Continuous representations of time-series gene expression data.

We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression profile is modeled as a cubic spline (piecewise polynomial) that is estimated from the observed data and every time point influences the overall smooth expression curve. We constrain the spline coefficients of genes in the same class to have similar expression patterns, while also allowing for gene specific parameters. We show that unobserved time points can be reconstructed using our method with 10-15% less error when compared to previous best methods. Our clustering algorithm operates directly on the continuous representations of gene expression profiles, and we demonstrate that this is particularly effective when applied to nonuniformly sampled data. Our continuous alignment algorithm also avoids difficulties encountered by discrete approaches. In particular, our method allows for control of the number of degrees of freedom of the warp through the specification of parameterized functions, which helps to avoid overfitting. We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results.     

Non-local interactions between light induced processes inCalliphora photoreceptors

Summary The prolonged depolarizing afterpotential (PDA) is a phenomenon which is tightly linked to visual pigment conversion. In order to determine whether processes underlying PDA induction and depression can spread in space, the PDA was recorded intracellularly in white-eyedCalliphora R1-6 photoreceptors and used to examine interactions between processes induced by activating statistically different photopigment molecules (Figs. 3–6). It was found that a PDA induced by converting some fraction of rhodopsin (R) molecules forward into the metarhodopsin (M) state can be completely depressed by equal or smaller amounts of pigment conversion, backward from metarhodopsin to rhodopsin even when largely different sets of pigment molecules were shifted in the respective directions, in agreement with previous experiments conducted on the barnacle. The characteristics of the afterpotentials obtained following the cessation of strong blue and green light stimuli which did not cause a net pigment conversion was examined (Figs. 7, 8). It was found that these afterpotentials, obtained when nonet R to M conversion took place, could not be depressed by an opposite net large M to R pigment conversion. Accordingly we propose to restrict the term PDA to an afterpotential which can be depressed by a net M to R pigment conversion. It is concluded: (a) that some processes underlying PDA induction and depression inCalliphora must interact at a distance which extends at least to the nearest neighboring pigment molecule, and (b) that inCalliphora photoreceptors net pigment conversion is required in order to induce and depress a PDA.Abbreviations R rhodopsin - M metarhodopsin - R to M rhodopsin to metarhodopsin pigment conversion - M to R metarhodopsin to rhodopsin pigment conversion - PDA prolonged depolarizing afterpotential - ERG electroretinogram - M potential metarhodopsin potential - ERP early receptor potential     

Lycopersicon esculentum: Trifoliate plants recovered from anther cultures of heterozygous tftf plants

The effects of the genotype and growth medium composition on callus induction and shoot regeneration from tomato (Lycopersicon esculentum Mill) anthers were studied. Five male sterile varieties, homozygous for the recessive gene ms 10³⁵, their isogenic fertile counterparts, and nineteen sterile mutants from an F₂ population segregating for ms 10³⁵, were tested. Callus induction and shoot formation were found to be affected by the genotype. The presence of the mutant gene ms 10³⁵ greatly increased callus induction. A significant interaction concerning callus induction was found between the ms 10³⁵ gene and the general genetic background. In most of the plants shoot regeneration from the anthers was associated with various degrees of callus production. However, there was no correlation between callus production and the ability to regenerate plants from that callus. Anthers isolated from plants which were heterozygous for the recessive leaf marker trifoliate, regenerated diploid plants with trifoliate leaves. The plants retained the trifoliate phenotype for over six months in culture under non-aseptic condition. Since the trifoliate phenotype appears only in the homozygous recessive state, the evidence that these trifoliate plants are doubled haploids of sporogenic origin is discussed.     

Morphological and physiological correlates of niche breadth in two species of Espeletia (Compositae) in the Venezuelan Andes

Summary We compared adaptive strategies in two plants of Venezuelan páramos (alpine areas): the widely distributed, caulescent, and pubescent Espeletia schultzii Wedd. with the acaulescent, nearly glabrous E. atropurpurea A.C. Smith which is restricted to mesic sites just above treeline. Both species occur together at 3,450 m, near treeline.Physiologically, E. schultzii was more drought resistant than E. atropurpurea, and was better adapted for carbon dioxide fixation under low temperatures. The densely pubescent leaves of E. schultzii are highly reflective; this increases the intensity of light needed for photosynthetic saturation and influences leaf temperature. Leaf pubescence may reduce the level of insect predation.Measurements of leaf productivity indicate higher values for E. atropurpurea during the rainy season and higher values for E. schultzii during the dry season. However, annual values of leaf productivity are similar for both species.Benefits of specialization in E. atropurpurea include reduced costs for stem and leaf hair production, higher growth rates during the rainy season and the ability to grow beneath canopies of some larger arborescent species. Costs of specialization include lower growth rates during the dry season, great susceptibility to insect predation and restriction to low elevation, mesic sites.     

Drosophila mutant with a transducer defect

The trp is a conditional phototransduction mutant of Drosophila. Direct electrical measurements and shot noise analysis suggest that a prolonged intense light causes in the mutant a reduction in the quantum efficiency for quantum bump production that does not arise from bleaching of the visual pigment. This effect depends on the duration of the light and only weakly on its intensity. In the normal fly, an intense blue light that shifts the visual pigment from rhodopsin to metarhodopsin, induces an excitatory process manifested by a prolonged depolarizing after potential (PDA). In the mutant, the PDA has a small amplitude and bump noise is superimposed on the response. It can thus be shown that the excitatory process underlying the PDA is also present in those trp mutants where the PDA voltage response is small or absent. It is suggested that the absence of the PDA voltage response in the mutant is probably due to a defect in an intermediate process, which links the excitatory process to the membrane conductance change.Presented at the EMBO-Workshop on Transduction Mechanism of Photoreceptors, Jülich, Germany, October 4–8, 1976     

Functional membrane vesicles from the nervous system of insects: I. Sodium- and chloride-dependent γ-aminobutyric acid transport

(1) A synaptosomal fraction obtained from locust nervous tissue has been shown to possess an active γ-aminobutyric acid transport mechanism. This activity is preserved and even enriched by the membrane vesicles derived from osmotically shocked synaptosomes. (2) Electron-microscopy examination indicates that the above membrane vesicles are derived predominantly from the neuronal plasma membrane and are devoid of any internal cellular organelles and components. Active transport of γ-aminobutyric acid into these vesicles has been demonstrated with artificially imposed ion gradients as the sole energy source. (3) γ-Aminobutyric acid transport can be driven by an Na⁺ gradient (out>in) and /or by a gradient of Cl^? (out>in). This process is absolutely dependent on the simultaneous presence of both types of ion in the external medium. The stimulation of the process by valinomycin indicates that γ-aminobutyric acid transport is an electrogenic process which is stimulated by a membrane potential (interior negative).     

Bud proliferation and plant regeneration in liquid-cultured philodendron treated with ancymidol and paclobutrazol

Philodendron plants propagated in liquid shake or bioreactor cultures proliferated profusely in the presence of paclobutrazol (PAC) and to a lesser extent in the presence of ancymidol (ANC). The growth retardants inhibited leaf development and induced the formation of bud clusters. Short transient treatments with low concentrations (1.7–3.4 M) of the growth retardants limited leaf growth and proliferation to a lesser extent than higher concentrations (6.8–17 M). The growth retardants had a carryover dwarfing effect in the semi-solid hardening medium, which was more pronounced at the higher concentrations or prolonged exposure periods. Regenerated plants resumed normal growth 3–6 weeks after transplanting. Treatment with growth retardants may become a useful method in the prevention of abnormal leaf growth in large-scale liquid cultures, as well as in enhancing bud proliferation.     

Measurement of stagnancy in a pipe line using a radioactive tracer and labelled bacteria

Summary A stainless steel T joint was used to simulate stagnant volume in a pipe-line. Residence time distribution in the lines was measured using a radiotracer (Cr⁵¹) which emitted radiation. The radiation was measured externally to the pipe line. From the experimental data the dead volume of the system was calculated. The effect of the depth of T and flow velocity on dead volume was evaluated. Labelled bacteria were used in some experiments instead of chromium. No significant difference in behavior between ionic chromium and bacteria labeled with chromium was found.     

Purification of peptidyl-tRNA on benzoylated DEAE-cellulose columns.

The o-nitrophenylsulfenyl group, and amino protecting group in the chemical synthesis of peptidyl-tRNA was used to attach newly synthesized peptidyl-tRNA to a benzoylated DEAE-cellulose column. This facilitated the isolation of a highly purified specific tRNA with a well defined peptide chain.