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Ribosomal Genes (ribosomal + gene)
Selected AbstractsKleptoplasty in an Antarctic dinoflagellate: caught in evolutionary transition?ENVIRONMENTAL MICROBIOLOGY, Issue 1 2007Rebecca J. Gast Summary Photosynthetic dinoflagellates contain a diverse collection of plastid types, a situation believed to have arisen from multiple endosymbiotic events. In addition, a number of heterotrophic (phagotrophic) dinoflagellates possess the ability to acquire chloroplasts temporarily by engulfing algae and retaining their chloroplasts in a functional state. These latter relationships typically last from a few days to weeks, at which point the chloroplasts lose function, are digested and replaced with newly acquired plastids. A novel and abundant dinoflagellate related to the icthyotoxic genera Karenia and Karlodinium was recently discovered by us in the Ross Sea, Antarctica. Sequencing of its plastid small subunit ribosomal gene indicated that it did not share evolutionary history with the plastids of Karenia or Karlodinium, but was closely related to the free-living haptophyte Phaeocystis antarctica, a species that often dominates phytoplankton blooms in the Ross Sea. Chloroplast uptake was observed to occur rapidly (within 2 days), with retention in cultures being long-lived (several months) but not permanent. The dinoflagellate was also incapable of growing indefinitely in continuous darkness with algae as prey. Our findings may indicate an emerging endosymbiotic event yielding a dinoflagellate that is presently neither purely phototrophic nor purely heterotrophic, but occupies a niche juxtaposed between these contrasting nutritional modes. [source] Species in the genus Turritopsis (Cnidaria, Hydrozoa): a molecular evaluationJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2007M. P. Miglietta Abstract Mitochondrial ribosomal gene sequences were used to investigate the status of several populations of hydromedusae belonging to the genus Turritopsis (family Oceaniidae). Several nominal species have been described for this genus, but most of them had been synonymized and attributed to one cosmopolitan species, Turritopsis nutricula. A recent revision based on morphological and reproductive characters, however, has shown that many different populations can be distinguished and that several of the nominal Turritopsis species are likely valid biological species. Our investigation using molecular sequence data of 16S mitochondrial gene confirms these results. The Mediterranean Turritopsis must be attributed to Turritopsis dohrnii and the Turritopsis of New Zealand must be referred to Turritopsis rubra. The situation of the Japanese Turritopsis is more complex, though all sampled populations are clearly distinct from T. nutricula, a species likely confined to the Western Atlantic. The Japanese Turritopsis fall into three widely separated lineages. One of them, corresponding likely to Turritopsis pacifica, is closely related to T. rubra. A second clade, which potentially represents an as yet undescribed species, produces smaller medusae than T. pacifica and is morphologically distinguishable from it. Finally, a third group was distinguished by a single haplotype sequence that is identical with a Mediterranean sample of T. dohrnii. It is postulated that the last group of Japanese Turritopsis is likely a recent introduction, most probably by human activity. A survey of all known and potentially valid Turritopsis species is given in table format to facilitate identifications and future revisory work. Sommario Sequenze del gene mitocondriale 16S sono state utilizzate per studiare lo stato tassonomico di idroidi appartenenti al genere Turritopsis (Famiglia Oceaniidae). In letteratura, tra le numerose specie nominali di TurritoSPSis descritte, molte di queste sono state successivamente messe in sinonimia e attribuite ad un'unica specie cosmopolita, Turritopsis nutricula. Una recente revisione, basata su dati morfologici e caratteri riproduttivi, ha comunque mostrato che diverse popolazioni di Turritopsis possono essere distinte in numerose specie nominali e probabilmente rappresentano valide specie biologiche. Il presente studio conferma questa recente interpretazione, mediante lo studio di sequenze molecolari del gene 16S. La popolazione mediterranea di Turritopsisè ora attribuita a T. dohrnii, mentre la popolazione neozelandese va ascritta alla specie T. rubra. La situazione nei mari giapponesi si presenta piu' complessa, sebbene tutte le popolazioni ivi campionate siano chiaramente distinte da T. nutricula, la quale risulta confinata unicamente all'Atlantico Orientale. Le sequenze ottenute da esemplari di Turritopsis provenienti dal Giappone formano tre cladi ben distinti. Uno di essi corrisponde a Turritopsis pacifica. Un secondo clade è costituito da popolazioni che producono meduse piu' piccole rispetto a Turritopsis pacifica ed e' dunque anche morfologicamente separato. Un terzo gruppo e' rappresentato da un solo aplotipo identico alle popolazioni mediterranee di T. dohrnii. La presenza di quest'ultimo gruppo di Turritopsis in Giappone e' molto probabilmente il risultato di un'introduzione recente, in seguito ad attività umana. Per facilitare futuri lavori di revisione, è inoltre presentata tavola che riassume le caratteristiche di tutte le specie di Turritopsis conosciute e potenzialmente valide. La tavola cerca di integrare i dati morfologici e riproduttivi già noti e dei dati molecolari ottenuti con questo studio. [source] Ribosomal RNA transcriptional activation and processing in hamster rubrospinal motoneurons: Effects of axotomy and testosterone treatmentTHE JOURNAL OF COMPARATIVE NEUROLOGY, Issue 4 2003Paul D. Storer Abstract Rubrospinal motoneurons (RSMN) represent a population of androgen receptor-expressing central motoneurons with limited regenerative potential relative to their peripheral counterparts. A key determinant of regenerative capability lies in the nucleolar reaction of injured neurons. To date, characterization of the nucleolar reaction in injured central motoneurons has not been accomplished. Furthermore, it has been documented that testosterone propionate (TP) augments peripheral motoneuron regeneration through regulation of the nucleolar reaction to injury. In this study, the effects of injury alone, or in conjunction with TP, on the nucleolar response of injured RSMN were examined using in situ hybridization (ISH) techniques. Castrated adult male hamsters were subjected to right spinal cord hemisection at the C7/T1 vertebral level. Half the animals were subcutaneously implanted with one Silastic TP capsule, with the other half sham implanted. ISH for precursor 45S and mature 28S rRNA was accomplished with a 3H-labeled ribosomal DNA probe specific to the external transcribed spacer region or to the 28S region of the ribosomal gene, respectively. Postoperative times of 2, 6, and 24 hours were selected for examination of precursor 45S rRNA (i.e., rRNA transcriptional activation) levels and 0.25, 2, 4, and 14 days for examination of mature rRNA (i.e., ribosome) levels. Transcriptional activation of the rRNA gene was rapidly and transiently increased in injured RSMN, analogously to previously documented effects of injury on rRNA transcription in peripheral motoneurons, but, in contrast, this did not translate into an increase in mature ribosomes. TP administration failed to affect positively the nucleolar response of injured RSMN at all. From this study, a key component underlying inherent differences in the regenerative capacity of peripheral vs. central motoneurons has been identified, which can be targeted in future experiments designed to enhance the regenerative potential of selective neuronal populations. J. Comp. Neurol. 458:326,333, 2003. © 2003 Wiley-Liss, Inc. [source] Rice root colonisation by mycorrhizal and endophytic fungi in aerobic soilANNALS OF APPLIED BIOLOGY, Issue 2 2009M. Vallino Abstract Arbuscular mycorrhizal (AM) fungi are ubiquitous root symbionts that form intimate associations with the majority of plants growing in aerobic soil; fungal endophytes live internally, either intercellularly or intracellularly, and asymptomatically within plant tissues. Their presence is correlated with an increased response to biotic and abiotic stress. The populations of AM and of endophytic fungi were studied in the roots of different rice varieties grown in aerobic condition, in experimental fields in Vercelli, North Italy. All the rice varieties resulted colonised by AM fungi with a percentage of arbuscularisation ranging between 4% and 28%. Preliminary molecular analyses on some rice varieties showed that the AM population was composed of fungi identified as Glomus intraradices, on the basis of 18S ribosomal gene. All the varieties analysed but one resulted in colonisation by endophytic fungi. About 300 fungal isolates were obtained, belonging mainly to the genera Neotyphodium, Stagonospora and Penicillium. [source] Morphological and Molecular Evidence of Arbuscular Mycorrhizal Fungal Associations in Costa Rican Epiphytic Bromeliads,BIOTROPICA, Issue 2 2005Annette R. Rowe ABSTRACT Arbuscular mycorrhizal fungi influence the growth, morphology, and fitness of a variety of plant species, but little is known of the arbuscular mycorrhizal (AM) fungal associations of plant species in forest canopies. Plant species' associations with AM fungi are most often elucidated by examining the roots for fungal structures; however, morphological data may provide a limited resolution on a plant's mycorrhizal status. We combined a traditional staining technique with a molecular marker (the 18S ribosomal gene) to determine whether or not a variety of epiphytic bromeliads form arbuscular mycorrhizal fungal associations. Using these methods we show that the epiphytic bromeliad Vriesea werkleana forms arbuscular mycorrhizal fungal associations with members of the genus Glomus. AM fungal sequences of this plant species formed three distinct clades nested within a larger Glomus clade; two of the clades did not group with any previously sequenced lineage of Glomus. Novel clades may represent novel species. Although Vriesea werkleana is associated with multiple AM fungal species, each individual plant is colonized by a single lineage. The combination of morphological and molecular methods provides a practical approach to the characterization of the mycorrhizal status of epiphytic bromeliads, and perhaps other tropical epiphytes. [source] Morphological and molecular characterization ofAquaticheirospora and phylogenetics of Massarinaceae (Pleosporales)BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007RAMPAI KODSUEB A morphologically interesting hyphomycete was collected from submerged wood in a stream in Doi Suthep-Pui National Park, Thailand. It is described as Aquaticheirospora lignicola gen. and sp. nov., and is characterized by euseptate conidia with divergent arms, which are vertically inserted in different planes to a basal cell. The genus differs from other chirosporous genera in having synnematous conidioma and conidia that are produced on conidiogenous cells borne at the apices of synnemata. The morphological characterization of this new fungus is reported and compared with similar chirosporous genera. To investigate the teleomorphic and phylogenetic relationships of this new taxon, three different regions of the ribosomal gene [18S rDNA, 28S rDNA, and internal transcribed spacer (ITS) including 5.8S] were sequenced and analysed. The results of phylogenetic analyses based on 18S, 28S, and partial ITS including 5.8S rDNA, employing different tree-making methods, indicate that Aquaticheirospora lignicola is closely related to the ascomycetes family Massarinaceae (Order: Pleosporales). The Massarinaceae as currently circumscribed is monophyletic. Massarina australiensis and M. bipolaris, however, appear to belong to the Lophiostomataceae. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 283,296. [source] A GyrB-GyrA fusion protein expressed in yeast cells is able to remove DNA supercoils but cannot substitute eukaryotic topoisomerase IIGENES TO CELLS, Issue 3 2002Sonia Trigueros Background: Type II topoisomerases are a highly conserved class of enzymes which transport one double-stranded DNA segment through a transient break in another. Whereas the eukaryotic enzymes are homodimers of a single polypeptide, their bacterial homologues are homodimers of two independently coded protein subunits. Unlike eukaryotic topoisomerase II and bacterial topoisomerase IV, DNA gyrase is a bacterial type II topoisomerase which specializes in intramolecular DNA transport. Results: We have fused the Escherichia coli coding sequences for the proteins GyrB and GyrA, which comprise DNA gyrase. This fusion was expressed in yeast cells and yielded the expected full-length protein product. When it was expressed in ,top1- top2-4 yeast cells, the fusion protein compensated their slow growth and reverted their elevated chromosomal excision of ribosomal genes. Furthermore, it removed DNA positive supercoils. The fusion protein, however, was unable to complement the temperature-dependent lethality of top2-4 cells. Conclusion: Fusion of the E. coli GyrB and GyrA proteins leads to a catalytically active topoisomerase which compensates several phenotypic traits attributed to unconstrained DNA supercoiling in topoisomerase-deficient cells. However, since the fusion protein cannot substitute for topoisomerase II, it may be efficient in intramolecular but not intermolecular DNA passage, resembling the catalytic properties of DNA gyrase. [source] Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes,HUMAN MUTATION, Issue 1 2009Anne Hartmann Abstract The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip® Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of ,99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of ,4,C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing. Hum Mutat 0,1,8, 2008. © 2008 Wiley-Liss, Inc. [source] On bivalve phylogeny: a high-level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence dataINVERTEBRATE BIOLOGY, Issue 4 2002Gonzalo Giribet Abstract. Bivalve classification has suffered in the past from the crossed-purpose discussions among paleontologists and neontologists, and many have based their proposals on single character systems. More recently, molecular biologists have investigated bivalve relationships by using only gene sequence data, ignoring paleontological and neontological data. In the present study we have compiled morphological and anatomical data with mostly new molecular evidence to provide a more stable and robust phylogenetic estimate for bivalve molluscs. The data here compiled consist of a morphological data set of 183 characters, and a molecular data set from 3 loci: 2 nuclear ribosomal genes (18S rRNA and 28S rRNA), and 1 mitochondrial coding gene (cytochrome c oxidase subunit I), totaling ,3 Kb of sequence data for 76 molluscs (62 bivalves and 14 outgroup taxa). The data have been analyzed separately and in combination by using the direct optimization method of Wheeler (1996), and they have been evaluated under 12 analytical schemes. The combined analysis supports the monophyly of bivalves, paraphyly of protobranchiate bivalves, and monophyly of Autolamellibranchiata, Pteriomorphia, Heteroconchia, Palaeoheterodonta, and Heterodonta s.l., which includes the monophyletic taxon Anomalodesmata. These analyses strongly support the conclusion that Anomalodesmata should not receive a class status, and that the heterodont orders Myoida and Veneroida are not monophyletic. Among the most stable results of the analysis are the monophyly of Palaeoheterodonta, grouping the extant trigoniids with the freshwater unionids, and the sister-group relationship of the heterodont families Astartidae and Carditidae, which together constitute the sister taxon to the remaining heterodont bivalves. Internal relationships of the main bivalve groups are discussed on the basis of node support and clade stability. [source] Phylogenetic signal and the utility of 12S and 16S mtDNA in frog phylogenyJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2004S. Hertwig Abstract Genes selected for a phylogenetic study need to contain conserved information that reflects the phylogenetic history at the specific taxonomic level of interest. Mitochondrial ribosomal genes have been used for a wide range of phylogenetic questions in general and in anuran systematics in particular. We checked the plausibility of phylogenetic reconstructions in anurans that were built from commonly used 12S and 16S rRNA gene sequences. For up to 27 species arranged in taxon sets of graded inclusiveness, we inferred phylogenetic hypotheses based on different a priori decisions, i.e. choice of alignment method and alignment parameters, including/excluding variable sites, choice of reconstruction algorithm and models of evolution. Alignment methods and parameters, as well as taxon sampling all had notable effects on the results leading to a large number of conflicting topologies. Very few nodes were supported in all of the analyses. Data sets in which fast evolving and ambiguously aligned sites had been excluded performed worse than the complete data sets. There was moderate support for the monophyly of the Discoglossidae, Pelobatoidea, Pelobatidae and Pipidae. The clade Neobatrachia was robustly supported and the intrageneric relationships within Bombina and Discoglossus were well resolved indicating the usefulness of the genes for relatively recent phylogenetic events. Although 12S and 16S rRNA genes seem to carry some phylogenetic signal of deep (Mesozoic) splitting events the signal was not strong enough to resolve consistently the inter-relationships of major clades within the Anura under varied methods and parameter settings. Zusammenfassung Zur Anwendung in einer phylogenetische Analyse müssen die ausgewählten Gene konservierte und detektierbare Information zum untersuchten phylogenetischen Niveau enthalten. Ribosomale Gene des Mitochondriums wurden für ein breites Spektrum phylogenetischer Fragestellungen bei verschiedenen Gruppen und insbesondere bei Froschlurchen eingesetzt. Wir untersuchten die Frage, ob Rekonstruktionen der Anuren-Phylogenie, basierend auf 12S und 16S rRNA Gensequenzen, plausibel sind. An einer Auswahl von 27 Arten, arrangiert in Taxa-Gruppen abgestufter Hierarchie, rekonstruierten wir phylogenetische Hypothesen unter verschiedenen, a priori festgelegten Bedingungen. Dazu gehörten die Auswahl verschiedener Alinierungsmethoden und,parameter, der Umgang mit variabel alinierten Positionen, die Auswahl der Algorithmen zur Baumkonstruktion sowie die Auswahl alternativer Modelle der Sequenzevolution. Die Methoden und Parameter der Alinierung und der Rekonstruktion, sowie die Auswahl der Taxa, hatten bedeutenden Einfluss auf die Resultate. Daraus resultierte eine große Anzahl alternativer Topologien, in denen nur sehr wenige Knoten in allen Analysen Unterstützung fanden. Ausschluss variabel alinierter Positionen ergaben Topologien mit niedrigem Grad der Auflösung. Die Sequenzen enthielten ein gewisses Signal für die Monophylie von Discoglossidae, Pelobatoidea, Pelobatidae und Pipidae. Der Knoten Neobatrachia wurde deutlich unterstützt. Die robuste Auflösung intragenerischer Phylogenien von Bombina und Discoglossus weisen auf eine besondere Eignung der Gene für die Untersuchung junger Aufspaltungsereignisse hin. Obwohl 12S und 16S rRNA-Gene eine heterogene Unterstützung für wenige frühe (mesozoische) phylogenetische Ereignisse zeigten, war das Signal nicht geeignet, um die Beziehungen der Taxa höherer Ordnung der Anura unter variierten Parametern und Analysemethoden konsistent aufzulösen. [source] Chromosome evolution in the genus Cicindela: physical mapping and activity of rDNA loci in the tiger beetle species Cicindela littoralis and C. flexuosaJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2003S. J. R. Proença Abstract Cicindela littoralis and Cicindela flexuosa were analysed at population level to determine the localization and activity of ribosomal genes. Fluorescence in situ hybridization (FISH), using a PCR-amplified 18S rDNA fragment as a probe, revealed the presence of polymorphism regarding the number of chromosomes with ribosomal genes as well as their localization within the genome. Nine populations of C. littoralis showed a consistent pattern of two loci located in an autosomal pair (active during spermatogenesis as shown by silver staining) and one locus located in one of the multiple X chromosomes (silent during spermatogenesis), whereas individuals from the population of Punta Entinas showed only signals in the autosomal pair, lacking the heterosomal locus. In C. flexuosa, two patterns were also observed. Nine populations showed two loci in an autosomal pair whereas individuals from the population of San Pedro del Pinatar showed the two loci located in the heterosomes (one of the multiple Xs and in the Y). The hypothesis that these two different populations may reflect a status of well-differentiated phylogenetic entities is not supported for C. littoralis after the phylogenetic analysis of a fragment of the cytochrome oxidase I gene. [source] DksA represses ribosomal gene transcription in Pseudomonas aeruginosa by interacting with RNA polymerase on ribosomal promotersMOLECULAR MICROBIOLOGY, Issue 4 2005Karl Perron Summary In Escherichia coli transcription of ribosomal RNA (rRNA) is regulated by the H-NS and Fis proteins, as well as by the small signal molecule ppGpp and the initiating nucleotides. During amino acid starvation, the concentration of ppGpp increases, and binding of this alarmone to RNA polymerase (RNAP) leads to inhibition of rRNA transcription, a regulatory event called stringent response. Here we show that in Pseudomonas aeruginosa DksA, a protein with pleiotropic effects, is a negative regulator of rRNA transcription both during exponential growth and stringent conditions. A dksA mutant overexpresses rRNA, without being affected in the production of ppGpp. Cell-fractionation and chromosome immunoprecipitation experiments demonstrate that DksA is associated with DNA, in particular with promoters of ribosomal genes in vivo. The binding to rRNA promoters specifically increases during stringent response, and correlates with the binding of RNAP to these regions. Moreover DksA can be copurified with RNAP subunits in vivo. DNA band shift experiments show that DksA, in synergy with ppGpp, increases the binding of RNAP to ribosomal promoters. Therefore DksA might be a new regulator of rRNA transcription in P. aeruginosa. [source] Morphological, Biochemical and Molecular Characterization of Herpetomonas samuelpessoai camargoi n. subsp., a Trypanosomatid Isolated from the Flower of the Squash Cucurbita moschataTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2001JOAO E. FIORINI ABSTRACT. We report the morphological, biochemical and molecular characteristics of a trypanosomatid isolated from the flower of Cucurbita moschata. Although the trypanosomatid was isolated from a plant, the lack of recognition of Phytomonas-spccific molecular markers based on spliced-leader and ribosomal genes as well as by monoclonal antibodies specific for Phytomonas argues against assigning it to this genus. Because the isolate displayed typical opisthomastigote forms in culture, it is assigned to the genus Herpetomonas. Analysis of randomly amplified polymorphic DNA (RAPD) patterns and characterization of ribosomal SSU and ITS markers suggest that it is more closely related to H. samuelpessoai than to any other species. However, the presence of spined flagellates in culture (displaying lateral expansions of the plasma membrane originating near the flagellar pocket) and isolate-specific RAPD fingerprints argue strongly that the trypanosomatid belongs to a new subspecies, for which the name Herpetomonas samuelpessoai camargoi n. subsp. is proposed. [source] Simultaneous analysis of basal Hymenoptera (Insecta): introducing robust-choice sensitivity analysisBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2003SUSANNE SCHULMEISTER Molecular characters are analysed on their own and in combination with morphological data to examine the phylogenetic relationships of the basal lineages of Hymenoptera (,Symphyta'). This study covers 47 sawfly genera and nine apocritan families and includes molecular sequences from five genes , 12S, 16S, 18S and 28S ribosomal genes and cytochrome oxidase 1 , as well as 343 morphological characters. A robust-choice sensitivity analysis is performed with the data. First, the simultaneous analysis is repeated three times, each time employing a different step matrix for weighting the transformations of the molecular characters. Then, the results of all three simultaneous analyses are summarized in a strict consensus in order to avoid basing the conclusions on a narrow set of assumptions. This methodology is discussed in the paper. The relationships among superfamilies largely confirm previous hypotheses, being (Xyeloidea (Tenthredinoidea s.l. (Pamphilioidea (Cephoidea (Siricoidea (Xiphydrioidea (Orussoidea Apocrita))))))), where Siricoidea is understood as Siricidae+Anaxyelidae. However, the relationships within Tenthredinoidea s.s. proposed here are novel: ({Argidae Pergidae}[Athalia{(Diprionidae Cimbicidae) Tenthredinidae minus Athalia}]). © 2003 The Linnean Society of London. Biological Journal of the Linnean Society, 2003, 79, 245,275. [source] Comparative transcriptome analysis to unveil genes affecting recombinant protein productivity in mammalian cellsBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2009Joon Chong Yee Abstract Low temperature culture (33°C) has been shown to enhance the specific productivity of recombinant antibodies in Chinese hamster ovary (CHO) cells but did not affect antibody productivity in hybridoma (MAK) cells. We probed the transcriptional response of both cells undergoing temperature shift using cDNA microarrays. Among the orthologous gene probes, common trends in the expression changes between CHO and MAK are not prominent. Instead, many transcriptional changes were specific to only one cell line. Notably, oxidative phosphorylation and ribosomal genes were downregulated in MAK but not in CHO. Conversely, several protein trafficking genes and cytoskeleton elements were upregulated in CHO but remained unchanged in MAK. Interestingly, at 33°C, immunoglobulin heavy and light chain showed no significant changes in CHO, but the immunoglobulin light chain was downregulated in MAK. Overall, a clear distinction in the transcriptional response to low temperature was seen in the two cell lines. To further elucidate the set of genes responsible for increased antibody productivity, the expression data of low temperature cultures was compared to that of butyrate treatment which increased specific antibody productivity in both cell lines. Genes which are commonly differentially expressed under conditions that increased productivity are likely to reflect functional classes that are important in the productivity changes. This comparative transcriptome analysis suggests that vesicle trafficking, endocytosis and cytoskeletal elements are involved in increased specific antibody productivity. Biotechnol. Bioeng. 2009;102: 246,263. © 2008 Wiley Periodicals, Inc. [source] A new model Gondwanan taxon: systematics and biogeography of the harvestman family Pettalidae (Arachnida, Opiliones, Cyphophthalmi), with a taxonomic revision of genera from Australia and New ZealandCLADISTICS, Issue 4 2007Sarah L. Boyer The phylogeny of the temperate Gondwanan harvestman family Pettalidae is investigated by means of a new morphological matrix of 45 characters, and DNA sequence data from five markers, including two nuclear ribosomal genes (18S rRNA and 28S rRNA), one nuclear protein coding gene (histone H3), and two mitochondrial genes,one protein coding (cytochrome c oxidase subunit I) and one ribosomal (16S rRNA). Phylogenetic analyses using an array of homology schemes (dynamic and static), criteria (parsimony and maximum likelihood), and sampling strategies (optimal trees versus Bayesian phylogenetics) all agree on the monophyly of Pettalidae as well as several of its subclades, each of which is restricted to a modern landmass. While most genera as traditionally defined are monophyletic, Rakaia and Neopurcellia, distributed across Queensland (Australia) and New Zealand, are not. Instead, the species from Queensland, previously described under three genera, constitute a well-supported clade, suggesting that in this case biogeography prevails over traditional taxonomy. A taxonomic emendation of the genera from Queensland and New Zealand is presented, and the new genus Aoraki is erected to include the species of the New Zealand denticulata group. A biogeographical hypothesis of the relationships of the former temperate Gondwana landmasses (with the exception of Madagascar) is presented, although ambiguity in the deep nodes of the pettalid tree renders such inference provisional. The data suggest that neither the South African fauna, the New Zealand fauna nor the Australian fauna is monophyletic but instead monophyly is found at smaller geographic scales (e.g., Western Australia, Queensland, NE South Africa). © The Willi Hennig Society 2007. [source] | ||||||||||