Distinguishing ulcerative colitis from autoimmunity

Lymphoid hyperplasia, autoimmunity, and compromised intestinal intraepithelial lymphocyte development in colitis-free gnotobiotic IL-2-deficient miceContractor, N.V. et al. (1998)J. Immunol. 160, 385–394     

Distinguishing ecological engineering from environmental engineering

This paper uses complex system thinking to identify key peculiarities of ecological engineering. In particular it focuses on the distinction between the purpose-driven design of structures in environmental engineering and the natural process of self-organization characteristic of life, which needs to be integrated into ecological engineering.Conventional engineering addresses the problem of fabrication of an organized structure, say a road, which reflects a goal at the outset, as well as considerations external to the road. At the outset there is an essence of which the organized structure is a realization. This realization belongs to a certain type (apartment building, suspension bridge). The type is in relation to: (a) the expected contexts (e.g. housing in Manhattan, a bridge in rural Africa) and (b) location-specific socio-economic constraints (low/high economic budget). Conventional engineering does not question the goals of the selected plan and can only object to the feasibility of a proposed typology in a given context. Engineers deal with the challenge of the realization of a plan at a given point in space and time.The central dogma of biology identifies organisms as informationally-closed and this makes possible their use as machines. Ecological systems, on the contrary, are informationally-open. They cannot be used as machines to create functional structures, because they are becoming in time. For engineered structures to work it is usually required that there is (1) stability of system components; (2) admissibility of a workable context; (3) validity of purpose and concept. Ecologically-engineered structures challenge these requirements because of specificity of required environments and lability of system parts over the time the engineered structure functions. Other engineering is better if it achieves flexibility, but ecological engineering must be so flexible as to take on a looping character that updates the system to meet changing requirements. Accordingly, the original goals cannot be taken for granted later in the process of ecological engineering. Ecological engineering has to be a flexible iterative process of design, in which the designer must continually update goals, essences, typologies and processes of realization.     

Distinguishing enzyme structures from non-enzymes without alignments

The ability to predict protein function from structure is becoming increasingly important as the number of structures resolved is growing more rapidly than our capacity to study function. Current methods for predicting protein function are mostly reliant on identifying a similar protein of known function. For proteins that are highly dissimilar or are only similar to proteins also lacking functional annotations, these methods fail. Here, we show that protein function can be predicted as enzymatic or not without resorting to alignments. We describe 1178 high-resolution proteins in a structurally non-redundant subset of the Protein Data Bank using simple features such as secondary-structure content, amino acid propensities, surface properties and ligands. The subset is split into two functional groupings, enzymes and non-enzymes. We use the support vector machine-learning algorithm to develop models that are capable of assigning the protein class. Validation of the method shows that the function can be predicted to an accuracy of 77% using 52 features to describe each protein. An adaptive search of possible subsets of features produces a simplified model based on 36 features that predicts at an accuracy of 80%. We compare the method to sequence-based methods that also avoid calculating alignments and predict a recently released set of unrelated proteins. The most useful features for distinguishing enzymes from non-enzymes are secondary-structure content, amino acid frequencies, number of disulphide bonds and size of the largest cleft. This method is applicable to any structure as it does not require the identification of sequence or structural similarity to a protein of known function.     

Distinguishing reversible from irreversible virus capsid assembly

Capsids of spherical viruses may be constructed from hundreds or thousands of copies of the major capsid protein(s). These assembly reactions are poorly understood. Here we consider the predicted behavior for assembly where the component reactions have weak association energy and are reversible and compare them to essentially irreversible reactions. The comparisons are based on mass action calculations and the behavior predicted from kinetic simulations where assembly is described as a cascade of low order reactions. Reversible reactions are characterized by a pseudo-critical concentration, whereas irreversible reactions consume all free subunits. Irreversible reactions are more susceptible to kinetic traps comprised of numerous small intermediates. In the case where only the ultimate step is irreversible, very low concentrations of intermediates slow the completion of the reaction so that overall it closely matches the predictions for the reversible reactions that make up the majority of the cascade. Data in the literature strongly support the hypothesis that most viruses are held together by many weak interactions.     

Distinguishing ecological from evolutionary approaches to transposable elements

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co‐evolutionary framework for explaining transposon‐host interactions. This review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole‐genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology.     

Distinguishing error from chaos in ecological time series

Over the years, there has been much discussion about the relative importance of environmental and biological factors in regulating natural populations. Often it is thought that environmental factors are associated with stochastic fluctuations in population density, and biological ones with deterministic regulation. We revisit these ideas in the light of recent work on chaos and nonlinear systems. We show that completely deterministic regulatory factors can lead to apparently random fluctuations in population density, and we then develop a new method (that can be applied to limited data sets) to make practical distinctions between apparently noisy dynamics produced by low-dimensional chaos and population variation that in fact derives from random (high-dimensional) noise, such as environmental stochasticity or sampling error. To show its practical use, the method is first applied to models where the dynamics are known. We then apply the method to several sets of real data, including newly analysed data on the incidence of measles in the United Kingdom. Here the additional problems of secular trends and spatial effects are explored. In particular, we find that on a city-by-city scale measles exhibits low-dimensional chaos (as has previously been found for measles in New York City), whereas on a larger, country-wide scale the dynamics appear as a noisy two-year cycle. In addition to shedding light on the basic dynamics of some nonlinear biological systems, this work dramatizes how the scale on which data is collected and analysed can affect the conclusions drawn.     

Beyond Benford's Law: Distinguishing Noise from Chaos

Determinism and randomness are two inherent aspects of all physical processes. Time series from chaotic systems share several features identical with those generated from stochastic processes, which makes them almost undistinguishable. In this paper, a new method based on Benford''s law is designed in order to distinguish noise from chaos by only information from the first digit of considered series. By applying this method to discrete data, we confirm that chaotic data indeed can be distinguished from noise data, quantitatively and clearly.     

被子植物早期近交衰退与晚期自交不亲和

被子植物自交后结籽率的降低通常由早期近交衰退(early-acting inbreeding depression)与晚期自交不亲和(self-incompatibility)导致.早期近交衰退是严格的合子后的作用机制,通常由多位点隐性有害基因的纯合导致,并在合子发育成成熟种子的过程中发生.发生在柱头表面或花柱中的自交不亲和是合子前的作用机制,而发生在子房内的晚期自交不亲和(late-acting ovarian self-incompatibility)可在合子前或合子后发生作用,与早期近交衰退很难区分.在合子前的子房内自交不亲和机制下,尽管花粉管能生长到子房甚至穿透胚珠,但通常不能形成合子.合子后的子房内自交不亲和能形成合子,但由于自交不亲和通常由单位点控制,合子败育集中发生在受精作用后的很短时间内.基于早期近交衰退和子房内自交不亲和的这种差异,己有研究提出了8种区分方法.通过解剖学方法观察授粉后生物学过程,比较自交和异交先后授粉和自交授粉处理的结籽率,以及通过一元线性回归模型考察自交和异交处理下成熟种子和败育种子数之和是否保持恒定,可以区分是合子前还是合子后过程导致的自交后种子产量降低.通过全同胞间杂交实验判断败育的遗传基础是单基因控制还是多位点有害隐性等位基因的纯和,可以区分合子后自交不亲和机制与早期近交衰退;或者通过这两种不同遗传基础导致的种子大小等表型性状的差异来区分.     

Distinguishing heat from light in debate over controversial fossils

Fossil organisms offer our only direct insight into how the distinctive body plans of extant organisms were assembled. However, realizing the potential evolutionary significance of fossils can be hampered by controversy over their interpretation. Here, as a guide to evaluating palaeontological debates, we outline the process and pitfalls of fossil interpretation. The physical remains of controversial fossils should be reconstructed before interpreting homologies, and choice of interpretative model should be explicit and justified. Extinct taxa lack characters diagnostic of extant clades because the characters had not yet evolved, because of secondary loss, or because they have rotted away. The latter, if not taken into account, will lead to the spurious assignment of fossils to basally branching clades. Conflicting interpretations of fossils can often be resolved by considering all the steps in the process of anatomical analysis and phylogenetic placement, although we must accept that some fossil organisms are simply too incompletely preserved for their evolutionary significance to be realized.     

Distinguishing species

Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious for closely related ones. A molecular marker giving a clear distinction would therefore be of immense benefit. The internal transcribed spacer 2 (ITS2) has been widely used for low-level phylogenetic analyses. Case studies revealed that a compensatory base change (CBC) in the helix II or helix III ITS2 secondary structure between two organisms correlated with sexual incompatibility. We analyzed more than 1300 closely related species to test whether this correlation is generally applicable. In 93%, where a CBC was found between organisms classified within the same genus, they belong to different species. Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species.     

Distinguishing benign from malignant pleural effusions by lectin immunocytochemistry

Since distinguishing malignant from benign cells in pleural effusions can be difficult, with reactive mesothelial cells simulating adenocarcinoma cells, the binding patterns of a battery of lectins on cells in eight benign and eight malignant effusions were studied using the avidin-biotin peroxidase complex method. The following lectins were used: concanavalin A, Dolichos biflorus agglutinin, peanut agglutinin, Phaseolus vulgaris agglutinin, Ricinus communis germ agglutinin, soybean agglutinin, Ulex europeaus agglutinin (UEA) and wheat germ agglutinin. Several patterns of staining were seen with the lectins, but only UEA was helpful in distinguishing between benign and malignant effusions. Sixty percent of the adenocarcinomas stained with UEA, whereas none of the cells in the benign effusions did. These results imply that UEA positivity is indicative of carcinoma and can be useful in separating reactive or atypical mesothelial cells from adenocarcinoma cells.