Entropy production and the Second Law in photosynthesis

An assertion that the primary photochemistry of photosynthesis can violate the Second Law of thermodynamics in certain efficient systems has been put forward by Jennings et al., who maintain their position strongly despite an argument to the contrary by Lavergne. We identify a specific omission in the calculation of Jennings et al. and show that no violation of the Second Law occurs, regardless of the photosynthetic efficiency.     

ATRX: Taming tandem repeats

Comment on: Law MJ, et al. Cell 2010; 143:367-78.     

The multiple faces of RIM

Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13.     

Three-dimensional trabecular alignment model

Trabecular alignment theory has been used to quantify Wolff's Law of bone remodeling. A three-dimensional finite element scheme was developed to analyze the bone remodeling phenomenon. The mathematical model proposed by Mullender et al. and later modified by Smith et al. was adopted to simulate the surface-based trabecular resorption and formation processes. Enhancements incorporated into the previous model include: mapping into three-dimensions, controlling the remodeling signal's passage through marrow, controlling the finite distance the signal may pass through the bone matrix, and including non-bone material in the finite element model. After the model is explained and thoroughly studied, three-dimensional implant surface geometries are simulated.     

THE LIFE CYCLE AND TOXICITY OF PFIESTERIA PISCICIDA REVISITED1

Despite use of excellent molecular techniques, Litaker et al. (2002) cannot provide insights about the life history of toxic Pfiesteria piscicida because they showed no data in support of having used toxic strains; rather they presented evidence that they used non‐inducible strains. Litaker et al. did not find amoeboid stages or a chrysophyte‐like cyst stage in several cultures and unequivocally concluded that the stages do not exist in all P. piscicida strains. Thus, they did not consider the tenet that absence of evidence does not constitute proof of absence. Apparent discrepancies between the research by Litaker et al. and previous research on Pfiesteria can be resolved as follows: First, Litaker et al. did not use toxic strains. We have reported findings (similar to Litaker et al.) showing few amoeboid transformations in non‐inducible strains, which manifest some but not all of the forms that have been documented in some toxic strains. We, and others, have documented active toxicity to fish, transformations to amoebae, and chrysophyte‐like cysts in some clonal toxic strains. Second, the data from several recent publications, which were available but not mentioned by Litaker et al. or by Coats (2002) in accompanying commentary, have verified P. piscicida amoebae, chrysophyte‐like cysts, and other stages in some toxic strains through a combination of approaches including PCR data from clonal cultures.     

Historical records of passerine introductions to New Zealand fail to support the propagule pressure hypothesis

Blackburn et al. (Biodiver Conserv 20:2189–2199, 2011) claim that a reanalysis of passerine introductions to New Zealand supports the propagule pressure hypothesis. The conclusions of Blackburn et al. (2011) are invalid for three reasons: First, the historical record is so flawed that there is no sound basis for identifying the mechanisms behind extinction following introduction, or whether species were successful because they were introduced in large numbers or were introduced in large numbers because earlier releases succeeded. Second, the GLIMMIX analysis of Blackburn et al. (2011) is biased in favor of the propagule pressure hypothesis. Third, the population viability analysis presented by Blackburn et al. (2011) is based on unjustified and questionable assumptions. It is likely that the outcome of passerine bird introductions to New Zealand depended on species characteristics, site characteristics, and human decisions more than on a simple summing of the numbers introduced.     

A note on efficient computation of haplotypes via perfect phylogeny.

The problem of inferring haplotype phase from a population of genotypes has received a lot of attention recently. This is partly due to the observation that there are many regions on human genomic DNA where genetic recombination is rare (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). A Haplotype Map project has been announced by NIH to identify and characterize populations in terms of these haplotypes. Recently, Gusfield introduced the perfect phylogeny haplotyping problem, as an algorithmic implication of the no-recombination in long blocks observation, together with the standard population-genetic assumption of infinite sites. Gusfield's solution based on matroid theory was followed by direct theta(nm2) solutions that use simpler techniques (Bafna et al., 2003; Eskin et al., 2003), and also bound the number of solutions to the PPH problem. In this short note, we address two questions that were left open. First, can the algorithms of Bafna et al. (2003) and Eskin et al. (2003) be sped-up to O(nm + m2) time, which would imply an O(nm) time-bound for the PPH problem? Second, if there are multiple solutions, can we find one that is most parsimonious in terms of the number of distinct haplotypes. We give reductions that suggests that the answer to both questions is "no." For the first problem, we show that computing the output of the first step (in either method) is equivalent to Boolean matrix multiplication. Therefore, the best bound we can presently achieve is O(nm(omega-1)), where omega < or = 2.52 is the exponent of matrix multiplication. Thus, any linear time solution to the PPH problem likely requires a different approach. For the second problem of computing a PPH solution that minimizes the number of distinct haplotypes, we show that the problem is NP-hard using a reduction from Vertex Cover (Garey and Johnson, 1979).     

Honeybee workers use cues other than egg viability for policing

Worker policing, wherein social insect workers prevent their sisters from reproducing by eating worker-laid eggs, is recognized as a textbook example of kin selection in action. However, the evolutionary basis of policing was recently challenged in a study that suggested that police-workers remove worker-laid eggs not because rearing workers' sons reduces worker fitness, but merely because worker-laid eggs have low viability. Here, we refute Pirk et al.'s conclusions. First, we confirm earlier work that showed equal viability of eggs laid by queens and workers. Second, a statistical analysis of the data of Pirk et al. reveals that their own data do not support the conclusion that worker-laid eggs are policed merely because of their low viability. Third, we present data that unequivocally show that police-workers cannot discriminate between dead and live eggs. Hence, our study seriously weakens the challenge to the kin-selected basis of policing in honeybees.     

A revisit on tests for homogeneity of the risk difference

Lipsitz et al. (1998, Biometrics 54, 148-160) discussed testing the homogeneity of the risk difference for a series of 2 x 2 tables. They proposed and evaluated several weighted test statistics, including the commonly used weighted least squares test statistic. Here we suggest various important improvements on these test statistics. First, we propose using the one-sided analogues of the test procedures proposed by Lipsitz et al. because we should only reject the null hypothesis of homogeneity when the variation of the estimated risk differences between centers is large. Second, we generalize their study by redesigning the simulations to include the situations considered by Lipsitz et al. (1998) as special cases. Third, we consider a logarithmic transformation of the weighted least squares test statistic to improve the normal approximation of its sampling distribution. On the basis of Monte Carlo simulations, we note that, as long as the mean treatment group size per table is moderate or large (> or = 16), this simple test statistic, in conjunction with the commonly used adjustment procedure for sparse data, can be useful when the number of 2 x 2 tables is small or moderate (< or = 32). In these situations, in fact, we find that our proposed method generally outperforms all the statistics considered by Lipsitz et al. Finally, we include a general guideline about which test statistic should be used in a variety of situations.     

陕西洋县药用植物群落土壤种子库特性研究

采用种子萌发法对洋县药用植物群落土壤种子库物种组成、单位面积种子密度、物种丰富度及与地上群落结构的关系进行了研究。结果显示,研究区内共有种子植物50种(包括药用植物21种),隶属于28科47属,其中草本植物45种、乔木5种;不同药用植物群落间土壤种子库种子密度差异显著,从大到小依次为:2年生凹叶厚朴(Magnolia officinalis Rehd.et Wils.subsp.biloba(Rehd.et Wils.)Law)4年生凹叶厚朴7年生凹叶厚朴11年生凹叶厚朴杜仲-凹叶厚朴(Eucommia ulmoides Oliver-Magnolia officinalis Rehd.et Wils.subsp.biloba(Rehd.et Wils.)Law)7年生厚朴(Magnolia officinalis Rehd.et Wils.)杜仲山茱萸(Cornus officinalis Sieb.et Zucc.)山茱萸-凹叶厚朴;土壤种子库具有表聚性,土层深度与种子数量成负相关;药用植物群落土壤种子库与地上群落结构相似性普遍较低。低林龄群落的土壤种子库密度大于高林龄群落,因此低林龄群落有利于天然更新,它们在植被恢复和生物多样性保护中的潜在价值更大。本研究结果可为洋县药用植物群落天然更新提供理论指导。     

On the matching and proportional laws of cybernetic models

The Matching and Proportional Laws are heuristic control policies that have found widespread use in cybernetic models of biological systems. Within this context, the laws serve as optimization surrogates for predicting the response of metabolic control circuits that modulate enzyme levels and activities. The key result of the current contribution is to demonstrate clearly the optimality properties of these laws and the assumptions that underlie their development. In doing so, we arrive at generalized versions of the Matching and Proportional Laws that are shown to collapse to the forms originally derived by Kompala et al. (Biotechnol. Bioeng. 1986, 28, 1044-1055) when certain simplifications are applied. As a further line of investigation, we show how Kompala et al.'s cybernetic laws compare with alternative control policies in their ability to describe diauxic growth behavior of microbial cultures. We find that Kompala et al.'s model describes the experimental observations more accurately than other limiting-case models that are either too aggressive or too passive in capturing the mixed-substrate growth rates and intermediate lag periods. Monte Carlo analysis of computational growth experiments in which strains obeying different regulatory policies directly compete for available nutrients reveals that the Matching and Proportional Law policy does not maximize the average growth rate of the culture. However, it allocates metabolic resources more frugally than other policies that outperform it and may be more realistic in reflecting the cell's true fitness-to-cost tradeoff as judged by its agreement with experimental growth data.     

Rare Genomic Characters Do Not Support Coelomata: RGC_CAMs

Recently there has been a lively debate about a new class of rare genomic characters, RGC_CAMs, and their implications for deep bilaterian phylogeny. Most recently, nine bilaterian species were analyzed along with subsets of six outgroups (Rogozin et al. 2007b), and support for a coelomate clade reported. The authors suggested that our previously reported support for an ecdysozoan clade (Irimia et al. 2007) reflected (i) one outgroup, Nematostella vectensis, being too closely related to bilaterians and (ii) lack of “rigorous statistical analysis.” Here, we report further studies of these characters. First, we discuss general issues of outgroup choice. Second, we point out that an argument used by Rogozin et al. against backmutation is not statistically significant. Third, we point out that the statistical method of Rogozin et al. fails to incorporate backmutations, leading to systematic placement of the long-branch taxon as the outgroup. A simple modification of the method yields very different results: 51 of 63 outgroup combinations favor Ecdysozoa, inlcuding 51 of 52 with at least eight phylogenetically informative characters, and all 19 with statistically significant signal. These results indicate that the Coelomata signal is a long-branch artifact.     

木兰科植物订正

对部分国产木兰科种类进行了订正,归并7个新异名,澄清Mognolia odoratissima Law et R.Z.Zhou和Michelia sphaerantha C.Y.WuexLaw et Y.F.Wu两个种分类上的混乱。     

A flux capacitor for moth pheromones

In this issue of Chemical Senses, Baker et al. propose a provocative and intriguing explanation for a commonly observed phenomenon in moth chemocommunication. Sex pheromones in moths typically consist of mixtures of long-chain unsaturated compounds in specific ratios. These ratios are correspondingly detected by male moths using separate olfactory sensory neurons for each pheromone component housed singly or multiply in long trichoid sensilla on the antennal surface. These neurons are often present in different proportions, typically with the neuron responding to the highest ratio component present in greatest abundance or with the largest dendritic diameter. In their article, Baker et al. postulate that these physical differences in neuron magnitudes arise to compensate for the higher molecular flux present with the most abundant pheromone components. Such a suggestion raises several questions concerning the physiological and behavioral nature of pheromone communication. Specifically, is the flux in a natural pheromone plume high enough to warrant increased flux detection for the most abundant components? Second, how can changes in neuronal number or size lead to increased flux detection? And finally, how would this increased flux detection be accomplished at molecular, cellular, and ultimately network scales? We address each of these questions and propose future experiments that could offer insight into the stimulating proposition raised by Baker et al.     

A thermodynamic and biomechanical theory of cell adhesion. Part I: General formulism

The equilibrium thermodynamics calculus of cell adhesion developed by Bell et al. (1984, Biophys. J. 45, 1051-1064) has been extended to the general non-equilibrium case. In contrast to previous models which could only compute the end results of equilibrium states, the present theory is able to calculate the kinetic process of evolution of adhesion, which may or may not approach towards equilibrium. Starting from a basic constitutive hypothesis for Helmholtz free energy, equations of balance of normal forces, energy balance at the edge of the contact area and rate of entropy production are derived using an irreversible thermodynamics approach, in which the restriction imposed by the Second Law of Thermodynamics takes the place of free energy minimization used by Bell et al. (1984). An explicit expression for adhesion energy density is derived for the general transient case as the difference of the usable work transduced from chemical energy liberation from bond formation of specific crosslinking molecules and the repulsive potential of non-specific interactions. This allows the energy balance to be used as an independent boundary equation rather than a practical way of computing the adhesion energy. Jump conditions are obtained from the conservation of crosslinking molecules across the edge of adhesion region which is treated as a singular curve. The bond formation and lateral motion of the crosslinking molecules are assumed to obey a set of reaction-diffusion equations. These equations and the force balance equation within the contact area, plus the jump conditions and the energy balance equation at the edge form a well-posed moving boundary problem which determines the propagation of the adhesion boundary, the separation distance between the two cell membranes over the contact area as well as the distributions of the crosslinking molecules on the cell surfaces. The behavior of the system depends on the relative importance of virtual convection, lateral diffusion and bond formation of the crosslinking molecules at the edge of the adhesion region, according to which two types of rate limiting cases are discussed, viz, reaction-limited and diffusion-limited processes.     

The Effects of Lethal Selection on the EST-6 to PGM Region of Chromosome 3 in DROSOPHILA MELANOGASTER

A powerful means of studying the effects of selection on chromosome segments in Drosophila melanogaster has been described by Clegg et. al. (1976, 1978). This method utilizes a recessive lethal, dominant visible allele whose selection dynamics can be accurately modelled to predict the fates of nonlethal alleles at linked loci. Results of these experiments indicate that strong epistatic interactions among loci occur that effect fitnesses associated with gametic types in the basal region of chromosome 3. We have used similar methods in studying a different segment of chromosome 3, that spanned by Est-6 (3-36.8) and Pgm (3-43.4), with the aim of determining whether the results of Clegg and his colleagues could be reproduced when a different region was studied. Our experiment showed that selection did operate on a region of the chromosome marked by Pgm, but that no evidence of selection at loci marked by Est-6 was apparent. Weak evidence for epistatic interactions among loci within the marked region was also found. Three possible explanations for the discrepancies between our experiments and those of Clegg et al. are suggested. First, the geographically homogeneous origin of our populations may preclude selectively significant changes as a result of recombination. Second, the results seen by Clegg et al. may have been unique to the regions they studied, which included the basal heterochromatin of the chromosomes. Finally, the three loci employed may not adequately mark the unit of selection, so that actual departures from predictions of selective neutrality may not have been apparent.     

Re-evaluation of phytohormone-independent division of tobacco protoplast-derived cells

We have used a [³H] thymidine incorporation assay and microscopic observation in order to reassess recently published data dealing with the response of tobacco protoplasts to phytohormones, lipochitooligosaccharides and peptides ( Harling et al . 1997 ; Hayashi et al . 1992 ; Miklashevichs et al . 1996 ; Miklashevichs et al . 1997 ; Röhrig et al . 1995 ; Röhrig et al . 1996 ; van de Sande et al . 1996 ; Walden et al . 1994 ). These proliferation assays reveal that, in contrast to published data, isolated cells of the investigated mutant plant lines axi159 ( Hayashi et al . 1992 ; Walden et al . 1994 ), axi4/1 ( Harling et al . 1997 ) and cyi1 ( Miklashevichs et al . 1997 ), which were generated by activation T-DNA tagging, were unable to grow in the absence of auxin or cytokinin. Furthermore, lipochitooligosaccharides which play a key role in the induction of nodules on roots of legumes were unable to promote auxin- or cytokinin-independent cell division in tobacco protoplasts as claimed by Röhrig et al . (1995 , 1996 ). The finding of van de Sande et al . (1996 ) that ENOD40 confers tolerance of high auxin concentration to wild-type tobacco protoplasts was also reinvestigated. The results of our investigations show that we were unable to reproduce the proliferation data presented in this study, which were obtained by counting tobacco protoplast-derived cells undergoing division. In total, none of the published data on phytohormone-independent division of tobacco cells could be reproduced.     

Two coupled oscillators as a model for the coordinated finger tapping by both hands

Recently, it was found that rhythmic movements (e.g. locomotion, swimmeret beating) are controlled by mutually coupled endogeneous neural oscillators (Kennedy and Davis, 1977; Pearson and Iles, 1973; Stein, 1974; Shik and Orlovsky, 1976; Grillner and Zangger, 1979). Meanwhile, it has been found out that the phase resetting experiment is useful to investigate the interaction of neural oscillators (Perkel et al., 1963; Stein, 1974). In the preceding paper (Yamanishi et al., 1979), we studied the functional interaction between the neural oscillator which is assumed to control finger tapping and the neural networks which control some tasks. The tasks were imposed on the subject as the perturbation of the phase resetting experiment. In this paper, we investigate the control mechanism of the coordinated finger tapping by both hands. First, the subjects were instructed to coordinate the finger tapping by both hands so as to keep the phase difference between two hands constant. The performance was evaluated by a systematic error and a standard deviation of phase differences. Second, we propose two coupled neural oscillators as a model for the coordinated finger tapping. Dynamical behavior of the model system is analyzed by using phase transition curves which were measured on one hand finger tapping in the previous experiment (Yamanishi et al., 1979). Prediction by the model is in good agreement with the results of the experiments. Therefore, it is suggested that the neural mechanism which controls the coordinated finger tapping may be composed of a coupled system of two neural oscillators each of which controls the right and the left finger tapping respectively.