There is a difference between scientific hypothesis and the "phylogenetic presumption" by Rasnitsyn (concerning the paper by I.Ia. Pavlinov, 2005. J. Gen. Biology. V. 66. No 5)

The arguments by Pavlinov against my critical analysis of the concept of the "phylogenetic presumptions" proposed by Rasnitsyn are briefly discussed. It is proved that these arguments are invalid because they are based on the substitution of terms. Instead of the term "phylogenetic presumption" introduced by Rasnitsyn just as an analogue of the presumption of innocence in jurisprudence, Pavlinov considers the presumption in the wider understanding, i.e. as a "preliminary statement".     

Application of multilevel models to morphometric data. Part 2. Correlations.

Multilevel organization of morphometric data (cells are "nested" within patients) requires special methods for studying correlations between karyometric features. The most distinct feature of these methods is that separate correlation (covariance) matrices are produced for every level in the hierarchy. In karyometric research, the cell-level (i.e., within-tumor) correlations seem to be of major interest. Beside their biological importance, these correlation coefficients (CC) are compulsory when dimensionality reduction is required. Using MLwiN, a dedicated program for multilevel modeling, we show how to use multivariate multilevel models (MMM) to obtain and interpret CC in each of the levels. A comparison with two usual, "single-level" statistics shows that MMM represent the only way to obtain correct cell-level correlation coefficients. The summary statistics method (take average values across each patient) produces patient-level CC only, and the "pooling" method (merge all cells together and ignore patients as units of analysis) yields incorrect CC at all. We conclude that multilevel modeling is an indispensable tool for studying correlations between morphometric variables.     

The affected sib method. III. Selection and recombination.

The affected sib-pair method has been used to investigate the mode of inheritance, and to estimate the "disease" allele frequency, for a number of HLA-associated diseases. One of the assumptions of the original sib-pair method is that the disease confers no selective disadvantage on affected individuals. This is obviously not the situation for most diseases. We have determined the expected HLA haplotype-sharing distribution among affected sib-pairs when selection against individuals with the disease is taken into account. We have shown that if the mode of inheritance of the selectively disadvantageous disease is recessive or additive, the original affected sib-pair analysis, ignoring selection, still estimates the true mode of inheritance, but usually yields an underestimate of the "disease" allele frequency. For intermediate and dominant models of disease predisposition, both the estimates of the degree of penetrance of the "disease" genotypes, and the "disease" allele frequency, are altered if selection is ignored in the analysis. Similarly, allowing for recombination between the "disease" locus and the HLA region does not affect the determination of the mode of inheritance of the disease if it is recessive or additive; in other cases, however, the estimate of the mode of inheritance is affected. The "disease" allele frequency is overestimated when nonzero recombination is ignored for all the modes of inheritance that have been studied.     

Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b

Several years ago, prochlorophyte picoplankton were discovered in the N. Atlantic. They have since been found to be abundant within the euphotic zone of the world's tropical and temperate oceans. The cells are extremely small, lack phycobiliproteins, and contain divinyl chlorophyll a and b as their primary photosynthetic pigments. Phylogenies constructed from DNA sequence data indicate that these cells are more closely related to a cluster of marine cyanobacteria than to their prochlorophyte relatives Prochlorothrix and Prochloron. Several strains of this organism have recently been brought into culture, and herewith are given the name Prochlorococcus marinus.     

Erratum to: Singh R.K. and Gunjan A. Histone tyrosine phosphorylation comes of age. Epigenetics 2011; 6:153-60.

We recently noticed that there is a major error in Figure 1 of our review published in Epignetics 2010, Volume 6, Issue 2. During the preparation of the figure, the human and yeast H2B tyrosines were numbered the same, making the human numbering incorrect. The correct Figure 1 with proper numbering of human tyrosines is below.Erratum to:Singh R.K. and Gunjan A. Histone tyrosine phosphorylation comes of age.Epigenetics 2011; 6:153-60.We recently noticed that there is a major error in Figure 1 of our review published in Epignetics 2010, Volume 6, Issue 2. During the preparation of the figure, the human and yeast H2B tyrosines were numbered the same, making the human numbering incorrect. The correct Figure 1 with proper numbering of human tyrosines is below.Open in a separate windowFigure 1. Tyrosine residues are highly conserved between budding yeast and mammalian core histones. The four canonical core histone proteins from the budding yeast Saccharomyces cerevisiae are indicated by the prefix “Sc” and denoted in blue. The mammalian core histones and the mammalian variant histone H2A.X are shown in black. The number of amino acid (aa) residues in each core histone is indicated on the right. The location of the a-helices in the secondary structure of the histone proteins is indicated by cylinders. Tyrosine residues are shown as balloons and the tyrosine residues essential for viability in budding yeast histones are indicated by red balloons. Tyrosines in mammalian histones have not yet been evaluated to determine the residues essential for viability. Note the high degree of conservation of the location as well as the spacing of all but one tyrosine residue between budding yeast and mammalian core histones (H3 Y54 being the exception). Tyrosine residues that have recently been shown to be phosphorylated in vivo are marked by yellow “explosion” signs and the letter “P.” Additional tyrosine residues that are predicted to be reasonably accessible in the nucleosomal context under certain conditions and can be potentially phosphorylated in vivo are indicated by a yellow halo only on the mammalian histones for clarity, but are likely to be just as applicable to the yeast histones. Solid yellow halo indicates higher probability of phosphorylation, while a dashed yellow halo indicates lower probability of phosphorylation.     

The endocrine cells of the rectum of adult ox.

In order to identify the endocrine cell types in various parts of the Ruminant gut, we have applied ultrastructural, both morphological and cytochemical, techniques, in parallel to the histochemical ones, to study the rectal mucosa of the adult Ox. In these studies we show that: "EC" cells, of the intestinal type, contain predominantly pleiomorphic granules, which are very electron dense and heavily reactive to "Masson" and "Grimelius" methods; "L" cells are recognizable by their numerous granules, which are fairly homogeneous in shape and osmiophilia. They do not react with "Masson" and are weak or negative to Grimelius s reaction. These granules occur near to others that are less dense, unreactive to "Masson", and that contain an argyrophilic matrix, with an eccentric electron dense core, which does not react with silver; "F-like" cells contain granules which are variable in shape, size and osmiophilia. They are unreactive to "Masson" and weak or unreactive to Grimelius silver; "H" cells contain few, small and uniformly osmiophilic granules. These are unreactive to "Masson" and uniformly reactive to "Grimelius". Our data suggest that the morphology, frequency and distribution of the cell types we have identified in the mucosa of the bovine rectum correspond with those reported in large intestine and rectum of Monogastrics, as by other authors described.     

Interaction between hydroxystilbamidine and DNA. II. Temperature jump relaxation study. Dynamics of nucleic acids and polynucleotides.

A temperature-jump relaxation study of the interaction of hydroxystilbamidine with DNA and synthetic polynucleotides has been performed. Two concentration dependent relaxation times tau1 and tau2 have been observed in the submillisecond range when detecting relaxation effects by means of light absorption. The longer of these two times (tau1) is also observed when using "blue" or "red" fluorescence detection. In the longer time scale the "red" fluorescence shows no other relaxation but the blue fluorescence shows two additional relaxation processes (tau3 and tau4) which correspond to an increase of fluorescence with temperature and which are independent of concentration. The experimental results clearly indicate that tau1 and tau2 are associated with the binding of the dye to strong and weak binding sites, respectively. A kinetic model is given to explain the results. It allows the determination of the four rate constants for the two binding reactions and yields equilibrium association constants in good agreement with those obtained from stoichiometric studies. The study of the effect of temperature, nature of the polymer, ionic strength and fraction of bound dye on tau3 and tau4 indicates that the dye acts only as a "blue" fluorescence probe of some processes involving the DNA or polynucleotide alone. These processes appear to be related with the dynamic structure of the polymers.     

Cholinergic sites in skeletal muscle. I. Denervation effects.

Cholinergic interactions in systems derived from rat skeletal mixed muscle are detailed. The isotherms of the binding of [125I]diiodo-alpha-bungarotoxin over the range of 10(-10)-10(-5) M toxin have been separated into a "nonspecific" component exclusive to the toxin and a "specific" component that binds both the toxin and d-tubocurarine. The "specific" component appears to reflect two independent sets of binding sites. One of the sets has an affinity constant on the order of 10(9) M-1. Following denervation, the number of sites in this high-affinity set begins to increase after 3 days, reaches a peak (28-fold higher than normal) on the 8th day, and begins to decline. Similar results are obtained when sensitivity of this set to an antibody derived from patients with myasthenia gravis is examined. This sensitivity is reflected by the inhibition of the alpha-bungarotoxin binding by the myasthenic IgG fraction. Following denervation, sensitivity first appears on day 3 progresses coincidentally with the increase in new sites in the set. The charcteristics of this set suggest that it represents the acetylcholine receptor and that the new sites appearing during the course of denervation are extrajunctional receptor sites. The interaction with the myasthenic IgG indicates an antigenic difference between junctional and extrajunctional receptors. The second set of specific binding sites has an affinity constant on the order of 10(5) M-1. The number of sites in this set increases only fivefold as a result of denervation. The increase also begins between days 2 and 3. The definition of this low affinity set of sites is not presently clear.     

Crop/Weed gene flow:Cucurbita argyrosperma Huber andC. fraterna L. H. Bailey (Cucurbitaceae)

A mixed population of Cucurbita at Vado El Mow in northern Tamaulipas, Mexico showed an anomalous pattern of fruit bitterness. Some domesticated plants (C. argyrosperma andC. moschata) expressed cucurbitacin bitterness whereas some sympatric free-living plants produced non-bitter fruits. This reversal of typical cucurbitacin expression suggested gene flow between crop and weed at the site. Isozyme analysis provided little insight as to taxa involved in gene exchange, although progeny from a single free-living plant carried IDH allozymes that are associated with Mexican landraces ofC. pepo. Synthetic hybridization revealed that fertile F, hybrids are produced from crosses involvingC. fraterna as the pistillate parent andC. argyrosperma as the staminate parent. Interspecific crop/weed hybrids can produce viable progeny upon self-pollination or backcrossingto either parent, andF₂ families display normal allozyme segregation. Hybrid fertility, as indicated by pollen stainability, increases in progeny produced by backcrossingfrom theC. argyrosperma parent. Interspecific hybridfertility represents a potential for crop/weed gene flow that would be realized under natural conditions if pollen flow occurs betweenC. fraterna andC. argyrosperma in the fields of Tamaulipas. Oligolectic “squash bees” (Teponapis), efficientCucurbita pollen vectors, are present at the site. Thus, it is likely that natural interspecific crop/weed hybridization has occurred at Vado El Moro and this might at least partially explain the anomalous distribution of fruit bitterness among extant populations at the site.     

The structure of kinetoplast DNA. 2. Characterization of a novel component of high complexity present in the kinetoplast DNA network of Crithidia luciliae.

1. Degradation of highly purified kinetoplast DNA (kDNA) networks with restriction endonucleases yields "extra" bands in agarose gels that are absent from digests of mini-circles. Each of the five endonucleases tested, i.e. AluI, HapII, EcoRI, Hsu and HindII + III, yields a unique set of "extra" bands. The "extra" bands consist of linear DNA; they are not mini-circle oligomers and their added molecular weight, calculated from mobility in gels, are around 2 X 10(7). Double digests with two restriction endonucleases yield a new set of "extra" bands, showing that the "extra" bands obtained with different enzymes are all derived from the same complex component of kDNA. In digests of 32P-labelled kDNA an average of 2.3% of the radioactivity is recovered in the "extra" bands. 2. Treatment of kDNA networks with the single-strand-specific S1 nuclease of Aspergillus oryzae preferentially releases a linear DNA with a molecular weight of 26 X 10(6), calculated from mobility in gels. We present evidence that the 'extra' bands obtained with restriction endonucleases are derived from this component. 3. DNA-DNA renaturation analysis of fragmented kDNA shows the presence of a minor complex component with a complexity of about 3 X 10(7), making up less than 10% of the total kDNA. 4. From these results we conclude that 3--5% of the kDNA consists of a homogeneous class of maxi-circles catenated in the mini-circle network. The molecular weight of these maxi-circles is about 26 X 10(6) and they contain a unique, non-repetitive, non-mini-circle nucleotide sequence. This component is a prime candidate for the true mitochondrial DNA of trypanosomes.     

The persistence of the R.A. Fisher-Sewall Wright controversy

This paper considers recent heated debates led by Jerry A. Coyne andMichael J. Wade on issues stemming from the 1929–1962 R.A. Fisher-Sewall Wrightcontroversy in population genetics. William B. Provine once remarked that theFisher-Wright controversy is central, fundamental, and very influential.Indeed,it is also persistent. The argumentative structure of therecent (1997–2000) debates is analyzed with the aim of eliminating a logicalconflict in them, viz., that the two sides in the debates havedifferent aims and that, as such, they are talking past each other. Given aphilosophical analysis of the argumentative structure of the debates,suggestions supportive of Wade's work on the debate are made that areaimed, modestly, at putting the persistent Fisher-Wright controversy on thecourse to resolution.     

Modeling Lignin Polymerization. I. Simulation Model of Dehydrogenation Polymers

Lignin is a heteropolymer that is thought to form in the cell wall by combinatorial radical coupling of monolignols. Here, we present a simulation model of in vitro lignin polymerization, based on the combinatorial coupling theory, which allows us to predict the reaction conditions controlling the primary structure of lignin polymers. Our model predicts two controlling factors for the β-O-4 content of syringyl-guaiacyl lignins: the supply rate of monolignols and the relative amount of supplied sinapyl alcohol monomers. We have analyzed the in silico degradability of the resulting lignin polymers by cutting the resulting lignin polymers at β-O-4 bonds. These are cleaved in analytical methods used to study lignin composition, namely thioacidolysis and derivatization followed by reductive cleavage, under pulping conditions, and in some lignocellulosic biomass pretreatments.Lignins are aromatic polymers that are predominantly present in secondarily thickened cell walls. These polymers make the cell wall rigid and impervious, allowing transport of water and nutrients through the vascular system and protecting plants against microbial invasion. Lignins are heterogeneous polymers derived from phenylpropanoid monomers, mainly the hydroxycinnamyl alcohols coniferyl alcohol (G-monomer) and sinapyl alcohol (S-monomer) and minor amounts of p-coumaryl alcohol (H-monomer). These monolignols differ in their degree of aromatic methoxylation (-OCH₃ group; Fig. 1). The resulting units in the lignin polymer are the guaiacyl (G), syringyl (S), and p-hydroxyphenyl (H) units. They are linked by a variety of chemical bonds (Fig. 2) that have different chemical properties (Boerjan et al., 2003; Ralph et al., 2004; Vanholme et al., 2008).Open in a separate windowFigure 1.Chemical structures of three monolignols. A, H-monomer (p-coumaryl alcohol). B, G-monomer (coniferyl alcohol). C, S-monomer (sinapyl alcohol). G- and S-monomers are considered in our simulations. The G-monomer is methoxylated (-OCH₃ group) on position 3, and the S-monomer is methoxylated on positions 3 and 5.Open in a separate windowFigure 2.Chemical structures resulting from the possible bonding between two monomers (A) or a monomer and the bindable end of an oligomer (B). X and Y in the monomers denote the absence (for a G-unit) or presence (for an S-unit) of a methoxyl group at position 5 (see Fig. 1). The red line indicates the bonds generated by couplings of the B position and B, 4, or 5 position.Lignification is the process by which monomers and/or oligomers are polymerized via radical coupling reactions and typically occurs after the polysaccharides have been laid down in the cell wall. Lignin composition varies among cell types and can even be different in individual cell wall layers (Ruel et al., 2009). Lignin composition is also influenced by environmental conditions; for example, lignin in compression wood is enriched in H-units (Timell, 1986). Hence, both developmental and environmental parameters influence the composition and thus the structure of the lignin polymer (Boerjan et al., 2003; Ralph et al., 2004).Lignin is one of the main negative factors in the conversion of lignocellulosic plant biomass into pulp and bioethanol (Lynd et al., 1991; Hill et al., 2006). In these processes, lignin needs to be degraded by chemical or mechanical processes that are expensive and often environmentally polluting. Hence, major research efforts are devoted toward understanding lignin biosynthesis and structure. It has already been shown that reducing lignin content and modifying its composition in transgenic plants can result in dramatic improvements in pulping efficiency (Pilate et al., 2002; Baucher et al., 2003; Huntley et al., 2003; Leplé et al., 2007) and in the conversion of biomass into bioethanol (Stewart et al., 2006; Chen and Dixon, 2007; Custers, 2009). These altered biomass properties are related to the alterations in lignin composition and structure in terms of the frequencies of the lignin units and the bond types connecting them and possibly also their interaction with hemicelluloses (Ralph et al., 2004; Ralph, 2006).To study the parameters that influence lignin structure, lignin polymerization has been mimicked in vitro by experiments with dehydrogenation polymers (DHPs; Terashima et al., 1995). Indeed, lignification can be mimicked by oxidizing monolignols using a peroxidase, such as horseradish peroxidase (HRP), and supplying its cofactor hydrogen peroxide, producing synthetic DHP lignins. Monolignol oxidation can also be achieved without enzymes (e.g. by using transition metal one-electron oxidants, such as copper acetate). Some of these biomimetic DHPs have been suggested to be better models for wood lignins than HRP-generated DHPs (Landucci, 2000).In DHP experiments, the monolignols are either added in bulk (Zulauf experiment) or dropwise (Zutropf experiment) to the reaction mixture, yielding lignin polymers with very different bond frequencies (Freudenberg, 1956). Zutropf experiments approach the in vivo formation of lignin, which depends on the slow introduction of monolignols into the wall matrix via diffusion to the site of incorporation (Hatfield and Vermerris, 2001). Because the exact reaction conditions are known, such in vitro experiments have provided insight into the lignification process in planta. In this way, numerous factors were shown to influence lignin structure, including the relative supply of the monolignols, the pH, the presence of polysaccharides, hydrogen peroxide concentrations, and cell wall matrix elements in general (Grabber et al., 2003; Vanholme et al., 2008).Computer simulations of lignin polymerization can help explain and predict lignin structure from low-level chemical kinetic factors, including subunit-coupling probabilities and monolignol synthesis rates. Such models are helpful in explaining the mechanism behind a range of controlling factors identified in the experimental work, including (1) the ratio of coniferyl versus sinapyl alcohol monolignols, (2) the monolignol supply rate, and (3) the abundance of alternative monomers present during lignin biosynthesis in mutants and transgenics. Thus, computer models will also help in suggesting new targets for controlled lignin biosynthesis.Here, we propose a simulation model of synthetic lignin polymerization that is based upon an emerging consensus from a variety of observations and derives from a series of previous models of lignin polymerization (Glasser and Glasser, 1974; Glasser et al., 1976; Jurasek, 1995; Roussel and Lim, 1995). Our model uses a symbolic grammar to describe a constructive dynamical system (Fontana, 1992) or a rule-based system (Feret et al., 2009) in which it is not necessary to define all possible products in advance. We assume that G- and S-monomers and newly formed oligomers couple in a well-mixed medium, depending on coupling rules and experimentally measured coupling probabilities. To develop the model, we have used information from DHP experiments rather than natural lignins, as they are formed in a well-mixed medium and their reaction conditions are well known (e.g. the influx rate of monomers). Using information from natural lignin would have further complicated our model, as the structures of natural lignin polymers are influenced by many factors, including the possible involvement of dirigent proteins (Davin and Lewis, 2005), steric hindrance by polysaccharides, spatiotemporal regulation, and modifications during isolation procedures (Boerjan et al., 2003; Ralph et al., 2004).Using our simulation models, we study how putative controlling factors of lignin primary structure, including the influx rate of monomers and the relative amount of S-monomers, affect in silico lignin synthesis, and we compare our predictions with in vitro experiments. To predict the degradability of lignins formed in our simulations, we apply an in silico thioacidolysis, which cleaves the polymers at their β-O-4 positions. This simulates the molecular action of two of the most used methods to analyze lignin composition, thioacidolysis (Lapierre, 1993; Baucher et al., 2003) and derivatization followed by reductive cleavage (Lu and Ralph, 1997). The G+S-monomer yield is often taken as a reflection of the fraction of units bound by β-O-4 bonds. Cleavage of β-O-4 bonds is also the most important reaction in kraft pulping of wood (Baucher et al., 2003). The model predicts from first principles (1) that DHP lignins formed under Zutropf conditions have a higher β-O-4 content than those formed under Zulauf conditions, (2) that DHP lignins formed with high S content have a higher β-O-4 content than those formed with high G content, and (3) that a higher β-O-4 content does not necessarily reduce the average length of lignin fragments generated during in silico thioacidolysis.     

DIVERSIONARY DISPLAY.–PART 1. CONNOTATION AND TERMINOLOGY

A more exact terminology than that current is suggested for behaviour having the effect of deflecting intruders from a bird's nest or chicks. The general term "diversionary display" is used to describe all such activities, and a distinction is made between "distraction display" and displacement activities having a diversionary function. Various sub-categories of distraction display are distinguished–injury-simulation, chick-simulation, eccentric deportment and advertising distraction display. Attention is called to the possibility that a number of displacement activities habitually performed when an intruder menaces the nest or chicks may have diversionary function.     

Effect of pore structure on energy barriers and applied voltage profiles. II. Unsymmetrical channels.

This paper examines "realistic" pores, i.e., ones that are neither symmetric nor of uniform diameter. Methods are described that permit estimation of the image potential for an ion in an aqueous pore spanning a lipid membrane and for the electric field produced in such a pore when a transmembrane potential is applied. They are used to model features of the delayed rectifier potassium channel. Constraints on the geometry of the exterior mouth, the dielectric properties of the narrow part of the pore and the conduction mechanism are determined for this channel.     

Gospel of Wealth, Gospel of Work: Counterhegemony in the U.S. Working Class

ABSTRACT  In this article, we marshal qualitative and quantitative evidence for a distinctive U.S. working-class perspective that criticizes and dissents from the society's consumerist orthodoxy. On the basis of ethnographic and archival research in white central New York and eastern Pennsylvania, Doukas suggested that the frugal, work-centered ideology of historical U.S. working classes—the "gospel of work"—persisted as counterhegemonic in today's "gospel of wealth" consumerism. Durrenberger quantitatively tested for "gospel of work" orientations and found confirmation among predominantly white central Pennsylvanian labor unionists. We argue that the combination of methods warrants a more confident generalization and that the "wage of whiteness" needs to be assessed in regional and historic context. We conclude that "gospel of work" values are widely held despite a century-long corporate-sponsored campaign to promote consumerism and caution against assuming consumerist hegemony in the United States.     

Gating current harmonics. IV. Dynamic properties of secondary activation kinetics in sodium channel gating.

The kinetics for sodium channel gating appear to involve three coupled processes: (a) "primary" activation, (b) "secondary" activation, and (c) inactivation. Gating current data obtained in dynamic steady states with sinusoidal voltage-clamp were analyzed to give further details about the secondary activation process in sodium channel gating. Unlike primary activation and inactivation, the secondary activation kinetics involve physical processes that become defined when the data are analyzed as a function of the sinusoid frequency in addition to mean membrane potential. The effects of these processes are described, and a physical interpretation is presented.     

Central equilibria in multilocus systems. I. Generalized nonepistatic selection regimes

The generalized nonepistatic selection regime encompasses combinations of multiplicative and neutral viability effects distributed across a set of loci. These subsume, in particular, mixtures of the classical modes of multiplicative and additive fitness evaluations for multilocus traits. Exact analytic conditions for existence and stability of a multilocus Hardy-Weinberg (H-W) polymorphic equilibrium configuration are ascertained. It is established that the central H-W polymorphism is stable only if the component loci are "over-dominant" and sufficient recombination is in force. The H-W central equilibrium is never stable for tight linkage whenever some multiplicative selection effects are contributed by at least two of the loci involved. In the case of additive selection expression and individual overdominant loci, the H-W polymorphism is stable independently of the level of recombination. In the context of "natural" recombination schemes, "more recombination" enhances the stability of the H-W polymorphic equilibrium.     

Justice for Marguerite.

In this paper are analyzed all the aleatory forefront and hinterground aspects of the procedures to which professor Kay has been submitted until she had been "terminated" for an unexisting "scientific misconduct". Particularly have been analyzed all the artefactual and insiduous factors elaborated penibly by the CAFT, which have conduced it to terminate professor Kay. But they are just these fragile elements which permit to conclude in their unsubstantial and unsuitable value that they are reducing the entire procedure to a juridical no true bill conducing to a total and definitive discharge.