Homology

Bioremediation is a possible mechanism for clean-up of hydrocarbon-contaminated soils in the Antarctic. Microbes indigenous to the Antarctic are required that degrade the hydrocarbon contaminants found in the soil, and that are able to survive and maintain activity under in situ conditions. Alkane- degrading bacteria previously isolated from oil-contaminated soil from around Scott Base, Antarctica, grew on a number of n-alkanes from hexane (C6) through to eicosane (C20) and the branched alkane pristane. Mineralization of 14C-dodecane was demonstrated with four strains. Representative isolates were identified as Rhodococcus species using 16S rDNA sequence analysis. Rhodococcus spp. strains 5/14 and 7/1 grew at −2°C but numbers of viable cells declined when incubated at 37°C. Both strains appear to have the major cold-shock gene cspA. Partial nucleotide sequence analyses of the PCR-amplified cspA open reading frame from Rhodococcus spp. strains 5/14 and 7/1 were approximately 60% identical to cspA from Escherichia coli.

We have evaluated the effects of the proline homologue Aze (1) (azetidine-2-carboxylic acid) on growth of Escherichia coli strains used to over-express recombinant forms of murine myelin basic protein (rmMBP), and on the degree of misincorporation. Addition of Aze to minimal media resulted in severe diminution of growth rate, but rmMBP could still be produced and purified. Mass spectrometry indicated that a detectable proportion of the rmMBP produced had incorporated Aze instead of proline (Pro), to a maximum of three of eleven possible sites. Molecular modelling of a proline-rich region of rmMBP illustrated that the misincorporation of Aze at any site would cause a severe bend in the polypeptide chain, and that multiple Pro ? Aze substitutions would completely disrupt a poly-proline type II structure that has been conjectured to be functionally significant.

1996), the traditional divisions grew at a rate of 40% The FASTA package of sequence comparison proper year, from 163 million to 317 million bases, but the grams has been expanded to include FASTX and entire GenBank grew from 173 million to 463 million FASTY, which compare a DNA sequence to a protein bases, because of the growth of the EST database. At sequence database, translating the DNA sequence in the end of 1996, about 40% of the bases in GenBank three frames and aligning the translated DNA sewere determined by high-throughput EST or genomic quence to each sequence in the protein database, sequencing. allowing gaps and frameshifts. Also new are TFASTX The DNA sequences produced by single-pass EST and TFASTY, which compare a protein sequence to a sequencing and high-throughput sequencing may be DNA sequence database, translating each sequence in of lower quality than traditional ''finished'' GenBank the DNA database in six frames and scoring alignsequences, which are typically based on multiple sements with gaps and frameshifts. FASTX and TFASTX quence reads from both strands of the DNA template. allow only frameshifts between codons, while FASTY As a result, EST sequences are more likely to contain and TFASTY allow substitutions or frameshifts within errors that produce frameshifts when translated into a codon. We examined the performance of FASTX and protein. Frameshift errors can be especially trouble-FASTY using different gap-opening, gap-extension, some in searches with single-pass EST sequences, beframeshift, and nucleotide substitution penalties. In cause these sequences are very likely to contain progeneral, FASTX and FASTY perform equivalently tein-coding regions, which are much more effectively when query sequences contain 0-10% errors. We also identified by protein, rather than DNA, sequence comevaluated the statistical estimates reported by FASTX parison. and FASTY. These estimates are quite accurate, except In an earlier paper (Zhang et al., 1997), we reported when an out-of-frame translation produces a low-complexity protein sequence. We used FASTX to scan the the development of rapid algorithms for comparing a Mycoplasma genitalium, Haemophilus influenzae, and translated DNA sequence to a protein sequence within Methanococcus jannaschii genomes for unidentified or a band, for incorporation into the optimization stage of misidentified protein-coding genes. We found at least the FASTA program (Pearson, 1990), and of a full 9 new protein-coding genes in the three genomes and Smith-Waterman translated-DNA-protein alignment. at least 35 genes with potentially incorrect boundaries. In this paper, we consider two methods for aligning a

Plant laccases are believed to be involved in dehydrogenative polymerisation of lignin. We report here the first cloning of monocot laccases. Five different laccase-encoding cDNA sequences were identified from ryegrass (Lolium perenne); four from stem and one from meristematic tissue. Three cDNA's contained entire coding sequences; LpLAC5-4 and LpLAC5-6 from stem, and LpLAC2-1 from meristem. LpLAC5-4 encodes a polypeptide of 610 amino acids with 14 potential N-glycosylation sites, and a calculated pI value of 5.0. Lack of an N-terminal signal peptide in LpLAC5-4 suggests that the mature protein is located intracellularly. A genomic clone, gLpLAC5-4 , has been isolated and represents the first exon Á/intron structure and promoter sequence of a plant laccase gene. LpLAC5-6 cDNA encodes a protein of 579 amino acids with an N-terminal signal peptide characteristic of secreted proteins, 13 potential N-glycosylation sites, and a pI value of 9.0. LpLAC2-1 was the only laccase found in a meristematic library. The cDNA encodes a protein of 578 amino acids with a predicted pI of 5.8, 9 putative N-glycosylation sites, and an N-terminal signal peptide. Ryegrass laccases are differentially expressed and are under tight transcriptional control. Sequence analyses have shown that the ryegrass genome encodes more than 25 different laccase genes. Plant laccases are distributed in different groups rather than being closely intraspecies related. High heterogeneity of plant laccases indicates that gene duplication events have occurred continuously before and after divergence of seedplants into gymnosperms, monocots, and dicots.

Penicillin binding proteins (PBPs) are involved in the biosynthesis of the peptidoglycan layer constitutive of the bacterial envelope. They have been targeted for more than half a century by extensively derived molecular scaffolds of penicillins and cephalosporins. Streptococcus pneumoniae resists the antibiotic pressure by inducing highly mutated PBPs that can no longer bind the β-lactam containing agents. To find inhibitors of PBP2x from Streptococcus pneumoniae (spPBP2x) with novel chemical scaffold so as to circumvent the resistance problems, a hierarchical virtual screening procedure was performed on the NCI database containing approximately 260000 compounds. The calculations involved ligand-based pharmacophore mapping studies and molecular docking simulations in a homology model of spPBP2x from the highly resistant strain 5204. A total of 160 hits were found, and 55 were available for experimental tests. Three compounds harboring two novel chemical scaffolds were identified as inhibitors of the resistant strain 5204-spPBP2x at the micromolar range. a Abbreviations: spPBP2x, penicillin Binding Protein 2x from Streptococcus pneumoniae; R6-PBP2x, 5204-PBP2x, sp328-PBP2x, PBP2x of Streptococcus pneumonia from respectively from the sensitive R6 strain and the resistant 5204 and 328 strains; NAG, N-acetylglucosamine; NAM, N-acetylmuramic acid; ASPRE, active-site penicillin recognizing enzymes; RA, residual activity; BSA, bovine serum albumin; S2d, Nbenzoyl-D-alanyl-thioglycolate; LTV, lactivicin; PLTV, phenoxyacetyllactivicin; CPH, common pharmacophore hypotheses.

The isocortex is a distinctive feature of the mammalian brain, with no clear counterpart in other amniotes. There have been long controversies regarding possible homologues of this structure in reptiles and birds. The brains of the latter are characterized by the presence of a structure termed dorsal ventricular ridge (DVR), which receives ascending auditory and visual projections, and has been postulated to be homologous to parts of the mammalian isocortex (i.e., the auditory and the extrastriate visual cortices). Dissenting views, now supported by molecular evidence, claim that the DVR originates from a region termed ventral pallium, while the isocortex may arise mostly from the dorsal pallium (in mammals, the ventral pallium relates to the claustroamygdaloid complex). Although it is possible that in mammals the embryonic ventral pallium contributes cells to the developing isocortex, there is no evidence yet supporting this alternative. The possibility is raised that the expansion of the cerebral cortex in the origin of mammals was product of a generalized dorsalizing influence in pallial development, at the expense of growth in ventral pallial regions. Importantly, the evidence suggests that organization of sensory projections is significantly different between mammals and sauropsids. In reptiles and birds, some sensory pathways project to the ventral pallium and others project to the dorsal pallium, while in mammals sensory projections end mainly in the dorsal pallium. We suggest a scenario for the origin of the mammalian isocortex which relies on the development of associative circuits between the olfactory, the dorsal and the hippocampal cortices in the earliest mammals. 

Seladin-1 Cholesterol biosynthesis Homology modelling MD simulation Enzymatic product egress a b s t r a c t Recent biochemical and clinical evidences unveiled that DHCR24 enzyme (3-␤-hydoxysterol-24 -reductase, also named seladin-1), which catalyzes the last step of the cholesterol biosynthesis, is implicated in relevant neuroprotective processes by modulating the level of cholesterol in membrane. The present study was undertaken with a view to model the DHCR24 enzyme and its catalytic site, analyzing the substrate recognition at an atomic level. A homology model of the enzyme was obtained based on plant Cytokinin Dehydrogenase, and its active site was found to bind the desmosterol plus a set of post-squalenic intermediates of the cholesterol biosynthesis in a binding mode conducive to catalysis, even if the docking results suggested that the enzyme has a clear preference for the last intermediates of such biosynthetic pathway. Since DHCR24 possesses a putative transmembrane segment, the enzyme was, then, inserted in a suitable membrane model and the membrane-anchored structure in complex with desmosterol and cholesterol underwent 10 ns MD simulations.

Two cDNAs, isolated from a Trypanosoma cruzi amastigote library immunoscreened with sera from patients with Chagas disease, encode proteins with sequence homology to eukaryotic components of the cellular sorting and recycling machinery. These proteins, denominated TcAGL, present an N-terminal lectin domain and a C-terminal region containing repetitive amino acids and a poly-glutamine tract. They are products of polymorphic alleles of a single copy gene constitutively expressed during the parasite life cycle. Polyclonal antibodies obtained from mice immunized with the recombinant antigen recognize proteins with apparent molecular weight ranging from 95 to 120 kDa in cell lysates from all three life stages and in various strains of the parasite. Sera from Chagas disease patients recognize the recombinant antigen in ELISA and immunoprecipitation assays but not in Western blot assays under denaturing conditions. Consistent with its proposed role in the glycoprotein secreting pathway, immunofluorescence analyses and expression of a green fluorescent protein-tagged TcAGL protein indicate a sub-cellular localization in the vicinity of the flagellar pocket membrane and the Golgi complex of the parasite. Ó

Four antigenically different strains of infectious bursal disease virus (IBDV), characterized by their reactivities with a panel of neutralizing monoclonal antibodies (MAbs), were selected to determine the molecular basis of antigenic variation. The large genome segment A, encoding the structural proteins of the U.S. variants GLS, DS326, E/Del and the vaccine strain D78, was cloned and sequenced. Comparison of the deduced amino acid sequences of the U.S. variants with other IBDV strains showed that most of the amino acid substitutions occur in the central region between residues 212 to 332, especially in the two hydrophilic regions between residues 212 to 223 and residues 314 to 324 of VP2 protein. By comparing the amino acid sequences of these variant viruses and their reactivities with IBDV specific MAbs, the putative amino acids involved in the formation of virus-neutralizing epitopes were identified. Comparison of the D78 versus PBG98 sequence showed that Gin at position 249 (Gln249) appears to be critical in binding with MAb B69. Similarly, comparison of the U.S. variant sequences with other serotype 1 sequences showed unique substitution(s) at residue Glu321 in GLS, residues Ile286, Asp318, Glu323 in E/Del, and residues Glu311 and Gln320 in DS326, which could be potential residue(s) involved in the recognition of MAb57, MAb67, and MAb179 epitopes, respectively. Comparison of the serotype 1 and serotype 2 sequences revealed that serotype 2 OH strain lacks the conserved amino acid sequence motif, S-W-S-AS -G-S, found in all virulent strains, as well as the second hydrophilic peak region, indicating a possible role of these residues in the serotype specificty or the pathogenic&y of the virus. Phylogenetic analysis of the IBDV proteins

Plant breeders have used disease resistance genes (R genes) to control plant disease since the turn of the century. Molecular cloning of R genes that enable plants to resist a diverse range of pathogens has revealed that the proteins encoded by these genes have several features in common. These findings suggest that plants may have evolved common signal transduction mechanisms for the expression of resistance to a wide range of unrelated pathogens. Characterization of the molecular signals involved in pathogen recognition and of the molecular events that specify the expression of resistance may lead to novel strategies for plant disease control.

Angesichts der Dominanz von Molekularbiologie, Entwicklungs-und Populationsgenetik sowie deren anwendungsorientierten Umsetzungen in den Bio-und Gentechniken mag es auf den ersten Blick merkwürdig überholt erscheinen Probleme der Morphologie nicht in einer ausschließlich wissenschaftshistorischen Perspektive, sondern sie als ein aktuelles wissenschaftsphilosophisches Problem zu thematisieren. Doch ein genauerer Blick auf die in den gegenwärtig dominanten Disziplinen der Biowissenschaften verhandelten theoretischen und methodischen Probleme zeigt sehr deutlich, dass viele der in der Morphologie behandelten Grundprobleme als ebensolche auch in der Molekularbiologie und den Genetiken zu verhandeln sind: Als erstes wären sicherlich zu nennen all die Probleme, die mit dem Vergleichen als einer Grundoperation jeglicher Wissenschaft verknüpft sind. Zum zweiten müssen auch die Genetiken auf einen Bauplan-Begriff rekurrieren, den sie weitgehend unreflektiert aus der morphologischen Tradition übernehmen. Drittens sehen sich die Genetiken konfrontiert mit Struktur-Funktionszusammenhängen, für deren Aufklärung das Wissen um zwar disziplinspezifisch gebrochene, aber methodisch entsprechende Debatten in der Morphologie hilfreich sein kann. Und schließlich wird mit dem Problemkreis von Modellen und Modellierungen ein Bereich angesprochen, der wiederum alle Wissenschaften in je spezifischer Weise betrifft.

In mammals, dosage compensation is achieved by X inactivation 1 and is regulated in cis by the X-inactivation centre 2 (Xic) and Xist (refs 3−5). The Xic controls X-chromosome counting, choice of X to inactivate and initiation of silencing. Xic action culminates in a change in Xist RNA property from a scarce, unstable RNA (refs 6,7) to highly expressed Xist RNA that coats the future inactive X (ref. 8). Deleting a 65-kb region downstream of Xist results in constitutive Xist expression and X inactivation, implying the presence of a cis-regulatory element 9 . In this region, we now report the discovery of a gene antisense to Xist. Tsix is a 40-kb RNA originating 15 kb downstream of Xist and transcribed across the Xist locus. Tsix sequence is conserved at the human XIC. Tsix RNA has no conserved ORFs, is seen exclusively in the nucleus and is localized at Xic. Before the onset of X inactivation, Tsix is expressed from both X chromosomes. At the onset of X inactivation, Tsix expression becomes monoallelic, is associated with the future active X and persists until Xist is turned off. Tsix is not found on the inactive X once cells enter the X-inactivation pathway. Tsix has features suggesting a role in regulating the early steps of X inactivation, but not the silencing step.

Sialidases (EC 3.2.1.18) are a group of glycohydrolytic enzymes, widely distributed in nature, that cleave sialic acid residues from the oligosaccharide components of glycoconjugates. All of the sialidase enzymes thus far characterized share an Asp block, repeated three to five times in the primary structure, and an F/YRIP sequence motif that is part of the active site. Using a sequence homology-based approach, we have identified a novel human gene, named NEU2, mapping to chromosome 2q37. The nucleotide sequence analysis of the gene has shown that it contains only one intron of about 1.25 kb, and the longest open reading frame encodes a protein of 380 amino acids, with a two-Asp block consensus, and the YRIP sequence. In the putative promoter sequence there are a classical TATAA box and four E boxes, which are consensus binding sites for muscle-specific transcription factors. Northern blot analysis revealed expression of the NEU2 transcript only in skeletal muscle.

The current situation in philosophy of science generally, and in philosophy of biology in particular, is most unsatisfactory. There are at least three general problems that many philosophers thought themselves near to solving twenty years ago, only to find that the anticipated solutions have come unglued. These are (1) the problem of characterizing and understanding the dynamics of conceptual change in science; (2) he problem of understanding the interrelationships among theories including particularly the reduction of one theory to another); and (3) he problem of scientific realism (i.e., the problem of how seriously to take the claims of theoretical science or, at least, of some theoretical scientists, to be describing the world literally--in terms of such theoretical entities as genes and protons, DNA molecules, and quarks). This general situation has significant effects on the philosophical study of particular sciences. In philosophy of biology, for example, although one finds a large number of elegant studies of particular topics, the sad fact is that there is no generally satisfactory large-scale synthesis n sight. We have no agreed-on foundation, no generally acceptable starting point from which to delimit and resolve the full range of theoretical problems of interest to scientists and philosophers regarding biology.

Homology is an essential idea of biology, referring to the historical continuity of characters, but it is also conceptually highly elusive. The main difficulty is the apparently loose relationship between morphological characters and their genetic basis. Here I propose that it is the historical continuity of gene regulatory networks rather than the expression of individual homologous genes that underlies the homology of morphological characters. These networks, here referred to as 'character identity networks', enable the execution of a character-specific developmental programme.

Characterization of the lectins from onion (Allium cepa), shallot (A. ascalonicum) and leek (A. porrum) has shown that these lectins differ from previously isolated Alliaceae lectins not only in their molecular structure but also in their ability to inhibit retrovirus infection of target cells. cDNA libraries constructed from poly(A)-rich RNA isolated from young shoots of onion, shallot and leek were screened for lectin cDNA clones using colony hybridization. Sequence analysis of the lectin cDNA clones from these three species revealed a high degree of sequence similarity both at the nucleotide and at the amino acid level. Apparently the onion, shallot and leek lectins are translated from mRNAs of ca. 800 nucleotides. The primary translation products are preproproteins (ca. 19 kDa) which are converted into the mature lectin polypeptides (12.5-13 kDa) after post-translational modifications. Southern blot analysis of genomic DNA has shown that the lectins are most probably encoded by a family of closely related genes which is in good agreement with the sequence heterogeneity found between different lectin cDNA clones of one species.

The extant land plants are unique among the monophyletic clade of photosynthetic eukaryotes, which consists of the green algae (chlorophytes), the charophycean algae (charophytes), numerous groups of unicellular algae (prasinophytes) and the embryophytes, by possessing, firstly, a sexual life cycle characterized by an alternation between a haploid, gametophytic and a diploid, sporophytic multicellular generation; secondly, the formation of egg cells within multicellular structures called archegonia; and, thirdly, the retention of the zygote and diploid sporophyte embryo within the archegonium. We review the developmental, paleobotanical and molecular evidence indicating that: the embryophytes descended from a charophyte-like ancestor; this common ancestor had a life cycle with only a haploid multicellular generation; and the most ancient (c. 410 Myr old) land plants (e.g. Cooksonia, Rhynia and Zosterophyllum) had a dimorphic life cycle (i.e. their haploid and diploid generations were morphologically different). On the basis of these findings, we suggest that the multicellular reproductive structures of extant charophytes and embryophytes are developmentally homologous, and that those of the embryophytes evolved by virtue of the co-option and re-deployment of ancient algal homeodomain gene networks.

Notre contribution montrera, sans doute pour la toute première fois, l’intérêt des réflexions sémiotiques des poètes surréalistes tchèques et français telles qu’elles s’expriment dans l’oeuvre collective "La civilisation surréaliste" (Payot 1976), publiée sous la direction du surréaliste parisien Vincent Bounoure, ancien ami d’André Breton depuis le milieu des années 1950. La contribution à cet ouvrage de Vratislav Effenberger, animateur du groupe pragois après la mort de Karel Teige, a également été majeure. Face au silence général observé sur ce travail par les experts du surréalisme et de la sémiotique, nous nous pencherons sur le nouveau jeu collectif des "récits parallèles", inventé dans les années 1970, et l’actualité des réflexions surréalistes sur le cours pris par l’usage du langage dans nos civilisations par le biais de la communication de masse, soumettant l’échange de signes à la logique de l’économie capitaliste et aux objectifs idéologiques du pouvoir politique. Par leur expérience ludique et poétique, les surréalistes ont compris le tournant négatif que prenait l’« universalité » du langage et de l’art. Ces idées sont confirmées et approfondies par quelques lettres et documents d’archives inédits, échangés entre Bounoure et Effenberger lors de la préparation du volume et jusqu’ici jamais pris en considération. Nous montrerons aussi l’existence de convergences implicites étonnantes entre cette sémiotique générale surréaliste et les théories des signes de Bakhtine et Rossi-Landi.

The furcula is a structure formed by the midline fusion of the clavicles. This is the element which is unique to theropods and is important for understanding the link between birds and other theropods. New specimens from basal theropods suggest that the furcula appeared very early in theropod history. We review furcula development, function, and morphology, as well as the anatomical terminology applied to it. Furcular morphology is highly variable in crown-group avians but is rather conserved among nonavian theropods. Here we review, or describe for the first time, the furculae in many nonavian theropods. Furculae occur in nearly all major clades of theropods, as shown by new theropod specimens from the Early Cretaceous of China and a close inspection of previously collected specimens. Informative phylogenetic characters pertaining to the furcula occur throughout Theropoda, though care should be take to consider taphonomic effects when describing furcular morphology.

Work on analogy has been done from a number of disciplinary perspectives throughout the history of Western thought. This work is a multidisciplinary guide to theorizing about analogy. It contains 1,406 references, primarily to journal articles and monographs, and primarily to English language material. Classical through to contemporary sources are included. The work is classified into eight different sections (with a number of subsections). A brief introduction to each section is provided. Keywords and key expressions of importance to research on analogy are discussed in the introductory material. Electronic resources for conducting research on analogy are listed as well.

This interpretation essay intends to investigate the nature of the Egyptian cosmotheology that underlies the theological discourse of the priestly texts of all ages. We turn to the notion of the Egyptian demiurge as: “The one in the multiple”, that we consider to be proper to the Egyptian monism of all its historical eras, which contrasts with the cosmovision of the dualistic classical philosophy which poses a different vision of the universe than the classical one that can be summed up in the phrase: “The one and the multiple”; summary of an entire equivocal position with regard to the Egyptian cosmovision, based on assigning an implicit platonic dualist worldview. This situation is exacerbated by a radical difference, not always assumed, founded in the contrast between the Egyptian inclusive multipurpose logic and the western a disjunctive causal logic that flies over the interpretations of Egyptian religion. What is striking in this cosmovision is that it presents a radicalized immanentist ontology and transnatural significance of the demiurge, synthesizable as a single substance; a single attribute of an eternal living one divided as their ways and forms in the cosmos; a single ontology. One of their core foundations is the concept of transformation–emanation as an expression of the demiurge and its creation that poses an ontological continuum without rupture characteristic of this cosmotheology and their religiosity. This essay is the attempt to revalue a paradigm of interpretation of the ancient Egyptian religious cosmovision, the monistic or unitarian cosmovision and its derivations, drafted in the 1980s by Nordic Egyptologists -Symposia of Uppsala (1987) and Bergen (1988)- and that projects the scholar to a divergent perception of the Egyptian experience of the sacred in respect of the interpretations currently in vogue.
ADENDA
-DETAILED CONTENTS-

SECOND PART. The homology and complementarity: nature and attribute of the divine in the monistic cosmovision of Ancient Egypt.

+Section 1: Nature of the One as First-Existent    p.  24:                                                           
+Section 2 : Cosmic and transnatural bionatural homology                                            p.  35;
+Section 3 : Ontological monism and homological reductionism                                          46;
+Section 4: Divine androgyny and coincidentia-oppositorum                                              59;
+Section 5: Integrative demiurge: cosmic transformation and circulation                            63;
+Section 6: First Existing:  Totalizing - ambiguous - creator                                    p.      89;
+Section 7: Maat cosmic and transnatural order                                                  p.        102;
+Section 8: Divinity and Power: spatiality - temporality – totality            p.            109;
+Section 9: Some reflections by way of synthesis                                      p.                  127;

PART THREE. Epilogue.
+The summoteism - One in All - All in One                                                          p. 137;                     

+Colophon                                                                                                       p.        145;

+Index of illustrations p.       146;
+Bibliography p.       147;
+The author p.       159.

The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin's theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for  years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from fourlegged terrestrial ancestors.

The emergence of dramatic morphological differences (disparity) and the ensuing bewildering increase in the number of species (diversity) documented in the fossil record at key stages of animal and plant evolution have defied, and still defy, the explanatory powers of Darwin's theory of evolution by natural selection. Among the best examples that have captured the imagination of the layman and the interest of scores of scientists for  years are the origins of land plants from aquatic green plants, of flowering plants from seed plants, of chordates from non-chordates and of tetrapod vertebrates from non-tetrapods; and the conquest of the land by amphibians; the emergence of endotherms from ectotherm animals; the recurrent invention of flight (e.g. in arthropods, birds and mammals) from non-flying ancestors; and the origin of aquatic mammals from fourlegged terrestrial ancestors.

Most geophilomorph centipedes have segmental clusters of exocrine glands whose opening pores are arranged in more or less well-defined sternal pore areas. We describe here the cuticular structures forming and:or accompanying the gland openings on the sternites and the shape of the pore areas along the body axis in representatives of most geophilomorph families. The cuticular ring around the pore may exhibit either of two forms. In Himantariidae (Himantarium) and in Dignathodontidae (Henia) the ring looks like a continuous ribbon with a visible suture, whereas in the representatives of the remaining families no suture is seen. As to the distribution of the pores on ventral surface of the body, we record the presence of pores on the last leg-bearing segment of Clinopodes flavidus, whereas that segment was described as poreless in all geophilomorphs. We also provide a taxonomic survey of shape and distribution of pore areas in the individual families, where the pore areas may take very different shapes that we regard as transformational homologues. As for the segmental distribution of sternal pore areas, there is a considerable amount of complexity along the trunk of geophilomorph centipedes, in contrast to the apparently uniform trunk structure.

The monophyly of the class Xiphosura is critically re-examined. For the first time a phylogenetic analysis of a number of synziphosurine and xiphosurid taxa is performed together with representatives of the other chelicerate orders also included as ingroup taxa. Xiphosura as currently defined is shown to be paraphyletic, and a revised classification is presented. Previous characteristics used to unite the xiphosurids (possessing a fused thoracetron) and a paraphyletic grade of synziphosurines (retaining freely articulating opisthosomal tergites) include the presence of a cardiac lobe, ophthalmic ridges, an axial region of the opisthosoma, and a reduced first opisthosomal segment. All of these characteristics are, however, here shown to be present in other chelicerate groups, leaving Xiphosura without any defining synapomorphies. A number of other characters, including the form of the chelicerae and appendage VII, indicate that xiphosurans may be paraphyletic with respect to a clade consisting of chasmataspidids, eurypterids, and arachnids. What ramifications this has for the evolution of basal chelicerates is briefly discussed, and it is recognized that most of the currently known ‘synziphosurine’ taxa represent offshoots from the main chelicerate lineage with ghost ranges extending into at least the Middle Ordovician.

Advances in developmental genetics and evo-devo in the last several decades have enabled the growth of novel developmental approaches to the classic theme of homology. These approaches depart from the more standard phylogenetic view by contending that homology between morphological characters depends on developmental-genetic individuation and explanation. This paper provides a systematic re-examination of the relationship between developmental and phylogenetic homology in light of current evidence from developmental and evolutionary genetics and genomics. I present a qualitative model of the processes that cause de-coupling of morphological and molecular evolution by developmental system drift (DSD), and hypothesize that DSD is a widespread and regular stochastic process that is predictable from parameters such as population size, pleiotropy, and regulatory redundancy. These theoretical findings support an integrative approach in which models of DSD aid in determining when developmental-genetic explanations of homology apply and when other explanations such as stabilizing selection are needed. I argue that a phylogenetic monism about the definition and criteria of homology supports the integration of different explanations into a theory of homology better than pluralism does.

Increasing fossil evidence surrounding the evolutionary origin of vertebrate limbs can be used to reconstruct the assembly of a limb ground-plan common to all tetrapods. The sequence of changes at the fin-to-limb transition can be compared to patterns of fin and limb ontogeny, and further comparisons can be made between phylogenetic changes at pectoral and pelvic levels. Such comparisons inform questions about the evolution of developmental autonomy (modularity). Limb evolution mostly concerns terminal additions and losses; from a developmental standpoint, these probably result either from minor adjustments to limb bud proportions or from the relative timing of gene expression or tissue growth. Evolutionary radiations of large clades are widely assumed to be marked by periods of rapid morphological diversification, raising further questions about the impact of restrictions imposed not only by ecology, but also by development and genetics. The early tetrapod data set is now large eno...

The concept of homology continues to attract more and more commentary. In systematic and evolutionary biology the meaning of homology as synapomorphic similarity inherited from a common ancestor has gained wide acceptance over the last three or four decades. In recent years, however, developmental biologists, in particular, have argued for a new approach to, and new definition for, homology that revolves around the desire to make it more process-oriented and more mechanistic. These efforts raise questions about the relationship between developmental and evolutionary biology as well as how the evolution of development is to be studied. It is argued in this paper that this new approach to homology seemingly decouples developmental biology from the study of the evolution of development rather than to facilitate that study. In contrast, applying the notion of historical, phylogenetic homology to developmental data is inherently comparative and therefore evolutionary.

Une présentation des plus complètes de la réflexion sémiotique de Ferruccio Rossi-Landi sur l'homologie de la reproduction sociale et l'idéologie comme pratique sociale, sans oublier ses enjeux actuels. Cette contribution a été lue et publiée dans le cadre du séminaire « Matérialité et écriture » organisé de 2014 à 2016 au sein du laboratoire Héritages et Constructions dans le Texte & l’Image de l'Université de Bretagne Occidentale .

A concept map for taking biodiversity to school is proposed here using a novel approach that combines systematics, evolutionary biology, and the nature of science. The concept map is tied to the recently published next generation science standards (NGSS). The problem of biodiversity is presented as a way to justify the need to take it to school. Biological classification is presented as a hypothesis about order in nature that is based on the evolutionary history of the organisms. Classification is the reference system of the entirety of biology with predictive and explanatory power. Homology is the concept that connects systematics to evolutionary biology. Evolutionary biology explains and systematics reflects the unity and diversity of life.

In 1991 de Pinna (Cladistics 7: 367–394) coined the term primary homology as the putative homology statements prior to tree reconstruction. However, some confusion still exists regarding the conjectural nature of homology and to the analysis of DNA sequences. By dividing de Pinna’s term primary homology into topographical identity and character state identity, we emphasize the sequential refinement of putative homology statements. We discuss the problem of transformational versus taxic homology and explain the application of our terms to DNA sequence data.

Due to their informative role in biological systems, the potential development of oligosaccharide utilization is very important. Today, their industrial application is increasing rapidly especially for their capability of specific stimulation of beneficial bacteria. Future development will require the access to specific oligosaccharides synthesized via processes compatible with technical and economical industrial constraints. In this context, glucansucrases are attractive tools allowing Ž . the production of different glucooligosaccharides GOS from simple substrates such as sucrose and maltose. These bacterial enzymes are responsible for the synthesis of glucan polymers. They can also synthesize oligomers when an acceptor molecule is introduced into the medium. A large variety of glucosidic bonds are formed corresponding to variable regiospecificities dependent on the enzyme origin. More than 30 glucansucrase-encoding genes have been cloned and sequenced. Many data were provided from studies on the structurerfunction relationship on these sucrose-converting Ž . glucosyltransferases GTF . Sequence alignment analysis allowed identification of essential amino acids and clearly showed analogies with enzymes from the large a-amylase family. It is now possible to list some determinants possibly involved in the glucansucrase specificity, but many additional investigations and data, especially about the three-dimensional structure, will be necessary for the rational design of specific enzymatic tools for GOS synthesis. q

The external morphology of a bilateral gynandromorphic tineid moth, Harmaclona tephrantha (Meyrick), is discussed. Both male and female sexual characters are approximately evenly divided between the left (female) and right (male) halves of the body, as shown by wing, abdominal, and genital structures. A brief review of the causes of gynandromorphism is provided, along with references to previous publications which discussed the genital morphology of gynandromorphic Lepidoptera.

Homology is the fundamental determinant of the sameness of biological characters or traits. When two characters stand in a relation of homology, they belong to the same character kind. For example, the eyes of humans and birds are homologous as vertebrate eyes – that is, they are the same kind of character: vertebrate eyes. Although the concept of homology originated in pre-Darwinian comparative anatomy, it was subsequently revealed to be an evolutionary phenomenon caused by common descent. Contemporary investigators work roughly within the following generic evolutionary conception of homology:

Homology: Two characters in distinct organisms or taxa are homologous if they are genealogically connected by continuous descent from a common ancestor that had the same character.

Molecular phylogenetic studies of Garcinia have identified a large clade whose component species can be identified by flowers that have nectariferous antesepalous appendages or intrastaminal rings and disks. One current hypothesis is that within Clusiaceae these structures represent an outer whorl of stamens, but the position of these structures in some mature flowers of Garcinia does not support this. To better understand the nature of these structures in Garcinia, the floral anatomy of mature staminate and pistillate flowers was studied in G. nervosa and G. xanthochymus. These detailed anatomical studies do not support the hypothesis that the nectariferous appendages or the rings and disks are of staminal origin, because they do not share any unique features with the stamens of staminate flowers or the staminodes of pistillate flowers. Disks in staminate flowers are supplied by several traces that arise directly from the floral stele, while the stamen bundles are supplied by a single trace arising from a petal-stamen bundle. The antesepalous appendages in pistillate flowers receive traces from the floral stele and from the antepetalous staminodes, while the antepetalous staminodes receive their vascularization directly from the stele.

Bu çalışma, Türk sinemasının son döneminde komedi türünde öne çıkan Cem Yılmaz’ın canlandırdığı ‘Arif’ karakteri ile Şahan Gökbakar’ın canlandırdığı ‘Recep İvedik’ karakterlilerinin toplumsal temsil ve alımlanma biçimi açısından karşılaştırmalı analizine dayanmaktadır. Analiz üç boyuttan oluşmaktadır. 1. Göstergebilimsel açıdan bu iki karakterin temsil niteliklerinin çözümlenişi; 2. Bu iki karakter ve isme dair yapılan nitel araştırmadan hareketle izleyicilerdeki alımlanma biçimlerinin yorumlanışı; 3. Bu iki ismin filmleri hakkında sosyal medyada yapılan yorumların değerlendirilişi. Çok keskin bir karşıtlık içermemekle birlikte filmlerdeki iki karakterin toplumda iki farklı sosyo-kültürel kategoriye karşılık geldiği gözlemlenmiştir. İçinde geçişkenlikler barındırsa da, bu karakterlerde iki farklı sosyal gruba karşılık gelen iki kültürel anlamlar dünyası keşfedilmiştir. Sosyal sınıfların kültürel yapısı ile filmlerdeki kurgu ve kahramanlık mitleri arasında homoloji olduğu görülmüştür. Söz konusu iki kültürel tabadaki zihinsel temsillerin analizi Kültürel Çalışmalar Okulu’nun yöntem repertuarından hareketle gerçekleştirilmiştir. İkisi arasındaki farklılaşma kültür-uygarlık ikiliği tartışması üzerinden yorumlanmıştır.
Anahtar kelimeler: Temsil, Güldürü, Homoloji, Kültür-Uygarlık İkiliği, Türk Sineması, Cem Yılmaz, Şahan Gökbakar.
Abstract:
This study is based on the comparative analysis of the recently prominent comedy-type characters of Turkish cinema
called as ‘Arif ’ performed by Cem Yılmaz and ‘Recep İvedik’ performed by Şahan Gökbakar with regard to social
representation and reception. The analysis has three dimensions: 1 Semiotic analysis of representation characteristics of
these two characters. 2. Interpretation of the audiences’ reception of these two characters from the point of the qualitative
research on these two characters and performers. 3. Evaluating the social media comments on the films of these
two performers. Although there is no strict contradiction, these two characters are observed as corresponding to two
different socio-cultural categories of society. Even if having transitivity, two culturally semantic worlds corresponding
to two different social groups have been found in these characters. There is a homology between the cultural structure of
social classes and the editing and heroic myths of the films. The analysis of mental representation of the mentioned two
cultural spheres was made from the point of the repertoire method of Cultural Studies. And the differentiation between
the two was explicated in terms of the discussion on culture-civilization duality.
Key Words: Representation, Comedy, Homology, Culture-Civilization Duality, Turkish Cinema, Cem Yılmaz, Şahan
Gökbakar.

Überraschend schnell hat unsere evolutionäre Erkenntnistheorie Anklang gefunden. Ihr Kernstück ist es, die Ordnungsmuster unseres Denkens als ein Selektionsprodukt an den Ordnungsmustern der Natur zu betrachten.

Und daß es nicht mein Selbstwertgefühl sein kann, das mich veranlaßt, hier von meiner persönlichen Denkwelt zu reden, wird man daran erkennen, daß die Schilderung meiner Unkenntnisse und Irrungen mehr Erklärungswert wird bieten können als die geglätteten und von Widersprüchen schon gesäuberten Ergebnisse, wie sie ja als Publikationen allen zur Verfügung stehen.

The first molecular phylogenetic analysis of Asaccus reveals high sequence divergence among the sampled species. Asaccus montanus is recovered as the sister to all other species. Two Arabian species (A. gallagheri, A. platyrhynchus) form a monophyletic group as suggested earlier by morphological analyses. Our data show that A. gallagheri from Nizwa, Oman likely represents a new species. Samples of two species (A. elisae, A. griseonotus) from north of the Persian Gulf form a well-supported clade. The traditional concept of A. elisae likely represents more than one species, as the samples included here are paraphyletic with respect to A. griseonotus. The taxonomy of A. elisae awaits comparison with samples from the type locality in Iraq. Our inability to resolve the phylogenetic position of two species (A. caudivolvulus and A. nasrullahi) prevents testing biogeographic hypotheses involving the occurrence of Asaccus on either side of the Persian Gulf.

The detailed external morphology and general anatomy of the majority of families and subfamilies of Poduromorpha were investigated and compared. This examination was done in relation to the three remaining orders of Collembola: Entomobryomorpha, Symphypleona and Neelipleona. Within Poduromorpha, homologies among the different families and subfamilies are established for general chaetotaxy, and chaeotaxy of head, buccal cone, sensilla of fourth antennal segment, anal valves and tibiotarsus. A consistent and comprehensive nomenclature is proposed for these morphological features unifying those applied in scattered existing studies. Observations on first instars are reported. Comparison of first instars and adult chaetotaxy suggests a possible paedomorphic trend in the evolution of Poduromorpha.

A novel red pigment, 2,2V -[3-methoxy-1Vamyl-5V -methyl-4-(1U-pyrryl)] dipyrryl-methene (MAMPDM), which has properties similar to those of prodigiosins, has been isolated for the first time from a bacterium putatively identified as Micrococcus sp. Our studies showed that MAMPDM inhibited proliferation of both human T as well as B cells and murine T cells, in response to polyclonal mitogens, in a concentration-dependent manner while murine B cell proliferation induced by lipopolysaccharide was inhibited only at high concentration. The effect of MAMPDM on constitutive cell cycling was ascertained using four mouse and human tumour cell lines. At 100 nM, the concentration that inhibited con A induced proliferation of mouse spleen cells, the viability of these cell lines was not affected. At 10 -100-fold higher concentration of MAMPDM, however, there was a decrease in cell viability with T cell-derived cell lines being more sensitive. MAMPDM did not block the secretion of IL-2 or expression of CD25 though it inhibited the proliferation of con A stimulated T cells. The higher amount of IL-2 in the supernatant of the con A stimulated T cells, cultured in the presence of the immunomodulator, indicated accumulation of IL-2 due to its reduced utilisation. At inhibitory concentration, MAMPDM induced apoptosis in con A stimulated cells. Thus, MAMPDM may have considerable and selective T cell immunosuppressive potential and appears to act by a mechanism distinct from that of other known immunosuppressors. D

The coloured patterns of the muricids may be divided in three main groups: (1) clear to dark uniform colour, (2) dark bands covering several spiral cords, (3) clear to dark cords contrasting with the main colour. The two last patterns, observed in Neogene muricids from the Western Atlantic region (USA), were unknown in Palaeogene species. In order to detect them in Palaeogene muricids, 35 species from 23 fossiliferous localities (Paris, Aquitaine and Loire-Atlantique basins) have been examined under Ultra-Violet light. On 1200 specimens, positive results have been obtained in two species (?Trophonopsis peregra (Beyrich, 1854), Rupelian and ?Paziella plini (de Raincourt, 1874), Middle Eocene). Both species bear the second type of pattern. In ?T. peregra (Auvers-St-Georges, Paris Basin), its occurrence is occasional. Conversely, in ?P. plini it is preserved from the Lutetian (Villiers-St-Frédéric, Paris basin) to the Bartonian (Bois-Gouët, Loire-Atlantique). The coloured bands seem similar in both species, but are probably not homologous. Effectively, the close analysis of the spiral sculpture shows that they differ by their place on the cords and even allows to reveal an intraspecific variation between the populations of ?P. plini.

TrruLB()Ri.r, R. A. (2006): Theropod dinosaurs, progenesis and birds: homology of digits in the manus. N. Jb. Geol. Paleont. Abh., Stuttgart. Abstract: Thc proposition that birds arose from theropod dinosaurs by the evolutionary meclranism of progencsis (accelerated development to sexual maturity) has important consequences for understanding of avian anatomy. One predictable consequence is an avian hand comprising digits 2-3-4 of thc pentadactyl format.

Table of Contents Acknowledgments p. iii Murphy and Tom Wysocki on chapters 1, 2, 3 and 4 respectively, and all provided helpful feedback on the respective chapters. Fifth, thanks to the Philosophy-Neuroscience-Psychology Dissertation Preparation Seminar, the members of which provided feedback on several different chapters at different stages of disorder, thanks especially to Mike Dacey, Nazim Keven, and Lauren Olin. Last but not least, thanks to Nate Adams, without whom I quite literally would not have made it through graduate school. He has been a constant source of clarity, on matters both philosophical and personal. Together, we shared meals, struggles, doubts, joys, ideas, and sci-fi readings. I wouldn't mind a zombie apocalypse so long as he was part of my tribe. v -To Juli, Sofia and Anabel I believe very strongly…that no one could ever deserve to suffer. Of the people in whose moral judgment I have the most confidence, some disagree. When some wrong-doers suffer, these people believe, this suffering is in itself good, or at least not in itself bad. Though this belief seems to me mistaken, I would be greatly relieved if I could explain why these people are making this mistake. This may be one of the cases in which an evolutionary explanation helps to undermine what it explains. This retributive belief may seem to justify certain natural reactive attitudes, such as an angry desire to hurt or the withdrawal of good will. These attitudes are like some simpler emotions that are had by the animals that are most like us. If evolution can explain why many people have these reactive attitudes, that might give some support to the view that these attitudes, and the widely held belief that such attitudes are justified, are not responses to reasons.