Distribution of effective field in the ising spin glass of the ±J model atT=0

The integral equation for the distribution function of effective field of the ±J random Ising model in the pair (Bethe) approximation is investigated. Its exact solutions atH (magnetic field)=0,T (temperature)=0 and forz (coordination number)=3 expressed as superpositions of 2N+1 (more than 3), delta functions are considered. Then the integral equation is reduced to a system of algebraic equations ofz ?1th degree withN+1 unknowns. The system of the equations is solved by the Gröbner basis method withN=1, 2, 3, 4. The number of physically acceptable solutions for a givenN is ω(N)+1 where ω(N) is the number of divisors ofN. The ground-state energy and entropy for these are calculated. They are very close in value (entropies are positive), and it is suggested that a number of physically acceptable solutions correspond to local stationary spin-glass states, as discussed in the literatures.     

Raman spectra of chemically modified lysozyme. Oxindole derivatives.

The Raman spectra of oxidation products of lysozyme have been investigated. The protein was oxidized by N-bromosuccinimide and dimethyl sulfoxide/HCl. Depending on the experimental conditions one to six tryptophan residues are oxidized to oxindole. The most prominent difference between the spectra of lysozyme and its oxindole derivatives is the strong band at 1017 cm^?1 which displaces the tryptophan peak at 1010 cm^?1. Other tryptophan bands are also weakened corresponding to the number of the tryptophan side chains destroyed. Shifts are observed in the amide I and in the amide III regions sensitive to conformational changes. These shifts indicate conformational differences in the higher oxidized species and in the native enzyme, although the amide III maxima overlap with a strong oxindole band. Similar effects are observed in the range of the C-C stretching vibrations of the peptide backbone. If more than one tryptophan side chain is oxidized changes have also been found in the S-S stretching range. The evaluation of this effect is difficult because of the strong oxindole vibration appearing in this region. In species oxidized by great excess of N-bromosuccinimide the tyrosine vibrations can no longer be detected, indicating the modification of this amino acid too.     

Learning Probabilistic Features for Robotic Navigation Using Laser Sensors

SLAM is a popular task used by robots and autonomous vehicles to build a map of an unknown environment and, at the same time, to determine their location within the map. This paper describes a SLAM-based, probabilistic robotic system able to learn the essential features of different parts of its environment. Some previous SLAM implementations had computational complexities ranging from O(Nlog(N)) to O(N²), where N is the number of map features. Unlike these methods, our approach reduces the computational complexity to O(N) by using a model to fuse the information from the sensors after applying the Bayesian paradigm. Once the training process is completed, the robot identifies and locates those areas that potentially match the sections that have been previously learned. After the training, the robot navigates and extracts a three-dimensional map of the environment using a single laser sensor. Thus, it perceives different sections of its world. In addition, in order to make our system able to be used in a low-cost robot, low-complexity algorithms that can be easily implemented on embedded processors or microcontrollers are used.     

Species patterns in foliar nitrogen concentration, nitrogen content and 13C abundance for understory saplings across light gradients

Soil nitrogen (N) supply and uptake by regenerating trees is an important ecosystem attribute but difficult to quantify in partial-cut forests where light availability varies. The foliar attributes of N concentration (N_%) and N per unit area (N_a) may help characterize the influence of soil nutrition, but ideally the relationship between soils and foliage would be tested separately by species across well-defined light gradients. To do this, we examined foliar attributes of four tree species across gradients of light availability in 12 year-old partially-cut forests in northwest British Columbia, Canada. There were no differences in forest floor or mineral soil N mineralization rates across the light gradients, and for western hemlock (Tsuga heterophylla) and hybrid white spruce (Picea glauca x sitchensis), this consistent level of soil N supply corresponded with unchanging foliar N_%. In contrast, foliar N_% of Betula papyrifera (paper birch) and Thuja plicata (western redcedar) declined with shading, perhaps due to shifts in root-shoot biomass allocation for B. papyrifera, and climatic constraints on shade tolerance for T. plicata. Leaf δ¹³C approached an asymptote at approx. 40% full light for the coniferous species, but increased linearly with light for B. papyrifera. Foliar N_a was linearly correlated with leaf δ¹³C for three species, reflecting the dual effect of light and nutrition on photosynthesis processes, and suggesting that foliar N_a may be a simple parameter to integrate both resource constraints on regenerating saplings. These results demonstrate both support for and limits to foliar attributes among species in isolating soil N effects against light constraints in partial-cut forests.     

Reproductive biology of the invasive Asian freshwater leech Barbronia weberi (Blanchard, 1897)

Barbronia weberi were collected from Hydrilla verticillata purchased from aquarium suppliers in Melbourne, Australia and additional B. weberi were obtained from aquatic plants in Canberra, ACT, Australia. Adult leeches fed Tubifex sp. ad libitum successfully reproduced under laboratory conditions (21 ± 5?°C ). Reproductively mature B. weberi produced cocoons every week for up to three months at which time the adults began to senesce. Cocoons contained one to five (barx=2.41±0.78 SD, N=58) eggs with juveniles leaving the cocoon within 27 ± 3.4 SD days (N=13) of cocoon production. Juvenile B. weberi reached reproductive maturity within four months (N=7) of hatching and had a maximum growth rate of 1.10 mm² d^?1 once they left the cocoon at around 30 days. Individual egg volume (r=0.63, scaling exponent = 1.21) and cocoon volume (r=0.65, scaling exponent = 1.24) showed a significant (P<0.001) and nearly isometric relationship when scaled with maternal body size. Because this species can grow rapidly and produce a large number of eggs over a short period of time and can piggyback with plant species and travel through the aquarium trade, there is potential for B. weberi to rapidly invade new localities.     

Identity Coefficients in Finite Populations. I. Evolution of Identity Coefficients in a Random Mating Diploid Dioecious Population

Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (N_e) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)³ and (1— f)⁶, where f is the mean inbreeding coefficient at time t. Tables are presented, for small N_e values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N _eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.     

Solution of Levinthal’s paradox is possible at the level of the formation and assembly of protein secondary structures

The complete volume of a protein’s conformation space is smaller by many orders of magnitude at the level of secondary-structure elements as compared with the conformation of amino-acid residues. According to Levinthal’s estimate, the latter is ~10^2L, with L being the number of residues in the chain, while the former, at the level of secondary structures, increases no faster than ~L^N with N being the number of the secondary-structure elements. N is approximately L/15 according to the statistics of protein structures. This drastic decrease in the exponent (L/15 instead of 2L) considerably reduces the sampling space and explains the reason that sampling of the conformation space at the level of secondary-structure elements does not prevent the protein chain from finding its most stable structure.     

Altitude modifies species richness–nutrient indicator value relationships in a country-wide survey of grassland vegetation

Nutrient enrichment is a threat to botanical diversity in Europe, and its assessment is part of biodiversity monitoring schemes. In Switzerland, this is done by calculating the average nutrient (N) indicator value of the vegetation based on a country-wide systematic vegetation survey. However, it is questionable whether N values indicate eutrophication and resulting species loss equally well across an entire country, which includes wide topographic gradients and distinct biogeographic regions. Here we analyze vascular plant species lists from 415 grassland plots (10 m²) between 365 and 2770 m a.s.l. throughout Switzerland to investigate how the relationship between N value and species richness differs with altitude and among regions. The N value strongly decreased with altitude (piecewise regression: r² = 0.77), particularly between 800 and 2000 m a.s.l., where this decrease was related to a decreasing proportion of fertilized grasslands. In the alpine belt, lower N values were associated with a greater frequency of acidic soils and a restricted species pool. Vascular plant species richness was maximal at intermediate altitude (piecewise regression: r² = 0.33) and intermediate N value (polynomial regression: r² = 0.46). When analyzed separately by altitudinal belt, the relationship between species richness and N value was negative in the lowlands and montane belt but unimodal in the subalpine belt. In the alpine belt, soil pH (R indicator values) explained most of the variation in species richness. Two indices of between-plot diversity (floristic dissimilarity and the contribution of individual plots to total species richness) were negatively related to N values from the lowlands to the subalpine belt but not in the alpine belt. All relationships differed little among the biogeographic regions of Switzerland, but they might be modified by changes in management and by the expansion of common lowland species into mountain grasslands.     

Effect of Water Vapor on Lyophilized Serratia marcescens and Escherichia coli

Dried Serratia marcescens ATTC 14014 and Escherichia coli ATTC 4157 cells were exposed to various partial pressures of purified water vapor. The colony-forming ability of the S. marcescens was unimpaired when the dried organisms were stored in water-vapor atmosphere such that P/P₀ < 0.55 or P/P₀ = 1.0 (where P is the pressure of the water vapor in contact with the organisms, and P₀ is vapor pressure of pure water at 25 C). During storage under water-vapor atmospheres with P/P₀ between 0.6 and 1.0, the colony-forming ability of the dried S. marcescens was destroyed. The inactivation by water vapor followed the expression — ln N/N₀ = Kt^1/2, where N₀ and N are the number of viable organisms before and after exposure, respectively, t is time, and K is a pseudo constant which is dependent upon the partial pressure of the water vapor at 25 C. Similar results were obtained with dried E. coli. The addition of solutes to the suspending media before freeze-drying was found to influence the stability of the organisms during exposure to water vapor.     

Diversity and community patterns of testate amoebae in Bau Sen and Bau Trang lakes in Binh Thuan Province,Vietnam

The species composition and distribution of testate amoebae in Bau Sen and Bau Trang lakes (Binh Thuan Province, Vietnam) were investigated. Fifty-three species, varieties and forms have been identified from the water column and sediments. Twenty-seven species, varieties and forms from the genera Arcella, Centropyxis, Cyclopyxis, Difflugia and Pyxidicula were found in Vietnam for the first time. The updated list of testate amoebae in Vietnam now includes 286 taxa. The genera Arcella, Centropyxis and Difflugia are characterized by the highest frequency of occurrence. The species diversity of Arcella, Centropyxis, Difflugia was the highest. Centropyxis aculeata, Arcella discoides, Difflugia schurmanni, Netzelia oviformis and Difflugia limnetica were the most common species. Many species have shown restricted distribution, some species have been found only in one lake and not been found in another lake. The number of observed species, varieties, and forms in each lake is 34. The average number of the species per sample on the shores of the lakes subjected to human agricultural activity was significantly higher than in the samples from the shores of the lakes with less anthropogenic disturbance. The curves of “cumulative species number vs. sampling effort” are well fitted by equations S = 7.60 N ^0.69 for Bau Sen lake and S = 12.52 N ^0.46 for Bau Trang. The curves are unsaturated, which indicates that more intensive investigations of testate amoebae should be expected to reveal more species.     

Analysis of ligand binding curves in terms of species fractions

The ligand binding curve for a macromolecular system presents the average number or ligand molecules bound per macromolecule as a function of the chemical potential or the logarithm of the ligand concentration. We show that various observable properties of this curve, for example its asymptotes and derivatives, are expressible in terms of linear combinations of the mole fractions α_i of macromolecules binding i molecules of ligand. Whenever enough such properties of the binding curve are known, the linear equations in α_i can be solved to give the mole fractions of each of the various macromolecular species. An application of these results is that a Hill plot for hemoglobin-ligand equilibrium where the asymptotes approach unit slope can be made to yield the four Adair constants by a simple algebraic method. A second use is that a knowledge of the first and second derivatives of the binding curve at points along the curve can yield the species fractions as functions of the degree of saturation without direct knowledge of the ligand binding constants. These methods are illustrated by some numerical examples.     

A region-based model framework for the rat urine concentrating mechanism

The highly structured organization of tubules and blood vessels in the outer medulla of the mammalian kidney is believed to result in preferential interactions among tubules and vessels; such interactions may promote solute cycling and enhance urine concentrating capability. In this study, we formulate a new model framework for the urine concentrating mechanism in the outer medulla of the rat kidney. The model simulates preferential interactions among tubules and vessels by representing two concentric regions and by specifying the fractions of tubules and vessels assigned to each of the regions. The model equations are based on standard expressions for transmural transport and on solute and water conservation. Model equations, which are derived in dynamic form, are solved to obtain steady-state solutions by means of a stable and efficient numerical method, based on the semi-Lagrangian semi-implicit method and on Newton’s method. In this application, the computational cost scales as O(N ²), where N is the number of spatial subintervals along the medulla. We present representative solutions and show that the method generates approximations that are second-order accurate in space and that exhibit mass conservation.     

The m6A‑methylase complex and mRNA export

During synthesis, mRNA undergoes a number of modifications such as capping, splicing and polyadenylation. These processes are coupled with the orderly deposition of the TREX complex on the mRNA and subsequent recruitment of the NXF1-P15 heterodimer which stimulates the nuclear export of mature mRNAs. mRNAs also undergo a number of internal modifications, the most common of which is the N⁶?methyladenosine (m⁶A) modification. In this review we discuss the recent evidence of coupling between the m⁶A modification, RNA processing and export.     

Factors influencing stable nitrogen isotope ratios in wing membranes of insectivorous bat species: A field study

Nitrogen stable isotope analysis studies have become a useful tool in dietary studies to quantify differences in diet composition among species or individuals. However, laboratory studies have revealed several factors that influence the nitrogen isotope ratios (δ¹⁵N) in animal tissues (e.g. habitat, amount of ingested food, and metabolic rate). The influence of these factors has not been validated for free-ranging bat species, which is important for interpreting nitrogen isotope data in field studies. In this study, we measured δ¹⁵N from wing membranes (δ¹⁵N_w) and habitat samples (δ¹⁵N_h; soil and leaf, or sediment) to test for effects of diet, age, and individual energy demand in three free-living bat species (Myotis daubentonii, Nyctalus noctula and Nyctalus leisleri). We hypothesised that based on differences in diet composition δ¹⁵N_w values should increase in the sequence M. daubentonii, N. leisleri, and highest N. noctula. Furthermore, juveniles should have significantly lower δ¹⁵N_w compared to their mothers. Thirdly, the δ¹⁵N_w values of reproductively active individuals should be significantly higher than those of non-reproductive individuals. Values of δ¹⁵N_w were significantly influenced by differences in feeding ecology among species and individual reproductive status, but not by animal age. Our results show that species feeding on primary consumers have lower δ¹⁵N_w values than species feeding on secondary and tertiary consumers. Further, independent young did not differ in their δ¹⁵N_w values from adults suggesting that their tissues already reflect the insect diet. The effect of reproductive status varied among species which might reflect intra-specific differences in foraging behaviour of generalist vs. specialist species. In this study, we demonstrated that δ¹⁵N can provide information on the dietary range of bats, but researchers should account for variation owing to reproductive status, habitat, and species.     

Fast calculation of the infrared spectra of large biomolecules

Vibrational spectra of proteins potentially give insight into biologically significant molecular motion and the proportions of different types of secondary structure. Vibrational spectra can be calculated either from normal modes obtained by diagonalizing the mass-weighted Hessian or from the time autocorrelation function derived from molecular dynamics trajectories. The Hessian matrix is calculated from force fields because it is not practical to calculate the Hessian from quantum mechanics for large molecules. As an alternative to molecular dynamics the spectral response can be calculated from a time autocorrelation derived from numerical solution of the harmonic equations of motion, resulting in calculations at least 4 times faster. Because the calculation also scales linearly with number of atoms, N, it is faster than normal-mode calculations that scale as N ³ for proteins with more then 4,700 atoms. Using this method it is practical to perform all-atom calculations for large biological systems, for example viral capsids, with the order of 10⁵ atoms.     

The ptychoid defensive mechanism in Euphthiracaroidea (Acari: Oribatida): A comparison of muscular elements with functional considerations

Ptychoidy is a mechanical predator defence in some groups of Oribatida (Acari), where the animals can retract their legs into the idiosoma and encapsulate. This mechanism is enabled by a number of morphological adaptations. We used the non-invasive technique of synchrotron X-ray microtomography to compare muscular elements involved in ptychoidy of two species from the Euphthiracaroidea (Oribotritia banksi and Rhysotritia ardua) which differ in a number of cuticular elements involved in ptychoidy. We hypothesize that a strong functional correlation exists between these cuticular structures and their corresponding musculature. We found a number of distinct differences concerning quantitative and qualitative muscle morphology. For testing the functional impact of different muscle configurations we simulated two conditions in silico (encapsulated / opened) and analysed the spatial relative force vectors of the prodorsum lateral adjustor muscles (pla) which are responsible for retraction and adjustment of the prodorsum during encapsulation. We show that the functional morphology of these muscles strongly differs between the two species and that this can be explained by the structure of corresponding cuticular elements. Furthermore, the dynamics of pla, as measured by the extent of contraction during encapsulation, is more than two times higher in R. ardua than in O. banksi.     

Alkylation of transfer RNA by N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea

The alkylation of a number of purified tRNA preparations by reaction with the carcinogens, N-methyl-N-nitrosourea and N-ethyl-N-nitrosourea was studied in order to investigate the role of nucleic acid structure on the distribution of alkylation products within the nucleotide sequence. The rate of alkylation was greatly increased by increasing the pH over the range 6 to 8 and the degree of alkylation (expressed as moles alkyl groups/mole tRNA) was directly proportional to the concentration of the nitrosamide added and independent of the amount of tRNA present. There was no significant difference in the degree of alkylation of any of the tRNA preparations tested. Reaction with N-ethyl-N-nitrosourea resulted in a degree of alkylation some 13 times less than that produced by reaction with a similar concentration of N-methyl-N-nitrosourea. The major product of the reaction was 7-alkylguanine amounting to about 80% of the total, but 3-methylcytosine, 6-O-methylguanine and 1-methyl-, 3-methyl-, and 7-methyladenine were also identified as products of the reaction of tRNA^fMet with N-methyl-N-nitrosourea.The possibility that preferential alkylation of certain residues within the polynucleotide sequence was produced by reaction with the nitrosamides was examined by degradation of the alkylated tRNA with pancreatic ribonuclease and separation of the oligonucleotide fragments by chromatography on DEAE cellulose. When tRNA^fMet which had been alkylated by reaction with N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea was analysed in this way, the distribution of 7-alkylguanine was, within the limits of experimental error, in agreement with that expected for a random reaction of the alkylating agent with all of the guanosine residues throughout the molecule. A similar result was seen when tRNA^Phe was examined. These results were obtained by alkylation under conditions where the native configuration of the tRNA was maintained and show that the tertiary structure of the nucleic acid does not impart any specificity to the reaction with the nitrosamide producing 7-alkylguanine but the possibility that such specificity does exist for the minor products of alkylation cannot be excluded.     

Sulphydryl groups of (Na+ +K+)-ATPase from rectal glands of Squalus acanthias: Titrations and classification

1. (Na⁺ +K⁺)-ATPase from rectal gland of Squlus acanthias contains 34 SH groups per mol (M_r 265000). 15 are located on the α subunit (M_r 106 000) and two on the β subunit (M_r 40 000). The β subunit also contains one disulphide bridge. 2. The reaction of (Na⁺ +K⁺)-ATPase with N-ethylmaleimide shows the existence of at least three classes of SH groups. Class I contains two SH groups on each α subunit and one on each β subunit. Reaction of these groups with N-methylmaleimide in the presence of 40% glycerol or sucrose does not alter the enzyme activity. Class II contains four SH groups on each α subunit, and the reaction of these groups with 0.1 mM N-ethylmaleimide in the presence of 150 mM K⁺ leads to an enzyme species with about 16% activity. The remaining enzyme activity can be completely abolished by reaction with 5–10 nM N-ethylmaleimide, indicating a third class of SH groups (Class III). This pattern of inactivation is different from that of the kidney enzyme, where only one class of SH groups essential to activity is observed. 3. It is also shown that N-ethylmaleimide and DTNB inactivate by reacting with the same Class II SH groups. 4. Spin-labelling of the (Na⁺ +K⁺)-ATPase with a maleimide derivative shows that Class II groups are mostly buried in the membrane, whereas Class I groups are more exposed. It is also shown that spin label bound to the Class I groups can monitor the difference between the Na⁺- and K⁺-forms of the enzyme.