Unidirectional Processes Research Articles

Tandem Duplication of rab Genes Followed by Sequence Divergence and Acquisition of Distinct Functions in Trypanosoma brucei

The Ras superfamily of small G proteins governs unidirectional cellular processes by virtue of GTP hydrolysis and concomitant conformational changes, which are in turn regulated by a number of accessory factors. Members of the Rab subfamily are important for correct targeting and fusion of intra-organellar vesicles loaded with trafficking proteins and lipids. During evolution from a prototype gene, novel functions may be acquired by duplicated daughter genes; for Rab proteins, this can be tested by location, which is specifically related to the function of each Rab. We have found an example of two rab genes in Trypanosoma brucei (trab genes) that clearly arose by tandem duplication, being highly related to each other and remaining juxtaposed in the genome, whose products have dramatically different subcellular locations, indicative of discrete functions. These two trab genes, isolated on a single genomic clone, are separated by a short intervening sequence and are in a head-to-tail orientation. The nucleotide sequences of the open reading frames and intervening sequence were determined and show that the genes are paralogues, probably arising from an ancient tandem duplication. Both genes are most homologous to ypt1 and sec4 in the Saccharomyces cerevisiae genome, while phylogenetic reconstruction indicates that although they have clearly diverged, the proteins are more closely related to each other than to other Rab protein sequences available in the data base. Immunofluorescence microscopy, using antibodies raised against the recombinant Trab proteins, clearly demonstrates that the native Trab proteins have completely distinct subcellular locations in the trypanosome. Trab1p is present in a widespread reticular location similar to BiP, suggesting an endoplasmic reticulum location, while Trab7p is observed in a discrete structure adjacent to the kinetoplast. Most interestingly, the Trab7p-positive compartment also appears to divide at the same time, or just prior to, the kinetoplast, i.e. early in mitosis, suggestive of association with structures in the flagellar pocket region. An estimate of the divergence time indicates that the trab1/trab7 duplication occurred approximately 100 million years ago, and therefore, the persistence of this pair suggests an essential role in the survival of T. brucei.

Self-similar regime of thermally controlled solidification of binary melts

When heat supply to a binary melt at its outer boundary is absent, macrokinetics of solidification are governed by progressive cooling of the melt rather than by withdrawal of an admixture. Because the former process is much faster than the latter one, a metastable region of concentrational supercooling arises and has time to expand before the ingot surface noticeably changes its position. This leads to bulk crystallization within such a region prior to solidification at the surface. If crystalline grains are forming and growing rapidly enough, the two-phase region is practically at the state of thermodynamic equilibrium. This case is considered under the assumptions that the melt phase diagram consists of straight liquidus and solidus lines with one eutectic point and that the physical parameters are constant. A simple self-similar solution of relevant equations is obtained which approximately describes unidirectional processes.

Identification of cholate as a shared substrate for the unidirectional efflux systems for methotrexate in L1210 mouse cells

The bidirectional transport properties of cholate have been examined in leukemic L1210 mouse cells and compared with the transport of methotrexate. The cell entry of [ 3H]cholate was Na +-independent, linear with increasing concentrations of substrate, enhanced by decreasing pH, and uneffected by excess unlabeled cholate or by various anion-transport inhibitors and hence had the characteristics of passive diffusion or a pH-dependent mediated process with a high K t for cholate. The efflux of [ 3H]cholate, however, could be attributed to carrier-mediated and energy-dependent transport. Efflux was rapid ( t 1 2 = 1.5 min ) and could be increased with glucose and decreased with metabolic inhibitors, and it was inhibited by various compounds including bromosulfophthalein, probenecid, prostaglandin A 1, reserpine, verapamil, quinidine, diamide, 1-methyl-3-isobutylxanthine and vincristine. The most potent inhibitor was prostaglandin A 1, which reduced efflux by 50% at a concentration of 0.10 μM. Half-maximal inhibition by vincristine occurred at 4.8 μM. The maximum extent of inhibition with most of the inhibitors was 95%, although a lower value was observed with bromosulfophthalein (85%). When cholate efflux was compared with the efflux of methotrexate, both processes responded similarly to changes in the metabolic state of the cell. Moreover, the various inhibitors of cholate efflux also inhibited the efflux of methotrexate and the same concentration of each inhibitor was required for half-maximal inhibition of both processes. The efflux of folate and urate also proceeded via outwardly directed, unidirectional processes which were sensitive to bromosulfophthalein and probenecid. The results suggest that L1210 cells have the capacity for the unidirectional extrusion of cholate, methotrexate and probably other large, structurally dissimilar organic anions and that this efflux occurs via two or more very similar transport systems with a broad anion specificity. The function of an organic anion efflux system in vivo may be to facilitate the extrusion of cytotoxic metabolic anions which are too large to exit via the general anion-exchange carrier of these cells. Similarities in inhibitor specificity were also apparent between unidirectional anion efflux in L1210 cells and the drug efflux pump which is over-produced in cells with multidrug resistance.

Unified approach to the temporal evolution of surface profiles in solid etch and deposition processes

The differential equation describing the temporal evolution of solid surfaces subject to etching or depositon is derived. Its general properties are discussed and solutions to particular problems are obtained. The differential equation explicitly shows the evolution of the shape of the surface to be the product of a geometric factor which is common to all etch/deposition processes and a rate factor which depends on the physics of the process considered. The rate factor must in general be derived from first principles. Here we limit consideration to rate factors that describe isotropic and unidirectional processes, as well as linear combinations of these two processes. The properties of the evolution of surface profiles are studied in detail for each case. A unidirectional etch with a rate factor dependent on the local surface curvature is shown to produce good agreement with the observed shapes of deep isolation trenches in silicon. Finally, the surface evolution equation is used to expore the ability of certain processes to smooth and polish initially rough surfaces.

Heat Transfer During Melting and Solidification of Metals

Recent advances in the understanding of melting and solidification heat transfer in metals and alloys are discussed. Since heat transfer is generally the rate-determining process, the emphasis in the paper is on fundamental heat transfer processes during solid–liquid phase transformation and comparison between mathematical-numerical model predictions with experimental data. After a brief discussion of theoretical considerations, unidirectional and multidirectional melting and solidification processes are reviewed. The important role played by buoyancy-driven fluid flow is discussed and problem areas needing research attention are identified.

Observational Study on the Dendritie Growth of Al–Mg Single Crystals by Real-Time X-Ray Topography

Real-time X-ray topography has been applied to a study of dendritic growth. Unidirectional melting and solidification processes of Al–Mg single crystals containing 0.5, 2.0 and 4.0 at%Mg were observed by real-time X-ray topography. Observations have been made on the following subjects: (1) sequential growth and morphology of dendrite arms during solidification as a function of the growth rate; (2) morphological changes of dendrite arms as a function of the Mg content; (3) morphological changes and solute redistribution during cooling and isothermal annealing after solidification; and, (4) observation of the melting process of a previously grown dendrite. Some valuable information which cannot be obtained by the conventional “ex post fact” method has been obtained by real-time X-ray topography.

The design and use of a hydraulically operated upward pressure-jump

The construction of hydraulically operated upward pressure-jump is described. Previous instruments with a comparable rate of pressration used helium gas to pressurize an observation cell to approximately half of the operating pressure reached with the present design. The above instrument, which can pressurize the observation cell in 1.8–3.8 ms. is safe to use and has a maximum working pressure of 30 MPa (300 atm). The device is compact in design and can easily be fitted to any observation cell capable of withstanding the transient change in pressure and of effectivekt damping cell resonances. The instrument finds specific application in the study of macromolecular equilibria with a large difference in volume between the equilibrium partners. This allow the system to be perturbed far from the equilibrium position at atmospheric pressure; the relaxations obtained can be analysed as essentially unidirectional processes. Kinetic data for the reaction would be obtained from experiments in a conventional downward pressure-jump. A study on the kinetics of the self-assembly of the myosin thick-filament is presented as a practical example.

Sulphur isotope rations in late and early Precambrian sediments and their implications regarding early environments and early life

The stable isotopes of sulphur are fractionated in equilibrium and unidirectional processes in the earth's crust and biosphere. By far the most important of these processes occur in the biological sulphur cycle characterized by the activity of sulphur oxidizing and reducing microbiota. In particular, the dissimilatory reduction of sulphate to hydrogen sulphide by anaerobic bacteria leads to isotope effects of from 0 to ∼60‰, the magnitude of the effect depending largely on metabolic rates. Actual isotope ratio (δ3 4S) patterns in sediments depends, therefore, on environmental conditions and the nature of sulphate reservoirs during reduction. Sulphur isotope ratios can and have been used to trace environmental conditions, sources, and modes of formation of certain Phanerozoic deposits.

Estimation of the longitudinal dispersion and sorption coefficients in saturated soils by straight-line methods / Recherche des coefficients de la dispersion longitudinale et de la sorption au milieu du sol saturé en utilisant des ‘straight lines’

Abstract This paper describes a graphical method for the estimation of the longitudinal dispersion and sorption coefficients K L and a of the unidirectional migration processes of pollutants in saturated homogenous soils. The migration process is regarded (comparable to the classical pumping test analysis) not only as a process in space with t = t i = constant, but also as a temporal process with x =x i = constant. This method is demonstrated by several laboratory experiments with Cl− and Ca2+ ions regarded as pollutants. It is also shown that the migration process calculated with K L and a estimated by this method, corresponds excellently with the measured data.

Polarity of actin at the leading edge of cultured cells.

VERTEBRATE non-muscle cells are known to contain considerable amounts of actin and myosin1–3, but the mechanisms underlying their motility have yet to be elucidated. Various theories have been proposed1,4–7 to explain the well known phenomena of cell migration, membrane ruffling and unidirectional growth processes, different emphasis being placed on the involvement of membrane components and contractile filament assemblies. These hypotheses have been limited, however, by the lack of information about the detailed structural organisation of the motile regions of the cytoplasm. As one approach to this problem we have developed procedures for the direct observation of the filamentous components of the lamella regions of cultured cells in the electron microscope8,9. The method, similar to that adopted by Brown et al.10, consists of the negative-staining of cells grown directly on electron microscope grids after removal of the cell membranes with Triton X-100. By this means, we demonstrate here a single polarity of actin at the leading edge of cultured cells, and consider its implications with regard to cell motility.

Wider application of multipass systems theory. Part 1: Multimachine and multicell systems

A general time-(distance-) domain representation of unidirectional multipass processes is presented which describes all previously identified examples.1 It is then shown that systems of multiple machines in which the signal flow is unidirectional could be simulated by the repeated simulation of a single machine, and that such a procedure is described by the same general time-domain formulation. The stability of this multipass-simulation sequence, and hence that of the multimachine system, can therefore be investigated analytically using the frequency-response approach previously applied1 to real life multipass processes. It is demonstrated how the approach can be applied also to discretised spatially-distributed processes, provided again that signal flow is unidirectional. The modelling and analysis techniques presented in the paper are shown to be unsuitable, however, in the presence of either counterflow signals or feedback controllers which are not of a local nature and uniformly distributed along the process. The identification of these limitations is an important objective and provides the motivation and starting point for a companion paper in which the multipass-systems approach is adapted to cope with this much wider class of processes.

Faradaic reaction noise

Expressions are derived for the small signal source impedance and the associated mean square noise voltage in the case of an irreversible redox reaction suitable for use when noise signals are studied by a novel cross-modulation method involving modulation of the electrochemical noise by an applied modulating signal. The analysis is based on the large signal aperiodic circuit for the faradaic reaction, the elementary sources of noise being evaluated by the application of the Nyquist, equation to diffusion resistance and a new equation, the semi-Nyquist equation, to resistance connected with unidirectional charge transfer processes. It is shown that the noise component of the current for a totally diffusion-controlled process is that predicted by the Schottky equation in agreement with results reported by Tyagai [2] and Levich [13]. The new most general form of the aperiodic circuit for a simple redox reaction contains a transformer, diodes and current sources in addition to the more usual speriodic circuit components but can be simplified somewhat with the aid of transitors.

Faradaic reaction noise

Expressions are derived for the small signal source impedance and the associated mean square noise voltage in the case of an irreversible redox reaction suitable for use when noise signals are studied by a novel cross-modulation method involving modulation of the electrochemical noise by an applied modulating signal. The analysis is based on the large signal aperiodic circuit for the faradaic reaction, the elementary sources of noise being evaluated by the application of the Nyquist, equation to diffusion resistance and a new equation, the semi-Nyquist equation, to resistance connected with unidirectional charge transfer processes. It is shown that the noise component of the current for a totally diffusion-controlled process is that predicted by the Schottky equation in agreement with results reported by Tyagai [2] and Levich [13]. The new most general form of the aperiodic circuit for a simple redox reaction contains a transformer, diodes and current sources in addition to the more usual speriodic circuit components but can be simplified somewhat with the aid of transitors.

On the localization of the origin of DNA replication in E. coli

The process of DNA replication in procaryotes with a circular chromosome is analyzed in terms of a stochastic model including the following features: (1) heterogeneity in the rate of DNA synthesis from cell to cell in a culture, (2) any degree of positive or negative correlation between mother and daughter cells and (3) drift of the origin and terminus in a chromosome from one generation to the next over a specified region or set of points in the chromosome. The model is applied to experimental data on E. coli cells in balanced growth, assuming the bidirectional replication process can be simulated by independent unidirectional processes along each arm. Comparison of calculated recovery profiles for label in a density pulse experiment reveals that there is remarkable latitude for drift of the origin from one generation to the next, with succeeding rounds capable of initiation at any site within a region of one half the total chromosomal length. The marker frequencies of genes at different positions on the chromosome measured by “equilibrium” assays similarly can be reconciled with unidirectional or bidirectional processes with a wandering origin. If as is suggested by results from kinetic experiments on populations with aligned chromosomes replication is bidirectional with a unique fixed site of origin, the results of the label recovery experiments are inconsistent with the available evidence for heterogeneity in replication times and growth rates.

SOME BIOSTRATIGRAPHICAL CONCEPTS

Time can be measured by observing unidirectional and nonreversible processes, or processes that proceed with a fixed periodicity. Geologic time is measured by observations of rock features that give evidence of previous existence of unidirectional or periodically repeated processes. Periodically recurrent processes do not provide world-wide time standards. The only natural processes that are of a unidirectional and nonreversible nature and that leave universally occurring testimony in the rocks are radioactive decay and evolution of life. The study of past life forms and their distribution in the rocks (paleontology and biostratigraphy) provides a reference system for determining the order of succession of geologic events from the Cambrian to the Recent. Radioactive dating supplies an approximative reference grid of dates in terms of absolute time. The biostratigraphic zone, which is an assemblage of rocks containing a defined fossil fauna or flora, is the basic and generally the smallest biostratigraphic unit on which world-wide correlations can be established. Application of biostratigraphy to geochronology is known as biochronology. Different plant and animal phyla change in biochronological value during their development, and at different periods during earth history, different groups of animals and plants attained varying degrees of biochronologic importance. The biochronological standard, based for each period on biostratigraphically important groups of fossils, is known as the orthochronologic standard. The basic unit of the orthochronologic standard is the time unit corresponding to the deposition of a biostratigraphic zone. A multiple biostratigraphic terminology is found unnecessary. Zone is accepted as the basic biostratigraphic unit, moment is recommended for the time unit during which a zone was deposited. Instant is suggested for a true “time plane” in stratigraphy. Biochron is suggested for the duration or survival time of taxonomic units, down to the species.

SULPHUR ISOTOPE EFFECTS IN THE BISULPHITE ADDITION REACTION OF ALDEHYDES AND KETONES: II. BOND-FORMATION EFFECT

The relative rates of formation of C12—S32 and C12—S34 bonds in the bisulphite addition reaction of heptanal, benzaldehyde, anisaldehyde, and 2-heptanone have been measured and found to approximate unity. This result has been interpreted in terms of the Bigeleisen treatment of isotope effects in unidirectional processes.