bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthesis of C
5
-dicarboxylic acids from C
2
-units involving crotonyl-CoA carboxylase/reductase: The ethylmalonyl-CoA pathway
Authors: Erb Tobias J. , Berg Ivan A. , Brecht Volker , Müller Michael , Fuchs Georg , Alber Birgit E.
Published: June 2007

Fifty years ago, Kornberg and Krebs established the glyoxylate cycle as the pathway for the synthesis of cell constituents from C
2
-units. However, since then, many bacteria have been described that do not contain isocitrate lyase, the key enzyme of this pathway. Here, a pathway termed the ethylmalonyl-CoA pathway operating in such organisms is described. Isotopically labeled acetate and bicarbonate were transformed to ethylmalonyl-CoA by cell extracts of acetate-grown, isocitrate lyase-negative
Rhodobacter sphaeroides
as determined by NMR spectroscopy. Crotonyl-CoA carboxylase/reductase, catalyzing crotonyl-CoA + CO
2
+ NADPH → ethylmalonyl-CoA
−
+ NADP
+
was identified as the key enzyme of the ethylmalonyl-CoA pathway. The reductive carboxylation of an enoyl-thioester is a unique biochemical reaction, unprecedented in biology. The enzyme from
R. sphaeroides
was heterologously produced in
Escherichia coli
and characterized. Crotonyl-CoA carboxylase/reductase (or its gene) can be used as a marker for the presence of the ethylmalonyl-CoA pathway, which functions not only in acetyl-CoA assimilation. In
Streptomyces
sp., it may also supply precursors (ethylmalonyl-CoA) for antibiotic biosynthesis. For methylotrophic bacteria such as
Methylobacterium extorquens
, extension of the serine cycle with reactions of the ethylmalonyl-CoA pathway leads to a simplified scheme for isocitrate lyase-independent C
1
assimilation.
Scm3, an essential
Saccharomyces cerevisiae
centromere protein required for G
2
/M progression and Cse4 localization
Authors: Stoler Sam , Rogers Kelly , Weitze Scott , Morey Lisa , Fitzgerald-Hayes Molly , Baker Richard E.
Published: June 2007

A universal mark of centromeric chromatin is its packaging by a variant of histone H3 known as centromeric H3 (CenH3). The mechanism by which CenH3s are incorporated specifically into centromere DNA or the specialized function they serve there is not known. In a genetic approach to identify factors involved in CenH3 deposition, we screened for dosage suppressors of a temperature-sensitive
cse4
allele in
Saccharomyces cerevisiae
(Cse4 is the
S. cerevisiae
CenH3). Independent screens yielded ORF YDL139C, which we named
SCM3
. Dosage suppression by
SCM3
was specific for alleles affecting the histone fold domain of Cse4. Copurification and two-hybrid studies showed that Scm3 and Cse4 interact
in vivo
, and chromatin immunoprecipitation revealed that Scm3, like Cse4, is found associated with centromere DNA. Scm3 contains two essential protein domains, a Leu-rich nuclear export signal and a heptad repeat domain that is widely conserved in fungi. A conditional
scm3
allele was generated to allow us to deplete Scm3. Upon Scm3 depletion, cells undergo a Mad2-dependent G
2
/M arrest, and centromere localization of Cse4 is perturbed. We suggest that
S. cerevisiae
Scm3 defines a previously undescribed family of fungal kinetochore proteins important for CenH3 localization.
Phenotypic characterization of human colorectal cancer stem cells
Authors: Dalerba Piero , Dylla Scott J. , Park In-Kyung , Liu Rui , Wang Xinhao , Cho Robert W. , Hoey Timothy , Gurney Austin , Huang Emina H. , Simeone Diane M. , Shelton Andrew A. , Parmiani Giorgio , Castelli Chiara , Clarke Michael F.
Published: June 2007

Recent observations indicate that, in several types of human cancer, only a phenotypic subset of cancer cells within each tumor is capable of initiating tumor growth. This functional subset of cancer cells is operationally defined as the “cancer stem cell” (CSC) subset. Here we developed a CSC model for the study of human colorectal cancer (CRC). Solid CRC tissues, either primary tissues collected from surgical specimens or xenografts established in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice, were disaggregated into single-cell suspensions and analyzed by flow cytometry. Surface markers that displayed intratumor heterogeneous expression among epithelial cancer cells were selected for cell sorting and tumorigenicity experiments. Individual phenotypic cancer cell subsets were purified, and their tumor-initiating properties were investigated by injection in NOD/SCID mice. Our observations indicate that, in six of six human CRC tested, the ability to engraft
in vivo
in immunodeficient mice was restricted to a minority subpopulation of epithelial cell adhesion molecule (EpCAM)
high
/CD44
+
epithelial cells. Tumors originated from EpCAM
high
/CD44
+
cells maintained a differentiated phenotype and reproduced the full morphologic and phenotypic heterogeneity of their parental lesions. Analysis of the surface molecule repertoire of EpCAM
high
/CD44
+
cells led to the identification of CD166 as an additional differentially expressed marker, useful for CSC isolation in three of three CRC tested. These results validate the stem cell working model in human CRC and provide a highly robust surface marker profile for CRC stem cell isolation.
Global distribution of negative cofactor 2 subunit-α on human promoters
Authors: Albert Thomas K. , Grote Korbinian , Boeing Stefan , Stelzer Gertraud , Schepers Aloys , Meisterernst Michael
Published: June 2007

Negative cofactor 2 (NC2) forms a stable complex with TATA-binding protein (TBP) on promoters
in vitro
. Its association with TBP prevents the binding of TFIIB and leads to inhibition of preinitiation complex formation. Here, we investigate the association of NC2 subunit-α with human RNA polymerase II promoter regions by using gene-specific ChIP and genome-wide promoter ChIPchip analyses. We find NC2α associated with a large number of human promoters, where it peaks close to the core regions. NC2 occupancy
in vivo
positively correlates with mRNA levels, which perhaps reflects its capacity to stabilize TBP on promoter regions. In single gene analyses, we confirm core promoter binding and in addition map the NC2 complex to enhancer proximal regions. High-occupancy histone genes display a stable NC2/TFIIB ratio during the cell cycle, which otherwise varies markedly from one gene to another. The latter is at least in part explained by an observed negative correlation of NC2 occupancy with the presence of the TFIIB recognition element in core promoter regions. Our data establish the genome-wide basis for general and gene-specific functions of NC2 in mammalian cells.
Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks
Authors: Bradford Justin A. , Dill Ken A.
Published: June 2007

We develop a computer model for how two different chemical catalysts in solution, A and B, could be driven to form AB complexes, based on the concentration gradients of a substrate or product that they share in common. If A's product is B's substrate, B will be attracted to A, mediated by a common resource that is not otherwise plentiful in the environment. By this simple physicochemical mechanism, chemical reactions could spontaneously associate to become chained together in solution. According to the model, such catalyst self-association processes may resemble other processes of “stochastic innovation,” such as Darwinian evolution in biology, that involve a search among options, a selection among those options, and then a lock-in of that selection. Like Darwinian processes, this simple chemical process exhibits cooperation, competition, innovation, and a preference for consistency. This model may be useful for understanding organizational processes in prebiotic chemistry and for developing new kinds of self-organization in chemically reacting systems.
Madden–Julian Oscillation analog and intraseasonal variability in a multicloud model above the equator
Authors: Majda Andrew J. , Stechmann Samuel N. , Khouider Boualem
Published: June 2007

The Madden–Julian Oscillation (MJO) is the dominant component of tropical intraseasonal variability, and a theory explaining its structure and successful numerical simulation remains a major challenge. A successful model for the MJO should have a propagation speed of 4–7 m/s predicted by theory; a wavenumber-2 or -3 structure for the planetary-scale, low-frequency envelope with distinct active and inactive phases of deep convection; an intermittent turbulent chaotic multiscale structure within the planetary envelope involving embedded westward- and eastward-propagating deep convection events; and qualitative features of the low-frequency envelope from the observational record regarding, e.g., its zonal flow structure and heating. Here, such an MJO analog is produced by using the recent multicloud model of Khouider and Majda in an appropriate intraseasonal parameter regime for flows above the equator so that rotation is ignored. Key features of the multicloud model are (
i
) systematic low-level moisture convergence with retained conservation of vertically integrated moist static energy, and (
ii
) the use of three cumulus cloud types (congestus, stratiform, and deep convective) together with their differing vertical heating structures. Besides all of the above structure in the MJO analog waves, there are accurate predictions of the phase speed from linear theory and transitions from weak, regular MJO analog waves to strong, multiscale MJO analog waves as climatological parameters vary. With all of this structure in a simplified context, these models should be useful for MJO predictability studies in a fashion akin to the Lorenz 96 model for the midlatitude atmosphere.
On the ability of the Viking gas chromatograph–mass spectrometer to detect organic matter
Authors: Biemann Klaus
Published: June 2007

A recent paper by Navarro-Gonzalez
et al.
[Navarro-Gonzalez R, Navarro KF, de la Rosa J, Iniguez E, Molina P, Miranda LD, Morales P, Cienfuegos E, Coll P, Raulin F,
et al.
(2006)
Proc Natl Acad Sci USA
103:16089–16094] claims to show that the Viking GCMS (gas chromatograph–mass spectrometer) experiment, which carried out a search for organic matter at the surface of Mars in 1976, “may have been blind to low levels of organics.” To rebut this assertion, the Viking experiment, test data, and results on Mars are reviewed, and the fallacies in the design, execution, and interpretation of the new experiments presented by Navarro-Gonzalez
et al.
are critically examined.
Monotherapy with a tumor-targeting mutant of
Salmonella typhimurium
cures orthotopic metastatic mouse models of human prostate cancer
Authors: Zhao Ming , Geller Jack , Ma Huaiyu , Yang Meng , Penman Sheldon , Hoffman Robert M.
Published: June 2007

Bacterial infection occasionally has a marked therapeutic effect on malignancies, as noted as early as the 19th century. Recently, there have been attempts to develop cancer treatment by using tumor-targeting bacteria. These treatments were developed to deliver therapeutic molecules specifically to tumors. Researchers used anaerobic microorganisms that preferentially grew in necrotic tumor areas. However, the resulting tumor killing was, at best, limited. We have developed a far more effective bacterial cancer therapy by targeting viable tumor tissue by using
Salmonella typhimurium
leu-arg auxotrophs. Although these bacteria grow in viable as well as necrotic areas of tumors, the nutritional auxo trophy severely restricts growth in normal tissue. In the current study, we measured the antitumor efficacy of the
S. typhimurium
A1-R mutant, which is auxotrophic for leu-arg and has increased antitumor virulence selected by tumor passage. A1-R was used to treat metastatic PC-3 human prostate tumors that had been orthotopically implanted in nude mice. GFP was used to image tumor and metastatic growth. Of the 10 mice with the PC-3 tumors that were injected weekly with
S. typhimurium
A1-R, 7 were alive and well at the time the last untreated mouse died. Four A1-R-treated mice remain alive and well 6 months after implantation. Ten additional nontumor-bearing mice were injected weekly to determine the toxicity of
S. typhimurium
A1-R. No toxic effects were observed. The approach described here, where bacterial monotherapy effectively treats metastatic prostate tumors, is a significant improvement over previous bacterial tumor-therapy strategies that require combination with toxic chemotherapy.
Raising plasma fatty acid concentration induces increased biogenesis of mitochondria in skeletal muscle
Authors: Garcia-Roves Pablo , Huss Janice M. , Han Dong-Ho , Hancock Chad R. , Iglesias-Gutierrez Eduardo , Chen May , Holloszy John O.
Published: June 2007

A number of studies have reported that a high-fat diet induces increases in mitochondrial fatty acid oxidation enzymes in muscle. In contrast, in two recent studies raising plasma free fatty acids (FFA) resulted in a decrease in mitochondria. In this work, we reevaluated the effects of raising FFA on muscle mitochondrial biogenesis and capacity for fat oxidation. Rats were fed a high-fat diet and given daily injections of heparin to raise FFA. This treatment induced an increase in mitochondrial biogenesis in muscle, as evidenced by increases in mitochondrial enzymes of the fatty acid oxidation pathway, citrate cycle, and respiratory chain, with an increase in the capacity to oxidize fat, as well as an increase in mitochondrial DNA copy number. Raising FFA also resulted in an increase in binding of peroxisome proliferator-activated receptor (PPAR) δ to the PPAR response element on the carnitine palmitoyltransferase 1 promoter. We interpret our results as evidence that raising FFA induces an increase in mitochondrial biogenesis in muscle by activating PPARδ.
CCR4-dependent regulatory T cell function in inflammatory bowel disease
Authors: Yuan Qian , Bromley Shannon K. , Means Terry K. , Jones Krister J. , Hayashi Fumitaka , Bhan Atul K. , Luster Andrew D.
Published: June 2007

Inflammatory bowel disease (IBD) is an idiopathic inflammatory disease of the intestine. CD4+ T lymphocytes play an important role in both initiating and regulating intestinal inflammatory immune responses. CD4+CD25+CD45RBlow regulatory T (T reg) cells are capable of preventing the development of colitis in a mouse model of IBD. The precise mechanism of T reg cell–mediated prevention of colitis in this model is unclear, and the role of chemokine receptors in the trafficking and function of T reg cells in this model has not been determined. We examined the role of the chemokine receptor CCR4 in in vivo trafficking and suppressive function of T reg cells in a mouse adoptive transfer model of IBD. CCR4-deficient T reg cells failed to accumulate in the mesenteric lymph nodes (MLNs) at early time points (2–5 d) after adoptive transfer, resulting in a failure to suppress the generation of pathogenic T cells and the development of colitis. Moreover, although CCR4-deficent T cells had equivalent in vitro suppressive activity and accumulated in MLNs at later time points (42–56 d), they were unable to suppress colitis. Our study demonstrates that CCR4 plays an important role in T reg cell trafficking in LNs and that this is critical for T reg cell suppressive function in vivo.
MyD88-dependent expansion of an immature GR-1+CD11b+ population induces T cell suppression and Th2 polarization in sepsis
Authors: Delano Matthew J. , Scumpia Philip O. , Weinstein Jason S. , Coco Dominique , Nagaraj Srinivas , Kelly-Scumpia Kindra M. , O'Malley Kerri A. , Wynn James L. , Antonenko Svetlana , Al-Quran Samer Z. , Swan Ryan , Chung Chun-Shiang , Atkinson Mark A. , Ramphal Reuben , Gabrilovich Dmitry I. , Reeves Wesley H. , Ayala Alfred , Phillips Joseph , LaFace Drake , Heyworth Paul G. , Clare-Salzler Michael , Moldawer Lyle L.
Published: June 2007

Polymicrobial sepsis alters the adaptive immune response and induces T cell suppression and Th2 immune polarization. We identify a GR-1+CD11b+ population whose numbers dramatically increase and remain elevated in the spleen, lymph nodes, and bone marrow during polymicrobial sepsis. Phenotypically, these cells are heterogeneous, immature, predominantly myeloid progenitors that express interleukin 10 and several other cytokines and chemokines. Splenic GR-1+ cells effectively suppress antigen-specific CD8+ T cell interferon (IFN) γ production but only modestly suppress antigen-specific and nonspecific CD4+ T cell proliferation. GR-1+ cell depletion in vivo prevents both the sepsis-induced augmentation of Th2 cell–dependent and depression of Th1 cell–dependent antibody production. Signaling through MyD88, but not Toll-like receptor 4, TIR domain–containing adaptor-inducing IFN-β, or the IFN-α/β receptor, is required for complete GR-1+CD11b+ expansion. GR-1+CD11b+ cells contribute to sepsis-induced T cell suppression and preferential Th2 polarization.
The uniquely human capacity to throw evolved from a non-throwing primate: an evolutionary dissociation between action and perception
Authors: Wood Justin N , Glynn David D , Hauser Marc D
Published: June 2007

Humans are uniquely endowed with the ability to engage in accurate, high-momentum throwing. Underlying this ability is a unique morphological adaptation that enables the characteristic rotation of the arm and pelvis. What is unknown is whether the psychological mechanisms that accompany the act of throwing are also uniquely human. Here we explore this problem by asking whether free-ranging rhesus monkeys (
Macaca mulatta
), which lack both the morphological and neural structures to throw, nonetheless recognize the functional properties of throwing. Rhesus not only understand that human throwing represents a threat, but that some aspects of a throwing event are more relevant than others; specifically, rhesus are sensitive to the kinematics, direction and speed of the rotating arm, the direction of the thrower's eye gaze and the object thrown. These results suggest that the capacity to throw did not coevolve with psychological mechanisms that accompany throwing; rather, this capacity may have built upon pre-existing perceptual processes. These results are consistent with a growing body of work showing that non-human animals often exhibit perceptual competencies that do not show up in their motor responses, suggesting evolutionary dissociations between the systems of perception that provide understanding of the world and those that mediate action on the world.
Female red deer prefer the roars of larger males
Authors: Charlton Benjamin D , Reby David , McComb Karen
Published: June 2007

Surprisingly little is known about the role of acoustic cues in mammal female mate choice. Here, we examine the response of female red deer (Cervus elaphus) to male roars in which an acoustic cue to body size, the formants, has been re-scaled to simulate different size callers. Our results show that oestrous red deer hinds prefer roars simulating larger callers and constitute the first evidence that female mammals use an acoustic cue to body size in a mate choice context. We go on to suggest that sexual selection through female mating preferences may have provided an additional selection pressure along with male–male competition for broadcasting size-related information in red deer and other mammals.
Hands-free circular motions of a benchmark bicycle
Authors: Basu-Mandal Pradipta , Chatterjee Anindya , Papadopoulos J.M
Published: June 2007

We write nonlinear equations of motion for an idealized benchmark bicycle in two different ways and verify their validity. We then present a complete description of hands-free circular motions. Three distinct families exist. (i) A handlebar-forward family, starting from capsize bifurcation off straight-line motion and ending in unstable static equilibrium, with the frame perfectly upright and the front wheel almost perpendicular. (ii) A handlebar-reversed family, starting again from capsize bifurcation but ending with the front wheel again steered straight, the bicycle spinning infinitely fast in small circles while lying flat in the ground plane. (iii) Lastly, a family joining a similar flat spinning motion (with handlebar forward), to a handlebar-reversed limit, circling in dynamic balance at infinite speed, with the frame near upright and the front wheel almost perpendicular; the transition between handlebar forward and reversed is through moderate-speed circular pivoting, with the rear wheel not rotating and the bicycle virtually upright. Small sections of two families are stable.
Boundary tracing and boundary value problems: I. Theory
Authors: Anderson Michael L , Bassom Andrew P , Fowkes Neville
Published: June 2007

Given an exact solution of a partial differential equation in two dimensions, which satisfies suitable conditions on the boundary of the domain of interest, it is possible to deform the boundary curve so that the conditions remain fulfilled. The curves obtained in this manner can be patched together in various ways to generate a remarkably broad range of domains for which the boundary constraints remain satisfied by the initial solution. This process is referred to as boundary tracing and works for both linear and nonlinear problems. This article presents a general theoretical framework for implementing the technique for two-dimensional, second-order, partial differential equations with a general flux condition imposed around the boundary. A couple of simple examples are presented that serve to demonstrate the analytical tools in action. Applications of more intrinsic interest are discussed in the following paper.
Colour preferences and colour vision in poultry chicks
Authors: Ham A.D , Osorio D
Published: June 2007

The dramatic colours of biological communication signals raise questions about how animals perceive suprathreshold colour differences, and there are long-standing questions about colour preferences and colour categorization by non-human species. This study investigates preferences of foraging poultry chicks (Gallus gallus) as they peck at coloured objects. Work on colour recognition often deals with responses to monochromatic lights and how animals divide the spectrum. We used complementary colours, where the intermediate is grey, and related the chicks' choices to three models of the factors that may affect the attractiveness. Two models assume that attractiveness is determined by a metric based on the colour discrimination threshold either (i) by chromatic contrast against the background or (ii) relative to an internal standard. An alternative third model is that categorization is important. We tested newly hatched and 9-day-old chicks with four pairs of (avian) complementary colours, which were orange, blue, red and green for humans. Chromatic contrast was more relevant to newly hatched chicks than to 9-day-old birds, but in neither case could contrast alone account for preferences; especially for orange over blue. For older chicks, there is evidence for categorization of complementary colours, with a boundary at grey.
Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium
Authors: Lechner Ute , Brodkorb Danny , Geyer Roland , Hause Gerd , Härtig Claus , Auling Georg , Fayolle-Guichard Françoise , Piveteau Pascal , Müller Roland H. , Rohwerder Thore
Published: June 2007

Strains L10T, L108 and CIP I-2052 were originally obtained from methyltert-butyl ether (MTBE)-contaminated groundwater and from a wastewater treatment plant, respectively. All share the ability to grow ontert-butanol, an intermediate of MTBE degradation. Cells are strictly aerobic, motile by a polar flagellum and exhibit strong pili formation. Polyβ-hydroxybutyrate (PHB) granules are formed. The DNA G+C content is 69–70.5 mol% and the main ubiquinone is Q-8. The major cellular fatty acids are 16 : 1cis-9 and 16 : 0 and the only hydroxy fatty acid is 10 : 0 3-OH. The major phospholipids are phosphatidylethanolamine (PE) 16 : 1/16 : 1 and phosphatidylglycerol 16 : 0/16 : 1. A significant amount of PE 17 : 0/16 : 1 is present. The 16S rRNA gene sequences of these strains are almost identical and form a separate line of descent in theRubrivivax–Roseateles–Leptothrix–Ideonella–Aquabacteriumbranch of theBetaproteobacteriawith 97 % similarity to 16S rRNA genes of the type strains ofRubrivivax gelatinosus,Leptothrix mobilisandIdeonella dechloratans. However, physiological properties, DNA–DNA relatedness values and the phospholipid and cellular fatty acid profiles distinguish the novel isolates from the three closely related genera. Therefore, it is concluded that strains L10T, L108 and CIP I-2052 represent a new genus and novel species for which the nameAquincola tertiaricarbonisgen. nov., sp. nov., is proposed. The type strain is strain L10T(=DSM 18512T=CIP 109243T).
Proposal of six species of moderately thermophilic, acidophilic, endospore-forming bacteria: Alicyclobacillus contaminans sp. nov., Alicyclobacillus fastidiosus sp. nov., Alicyclobacillus kakegawensis sp. nov., Alicyclobacillus macrosporangiidus sp. nov., Alicyclobacillus sacchari sp. nov. and Alicyclobacillus shizuokensis sp. nov.
Authors: Goto Keiichi , Mochida Kaoru , Kato Yuko , Asahara Mika , Fujita Rieko , An Sun-Young , Kasai Hiroaki , Yokota Akira
Published: June 2007

Moderately thermophilic, acidophilic, spore-forming bacteria (146 strains) were isolated from various beverages and environments. Based on the results of sequence analysis of the hypervariable region of the 16S rRNA gene, eight of the strains represent novel species of the genusAlicyclobacillus. These strains were designated 3-A191T, 4-A336T, 5-A83JT, 5-A167N, 5-A239-2O-AT, E-8, RB718Tand S-TABT. Phylogenetic analyses of 16S rRNA and DNA gyrase B subunit (gyrB) nucleotide sequences confirmed that the eight strains belonged to theAlicyclobacillusclade. Cells of the eight strains were Gram-positive or Gram-variable, strictly aerobic and rod-shaped. The strains grew well under acidic and moderately thermal conditions, produced acid from various sugars, contained menaquinone 7 as the major isoprenoid quinone and did not produce guaiacol.ω-Alicyclic fatty acids were the predominant lipid component of strains 4-A336T, 5-A83JT, 5-A167N, RB718Tand S-TABT. Noω-alicyclic fatty acids were detected in strains 3-A191T, 5-A239-2O-ATor E-8, but iso- and anteiso-branched fatty acids and small amounts of straight-chain saturated fatty acids were detected instead. According to the DNA–DNA hybridization data and distinct morphological, physiological, chemotaxonomical and genetic traits, the eight strains represent six novel species within the genusAlicyclobacillus, for which the following names are proposed:Alicyclobacillus contaminanssp. nov. (type strain 3-A191T=DSM 17975T=IAM 15224T),Alicyclobacillus fastidiosussp. nov. (type strain S-TABT=DSM 17978T=IAM 15229T),Alicyclobacillus kakegawensissp. nov. (type strain 5-A83JT=DSM 17979T=IAM 15227T),Alicyclobacillus macrosporangiidussp. nov. (type strain 5-A239-2O-AT=DSM 17980T=IAM 15370T),Alicyclobacillus saccharisp. nov. (type strain RB718T=DSM 17974T=IAM 15230T) andAlicyclobacillus shizuokensissp. nov. (type strain 4-A336T=DSM 17981T=IAM 15226T).
Corynebacterium ureicelerivorans sp. nov., a lipophilic bacterium isolated from blood culture
Authors: Yassin A. F.
Published: June 2007

A lipophilic coryneform bacterium isolated from a blood culture from a patient with signs of septicaemia was characterized by means of phenotypic and molecular taxonomic methods. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and short-chain mycolic acids, which are consistent with the genusCorynebacterium. The isolate was characterized biochemically by the very rapid (approx. 60 s) positive result that was obtained in a urease test in the API Coryne system. Comparative 16S rRNA gene sequencing demonstrated that the isolate belonged phylogenetically to the genusCorynebacterium. The values for sequence divergence (⩾1.4 %) with respect to knownCorynebacteriumspecies, together with phenotypic differences, show that the unidentified bacterium represents a novel member of this genus. On the basis of both the phenotypic and phylogenetic data, this isolate should be classified within a novel species of the genusCorynebacterium, for which the nameCorynebacterium ureicelerivoranssp. nov. is proposed. The type strain is IMMIB RIV-2301T(=DSM 45051T=CCUG 53377T).
Psychromonas hadalis sp. nov., a novel piezophilic bacterium isolated from the bottom of the Japan Trench
Authors: Nogi Yuichi , Hosoya Shoichi , Kato Chiaki , Horikoshi Koki
Published: June 2007

An obligately piezophilic bacterium was isolated from sediment collected from the bottom of the Japan Trench at a depth of 7542 m. The isolated strain, designated K41GT, was closely affiliated with members of the genusPsychromonason the basis of 16S rRNA gene sequence analysis. Levels of DNA–DNA relatedness between strain K41GTandPsychromonasreference strains were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of strain K41GTwere 6 °C and 60 MPa, respectively. The DNA G+C content was 39.1 mol%. Whole-cell fatty acids consisted of significant amounts of unsaturated fatty acids C16 : 1(37 %) and C14 : 1(17 %), saturated fatty acid C16 : 0(31 %) and polyunsaturated fatty acid C22 : 6(8 %). Based on the taxonomic differences observed, strain K41GTis considered to represent a novel obligately piezophilicPsychromonasspecies. The namePsychromonas hadalis(type strain, K41GT=JCM 11830T=ATCC BAA-638T) is proposed. This is the second species of obligately piezophilic bacteria to be proposed in the genusPsychromonas.
Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium
Authors: Wang Ya-Nan , Cai Hua , Chi Chang-Qiao , Lu An-Huai , Lin Xian-Gui , Jiang Zheng-Feng , Wu Xiao-Lei
Published: June 2007

A moderately halophilic bacterium, designated strain SL014B-85T, was isolated from a crude-oil-contaminated saline soil from Shengli oilfield, Shandong Province, China. Cells were Gram-negative, aerobic, short rods with lateral flagella. Growth occurred at NaCl concentrations of 0–15 % (optimum 5–15 %), at 10–42 °C (optimum 30 °C) and at pH 8.0–9.0 (optimum pH 8.5). The only respiratory quinone was Q9, and the main cellular fatty acids were C18 : 1
ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The G+C content of the DNA was 66.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SL014B-85T belonged to the genus Halomonas in the Gammaproteobacteria, with highest sequence similarity of 98.1 and 97.8 % to Halomonas alimentaria DSM 15356T and Halomonas ventosae DSM 15911T, respectively. DNA–DNA relatedness values were below 40 % with members of closely related Halomonas species. Results of phenotypic, biochemical and phylogenetic analyses revealed that strain SL014B-85T could be classified as representing a novel species of the genus Halomonas, for which the name Halomonas shengliensis sp. nov. is proposed. The type strain is SL014B-85T (=CGMCC 1.6444T=LMG 23897T).
Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan
Authors: Hosoya Shoichi , Yokota Akira
Published: June 2007

Two strains of gliding, agarolytic bacteria, strains YS10T and YML5, were isolated from coastal seawater off Kamogawa, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolates represent a separate lineage within the genus Flammeovirga. DNA–DNA hybridization values between these isolates and the type strains of species of the genus Flammeovirga were significantly lower than those accepted as threshold values for the phylogenetic definition of a species. Furthermore, some of the phenotypic characteristics indicate that the isolates differ from other Flammeovirga species. Based on these differences, it is suggested that the isolates represent a novel species, for which the name Flammeovirga kamogawensis sp. nov. is proposed. The type strain is YS10T (=IAM 15451T=NCIMB 14281T).
Differential accumulation of U1 and U4 small nuclear RNAs during Xenopus development.
Authors: Lund E , Dahlberg J E
Published: June 2007

We showed previously that those U1 small nuclear RNA (snRNA) genes of Xenopus laevis which are transcribed very actively in early embryos are quiescent in mature (stage VI) oocytes (Forbes et al. 1984). Although that study demonstrated that differential control of snRNA genes occurred, it did not describe snRNA accumulation during development. Using high-resolution polyacrylamide gels in combination with Northern blot hybridization and RNA sequence analyses, we show here that Xenopus has at least three classes of U1 and U4 snRNAs that are distinguishable by their differential expression of oocytes, embryos, tadpoles, and frogs. Adult snRNAs appear to be synthesized constitutively throughout Xenopus development and comprise the major species in tissues from large tadpoles and frogs. Embryonic snRNAs are the principal species accumulating during the two periods of rapid snRNA synthesis, i.e., in previtellogenic oocytes and early embryos. Tadpole RNAs are minor species that are most prominent in young feeding tadpoles. Transcription of both embryonic and adult snRNA genes is activated at the midblastula transition (MBT), but expression of the embryonic genes is switched off selectively within a few days after MBT. Although the precise timing of this inactivation differs significantly for U1 and U4 genes, the overall pattern of differential expression is common to U1 and U2 snRNA genes. Because of sequence differences between the snRNAs accumulating at various stages, the resulting populations of snRNPs could have different splice-site specificities leading to altered patterns of pre-mRNA splicing during development.
The transcription of Xenopus laevis embryonic U1 snRNA genes changes when oocytes mature into eggs.
Authors: Lund E , Bostock C J , Dahlberg J E
Published: June 2007

X. laevis stage VI oocytes respond differently from unfertilized eggs when injected with the genes for X. laevis embryonic U1 RNAs, xU1b1, and xU1b2. Upon maturation of oocytes into eggs, the efficiency of transcription decreases greatly and the ratio of xU1b1 to xU1b2 RNA transcription changes. Moreover, DNA replication is now required for transcription. Because of differences in the 5'-flanking regions of the two xU1b genes, xU1b2 RNA transcription predominates after injection into oocytes; in contrast, xU1b1 RNA transcription predominates after injection into unfertilized eggs. Our results also indicate that in oocytes a factor that interacts with sequences close to the coding region is limiting, whereas in eggs a factor that recognizes far-upstream sequences required for enhancer activity is limiting. Qualitatively, expression of the embryonic xU1b genes injected into eggs closely resembles that of the endogenous genes during early embryogenesis.
The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity.
Authors: Schirm S , Jiricny J , Schaffner W
Published: June 2007

The SV40 enhancer is known to be active in a wide variety of tissues and species. It contains a number of sequence motifs that can be bound by protein factors and whose integrity is essential for full enhancer activity. We have individually analyzed three synthetic oligonucleotides derived from sequences present within the SV40 enhancer: two oligonucleotides contain variants of the enhancer "core" sequence (designated corePVUII and coreC) and the third represents a region containing a decanucleotide homology to the immunoglobulin promoters/enhancers (designated SPHI). The oligonucleotides were multimerized and linked to a beta-globin test gene. Transcripts of the test gene were analyzed following transient expression in 10 cell lines representing a broad spectrum of tissues. We show that each of the three short segments can individually act as an enhancer when present in multiple copies. None of these enhancers is ubiquitously active; however, each shows activity in a distinctive subpopulation of cell lines. This cell type specificity is most remarkable in the case of the two oligonucleotide segments containing the core sequences. One of these is primarily active in CV-1 cells, whereas the other exhibits a cell type specificity identical to that of the entire enhancer, possibly identifying it as the most important sequence element within the native SV40 enhancer. Our data suggest that a particular cell type specificity is typical for individual enhancer segments, and that enhancers of differing specificity can be assembled from the individual sequence motifs by combining them in different patterns.
Thyroid hormone induction of keratin genes: a two-step activation of gene expression during development.
Authors: Mathisen P M , Miller L
Published: June 2007

To determine the mechanism of action of the thyroid hormone triiodothyronine (T3) during metamorphosis of the amphibian epidermis, we have investigated the developmental activation of the 63-kD keratin genes in the frog Xenopus laevis. These genes code for three closely related keratins that first appear in the larval epidermis and accumulate during metamorphosis to become the most abundant proteins in the adult epidermis. We report here that the 63-kD keratins and their mRNAs first appear at stages 48-52. The level of 63-kD keratin gene expression remains relatively low until stage 56 and then increases dramatically. Quantitative analysis of the concentration of 63-kD keratin mRNA demonstrates low levels until stage 55/56, followed by an increase greater than 300-fold from stage 55/56 to the adult. Each adult cell contains approximately 55,000 molecules of the 63-kD keratin mRNAs. T3 is not required for the initial activation of the 63-kD keratin genes, but high-level expression is absolutely dependent on T3. High-level expression is prevented by propylthiouracil, which inhibits thyroid hormone synthesis and can be induced precociously both in vivo and in vitro with exogenous T3 as early as stage 48, but not prior to that time. Thus, the full activation of the 63-kD keratin genes during development requires two regulatory steps, one independent and one dependent on T3.
Stage-specific selection of alternative transcriptional initiation sites from the 5C actin gene of Drosophila melanogaster.
Authors: Vigoreaux J O , Tobin S L
Published: June 2007

The transcription unit of the 5C actin gene exhibits a complex organization that is unique among the six actin genes of Drosophila melanogaster. Three different mRNA size classes showing distinct patterns of accumulation throughout development are detected on Northern blots. We have determined the structure of the various 5C actin transcripts by exon mapping using strand-specific RNA probes, primer extension analysis, and DNA sequences analysis of both cDNA and genomic clones. All the transcripts share a single protein-coding nucleotide sequence but are heterogeneous in the 5' and 3' untranslated regions. The 5' untranslated region of each transcript consists of either one of two small exons (exon 1 and exon 2) which are alternatively spliced to a single acceptor site 8 bp upstream from the translation initiation codon in exon 3. Results from primer extension analysis suggest that transcription can initiate from either exon 1 or exon 2, and also from a third site within exon 2. We detect an increase in the relative abundance of exon 1-containing transcripts at larval and pupal stages, as well as a change in the proportion of transcripts that initiate at either of the two exon 2 sites. Five polyadenylation sites have been found within three termination/processing regions that define the three size classes of polyadenylated transcripts. The results of our experiments indicate the existence in vivo of all possible combinations of 5' exon with 3' polyadenylation site. However, particular combinations of 5' initiation site and 3' polyadenylation site are preferred at certain developmental stages.
Meiotic maturation of mouse oocytes triggers the translation and polyadenylation of dormant tissue-type plasminogen activator mRNA.
Authors: Huarte J , Belin D , Vassalli A , Strickland S , Vassalli J D
Published: June 2007

The serine protease tissue-type plasminogen activator (t-PA) is synthesized by murine oocytes undergoing meiotic maturation, but not by arrested primary oocytes. Dormant, stable t-PA mRNA accumulates during oocyte growth, so that fully grown, arrested primary oocytes contain in their cytoplasm approximately 10,000 copies of this molecule. Translation of t-PA mRNA is triggered upon resumption of meiosis and is accompanied by a progressive and concerted increase in its size. This structural change can be accounted for by increased polyadenylation at the 3' end of the molecule. Following its translation, t-PA mRNA is degraded; it is no longer detectable in fertilized eggs. The identification of a dormant mRNA in murine oocytes and the demonstration that its translational activation is accompanied by elongation of its poly(A) tail may provide insights into the control of gene expression during meiotic maturation and early mammalian development.
Structure of two genes at the gooseberry locus related to the paired gene and their spatial expression during Drosophila embryogenesis.
Authors: Baumgartner S , Bopp D , Burri M , Noll M
Published: June 2007

The gooseberry (gsb) locus contains two closely linked genes, BSH9 and BSH4, which are structurally related to each other and to the paired (prd) gene. Sequence analysis of genomic DNA and cDNA shows that BSH9 and BSH4 can encode proteins of 427 and 452 amino acids, respectively. The structural homology between these two putative proteins and the prd protein consists essentially of two domains forming most of the amino-terminal halves of the proteins: the prd domain of 128 amino acids and a prd-type homeo domain of 60 amino acids, which is extended by 18 amino acids at its amino-terminal end. The temporal profiles of BSH9 and BSH4 transcripts, as characterized by Northern analysis, show a peak shortly after the peak of prd transcripts. The spatial distributions of BSH9 and BSH4 transcripts have been analyzed by in situ hybridization to whole-mount and sectioned embryos. BSH9 transcripts appear in the posterior ventrolateral part of each primordial segment throughout the embryo, including head and tail segments. Transcripts are initially restricted to the ectoderm, in which they arise as two spatially shifted and temporally delayed waves exhibiting double-segment periodicity and anteroposterior polarity. During germ-band extension, BSH9 is induced in the mesoderm in register with the ectoderm and neurectoderm and in the tail segments A9-A11. In contrast, BSH4 transcripts appear with a single-segment repeat, first, in the neurectoderm during germ-band extension and, later, in single neurons during neuronal differentiation. BSH9, BSH4, and prd are activated in cells that are in register along the anteroposterior axis of the embryo in the posterior parts of primordial segments comprising the posterior compartments of engrailed expression.
The human myc gene family: structure and activity of L-myc and an L-myc pseudogene.
Authors: DePinho R A , Hatton K S , Tesfaye A , Yancopoulos G D , Alt F W
Published: June 2007

We have determined the nucleotide sequence and transforming activity of the human L-myc gene and a processed L-myc pseudogene (L-myc psi). We demonstrate by cotransformation assays that a 10.6-kb EcoRI fragment derived from a human placental library contains a complete and functional L-myc gene including transcriptional regulatory sequences sufficient for expression in rat embryo fibroblasts. Organization of the L-myc gene was determined by comparing its sequence to those of the L-myc psi gene and an L-myc cDNA clone derived from a human small cell lung carcinoma. Our results show that L-myc has a three-exon organization similar to that of the c-myc and N-myc genes. The putative L-myc gene product consists of 364 amino acids and contains five of the seven homology regions highly conserved between c-myc and N-myc. These conserved regions are located along the entire length of the putative L-myc protein and are interspersed among nonconserved regions. While the putative L-myc gene product is of a smaller size when compared to the c- and N-myc proteins, the relative positions of certain conserved residues occur in corresponding locations along the peptide backbone of the three proteins. In addition, comparison of the human and murine L-myc gene sequences indicate that the relatively large 5' and 3' untranslated regions are evolutionarily conserved, but that these sequences are totally divergent between the L-, c-, and N-myc genes. Finally, we demonstrate that, like the N- and c-myc genes, the L-myc gene can cooperate with a mutant Ha-ras gene to cause malignant transformation of rat embryo fibroblasts in culture. Our analyses clearly prove that L-myc represents a functional member of the myc oncogene family and further delineate structural features that may be important for the common and divergent functions of the members of this gene family.
Transabdominal, a dominant mutant of the Bithorax Complex, produces a sexually dimorphic segmental transformation in Drosophila.
Authors: Celniker S E , Lewis E B
Published: June 2007

Transabdominal (Tab), a dominant mutation in the Bithorax Complex (BX-C) of Drosophila, creates a sexually dimorphic pattern of segmental transformation that has complete penetrance and expressivity. Specific regions within the notum of the second thoracic segment (T2) are transformed into abdominal-like cuticle; thus, the Tab/ + notum has sets of short stripes that are black in males and only bordered with black in females. Also, Tab/ + abdominal tergites, A1-A6, inclusive, have small patches of A7-like tergite cuticle. Tab is inseparable from an 89E/90D inversion, whose DNA breakpoint in 89E is at +188 kb in the infra-abdominal-8 (iab-8) region of the BX-C. When probed with a pupal cDNA from the iab-7 region, labeling above background was not detected in wild-type wing discs but was detected in, and confined to, the notal region of Tab/ + wing discs. The Tab/ + phenotype is assumed to result from cis-overexpression of iab-7 in localized regions of segments T2-A6, inclusive.
Transcription antitermination by phage lambda gene Q protein requires a DNA segment spanning the RNA start site.
Authors: Yang X J , Hart C M , Grayhack E J , Roberts J W
Published: June 2007

The gene Q protein of phage lambda is a transcription antiterminator that modifies RNA polymerase near the phage late gene promoter and thereby causes antitermination at distant sites. To define the site of action of Q protein, we have reconstructed the regulatory system on plasmids that allow the intracellular concentration of Q protein to be regulated, and that allow the effect of Q protein on transcription from variant promoter segments to be measured in vivo and in vitro. We show that DNA sequences essential for Q protein-mediated antitermination span the RNA start site, but do not extend beyond nucleotide 18 of the late RNA coding region. We also show that the modification that permits antitermination persists while RNA polymerase passes at least two terminators in vivo and in vitro.