Pteridophytic evolution: an often underappreciated phytological success story

The role and success of pteridophytes in the vascular land flora from the Silurian to Recent are examined. Success is defined as the ability of plants to occupy physical and ecological space through time, and evaluated in terms of species richness and percent cover. These factors are examined for vascular plants of successively more specialized grades of life cycles. Four grades, including homospory, heterospory, extreme heterospory, and angiospermy are recognized, with angiospermy providing for the greatest species richness and percent cover in the modern flora. In terms of percent cover, gymnosperms are also relatively successful, but in terms of species richness homosporous pteridophytes are more successful than all other non-angiospermous grades combined. The diversity of growth forms and life history patterns that have helped pteridophytes become successful throughout time is examined, and evidence for rhizomatous herbs, vines, epiphytes, trees of diverse architectures, and specialized modes of growth and vegetative propagation are reviewed. Comparison of several analyses of land plant diversity through the Phanerozoic suggests that plants with pteridophytic reproduction were dominant in most floras long after the origin of seed plants, and that pteridophytes probably have continued to increase in species richness up to the present. The loss of pteridophytic dominance in terms of percent cover at the end of the Paleozoic was associated with species turnover in which arborescent pteridophytes of several clades became extinct, but some herbaceous pteridophytes may have retained dominance in many floras into the Paleogene.     

Purification of Recombinant Human Serum Albumin Efficient purification using STREAMLINE

Two inter-related challenges must be overcome to develop a recombinant human serum albumin process. One is purity; the other is cost. Regarding cost, our goal is to produce recombinant human serum albumin at least as economically as plasma derived human serum albumin. To control production costs, maximum quantities of albumin must be produced from minimum volumes of cell culture, followed by high efficiency, high-yield purification methods. By introducing STREAMLINE technology, we have improved productivity by roughly 50% in terms of processing time and 45% in terms of yield. Furthermore, the life time of the gel and column are very long. After more than 1000 process cycles, performance remained unchanged.     

Rapid measurement of protein osmotic second virial coefficients by self-interaction chromatography

Weak protein interactions are often characterized in terms of the osmotic second virial coefficient (B(22)), which has been shown to correlate with protein phase behavior, such as crystallization. Traditional methods for measuring B(22), such as static light scattering, are too expensive in terms of both time and protein to allow extensive exploration of the effects of solution conditions on B(22). In this work we have measured protein interactions using self-interaction chromatography, in which protein is immobilized on chromatographic particles and the retention of the same protein is measured in isocratic elution. The relative retention of the protein reflects the average protein interactions, which we have related to the second virial coefficient via statistical mechanics. We obtain quantitative agreement between virial coefficients measured by self-interaction chromatography and traditional characterization methods for both lysozyme and chymotrypsinogen over a wide range of pH and ionic strengths, yet self-interaction chromatography requires at least an order of magnitude less time and protein than other methods. The method thus holds significant promise for the characterization of protein interactions requiring only commonly available laboratory equipment, little specialized expertise, and relatively small investments of both time and protein.     

Fractal methods to analyze ion channel kinetics

We describe the traditional nonfractal and the new fractal methods used to analyze the currents through ion channels in the cell membrane. We discuss the hidden assumptions used in these methods and how those assumptions lead to different interpretations of the same experimental data. The nonfractal methods assumed that channel proteins have a small number of discrete states separated by fixed energy barriers. The goal was to determine the parameters of the kinetic diagram, which are the number of states, the pathways between them, and the kinetic rate constants of those pathways. The discovery that these data have fractal characteristics suggested that fractal approaches might provide more appropriate tools to analyze and interpret these data. The fractal methods determine the characteristics of the data over a broad range of time scales and how those characteristics depend on the time scale at which they are measured. This is done by using a multiscale method to accurately determine the probability density function over many time scales and by determining how the effective kinetic rate constant, the probability of switching states, depends on the effective time scale at which it is measured. These fractal methods have led to new information about the physical properties of channel proteins in terms of the number of conformational substates, the distribution of energy barriers between those states, and how those energy barriers change with time. The new methods developed from the fractal paradigm shifted the analysis of channel data from determining the parameters of a kinetic diagram to determining the physical properties of channel proteins in terms of the distribution of energy barriers and/or their time dependence.     

叶物候、构建消耗和偿还时间对入侵植物碳积累的影响

随着全球经济一体化进程的深入,生物入侵已成为严重的全球性问题之一.外来种入侵打破了物种生存的自然平衡,导致生态系统趋于均质化,并给社会经济发展和人类健康造成了无法估量的损失.然而,目前人们对外来种的入侵机理仍不十分清楚.叶物候如叶片发生时间、凋落时间、及由二者决定的叶寿命和叶片发育进程是植物在季节和非季节性变化的环境中为了获得碳收益所采取的适应策略.叶构建消耗是植物碳收获过程中必要的成本投入,反映了植物在叶片水平上的能量分配策略.偿还时间能在一定程度上反映叶片碳的积累情况.从叶物候、构建消耗和偿还时间入手,分析了入侵植物的资源捕获能力和成本对其碳积累的影响,并提出了今后的研究方向.     

Flocking and predator surveillance in house sparrows: Test of an hypothesis

The argument that individuals benefit from foraging in flocks through spending less time in predator surveillance and hence more time foraging and feeding, has been formalized in terms of a mathermatical relationship (Pulliam 1973). We have tested the model using house sparrows (Passer domesticus), and our results support its prediction of an inverse relationship between the time spent in predator surveillance and the flock size. The data did not fit the model exactly, and we attribute this to an unrealistic assumption.     

Rapid parallel evolution of aberrant traits in the diversification of the Gulf of Guinea white-eyes (Aves, Zosteropidae)

Archipelago-endemic bird radiations are familiar to evolutionary biologists as key illustrations of evolutionary patterns. However, such radiations are in fact rare events. White-eyes (Zosteropidae) are birds with an exceptionally high colonization and speciation potential; they have colonized more islands globally than any other passerine group and include the most species-rich bird genus. The multiplication of white-eye island endemics has been consistently attributed to independent colonizations from the mainland; the white-eyes of the Gulf of Guinea archipelago had been seen as a classic case, spanning as great a breadth of phenotypic diversity as the family worldwide. Contrary to this hypothesis, our molecular phylogenetic analysis places the Gulf of Guinea white-eyes in just two radiations, one grouping all five oceanic island taxa and the other grouping continental island and land-bridge taxa. Numerous 'aberrant' phenotypes (traditionally grouped in the genus Speirops) have evolved independently over a short space of time from nonaberrant (Zosterops) phenotypes; the most phenotypically divergent species have separated as recently as 0.22 Ma. These radiations rival those of Darwin's finches and the Hawaiian honeycreepers in terms of the extent of adaptive radiation per unit time, both in terms of species numbers and in terms of phenotypic diversity. Tempo and patterns of morphological divergence are strongly supportive of an adaptive radiation in the oceanic islands driven by ecological interactions between sympatric white-eyes. Here, very rapid phenotypic evolution mainly affected taxa derived from the youngest wave of colonization, in accordance with the model of asymmetric divergence owing to resource competition in sympatry.     

Statistical energy potential: reduced representation of Dehouck–Gilis–Rooman function by selecting against decoy datasets

Statistical effective energy function (SEEF) is derived from the statistical analysis of the database of known protein structures. Dehouck-Gilis-Rooman (DGR) group has recently created a new generation of SEEF in which the additivity of the energy terms was manifested by decomposing the total folding free energy into a sum of lower order terms. We have tried to optimize the potential function based on their work. By using decoy datasets as screening filter, and through modification of algorithms in calculation of accessible surface area and residue-residue interaction cutoff, four new combinations of the energy terms were found to be comparable to DGR potential in performance test. Most importantly, the term number was reduced from the original 30 terms to only 5 in our results, thereby substantially decreasing the computation time while the performance was not sacrificed. Our results further proved the additivity and manipulability of the DGR original energy function, and our new combination of the energy could be used in prediction of protein structures.     

Lagrangian description of zooplankton swimming trajectories

Three-dimensional swimming, in 20 trajectories of Daphnia pulex,was characterized in terms of its kinematic properties. Resultsshow that the random component was stronger than the deterministiccomponent at time scales >1–2 s. Such random movementsmay have evolved to outwit potential predators and prey.     

Markov modelling of immunological and virological states in HIV-1 infected patients

The purpose of this study was to evaluate the evolution of HIV infected patients and to bring out some significant factors associated with this pathology. The main criteria revealing the State of illness is viral load measurement (VL). However the CD4 lymphocytes also represent an important marker as these reflect the State of the immune reservoir. Many studies have been carried out in this field and different models have been proposed with a view to a better understanding of this disease. Multi State Markov models defined in terms of CD4 counts, or in terms of viral load, have proved to be very useful tools for modelling HIV disease progression. The model we have developed in this study is based on both the CD4 lymphocytes counts and VL. Markov models are characterized by transition intensities. In this paper we explored several structures in succession. First, we used a homogeneous continuous time Markov process with four states defined by crossed values of CD4 and VL in a given patient at a given time. Then, the effect of certain covariates on the infection process was introduced into the model via the transition intensity functions, as with a Cox regression model. Since the hypothesis of homogeneity may be unrealistic in certain cases, we also considered piecewise homogeneous Markov models. Finally, the effects of covariates and time were combined in a piecewise homogeneous model with a covariate. We applied these methods to data from 1313 HIV-infected patients included in the NADIS cohort.     

Learning in Spiders

After the spider, Zygiella x-notata Cl. has been enticed toleave the retreat and catch a fly in a web turned upside-down,it takes a relatively long time to return to the retreat. Thereturn-time is divided into periods of active searching andmotionlessness. Several factors have been found to shorten significantlythe searching and motionless time; among them are youth of theanimals, small number of webs previously built, the positionof the web before and between experiments, and repetition oftrials at certain time intervals. The observed phenomenon andvariations in time are explained in terms of current conceptsof memory function and information processing.     

Timing of mate-locating by males in relation to female activity in the carpenter beeXylocopa varipuncta (Hymenoptera: Apidae)

Males of the carpenter beeXylocopa varipuncta Patton wait for females to visit them as they hover at landmark territories along ridgelines on some spring afternoons. While hovering, males advertize their presence by releasing a pheromone that attracts passing females. If males have limited time to invest in territorial hovering and signaling, then they should engage in these activities more often at times when mate-searching females are most likely to visit landmark territories. The number of females flying near male territories varies greatly over the course of afternoons and from day to day. Measures of female activity and male territorial activity were highly correlated at one study site, both in terms of changes within afternoons and in terms of day-to-day fluctuations. This result supports the hypothesis that males ofX. varipuncta time their mateattracting behavior to maximize contacts with receptive females.     

Measurements of protein self-association as a guide to crystallization

The challenge of crystallizing proteins has led to a significant amount of research in understanding protein self-association and assembly. Arguably the most influential finding in this field in the past decade has been that weakly attractive protein interactions, characterized in terms of the osmotic second virial coefficient, correlate with solution conditions that are conducive to crystallization. Recent work in this area has focused on the development of more efficient techniques for measuring the second virial coefficient, as traditional characterization methods suffer from poor efficiency in terms of time and protein consumption. The resulting measurements have provided new insights into patterns of protein interactions and their relation to protein phase behavior.     

An application of the theory of neural nets to the study of motion sickness

The results from a study by M. F. Morales on the labyrinthine response to motion are used, together with results of neural net theory, to enable one to calculate, in terms of a small number of parameters, the percentage of individuals who have motion sickness when exposed to rather general patterns of motion which may vary with time.     

Redefining Industrial Symbiosis

The most commonly cited definition of industrial symbiosis (IS), by Chertow (2000) , has served well to foster discussion and research for more than a decade. The definition reflected the state of research and practice at the time; as both have advanced, some terms have been interpreted in substantially different ways. In this article we analyze those generally used terms for their connection to the ecological metaphor that is the root of industrial ecology, and their varied interpretations in IS research and practice over time. We then propose an updated definition intended to communicate the essence of IS as a tool for innovative green growth: IS engages diverse organizations in a network to foster eco‐innovation and long‐term culture change. Creating and sharing knowledge through the network yields mutually profitable transactions for novel sourcing of required inputs and value‐added destinations for non‐product outputs, as well as improved business and technical processes. We posit that, although geographic proximity is often associated with IS, it is neither necessary nor sufficient—nor is a singular focus on physical resource exchange.     

Costs and cost-minimisation analysis.

Whatever kind of economic evaluation you plan to undertake, the costs must be assessed. In health care these are first of all divided into costs borne by the NHS (like drugs), by patients and their families (like travel), and by the rest of society (like health education). Next the costs have to be valued in monetary terms; direct costs, like wages, pose little problem, but indirect costs (like time spent in hospital) have to have values imputed to them. And that is not all: costs must be further subdivided into average, marginal, and joint costs, which help decisions on how much of a service should be provided. Capital costs (investments in plant, buildings, and machinery) are also important, as are discounting and inflation. In this second article in the series Ray Robinson defines the types of costs, their measurement, and how they should be valued in monetary terms.     

Separation of ketoconazole enantiomers by chiral subcritical-fluid chromatography

The separation of ketoconazole enantiomers by subcritical-fluid chromatography using an amylose-based column is described. Drastic changes in the resolution have been obtained for the different organic modifiers evaluated, with ethanol providing the best results. Other chromatographic parameters such as temperature, pressure and flow-rate have also been studied. The best results in terms of resolution and analysis time were obtained using 30% ethanol (containing 0.1% triethylamine and 0.1% trifluoroacetic acid), a pressure of 300 bar, a temperature of 35 degrees C and a flow-rate of 3 ml/min. Under these conditions the ketoconazole enantiomers are resolved in a short time (less than 7 min) and with high resolution (4.29).     

Origin of multicellular eukaryotes - insights from proteome comparisons

The complete genomes of the yeast Saccharomyces cerevisiae and the nematode worm Caenorhabditis elegans have recently become available allowing the comparison of the complete protein sets of a unicellular and multicellular eukaryote for the first time. These comparisons reveal some striking trends in terms of expansions or extensive shuffling of specific domains that are involved in regulatory functions and signaling. Similar comparisons with the available sequence data from the plant Arabidopsis thaliana produce consistent results. These observations have provided useful insights regarding the origin of multicellular organisms.     

A Novel Byte-Substitution Architecture for the AES Cryptosystem

The performance of Advanced Encryption Standard (AES) mainly depends on speed, area and power. The S-box represents an important factor that affects the performance of AES on each of these factors. A number of techniques have been presented in the literature, which have attempted to improve the performance of the S-box byte-substitution. This paper proposes a new S-box architecture, defining it as ultra low power, robustly parallel and highly efficient in terms of area. The architecture is discussed for both CMOS and FPGA platforms, and the pipelined architecture of the proposed S-box is presented for further time savings and higher throughput along with higher hardware resources utilization. A performance analysis and comparison of the proposed architecture is also conducted with those achieved by the existing techniques. The results of the comparison verify the outperformance of the proposed architecture in terms of power, delay and size.     

Characteristics of root apical meristem cell population kinetics: A review of analyses and concepts

Various conclusions have been reached in the literature concerning the organization of root meristems in terms of cell proliferation and quiescence. In this article the methods used in such analyses are examined in order to assess the validity of the results obtained. Cells in root meristems are clearly heterogeneous in terms of cycle time. The existence of quiescent populations of cells outside the quiescent center, however, is more problematic because (i) it is difficult to define clearly the proximal boundary of the root apical meristem and (ii) present techniques used to measure the size of the proliferative cell fraction are likely to be, in many, if not all cases, highly inaccurate. We have concluded that non-cycling cells, other than those of the quiescent center, do not exist within the meristem proper at the apex of the proliferating angiosperm root.