The Development of the Sauropsid Integument: A Contribution to the Problem of the Origin and Evolution of Feathers

Developmental anatomical data are insufficient to discuss plausibleintermediates between an ancestral, scaled, reptilian skin andappendage-bearing, avian skin. We also review adult tissue replacementand ubiquitous mechanisms underlying skin morphogenesis. Combiningdevelopmental data sensu lato with consideration of necessarybiological roles permits evaluation of major form/function trendsin skin evolution. New data on feathers reveal retention ofthe sauropsid synapomorphy of vertical alteration of - and ß-keratogenesis.By identifying roles that were obligatorily maintained throughoutevolution, we demonstrate constraints on hypothetical skin morphologiesin preavian taxa. We analyze feather origins as a problem ofemergence of complex form via modulations of morphogenesis.While existing data do not permit presentation of sequential,hypothetical, intermediates culminating in a plumage, the analysis:(1) implies that a protofeather and its follicle are most easilyderived from isolated, flattened, elongate, reptilian scales;(2) explains diversification of feather morphs from a contour-like"basic" feather and the similarity between feather and hairfollicles; and thus (3) reveals several developmental constraintson structures proposed as antecedent to avian feathers, whetherhypothetical constructs or palaeontological interpretations.Although these conclusions do not depend on any previous scenario,they are consistent with Regal's (1975) model and the limited,fossil evidence, especially that of the "basal archosaur" Longisquama.     

Caenorhabditis elegans Heterochromatin protein 1 (HPL-2) links developmental plasticity, longevity and lipid metabolism

Background

Heterochromatin protein 1 (HP1) family proteins have a well-characterized role in heterochromatin packaging and gene regulation. Their function in organismal development, however, is less well understood. Here we used genome-wide expression profiling to assess novel functions of the Caenorhabditis elegans HP1 homolog HPL-2 at specific developmental stages.

Results

We show that HPL-2 regulates the expression of germline genes, extracellular matrix components and genes involved in lipid metabolism. Comparison of our expression data with HPL-2 ChIP-on-chip profiles reveals that a significant number of genes up- and down-regulated in the absence of HPL-2 are bound by HPL-2. Germline genes are specifically up-regulated in hpl-2 mutants, consistent with the function of HPL-2 as a repressor of ectopic germ cell fate. In addition, microarray results and phenotypic analysis suggest that HPL-2 regulates the dauer developmental decision, a striking example of phenotypic plasticity in which environmental conditions determine developmental fate. HPL-2 acts in dauer at least partly through modulation of daf-2/IIS and TGF-β signaling pathways, major determinants of the dauer program. hpl-2 mutants also show increased longevity and altered lipid metabolism, hallmarks of the long-lived, stress resistant dauers.

Conclusions

Our results suggest that the worm HP1 homologue HPL-2 may coordinately regulate dauer diapause, longevity and lipid metabolism, three processes dependent on developmental input and environmental conditions. Our findings are of general interest as a paradigm of how chromatin factors can both stabilize development by buffering environmental variation, and guide the organism through remodeling events that require plasticity of cell fate regulation.     

The genetic basis of phenotypic convergence in beach mice: similar pigment patterns but different genes

Convergent evolution is a widespread phenomenon seen in diverseorganisms inhabiting similar selective environments. However,it is unclear if similar phenotypes are produced by the sameor different genes and mutations. Here we analyze the molecularmechanisms underlying convergent pigment pattern among subspeciesof the beach mouse (Peromyscus polionotus) inhabiting the Gulfand Atlantic coasts of Florida. In these two geographic regions,separated by more than 300 km, "beach mice" have lighter coloredcoats than do their mainland counterparts, produced by naturalselection for camouflage against the pale coastal sand dunes.We measured color pattern in eight beach mouse subspecies andshowed that three of the Gulf Coast subspecies are more phenotypicallysimilar to an Atlantic coast subspecies than to their Gulf Coastneighbors. However, light-colored beach mice do not form a monophyleticgroup. Previous results implicated a single derived amino acidchange in the melanocortin-1 receptor (Mc1r) as a major contributorto pigment pattern in the Gulf Coast beach mice; despite phenotypicsimilarities, the derived Mc1r allele was not found in the Atlanticcoast beach mouse populations. Here we show that Atlantic coastbeach mice have high levels of Mc1r polymorphism but they lackunique alleles. Functional assays revealed that single aminoacid mutations segregating in Atlantic coast beach mice do notcause any change in Mc1r activity compared with the activityof Mc1r from dark-colored mice. These joint results show thatconvergent pigment patterns in recently diverged beach mousesubspecies—whose developmental constraints are presumablysimilar—have evolved through a diversity of genetic mechanisms.     

Roles of the Af and Tl Genes in Pea Leaf Morphogenesis: Shoot Ontogeny and Leaf Development in the Heterozygotes

The wildtype leaf blade of Pisum sativum possesses proximalleaflets and distal tendrils, which may be altered by two recessivemutations that affect pinna morphology, afila (afaf) and tendrilless(tltl). Using morphological observations and SEM, the variationin leaf forms along the plant axis and leaf development werecharacterized for plants heterozygous at the Af and/or Tl loci.The Af and Tl genes interacted to affect many characteristicsof shoot ontogeny, including rate changes in leaf blade lengthand complexity increases, as well as time to flowering. TheAf gene retarded early vegetative development and acceleratedthe time to flowering. The leaf phenotypes of these heterozygousgenotypes were specified mainly by changes in the timing ofmajor developmental events. The data support the hypothesesthat both genes are heterochronic in nature and that the pealeaf blade consists of three genetically- and developmentally-determined regions: proximal, distal and terminal. Copyright2000 Annals of Botany Company Heterochrony, leaf development, shoot ontogeny, Pisum sativum L., garden pea, afila,tendrilless .     

家蚕Hox基因研究进展

Hox基因（homeobox genes）在昆虫躯体模式（body plan）的发育调控机制中扮演着重要角色,其表达具有严格的组织特异性和胚胎发育的程序性。家蚕Bombyx mori作为鳞翅目昆虫的代表,其Hox基因也陆续得到鉴定。在家蚕中存在一个拟复等位基因群--E群基因,其突变表型均与过剩斑纹和过剩附肢有关,这可能与Hox基因有着密切联系。家蚕全基因组测序完成后,发现其Hox基因簇中存在12个特有的homeobox基因（Bmshx1~Bmshx12）, 说明家蚕Hox基因可能具有独特的生物学意义。我们还利用家蚕基因芯片数据分析了Bmlab与Bmpb基因的组织表达特征。通过对家蚕Hox基因的研究,探索家蚕躯体模式建立机制,可望为解析其他鳞翅目昆虫的躯体模式的建立机制提供理论依据。本文就家蚕Hox基因的表达、功能及其与E群突变的关系等方面进行了综述。     

Hox and ParaHox Genes in Flatworms: Characterization and Expression

Flatworms (phylum Platyhelminthes) are favourite organisms inDevelopmental Biology and Zoology because of their extraordinarypowers of regeneration and because they may hold a pivotal placein the origin and evolution of the Bilateria. Hox genes playkey roles in both processes: setting up the new anteroposteriorpattern in the former, and as qualitative markers of phylogeneticaffinities among bilaterian phyla in the latter. We have searchedfor Hox and ParaHox genes in several flatworm groups spanningfrom freshwater triclads to marine polyclads and, more recently,in the acoels, the likely earliest extant bilaterian. We haveisolated and sequenced eight Hox genes from the freshwater tricladGirardia tigrina and three Hox and two ParaHox genes from thepolyclad Discocelis tigrina. Data from the acoels Paratomellarubra and Convoluta roscoffensis is also reported. FlatwormHox sequences and 18S rDNA sequence data support clear affinitiesof Platyhelminthes to spiralian lophotrochozoans. The basalposition of acoel flatworms supported from recent 18S rDNA data,remains still uncertain. Expression of Hox genes in intact andregenerating adult organisms show nested patterns with gradedanterior expression boundaries, or ubiquitous expression. Newapproaches to study the function of Hox genes in flatworms,such as RNA interference are briefly discussed.     

Developmental Gene Expression in Amphioxus: New Insights into the Evolutionary Origin of Vertebrate Brain Regions, Neural Crest, and Rostrocaudal Segmentation

SYNOPSIS. Amphioxus is widely held to be the closest invertebraterelative of the vertebrates and the best available stand-infor the proximate ancestor of the vertebrates. The spatiotemporalexpression patterns of developmental genes can help suggestbody part homologies between vertebrates and amphioxus. Thisapproach is illustrated using five homeobox genes (AmphiHoxl,AmphiHox2, AmphiOtx, AmphiDll, and AmphiEri) to provide insightsinto the evolutionary origins of three important vertebratefeatures: the major brain regions, the neural crest, and rostrocaudalsegmentation. During amphioxus development, the neural expressionpatterns of these genes are consistent with the presence ofa forebrain (detailed neuroanatomy indicates that the forebrainis all diencephalon without any telencephalon) and an extensivehindbrain; the possible presence of a midbrain requires additionalstudy. Further, during neurulation, the expression pattern ofAmphiDll as well as migratory cell behavior suggest that theepidermal cells bordering the neural plate may represent a phylogeneticprecursor of the vertebrate neural crest. Finally, when theparaxial mesoderm begins to segment, the earliest expressionof AmphiEn is detected in the posterior part of each nascentand newly formed somite. This pattern recalls the expressionof the segment-polarity gene engrailed during establishmentof the segments of metameric protostomes. Thus, during animalevolution, the role of engrailed in establishing and maintainingmetameric body plans may have arisen in a common segmented ancestorof both the protostomes and deuterostomes.     

Developmental Genetics and Morphological Evolution of Flowering Plants, Especially Bladderworts (Utricularia): Fuzzy Arberian Morphology Complements Classical Morphology

This review compares new developmental models on flowering andother vascular plants with evolutionary hypotheses formulatedby Agnes Arber (1879–1960) and like-minded botanists.Special emphasis is laid on philosophical basics such as perspectivism,pluralism about evolutionary modelling, continuum way of thinking,and fuzzy logic. Arber's perspective is best labelled as F uzzyA rberian M orphology (FAM Approach). Its proponents (‘FAMmers’)treat structural categories (e.g. ‘roots’, ‘shoots’,‘stems’, ‘leaves’, ‘stipules’)in vascular plants as concepts with fuzzy borderlines allowingintermediates (including transitional forms, developmental mosaics).The FAM Approach complements Cla ssical Plant M orphology (ClaMApproach), which is the traditional approach in botany. ClaMproponents (‘ClaMmers’) postulate that the structuralcategories of vascular plants are regarded as concepts withclear-cut borderlines and without intermediates. However, duringthe evolution of vascular plants, the root-shoot distinctionand the stem-leaf distinction have become blurred several timesdue to developmental changes, resulting in organs with uniquecombinations of features. This happened, for example, in thebladderworts (Utricularia, Lentibulariaceae). When focusingon the ‘leaf’, the FAM Approach is identical toArber's ‘partial-shoot theory of the leaf’ and Sinha's‘leaf shoot continuum model’. A compound leaf canrepeat the developmental pathway of the whole shoot, at leastto some degree. For example, compound leaves of Chisocheton(Meliaceae)with indeterminate apical growth and three-dimensional branchingmay be seen as developmental mosaics sharing some growth processeswith whole shoots! We focus here on the FAM Approach becausethis perspective is especially promising for developmental geneticistsstudying flowering and other vascular plants. Copyright 2001Annals of Botany Company Review, body plan, developmental mosaics, leaf development, history of botany, homeosis, homeotic genes, Lentibulariaceae, morphological evolution, process morphology, stipules, Utricularia, flowering plants     

Assignment of 82 Known Genes and Gene Clusters on the Genome of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC6803

We have previously constructed the physical map of a cyanobacterium,Synechoystis sp. strain PCC6803 on the basis of restrictionand linking clone analysis. Since a total of 82 genes and geneclusters have been isolated from this strain, most of whichare involved in oxygenic photosynthesis, portions of their sequenceswere amplified by the PCR method and assigned on the physicalmap of the genome by hybridization with restriction fragments,ordered clones, which were obtained from cosmid and libraries,and long PCR-products. An exception was the gene psbG2 whichwas mapped on an extra-chromosomal unit of 45 kb. Since geneticmaps of some of genes assigned above, especially those for photosynthesis,have been reported for two other cyanobacterial strains, Anabaenasp. PCC7120 and Synechococcus sp. PCC7002, gene organizationswere compared among the three strains. However, no significantcorrelation was observed, suggesting that rearrangement of genesoccurred in the respective strains during or after establishmentof the species.     

Analysis of the reticulon gene family demonstrates the absence of the neurite growth inhibitor Nogo-A in fish

Reticulons (RTNs) are a family of evolutionary conserved proteinswith four RTN paralogs (RTN1, RTN2, RTN3, and RTN4) presentin land vertebrates. While the exact functions of RTN1 to RTN3are unknown, mammalian RTN4-A/Nogo-A was shown to inhibit theregeneration of severed axons in the mammalian central nervoussystem (CNS). This inhibitory function is exerted via two distinctregions, one within the Nogo-A–specific N-terminus andthe other in the conserved reticulon homology domain (RHD).In contrast to mammals, fish are capable of CNS axon regeneration.We performed detailed analyses of the fish rtn gene family todetermine whether this regeneration ability correlates withthe absence of the neurite growth inhibitory protein Nogo-A.A total of 7 rtn genes were identified in zebrafish, 6 in pufferfish,and 30 in eight additional fish species. Phylogenetic and syntenicrelationships indicate that the identified fish rtn genes areorthologs of mammalian RTN1, RTN2, RTN3, and RTN4 and that severalparalogous fish genes (e.g., rtn4 and rtn6) resulted from genomeduplication events early in actinopterygian evolution. Accordingly,sequences homologous to the conserved RTN4/Nogo RHD are presentin two fish genes, rtn4 and rtn6. However, sequences comparableto the first 1,000 amino acids of mammalian Nogo-A includinga major neurite growth inhibitory region are absent in zebrafish.This result is in accordance with functional data showing thataxon growth inhibitory molecules are less prominent in fisholigodendrocytes and CNS myelin compared to mammals.     

Functional mapping imprinted quantitative trait loci underlying developmental characteristics

Background

Genomic imprinting, a phenomenon referring to nonequivalent expression of alleles depending on their parental origins, has been widely observed in nature. It has been shown recently that the epigenetic modification of an imprinted gene can be detected through a genetic mapping approach. Such an approach is developed based on traditional quantitative trait loci (QTL) mapping focusing on single trait analysis. Recent studies have shown that most imprinted genes in mammals play an important role in controlling embryonic growth and post-natal development. For a developmental character such as growth, current approach is less efficient in dissecting the dynamic genetic effect of imprinted genes during individual ontology.

Results

Functional mapping has been emerging as a powerful framework for mapping quantitative trait loci underlying complex traits showing developmental characteristics. To understand the genetic architecture of dynamic imprinted traits, we propose a mapping strategy by integrating the functional mapping approach with genomic imprinting. We demonstrate the approach through mapping imprinted QTL controlling growth trajectories in an inbred F₂ population. The statistical behavior of the approach is shown through simulation studies, in which the parameters can be estimated with reasonable precision under different simulation scenarios. The utility of the approach is illustrated through real data analysis in an F₂ family derived from LG/J and SM/J mouse stains. Three maternally imprinted QTLs are identified as regulating the growth trajectory of mouse body weight.

Conclusion

The functional iQTL mapping approach developed here provides a quantitative and testable framework for assessing the interplay between imprinted genes and a developmental process, and will have important implications for elucidating the genetic architecture of imprinted traits.     

MMG: a probabilistic tool to identify submodules of metabolic pathways

Motivation: A fundamental task in systems biology is the identificationof groups of genes that are involved in the cellular responseto particular signals. At its simplest level, this often reducesto identifying biological quantities (mRNA abundance, enzymeconcentrations, etc.) which are differentially expressed intwo different conditions. Popular approaches involve using t-teststatistics, based on modelling the data as arising from a mixturedistribution. A common assumption of these approaches is thatthe data are independent and identically distributed; however,biological quantities are usually related through a complex(weighted) network of interactions, and often the more pertinentquestion is which subnetworks are differentially expressed,rather than which genes. Furthermore, in many interesting cases(such as high-throughput proteomics and metabolomics), onlyvery partial observations are available, resulting in the needfor efficient imputation techniques. Results: We introduce Mixture Model on Graphs (MMG), a novelprobabilistic model to identify differentially expressed submodulesof biological networks and pathways. The method can easily incorporateinformation about weights in the network, is robust againstmissing data and can be easily generalized to directed networks.We propose an efficient sampling strategy to infer posteriorprobabilities of differential expression, as well as posteriorprobabilities over the model parameters. We assess our methodon artificial data demonstrating significant improvements overstandard mixture model clustering. Analysis of our model resultson quantitative high-throughput proteomic data leads to theidentification of biologically significant subnetworks, as wellas the prediction of the expression level of a number of enzymes,some of which are then verified experimentally. Availability: MATLAB code is available from http://www.dcs.shef.ac.uk/~guido/software.html Contact: guido{at}dcs.shef.ac.uk Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Jonathan Wren     

Evolution of sensory structures in basal metazoa

Cnidaria have traditionally been viewed as the most basal animalswith complex, organ-like multicellular structures dedicatedto sensory perception. However, sponges also have a surprisingrange of the genes required for sensory and neural functionsin Bilateria. Here, we: (1) discuss "sense organ" regulatorygenes, including; sine oculis, Brain 3, and eyes absent, thatare expressed in cnidarian sense organs; (2) assess the sensoryfeatures of the planula, polyp, and medusa life-history stagesof Cnidaria; and (3) discuss physiological and molecular datathat suggest sensory and "neural" processes in sponges. We thendevelop arguments explaining the shared aspects of developmentalregulation across sense organs and between sense organs andother structures. We focus on explanations involving divergentevolution from a common ancestral condition. In Bilateria, distinctsense-organ types share components of developmental-gene regulation.These regulators are also present in basal metazoans, suggestingevolution of multiple bilaterian organs from fewer antecedentsensory structures in a metazoan ancestor. More broadly, wehypothesize that developmental genetic similarities betweensense organs and appendages may reflect descent from closelyassociated structures, or a composite organ, in the common ancestorof Cnidaria and Bilateria, and we argue that such similaritiesbetween bilaterian sense organs and kidneys may derive froma multifunctional aggregations of choanocyte-like cells in ametazoan ancestor. We hope these speculative arguments presentedhere will stimulate further discussion of these and relatedquestions.     

Expression of Plasma Membrane Water Channel Genes under Water Stress in Nicotiana excelsior

Deduced amino acid sequences encoded by the cDNAs related tothe MIP gene family from Nicotiana excelsior were characterized.Phylogenetic characterization of the products of correspondinggenes named NeMip1, NeMip2, and NeMip3 strongly suggested thatthey are water channel proteins localized in the plasma membrane.Organ specificity of the gene expression was examined in leaves,roots, and reproductive organs. NeMip1 was expressed in rootsand reproductive organs; however, it was hardly detectable inleaves. Two other genes, NeMip2 and NeMip3, were expressed inall of organs examined. mRNA accumulation from the genes wasinvestigated in leaves under salt- and drought-stresses. Theresults demonstrated that mRNA accumulation from all three genesincreased under salt- and drought-stresses within one day. However,they showed different accumulation patterns. In addition totheir up-reg-ulation under salt- and drought-stresses, dailychanges in NeMip2 and NeMip3 mRNA accumulation was observedunder unstressed conditions in leaves. (Received May 2, 1997; Accepted September 3, 1997)