An evolutionary analytical model of a complementary circular code simulating the protein coding genes, the 5′ and 3′ regions

The self-complementary subset ∪{AAA,TTT} with = {AAC, AAT, ACC, ATC, ATT, CAG, CTC, CTG, GAA, GAC, GAG, GAT, GCC, GGC, GGT, GTA, GTC, GTT, TAC, TTC} of 22 trinucleotides has a preferential occurrence in the frame 0 (reading frame established by the ATG start trinucleotide) of protein (coding) genes of both prokaryotes and eukaryotes. The subsets ∪{CCC} and ∪{GGG} of 21 trinucleotides have a preferential occurrence in the shifted frames 1 and 2 respectively (frame 0 shifted by one and two nucleotides respectively in the 5′-3′ direction). and are complementary to each other. The subset contains the subset which has the rarity property (6 × 10⁻⁸) to be a complementary maximal circular code with two permutated maximal circular codes and in the frames 1 and 2 respectively. is called a C³ code. A quantitative study of these three subsets in the three frames 0, 1, 2 of protein genes, and the 5′ and 3′ regions of eukaryotes, shows that their occurrence frequencies are constant functions of the trinucleotide positions in the sequences. The frequencies of in the frame 0 of protein genes are 49, 28.5 and 22.5% respectively. In contrast, the frequencies of in the 5′ and 3′ regions of eukaryotes, are independent of the frame. Indeed, the frequency of in the three frames of 5′ (respectively 3′) regions is equal to 35.5% (respectively 38%) and is greater than the frequencies and , both equal to 32.25% (respectively 31%) in the three frames. Several frequency asymmetries unexpectedly observed (e.g. the frequency difference between and in the frame 0), are related to a new property of the subset involving substitutions. An evolutionary analytical model at three parameters (p, q, t) based on an independent mixing of the 22 codons (trinucleotides in frame 0) of with equiprobability (1/22) followed by t ≈ 4 substitutions per codon according to the proportions p ≈ 0.1; q ≈ 0.1 and r = 1 − p − q ≈ 0.8 in the three codon sites respectively, retrieves the frequencies of observed in the three frames of protein genes and explains these asymmetries. Furthermore, the same model (0.1, 0.1, t) after t ≈ 22 substitutions per codon, retrieves the statistical properties observed in the three frames of the 5′ and 3′ regions. The complex behaviour of these analytical curves is totally unexpected and a priori difficult to imagine.     

Modelling the dynamics of West Nile Virus

In this work we formulate and analyze a mathematical model for the transmission of West Nile Virus (WNV) infection between vector (mosquito) and avian population. We find the Basic Reproductive Number in terms of measurable epidemiological and demographic parameters. is the threshold condition that determines the dynamics of WNV infection: if the disease fades out, and for the disease remains endemic. Using experimental and field data we estimate for several species of birds. Numerical simulations of the temporal course of the infected bird proportion show damped oscillations approaching the endemic value.     

A simple classification of the volvocine algae by formal languages

There are several explanations of why certain primitive multicellular organisms aggregate in particular forms and why their constituent cells cooperate with one another to a particular degree. Utilizing the framework of formal language theory, we have derived one possible simple classification of the volvocine algae—one of the primitive multicells—for some forms of aggregation and some degrees of cooperation among cells. The volvocine algae range from the unicellular Chlamydomonas to themulticellular Volvox globator, which has thousands of cells. The classification we use in this paper is based on the complexity of Parikh sets of families on Chomsky hierarchy in formal language theory. We show that an alga with almost no space closed to the environment, e.g., Gonium pectorale, can be characterized by , one with a closed space and no cooperation, e.g., Eudorina elegans, by , and one with a closed space and cooperation, e.g., Volvox globator, by . This classification should provide new insights into the necessity for specific forms and degrees of cooperation in the volvocine algae.     

High groundwater nitrate concentrations inhibit eutrophication of sulphate-rich freshwater wetlands

During the last 60 years, pollution of the groundwater with has greatly increased in many parts of Europe, as a consequence of excessive use of manure and synthetic fertilisers. Monitoring of groundwater-fed wetlands indicated that sediments with high concentrations had the lowest Fe and concentrations in the pore water. A comparison of two restored open water fens, differing in supply via the groundwater, indicated that the redox potential and the sulphate ( ) reduction rate were lower when the groundwater contained not only but also high concentrations. The lower reduction rates in the -rich open water fen were associated with lower concentrations and the presence of plant species characteristic of clear water. In contrast, the higher reduction rates in the -poor open water fen were associated with very high concentrations and massive development of plant species characteristic of eutrophic environments. Investigations at -rich seepage sites in black alder carrs, showed that high concentrations in the pore water caused chlorosis in the alder carr vegetation, due to lower availability of Fe in the pore water and less Fe uptake by the plants. Experimental desiccation of sediments proved that the -rich seepage sites contained no oxidisable FeS _x , contrary to -poor locations, which became acidified and mobilised extremely high amounts of due to FeS _x oxidation. A laboratory experiment showed that addition to sediments led to reduced releases of Fe, and S^2–, very likely due to the oxidation of reduced Fe and S compounds. Overall, the results confirmed that is an energetically more favourable electron acceptor in anaerobic sediments than Fe and , and that high loads function as a redox buffer, preventing reduction of Fe and . Limited reduction prevents S^2– -mediated mobilisation of from Fe- complexes. At a higher redox potential, reduced Fe, including FeS _x , was oxidised, increasing the content of Fe(III) capable of binding . This prevented increased availability and the concomitant massive development of plant species characteristic of eutrophic environments.     

A model of oxygen uptake kinetics in response to exercise: Including a means of calculating oxygen demand/deficit/debt

We present a new model of the underlying dynamics of the oxygen uptake kinetics for various exercise intensities. This model is in the form of a set of nonlinear coupled vector fields for the and , the derivative of the exercise intensity with respect to time. We also present a new and novel means for calculating the oxygen demand, D(v, t), and hence also the oxygen deficit and debt, given the time series of the . This enables us to give better predictions for these values especially for when exercising at or close to maximal exercise intensities. Our model also allows us to predict the oxygen uptake time series given the time series for the exercise intensity as well as to investigate the oxygen uptake response to nonlinear exercise intensities. Neither of these features is possible using the currently used three-phase model. We also present a review of both the underlying physiology and the three-phase model. This includes for the first time a complete set of the analytical solutions of the three-phase model for the oxygen deficit and debt.     

Some results in graph theory and their application to abstract relational biology

It has been shown in earlier work that one approach to what Rashevsky has called “abstract biology” is through the study of the class of ( )-systems that can be formed in an arbitrary subcategory of the category of sets. The concept of the ( )-system, however, depends on the availability of mappings that contain other mappings in their range. It is shown that, by introducing an appropriate measure for this property, the problem of characterizing those categories suitable for a rich theory of ( )-systems reduces to a problem familiar from the general theory of graphs. Some new results in these directions are obtained, and it is then shown that any category with mappings that possess properties we might expect to hold in the physical world will also admit a rich theory of ( )-systems. In particular, it is shown that a sufficiently large family of mappings drawn at random from such a category will with overwhelming probability contain an ( )-system. This research was supported by the United States Air Force through the Air Force Office of Scientific Research of the Air Research and Development Command, under Grant No. AF-AFOSR-9-63.     

The nucleotide sequence ofBeneckea harveyi 5S rRNA

Summary The complete sequence of the 5S rRNA from the bioluminescent bacterium,Beneckea harveyi has been determined to be p U G C U U G G C G C C A U A G C G A U U-G G A C C C A C U G A (U) C U U C A U U C C-G A A C C A G A A G U G A A C G A A U U A-G G C C G A U G G U G U G U G G G G C U-C C C C A U G U A G A G U A G G A A U C G-C C A G G U (U)_OH.Two sites of sensitivity to ribonuclease T₂ cleavage were identified; at A₄₁ and either A₅₄ or A₅₅. Comparison with existing sequence information fromEscherichia coli andPhotobacterium phosphoreum clarifies the amount of diversity among the bioluminescent bacteria and provides further insight into their phylogenetic position. Sequence heterogeneities were encountered and the importance of these in interpreting 5S rRNA data is discussed.     

Compensatory changes in Photosystem II electron turnover rates protect photosynthesis from photoinhibition

Exposure of algae or higher plants to bright light can result in a photoinhibitory reduction in the number of functional PS II reaction centers (n) and a consequential decrease in the maximum quantum yield of photosynthesis. However, we found that light-saturated photosynthetic rates (P_max) in natural phytoplankton assemblages sampled from the south Pacific ocean were not reduced despite photoinhibitory decreases in n of up to 52%. This striking insensitivity of P_max to photoinhibition resulted from reciprocal increases in electron turnover ( )through the remaining functional PS II centers. Similar insensitivity of P_max was also observed in low light adapted cultures of Thalassiosira weissflogii (a marine diatom), but not in high light adapted cells where P_max decreased in proportion to n. This differential sensitivity to decreases in n occurred because was close to the maximum achievable rate in the high light adapted cells, whereas was initially low in the low light adapted cells and could thus increase in response to decreases in n. Our results indicate that decreases in plant productivity are not necessarily commensurate with photoinhibition, but rather will only occur if decreases in n are sufficient to maximize or incident irradiance becomes subsaturating.     

Use of the force-velocity test to determine the optimal braking force for a sprint exercise on a friction-loaded cycle ergometer

A group of 15 untrained male subjects pedalled on a friction-loaded cycle ergometer as fast as possible for 5–7 s to reach the maximal velocity (V{immax}) against different braking forces (F _B). Power was averaged during a complete crank rotation by adding the power dissipated againstF _B to the power necessary to accelerate the flywheel. For each sprint, determinations were made of peak power output ( ) power output attained atV _max ( ) calculated as the product ofV _max andF _B and the work performed to reachV _max expressed in mean power output ( ). The relationships between these parameters andF _B were examined. A biopsy taken from the vastus lateralis muscle and tomodensitometric radiographs of both thighs were taken at rest to identify muscle metabolic and morphometric properties. The value was similar for allF _B. Therefore, the average of values was defined as corrected maximal power ( ). This value was 11 higher than the maximal power output uncorrected for the acceleration. Whereas the determination did not require high loads, the highest value ( ) was produced when loading was heavy, as evidenced by the -F _B parabolic relationship. For each subject, the braking force ( ) giving was defined as optimal. The , equal to 0.844 (SD 0.108) N · kg⁻¹ bodymass, was related to thigh muscle area (r = 0.78,P < 0.05). The maximal velocity ( ) reached against this force seemed to be related more to intrinsic fibre properties (% fast twitch b fibre area and adenylate kinase activity). Thus, from the determination, it is suggested that it should be possible to predict the conditions for optimal exercise on a cycle ergometer.     

Regulation of mineral nitrogen uptake in plants

In the biosphere plants are exposed to different forms of N, which comprise mineral and organic N forms in soils as well as gaseous NH3, NOx, and molecular N2 in the atmosphere. The form of N uptake is mainly determined by its abundance and accessibility, which make and the most important N forms for plant nutrition under agricultural conditions. With minor importance, the form of N uptake is also subject to plant preferences, by which plants maintain their cation/anion balance during uptake. However, some species seem to have an obligatory preference which even prevents their growth on certain other N sources. In general, uptake of a certain N form closely matches the growth-related demand of the plant, at least when N transport to the root surface is not limiting. In addition, many plants accumulate large pools of N during vegetative growth which are remobilized in the generative stage. As a consequence, systems responsible for N transport need to be tightly regulated in their expression and activity upon sensing N availability and plant demand. Employing the tools of molecular genetics, the first plant genes encoding transporters for inorganic N have recently been isolated and characterized. These data can now complete the wealth of physiological and nutritional studies on N uptake. The present article will focus on the uptake of and into root cells and tries to link data derived from physiological, genetic and molecular studies.     

On the derivation of a mean growth equation for cell cultures

IfN(t) is the expected number of cells in a culture at timet, the corresponding time derivative, andf(t−τ)dt the probability that a cell of aget−τ at timet will divide in the succeeding time intervaldt, then according to Hirsch and Engelberg (this issue) there obtains the integral equation for describing the dynamics of the cell population. It is the purpose of this note to give two alternative derivations of this equation, one based on the age density equation of Von Foerster, and the other based on a generalized form of the Harris-Bellman equation describing the first moment of an age dependent, branching process. In addition, a probability model is posed from which the Von Foerster equation and, hence, the Hirsch-Engelberg equation readily follows.     

Activity and oxygen consumption during hypoxic exposure in high altitude and lowland sceloporine lizards

Summary Resting rates of O₂ consumption against , exercise endurance times and during recovery from vigorous exercise were measured inSceloporus occidentalis captured near sea level and inS. graciosus captured above 2850 m. Oxygen consumption against was also measured inS. occidentalis captured above 2850 m. When was recorded continuously, as ambient was slowly reduced from 155 Torr, it became directly dependent upon ambient between 110 and 120 Torr. The critical for the high altitude lizards was lower than that for the lowland lizards, which enabled the former to maintain relatively higher 's when ambient was reduced below 120 Torr. The high altitude lizards also had significantly greater endurance when stimulated to exercise at 1600 m ( 130 Torr). Both the higher under hypoxia and the greater endurance roughly parallel a significantly greater maximum in the high altitude lizards. At a simulated altitude of 3600 m ( 100 Torr), maximum and rate of recovery of the O₂ debt calculated from post active were significantly reduced in the lowland but not the high altitude lizards. The effects of simulated altitude conditions on the lowland but not the mountaine animals indicate adaptations to altitude in these sceloporine lizards. We did not find any consistent relationship between organ/body weight ratios or hematocrit and our measures of endurance or the altitude at which the lizards were captured.     

Dynamics of cardiorespiratory function in Standardbred horses during different intensities of constant-load exercise

Summary Six Standardbred horses were used to evaluate the time course of pulmonary gas exchange, ventilation, heart rate (HR) and acid base balance during different intensities of constant-load treadmill exercise. Horses were exercised at approximately 50%, 75% and 100% maximum oxygen uptake ( max) for 5 min and measurements taken every 30 s throughout exercise. At all work rates, the minute ventilation, respiratory frequency and tidal volume reached steady state values by 60 s of exercise. At 100% max, the oxygen consumption ( ) increased to mean values of approximately 130 ml/kg·min, which represents a 40-fold increase above resting . At the low and moderate work rates, showed no significant change from 30 s to 300 s of exercise. At the high work rate, the mean at 30 s was 80% of the value at 300 s. The HR showed no significant change over time at the moderate work rate but differing responses at the low and high work rates. At the low work rate, the mean HR decreased from 188 beats/min at 30 s to 172 beats/min at 300 s exercise, whereas at the high work rate the mean HR increased from 204 beats/min at 30 s to 221 beats/min at 300 s exercise. No changes in acid base status occurred during exercise at the low work rate. At the moderate work rate, a mild metabolic acidosis occurred which was nonprogressive with time, whereas the high work rate resulted in a progressive metabolic acidosis with a base deficit of 16 mmol/l by 300 s exercise. It is concluded that the kinetics of gas exchange during exercise are more rapid in the horse than in man, despite the relatively greater change in in the horse when going from rest to high intensity exercise.Symbols and abbreviations E minute ventilation - V _T tidal volume - oxygen uptake - carbon dioxide output - oxygen pulse - ventilatory equivalent for oxygen - ventilatory equivalent for carbon dioxide - R respiratory exchange ratio - HR heart rate - SBC standard bicarbonate - STPD standard temperature and pressure dry - BTPS body temperature and pressure saturated - arterial oxygen content - arteriovenous oxygen content difference - Rf respiratory frequency     

Heterogeneous organ models

A theoretical study is made of three organ flow models with heterogeneity of capillary transit times. A new parametrization of Rose and Goresky's Model III facilitates in many cases a reduction to Goresky's Model II, accomplished by a special time shift. The shift parameter defined here is critical in this analysis of Model III. A new expression of the series for outflow concentration in Model III is given and proves useful in examining the model as an operator and in relating it to Models I and II. A result on parameter optimization is given: if then Model III cannot fit better than Model II. This is applied to some data from Rose and Goresky [Circulation Res. 39, 541–544 (1976)] and raises a new question about their model. A heart model of Levin and Bassingthwaighte based on regional flow measurement is shown to be a discretized generalization of Model II. This work supported in part by PHS Grant Nos. HL-19153 (SCOR for Pulmonary Vascular Disease) and HL-19370 at Vanderbilt University.     

The Influence of Hydroregime on Catch, Abundance And Recruitment of the Catfish, Chrysichthys Nigrodigitatus (Bagridae) and the Bonga, Ethmalosa Fimbriata (Clupeidae) of Southeastern Nigeria's Inshore Waters

This paper investigates the relationship between the hydroclimatic parameters (rainfall and flood index) and the catch, stock abundance and recruitment of the catfish, Chrysichthys nigrodigitatus (Bagridae) and the bonga, Ethmalosa fimbriata (Clupeidae) of southeastern Nigeria's inshore waters. For C. nigrodigitatus, most peaks in the mean biomass and recruitment curves occurred during the 'wet' years, i.e., years for which the percentage deviations of rainfall and flood index from their means remained above their averages. Catch and abundance respectively showed good positive linear correlation with the flood index. E. fimbriata behaved differently; some peaks in the and curves occurred in the 'wet' and some in the 'dry' years; and there was no correlation between the annual catch of bonga and either the rainfall or the flood index. The hypothesis, that linear relationships exist between the interannual variations in the hydroregime and the yearly fluctuations in the catch and population structure of some coastal and estuarine fishes, holds true for the catfish, C. nigrodigitatus, but not for bonga, E. fimbriata.     

Results of the oxygen Fick method in a closed blood circulation model including “total arteriovenous diffusive shunt of oxygen”

It is considered that arteriovenous diffusive shunts of oxygen may cause inaccuracy of the oxygen Fick method as where is the pulmonary oxygen uptake, is the cardiac output, and CaO₂ and CvO₂ are the arterial and venous oxygen contents, respectively. A simple circulation model, including the whole circulation with nine well-mixed compartments (C1, ... C9), is constructed: the is assigned as constant as 6000 ml min⁻¹; the blood portions of 60 ml move at an interval of 600 ms. C1 and C2 compartments, each having 60 ml volume, represent the blood of pulmonary microcirculation, C3 represents the arterial blood with a volume of 1500 ml, C4, ..., C8, each also having a volume of 60 ml, represent the blood of peripheral microcirculation, whereas C9 represents the venous blood with a volume of 3000 ml. The pulmonary oxygen uptake , related to C1 and C2, the oxygen release , related to C4,...,C8, as well as a “total arteriovenous diffusive shunt of oxygen” , from the arterial blood (C3) to the venous blood (C9), are calculated simultaneously. The alveolar gas has a constant oxygen partial pressure, and the pulmonary diffusion capacity is also constant; similar to modeling the pulmonry, oxygen diffusion, constant partial oxygen pressures for all peripheral tissues as well as constant diffusion capacities for all peripheral oxygen diffusion are also assigned. The diffusion capacities for the (between C3 and C9) are arbitrarily assigned. The Fick method gives incorrect results depending on the total arteriovenous diffusive shunt of oxygen . But the mechanism determining the magnitude of remains unclear.     

A kinetics model of abrin binding in a virus transformed lymphocyte cell culture

The second order nonlinear differential equation arises from a kinetics model of abrin binding in an Epstein-Barr virus-transformed lymphocyte culture. Some results on the dynamical behavior of this equation are given. These results are then discussed in relation to the known kinetics behavior of abrin in an EBV-lymphocyte cell culture.     

(H)NCAHA and (H)CANNH experiments for the determination of vicinal coupling constants related to the ϕ-torsion angle

Summary A set of three-dimensional triple-resonance experiments is described which provide , , and coupling constants. The pulse sequences generate E.COSY-like multiplet patterns and comprise a magnetization transfer from the amide proton to the α-proton or vice versa via the directly bound heteronuclei. For residues with the ¹H^α spin resonating close to the H₂O signal, a modified HNCA experiment can be employed to measure the vicinal ¹H^N,¹H^α couplings. Ambiguities associated with the conversion of values into ϕ-angle constraints for protein structure determination can be resolved with the knowledge of the heteronuclear ³J-couplings. In favourable cases, stereospecific assignments of glycine α-protons can be obtained by employing the experiments described here in combination with NOE data. The methods are applied to flavodoxin from Desulfovibrio vulgaris.     

Differentiation between acetate and higher volatile acids in the modeling of the anaerobic biomethanation process

This paper presents a model for the single-stage completely-mixed anaerobic digestion of complex substrates containing no volatile acids. In the model, volatile acids produced by the acidogenic bacteria are no longer considered together. Acetate is assumed to be representative of the substrate and propionate and butyrate act only as inhibitors for the methanogenic bacteria.Nomenclature ···0 represents factors associated with the influent - ···1 represents factors associated with the acidogenic bacteria - ···2 represents factors associated with the methanogenic bacteria - Q hydraulic flow (1/d) - V reactor liquid volume (1) - T temperature of the mixed liquor (° C) - S microorganisms concentration (mg/1) - L volatile solids concentration (mg VS/1) - Lb biodegradable volatile solids concentration (mg VS/1) - VA2 acetate concentration (mg/1) - VA3 volatile acids with 3 to 5 carbon atoms concentration (mg/1) - methane rate production (1 CH₄/1_digester.d) - Km saturation coefficient (mg/l) - Ki inhibition coefficient (mg/l) - specific growth rate (1/d) - maximum specific growth rate (1/d) - b biological decay coefficient (1/d) - Arrhénius coefficient (–) - yield of acidogenic bacteria per mg of biodegradable matter consumed (mg S₁/mg L_b) | (mg S₂/mg VA2) - yield of methanogenic bacteria per mg of VA2 consumed - yield of methane production per mg of S₂ formed (1 CH₄/mg S₂) - proportion of VA2 produced per mg of S₁ biosynthetised - proportion of VA3 produced per mg of S₁ biosynthetised - Y_sp volume of CH₄ produced per g of volatile solids eliminated