Discovering Periodic Patterns in Historical News

We address the problem of observing periodic changes in the behaviour of a large population, by analysing the daily contents of newspapers published in the United States and United Kingdom from 1836 to 1922. This is done by analysing the daily time series of the relative frequency of the 25K most frequent words for each country, resulting in the study of 50K time series for 31,755 days. Behaviours that are found to be strongly periodic include seasonal activities, such as hunting and harvesting. A strong connection with natural cycles is found, with a pronounced presence of fruits, vegetables, flowers and game. Periodicities dictated by religious or civil calendars are also detected and show a different wave-form than those provoked by weather. States that can be revealed include the presence of infectious disease, with clear annual peaks for fever, pneumonia and diarrhoea. Overall, 2% of the words are found to be strongly periodic, and the period most frequently found is 365 days. Comparisons between UK and US, and between modern and historical news, reveal how the fundamental cycles of life are shaped by the seasons, but also how this effect has been reduced in modern times.     

T-DNA标签在转基因水稻基因组中的整合特点

利用热不对称交错PCR (TAIL-PCR),对200个含T-DNA插入的转基因水稻株系进行分析,获得了159个T-DNA右边界侧翼序列. 其中,92个序列含有T-DNA右边界和侧邻的水稻基因组序列,78个序列与已公布的水稻BAC/PAC克隆有97%～100%的同源性,从而可作为T-DNA标签定位在水稻的12条染色体上. 结合先前定位的169个T-DNA标签,对T-DNA在水稻基因组中的整合特点进行了分析. 结果发现,在T-DNA右边界和侧邻的水稻基因组序列的连接处,14.6%的T-DNA标签含有3～74bp的填充序列. 在不含填充序列的连接处,21.3%的T-DNA标签,在整合后的T-DNA右边界与侧翼的水稻基因组序列之间显示出3～5 bp的微同源性. 填充序列和微同源性的存在,揭示了T-DNA在水稻基因组中的整合既存在双链断裂修补机制,又存在单链裂缝修补机制. T-DNA倾向于整合到富含A/T核苷酸的基因组区域,即主要在基因的5′和3′端调控区以及内含子中.     

Developmental Integration and the Evolution of Pleiotropy

The different forms of morphological integration, developmental,functional, genetic, and evolutionary are defined and theirtheoretical relationships explored. Quantitative genetic modelspredict that the co-selection of traits involved in a commonfunction will lead to pleiotropic effects at the loci affectingthem while functionally-unrelated traits will be affected byseparate sets of loci (Wagner, 1996). The patterns of geneticvariation produced by these pleiotropic mutations and stabilizingselection for functionally and developmentally interacting traitsresults in their specific co-inheritance relative to other traits.This in turn leads to their co-ordinated response to selection.Therefore, functional and developmental integration lead togenetic integration which, in turn leads to evolutionary integration.Three examples of how developmental integration structures pleiotropyand morphological variation in non-human primate crania, artificially-modifiedhuman crania, and for the effects ofindividual genes on murinemandibular morphology are presented.     

Building Developmental Integration into Functional Systems: Function-Induced Integration of Mandibular Shape

The mammalian mandible is a developmentally modular but functionally integrated system. Whether morphological integration can evolve to match the optimal pattern of functional integration may depend on the developmental origin of integration, specifically, on the role that direct epigenetic interactions play in shaping integration. These interactions are hypothesized to integrate modules and also to be highly conservative, potentially constraining the evolution of integration. Using the fox squirrel (Sciurus niger) mandible as a model system, we test five a priori developmental hypotheses that predict mandibular integration and we also explore for correlations between shapes of mandibular regions not anticipated by any of the developmental models. To determine whether direct epigenetic interactions are highly conserved in rodents, we examine the correlation structure of fluctuating asymmetry, and compare integration patterns between fox squirrels and prairie deer mice (Peromyscus maniculatus bairdii). In fox squirrels, we find a correlation structure unanticipated by all a priori developmental models: adjacent parts along the proximodistal jaw axis are correlated whereas more distant ones are not. The most notable exception is that the shape of the anterior incisor alveolus is correlated with the shape of the ramus (FA component) or coronoid (symmetric component). Those exceptions differ between species; in prairie deer mice, the molar alveolus is connected to more parts, and the incisor alveolus to fewer, than in fox squirrels. The structure of integration suggests that the mandible cannot be decomposed into parts but rather is a single connected unit, a result consistent with its functional integration. That match between functional and developmental integration may arise, at least in part, from function-induced growth, building developmental integration into the functional system and enabling direct epigenetic interactions to evolve when function does.     

Patterns of Integration and Expression of Retroviral,Non-Replicative Vectors in Avian Embryos: Embryo Developmental Stage and Virus Subgroup Envelope Modulate Tissue-Tropism

We previously demonstrated that Avian Leukemia Viruses (ALV) carrying the v-myc gene specifically induce two types of tumors, cardiomyocytic tumors when the virus is injected before embryonic day 3 (E3), skin tumors when the virus is injected at E3 or E5.

Aiming to elucidate the mechanisms which determine this time-dependent change in target, we infected chick and quail embryos at E3 and E5 with replication-deficient, lacZ gene-carrying, ALV-based viruses produced by a packaging cell line. Three constructs driven by 3 different Long Terminal Repeats (LTRs) were tested and yielded similar results. When the constructs were inoculated at E3 and the lacZ gene product revealed 5 days later, around 70% of the embryos carried lacZ+ clones in the heart, around 50% had positive clones in the skin anywhere on the body, while a few embryos displayed clones in internal organs (liver, stomach, lungs). Immunocytological identification of the heart cell type(s) expressing the virus revealed that the only cells infected were cardiomyocytes. When the constructs were inoculated at E5, no lacZ+ clones appeared in the heart but all were located in the cephalic skin. In order to examine the relationship between viral integration and expression, DNA of different organs or tissues from lacZ stained embryos was analyzed by PCR. A tight correlation between integration and expression in the heart and in the skin was revealed in most cases. In contrast, a significant PCR signal was often detected in the liver or the stomach despite weak or absent expression as revealed by lacZ+ clones.

We then investigated the influence of envelope glycoprotein subgroups on the tropism of these constructs. The lacZ vector driven by RAV-2 LTRs was packaged as subgroups A, B or E viral particles. The A subgroup, used in the part of the study described above, infects both chick and quail while the B and E subgroups are specific for chick or quail respectively. These B and E subgroups induced lacZ+ clones in the heart (after E3 injection) while no clones or only a few were detected in the skin either after E3 or E5 injection. The following conclusions can be drawn: 1) cardiomyocytes are at E3 the major target for integration and expression of ALV-derived viruses in vivo; 2) targets change rapidly with embryonic age; and 3) tissue-specific infections depend on the envelope subgroup, thus presumably on the presence of the cognate receptor. This study clearly indicates that E3 inoculation of ALV-based retroviral vectors is a simple and powerful method to transfer gene sequences into cardiomyocytes and epidermal cells.     

Patterns of Integration and Expression of Retroviral, Non-Replicative Vectors in Avian Embryos: Embryo Developmental Stage and Virus Subgroup Envelope Modulate Tissue-Tropism

We previously demonstrated that Avian Leukemia Viruses (ALV) carrying the v-myc gene specifically induce two types of tumors, cardiomyocytic tumors when the virus is injected before embryonic day 3 (E3), skin tumors when the virus is injected at E3 or E5.

Aiming to elucidate the mechanisms which determine this time-dependent change in target, we infected chick and quail embryos at E3 and E5 with replication-deficient, lacZ gene-carrying, ALV-based viruses produced by a packaging cell line. Three constructs driven by 3 different Long Terminal Repeats (LTRs) were tested and yielded similar results. When the constructs were inoculated at E3 and the lacZ gene product revealed 5 days later, around 70% of the embryos carried lacZ+ clones in the heart, around 50% had positive clones in the skin anywhere on the body, while a few embryos displayed clones in internal organs (liver, stomach, lungs). Immunocytological identification of the heart cell type(s) expressing the virus revealed that the only cells infected were cardiomyocytes. When the constructs were inoculated at E5, no lacZ+ clones appeared in the heart but all were located in the cephalic skin. In order to examine the relationship between viral integration and expression, DNA of different organs or tissues from lacZ stained embryos was analyzed by PCR. A tight correlation between integration and expression in the heart and in the skin was revealed in most cases. In contrast, a significant PCR signal was often detected in the liver or the stomach despite weak or absent expression as revealed by lacZ+ clones.

We then investigated the influence of envelope glycoprotein subgroups on the tropism of these constructs. The lacZ vector driven by RAV-2 LTRs was packaged as subgroups A, B or E viral particles. The A subgroup, used in the part of the study described above, infects both chick and quail while the B and E subgroups are specific for chick or quail respectively. These B and E subgroups induced lacZ+ clones in the heart (after E3 injection) while no clones or only a few were detected in the skin either after E3 or E5 injection. The following conclusions can be drawn: 1) cardiomyocytes are at E3 the major target for integration and expression of ALV-derived viruses in vivo; 2) targets change rapidly with embryonic age; and 3) tissue-specific infections depend on the envelope subgroup, thus presumably on the presence of the cognate receptor. This study clearly indicates that E3 inoculation of ALV-based retroviral vectors is a simple and powerful method to transfer gene sequences into cardiomyocytes and epidermal cells.     

Starting Points for a Developmental Genetics of Nerve Patterns

SYNOPSIS. The genie control of the development of neural morphologyand specific neural connections is little known, primarily becauseof a paucity of neurological mutants in animal models suitablefor experimental manipulation. However, by using cell markers—suchas tetraploidy, a large cell marker whose development is describedhere—the development of single retinal cells in tetraploidembryos, the growth of marked polyclones in chimeric eyes, andthe central connections of various chimeric eyes have been analyzedto identify the strategies used in molding eye morphology andestablishing precise central connections. Theoretical modelsand computer simulations were used to draw inferences aboutthe information used to accomplish the identified strategies.This analysis resulted in predictions about the sorts of mutantgenes which might be found to affect neural ontogeny.     

Heavy-Metal Stress and Developmental Patterns of Arbuscular Mycorrhizal Fungi

The rate of global deposition of Cd, Pb, and Zn has decreased over the past few decades, but heavy metals already in the soil may be mobilized by local and global changes in soil conditions and exert toxic effects on soil microorganisms. We examined in vitro effects of Cd, Pb, and Zn on critical life stages in metal-sensitive ecotypes of arbuscular mycorrhizal (AM) fungi, including spore germination, presymbiotic hyphal extension, presymbiotic sporulation, symbiotic extraradical mycelium expansion, and symbiotic sporulation. Despite long-term culturing under the same low-metal conditions, two species, Glomus etunicatum and Glomus intraradices, had different levels of sensitivity to metal stress. G. etunicatum was more sensitive to all three metals than was G. intraradices. A unique response of increased presymbiotic hyphal extension occurred in G. intraradices exposed to Cd and Pb. Presymbiotic hyphae of G. intraradices formed presymbiotic spores, whose initiation was more affected by heavy metals than was presymbiotic hyphal extension. In G. intraradices grown in compartmentalized habitats with only a portion of the extraradical mycelium exposed to metal stress, inhibitory effects of elevated metal concentrations on symbiotic mycelial expansion and symbiotic sporulation were limited to the metal-enriched compartment. Symbiotic sporulation was more sensitive to metal exposure than symbiotic mycelium expansion. Patterns exhibited by G. intraradices spore germination, presymbiotic hyphal extension, symbiotic extraradical mycelium expansion, and sporulation under elevated metal concentrations suggest that AM fungi may be able to survive in heavy metal-contaminated environments by using a metal avoidance strategy.     

Developmental Patterns of Tree Dimensions in a Neotropical Deciduous Forest1

For 26 tree species in very dry tropical forest in Mexico, the developmental trends of relationships among trunk diameter, tree height, and crown diameter were inferred from a one‐time measurement of dispersed individuals across the size range from saplings to large, mature trees. On hillside sites in this high diversity forest, maximum dimensions were usually <10‐m height, 4‐m crown diameter, and 0.3‐m trunk diameter. The relationship of height to trunk diameter was characterized by an asymptotic, three‐parameter model. Crown diameter was a linear function of trunk diameter. The parameter values for both models varied widely among the species. In general, the dispersion among species of the height–crown diameter relationship increased linearly with trunk diameter (up to 0.2 m). Arborescent cacti were distant from other species at all sizes, although they were well modeled using the same equations. Empirical and theoretical features and limitations of the present and previous models, including mechanical buckling and water‐stress theories, are considered.     

Homology, Hox Genes, and Developmental Integration

The establishment and inheritance of individualized structuralunits is a key feature of morphological evolution, embodiedin the concept of homology. In current debates, homology isoften equated with identical genetic encoding. The empiricalevidence for this assumption is ambiguous. Genetic identitycan indicate morphological identity in some cases, but severalexamples show that gene expression patterns and regulatory systemsof development may be highly conserved while morphological charactersundergo dramatic evolutionary innovation. This indicates someindependence of structural homology from its genetic and developmentalmakeup. It is proposed that phenotypic evolution depends stronglyon the epigenetic context in which genetic redundancy becomesavailable for the control of new developmental interactions.The integrated character of developmental systems may representan important factor in the origin and identity of morphologicalcharacters and can stabilize incipient structures before theirfull genetic integration. The origin of the autopod sectionof the tetrapod limb is an example which suggests that novelhomologues can arise in evolution as a consequence of changingthe epigenetic context of conserved gene function.     

叉蕨科4属5种植物配子体的发育模式及其系统学意义

利用光学显微镜详细观察了叉蕨科（Aspidiaceae）4属5种植物,即肋毛蕨属（Ctenitis（C．Chr．）C．Chr．）的亮鳞肋毛蕨（C．subglandulosa（Hance）Ching）和海南肋毛蕨（C．decurrenti-pmnata（Ching）Ching）、轴脉蕨属（Ctenitopsis Ching ex Tard-Blot et C．Chr．）的轴脉蕨（C．sagenioides（Mett．）Ching）、黄腺羽蕨属（Pleocnemia Presl）的黄腺羽蕨（P．winitti Holtt．）以及叉蕨属（Tectaria Cav．）的剑叶叉蕨（T.leptophylla（C．H．Wright）Ching）的配子体发育过程,记录了配子体各发育阶段的模式特征,认为这5种植物的孢子、丝状体、片状体、生长点、翼片、细胞、毛状体和假根等具有稳定的系统学意义。检索结果与该科的经典分类结果基本相似,并在此基础上编写了各分类群的检索表。本研究为叉蕨科系统学研究积累了详实的配子体形态学资料。     

叉蕨科4属5种植物配子体的发育模式及其系统学意义

利用光学显微镜详细观察了叉蕨科(Aspidiaceae)4属5种植物, 即肋毛蕨属(Ctenitis (C. Chr.)C. Chr.)的亮鳞肋毛蕨 (C. subglandulosa (Hance)Ching)和海南肋毛蕨(C. decurrenti-pinnata (Ching)Ching)、轴脉蕨属(Ctenitopsis Ching ex Tard.-Blot et C. Chr.)的轴脉蕨(C. sagenioides (Mett.)Ching)、黄腺羽蕨属(Pleocnemia Presl )的黄腺羽蕨(P. winitti Holtt.)以及叉蕨属(Tectaria Cav.)的剑叶叉蕨(T. leptophylla (C. H. Wright)Ching)的配子体发育过程, 记录了配子体各发育阶段的模式特征, 认为这5种植物的孢子、丝状体、片状体、生长点、翼片、细胞、毛状体和假根等具有稳定的系统学意义。检索结果与该科的经典分类结果基本相似, 并在此基础上编写了各分类群的检索表。本研究为叉蕨科系统学研究积累了详实的配子体形态学资料。     

以发育模块重复征用和整合为基础的进化创新机制

进化新征的起源和分化是进化发育生物学研究的核心问题。通过对多细胞生物早期发育调控机制的比较分析,发现亲缘关系较远的生物所共有的一些形态特征受保守的发育调控程序调节（深同源性）。许多创新性状的发生是基于对预先存在的基因或发育调控模块的重复利用和整合。发育基因调控网络在结构和功能上高度模块化,因此不仅可以通过模块拆分和重复征用改变发育程式,而且也增强了调控网络自身的进化力。研究基因调控网络和发育系统的进化动态将有助于更深入地认识生物演化过程中创新性状发生和表型进化的分子机制。     

皖南花猪11种血液生化指标的发育性变化及性别差异

随机选择出生30、45、90、180日龄的皖南花猪公母各5头,测定了11项血清生化指标.结果显示:血糖(GLU)、总胆固醇(TC)、高密度脂蛋白胆固醇(HDL-C)、游离脂肪酸(FFA)、脂联素(ADP)、瘦素(leptin)和IgG有极显著的发育性变化(P0.01);而甘油三酯(TG)、低密度脂蛋白胆固醇(LDL-C)、IgA和IgM等没有明显的发育性变化.母猪的TG、TC、HDL-C和IgM极显著或显著大于公猪(P0.01或P0.05),其他血清生化指标虽在总体上没有性别差异,但在有些日龄差异明显,大多表现为母猪在90或180日龄大于公猪.结果表明:皖南花猪血液生化指标有特定的发育性模式,并存在不同程度的性别差异.     

Patterns of Genomic Integration of Nuclear Chloroplast DNA Fragments in Plant Species

The transfer of organelle DNA fragments to the nuclear genome is frequently observed in eukaryotes. These transfers are thought to play an important role in gene and genome evolution of eukaryotes. In plants, such transfers occur from plastid to nuclear [nuclear plastid DNAs (NUPTs)] and mitochondrial to nuclear (nuclear mitochondrial DNAs) genomes. The amount and genomic organization of organelle DNA fragments have been studied in model plant species, such as Arabidopsis thaliana and rice. At present, publicly available genomic data can be used to conduct such studies in non-model plants. In this study, we analysed the amount and genomic organization of NUPTs in 17 plant species for which genome sequences are available. The amount and distribution of NUPTs varied among the species. We also estimated the distribution of NUPTs according to the time of integration (relative age) by conducting sequence similarity analysis between NUPTs and the plastid genome. The age distributions suggested that the present genomic constitutions of NUPTs could be explained by the combination of the rapidly eliminated deleterious parts and few but constantly existing less deleterious parts.