monitor natural infections. Live $\text{T}$. $\text{bullocki}$ were incubated in plasma from fish at each temperature to monitor the host's humoral response. Trypanoplasmacidal lysis occurred in experimental infections maintained at 24°C and in natural infections over a range of 10°C to 22°C. Complete elimination of trypanoplasms occurred in experimental infections at 24°C and in natural infections at 22°C. Differences in temperature where lytic activity occurred was mainly attributable to the short time exposure of experimental infections to increasing temperatures in contrast to that occurring in nature. Trypanoplasmacidal lysis with increasing water temperatures in flounder indicates that the fish's humoral immunity is responsible for the annual spring decline in prevalence and eventual elimination of $\text{T}$. $\text{bullocki}$ infections.     

Ultraviolet carcinogenesis in the teleost fish,Poecilia formosa

A calculation is made of the fraction of a population of $\text{Poecilia}$, $\text{formosa}$, that develop ultraviolet induced tumors and the result compared with the experimental data. Reasonable correlation is obtained.     

Terminal rearrangements in the genome of adenovirus type 12 mutants adapted to growth in two human tumor cell lines

After serial passage of adenovirus type 12 in cells of the human melanoma line Nki4 virus mutants with enhanced growth potential have been isolated which carry additional sequences of regularly increasing size at the right end of the genome. DNA sequence analysis was performed'to characterize these genomic alterations as well as those of the previously described Ad12 $\text{C}\text{4}\text{1}$ mutants adapted to growth in the human carcinoma cell line $\text{C}\text{4}\text{1}$ (I. Kruczek, E. Schwarz, and H. zur Hausen (1981)Int. J. Cancer27, 139–143). Duplication of the inverted terminal repetition (ITR) emerged as the common feature of the right terminal alterations of all the mutant genomes analyzed. The sequences present between the ITR repeats were of either right-end or left-end origin, the latter suggesting that left-end sequences comprising the ITR and parts of the adjacent unique sequences have been transferred to the right end of the genome. The different sizes of the additional sequences in Ad12 Nki-4 DNA could be explained by varying degrees of amplification of a basic additional sequence of 342 base pairs.     

Immunodetente and the ‘see-saw’

The materno-fetal relationship is governed by critical levels of progesterone (P) and prostaglandin F2alpha (PGF2alpha). The ‘see-saw’ in concentration of these molecules maintain and terminate pregnancy in placental mammals. Apart from the enhancement or suppression of uterine contractility by PGF2alpha and P respectively, the hypothesis in these pages is that the initiating event of parturition is a maternal immunologic repudiation of the feto-placental unit. This $\text{immunoregulative}$, $\text{theory}$, $\text{of}$, $\text{parturition}$ is not in contradiction to other physico-endocrinologic theories of labour; but is here presented to further explain some, herefore, puzzling empirical data witnessed in complications of pregnancy and induced abortion, when Pgs are employed as abortifacients.     

Short stature and delayed skeletal maturation in children with allergic disease

The frequency of short stature was assessed in 598 children (66% boys, 34% girls) referred consecutively because of asthma or allergic rhinitis. Six percent were of small stature, with heights of less than the third percentile for age. A total of 66 children with small stature were subsequently studied, 36 of whom had asthma. None had received steroids. Children with short stature were predominantly boys (83%, p < 0.005) and had delayed bone age (<2 SD of mean, $\text{34}\text{45}$), correspondence of bone age with height age (r = 0.93), normal serum thyroxine but increased tri-iodothyronine levels ($\text{11}\text{24}$), and normal insulin-induced growth hormone secretion ($\text{12}\text{12}$). Their heights corresponded only in part to midparental height. The results were the same for those with and without asthma, and the severity of asthma was not related to the degree of growth retardation. The findings suggest that short stature is more common than expected in children with allergic respiratory disease, both asthmatic and nonasthmatic, that their growth potential is good, and that impaired linear growth is not necessarily a result only of asthma but of a more fundamental abnormality possibly associated with the atopic state. They emphasize the importance of considering allergic respiratory disease in the clinical evaluation of children with small stature.     

A pocket calculator program for the evaluation of the oxygen diffusion to perfusion ratio

A pocket calculator program has been written for the evaluation of the oxygen difusion to perfusion ratio (). It allows one to avoid the computational errors involved by approximating the oxygen dissociation curve through a straight line.     

Simulated and experimental temperature responses in man during exercise in varying environments

Stolwijk's mathematical model of thermoregulation is validated against reported human experience.Computed temperatures from the model were compared against experimental data obtained, using various matched environmental conditions. Three fit male subjects 168.5 ± 1.8 cm, 64.2 ± 1.9 kg, 24.5 ± 2.6 yr. (mean ± range) underwent pre-work and incremented work phases in the various conditions. Measurements of rectal temperature (T_R), tympanic temperature (T_T), and four skin sites ($\text{T}$_S) were taken. Air temperature (T_AIR), air velocity (V), relative humidity (RH) and work (W), were manipulated.Good simulations were achieved at 30°C air temperature, rectal temperature deviation $\text{d}$ < 0.10°C. As lower ambient temperatures were encountered initial transient drop of simulated core temperature was emphasized, and this was not reflected in experimental data. It is proposed that the process of thermoregulation during exercise in the cold requires further conceptual refinement in the model. By subdivision of active muscular layers in the passive system of the model superior simulations at low air temperatures, may be achieved.     

Evidence of nucleosomes in situ and their organization in chromatin and chromosomes of Chinese hamster cells

Freeze-fracture studies of intact metaphase Chinese hamster cells indicate that the chromosomes are composed of compactly aligned, flat and hexagonally shaped bipartite disks. The overall dimensions of a bipartite disk are about $\text{140 ± 25}\text{A}\text{?}$ in height, $\text{100 ± 20}\text{A}\text{?}$ in width, and $\text{54 ± 4}\text{A}\text{?}$ in thickness. The center-to-center distance of two units of a bipartite disk is about $\text{34 ± 3}\text{A}\text{?}$. The core of a disk appears to contain four substructures that measure about $\text{25 ± 5}\text{A}\text{?}$ in diameter. Through the center of the disk core there is an axial structure measuring about $\text{20 ± 5}\text{A}\text{?}$ in diameter, which spans and interconnects similar bipartite disks to form a continuous linear array. A structure measuring $\text{20 ± 4}\text{A}\text{?}$ in diameter is wound around the edges of the disk core and interconnects with the next bipartite disk. The connecting strand is parallel to the axial structure. In addition, there appear to be bridgings between the curled structure and disk core. The chromatin of intact interphase cell nuclei shows similar bipartite disks with dimensions and features similar to those of metaphase chromosomes. The bipartite disks are aligned in a linear array in both chromatin and chromosomes.     

Selective resolution of plaques and treatment of Atherosclerosis by biophysical alteration of “cellular” and “intracellular” properties

Presenting a totally new approach to the effective treatment of Atherosclerosis through the alteration of biophysical properties both “intracellularly” and “extracellularly.” The experimental data is preliminary but the results obtained indicate that by allowing the atherosclerotic lesions to take up the magnetically excitable submicron particles and then applying an external alternating electro-magnetic field, the atherosclerotic lesions may be $\text{selectively}$ resolved $\text{without}$ damaging normal blood vessels. This concept suggests many areas of investigation since there are a variety of means of biophysically altering the atherosclerotic plaques, and many substances may be utilized to enhance the process. This new technology and this initial experimentation introduces a “new era” in the $\text{effective}$ treatment of Atherosclerosis.     

The invitro generation of an antibacterial activity from the fat body and hemolymph of non-immunized larvae of Galleriamellonella

A state of immunity in $\text{Galleria}$$\text{mellonella}$ against the pathogen $\text{Pseudomonas}$$\text{aeruginosa}$ is known to be induced by the injection of lipopolysaccharide (LPS), isolated from the homologous organism. An $\text{in}$$\text{vitro}$ mixture of the LPS and whole or cell-free hemolymph from non-immunized larvae is not antibacterial. $\text{In}$$\text{vitro}$ mixtures of fat body and cell-free hemolymph from non-immunized larvae, incubated at 25°C for 20 hours generated a proteinaceous antibacterial activity. The generation of this activity was enhanced by the presence in the incubation mixture of LPS and/or hemocytes from non-immunized larvae. It is suggested that LPS causes the release of a hemocyte factor(s) which acts in conjunction with or directly on the fat body resulting in an enhanced production of antibacterial factors.