T-cell receptor and immunoglobulin genes are rearranged together in Abelson virus-transformed pre-B and pre-T cells.

We have assessed the state of rearrangement and expression of B- and T-cell antigen receptor genes in cells of Abelson murine leukemia virus-transformed thymomas and other tumors. We found that unrearranged TcR gamma genes are expressed, as are unrearranged C mu genes, in pre-T, pre-B, and myeloid cells. We also found TcR gamma genes rearranged and expressed in putative pre-T cells and in cells apparently committed to the B-cell lineage. This is in contrast to the data from more mature T- and B-cell tumors. We conclude that in immature lymphoid cells both immunoglobulin and TcR gamma genes are accessible for rearrangement. We discuss the implications of these observations for an understanding of the B-T lymphoid differentiation event.     

Testing the correlation for clustered categorical and censored discrete time-to-event data when covariates are measured without/with errors

In the analysis of clustered categorical data, it is of common interest to test for the correlation within clusters, and the heterogeneity across different clusters. We address this problem by proposing a class of score tests for the null hypothesis that the variance components are zero in random effects models, for clustered nominal and ordinal categorical responses. We extend the results to accommodate clustered censored discrete time-to-event data. We next consider such tests in the situation where covariates are measured with errors. We propose using the SIMEX method to construct the score tests for the null hypothesis that the variance components are zero. Key advantages of the proposed score tests are that they can be easily implemented by fitting standard polytomous regression models and discrete failure time models, and that they are robust in the sense that no assumptions need to be made regarding the distributions of the random effects and the unobserved covariates. The asymptotic properties of the proposed tests are studied. We illustrate these tests by analyzing two data sets and evaluate their performance with simulations.     

Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies

Regressions of biological variables across species are rarely perfect. Usually, there are residual deviations from the estimated model relationship, and such deviations commonly show a pattern of phylogenetic correlations indicating that they have biological causes. We discuss the origins and effects of phylogenetically correlated biological variation in regression studies. In particular, we discuss the interplay of biological deviations with deviations due to observational or measurement errors, which are also important in comparative studies based on estimated species means. We show how bias in estimated evolutionary regressions can arise from several sources, including phylogenetic inertia and either observational or biological error in the predictor variables. We show how all these biases can be estimated and corrected for in the presence of phylogenetic correlations. We present general formulas for incorporating measurement error in linear models with correlated data. We also show how alternative regression models, such as major axis and reduced major axis regression, which are often recommended when there is error in predictor variables, are strongly biased when there is biological variation in any part of the model. We argue that such methods should never be used to estimate evolutionary or allometric regression slopes.     

Simple mathematical model of pathologic microsatellite expansions: when self-reparation does not work

We propose a simple model of pathologic microsatellite expansion, and describe an inherent self-repairing mechanism working against expansion. We prove that if the probabilities of elementary expansions and contractions are equal, microsatellite expansions are always self-repairing. If these probabilities are different, self-reparation does not work. Mosaicism, anticipation and reverse mutation cases are discussed in the framework of the model. We explain these phenomena and provide some theoretical evidence for their properties, for example, the rarity of reverse mutations.     

Intrasexually selected weapons

We propose a practical concept that distinguishes the particular kind of weaponry that has evolved to be used in combat between individuals of the same species and sex, which we term intrasexually selected weapons (ISWs). We present a treatise of ISWs in nature, aiming to understand their distinction and evolution from other secondary sex traits, including from ‘sexually selected weapons’, and from sexually dimorphic and monomorphic weaponry. We focus on the subset of secondary sex traits that are the result of same‐sex combat, defined here as ISWs, provide not previously reported evolutionary patterns, and offer hypotheses to answer questions such as: why have only some species evolved weapons to fight for the opposite sex or breeding resources? We examined traits that seem to have evolved as ISWs in the entire animal phylogeny, restricting the classification of ISW to traits that are only present or enlarged in adults of one of the sexes, and are used as weapons during intrasexual fights. Because of the absence of behavioural data and, in many cases, lack of sexually discriminated series from juveniles to adults, we exclude the fossil record from this review. We merge morphological, ontogenetic, and behavioural information, and for the first time thoroughly review the tree of life to identify separate evolution of ISWs. We found that ISWs are only found in bilateral animals, appearing independently in nematodes, various groups of arthropods, and vertebrates. Our review sets a reference point to explore other taxa that we identify with potential ISWs for which behavioural or morphological studies are warranted. We establish that most ISWs come in pairs, are located in or near the head, are endo‐ or exoskeletal modifications, are overdeveloped structures compared with those found in females, are modified feeding structures and/or locomotor appendages, are most common in terrestrial taxa, are frequently used to guard females, territories, or both, and are also used in signalling displays to deter rivals and/or attract females. We also found that most taxa lack ISWs, that females of only a few species possess better‐developed weapons than males, that the cases of independent evolution of ISWs are not evenly distributed across the phylogeny, and that animals possessing the most developed ISWs have non‐hunting habits (e.g. herbivores) or are faunivores that prey on very small prey relative to their body size (e.g. insectivores). Bringing together perspectives from studies on a variety of taxa, we conceptualize that there are five ways in which a sexually dimorphic trait, apart from the primary sex traits, can be fixed: sexual selection, fecundity selection, parental role division, differential niche occupation between the sexes, and interference competition. We discuss these trends and the factors involved in the evolution of intrasexually selected weaponry in nature.     

Convergence Time towards Periodic Orbits in Discrete Dynamical Systems

We investigate the convergence towards periodic orbits in discrete dynamical systems. We examine the probability that a randomly chosen point converges to a particular neighborhood of a periodic orbit in a fixed number of iterations, and we use linearized equations to examine the evolution near that neighborhood. The underlying idea is that points of stable periodic orbit are associated with intervals. We state and prove a theorem that details what regions of phase space are mapped into these intervals (once they are known) and how many iterations are required to get there. We also construct algorithms that allow our theoretical results to be implemented successfully in practice.     

Membrane fusion proteins are required for oskar mRNA localization in the Drosophila egg chamber

We used a genetic screen in Drosophila to identify mutations which disrupt the localization of oskar mRNA during oogenesis. Based on the hypothesis that some cytoskeletal components which are required during the mitotic divisions will also be required for oskar mRNA localization during oogenesis, we designed the following genetic screen. We screened for P-element insertions in genes which slow down the blastoderm mitotic divisions. A secondary genetic screen was to generate female germ-line clones of these potential cell division cycle genes and to identify those which cause the mislocalization of oskar mRNA. We identified mutations in ter94 which disrupt the localization of oskar mRNA to the posterior pole of the oocyte. Ter94 is a member of the CDC48p/VCP subfamily of AAA proteins which are involved in homotypic fusion of the endoplasmic reticulum during mitosis. Consistent with the function of the yeast ortholog, ter94-mutant egg chambers are defective in the assembly of the endoplasmic reticulum. We tested whether other membrane biosynthesis genes are required for localizing oskar mRNA during oogenesis. We found that ovaries that are mutant for syntaxin-1a, rop, and synaptotagmin are also defective in oskar mRNA localization during oogenesis. We suggest a pathway for the role of membrane assembly proteins on oskar mRNA localization.     

Two distinct classes of prestalk-enriched mRNA sequences in Dictyostelium discoideum

We have isolated cDNA clones derived from three mRNA sequences which are inducible by DIF, the putative stalk-specific morphogen of Dictyostelium. The three mRNA sequences are selectively expressed in cells on the stalk cell pathway of differentiation and we have compared them with previously characterized prestalk-enriched mRNA sequences. We find these latter sequences are expressed without a dependence on DIF, are much less highly enriched in prestalk over prespore cells and are expressed earlier during development than the DIF-inducible mRNA sequences. We propose two distinct mechanisms whereby a mRNA may become enriched in prestalk cells. An apparently small number of genes, represented by those we have isolated, is inducible by DIF and accumulates only in prestalk cells. We suggest that a second class of prestalk-enriched mRNA sequences are induced by cAMP to accumulate in all cells during aggregation and then become enriched in prestalk cells by selective loss from prespore cells.     

Towards linkage analysis with markers in linkage disequilibrium by graphical modelling

We review recent developments of MCMC integration methods for computations on graphical models for two applications in statistical genetics: modelling allelic association and pedigree based linkage analysis. We discuss and illustrate estimation of graphical models from haploid and diploid genotypes, and the importance of MCMC updating schemes beyond what is strictly necessary for irreducibility. We then outline an approach combining these methods to compute linkage statistics when alleles at the marker loci are in linkage disequilibrium. Other extensions suitable for analysis of SNP genotype data in pedigrees are also discussed and programs that implement these methods, and which are available from the author's web site, are described. We conclude with a discussion of how this still experimental approach might be further developed.     

Behavioural strategies of cormorants (Phalacrocoracidae) foraging under challenging light conditions

Diving is indicative of foraging in cormorants (Phalacrocoracidae). We have investigated a range of parameters associated with diving in Great Cormorants Phalacrocorax carbo to provide insight into the bases of cormorant predatory strategies. We hypothesize that if vision is important in cormorant foraging behaviour, and if they are not constrained by the position of their prey in the water column, then diving behaviour will be modulated primarily in response to the diel variation in ambient light levels. Specifically, we propose that cormorants forage at shallower depths when light levels are low, and more deeply when light levels are high. We provide evidence that this is the case. We recorded the occurrence of cormorant diving behaviour using implanted data loggers and recorded ambient light levels and water temperature using leg-mounted loggers in a sample of free-living Great Cormorants in Greenland. Our results show that dives are shallower at the beginning and end of each day when light levels are lower. We suggest that these data support the hypothesis that cormorant foraging is visually-guided even though recent evidence has shown that their underwater visual acuity is poor.     

Travelling wave dynamics and self-organization in a spatio-temporally structured population

We analyse spatial population dynamics showing that periodic or period-like chaotic dynamics produce self-organization structures, such as travelling waves. We suggest that self-organized patterns are associated with spatial synchrony patterns that often depend on geographical distance between subpopulations. The population dynamics also show statistical spatial autocorrelation patterns. We contrast our theoretical simulations with empirical data on annual damages in young sapling stands caused by voles. We conclude, on the basis of the periodicity, synchrony, and spatial autocorrelation patterns, and our simulation results, that vole dynamics represent travelling waves in population dynamics. We suggest that because such synchrony patterns are frequently observed in natural populations, spatial self-organization may be more common in population dynamics than reported in the literature.     

Great Expectations: Teaching Ethics to Medical Students in South Africa

Many academic philosophers and ethicists are appointed to teach ethics to medical students. We explore exactly what this task entails. In South Africa the Health Professions Council's curriculum for training medical practitioners requires not only that students be taught to apply ethical theory to issues and be made aware of the legal and regulatory requirements of their profession, it also expects moral formation and the inculcation of professional virtue in students. We explore whether such expectations are reasonable. We defend the claim that physicians ought to be persons of virtuous character, on the grounds of the social contract between society and the profession. We further argue that since the expectations of virtue of health care professionals are reasonable, it is also sound reasoning to expect ethics teachers to try to inculcate such virtues in their students, so far as this is possible. Furthermore, this requires of such teachers that they be suitable role models of ethical practice and virtue, themselves. We claim that this applies to ethics teachers who are themselves not members of the medical profession, too, even though they are not bound by the same social contract as doctors. We conclude that those who accept employment as teachers of ethics to medical students, where as part of their contractual obligation they are expected to inculcate moral values in their students, ought to be prepared to accept their responsibility to be professionally ethical, themselves.     

Hierarchically organized populations: interactions between individual,population, and ecosystem levels

We consider a population of individuals which can be distributed in different equivalence classes. These classes are gathered in groups so that intragroup transformations are much more frequent than intergroup ones. We study linear systems in general, illustrated by the example of coupled individual and population levels. Then, we study nonlinear systems with the example of coupled population and ecosystem levels. We give methods to derive the dynamical equations for the different levels and to calculate interlevel coupling terms. We compare the coupling effects in the linear and in the nonlinear case.     

中国受胁鸟类的分布与现状分析

参照《Threatened Birds of Asia》(《亚洲受胁鸟类红皮书》),将其中记载的在中国有分布的物种与《中国濒危动物红皮书·鸟类》的物种进行比较。两者的物种组成有明显差异,仅69种鸟同时出现在两个红皮书中;《亚洲受胁鸟类红皮书》中雀形目鸟类占比例最大,而《中国濒危动物红皮书·鸟类》中鸡形目鸟类占比例最大。两个红皮书中的受胁鸟类均以森林、湿地和灌丛为主要栖息生境,而导致物种受胁的主要原因是人为干扰所造成的栖息地破坏。在地理分布方面,应用Arcview 3.2的数据处理与叠加功能,发现西南山地亚区、东部丘陵平原亚区和黄淮平原亚区以及台湾亚区受胁鸟类物种丰富度较高,其中留鸟在西南山地亚区及其周边地区相对集中,迁徙鸟在东部丘陵平原亚区及其周边地区相对集中。在保护方面,中国的显著重要鸟区中有51个是在自然保护区范围内,但还有6个尚未建立保护区,建议予以保护和重视。作者认为西南山地和台湾、海南地区的受胁鸟类面临更大的灭绝威胁,而恢复和重建退化的生态系统是保护鸟类的重要前提。     

Domain deletions and substitutions in the modular protein evolution

The main mechanisms shaping the modular evolution of proteins are gene duplication, fusion and fission, recombination and loss of fragments. While a large body of research has focused on duplications and fusions, we concentrated, in this study, on how domains are lost. We investigated motif databases and introduced a measure of protein similarity that is based on domain arrangements. Proteins are represented as strings of domains and comparison was based on the classic dynamic alignment scheme. We found that domain losses and duplications were more frequent at the ends of proteins. We showed that losses can be explained by the introduction of start and stop codons which render the terminal domains nonfunctional, such that further shortening, until the whole domain is lost, is not evolutionarily selected against. We demonstrated that domains which also occur as single-domain proteins are less likely to be lost at the N terminus and in the middle, than at the C terminus. We conclude that fission/fusion events with single-domain proteins occur mostly at the C terminus. We found that domain substitutions are rare, in particular in the middle of proteins. We also showed that many cases of substitutions or losses result from erroneous annotations, but we were also able to find courses of evolutionary events where domains vanish over time. This is explained by a case study on the bacterial formate dehydrogenases.     

Bark beetles and pinhole borers (Curculionidae, Scolytinae, Platypodinae) alien to Europe

Invasive bark beetles are posing a major threat to forest resources around the world. DAISIE's web-based and printed databases of invasive species in Europe provide an incomplete and misleading picture of the alien scolytines and platypodines. We present a review of the alien bark beetle fauna of Europe based on primary literature through 2009. We find that there are 18 Scolytinae and one Platypodinae species apparently established in Europe, from 14 different genera. Seventeen species are naturalized. We argue that Trypodendron laeve, commonly considered alien in Europe, is a native species; conversely, we hypothesize that Xyleborus pfeilii, which has always been treated as indigenous, is an alien species from Asia. We also point out the possibility that the Asian larch bark beetle Ips subelongatus is established in European Russia. We show that there has been a marked acceleration in the rate of new introductions to Europe, as is also happening in North America: seven alien species were first recorded in the last decade.We present information on the biology, origins, and distributions of the alien species. All but four are polyphagous, and 11 are inbreeders: two traits which increase invasiveness. Eleven species are native to Asia, six to the Americas, and one is from the Canary Islands. The Mediterranean is especially favorable for invasives, hosting a large proportion of the aliens (9/19). Italy, France and Spain have the largest numbers of alien species (14, 10 and 7, respectively). We point out that the low numbers for at least some countries is likely due to under-reporting.Finally, we discuss the difficulties associated with identifying newly invasive species. Lack of good illustrations and keys hinder identification, particularly for species coming from Asia and Oceania.     

Location of 2(')-O-methyl nucleotides in 26S rRNA and methylation guide snoRNAs in Caenorhabditis elegans

Many nucleotides in rRNAs are modified. We devised a method to locate 2(')-O-methyl nucleotide residues using a conventional DNA sequencer. We found 38 2(')-O-methyl nucleotides in the 26S rRNA of Caenorhabditis elegans using this method. Fourteen of the 38 residues are conserved in both human and yeast rRNAs and 14 residues are conserved in either human or yeast rRNA. The remaining 10 nucleotides are uniquely methylated in C. elegans 26S rRNA. We searched the C. elegans genomic sequence for small nucleolar RNAs (snoRNAs), which guide the methylation of ribose residues, and predicted 18 snoRNA sequences that are expected to guide the methylation of some of these nucleotide residues.     

Tubers as fallback foods and their impact on Hadza hunter-gatherers

The Hadza are hunter-gatherers in Tanzania. Their diet can be conveniently categorized into five main categories: tubers, berries, meat, baobab, and honey. We showed the Hadza photos of these foods and asked them to rank them in order of preference. Honey was ranked the highest. Tubers, as expected from their low caloric value, were ranked lowest. Given that tubers are least preferred, we used kilograms of tubers arriving in camp across the year as a minimum estimate of their availability. Tubers fit the definition of fallback foods because they are the most continuously available but least preferred foods. Tubers are more often taken when berries are least available. We examined the impact of all foods by assessing variation in adult body mass index (BMI) and percent body fat (%BF) in relation to amount of foods arriving in camp. We found, controlling for region and season, women of reproductive age had a higher %BF in camps where more meat was acquired and a lower %BF where more tubers were taken. We discuss the implications of these results for the Hadza. We also discuss the importance of tubers in human evolution. Am J Phys Anthropol, 140:751–758, 2009. © 2009 Wiley-Liss, Inc.     

Estimation of Coupling Strength in Regenerated Lamprey Spinal Cords Based on a Stochastic Phase Model

We present a simple stochastic model of two coupled phase oscillators and a method of fitting the model to experimental spike-train data or to sequences of burst times. We apply the method to data from lesioned isolated lamprey spinal cords. The remaining tracts at the lesion site are either regenerated medial tracts, regenerated lateral tracts, control medial tracts, or control lateral tracts. We show that regenerated tracts on average provide significantly weaker coupling than control tracts. We compare our model-dependent estimate of coupling strength to a measure of coordination based on the size of deflections in the spike-train cross-correlation histogram (CCH). Using simulated data, we show that our estimates are able to detect changes in coupling strength that do not change the size of deflections in the CCH. Our estimates are also more resistant to changes in the level of dynamic noise and to changes in relative oscillator frequency than is the CCH. In simulations with high levels of dynamic noise and in one experimental preparation, we are able detect significant coupling strength although there are no significant deflections in the CCH.