Theoretical basis of the Beavis effect

The core of statistical inference is based on both hypothesis testing and estimation. The use of inferential statistics for QTL identification thus includes estimation of genetic effects and statistical tests. Typically, QTL are reported only when the test statistics reach a predetermined critical value. Therefore, the estimated effects of detected QTL are actually sampled from a truncated distribution. As a result, the expectations of detected QTL effects are biased upward. In a simulation study, William D. Beavis showed that the average estimates of phenotypic variances associated with correctly identified QTL were greatly overestimated if only 100 progeny were evaluated, slightly overestimated if 500 progeny were evaluated, and fairly close to the actual magnitude when 1000 progeny were evaluated. This phenomenon has subsequently been called the Beavis effect. Understanding the theoretical basis of the Beavis effect will help interpret QTL mapping results and improve success of marker-assisted selection. This study provides a statistical explanation for the Beavis effect. The theoretical prediction agrees well with the observations reported in Beavis's original simulation study. Application of the theory to meta-analysis of QTL mapping is discussed.     

A community effect in muscle development

BACKGROUND: Most vertebrate tissues arise by embryonic induction, as a result of which new cell layers are formed. These are subsequently subdivided into discrete groups of homogeneous cell populations, each containing different cell-types with specific gene expression. There is preliminary evidence from previous work that the mesoderm-forming induction in amphibian development may be followed by a further interaction among some of the induced mesoderm cells, and that this could be required for muscle gene activation in uniform cell populations. RESULTS: We have established the existence, time and place of this further cell interaction by transplanting muscle progenitor cells from Xenopus mid-gastrulae into ectoderm sandwiches, and then culturing these constructs until the time of muscle gene activation. We find that cells implanted as reaggregates, but not those implanted as single cells, activate early myogenic genes and later muscle-specific genes. More than 100 cells must be near each other for muscle gene activation. These cells can induce non-muscle mesoderm cells to express muscle genes by emitting a signal that differs from the preceding mesoderm induction signal. Muscle gene activation under these conditions does not require gap junction communication. CONCLUSION: Cells within the muscle progenitor region of a Xenopus embryo need to interact with each other in order to activate muscle genes in homogeneous cell groups. This exemplifies the 'community effect', which may be a widespread developmental mechanism used to increase the homogeneity within, and demarkation between, embryonic tissues.     

Theoretical basis of the plant domestication

Summary Plant domestication is stimulated by economic demands. Crop plant formation is controlled primarily by natural selection in cultivation; artificial selection is only a useful addition. The ecotypical nature of the initial material has great bearing on the success of domestication. The weeds of a convergent group were well adapted to being cultivated; weeds of a divergent group can be domesticated only with difficulty. Wild plants in nature are extremely varied ecotypically: some can be domesticated easily, others with difficulty. Some wild plants and weeds can be cultivated without genetic change (naturalization), while a genetic transmutation is necessary for the domestication of others (acclimatization). New domesticated ecotypes can be produced: 1. as a result of reconstruction of the initial populations and new ecotype synthesis on the basis of individual genotypes; 2. by means of hybridization of wild or weed initial genotypes with cultivated ones; 3. by use of new mutations in cultivation and further plant breeding.     

Theoretical basis for predicting climate-induced abrupt shifts in the oceans

Among the responses of marine species and their ecosystems to climate change, abrupt community shifts (ACSs), also called regime shifts, have often been observed. However, despite their effects for ecosystem functioning and both provisioning and regulating services, our understanding of the underlying mechanisms involved remains elusive. This paper proposes a theory showing that some ACSs originate from the interaction between climate-induced environmental changes and the species ecological niche. The theory predicts that a substantial stepwise shift in the thermal regime of a marine ecosystem leads indubitably to an ACS and explains why some species do not change during the phenomenon. It also explicates why the timing of ACSs may differ or why some studies may detect or not detect a shift in the same ecosystem, independently of the statistical method of detection and simply because they focus on different species or taxonomic groups. The present theory offers a way to predict future climate-induced community shifts and their potential associated trophic cascades and amplifications.     

Theoretical basis of protocols for seed storage

The protocols presently established for optimum seed storage do not account for the chemical composition of different seed species, the physiological status of the seed, and the physical status of water within the seed. The physiological status of seeds from five species with varying chemical compositions was determined by measurements of rates of oxygen uptake and seed deterioration. The physical status of water was determined by water sorption characteristics. For each species studied, there was a specific moisture content for the onset of respiration, chemical reactions, and accelerated aging rates. The moisture contents at which these physiological levels were observed varied among the species and correlated with the lipid content of the seed. However, the changes in physiological activities and the physical status of water occurred at specific relative humidities: 91% for the onset of respiration, 27% for the increased rates of thermal-chemical reactions, and 19% for optimum longevity. Based on these observations, we propose that equilibrating seeds between 19 and 27% relative humidity provides the optimum moisture level for maintaining seed longevity during longterm storage.     

The basis of the hydrophobic effect

The property of a molecule that most reliably determines the magnitude of the hydrophobic effect that it will experience is the number of hydrogen–carbon bonds it contains not the accessible surface area of its nonpolar portions. This conclusion follows from an examination of the standard free energies of transfer of alkanes, alkenes, alkadienes, and arenes from water to hexadecane. When the standard free energies of transfer for hydrocarbons in these different classes are plotted as a function of the number of hydrogen–carbon bonds they contain, all of the data fall upon the same line. These standard free energies of transfer are also directly proportional to the number of hydrogen–carbon bonds the hydrocarbons contain. When the same standard free energies of transfer are plotted as a function of the accessible surface areas of the hydrocarbons, the data do not fall upon the same line nor are the standard free energies of transfer directly proportional to the accessible surface areas. An examination of the standard free energies of transfer for the different classes of hydrocarbons from the gas phase to water and from the gas phase to hexadecane reinforces the conclusion that the number of hydrogen–carbon bonds in a molecule rather than its accessible surface area is the basis of the hydrophobic effect. Consequently, estimates of the contribution of different functional groups to the hydrophobic effect providing the free energy of folding of a molecule of protein or providing the free energy of dissociation for the association of two proteins or the association of a ligand with a protein should be made by counting the number of hydrogen–carbon bonds excluded from water rather than computing the accessible surface areas excluded from water.     

Theoretical basis of single breath gas absorption tests

Absorption of gas from alveoli is examined in a simplified model of the respiratory system during a stylized single breath consisting of constant inspiratory flow, constant expiratory flow, and breathholding. The equations describing gas behavior are general since they are based upon conservation of mass. The equations simplify considerably when gases that are not soluble in pulmonary tissue and/or blood are utilized. In a three-compartment model, diffusing capacity of the lung for carbon monoxide (D _CO ) will be underestimated except when both uneven distribution of lung volume andD _CO are present; under most circumstances, the standard clinical 10-s method [9] is at least as accurate as any other. When pulmonary capillary blood flow is calculated by the one point method [2] in a one-compartment lung, it is underestimated; in the three-compartment model, it is underestimated except when both uneven distribution of . and lung volume are present. The multiple single breath method [2] accurately measuresD _CO and . Measurement of pulmonary tissue volume is improved by correcting the value of the intercept of acetylene absorption to the time when carbon monoxide apparently began rather than utilizing the beginning of inspiration.Nomenclature D _CO diffusing capacity of the lung for CO (ml CO, STPD/min/mm Hg) - pulmonary capillary blood flow rate (L/min) - V _t pulmonary tissue volume (L) - V _A alveolar compartment volume (L) - V _Ao alveolar compartment volume at conclusion of inspiratory flow (L) - inspiratory flow rate (L/sec) - expiratory flow rate (L/sec) - Bunsen coefficient of pulmonary tissue for test gas (ml test gas/ml tissue/atm) - Bunsen coefficient of pulmonary tissue for test gas (ml test gas/ml blood/atm) - F _A fractional pressure of test gas in the alveolar compartment (atm)     

The epigenetic basis of the Warburg effect

Cancer development results from the accumulation of genetic and epigenetic changes. By interacting with intracellular signaling to promote carcinogenesis, epigenetic networks can actively transform cancer–promoting signals from tumor-permissive microenvironment to coordinate cellular proliferation and metabolism in the initiation and progression of cancers. As reported recently, NF-kappaB which can be activated by many soluble bioactive factors enriched in tumor microenvironments can promote the switch of cellular glucose metabolism from oxidative phosphorylation to oxygen-independent glycolysis in tumor cells, in addition to its well-known anti-apoptosis functions. Such epigenetic trans-generation of microenvironmental factors plays important roles in the development of cancers, particularly inflammation-related or sporadic cancers.     

The effect of lactating rabbit does on the development of the caecal microbial community in the pups they nurture

AIMS: To study the effect of microbial community of the rabbit does as influenced by dietary factors, on the development of the gut microbiota of their litters. METHODS AND RESULTS: Twenty-four lactating does were given a diet unsupplemented (NAB) or with 100 ppm of bacitracin (BAC) or tiamulin (TIA) to modify their digestive microbiota. Litters were adjusted to six pups. In Trial 1, four does per diet milked their own six pups. In Trial 2, two does per diet nursed three of their pups and three fostered from the doe given the same diet. In Trial 3, two does on each diet nursed three of their pups and three fostered from another doe fed on another diet. Denaturing gradient gel electrophoresis (DGGE) analyses of the litter microbiota showed that the effect of the milking mother was greater than the influence of the biological mother. TIA had a strong effect on the bacterial profile even prevailing over that of the milking mother, in contrast to BAC. CONCLUSIONS: Nursing mother microbiota plays an important role over that of the litter. Caecal colonization that occurs during the lactation process prevailed over that during the partum. SIGNIFICANCE AND IMPACT OF THE STUDY: Manipulation of the mother's microbiota may help for adaptation of the litter microbial community against pathologic digestive processes.     

Molecular basis of the Bohr effect in arthropod hemocyanin

Flash photolysis and K-edge x-ray absorption spectroscopy (XAS) were used to investigate the functional and structural effects of pH on the oxygen affinity of three homologous arthropod hemocyanins (Hcs). Flash photolysis measurements showed that the well-characterized pH dependence of oxygen affinity (Bohr effect) is attributable to changes in the oxygen binding rate constant, k(on), rather than changes in k(off). In parallel, coordination geometry of copper in Hc was evaluated as a function of pH by XAS. It was found that the geometry of copper in the oxygenated protein is unchanged at all pH values investigated, while significant changes were observed for the deoxygenated protein as a function of pH. The interpretation of these changes was based on previously described correlations between spectral lineshape and coordination geometry obtained for model compounds of known structure (Blackburn, N. J., Strange, R. W., Reedijk, J., Volbeda, A., Farooq, A., Karlin, K. D., and Zubieta, J. (1989) Inorg. Chem., 28, 1349-1357). A pH-dependent change in the geometry of cuprous copper in the active site of deoxyHc, from pseudotetrahedral toward trigonal was assigned from the observed intensity dependence of the 1s --> 4p(z) transition in x-ray absorption near edge structure (XANES) spectra. The structural alteration correlated well with increase in oxygen affinity at alkaline pH determined in flash photolysis experiments. These results suggest that the oxygen binding rate in deoxyHc depends on the coordination geometry of Cu(I) and suggest a structural origin for the Bohr effect in arthropod Hcs.     

半干旱地区林业发展的理论基础评介<中国沙地森林生态系统>一书

沙地森林是分布在我国半干旱草原区沙地上的以大 (中 )高位芽植物为建群种形成的森林群落。由于其独特的生态条件、丰富的生物多样性和重要的生态系统功能 ,对我国北方防风固沙、控制土地沙漠化、“三北”防护林体系建设 ,以及对我国西部大开发具有重大的生态效益、经济效益和社会效益。《中国沙地森林生态系统》是由我国植物生态学家徐文铎研究员和邹春静副研究员等 8位专家 ,潜心研究多年 ,共同完成 ,已于 1 998年 1 2月由国家科学技术学术著作出基金资助 ,中国林业出版社出版。它是我国沙地天然林生态系统研究的专著 ,是研究半干旱地区林…     

Genetic basis of skin appendage development

Morphogenesis of hair follicles, teeth, and mammary glands depends on inductive epithelial-mesenchymal interactions mediated by a conserved set of signalling molecules. The early development of different skin appendages is remarkably similar. Initiation of organogenesis is marked by the appearance of a local epithelial thickening, a placode, which subsequently invaginates to produce a bud. These early developmental stages require many of the same genes and signalling circuits and consequently alterations in them often cause similar phenotypes in several skin appendages. After the bud stage, these organs adopt diverse patterns of epithelial growth, reflected in the usage of more divergent genes in each.     

Theoretical analysis of the DNA duplication mechanisms in the prokaryotic genomes on the basis of repeats

In the present work a theoretical analysis of the molecular mechanisms on duplications emergence in the genomes of prokaryotes on the basis of direct repeats has been carried out. The correlations obtained have shown, that the duplication rate depends on such parameters as the distance between repeated regions, repeats nucleotide composition and the number of homology damages in them. It has been revealed that the rate of duplications decreases more readily than the deletion rate upon the growth of the distance between the repeats. Such prevalence of deletions over duplications must lead to the elimination of various types of direct repeats from the prokaryotic genomes in the course of their evolution.     

The neural basis of the behavioral face-inversion effect

Two of the most robust markers for "special" face processing are the behavioral face-inversion effect (FIE)-the disproportionate drop in recognition of upside-down (inverted) stimuli relative to upright faces-and the face-selective fMRI response in the fusiform face area (FFA). However, the relationship between these two face-selective markers is unknown. Here we report that the behavioral FIE is closely associated with the fMRI response in the FFA, but not in other face-selective or object-selective regions. The FFA and the face-selective region in the superior temporal sulcus (f_STS), but not the occipital face-selective region (OFA), showed a higher response to upright than inverted faces. However, only in the FFA was this fMRI-FIE positively correlated across subjects with the behavioral FIE. Second, the FFA, but not the f_STS, showed greater neural sensitivity to differences between faces when they were upright than inverted, suggesting a possible neural mechanism for the behavioral FIE. Although a similar trend was found in the occipital face area (OFA), it was less robust than the FFA. Taken together, our data suggest that among the face-selective and object-selective regions, the FFA is a primary neural source of the behavioral FIE.