Some comments on re-estalishability

The present note consists of two separate but related parts. In the first, a new graphtheoretic proof is presented that an (ℳ,R)-system must always contain a nonreestablishable component. The second considers some questions concerning the relation between re-establishability and the time-lag structure in (ℳ,R)-systems. It is supposed that the reader is familiar with the terminology of the author's previous work on (ℳ,R)-systems, particularly R. Rosen,Bull. Math. Biophysics,20, 245–260, 1958.     

Abstract biological systems as sequential machines II: Strong connectedness and reversibility

It was previously shown that the abstract biological systems called. (ℳ, ℛ)-systems could be regarded formally as sequential machines, and that when this was done, the reversibility of environmentally induced structural changes in these systems was closely related to the strong connectedness of the corresponding machines. In the present work it is shown that the sequential machines arising in this way are characterized by the property that the size of the input alphabet is very small compared with the size of the set of states of the machine. It is further shown that machines with this property almost always fail to be strongly connected. Therefore, it follows that one of the following alternatives holds: either most environmentally induced structural alterations are not environmentally reversible, or else many mappings in the category from which the (ℳ, ℛ)-systems are formed must not be physically realizable.     

Abstract biological systems as sequential machines

It is shown that a rather close relationship exists between the (ℳ,ℛ)-systems, defined previously as prototypes of abstract biological systems, and the sequential machines which have been studied by various authors. The theory of sequential machines is reformulated in a way suitable for its application to the study of the intertransformability of (ℳ,ℛ)-systems as a result of environmental alteration. The important concept of strong connectedness is most useful in this direction, and is used to derive a number of results on intertransformability. Some suggestions are made for further studies along these lines.     

Functionality of biphenyl 2,3-dioxygenase components in naphthalene 1,2-dioxygenase

Naphthalene 1,2-dioxygenase (Nap dox) and biphenyl 2,3-dioxygenase (Bph dox) are related enzymes that have differentiated during evolution as their specificity has changed. Although their component arrangement is similar, the structure of each component has been modified quite extensively. The purpose of this work was to determine the catalytic capacity of purified Nap dox toward chlorobiphenyls and to investigate the functionality of Bph dox components in the Nap dox system. Both enzyme systems were purified by affinity chromatography as histidine-tagged fused proteins. Data show for the first time that Nap dox can catalyze the oxygenation of all three monochlorobiphenyl isomers, but it is unable to hydroxylate 2,5-, 2,2′-, 3,3′-, 4,4′-di- and 2,2′,5,5′-tetrachlorobiphenyl. The rates of cytochrome c reduction by the ferredoxin components of the two enzymes were identical when the Bph dox reductase component was used in the assay, showing an efficient electron transfer between the Bph dox reductase component and the Nap dox ferredoxin. However, when the Bph dox ferredoxin was used to reconstitute a hybrid Nap dox, the enzyme was only 22% as active as the parental enzyme. These data are discussed in terms of the potential use of Nap dox for the development of enhanced chlorobiphenyl-degrading dioxygenases. Received: 15 October 1998 / Received revision: 21 January 1999 / Accepted: 31 January 1999     

Conformational change of human lens insoluble α-crystallin

Human lens α-crystallin becomes progressively insoluble with age and is the major crystallin component in the water-insoluble (WI) fraction. The mechanism that causes the originally water-soluble (WS) α-crystallin to become insoluble is unknown. A conformational change by chemical modification may be the cause, but the nature of insolubility renders it impossible to study protein conformation in the WI fraction by most spectroscopic measurements. In the present study, α-crystallin in the WI fraction was extracted by urea and reconstituted to a folded protein by dialysis. The refolded urea-soluble (US) α-crystallin was compared with WS α-crystallin. The US α-crystallin has a greater amount of polymeric species, but fewer degraded subunits than the WS α-crystallin as shown by SDS-PAGE and Western blot. Circular dichroism (CD) measurements indicate that they have the same secondary structure but a different tertiary structure, possibly a partial unfolding in the US α-crystallin. This is supported by fluorescence measurements: Trp residues are more exposed and protein has a more-hydrophobic surface in the US than in the WS α-crystallin. Blue fluorescence further indicates that the US α-crystallin has a greater amount of pigment than the WS α-crystallin. Together, these results indicate that the US α-crystallin is a chemically and conformationally modified protein.     

Conformational change of human lens insoluble α-crystallin

Human lens α-crystallin becomes progressively insoluble with age and is the major crystallin component in the water-insoluble (WI) fraction. The mechanism that causes the originally water-soluble (WS) α-crystallin to become insoluble is unknown. A conformational change by chemical modification may be the cause, but the nature of insolubility renders it impossible to study protein conformation in the WI fraction by most spectroscopic measurements. In the present study, α-crystallin in the WI fraction was extracted by urea and reconstituted to a folded protein by dialysis. The refolded urea-soluble (US) α-crystallin was compared with WS α-crystallin. The US α-crystallin has a greater amount of polymeric species, but fewer degraded subunits than the WS α-crystallin as shown by SDS-PAGE and Western blot. Circular dichroism (CD) measurements indicate that they have the same secondary structure but a different tertiary structure, possibly a partial unfolding in the US α-crystallin. This is supported by fluorescence measurements: Trp residues are more exposed and protein has a more-hydrophobic surface in the US than in the WS α-crystallin. Blue fluorescence further indicates that the US α-crystallin has a greater amount of pigment than the WS α-crystallin. Together, these results indicate that the US α-crystallin is a chemically and conformationally modified protein.     

Nanocomposite regeneration systems for wound healing

The regeneration system “Biokol” based on the principles of combining synthetic and natural biopolymers has been investigated. The wound dressing consists of “large” (200–250 nm) particles of a synthetic biopolymer and a gel component, which consists of “small” polysaccharide elements 10–20 nm in size. The system can be used both separately and in combination with the gel complex and cell cultures. In properties (vapor and gas permeability, mechanical properties, conductivity, resistance to microbes, etc.), it corresponds to the upper layer of the skin. When applied to the wound, the dressing changes its adhesiveness: first, owing to its hydrophilicity and low hydrophobicity, it closely adheres to the wound surface, and after some time, which corresponds to the time the polysaccharide complex is released from the dressing, it becomes hydrophobic and easily separates from the wound. Owing to these properties, the system can be used at all stages of wound healing.     

Neutron versus Á-ray risk estimates

While it is recognized that neutrons contributed to the excess cancer incidence and mortality among the atomic bomb survivors in Hiroshima, there is no possibility to deduce the magnitude of this contribution from the data. This remains true even if the neutron doses in the dosimetry system DS86 are corrected upwards in line with recent neutron activation measurements. In spite of this fact, important information can be obtained in the form of an inverse relation of the risk coefficients for γ-rays and neutrons. Such an interrelation must apply because the observed excess incidence or mortality is made up of a γ-ray and a neutron component; increased attribution to neutrons decreases the attribution to photons. Computations with the uncorrected and the corrected DS86 are performed for the mortality and the incidence of solid tumors combined. They refer to doses up to 2 Gy and employ the constant relative risk model and a linear-quadratic dose dependence with variable ratio – the neutron relative biological effectiveness (RBE) at low doses – of the linear component for neutrons and γ-rays. In line with past analyses, no quadratic component is obtained with the uncorrected DS86, but it is seen, even in these calculations, that the assumption of increased neutron RBEs does not translate into proportional increases of the risk coefficients of neutrons, because it leads to substantially reduced risk estimates for γ-rays. Calculations with the corrected dosimetry bring out this reciprocity even more clearly. High values of the neutron RBE reduce – in line with recent suggestions by Rossi and Zaider – the risk estimates for γ-rays substantially. Even a purely quadratic dose relation for γ-rays is consistent with the data; it requires no major increase of the nominal risk coefficients for neutrons over the currently assumed values. The cancer data from Hiroshima can still provide `prudent' risk estimates for photons, but with the corrected DS86, they do not prove that there is a linear component in the dose dependence for photons. Received: 20 January 1997 / Accepted in revised form: 14 March 1997     

Effect of Abrading the Cuticle Using Emery

Abrading the cuticle is sometimes required in order to measureauxin-stimulated acidification. We have determined, however,that the process should be used with caution. The diameter ofthe Edmund Scientific emery No. 305 particles was found to benear 40 times greater than cuticle thickness (0 –14 µm).Thus it was not surprising to find that even gentle abrasionmight cause damage to the epidermal cells. The resultant woundingmay complicate interpretastion of experimental results becausethe healing process shown to follow the wounding is likely tohave an auxin – regulated component. Experiments shouldbe designed to differentiate wound – related auxin effectsfrom elongation-related auxin effects.     

Evolution of the Aldose Reductase-Related Gecko Eye Lens Protein ρB-Crystallin: A Sheep in Wolf's Clothing

ρB-crystallin (AJ245805) is a major protein component (20%) in the eye lens of the gecko Lepidodactylus lugubris. Limited peptide sequence analysis earlier revealed that it belongs to the aldo-keto reductase superfamily, as does the frog lens ρ-crystallin. We have now determined the complete cDNA sequence of ρB-crystallin and established that it is more closely related to the aldose reductase branch of the superfamily than to frog ρ-crystallin. These gecko and frog lens proteins have thus independently been recruited from the same enzyme superfamily. Aldose reductase is implicated in the development of diabetic cataract in mammals, and, if active, ρB-crystallin might be a potential risk for the gecko lens. Apart from a replacement 298 Cys → Tyr, ρB-crystallin possesses all amino acid residues thought to be required for catalytic activity of the aldose reductases. However, modeling studies of the ρB-crystallin structure indicate that substrate specificity and nicotinamide cofactor affinity might be affected. Indeed, neither recombinant ρB-crystallin nor the reverse mutant 298 Tyr → Cys showed noticeable activity toward aliphatic and aromatic substrates, although cofactor binding was retained. Various other oxidoreductases are known to be recruited as abundant lens proteins in many vertebrate species; ρB-crystallin demonstrates that an aldose reductase-related enzyme also can be modified to this end. Received: 18 July 2000 / Accepted: 3 November 2000     

Time lags in algal growth: generality, causes and consequences

Lagged algal growth responses are argued to be general phenomenaoccurring, whenever algal growth is enhanced by some growthstimulus, in all aquatic environments supporting planktonicor epiphytic communities. Lag phenomena can be accounted forthrough a hierarchical conception of microalgal ecology, involvingthe partition of lagged responses into an ‘intrinsic’component, due to biochemical reorganization needed for rapidcell division, and ‘extrinsic’ component, due tovariability in algal growth and loss rates that result in alag between enhanced cell division and population growth. Theplausibility of such an ‘extrinsic’ lag componentwas confirmed by simulation modelling, which also revealed thatlag duration should decrease exponentially with increasing growthrate, and increase linearly with increasing variability in growthrate. Lag phenomena in algal growth may be of paramount importancein structuring aquatic ecosystems, because it results in thetemporal (and spatial, in systems with important advective components)uncoupling between growth stimuli and algal growth. Further,lag phenomena impinge directly upon the interpretation of fielddata relating algal growth to contemporary environmental conditions.     

What history tells us

The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists — and in particular biologists — can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.     

Universal primers for the PCR-mediated amplification of DNA β

DNA β is an approx 1350 nucleotide, single-stranded DNA molecule which has been shown to be associated with some monopartite geminiviruses of the genus Begomovirus. This component requires the helper begomovirus for replication in the cells of host plants and for insect transmission, possibly by trans-encapsidation. Sequence comparisons of the two available DNA β sequences has identified a highly conserved region upstream of a predicted hairpin structure. Abutting primers designed to this conserved region allows PCR-mediated amplification of the full-length DNA β component from total nucleic acid extracts isolated from infected plants originating from a variety of geographically distinct sources and host plants.     

Use of zinc ions for fractionation of pig γ-G-globulin and its structural subunits

The different behaviour of the two fractions of pig γ-G-globulin prepared by interaction with zinc ions during oxidative sulphitolysis is described. The γ-G-globulin fraction which is not precipitated by zinc ions is dissociated more readily, as seen from the finding that, unlike the other fraction, it contains practically no incompletely dissociated molecules. Fractions of the light chains, with different molecular weights, were also isolated from this fraction. A technique was elaborated for separation of the component with H antigenic specificity which is present in the light chain preparation. Detailed study of this component showed that it is probably part of the heavy chain. The origin and formation of the component is discussed.     

Single-event-related potential analysis by means of fragmentary decomposition

 A recently developed fragmentary decomposition method is employed to analyse single-trial event-related potentials (ERPs), thereby extending the traditional method of averaging. Using a conventional auditory oddball paradigm with 40 target stimuli, single-trial ERPs in 40 normal subjects were analysed for midline scalp (Fz, Cz and Pz) recording sites. The normalization effect, reported in our previous study of eye blink EMGs and proposed to be a characteristic property of a wide class of non-stationary physiological processes, was found to apply to these single-trial ERPs. Fragmentary decomposition of single-trial ERPs may be regarded as re-statement of the normalization effect. This allows both pre-stimulus EEGs and post-stimulus ERPs to be regarded as overlapping generic mass potentials (GMPs), with a characteristic Gaussian amplitude spectrum. On theoretical and empirical grounds we uniquely deduce a model GMP using an introduced “bud” function, and physically support it by the resting and transient conditions. The model takes into account the shape of the component, which suggests a simple relationship between the peak latency and the time of the component onset. Given that GMPs may be manipulated and sorted out, we present principles of the fragmentary synthesis, i.e. probabilistic ERP reconstructions on the basis of individual and ensemble properties of its identified components. Summarizing the component quantification in the form of the dynamic model provides for the first time the opportunity to quantify all significant components in single-trial ERPs. This method of single-trial analysis opens up new possibilities of exploring the dynamical ERP changes within a recording trial, particularly in late component “cognitive” paradigms. Received: 29 August 2000 / Accepted in revised form: 5 February 2001     

The Out-of-India hypothesis: What do molecules suggest?

The remarkable geological and evolutionary history of peninsular India has generated much interest in the patterns and processes that might have shaped the current distributions of its endemic biota. In this regard the “Out-of-India” hypothesis, which proposes that rafting peninsular India carried Gondwanan forms to Asia after the break-up of Gondwana super continent, has gained prominence. Here we have reviewed molecular studies undertaken on a range of taxa of supposedly Gondwanan origin to better understand the Out-of-India scenario. This re-evaluation of published molecular studies indicates that there is mounting evidence supporting Out-of-India scenario for various Asian taxa. Nevertheless, in many studies the evidence is inconclusive due to lack of information on the age of relevant nodes. Studies also indicate that not all Gondwanan forms of peninsular India dispersed out of India. Many of these ancient lineages are confined to peninsular India and therefore are relict Gondwanan lineages. Additionally, for some taxa an “Into India” rather than “Out-of-India” scenario better explains their current distribution. To identify the “Out-of-India” component of Asian biota it is imperative that we understand the complex biogeographical history of India. To this end, we propose three oversimplified yet explicit phylogenetic predictions. These predictions can be tested through the use of molecular phylogenetic tools in conjunction with palaeontological and geological data.     

Modelling the Components of Plant Respiration: Representation and Realism

This paper outlines the different ways in which plant respirationis modelled, with reference to the principles set out in Cannelland Thornley (Annals of Botany85: 55–67, 2000), firstin whole-plant ‘toy’ models, then within ecosystemor crop models using the growth-maintenance paradigm, and finallyrepresenting many component processes within the Hurley Pasture(HPM) and Edinburgh Forest Models (EFM), both of which separateC and N substrates from structure. Whole-plant models can beformulated so that either maintenance or growth respirationtake priority for assimilates, or so that growth respirationis the difference between total respiration and maintenanceassociated with the resynthesis of degraded tissues. All threeschemes can be converted to dynamic models which give similar,reasonable predictions of plant growth and respiration, butall have limiting assumptions and scope. Ecosystem and cropmodels which use the growth-maintenance respiration paradigmwithout separating substrates from structure, implicitly assumethat maintenance respiration is a fixed cost, uncoupled to assimilatesupply, and use fixed rate coefficients chosen from a rangeof measured values. Separation of substrates in the HPM andEFM enables estimates to be made of respiration associated withlocal growth, phloem loading, ammonium and nitrate N uptake,nitrate reduction, N₂fixation and other mineral ion uptake,leaving a ‘residual maintenance’ term. The lattercan be explicitly related to C substrate supply. Simulated changesin grassland respiration over a season and forest respirationover a rotation show that the ratio of total respiration togross canopy photosynthesis varies within the expected limitedrange, that residual maintenance accounts for 46–48% oftotal respiration, growth 36–42%, phloem loading 10–12%and the other components for the small remainder, with the ratiosbetween components varying during a season or forest rotation.It is concluded that the growth-maintenance approach to respiration,extended to represent many of the component processes, has considerablemerit. It can be connected to reality at many points, it givesmore information, it can be examined at the level of assumptionsas well as at the level of predictions, and it is open to modificationas more knowledge emerges. However, currently, there are stillparameters that require adjustment so that the predictions ofthe model are acceptable. Copyright 2000 Annals of Botany Company Respiration, photosynthesis, growth, maintenance, substrate, N uptake, mineral uptake, phloem loading, model.     

Hourglass and rhythmic components of photoperiodic time measurement in the pitcher plant mosquito, Wyeomyia smithii

The mosquito, Wyeomyia smithii, enters a larval dormancy or diapause that is initiated, maintained, and terminated by photoperiod. The median or critical photoperiod regulating diapause increases from 12 h of light per day along the Gulf of Mexico, USA (30° N), to over 15 h in southern Canada (49° N). Photoperiodic time measurement in W. smithii comprises both rhythmic and hourglass (interval timer) components. Using interrupted-night and resonance experiments, we show that both the rhythmic and hourglass components are prominent in the southern (ancestral) populations and that the influence of the rhythmic component declines with increasing latitude, while the hourglass component remains strong in northern (derived) populations. Previously, it has been shown that the genetic differences in critical photoperiod between northern populations and their southern ancestors involve not only the additive (independent) effects of genes, but also gene-gene interaction (epistasis). We therefore conclude that adaptive evolution of W. smithii has probably involved the progressive epistatic masking of the ancestral rhythmic component resulting in photoperiodic time measurement in northern populations accomplished principally through a day-interval timer. A comparison of W. smithii with previous studies indicates that the decline in critical photoperiod with increasing latitude represents an overall decrease in response to light rather than a shift in the timing of photosensitivity among arthropods in general. We propose that the underlying functional components of photoperiodic time measurement, as well as the overt photoperiodic response, are either homologous or are themselves responding directly to selection over latitudinal gradients in seasonality. Received: 18 May 1998 / Accepted: 14 September 1998