bluuebunny/crossref_metadata_2025 huggingface dataset:
Zoonotic orthopoxviruses encode a high-affinity antagonist of NKG2D
Authors: Campbell Jessica A. , Trossman David S. , Yokoyama Wayne M. , Carayannopoulos Leonidas N.
Published: June 2007

NK and T lymphocytes express both activating and inhibiting receptors for various members of the major histocompatibility complex class I superfamily (MHCISF). To evade immunologic cytotoxicity, many viruses interfere with the function of these receptors, generally by altering the displayed profile of MHCISF proteins on host cells. Using a structurally constrained hidden Markov model, we discovered an orthopoxvirus protein, itself distantly class I–like, that acts as a competitive antagonist of the NKG2D activating receptor. This orthopoxvirus MHC class I–like protein (OMCP) is conserved among cowpox and monkeypox viruses, secreted by infected cells, and bound with high affinity by NKG2D of rodents and humans (KD ∼ 30 and 0.2 nM, respectively). OMCP blocks recognition of host-encoded ligands and inhibits NKG2D-dependent killing by NK cells. This finding represents a novel mechanism for viral interference with NKG2D and sheds light on intercellular recognition events underlying innate immunity against emerging orthopoxviruses.
Dendritic cell quiescence during systemic inflammation driven by LPS stimulation of radioresistant cells in vivo
Authors: Nolte Martijn A. , LeibundGut-Landmann Salomé , Joffre Olivier , Sousa Caetano Reis e
Published: June 2007

Dendritic cell (DC) activation is a prerequisite for T cell priming. During infection, activation can ensue from signaling via pattern-recognition receptors after contact with pathogens or infected cells. Alternatively, it has been proposed that DCs can be activated indirectly by signals produced by infected tissues. To address the contribution of tissue-derived signals, we measured DC activation in a model in which radioresistant cells can or cannot respond to lipopolysaccharide (LPS). We report that recognition of LPS by the radioresistant compartment is sufficient to induce local and systemic inflammation characterized by high circulating levels of tumor necrosis factor (TNF) α, interleukin (IL) 1β, IL-6, and CC chemokine ligand 2. However, this is not sufficient to activate DCs, whether measured by migration, gene expression, phenotypic, or functional criteria, or to render DC refractory to subsequent stimulation with CpG-containing DNA. Similarly, acute or chronic exposure to proinflammatory cytokines such as TNF-α ± interferon α/β has marginal effects on DC phenotype in vivo when compared with LPS. In addition, DC activation and migration induced by LPS is unimpaired when radioresistant cells cannot respond to the stimulus. Thus, inflammatory mediators originating from nonhematopoietic tissues and from radioresistant hematopoietic cells are neither sufficient nor required for DC activation in vivo.
Complement factor H and the hemolytic uremic syndrome
Authors: Atkinson John P. , Goodship Timothy H.J.
Published: June 2007

Immune recognition is coupled to powerful proinflammatory effector pathways that must be tightly regulated. The ancient alternative pathway of complement activation is one such proinflammatory pathway. Genetic susceptibility factors have been identified in both regulators and activating components of the alternative pathway that are associated with thrombotic microangiopathies, glomerulonephritides, and chronic conditions featuring debris deposition. These observations indicate that excessive alternative pathway activation promotes thrombosis in the microvasculature and tissue damage during debris accumulation. Intriguingly, distinct genetic changes in factor H (FH), a key regulator of the alternative pathway, are associated with hemolytic uremic syndrome (HUS), membranoproliferative glomerulonephritis (dense deposit disease), or age-related macular degeneration (AMD). A mouse model of HUS designed to mirror human mutations in FH has now been developed, providing new understanding of the molecular pathogenesis of complement-related endothelial disorders.
An integrable equation governing short waves in a long-wave model
Authors: Faquir M , Manna M.A , Neveu A
Published: June 2007

The dynamics of a nonlinear and dispersive long surface capillary-gravity wave model equation is studied analytically in its short-wave limit. We exhibit its Lax pair and some non-trivial conserved quantities. Through a change of functions, an unexpected connection between this classical surface water-wave model and the sine-Gordon (or sinh-Gordon) equation is established. Numerical and analytical studies show that in spite of integrability their solutions can develop singularities and multivaluedness in finite time. These features can be traced to the fact that the surface tension term in the energy involves second-order derivatives. It would be interesting to see in an experiment whether such singularities actually appear, for which surface tension would be specifically responsible.
An experimental test of frequency-dependent selection on male mating strategy in the field
Authors: Bleay C , Comendant T , Sinervo B
Published: June 2007

We provide field-based experimental evidence for the frequency-dependent nature of the fitness of alternative mating strategies. We manipulated the frequency of genetically determined phenotypic strategies in six wild populations of the side-blotched lizard,Uta stansburiana. The within-population pattern of mating was assessed using nine microsatellite loci to assign paternity. Within populations of the side-blotched lizard exist three colour morphs (orange, blue and yellow) associated with male mating strategy. The frequency of these morphs has previously been found to oscillate over a 4- to 5-year period. We found, as predicted, that the common phenotype lost fitness to its antagonist. The mating patterns of all six populations adhered toa prioripredictions that were derived from previous empirical and theoretical observations on this system. We found that the frequency-dependent nature of male fitness could be accounted for by the composition of their competitors at a small local population level, driven by associations within a focal female's social neighbourhood.
Climatically driven synchrony of gerbil populations allows large-scale plague outbreaks
Authors: Linné Kausrud Kyrre , Viljugrein Hildegunn , Frigessi Arnoldo , Begon Mike , Davis Stephen , Leirs Herwig , Dubyanskiy Vladimir , Stenseth Nils Chr
Published: June 2007

In central Asia, the great gerbil (
Rhombomys opimus
) is the main host for the bacterium
Yersinia pestis
, the cause of bubonic plague. In order to prevent plague outbreaks, monitoring of the great gerbil has been carried out in Kazakhstan since the late 1940s. We use the resulting data to demonstrate that climate forcing synchronizes the dynamics of gerbils over large geographical areas. As it is known that gerbil densities need to exceed a threshold level for plague to persist, synchrony in gerbil abundance across large geographical areas is likely to be a condition for plague outbreaks at similar large scales. Here, we substantiate this proposition through autoregressive modelling involving the normalized differentiated vegetation index as a forcing covariate. Based upon predicted climate changes, our study suggests that during the next century, plague epizootics may become more frequent in central Asia.
The age and evolution of an antiviral resistance mutation inDrosophila melanogaster
Authors: Bangham Jenny , Obbard Darren J , Kim Kang-Wook , Haddrill Penelope R , Jiggins Francis M
Published: June 2007

What selective processes underlie the evolution of parasites and their hosts? Arms-race models propose that new host-resistance mutations or parasite counter-adaptations arise and sweep to fixation. Frequency-dependent models propose that selection favours pathogens adapted to the most common host genotypes, conferring an advantage to rare host genotypes. Distinguishing between these models is empirically difficult. The maintenance of disease-resistance polymorphisms has been studied in detail in plants, but less so in animals, and rarely in natural populations. We have made a detailed study of genetic variation in host resistance in a natural animal population,Drosophila melanogaster, and its natural pathogen, the sigma virus. We confirm previous findings that a single (albeit complex) mutation in the generef(2)Pconfers resistance against sigma and show that this mutation has increased in frequency under positive selection. Previous studies suggested thatref(2)Ppolymorphism reflects the progress of a very recent selective sweep, and that in Europe during the 1980s, this was followed by a sweep of a sigma virus strain able to infect flies carrying this mutation. We find that theref(2)Presistance mutation is considerably older than the recent spread of this viral strain and suggest that—possibly because it is recessive—the initial spread of the resistance mutation was very slow.
Clostridium aestuarii sp. nov., from tidal flat sediment
Authors: Kim Seil , Jeong Hyunyoung , Chun Jongsik
Published: June 2007

A strictly anaerobic, halophilic, motile, endospore-forming, rod-shaped bacterium, designated strain HY-45-18T, was isolated from a sediment sample of a tidal flat in Korea. The isolate produced butyric acid, propionic acid, glycerol and H2as fermentation end products from glucose. Strain HY-45-18Tis halophilic as it was unable to grow in the absence of sea salts. A 16S rRNA gene sequence analysis clearly indicated that the tidal flat isolate is a member of cluster I of the orderClostridiales, which contains the type species ofClostridium,Clostridium butyricum. The closest phylogenetic neighbour of strain HY-45-18TwasClostridium ganghwenseKCTC 5146T(96.5 % 16S rRNA gene sequence similarity). Several phenotypic characteristics can be readily used to differentiate the isolate from phylogenetically related clostridia. Therefore, strain HY-45-18Trepresents a novel species of the genusClostridium, for which the nameClostridium aestuariisp. nov. is proposed. The type strain is HY-45-18T(=IMSNU 40129T=KCTC 5147T=JCM 13194T).
Aerococcus suis sp. nov., isolated from clinical specimens from swine
Authors: Vela A. I. , García N. , Latre M. V. , Casamayor A. , Sánchez-Porro C. , Briones V. , Ventosa A. , Domínguez L. , Fernández-Garayzábal J. F.
Published: June 2007

Biochemical and molecular genetic studies were performed for five isolates of unknown Gram-positive, catalase-negative, cocci-shaped micro-organisms obtained from clinical samples from pigs. The micro-organisms were tentatively identified as Aerococcus species on the basis of the results from cellular morphological and biochemical tests. 16S rRNA gene sequencing studies confirmed the provisional identification of the isolates as members of the genus Aerococcus, but the micro-organism did not correspond to any recognized species of this genus. The nearest phylogenetic relatives of these unknown cocci isolated from pigs were Aerococcus viridans (95.9 % 16S rRNA gene sequence similarity) and Aerococcus urinaeequi (95.8 %). The unknown bacterium, however, was distinguishable from these two species and from other animal aerococci by using biochemical tests. On the basis of both phenotypic and phylogenetic findings, the isolates represent a novel species of the genus Aerococcus, for which the name Aerococcus suis sp. nov. is proposed. The type strain is 1821/02T (=CECT 7139T=CCUG 52530T).
Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest
Authors: Zhang Li , Xu Zhihong , Patel Bharat K. C.
Published: June 2007

An aerobic bacterium, designated strain E1HC-02T, was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02Twere short irregular rods (0.5–1.0×0.2–0.4 μm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 °C and at a pH of 9.1. Strain E1HC-02Tmetabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02Tshowed that it was a member of the familyMicrobacteriaceae, phylumActinobacteria. The cell wall contained a type B2βpeptidoglycan, the dominant cellular fatty acid was 18 : 1ω7cand the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02Twere distinctly different to all of the 17 genera of the familyMicrobacteriaceaeand hence strain E1HC-02Tis designated as representing a novel species of a new genus,Frondicola australicusgen. nov., sp. nov. The type strain of the type species is E1HC-02T(=JCM 13598T=DSM 17894T).
Leeia oryzae gen. nov., sp. nov., isolated from a rice field in Korea
Authors: Lim Jee-Min , Jeon Che Ok , Lee Gye Suk , Park Dong-Jin , Kang Ui-Gum , Park Chang-Young , Kim Chang-Jin
Published: June 2007

A strictly aerobic, non-spore-forming, Gram-negative bacterium, designated strain HW7T, was isolated from a rice field in Korea. Cells of strain HW7T were short rod-shaped and motile with single polar flagella. The major cellular fatty acids of strain HW7T were C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH). The genomic DNA G+C content was 56 mol% and the major isoprenoid quinone was Q-8. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HW7T forms a distinct lineage with respect to closely related genera within the class Betaproteobacteria and that the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93 %. On the basis of the physiological and phylogenetic data, strain HW7T represents a novel genus and species of the Betaproteobacteria, for which the name Leeia oryzae gen. nov., sp. nov. is proposed. The type strain is HW7T (=KCTC 12585T=DSM 17879T).
Parapedobacter koreensis gen. nov., sp. nov.
Authors: Kim Myung Kyum , Na Ju-Ryun , Cho Dong Ha , Soung Nak-Kyun , Yang Deok-Chun
Published: June 2007

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1
ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).
Marichromatium bheemlicum sp. nov., a non-diazotrophic, photosynthetic gammaproteobacterium from a marine aquaculture pond
Authors: Kumar P. Anil , Jyothsna T. S. Sasi , Srinivas T. N. R. , Sasikala Ch. , Ramana Ch. V. , Imhoff J. F.
Published: June 2007

A rod-shaped, phototrophic, purple sulfur bacterium, strain JA124T, was isolated in pure culture from a marine aquaculture pond, located near Bhimunipatnam, in a medium that contained 3 % NaCl (w/v). Strain JA124T is a Gram-negative, motile rod with a single polar flagellum. Strain JA124T has a requirement for NaCl, with optimum growth at 1.5–8.5 %, and tolerates up to 11 % NaCl. Intracellular photosynthetic membranes are of the vesicular type. Bacteriochlorophyll a and probably carotenoids of the spirilloxanthin series are present as photosynthetic pigments. Strain JA124T was able to utilize sulfide, sulfate, thiosulfate, sulfite, thioglycollate and cysteine as sulfur sources. Strain JA124T was able to grow photolithoautotrophically, photolithoheterotrophically and photo-organoheterotrophically. Chemotrophic and fermentative growth could not be demonstrated. Strain JA124T lacks diazotrophic growth and acetylene reduction activity. Pyridoxal phosphate is required for growth. During growth on reduced sulfur sources as electron donors, sulfur is deposited intermediately as a number of small granules within the cell. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA124T clusters with species of the genus Marichromatium belonging to the class Gammaproteobacteria. The highest sequence similarities of strain JA124T were found with the type strains of Marichromatium indicum (98 %), Marichromatium purpuratum (95 %) and Marichromatium gracile (93 %). However, DNA–DNA hybridization with Marichromatium indicum DSM 15907T revealed relatedness of only 65 % with strain JA124T. The DNA base composition of strain JA124T was 67 mol% G+C (by HPLC). Based on 16S rRNA gene sequence analysis, morphological and physiological characteristics and DNA–DNA hybridization studies, strain JA124T (=ATCC BAA-1316T=JCM 13911T) is sufficiently different from other Marichromatium species to merit its description as the type strain of a novel species, Marichromatium bheemlicum sp. nov.
Rhodobium pfennigii sp. nov., a phototrophic purple non-sulfur bacterium with unusual bacteriochlorophyll a antennae, isolated from a brackish microbial mat on Rangiroa atoll, French Polynesia
Authors: Caumette Pierre , Guyoneaud Rémy , Duran Robert , Cravo-Laureau Cristiana , Matheron Robert
Published: June 2007

A novel budding purple non-sulfur bacterium (strain AR2102T) was isolated in pure culture from a microbial mat that had developed in brackish-water ponds on the coral rim of the atoll of Rangiroa (Tuamotu Islands, French Polynesia). Single cells of this strain were rod-shaped and motile by means of polar flagella and divided by budding. Their intracellular photosynthetic membranes were of the lamellar type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series, with spirilloxanthin as the main carotenoid, were present as photosynthetic pigments. Bacteriochlorophyll a absorption in the infrared portion of the light spectrum exhibited an unusual in vivo absorption peak at 909 nm. The strain grew optimally under photoheterotrophic conditions, but could grow photolithotrophically on thiosulfate or chemo-organotrophically under micro-oxic conditions. Optimal growth occurred in the presence of 1–2 % NaCl. Comparative sequence analysis of the 16S rRNA gene placed strain AR2102T within the class Alphaproteobacteria, in a cluster with Rhodobium species. Representatives of this cluster form a closely related group of slightly to moderately halotolerant to halophilic, rod-shaped, purple non-sulfur bacteria that divide by budding. The new isolate exhibited some differences in physiology (no utilization of alcohols or carbohydrates) and genetic characteristics (low relatedness in DNA–DNA hybridization) as well as in its relation to light (differences in absorption wavelengths) from previously described Rhodobium species. Consequently, we propose that strain AR2102T (=DSM 17143T=ATCC BAA-1145T) should be considered as the type strain of a novel species within the genus Rhodobium, Rhodobium pfennigii sp. nov.
Nocardia acidivorans sp. nov., isolated from soil of the island of Stromboli
Authors: Kämpfer Peter , Huber Birgit , Buczolits Sandra , Thummes Kathrin , Grün-Wollny Iris , Busse Hans-Jürgen
Published: June 2007

A Gram-positive, non-spore-forming bacterium (strain GW4-1778T) was isolated from soil of the Italian island of Stromboli. 16S rRNA gene sequence similarity studies showed that strain GW4-1778T is a member of the genus Nocardia, most closely related to Nocardia pseudobrasiliensis (GenBank accession no. DQ659914; 98.6 %), Nocardia nova (Z36930; 98.6 %), Nocardia niigatensis (AB092563; 98.4 %), Nocardia jiangxiensis (AY639902; 98.0 %), Nocardia uniformis (Z46752; 98.0 %) and Nocardia miyunensis (AY639901; 97.8 %). Strain GW4-1778T could be distinguished from any other established Nocardia species by sequence similarity values of less than 97.5 %. Strain GW4-1778T exhibited a quinone system with the predominant compound MK-8 (H4, ω-cycl) (99.5 %) and traces of MK-8 (H4), characteristic for the genus Nocardia. The polar lipid profile of strain GW4-1778T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine, phosphatidylinositol, two phosphatidylinositol mannosides, a unknown polar lipid and trace amounts of two unknown lipids and the major fatty acids were C15 : 0, C16 : 0, C17 : 1
ω8c and 10-methyl C17 : 0. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW4-1778T from related species with 16S rRNA gene similarities of >97.5 %. Therefore, strain GW4-1778T merits species status, for which the name Nocardia acidivorans sp. nov. is proposed, with the type strain GW4-1778T (=CCUG 53410T=CIP 109315T=DSM 45049T).
Pigmentiphaga daeguensis sp. nov., isolated from wastewater of a dye works, and emended description of the genus Pigmentiphaga
Authors: Yoon Jung-Hoon , Kang So-Jung , Kim Wonyong , Oh Tae-Kwang
Published: June 2007

A Gram-negative, non-spore-forming, rod-shaped Pigmentiphaga-like bacterial strain, K110T, was isolated from wastewater collected from a dye works in Korea and was subjected to a polyphasic taxonomic analysis. Strain K110T grew optimally at pH 7.0–-8.0 and 37 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and C16 : 0, cyclo C17 : 0 and cyclo C19 : 0
ω8c as the major fatty acids. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified aminolipids. The DNA G+C content was 67.4 mol%. In a neighbour-joining phylogenetic tree constructed on the basis of 16S rRNA gene sequences, strain K110T joined Pigmentiphaga kullae, the sole species of the genus, at a bootstrap confidence level of 100 %. Strain K110T exhibited a 16S rRNA gene sequence similarity of 99.4 % with respect to the type strain of P. kullae. Although strain K110T was found to be similar to P. kullae in terms of phenotypic properties, it differed in terms of motility, polar lipids, DNA–DNA relatedness and repetitive extragenic palindromic PCR genomic fingerprinting patterns. On the basis of phenotypic, phylogenetic and genetic data, strain K110T represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga daeguensis sp. nov. is proposed. The type strain is K110T (=KCTC 12838T=JCM 14330T).
Alcanivorax balearicus sp. nov., isolated from Lake Martel
Authors: Rivas Raúl , García-Fraile Paula , Peix Alvaro , Mateos Pedro F. , Martínez-Molina Eustoquio , Velázquez Encarna
Published: June 2007

A bacterial strain designated MACL04T was isolated from Lake Martel, a subterraneous saline lake in Mallorca (Spain). The complete 16S rRNA gene sequence of this strain showed nearly 100 % similarity to that of Alcanivorax dieselolei B-5T. Despite this high similarity, strain MACL04T showed phenotypic, chemotaxonomic and molecular differences with respect to A. dieselolei, indicating that strain MACL04T represents a separate species. Cells of strain MACL04T were motile by means of a single polar or subpolar flagellum and colonies formed on media containing 1 % (v/v) Tween 20 were opaque and mucoid, with blue–green iridescence. The generation time of strain MACL04T in this medium was approximately half that of A. dieselolei B-5T and strain MACL04T did not produce lipases after incubation for 5 days. Strain MACL04T did not require NaCl for growth and grew in the presence of up to 15 % (w/v) NaCl. The strain was able to use alkanes as a sole carbon source; however, glucose could also be used, albeit weakly, as a carbon source. Several amino acids and organic acids were used as carbon sources. Strain MACL04T produced acid in media containing pyruvate as the sole carbon source. The major fatty acids were C19 : 0 cyclo ω8c and C16 : 0. The fatty acid C16 : 1
ω8c, present in strain MACL04T, was not detected in the recognized Alcanivorax species. The sequences of the large and short 16S–23S intergenic spacer regions showed similarities of 97.2 and 98.8 % (ungapped) with respect to A. dieselolei B-5T. Partial sequences of gyrB and alkb genes showed 94.0 % similarity between strain MACL04T and A. dieselolei B-5T. The G+C content of strain MACL04T was 62.8 mol%. The data from this polyphasic study indicate that strain MACL04T represents a novel species of the genus Alcanivorax, for which the name Alcanivorax balearicus sp. nov. is proposed. The type strain is MACL04T (=LMG 22508T=CECT 5683T).
Use of the novel phylogenetic marker dnaJ and DNA–DNA hybridization to clarify interrelationships within the genus Aeromonas
Authors: Nhung Pham Hong , Hata Hiroyuki , Ohkusu Kiyofumi , Noda Makiko , Shah Mohammad Monir , Goto Keiichi , Ezaki Takayuki
Published: June 2007

The interrelationships of 27Aeromonasstrains were investigated usingdnaJsequences and DNA–DNA hybridization.dnaJsequence similarities showed a stronger relationship with DNA–DNA relatedness values than did 16S rRNA gene sequence similarities. Additionally,dnaJsequence analysis, with interspecies divergence over 5.2 % in most cases, gave better resolution than 16S rRNA gene sequences for the differentiation of strains at the species level. Relationships amongAeromonasspecies were therefore elucidated on the basis ofdnaJsequences and DNA–DNA reassociation. Strains ofAeromonas encheleiaandAeromonassp. HG11 were unquestionably grouped in the same genetic species, since they shared 98.7 %dnaJsequence similarity and 82–85 % genomic relatedness. The phylogenetically close relationships obtained fromdnaJsequence analysis (1.7–3.3 % genetic distance) were corroborated by high DNA–DNA relatedness (73–97 %) to support the previous suggestion thatAeromonas culicicolaandAeromonas allosaccharophilaare later heterotypic synonyms ofAeromonas veronii. Our findings will contribute to the clarification of controversial relationships in the genusAeromonasand also demonstrate that analysis ofdnaJsequences can be a powerful tool for interspecies study of the genus.
Cloning of nucleoplasmin from Xenopus laevis oocytes and analysis of its developmental expression.
Authors: Bürglin T R , Mattaj I W , Newmeyer D D , Zeller R , De Robertis E M
Published: June 2007

Nucleoplasmin is the most abundant protein in the nucleus of Xenopus laevis oocytes. We cloned a cDNA coding for nucleoplasmin from an expression library of immature Xenopus laevis oocytes. The deduced amino acid sequence shows that the carboxyl terminus is very hydrophilic and contains an unusual stretch of 12 glutamic acid residues, which is consistent with one of the proposed functions of nucleoplasmin--that of promoting chromatin assembly. The last 50 amino acids are lysine- and alanine-rich and contain short stretches of homology to histone H1. These regions could be involved in interactions with nucleosomes. The levels of nucleoplasmin mRNA and protein during oogenesis and embryogenesis were investigated using Northern blots, Western blots, and in situ hybridization to oocyte sections. The mRNA is detected during oogenesis but not during embryogenesis, suggesting that nucleoplasmin may be an exclusively maternally expressed gene. However, the protein is present throughout embryogenesis and undergoes pronounced changes in its level of phosphorylation during maturation of the oocyte and just after midblastula transition. These results support the notion that nucleoplasmin is not only important in oocytes but also plays a major role during the rapid cleavages of early embryogenesis.
Differences in DNA methylation during oogenesis and spermatogenesis and their persistence during early embryogenesis in the mouse.
Authors: Sanford J P , Clark H J , Chapman V M , Rossant J
Published: June 2007

We have examined the relative methylation levels of several dispersed repeated and low-copy-number gene sequences during gametogenesis and early embryogenesis. Southern blot analyses revealed that L1, intercisternal A particle (IAP), and major urinary protein (MUP) sequences were undermethylated extensively at MspI sites in DNA from diplotene oocytes. In contrast, the same sequences were highly methylated in DNA from pachytene spermatocytes, round spermatids, and epididymal sperm. These results indicate that there are genome-wide DNA methylation differences between oogenesis and spermatogenesis. Repeated sequences in DNA from cleavage-stage embryos and inner cell masses (ICM) were methylated at intermediate levels, consistent with transient maintenance of gametic methylation levels during early embryogenesis. Gametic differences in DNA methylation observed here indicate that methylation could provide a mechanism for imprinting maternal and paternal genomes resulting in differential regulation of parental genomes during early development.
Expression in transgenic mice of two genes of different tissue specificity integrated into a single chromosomal site.
Authors: Einat P , Bergman Y , Yaffe D , Shani M
Published: June 2007

Transgenic mice were used to study the expression of pairs of genes with distinctly different tissue specificities, covalently linked and integrated into the same chromosomal site. A transgenic strain carrying, in close proximity and in the same orientation, the rat fast skeletal muscle myosin light-chain 2 (MLC2) gene and the mouse rearranged immunoglobulin kappa light-chain gene expressed the immunoglobulin gene specifically in the lymphoid tissues, whereas rat MLC2 transcripts were found in skeletal muscle but not in the spleen or the other tissues that were tested. In another transgenic strain, carrying the rat MLC2 gene and a modified rat skeletal muscle actin gene (actin-globin chimeric gene), transcripts of the rat MLC2 gene were detected in skeletal muscle only, whereas the actin-globin transcripts were detected in skeletal muscle as well as in the heart. Moreover, the expression of the chimeric gene was also developmentally regulated. Expression was higher in cardiac muscle than in the skeletal muscle of neonatal mice, whereas expression was higher in skeletal muscle in adult mice. This pattern is consistent with the regulation of the expression of the endogenous skeletal muscle actin gene. Thus, in those transgenic strains that expressed both genes, each gene retained its tissue specificity, in spite of their close proximity. These results indicate a high degree of autonomy of the control elements included in the cloned genomic DNA fragment and demonstrate that a single chromosomal site can be permissive for the proper expression of two genes with different tissue specificities.
Expression and assembly of a human neurofilament protein in transgenic mice provide a novel neuronal marking system.
Authors: Julien J P , Tretjakoff I , Beaudet L , Peterson A
Published: June 2007

To investigate the regulation of neurofilament gene expression, we have generated several lines of transgenic mice carrying multiple copies of a cloned human neurofilament (NF-L) gene. We show that a 21.5-kb DNA fragment including the human NF-L gene contains essential information for correct expression in nervous tissue of transgenic mice. The integrated genes are arranged in multiple tandem arrays, but the extent of transgene expression does not correlate with copy number nor does it influence the expression of the endogenous neurofilament genes. However, the levels of human NF-L protein recovered in neurofilament preparations from brains of transgenic mice correlate directly with the relative abundance of human NF-L mRNA detected in each line. There is an apparent delay in the accumulation of human NF-L protein during development, as determined by immunoblotting with a human-specific monoclonal antibody. Finally, immunohistochemical localization of the human NF-L protein results in the specific staining of neurons and their processes in transgenic mice.
A 100-kD HeLa cell octamer binding protein (OBP100) interacts differently with two separate octamer-related sequences within the SV40 enhancer.
Authors: Sturm R , Baumruker T , Franza B R , Herr W
Published: June 2007

Numerous eukaryotic upstream promoter and enhancer regions contain a functional octamer sequence ATGCAAAT. We have examined the interactions between an octamer binding protein isolated from HeLa cells and the SV40 and immunoglobulin heavy-chain (IgH) gene enhancers. A partially purified octamer binding activity forms a single complex with the IgH enhancer octamer in a gel retardation assay, but two complexes with a SV40 enhancer fragment containing a single 72-bp element. By using point mutants and both dimethyl sulfate and diethyl pyrocarbonate modification interference assays, we show that the SV40 complexes result from binding of a factor to the octamer-related sequence ATGCAAAG (Octa1) and to an adjacent previously unidentified octamer-related sequence ATGCATCT (Octa2). The base-specific interactions with Octa1 and Octa2 differ; chemical modifications over a 10-bp sequence TATGCAAAGC affect Octa1 binding whereas Octa2 binding is affected by modifications spanning a 13-bp sequence ATGCATCTCAATT in which the octamer-like sequence is not centered. The octamer binding activity has been purified extensively by a DNA affinity precipitation procedure and SDS-polyacrylamide gel electrophoresis. The purified protein, OBP100, has an apparent molecular weight of 100 kD and binds both SV40 Octa1 and Octa2, as well as the IgH enhancer. The distinct interactions of OBP100 with the differently sized Octa1 and Octa2 binding sites suggest remarkably flexible sequence recognition between OBP100 and its binding sites.
Changing patterns of transcriptional and post-transcriptional control of liver-specific gene expression during rat development.
Authors: Panduro A , Shalaby F , Shafritz D A
Published: June 2007

Genes coding for unique or tissue-specific (differentiated) functions in the liver are induced at different times during development. It has generally been felt that transcriptional control represents the dominant mechanism for regulating expression of these genes. We have determined the relative transcription rates and mRNA steady-state levels for a series of genes specifically or preferentially expressed in rat liver and find examples of transcriptional control (albumin, alpha-fetoprotein, alpha 1-antitrypsin, tyrosine aminotransferase, transferrin, and cytochrome P450, TF-1) and post-transcriptional control (alpha 1-acid glycoprotein, apolipoproteins A-1 and E, malic enzyme, and ATP citrate lyase), as well as "mixed" regulation (ligandin and cytochrome P450, R17). Examples have been identified in which the predominant mode for regulating expression of preferentially expressed genes changes from transcriptional to post-transcriptional at different stages of liver development and some members of multigene families (cytochrome P450s and apolipoprotein genes) also show independent and sometimes contrasting modes of regulation. Therefore, it appears that regulation of specific gene expression in the liver is a dynamic process, far more complex than heretofore suspected, and a much greater contribution of post-transcriptional regulation accounts for changes in expression of genes representing major functions of the liver.
Species- and tissue-specific expression of human alpha 1-antitrypsin in transgenic mice.
Authors: Kelsey G D , Povey S , Bygrave A E , Lovell-Badge R H
Published: June 2007

alpha 1-Antitrypsin (alpha 1AT) is an abundant serum protein whose major site of synthesis is in the hepatocyte. alpha 1AT transcripts are also present, albeit at a lower level, in a variety of other human tissues. This pattern of expression is partly related to initiation of transcription at sites with distinct tissue specificities. The mouse alpha 1AT gene, in contrast, is more strictly liver specific in its expression. To explore the regulation of the alpha 1AT gene we have microinjected a cosmid insert carrying the human gene into fertilized mouse eggs. In three lines obtained from transgenic mice, inheritance of copies of the human gene is accompanied by a high serum concentration of the human protein. Human alpha 1AT RNA accumulates to the highest level in liver of transgenic animals. The presence of transcripts in other tissues indicates that the human pattern of expression is maintained, whereas the temporal activity of the introduced gene parallels that of the endogenous one during mouse embryogenesis.
A novel role for the 3' region of introns in pre-mRNA splicing of Saccharomyces cerevisiae.
Authors: Rymond B C , Torrey D D , Rosbash M
Published: June 2007

To investigate the importance of sequences between the yeast (Saccharomyces cerevisiae) branch point (TACTAAC box) and 3' splice site (AG), we generated a series of pre-mRNA substrates that differed in the length of RNA retained on the 3' side of the TACTAAC box. These pre-mRNAs were compared as substrates for the first step of in vitro splicing (5' cleavage and lariat formation) and in vitro spliceosome assembly (complex formation) in a whole-cell yeast extract. The results indicate that for rp51A pre-mRNA at least 29 nucleotides of RNA on the 3' side of the TACTAAC box are required for 5' cleavage and lariat formation, as smaller substrates fail to manifest any detectable cleavage or ligation events. Analysis of splicing complex assembly indicates that these smaller substrates undergo efficient yet incomplete complex formation; they are blocked at a late stage of spliceosome assembly, the complex I to complex II transition (Pikielny et al. 1986), a result which suggests that the failure to form lariats is due to a specific assembly defect. The lariat formation block (and assembly defect) can be relieved by the addition of ribohomopolymer "tails" to the 3' end of the shortened rp51A pre-mRNAs, and similar results were obtained with shortened actin pre-mRNAs. The results of this study indicate that this region of the pre-mRNA serves a specific function late in in vitro spliceosome assembly.
An albumin enhancer located 10 kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice.
Authors: Pinkert C A , Ornitz D M , Brinster R L , Palmiter R D
Published: June 2007

Transgenic mice were used to locate the cis-acting DNA elements that are important for efficient, tissue-specific expression of the mouse albumin gene in the adult. Chimeric genes with up to 12 kb of mouse albumin 5'-flanking region fused to a human growth hormone (hGH) reporter gene were tested. Remarkably, a region located 8.5-10.4 kb upstream of the albumin promoter was essential for high-level expression in adult liver and the region in between -8.5 and -0.3 kb was dispensable. The far-upstream region behaved like an enhancer in that its position and orientation relative to the albumin promoter were not critical; however, it did not function well with a heterologous promoter. Two of four DNase hypersensitive sites found in the 5'-flanking region of the albumin gene map to the far-upstream and promoter regions; the others may reflect regions involved in developmental or environmental control of this gene.
The lin-14 locus of Caenorhabditis elegans controls the time of expression of specific postembryonic developmental events.
Authors: Ambros V , Horvitz H R
Published: June 2007

The lin-14 locus of Caenorhabditis elegans plays an important role in specifying the normal timing and sequence of developmental events in the lateral hypodermal cell lineages. The results of gene dosage, complementation, and temperature-shift experiments indicate that the fates expressed by cells at successive stages of these cell lineages are specified by the level of lin-14 activity and that lin-14 acts at multiple times during development to control stage-specific choices of cell fate. Our observations suggest that during normal development a reduction in the level of lin-14 gene function causes the sequential expression of stage-specific cell fates.
A trans-acting suppressor restores splicing of a yeast intron with a branch point mutation.
Authors: Couto J R , Tamm J , Parker R , Guthrie C
Published: June 2007

Splicing of introns from Saccharomyces cerevisiae pre-mRNA requires the conserved sequence TACTAAC; the 3'-most A residue is utilized as the site of branch formation. We showed previously that the transcript from an actin-HIS4 gene fusion containing the mutation TACTAAC to TACTACC (designated C259) is spliced inefficiently, thereby preventing growth on the histidine precursor histidinol. By selecting for growth on histidinol, we have identified a mutant in which the splicing of the C259 transcript is increased fourfold; splicing of other mutated introns is not significantly improved. The mutant locus encodes a trans-acting suppressor. A single mutation, rna16-1, is sufficient for suppression; however, suppression is maximized in heterozygous diploids containing both rna16-1 and the wild-type allele RNA16. In addition, wild-type pre-mRNAs (and lariat intermediates) accumulate in rna16-1 cells. We propose that the RNA16 locus encodes a component of the splicing machinery.
Relative position and strengths of poly(A) sites as well as transcription termination are critical to membrane versus secreted mu-chain expression during B-cell development.
Authors: Galli G , Guise J W , McDevitt M A , Tucker P W , Nevins J R
Published: June 2007

During B-cell differentiation, there is a dramatic switch in the RNA products of the immunoglobulin mu heavy chain transcription unit. In the mature B cell there is roughly equal production of the microseconds and the micron RNA, whereas in the antibody-secreting plasma cell there is nearly exclusive production of the microseconds RNA. A plasmid containing the entire mu transcription unit was properly regulated when assayed by transient transfection in a B lymphoma and a plasmacytoma. In contrast, no such regulation was observed with separate plasmids that could produce only one or the other RNA. Instead, the micron poly(A) site was utilized more efficiently than the microseconds poly(A) site, irrespective of the cell type. We also found that transcription termination prior to the micron poly(A) site in plasmacytomas contributes to preferential production of microseconds RNA in these cells. Finally, reducing the distance between the two poly(A) sites improved the use of the micron site at the expense of the use of the microseconds in B lymphoma cells, suggesting a competition for a limiting factor. Such competition was not apparent in plasmacytomas. We conclude that relative poly(A) site strength and the position of the poly(A) sites within the transcription unit, coupled with a changing concentration of a limiting factor, as well as transcription termination prior to the micron poly(A) site, all play a role in determining the expression of the mu locus during B-cell development.
DNA specificity determinants of Escherichia coli tryptophan repressor binding.
Authors: Bass S , Sugiono P , Arvidson D N , Gunsalus R P , Youderian P
Published: June 2007

We have analyzed the sequence-specific interaction between the Escherichia coli tryptophan (Trp) repressor and its operator using challenge phage vectors. These phages, derivatives of Salmonella phage P22 that have substitutions of synthetic, symmetric trp operators for the P22 mnt operator, provide a genetic assay for DNA binding in vivo. Phages carrying operators that retain the determinants of Trp repressor binding efficiently lysogenize cells producing repressor; in contrast, phages with operators missing critical determinants kill such hosts. The binding determinants revealed by this assay corroborate a simple docking model for the Trp repressor-operator interaction postulated from the repressor crystal structure, and account for both the specificity of repressor binding and the ability of Trp repressor to recognize multiple, tandem DNA sites.
Use of repetitive sequences to identify DNA polymorphisms linked to regA, a developmentally important locus in Volvox.
Authors: Harper J F , Huson K S , Kirk D L
Published: June 2007

The regA locus plays a centrally important role in Volvox development by preventing somatic cells from redifferentiating as germ cells; until now, approaches to cloning regA, as a preliminary to molecular analysis of its function, have been lacking. Here a novel approach is described that uses repetitive-sequence probes to rapidly identify restriction fragment length polymorphisms (RFLPs) linked to regA. Genomic DNA was cut with restriction enzymes having 4-base recognition sequences and then electrophoresed long enough to run most fragments off the gel; the remaining long (1- to 20-kb) fragments were resolved into numerous, reproducibly identifiable bands. On Southern blots of such preparations, six repetitive-sequence probes were used to identify 1232 bands, 24% of which were polymorphic between two closely related strains. Ninety-four RFLPs, for which inheritance patterns have been analyzed, fall into 36 "segregation groups," within which no recombination was observed in the limited progeny sample analyzed. Eight RFLPs cosegregated perfectly with alleles at the mating-type (mt) locus. More significantly, four RFLPs exhibited linkage to the regA locus, providing a potential starting place for a chromosome walk designed to clone the locus.
Human muscle carbonic anhydrase: gene structure and DNA methylation patterns in fetal and adult tissues.
Authors: Lloyd J , Brownson C , Tweedie S , Charlton J , Edwards Y H
Published: June 2007

We report the isolation and analysis of genomic clones comprising the entire gene coding for the human muscle carbonic anhydrase, CAIII. The gene spans 10.3 kb and has a seven-exon/six-intron structure. A noncanonical TATA box, a CCAAT motif, and two CCGCCC elements are present in the sequences upstream of exon 1. Although the expression of CAIII shows strict tissue specificity, the gene exhibits a number of features normally associated with housekeeping enzymes. For example, there is 48% homology with a 25-bp consensus sequence between the TATA box and the cap site and there is a CpG-rich island spanning a 469-bp sequence near to the origin of transcription. Methylation studies suggest that some CCGG sites clustered in the CpG-rich island are undermethylated in DNA from fetal and adult muscle and in other tissues irrespective of CAIII expression. In contrast, several nonclustered CCGG sites show a methylation pattern that correlates with gene expression. However DNA from differentiated type II adult muscle fibers is undermethylated at these sites even though CAIII is not expressed.