A catalogue of phi, psi and omega torsion angles for tetrapeptides in proteins

This work examined the degree of consistency, over multiple occurrences in several proteins, of conformations of tetrapeptides. A data base of 114 proteins was taken from the Brookhaven Data Bank. The number of occurrences of every tetrapeptide in these proteins was counted. For each tetrapeptide which occurred more than 6 times all phi, psi and omega angles were calculated and averaged over the occurrences. Due to the limitations of the data base there were only 24 tetrapeptides in this category. This does not provide sufficient information for the extensive prediction of structures which are not homologous to those already in the data base but the effectiveness of structure prediction can be expected to increase with the size of the data base.     

Olfactory networks: from sensation to perception

Olfactory networks, comprised of sensory neurons and interneurons, detect and process changes in the chemical environment to drive animal behavior. Recent studies combining genetics with behavioral analyses and imaging in worms, flies and mice have revealed new insights into the mechanisms of olfaction. In this discussion, we focus on three interesting findings. First, sensory neuron responses to odor are modulated by neuropeptides. This modulation might serve to extend the range of responses of the sensory neurons and also to integrate internal state information into the chemosensory circuit. Second, genetic tracing studies in mice and flies have shown that the first layer of connections in chemosensory circuits from olfactory epithelium to the glomeruli are stereotyped, while the subsequent connections to higher order sensory processing regions are not. Distributed connectivity to the higher order sensory processing regions has profound implications for how odors are represented in those regions. Third, recent work has revealed that odors are surprisingly sparsely represented in the piriform cortex. The sparse coding in the higher brain centers implies a much greater role for experience and learning in mediating responses to olfactory cues. Analyzing olfactory network function in various species provides us with fascinating clues about how sensory information is acquired, processed and represented at multiple levels within the nervous system.     

Introduction. The perception of speech: from sound to meaning

Spoken language communication is arguably the most important activity that distinguishes humans from non-human species. This paper provides an overview of the review papers that make up this theme issue on the processes underlying speech communication. The volume includes contributions from researchers who specialize in a wide range of topics within the general area of speech perception and language processing. It also includes contributions from key researchers in neuroanatomy and functional neuro-imaging, in an effort to cut across traditional disciplinary boundaries and foster cross-disciplinary interactions in this important and rapidly developing area of the biological and cognitive sciences.     

Motion perception and motion estimation by total-least squares

A computational model of motion perception is proposed. The model, which is gradient-based, adheres to the neural constraint that transmitted signals are positive-valued functions by posing the estimation of image motion as a quadratic programming problem combined with total-least squares: a model that assumes that image signals are contaminated by noise in both the spatial and temporal dimensions. By shrinking motion estimates with a regularizer whose subtractive effect introduces a contrast dependent speed threshold into motion computations, it is shown that the total-least squares model when posed as a quadratic programming problem, is capable of explaining both increases and decreases in perceived speed as these effects were reported by Thompson (1982) to vary as a function of image contrast and temporal frequency. The correlation that exists between the model's contrast speed response and results reported from visual psychophysics is consistent with the view that the visual system assumes that image signals may be contaminated by noise in both the spatial and the temporal domain, and that visual motion is influenced by the consequence of these assumptions.     

Partial purification of "omega" protein from calf thymus.

Proteins which relax supercoiled DNA, called "omega" proteins, are thought to be involved in DNA replication. Calf thymus is a plentiful source of "omega" protein activity. It has been extensively purified and has been characterized as behaving similarly to other eukaryotic "omega" proteins in completely relaxing either positively or negatively supercoiled DNA, requiring a salt concentration of about 0.2 M NaCl or KCl, and not requiring Mg2+. A transient nick must occur but could not be detected. A new assay for "omega" activity is described which is rapid and sensitive, and depends on the fluorescence enhancement of ethidium intercalating duplex DNA.     

Assessment of essential fatty acid and omega3-fatty acid status by measurement of erythrocyte 20:3omega9 (Mead acid), 22:5omega6/20:4omega6 and 22:5omega6/22:6omega3

BACKGROUND: Early suspicion of essential fatty acid deficiency (EFAD) or omega3-deficiency may rather focus on polyunsaturated fatty acid (PUFA) or long-chain PUFA (LCP) analyses than clinical symptoms. We determined cut-off values for biochemical EFAD, omega3-and omega3/22:6omega3 [docosahexaenoic acid (DHA)]-deficiency by measurement of erythrocyte 20:3omega9 (Mead acid), 22:5omega6/20:4omega6 and 22:5omega6/22:6omega3, respectively. METHODS: Cut-off values, based on 97.5 percentiles, derived from an apparently healthy omnivorous group (six Dominica breast-fed newborns, 32 breast-fed and 27 formula+LCP-fed Dutch low-birth-weight infants, 31 Jerusalem infants, 33 Dutch 3.5-year-old infants, 69 omnivorous Dutch adults and seven Dominica mothers) and an apparently healthy group with low dietary LCP intake (81 formula-fed Dutch low-birth-weight infants, 12 Dutch vegans). Cut-off values were evaluated by their application in an EFAD suspected group of 108, mostly malnourished, Pakistani children, three pediatric patients with chronic fat-malabsorption (abetal-ipoproteinemia, congenital jejunal and biliary atresia) and one patient with a peroxisomal beta-oxidation disorder. RESULTS: Erythrocyte 20:3omega9, 22:5omega6/20:4omega6 and 22:5omega6/22:6omega3 proved age-dependent up to 0.2 years. Cut-off values for ages above 0.2 years were: 0.46mol% 20:3omega9 for EFAD, 0.068mol/mol 22:5omega6/20:4omega6 for omega3-deficiency, 0.22mol/mol 22:5omega6/22:6omega3 for omega3/DHA-marginality and 0.48mol/mol 22:5omega6/22:6omega3 for omega3/DHA-deficiency. Use of RBC 20:3omega9 and 22:5omega6/20:4omega6 cut-off values identified 20.4% of the Pakistani subjects as EFAD+omega3-deficient, 12.9% as EFAD+omega3-sufficient, 38.9% as EFA-sufficient+omega3-deficient and 27.8% as EFA-sufficient+omega3-sufficient. The patient with the peroxisomal disorder was classified as EFA-sufficient, omega3-sufficient (based on RBC 22:5omega6/20:4omega6) and omega3/DHA-deficient (based on RBC 22:5omega6/22:6omega3). The three other pediatric patients were classified as EFAD, omega3-deficient and omega3/DHA-deficient. CONCLUSION: Use of the combination of the present cut-off values for EFA, omega3 and omega3/DHA status assessment, as based on 97.5 percentiles, may serve for PUFA supplement intervention until better concepts have emerged.     

Motion perception and visual signal design in Anolis lizards

Anolis lizards communicate with displays consisting of motion of the head and body. Early portions of long-distance displays require movements that are effective at eliciting the attention of potential receivers. We studied signal-motion efficacy using a two-dimensional visual-motion detection (2DMD) model consisting of a grid of correlation-type elementary motion detectors. This 2DMD model has been shown to accurately predict Anolis lizard behavioural response. We tested different patterns of artificially generated motion and found that an abrupt 0.3° shift of position in less than 100 ms is optimal. We quantified motion in displays of 25 individuals from five species. Four species employ near-optimal movement patterns. We tested displays of these species using the 2DMD model on scenes with and without moderate wind. Display movements can easily be detected, even in the presence of windblown vegetation. The fifth species does not typically use the most effective display movements and display movements cannot be discerned by the 2DMD model in the presence of windblown vegetation. A number of Anolis species use abrupt up-and-down head movements approximately 10 mm in amplitude in displays, and these movements appear to be extremely effective for stimulating the receiver visual system.     

Comparative properties of bacteriophage phi6 and phi6 nucleocapsid.

Nonionic detergent treatments released a nucleocapsid from the enveloped bacteriphage phi6. The nucleocapsid sedimented at nearly the same rate as the whole phage in sucrose density gradients, but the buoyant density in Cs2S04 changed from 1.22 g/cm3 for the whole phage to 1.33 g/cm3 for the nucleocapsid. The detergent completely removed the lipid and 5 of the 10 proteins from the phage. Surface labeling of the phage and nucleocapsid with 125I revealed that protein P3 was on the outer surface of the whole phage and P8 was on the surface of the nucleocapsid. Both the phage and the nucleocapsid were stable between pH 6.0 and 9.5. Low concentrations of EDTA (10-4 M) dissociated the nucleocapsid but had no effect on the whole phage. The nucleocapsid contained all three double-stranded RNA segments, as well as RNA polymerase activity.     

Age-related decrease in omega conotoxin binding to rat cardiac synaptosomes.

A cardiac synaptosomal preparation developed by this laboratory was used to study neuronal calcium channels in aging rat heart. Ca2+ channels were quantified by measuring binding of iodinated omega conotoxin, which is reported to specifically block neuronal Ca2+ channels. We determined the binding of [125I]-omega conotoxin GVIA to a synaptosomal preparation from the hearts of 6- and 24-month-old male Fisher 344 rats. The maximum number of binding sites (Bmax +/- SD, fmol/mg protein) is lower in preparations from 24-month (2.2 +/- 0.6) than from 6-month (3.4 +/- 0.7)-old rats. This decrease in number of binding sites suggests an age-related reduction in the number of neuronal calcium channels. Since calcium is essential for exocytotic release of norepinephrine and is made available intracellularly through neuronal calcium channels, the reduction in neuronal calcium channel number may explain, in part, our previous observations of diminished release of norepinephrine in senescent hearts.     

The mechanism of replication of phi X 174. XVIII. Gene A and A* proteins of phi X 174 bind tightly to phi X 174 replicative form DNA

Evidence is presented that the gene A and A * proteins of bacteriophage phi X 174 form covalent associations with the 5' ends of the DNA molecules when superhelical phi X replicative form DNA is nicked by a combination of these proteins in vitro. This evidence is: 1, The 5' ends of the DNA molecules nicked by the gene A protein and reacted with bacterial alkaline phosphatase were protected against subsequent phosphorylation by polynucleotide kinase even after treatment of the nicked DNA with SDS and pronase followed by centrifugation on a high-salt neutral sucrose gradient. 2, Iodinated pronase-sensitive material remained attached to the nicked replicative form DNA and could not be removed by exposure to SDS or 2 M NaCl, either by sedimentation through high-salt neutral sucrose gradients, or by CsCl equilibrium centrifugation. 3, Iodinated pronase-sensitive material was detected on DNA that had been nicked during the reaction, but not on unreacted DNA. 4, Electrophoresis of the iodinated pronase-sensitive, DNA-bound material in SDS-polyacrylamide gels after DNAse digestion revealed that it was composed almost entirely polypeptides with electrophoretic mobilities similar to those of the gene A and A * proteins. We speculate that the gene * protein may be essential for normal progeny single-stranded DNA synthesis in vivo.     

Protein synthesis and degradation in isolated muscle. Effect of omega 3 and omega 6 fatty acids.

The ability of derivatives of the essential fatty acids linoleic acid (C18:2, omega 6) and alpha-linolenic acid (C18:3, omega 3) to stimulate rates of protein synthesis and degradation was investigated in isolated intact muscles from fasted rabbits. Both omega 6 derivatives examined, arachidonic acid (C20:4, omega 6) and dihomo-gamma-linolenic acid (C20:3, omega 6), when added at concentrations up to 1 microM, stimulated the rate of protein synthesis and the release of prostaglandin F2 alpha (PGF2 alpha). Metabolites of the omega 6 series, namely eicosapentaenoic acid (C20:5, omega 3) and docosahexaenoic acid (C22:6, omega 3), were without effect on the rate of protein synthesis and resulted in a decrease in the release of PGF2 alpha. None of the fatty acids had a significant effect on the rate of protein degradation. Although insulin (100 mu units/ml) also stimulated rates of protein synthesis when added alone, none of the omega 3 or omega 6 fatty acids, when added with insulin at concentrations of 0.2 microM, potentiated the effect of the hormone.     

Transition from initiation to elongation in protein-primed phi 29 DNA replication: salt-dependent stimulation by the viral protein p6.

The transition step from the p3-dAMP initiation complex to the first elongated products, p3-(dAMP)2 and p3-(dAMP)3, requires a dATP concentration higher than that needed for the initiation reaction or for the further elongation of the p3-(dAMP)3 complex. The elongation in phi 29 DNA-protein p3 replication in vitro was strongly inhibited by salt. Under inhibitory salt concentration, the viral protein p6 greatly stimulated phi 29 DNA-protein p3 replication. The effect of protein p6 was not on the rate of elongation but on the amount of elongated product, stimulating the transition from initiation to formation of the first elongation products.     

Radioimmunoassay of an antibody to phi X 174 DNA.RNA hybrid.

A fast and simple radioimmunoassay (RIA) technique was developed for an antibody to DNA·RNA hybrid using protein A-bearing Staphylococcus aureus cells as immuno-adsorbent and a glass microfiber filter for the deparation of free antigen and antibody-antigen complex. A simple method for preparing ³H-labeled DNA·RNA hybrid using single-stranded circular DNA of viruses and Escherichia coli RNA polymerase (nucleosidetri-phosphate: RNA nucleotidyltransferase, EC 2.7.7.6) is also described. In comparison to a hybrid made of natural sequences, a synthetic homopolymer hybrid poly (A)·poly(dT) was found to be a poor competitor for the antibody by this RIA technique.     

Cloning of restriction fragments of DNA from staphylococcal bacteriophage phi 11.

EcoRI fragments of Staphylococcus aureus bacteriophage phi 11 DNA were cloned in vector plasmid pSA2100 in S. aureus. The clones were analyzed in marker rescue experiments with suppressor- and temperature-sensitive mutants of phi 11 to correlate the genetic and physical map. Several mutants could be identified on the physical map, and a clone containing fragment EcoRI-B of phi 11 DNA expressed immunity to phage infection. In addition, it was found that recombinant plasmids containing phi 11 DNA sequences can be transferred by high-frequency transduction after phage phi 11 infection of host cells.     

Whole-body beta-oxidation of 18:2omega6 and 18:3omega3 in the pig varies markedly with weaning strategy and dietary 18:3omega3

Segregated early weaning (SEW) into a cleaner nursery increases food intake and growth in pigs, presumably because of reduced immune stimulation compared with conventionally reared, nonsegregated pigs (NSW). The aim of the present study was to evaluate the oxidation of linoleic acid (18:2omega6) and alpha-linolenic acid (18:3omega3) in SEW and NSW pigs. Pigs consumed a control or high 18:3omega3 diet (omega6 PUFA/omega3 PUFA; 21.3 vs. 2.5, respectively) and were weaned at either 14 days old into a SEW nursery or at 21 days old into a conventional NSW nursery. The major acute-phase protein of pigs but not haptoglobin increased in 35-day-old NSW pigs. NSW pigs had 15-25% lower carcass 18:2omega6 and 20-30% lower carcass 18:3omega3 (% composition) at 49 days old. Between 35- and 49-days-old, NSW pigs had a higher whole-body oxidation of 18:2omega6 (40-120%) and 18:3omega3 (30-80%). The high 18:3omega3 diet decreased the whole-body oxidation of 18:2omega6 by 73% and of 18:3omega3 by 63% in NSW pigs. We conclude that moderately cleaner housing SEW significantly decreases 18:2omega6 and 18:3omega3 oxidation in pigs.     

Bacteriophage phi29 terminal protein: its association with the 5' termini of the phi29 genome.

The location of the protein bound to bacteriophage phi29 DNA has been studied with restriction endonucleases, exonucleases, and polynucleotide kinase. The protein is invariably associated with the two terminal DNA fragments generated by restriction endonucleases. The phi29 DNA prepared with or without proteinase K treatment is resistant to the action of the 5'-terminal-specific exonucleases, lambda-exonuclease and T7 exonuclease. The phi29 DNA is also inaccessible to phosphorylation by polynucleotide kinase even after treatment with alkaline phosphatase. On the other hand, phi29 DNA is sensitive to exonuclease III, and the 3' termini of the DNA can be labeled by incubating with alpha-[32P]ATP and terminal deoxynucleotidyl transferase. The protein remains associated with the phi29 DNA after treatment with various chaotropic agents, including 8 M urea, 6 M guanidine-hydrochloride, 4 M sodium perchlorate, 2 M sodium thiocyanate, and 2 M LiCl. These results are consistent with the notion that the protein is linked covalently to the 5' termini of the phi29 DNA.