Gondolelloid multielement conodont apparatus (Scythogondolella) from the Lower Triassic of Jiangsu,East China,revealed by high-resolution X-ray microtomography

The application of high-resolution X-ray microtomography on conodont natural assemblages has provided new information on the structure of the elements and enabled the three-dimensional reconstruction of apparatuses. We herein report four conodont natural assemblages from uppermost Lower Qinglong Formation, Longtan, Nanjing, East China. Using X-ray microtomography, we reconstructed the apparatus of the end-Smithian (Olenekian, Early Trassic) Scythogondolella milleri. Our result confirms that Scythogondolella has an octomembrate apparatus composed of 15 elements (a single S₀ element, two pairs of S_1–4, M and P_1–2 elements) like other gondolelloid apparatuses that have been tested by their corresponding natural assemblages, including Neogondolella, Novispathodus and Nicoraella. Element morphology of Scythogondolella closely resembles that of Neogondolella apparatus from the Illyrian (Anisian, Middle Triassic) of Monte San Giorgio: an alate (hibbardellan) S₀ element with two long lateral processes that meet at a denticle anterior of the cusp, a bipennate (hindeodellan) S₃ element with a bifurcated anterior process branching from the third denticle anterior of the cusp and an enantiognathiform S₂ element with two dissimilar processes of nearly equal in length. It differs from the latter in the length of the inner-lateral process of M element and the posterior process of S₀ and S_3–4 elements without considering the obvious morphological differences in P elements between them. The element positional homologues of Scythogondolella conforms to those of the standard 15-element plan shared primitively among ozarkodinin, prioniodinin and prioniodontid conodonts, and again confirms that the breviform digyrate elements of cypridodellan and enantiognathiform morphotypes occupy the S₁ and S₂ positions, respectively, within the superfamily Gondolelloidea.     

There is no general model for occlusal kinematics in conodonts

Knowledge of conodont element function is based largely on analysis of morphologically similar P₁ elements of few comparatively closely related species known from abundant articulated remains. From these, a stereotypical pattern of rotational occlusion has been inferred, leading to the suggestion that this may represent a general model for ozarkodinin P₁ elements at the very least. We test the generality of this occlusal model through functional analysis of Pseudofurnishius murcianus P₁ elements which, though superficially similar to homologous elements in gnathodids, evolved their platform morphology independently, through a different mode of morphogenesis, and in a different topological position within the element. Our integrated functional analysis of several articulated clusters of P₁ elements encompassed physical and virtual occlusal analyses, constrained by microwear and sharpness analyses. All of the evidence supports an occlusal model in which the Pseudofurnishius P₁ elements occluded with the dextral blade located between the rostral face of the sinistral blade and the first cusp of the rostral primary process. In achieving this, the dorsal and ventral blades guided the opposing elements, and the rostral processes of both elements guided the final stages of precise occlusion. Spalling and microwear on the non‐occlusal side of the element evidence malocclusion, requiring the complete separation of elements within the occlusal cycle. This occlusal cycle is entirely linear, orthogonal to the plane of attachment of the elements. Evidently, the rotational occlusal model is not general for P₁ elements, even for ozarkodinins, and it is likely that among conodonts occlusal kinematics are as disparate as element morphologies. Attempts to elucidate the diversity of occlusal kinematics and, therefore, feeding ecologies of conodonts will be repaid by an understanding of the role of this important abundant and diverse clade in Palaeozoic and Mesozoic marine ecosystems.     

On the ontogeny and orientation of the Triassic Conodont P1-element in Pseudofurnishius murcianus Van den Boogaard, 1966

Successive growth stages of P1-elements in the Middle to early Late Triassic species Pseudofurnishius murcianus allows the observation of a detailed ontogeny. Besides the gradual enlargement of its curved blade and the growing number of its denticles, a small internal platform develops, eventually followed by an external one, both bearing denticles. The number of denticles on the blade and internal platform increases from five and one in the smallest specimens, respectively, to 14 and 9 in fully developed ones, whereby the distribution pattern of platform-denticles, on the inner one in particular, is of great morphological variety. For the orientation of the P1-element of P. murcianus, the comparison of the early development stages of Pseudofurnishius and Sephardiella, that share a common ancestry, permits to adhere to the orientation used by Diebel rather than to the one proposed by Van den Boogaard.     

Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography

The composition of conodont apparatuses is crucial for understanding the feeding mechanisms of these early vertebrates. However, the multielement apparatus reconstructions of most species remain equivocal because they have been inferred from loose element collections, guided by knowledge from rare articulated ‘bedding plane assemblages’ and fused clusters, often from distantly related taxa. Even these natural assemblages can be difficult to interpret because the component elements can be closely juxtaposed or embedded in matrix, making it hard to discern the morphology of each element and their relative positions within the architecture of the feeding apparatus. Here we report five exceptionally preserved conodont clusters from the Middle Triassic Luoping Biota, Yunnan Province, Southwest China. These materials were scanned using synchrotron radiation X-ray tomographic microscopy (SRXTM), revealing the morphology and positional homology of the component elements in the fused clusters. We confirm that the apparatus of Nicoraella was composed of eight types of elements, comprising a total of 15 elements. SRXTM reveals the positional homologies of the component elements, viz. a single alate element is located in the S₀ position, flanked successively abaxially by pairs of breviform digyrate S₁ and S₂ elements, bipennate S₃ and S₄ elements, and a pair of inwardly curved breviform digyrate M elements. Carminate elements occupy the P₁ and P₂ positions. The apparatus of Nicoraella is among the most completely characterised of all conodonts and serves as a template for the reconstruction of gondollellids.     

Transposon-like properties of the major, long repetitive sequence family in the genome of Physarum polycephalum

A family of long, highly-repetitive sequences, referred to previously as `HpaII-repeats', dominates the genome of the eukaryotic slime mould Physarum polycephalum. These sequences are found exclusively in scrambled clusters. They account for about one-half of the total complement of repetitive DNA in Physarum, and represent the major sequence component found in hypermethylated, 20-50 kb segments of Physarum genomic DNA that fail to be cleaved using the restriction endonuclease HpaII. The structure of this abundant repetitive element was investigated by analysing cloned segments derived from the hypermethylated genomic DNA compartment. We show that the `HpaII-repeat' forms part of a larger repetitive DNA structure, ~8.6 kb in length, with several structural features in common with recognised eukaryotic transposable genetic elements. Scrambled clusters of the sequence probably arise as a result of transposition-like events, during which the element preferentially recombines in either orientation with target sites located in other copies of the same repeated sequence. The target sites for transposition/recombination are not related in sequence but in all cases studied they are potentially capable of promoting the formation of small `cruciforms' or `Z-DNA' structures which might be recognised during the recombination process.     

Synthesis of sialyllactosamine clusters using carbosilane as core scaffolds by means of chemical and enzymatic approaches

An efficient synthesis of sialyllactosamine (SiaLacNAc) clusters using carbosilanes as core scaffolds has been accomplished by means of chemical and enzymatic approaches. N-Acetyl-d-glucosamine (GlcNAc) clusters having O-glycosidic linkage or S-glycosidic linkage were chemically synthesized from known intermediates in high yields. The GlcNAc clusters were first used as substrates for β1,4 galactosyl transferase using UDP-galactose (UDP-Gal) as a sugar source to provide corresponding N-acetyllactosamine clusters. Further sugar elongation of the LacNAc clusters was demonstrated using α2,3 sialyl transferase and CMP-neuraminic acid (CMP-NANA) to yield the corresponding SiaLacNAc clusters.     

Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida

Pseudomonas putida KT2440 is a soil bacterium that effectively colonises the roots of many plants and degrades a variety of toxic aromatic compounds. Its genome has recently been sequenced. We describe that a 35 bp sequence with the structure of an imperfect palindrome, originally found repeated three times downstream of the rpoH gene terminator, is detected more than 800 times in the chromosome of this strain. The structure of this DNA segment is analogous to that of the so-called enterobacteriaceae repetitive extragenic palindromic (REP) sequences, although its sequence is different. Computer-assisted analysis of the presence and distribution of this repeated sequence in the P.putida chromosome revealed that in at least 80% of the cases the sequence is extragenic, and in 82% of the cases the distance of this extragenic element to the end of one of the neighbouring genes was <100 bp. This 35 bp element can be found either as a single element, as pairs of elements, or sometimes forming clusters of up to five elements in which they alternate orientation. PCR scanning of chromosomes from different isolates of Pseudomonas sp. strains using oligonucleotides complementary to the most conserved region of this sequence shows that it is only present in isolates of the species P.putida. For this reason we suggest that the P.putida 35 bp element is a distinctive REP sequence in P.putida. This is the first time that REP sequences have been described and characterised in a group of non-enterobacteriaceae.     

Acquisition and Evolution of Plant Pathogenesis–Associated Gene Clusters and Candidate Determinants of Tissue-Specificity in Xanthomonas

Background

Xanthomonas is a large genus of plant-associated and plant-pathogenic bacteria. Collectively, members cause diseases on over 392 plant species. Individually, they exhibit marked host- and tissue-specificity. The determinants of this specificity are unknown.

Methodology/Principal Findings

To assess potential contributions to host- and tissue-specificity, pathogenesis-associated gene clusters were compared across genomes of eight Xanthomonas strains representing vascular or non-vascular pathogens of rice, brassicas, pepper and tomato, and citrus. The gum cluster for extracellular polysaccharide is conserved except for gumN and sequences downstream. The xcs and xps clusters for type II secretion are conserved, except in the rice pathogens, in which xcs is missing. In the otherwise conserved hrp cluster, sequences flanking the core genes for type III secretion vary with respect to insertion sequence element and putative effector gene content. Variation at the rpf (regulation of pathogenicity factors) cluster is more pronounced, though genes with established functional relevance are conserved. A cluster for synthesis of lipopolysaccharide varies highly, suggesting multiple horizontal gene transfers and reassortments, but this variation does not correlate with host- or tissue-specificity. Phylogenetic trees based on amino acid alignments of gum, xps, xcs, hrp, and rpf cluster products generally reflect strain phylogeny. However, amino acid residues at four positions correlate with tissue specificity, revealing hpaA and xpsD as candidate determinants. Examination of genome sequences of xanthomonads Xylella fastidiosa and Stenotrophomonas maltophilia revealed that the hrp, gum, and xcs clusters are recent acquisitions in the Xanthomonas lineage.

Conclusions/Significance

Our results provide insight into the ancestral Xanthomonas genome and indicate that differentiation with respect to host- and tissue-specificity involved not major modifications or wholesale exchange of clusters, but subtle changes in a small number of genes or in non-coding sequences, and/or differences outside the clusters, potentially among regulatory targets or secretory substrates.     

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium

Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.     

The structure of rooster-comb dermatan sulfate. Fragmentation of the polysaccharide chains by chondroitinase AC-II digestion,and by periodate oxidation,followed by alkali cleavage

The polysaccharide-chain fragments of rooster-comb dermatan sulfates (RC-20 and RC-30) were obtained by chondroitinase AC-II digestion and by periodate oxidation, followed by alkaline cleavage, and their structures analyzed both quantitatively and qualitatively. RC-20 having a lower d-glucuronic acid content (22.6%) is composed preponderantly of large clusters of N-acetyldermosine sulfate (M_r～17 600–41 000) at the nonreducing terminal, whereas RC-30, having a higher d-glucuronic acid content, (41.4%) is poor in this cluster. Both RC-20 and RC-30 have an N-acetyldermosine sulfate cluster (M_r 6500–7300) within the polysaccharide chains. Most N-acetylchondrosine sulfate units of RC-20 and RC-30 exist as clusters, the large clusters (M_r～17 600) being preponderant in RC-30; both RC-20 and RC-30 contain a large proportion of N-acetylchondrosine sulfate clusters (M_r 3500 and 9000) that corresponds to the uronic acid content. In RC-30, most N-acetyldermosine disulfate units (13.4%) are linked to N-acetylchondrosine sulfate units or clusters.     

CHERUB: power consumption aware cluster resource management

This paper presents an evaluation of ACPI energy saving modes, and deduces the design and implementation of an energy saving daemon for clusters called cherub. The design of the cherub daemon is modular and extensible. Since the only requirement is a central approach for resource management, cherub is suited for Server Load Balancing (SLB) clusters managed by dispatchers like Linux Virtual Server (LVS), as well as for High Performance Computing (HPC) clusters. Our experimental results show that cherub’s scheduling algorithm works well, i.e. it will save energy, if possible, and avoids state-flapping.     

Genetics and Evolution of the Salmonella Galactose-Initiated Set of O Antigens

This paper covers eight Salmonella serogroups, that are defined by O antigens with related structures and gene clusters. They include the serovars that are now most frequently isolated. Serogroups A, B1, B2, C2-C3, D1, D2, D3 and E have O antigens that are distinguished by having galactose as first sugar, and not N-acetyl glucosamine or N-acetyl galactosamine as in the other 38 serogroups, and indeed in most Enterobacteriaceae. The gene clusters for these galactose-initiated appear to have entered S. enterica since its divergence from E. coli, but sequence comparisons show that much of the diversification occurred long before this. We conclude that the gene clusters must have entered S. enterica in a series of parallel events. The individual gene clusters are discussed, followed by analysis of the divergence for those genes shared by two or more gene clusters, and a putative phylogenic tree for the gene clusters is presented. This set of O antigens provides a rare case where it is possible to examine in detail the relationships of a significant number of O antigens. In contrast the more common pattern of O-antigen diversity within a species is for there to be only a few cases of strains having related gene clusters, suggesting that diversity arose through gain of individual O-antigen gene clusters by lateral gene transfer, and under these circumstances the evolution of the diversity is not accessible. This paper on the galactose-initiated set of gene clusters gives new insights into the origins of O-antigen diversity generally.     

Clostridium botulinum Strain Af84 Contains Three Neurotoxin Gene Clusters: Bont/A2, bont/F4 and bont/F5

Sanger and shotgun sequencing of Clostridium botulinum strain Af84 type Af and its botulinum neurotoxin gene (bont) clusters identified the presence of three bont gene clusters rather than the expected two. The three toxin gene clusters consisted of bont subtypes A2, F4 and F5. The bont/A2 and bont/F4 gene clusters were located within the chromosome (the latter in a novel location), while the bont/F5 toxin gene cluster was located within a large 246 kb plasmid. These findings are the first identification of a C. botulinum strain that contains three botulinum neurotoxin gene clusters.     

The building block structure of barley amylopectin

Amylopectin branchpoints are present in amorphous lamellae of starch granules and organised into densely branched areas, referred to as building blocks. One single amylopectin cluster contains several building blocks. This study investigated the building block structure of domains (groups of clusters) and clusters in four different barley genotypes. Two of the barleys possessed the amo1 mutation, Glacier Ac38 and the double recessive SW 49427 with both wax and amo1 mutations, and were compared with the two waxy type barleys Cinnamon and Cindy. A previous detailed study on these four barley genotypes showed that the amo1 mutation affected the internal structure of amylopectin as manifested in the composition of clusters. In this work the building blocks were isolated from domains and clusters by extensive treatment with liquefying α-amylase of Bacillus subtilis and structurally characterised with enzymatic and chromatographic techniques. The proportion of large building blocks with a high number of chains was increased in the amo1 barleys, and the chain length between the blocks was short, which explained the previous findings of large clusters with more dense structure in the amo1 amylopectins.     

Reactions of mass-selected Fen cluster ions (n=1-5) with dimethyl carbonate

The reactions of mass-selected iron clusters Fe_n ⁺ (n=1-5) with dimethyl carbonate, (CH₃O)₂CO, are examined by means of Fourier-transform ion-cyclotron-resonance mass spectrometry. For the bare metal cation Fe⁺, loss of a methyl radical prevails which leads to the iron carbonate species FeOC(O)OCH₃ ⁺. For the corresponding Fe_n ⁺ clusters, this type of reaction is not observed anymore. Instead, the clusters show a strong tendency for a formal O-atom abstraction leading to the formation of the corresponding monoxide clusters Fe_nO⁺ In addition, several bond activations of dimethyl carbonate are observed which markedly differ from the behavior of the mononuclear cation. Nevertheless, a mechanistic analysis implies that the initial steps are the same for bare Fe⁺ as well as small Fe_n ⁺ clusters.