Deviations from Hardy-Weinberg Proportions: Sampling Variances and Use in Estimation of Inbreeding Coefficients

An analysis is made of the distribution of deviations from Hardy-Weinberg proportions with k alleles and of estimates of inbreeding coefficients (f) obtained from these deviations.—If f is small, the best estimate of f in large samples is shown to be 2Σ _i(T_ii/N_i)/(k - 1), where T_ii is an unbiased measure of the excess of the ith homozygote and N_i the number of the ith allele in the sample [frequency = N_i/(2N)]. No extra information is obtained from the T_ij, where these are departures of numbers of heterozygotes from expectation. Alternatively, the best estimator can be computed from the T_ij, ignoring the T_ii. Also (1) the variance of the estimate of f equals 1/(N(k - 1)) when all individuals in the sample are unrelated, and the test for f = 0 with 1 d.f. is given by the ratio of the estimate to its standard error; (2) the variance is reduced if some alleles are rare; and (3) if the sample consists of full-sib families of size n, the variance is increased by a proportion (n - 1)/4 but is not increased by a half-sib relationship.—If f is not small, the structure of the population is of critical importance. (1) If the inbreeding is due to a proportion of inbred matings in an otherwise random-breeding population, f as determined from homozygote excess is the same for all genes and expressions are given for its sampling variance. (2) If the homozygote excess is due to population admixture, f is not the same for all genes. The above estimator is probably close to the best for all f values.     

Peak Torque and Rate of Torque Development Influence on Repeated Maximal Exercise Performance: Contractile and Neural Contributions

Rapid force production is critical to improve performance and prevent injuries. However, changes in rate of force/torque development caused by the repetition of maximal contractions have received little attention. The aim of this study was to determine the relative influence of rate of torque development (RTD) and peak torque (T_peak) on the overall performance (i.e. mean torque, T_mean) decrease during repeated maximal contractions and to investigate the contribution of contractile and neural mechanisms to the alteration of the various mechanical variables. Eleven well-trained men performed 20 sets of 6-s isokinetic maximal knee extensions at 240°·s^-1, beginning every 30 seconds. RTD, T_peak and T_mean as well as the Rate of EMG Rise (RER), peak EMG (EMG_peak) and mean EMG (EMG_mean) of the vastus lateralis were monitored for each contraction. A wavelet transform was also performed on raw EMG signal for instant mean frequency (if_mean) calculation. A neuromuscular testing procedure was carried out before and immediately after the fatiguing protocol including evoked RTD (eRTD) and maximal evoked torque (eT_peak) induced by high frequency doublet (100 Hz). T_mean decrease was correlated to RTD and T_peak decrease (R²=0.62; p<0.001; respectively β=0.62 and β=0.19). RER, eRTD and initial if_mean (0-225 ms) decreased after 20 sets (respectively -21.1±14.1, -25±13%, and ~20%). RTD decrease was correlated to RER decrease (R²=0.36; p<0.05). The eT_peak decreased significantly after 20 sets (24±5%; p<0.05) contrary to EMG_peak (-3.2±19.5 %; p=0.71). Our results show that reductions of RTD explained part of the alterations of the overall performance during repeated moderate velocity maximal exercise. The reductions of RTD were associated to an impairment of the ability of the central nervous system to maximally activate the muscle in the first milliseconds of the contraction.     

Studies of the induction of mitotic gene conversion by ultraviolet irradiation: II. Action spectra

Action spectra for the induction of intragenic mitotic recombination (gene conversion) at the trp5 locus by UV are presented for three cell stages (T₀, T₉ and T₁₆) taken from synchronously growing cultures of Saccharomyces cerevisiae. The spectra over the range from 230 to 300 nm were taken mostly in 5-nm steps. The peak of action spectra was significantly shifted, regardless of the stage, toward the longer wavelengths as compared with that of the absorption spectrum of DNA (258 nm) or even that of thymine (265 nm). In one extreme case (T₁₆), the peak was shifted 17 nm from the absorption peak of DNA. Further, the spectrum changed its shape at the cell stage advanced from non-dividing (unbudded) (T₀) to a dividing phase (T₁₆). Furthermore, the induction cross section decreased by a large factor (about 40), regardless of the wavelength, in going from T₀ to T₁₆. From observations of the high photoreversibility of induced conversions, the major primary damage was thought to be pyrimidine dimers in the DNA.One plausible explanation, though not quite satisfactory from the quantitative viewpoint for these findings was that the increasing RNA during growth would screen the incident UV differentially with respect to the stage. If this explanation is correct, thymine dimers may still be considered, in spite of the shifts and deformations in the action spectra, as the major primary damage that triggers the long series of processes leading to gene conversion. Conventional methods for obtaining action spectra are discussed in comparison with the present method, which was based on sensitivity parameter a in the proposed dose (t)-frequency (f) relation, f = (at)^α (α is the multiplicity parameter).     

Some theorems in topology and a possible biological implication

In a previous paper (Bull. Math. Biophysics,16, 317–48, 1954) a transformationT of one graph into another was suggested, which may describe the relations between organisms of different complexity. In this paper some topological properties of the transformationT are studied. It is shown that the fundamental group of the transformed graph is homomorph to the fundamental group of the original graph. An expression is derived for the number of points in a point base of the transformed graph in terms of the number of points of the point base of the original when the point base of the latter consists only of residual points, and it is shown that the ratio of the number of points of the point base to the total number of points of the graph is in that case greater in the transformed graph than in the original. A combinatorial problem arising in connection with the transformationT is solved by deriving the number of possible ways in whichn-n _i indistinguishable elements may be arranged inn _i classes, permitting some of then _i classes to be empty. The possible biological meaning of the increased ratio of the number of points of the point base to the total number of points of the graph is discussed. It is suggested that it may be interpreted as a decrease of regenerating ability with increase of differentiation of the organism. Those considerations suggest the possibility of deriving some general biological laws from the consideration of the properties of the transformation only, regardless of the choice of the primordial graph.     

Damage functions and thermal requirements of Meloidogyne javanica and Meloidogyne incognita on watermelon

The relationship between the initial (P_i) and final (P_f) population densities of Meloidogyne javanica and yield of watermelon, Citrullus lanatus, cv. Sugar Baby were determined in pot and field experiments. In the pots, the maximum reproduction rate of the nematode was 14, and the equilibrium density was 49 400 eggs/100 cm³ of soil. Yield data represented as fresh top weight fitted the Seinhorst damage function (P < 0.001, R² = 0.7), and the minimum relative yield (m) was 0.65 at P_i ≥ 3200 eggs/100 cm³ of soil and the tolerance limit (T) 74 eggs/100 cm³. In the field experiments (2011 and 2012), the maximum reproduction rate was 73 and 70, and the equilibrium density 32 and 35 second‐stage juveniles (J2)/100 cm³ soil. Yield data represented as fruit weight fitted the Seinhorst damage function in 2011 (P < 0.001, R² = 0.92) and the m‐ and T‐values were 0.63 and 20 J2/100 cm³ of soil, respectively. Meloidogyne incognita and M. javanica needed similar length of time for development to egg‐laying females and life cycle completion at 24.4°C.     

Purification and properties of a methionine formylmethionyl-tRNA-binding initiation factor from pig liver

(i) A factor, EIF-2, that binds methionyl-tRNA_f^Met in the presence of GTP has been isolated from pig liver. (ii) Dodecylsulfate-gel electrophoresis and sedimentation equilibrium centrifugation indicate that the factor has a molecular weight of 122,000 and that it consists of three unequal subunits. (iii) The apparent K_D for binding of methionyl-tRNA_f^Met varies with factor concentration. GTP participates in the binding with a K_D of 0.5 μm. β,γ-Methylene-guanosine triphosphate supports 40% of the binding observed with GTP. GDP is a competitive inhibitor with a K_i of 0.2 μm. The optimal, free Mg²⁺ concentration is approximately 50 μm. GTP and Mg²⁺ stabilize the factor against thermal inactivation and inactivation by N-ethyl maleimide. (iv) The factor is required for the formation of a sucrose gradient-stable complex between methionyl-tRNA_f^Met and the 40S ribosomal subunit. The presence of template is not necessary, but poly(A,U,G) increases the binding observed 1.5-fold. (v) The factor markedly stimulates synthesis in a reconstituted protein-synthesizing system with globin messenger RNA as template.     

Temperature-Dependent Gas Exchange and Stomatal/Non-Stomatal Limitation to CO2 Assimilation of Quercus Liaotungensis under Midday High Irradiance

The effects of varying leaf temperature (T ₁) on some ecophysiological characteristics of photosynthesis for Quercus liaotungensis Koiz. under ambient radiation stress around midday on clear summer days were investigated using an IRGA equipped with a temperature-controlled cuvette. Net photosynthetic rate (P _N) decreased as T ₁ increased from 30 to 35 °C as a result of stomatal closure, whereas non-stomatal limitation led to decreased P _N in the T ₁ range of 35–45 °C. Decreased transpiration rate (E) and stomatal conductance (g _s) at leaf temperatures above 30 °C were interpreted as a combined feedward effect as a result of enhanced leaf-air vapour pressure deficit (VPD) and stomatal closure. Changes in E from T ₁ 30 to 20 °C depended on VPD when g _s was maintained constant. Water use efficiency (WUE) varied inversely with T ₁ by following a hyperbola. A decrease in intercellular CO₂ concentration (C _i) occurred as a result of stomatal closure and a relatively high carboxylation capacity, whereas inactivation of mesophyll carboxylation in combination with photorespiration might be associated with the observed increase in C _i in the T ₁ range of 40 to 45 °C.     

Propulsive forces on the flagellum during locomotion of Chlamydomonas reinhardtii

The distributed propulsive forces exerted on the flagellum of the swimming alga Chlamydomonas reinhardtii by surrounding fluid were estimated from experimental image data. Images of uniflagellate mutant Chlamydomonas cells were obtained at 350 frames/s with 125-nm spatial resolution, and the motion of the cell body and the flagellum were analyzed in the context of low-Reynolds-number fluid mechanics. Wild-type uniflagellate cells, as well as uniflagellate cells lacking inner dynein arms (ida3) or outer dynein arms (oda2) were studied. Ida3 cells exhibit stunted flagellar waveforms, whereas oda2 cells beat with lower frequency. Image registration and sorting algorithms provided high-resolution estimates of the motion of the cell body, as well as detailed kinematics of the flagellum. The swimming cell was modeled as an ellipsoid in Stokes flow, propelled by viscous forces on the flagellum. The normal and tangential components of force on the flagellum (f_N and f_T) were related by resistive coefficients (C_N and C_T) to the corresponding components of velocity (V_N and V_T).The values of these coefficients were estimated by satisfying equilibrium requirements for force and torque on the cell. The estimated values of the resistive coefficients are consistent among all three genotypes and similar to theoretical predictions.     

Kinetic study on unzippering of polynucleotides and order-order transition in polypeptides

Solutions are presented for N + 1 sequential and reversible first-order reactions for which the magnitude of the reverse rate constant, k_b, for all steps except the last is identical. Also the magnitude of the forward rate constant, k_f, for all steps except the first and last is identical. The initial and final steps are nucleation reactions; therefore, the initial and final k_f are modified by the factors σ′ and γ respectively. The final k_b is modified by the factor γ σ. The ratio k_b/k_f is defined as s, which has the same meaning as s in the Zimm-Bragg theory. The mathematical model is intended to apply to polymeric molecules of N segments and allows the calculation of the mole fraction of molecules in state i at any time t, C_i(t). A molecule in state i has i unreacted segments and N – i reacted ones. Because the reactions are sequential, all reacted segments are contiguous. Our numerical results show that when σ′ is much less than unity and the forward reaction is favored, the relaxation curve is sigmoidal. If, however, the forward and reverse reactions are equally favored (i.e., s ? 1) the relaxation curve is a straight line. When s and σ′ are near unity, the curve is exponential for a considerably large fraction of the reaction. Further, in the exponential for a considerably large fraction of the reaction. Further, in the exponential phase of the reaction, the relaxation time is proportional to N² for highly cooperative systems (i.e., Nσ ? 1). As found by Pipkin and Gibbs, if N is sufficiently large and s is less than unity (e.g., N ? 50 and s ?0.9) the relaxation curve is largely linear with a slope inversely proportional to N. Applications are given for the unwinding of double-helical poly(A·U) and the order–order transition in poly-L -proline.     

The qualitative analysis of a difference equation of population growth

The difference equation f _b :[0,1]–[0,1] defined by f _b (x)=b x(1–x) is studied. In particular complete qualitative information is obtained for the parameter value b=3.83. For example the number of fixed points of (f _b )ⁱ is given by

Z-Spectrum Analysis Provides Proton Environment Data (ZAPPED): A New Two-Pool Technique for Human Gray and White Matter

A new technique – Z-spectrum Analysis Provides Proton Environment Data (ZAPPED) – was used to map cross-relaxing free and restricted protons in nine healthy subjects plus two brain tumor patients at 3T. First, MT data were acquired over a wide symmetric range of frequency offsets, and then a trio of quantitative biomarkers, i.e., the apparent spin-spin relaxation times (T_2,f, T_2,r) in both free and restricted proton pools as well as the restricted pool fraction F_r, were mapped by fitting the measured Z-spectra to a simple two-Lorentzian compartment model on a voxel-by-voxel basis. The mean restricted exchangeable proton fraction, F_r, was found to be 0.17 in gray matter (GM) and 0.28 in white matter (WM) in healthy subjects. Corresponding mean values for apparent spin-spin relaxation times were 785 µs (T_2,f) and 17.7 µs (T_2,r) in GM, 672 µs (T_2,f) and 23.4 µs (T_2,r) in WM. The percentages of F_f and F_r in GM are similar for all ages, whereas F_r shows a tendency to decrease with age in WM among healthy subjects. The patient ZAPPED images show higher contrast between tumor and normal tissues than traditional T₂-weighted and T₁-weighted images. The ZAPPED method provides a simple phenomenological approach to estimating fractions and apparent T₂ values of free and restricted MT-active protons, and it may offer clinical useful information.     

Multifrequency permittivity measurements enable on‐line monitoring of changes in intracellular conductivity due to nutrient limitations during batch cultivations of CHO cells

Lab and pilot scale batch cultivations of a CHO K1/dhfr^? host cell line were conducted to evaluate on‐line multifrequency permittivity measurements as a process monitoring tool. The β‐dispersion parameters such as the characteristic frequency (f_C) and the permittivity increment (Δε_max) were calculated on‐line from the permittivity spectra. The dual‐frequency permittivity signal correlated well with the off‐line measured biovolume and the viable cell density. A significant drop in permittivity was monitored at the transition from exponential growth to a phase with reduced growth rate. Although not reflected in off‐line biovolume measurements, this decrease coincided with a drop in OUR and was probably caused by the depletion of glutamine and a metabolic shift occurring at the same time. Sudden changes in cell density, cell size, viability, capacitance per membrane area (C_M), and effects caused by medium conductivity (σ_m) could be excluded as reasons for the decrease in permittivity. After analysis of the process data, a drop in f_C as a result of a fall in intracellular conductivity (σ_i) was identified as responsible for the observed changes in the dual‐frequency permittivity signal. It is hypothesized that the β‐dispersion parameter f_C is indicative of changes in nutrient availability that have an impact on intracellular conductivity σ_i. On‐line permittivity measurements consequently not only reflect the biovolume but also the physiological state of mammalian cell cultures. These findings should pave the way for a better understanding of the intracellular state of cells and render permittivity measurements an important tool in process development and control. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

Exogenous application of trehalose induced H2O2 production and stomatal closure in Vicia faba

Trehalose can reduce stomatal aperture by a hydrogen-peroxide-dependent pathway in Vicia faba L. (cv. Daqingpi) resulting in significantly lower values of net photosynthetic rate (P_N), stomatal conductance (g_s), and transpiration rate (E). At 8 and 24 h, the lower P_N in trehalose-treated plants was accompanied by significant decrease in intercellular CO₂ concentration (c_i) suggesting that the reduction of P_N was caused by stomatal limitation. At 48 and 72 h, trehalose decreased apparent carboxylation efficiency (P_N/c_i) and did not decrease c_i and g_s compared with controls; therefore the reduction in photosynthesis was caused by non-stomatal limitation. Trehalose treatment resulted in significantly higher effective photochemical efficiency of PS II (Φ_PSII) and did not affect maximum photochemical efficiency of PS II (F_v/F_m). At 24, 48, and 72 h, trehalose decreased non-photochemical quenching (NPQ) and increased photochemical quenching (qP). Our results suggest that trehalose did not damage photosynthetic reaction centers.     

Estimation of intracellular pH in muscle of fishes from different thermal environments

A technique based on homogenisation of rapidly frozen tissue was used to investigate the regulation of intracellular pH (pH_i) in freshwater and marine fish from diverse environmental temperatures. The following species were held at ambient temperatures of ca. 1°C (Notothenia coriiceps; Antarctica), 5°C (Pleuronectes platessa, Myoxocephalus scorpius; North Sea), and 26°C (Oreochromis niloticus; African lakes). The effects of seasonal acclimatisation to 4, 11 and 18°C were also examined in rainbow trout in the winter, autumn and summer, respectively. Extracellular (whole blood) pH (pH_e) did not follow the constant relative alkalinity relationship, where pH⁺=pOH⁻ for any particular temperature, over a range of 1–26°C (overall δpH_e/δT=0.009±0.002 U °C⁻¹; P<0.001), apparently being regulated by ionic fluxes and ventilation. Intracellular pH (pH_i) was also regulated independently of pN(=0.5 pK water) in all species of fish examined. The inverse relationship between pH_i and environmental temperature gave an overall δpH_i/δT of −0.010±0.001 U °C⁻¹ (for both white and red muscle) and −0.004±0.003 U °C⁻¹ (cardiac muscle). However, between 1 and 11°C δpH_i/δT was much higher (P<0.001), −0.022±0.003 U °C⁻¹ (white muscle) and −0.022±0.004 U °C⁻¹ (red muscle). The possible adaptive roles for these different acid–base responses to environmental temperature variation among tissues and species, and the potential difficulties of estimating pH_i, are discussed.     

Photorespiration and photoprotection of grapevine (<Emphasis Type="Italic">Vitis vinifera</Emphasis> L. cv. Cabernet Sauvignon) under water stress

In order to investigate the photoprotective function of photorespiration in grapevine under water stress, potted grapevines (Vitis vinifera L. cv. Cabernet Sauvignon) were randomly divided into three uniform groups for well-watered [watered every morning to keep the relative water content (RWC) of soil over 70 %], water-stress adapted (drought-adapted at 30 % relative soil water content for 30 days), and water stress without adaptation treatment (water-stressed to 30 % relative soil water content for 3 days). Net assimilation rate (A _N), stomatal conductance (g _s), substomatal CO₂ concentration (C _i), transpiration rate (E), actual photochemical efficiency of PSII (Φ_PSII), and maximum photochemical efficiency of PSII (F_v/F_m) were recorded by combining measurements of gas exchange and chlorophyll fluorescence. Gross photorespiration (P_r), photosynthetic electron partitioning (J_C/J_T), photochemical quenching coefficient (qP), and non-photochemical quenching (NPQ) were also calculated. The ratio of net assimilation rate to transpiration rate (A _N/E) was used as an indicator of water use efficiency (WUE). A _N, apparent P_r, Φ_PSII, F_v/F_m, qp, and g _s decreased, NPQ increased, and gross P_r sustained at a high level under water stress. This suggests that both photorespiration and energy dissipation play important roles in protecting photosynthetic apparatus against photoinhibition. C _i in water-stressed plants without adaptation treatment increased, which indicates the leaves suffered a non-stomatal limitation, while the water-stress adaped plants only suffered a stomatal limitation indicated by low C _i.     

Considerations of correlated fertility between genders on genetic diversity: the Pinus densiflora seed orchard as a model

The correlation between 99 clone female and male fertilities in a first generation seed orchard of Pinus densiflora was studied over 6 years. The effective number of the parent (N_p) and the variance effective population number [N_e^(v)] were used to assess the impact of total (O_T), female (N_f) and male (N_m) fertility variation. A theoretical framework was developed to account for female and male fertility correlations as well as the impact of possible pollen contamination. Total fertility variation was described by the sibling coefficient (O_T: the probability that two genes randomly chosen from the gamete gene pool originate from the same parent), which was further subdivided into N_f and N_m. These parameters were compared under various conditions including the total seed harvest, imposing on equal seed harvest among the orchard's clones and two contamination scenarios (M = 0 and 20%). Fertility variations among females, males and clones were observed within and among years. Sibling coefficients (O_T) were lower, but the effective number of parent (N_p) and variance effective population number (N_e^(v)) were higher in years with moderate female and good male strobilus production. N_p for female and male reproductive outputs varied from 49 to 82 and from 57 to 93, respectively. N_p was higher for males than females. When the crop of the 6 years was pooled, N_p for female, male and the clone were 73, 87 and 85, respectively. The impact of female-male fertility correlation for conditions with no-, positive- and negative-correlations were assessed and their impact on O_T, N_p and N_e^(v) was also evaluated. It was demonstrated that the practice of equal seed harvesting from every clone, or the mixing of seeds from several years, would substantially improve the genetic diversity and the genetic representation of the seed orchard population when a positive correlation between gender fertilities was observed. The relevance of these results to supplemental-mass-pollination was discussed under two cases where equal- and un-equal amounts of pollen from clones were included in the pollen mixes.     

Analysis of protein crystallographic structural data: analysis of the orientation of peptide planes

A new dihedral angle parameter θ′, defined by C_i?1|N_i…C_i|N_i+1, involving pairs of backbone atoms in two adjacent peptide planes is used in this paper to analyse the relative orientation of the peptide planes in a protein chain. The equiangle contours for this parameter on the ?+ψ in an approximately linear way. Thus, θ′ serves as a good single parameter representation for chainfolding characterization by bringing out the relative orientation of successive peptide planes. Unlike the earlier proposed θ which gives the gross folding features, θ′ can be applied for nonregular helical features. Its utility in the detection of bend regions in protein chains is compared with that of θ through theoretically calculated tables as well as examples from actual proteins.     

Effect of incubation temperature and androgens on dopaminergic activity in the leopard gecko, Eublepharis macularius

Male leopard geckos that hatch from eggs incubated at a female‐biased temperature (T_f) behave differently when compared with males hatching at a temperature which produces a male‐biased sex ratio (T_m). We investigated the effect of incubation temperature and androgen implantation on aspects of the dopaminergic system of T_f and T_m males. Our data suggest that more dopamine (DA) is stored in the nucleus accumbens of naive T_f males compared with naïve T_m males when they encounter a receptive female conspecific across a barrier. No difference was measured in the preoptic area and the ventral tegmental area (VTA). This difference in intracellular DA levels in a motivation‐related brain nucleus might be correlated with differences in sociosexual behavior observed between the two morphs. There were no differences in tyrosine hydroxylase (TH) expressing cell numbers in the VTA of cholesterol (CH)‐implanted naive castrated T_f and T_m males. Only T_f males implanted with testosterone had significantly higher TH immunopositive cell numbers in the VTA compared with CH‐ and dihydrotestosterone‐implanted T_f males. These data indicate that both the embryonic environment as well as the circulating hormonal milieu can modulate neurochemistry, which might in turn be a basis for individual variation in behavior. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007