Mathematical Models of Plasma in Morozov’s Projects

Plasma Physics Reports - Mathematical models and simulations of plasma processes in scientific and technological projects proposed and, to a large extent, implemented by A.I. Morozov are reviewed....     

Role of Concentration-dependent Unloading in Mathematical Models of Münch Transport

It has been erroneously claimed (Goeschl et al. [1976] Plant Physiol. 58: 556-562) that concentration-dependent unloading is required for a correct mathematical solution for Münch phloem transport. Although it may prove to be physiologically correct, concentration-dependent unloading is not a mathematical necessity. Furthermore, its use in a mathematical model may not be desirable, because there is an infinite family of solutions for any given unloading distribution, irrespective of whether concentration-dependent unloading is assumed. Some illustrative numerical results are presented.     

Not Just a Sum? Identifying Different Types of Interplay between Constituents in Combined Interventions

Motivation

Experiments in which the effect of combined manipulations is compared with the effects of their pure constituents have received a great deal of attention. Examples include the study of combination therapies and the comparison of double and single knockout model organisms. Often the effect of the combined manipulation is not a mere addition of the effects of its constituents, with quite different forms of interplay between the constituents being possible. Yet, a well-formalized taxonomy of possible forms of interplay is lacking, let alone a statistical methodology to test for their presence in empirical data.

Results

Starting from a taxonomy of a broad range of forms of interplay between constituents of a combined manipulation, we propose a sound statistical hypothesis testing framework to test for the presence of each particular form of interplay. We illustrate the framework with analyses of public gene expression data on the combined treatment of dendritic cells with curdlan and GM-CSF and show that these lead to valuable insights into the mode of action of the constituent treatments and their combination.

Availability and Implementation

R code implementing the statistical testing procedure for microarray gene expression data is available as supplementary material. The data are available from the Gene Expression Omnibus with accession number GSE32986.     

The Genetic Code—More Than Just a Table

The standard codon table is a primary tool for basic understanding of molecular biology. In the minds of many, the table’s orderly arrangement of bases and amino acids is synonymous with the true genetic code, i.e., the biological coding principle itself. However, developments in the field reveal a much more complex and interesting picture. In this article, we review the traditional codon table and its limitations in light of the true complexity of the genetic code. We suggest the codon table be brought up to date and, as a step, we present a novel superposition of the BLOSUM62 matrix and an allowed point mutation matrix. This superposition depicts an important aspect of the true genetic code—its ability to tolerate mutations and mistranslations.     

Sympatric Speciation in the Post “Modern Synthesis” Era of Evolutionary Biology

Sympatric speciation is among the most controversial and challenging concepts in evolution. There are a multitude of definitions of speciation alone, and when combined with the biogeographic concept of sympatric range overlap, consensus on what sympatric speciation is, whether it happens, and its importance, is even more difficult to achieve. Providing the basis upon which to define and judge sympatric speciation, the Modern Evolutionary Synthesis (Huxley in Evolution: the modern synthesis. MIT Press, Cambridge, 1942) led to the conclusion that sympatric speciation is an inconsequential process in the generation of species diversity. In the post Modern Synthesis era of evolutionary biology, the PCR revolution and associated accumulation of DNA sequence data from natural populations has led to a resurgence of interest in sympatric speciation, and more importantly, the role of natural selection in lineage diversification. Much effort is currently being devoted to elucidating the processes by which the constituents of an initially panmictic population can become reproductively isolated and evolve some level of reproductive incompatibility without the complete cessation of gene flow due to geographic barriers. The evolution of reproductive isolation solely due to natural selection is perhaps the most controversial manner by which sympatric speciation occurs, and it is that which we focus upon in this review. Mathematical model simulations indicate that even strict definitions of sympatric speciation are possible to satisfy, empirical data consistent with sympatric divergence are accumulating, but irrefutable evidence of sympatric speciation in natural populations remains elusive. Genomic investigations are advancing our ability to identify genetic patterns caused by natural selection, thereby advancing our understanding of the power of natural selection relative to gene flow. Overall, sympatric lineage divergence, especially at the sub-species level, may have led to a substantial portion of biodiversity.     

The avoidance of superparasitism in four species of parasitic wasp—Mathematical models and experimental results

Experimental results, and interpretation, are presented which relate to oviposition behaviour in four species of parasitic wasp (Hymenoptera: Chalcidoidea). All lay their eggs in pupae of the common house fly (Musca domestica) and of other flies associated with man. Probability models suggested byD. J. Daley for describing the avoidance of superparasitism are used to analyse the data. Certain of the models considered by previous authors appear as specieal cases. A satisfactory fit was obtained either by assuming a fixed probability of oviposition in an already parasitised pupa, or by using a model motivated by supposing that a female will tolerate without oviposition some fixed number of visits to already parasitised pupae. A third model was considered which makes the probability depend on the number of previous ovipositions in the pupae now visited. In all four species the presence of other females (with parasite: host ratio unchanged) increased the probability of oviposition upon encountering an already parasitised pupa. In the presence of other females Spalangia endius laid an increased number of eggs, whereas the other three species laid fewer eggs.     

From Here to Eternity—The Theory and Practice of a Really Long Experiment

In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.     

(Too Many) Mathematical Models of Circadian Clocks (?)

Many mathematical models derived from the principles obtained from empirical observations in chronobiology have been proposed and explored. They cover several organisms and phenomena, and utilize quite different formal approaches. These models can be divided into the ones that intend to describe pacemaker core function, such the Goodwin-oscillator family, non-genetic approaches or purely mathematical (i.e., without clear biochemical correlations) models, and the ones that represent events depending on pacemaker activity, i.e., photoperiodic phenomena. We aim to illustrate the diversity of mathematical and methodological approaches to describe circadian systems and related matters.     

Evolutionary Psychology��s Place in Evolutionary Studies: a Tale of Promise and Challenge

The Evolutionary Studies (EvoS) Consortium and the academic programs born from its creation have been wildly successful in their initial ventures. These achievements are marked by feedback from across the EvoS campuses, the resultant scholarly work produced by participating students, and faculty collaborations spurred by exposure to the organization. The success of EvoS is probably best marked by the recent National Science Foundation grant (CCLI Award #0817337), awarded jointly to SUNY New Paltz and Binghamton University, with the purpose of expanding EvoS beyond the bounds of these two institutions. A particularly noteworthy element of many EvoS programs is the role of Evolutionary Psychology (EP), a perspective in the behavioral sciences that addresses questions of human behavior from the perspective of evolution. In light of several forms of data, including analyses of a variety of disciplines drawn on from evolutionary psychologists in their work, we argue that evolutionary psychologists may well be the most naturally interdisciplinary scholars within the behavioral sciences, making them highly appropriate for inclusion in EvoS. But our research shows not only promise regarding the relationship between EP and EvoS—challenges are raised as well. We present additional data showing that EP is currently represented disproportionately within the EvoS world—a fact that clearly shows that there are currently limitations to the potential impact of EvoS in modern academia. Scholars from other disciplines, particularly within the humanities and social sciences, seem to be missing the evolution revolution. Implications regarding how EvoS can broaden its scope to be even more powerful in its integrative scope are discussed.     

Does the Segregation of Evolution in Biology Textbooks and Introductory Courses Reinforce Students’ Faulty Mental Models of Biology and Evolution?

The well-established finding that substantial confusion and misconceptions about evolution and natural selection persist after college instruction suggests that these courses neither foster accurate mental models of evolution’s mechanisms nor instill an appreciation of evolution’s centrality to an understanding of the living world. Our essay explores the roles that introductory biology courses and textbooks may play in reinforcing undergraduates’ pre-existing, faulty mental models of the place of evolution in the biological sciences. Our content analyses of the three best-selling introductory biology textbooks for majors revealed the conceptual segregation of evolutionary information. The vast majority of the evolutionary terms and concepts in each book were isolated in sections about evolution and diversity, while remarkably few were employed in other sections of the books. Standardizing the data by number of pages per unit did not alter this pattern. Students may fail to grasp that evolution is the unifying theme of biology because introductory courses and textbooks reinforce such isolation. Two goals are central to resolving this problem: the desegregation of evolution as separate “units” or chapters and the active integration of evolutionary concepts at all levels and across all domains of introductory biology.     

The effects of mechanically-induced stress in plants — a review

Mechanically-induced stress (MIS) occurs naturally in plants as the aerial parts are moved, usually by wind, but also by such agents as rain and animals. It can be induced indoors by various actions such as rubbing or bending the stem or shaking or brushing the entire shoot. The most noticeable effect of MIS is a reduction in stem, leaf or petiole length invariably resulting in plants which are smaller and more compact than unstressed controls. However, the response of other variables can often differ between species and there may be either increases or decreases in stem or petiole diameter, root: shoot weight ratio, chlorophyll content or drought resistance. Why species should differ in this way, and what is the endogenous control mechanism for MIS responses, are inanswered questions. Ethylene, which increases as a result of MIS in several species may cause some MIS responses such as increased stem diameter, epinasty or a change in sex expression. However, evidence suggests that MIS retardation of extension growth may equally be due to lower or supraoptimal auxin levels or lower gibberellin levels.The uses in the field of the growth promoter gibberellin or the growth retardant chlormequat chloride (CCC) appear to be examples of respectively reversing or stimulating MIS growth response. MIS may be applied indoors if short compact plants are needed, either for aesthetic purposes as with floral crops, or if hardier and more manageable plants are needed, such as seedlings for transplanting in the field. Much more research is needed to estimate the importance of MIS in the field and to assess how such knowledge may be used to improve crop yield.     

The HSP70 Molecular Chaperone Is Not Beneficial in a Mouse Model of α-synucleinopathy

Background

Aggregation and misfolded α-synuclein is thought to be central in the pathogenesis of Parkinson''s disease (PD). Heat-shock proteins (HSPs) that are involved in refolding and degradation processes could lower the aggregate load of α-synuclein and thus be beneficial in α-synucleinopathies.

Methodology/Principal Findings

We co-overexpressed human A53T point-mutated α-synuclein and human HSP70 in mice, both under the control of Thy1 regulatory sequences. Behavior read-outs showed no beneficial effect of HSP70 expression in mice. In contrast, motor coordination, grip strength and weight were even worse in the α-synucleinopathy model in the presence of HSP70 overexpression. Biochemical analyses revealed no differences in α-synuclein oligomers/aggregates, truncations and phosphorylation levels and α-synuclein localization was unchanged in immunostainings.

Conclusion/Significance

Overexpressing HSP70 in a mouse model of α-synucleinopathy did not lower the toxic load of α-synuclein species and had no beneficial effect on α-synuclein-related motor deficits.     

Belief in a Just What? Demystifying Just World Beliefs by Distinguishing Sources of Justice

People’s Belief in a Just World (BJW) plays an important role in coping with misfortune and unfairness. This paper demonstrates that understanding of the BJW concept, and its consequences for behavior, is enhanced if we specify what (or who) the source of justice might be. We introduce a new scale, the 5-Dimensional Belief in a Just Treatment Scale (BJT5), which distinguishes five causal dimensions of BJW (God, Nature, Other People, Self, Chance). We confirm the 5-factor structure of the BJT5. We then address whether the BJW should be considered a uni- and/or multi-dimensional construct and find support for our multi-dimensional approach. Finally, we demonstrate convergent and discriminant validity with respect to important correlates of BJW as well as action in response to important negative life events and societal attitudes. This work illustrates the importance of distinguishing causal dimensions with regard to who distributes justice.