bluuebunny/crossref_metadata_2025 huggingface dataset:
Actor's and observer's primary motor cortices stabilize similarly after seen or heard motor actions
Authors: Caetano Gina , Jousmäki Veikko , Hari Riitta
Published: May 2007

We quantified rhythmic brain activity, recorded with whole-scalp magnetoencephalography (MEG), of 13 healthy subjects who were performing, seeing, or hearing the tapping of a drum membrane with the right index finger. In the actor's primary motor (M1) cortex, the level of the ≈20-Hz brain rhythms started to decrease, as a sign of M1 activation, ≈2 s before the action and then increased, with a clear rebound ≈0.6 s after the tapping, as a sign of M1 stabilization. A very similar time course occurred in the M1 cortex of the observer: the activation, although less vigorous than in the actor, started ≈0.8 s before the action and was followed by a rebound. When the subject just heard the tapping sound, no preaction activation was visible, but a rebound followed the sound. The ≈10-Hz somatosensory rhythm, which also started to decrease before own and viewed actions, returned to the baseline level ≈0.6 s later after own actions than observed actions. This delay likely reflects proprioceptive input to the cortex, available only during own actions, and therefore could be related to the brain signature of the sense of agency. The strikingly similar motor cortex reactivity during the first and third person actions expands previous data on brain mechanisms of intersubjective understanding. Besides motor cortex activation before own and observed (predicted) actions, the M1 cortex of both the viewer and the listener stabilized in a very similar manner after brisk motor actions.
Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends
Authors: Tsai Chun J. , Kim Sunny A. , Chu Gilbert
Published: May 2007

Nonhomologous end-joining (NHEJ) repairs DNA double-strand breaks created by ionizing radiation or V(D)J recombination of the immunoglobulin genes. The breaks often leave mismatched or nonligatable ends, and NHEJ must repair the breaks with high efficiency and minimal nucleotide loss. Here, the NHEJ proteins Ku, DNA-dependent protein kinase catalytic subunit, XRCC4/Ligase IV, and Cernunnos/XRCC4-like factor joined mismatched and noncohesive DNA ends in the absence of processing factors. Depending on the mismatch, Cernunnos stimulated joining 8- to 150-fold. For substrates with a blunt end and a 3′ overhanging end, Ku, XRCC4/Ligase IV, and Cernunnos ligated the 3′ overhanging hydroxyl group to the 5′ phosphate of the blunt end, leaving the other strand unjoined. This activity provides a mechanism for retaining 3′ overhang sequences, as observed during V(D)J recombination
in vivo
. Thus, Cernunnos/XRCC4-like factor promotes a mismatched end (MEnd) DNA ligase activity to facilitate joining and to preserve DNA sequence. Furthermore, MEnd ligase activity may have applications in recombinant DNA technology.
Two atomic constraints unambiguously position the S4 segment relative to S1 and S2 segments in the closed state of Shaker K channel
Authors: Campos Fabiana V. , Chanda Baron , Roux Benoît , Bezanilla Francisco
Published: May 2007

It is now well established that the voltage-sensing S4 segment in voltage-dependent ion channels undergoes a conformational change in response to varying membrane potential. However, the magnitude of the movement of S4 relative to the membrane and the rest of the protein remains controversial. Here, by using histidine scanning mutagenesis in the Shaker K channel, we identified mutants I241H (S1 segment) and I287H (S2 segment) that generate inward currents at hyperpolarized potentials, suggesting that these residues are part of a hydrophobic plug that separates the water-accessible crevices. Additional experiments with substituted cysteine residues showed that, at hyperpolarized potentials, both I241C and I287C can spontaneously form disulphide and metal bridges with R362C, the position of the first charge-carrying residue in S4. These results constrain unambiguously the closed-state positions of the S4 segment with respect to the S1 and S2 segments, which are known to undergo little or no movement during gating. To satisfy these constraints, the S4 segment must undergo an axial rotation of ≈180° and a transmembrane (vertical) movement of ≈6.5 Å at the level of R362 in going from the open to the closed state of the channel, moving the gating charge across a focused electric field.
A fundamental system of cellular energy homeostasis regulated by PGC-1α
Authors: Rohas Lindsay M. , St-Pierre Julie , Uldry Marc , Jäger Sibylle , Handschin Christoph , Spiegelman Bruce M.
Published: May 2007

Maintenance of ATP levels is a critical feature of all cells. Mitochondria are responsible for most ATP synthesis in eukaryotes. We show here that mammalian cells respond to a partial chemical uncoupling of mitochondrial oxidative phosphorylation with a decrease in ATP levels, which recovers over several hours to control levels. This recovery occurs through an increased expression of the transcriptional coactivator peroxisome proliferator-activated receptor-coactivator 1α (PGC-1α) and mitochondrial genes. Cells and animals lacking PGC-1α lose this compensatory mechanism and cannot defend their ATP levels or increase mitochondrial gene expression in response to reduced oxidative phosphorylation. The induction of PGC-1α and its mitochondrial target genes is triggered by a burst of intracellular calcium, which causes an increase in cAMP-response-element-binding protein and transducer of regulated cAMP-response-element-binding proteins actions on the PGC-1α promoter. These data illustrate a fundamental transcriptional cycle that provides homeostatic control of cellular ATP. In light of this compensatory system that limits the toxicity of mild uncoupling, the use of chemical uncoupling of mitochondria as a means of treating obesity should be re-evaluated.
Long-term effects of chronic nicotine exposure on brain nicotinic receptors
Authors: Besson Morgane , Granon Sylvie , Mameli-Engvall Monica , Cloëz-Tayarani Isabelle , Maubourguet Nicolas , Cormier Anne , Cazala Pierre , David Vincent , Changeux Jean-Pierre , Faure Philippe
Published: May 2007

Chronic nicotine exposure results in long-term homeostatic regulation of nicotinic acetylcholine receptors (nAChRs) that play a key role in the adaptative cellular processes leading to addiction. However, the relative contribution of the different nAChR subunits in this process is unclear. Using genetically modified mice and pharmacological manipulations, we provide behavioral, electrophysiological, and pharmacological evidence for a long-term mechanism by which chronic nicotine triggers opposing processes differentially mediated by β2*- vs. α7*nAChRs. These data offer previously undescribed insights into the understanding of nicotine addiction and the treatment of several human pathologies by nicotine-like agents chronically acting on β2*- or α7*nAChRs.
LKB1 and AMPK maintain epithelial cell polarity under energetic stress
Authors: Mirouse Vincent , Swick Lance L. , Kazgan Nevzat , St Johnston Daniel , Brenman Jay E.
Published: May 2007

LKB1 is mutated in both familial and spontaneous tumors, and acts as a master kinase that activates the PAR-1 polarity kinase and the adenosine 5′monophosphate–activated kinase (AMPK). This has led to the hypothesis that LKB1 acts as a tumor suppressor because it is required to maintain cell polarity and growth control through PAR-1 and AMPK, respectively. However, the genetic analysis of LKB1–AMPK signaling in vertebrates has been complicated by the existence of multiple redundant AMPK subunits. We describe the identification of mutations in the single Drosophila melanogaster AMPK catalytic subunit AMPKα. Surprisingly, ampkα mutant epithelial cells lose their polarity and overproliferate under energetic stress. LKB1 is required in vivo for AMPK activation, and lkb1 mutations cause similar energetic stress–dependent phenotypes to ampkα mutations. Furthermore, lkb1 phenotypes are rescued by a phosphomimetic version of AMPKα. Thus, LKB1 signals through AMPK to coordinate epithelial polarity and proliferation with cellular energy status, and this might underlie the tumor suppressor function of LKB1.
Molecular dissection of the myelin-associated glycoprotein receptor complex reveals cell type–specific mechanisms for neurite outgrowth inhibition
Authors: Venkatesh Karthik , Chivatakarn Onanong , Sheu Shey-Shing , Giger Roman J.
Published: May 2007

Neuronal Nogo66 receptor-1 (NgR1) binds the myelin inhibitors NogoA, OMgp, and myelin-associated glycoprotein (MAG) and has been proposed to function as the ligand-binding component of a receptor complex that also includes Lingo-1, p75NTR, or TROY. In this study, we use Vibrio cholerae neuraminidase (VCN) and mouse genetics to probe the molecular composition of the MAG receptor complex in postnatal retinal ganglion cells (RGCs). We find that VCN treatment is not sufficient to release MAG inhibition of RGCs; however, it does attenuate MAG inhibition of cerebellar granule neurons. Furthermore, the loss of p75NTR is not sufficient to release MAG inhibition of RGCs, but p75NTR−/− dorsal root ganglion neurons show enhanced growth on MAG compared to wild-type controls. Interestingly, TROY is not a functional substitute for p75NTR in RGCs. Finally, NgR1−/− RGCs are strongly inhibited by MAG. In the presence of VCN, however, NgR1−/− RGCs exhibit enhanced neurite growth. Collectively, our experiments reveal distinct and cell type–specific mechanisms for MAG-elicited growth inhibition.
Identification of an IL-17–producing NK1.1neg iNKT cell population involved in airway neutrophilia
Authors: Michel Marie-Laure , Keller Alexandre Castro , Paget Christophe , Fujio Masakazu , Trottein François , Savage Paul B. , Wong Chi-Huey , Schneider Elke , Dy Michel , Leite-de-Moraes Maria C.
Published: May 2007

Invariant natural killer T (iNKT) cells are an important source of both T helper type 1 (Th1) and Th2 cytokines, through which they can exert beneficial, as well as deleterious, effects in a variety of inflammatory diseases. This functional heterogeneity raises the question of how far phenotypically distinct subpopulations are responsible for such contrasting activities. In this study, we identify a particular set of iNKT cells that lack the NK1.1 marker (NK1.1neg) and secrete high amounts of interleukin (IL)-17 and low levels of interferon (IFN)-γ and IL-4. NK1.1neg iNKT cells produce IL-17 upon synthetic (α-galactosylceramide [α-GalCer] or PBS-57), as well as natural (lipopolysaccharides or glycolipids derived from Sphingomonas wittichii and Borrelia burgdorferi), ligand stimulation. NK1.1neg iNKT cells are more frequent in the lung, which is consistent with a role in the natural immunity to inhaled antigens. Indeed, airway neutrophilia induced by α-GalCer or lipopolysaccharide instillation was significantly reduced in iNKT-cell–deficient Jα18−/− mice, which produced significantly less IL-17 in their bronchoalveolar lavage fluid than wild-type controls. Furthermore, airway neutrophilia was abolished by a single treatment with neutralizing monoclonal antibody against IL-17 before α-GalCer administration. Collectively, our findings reveal that NK1.1neg iNKT lymphocytes represent a new population of IL-17–producing cells that can contribute to neutrophil recruitment through preferential IL-17 secretion.
A critical role for IRAK4 kinase activity in Toll-like receptor–mediated innate immunity
Authors: Kim Tae Whan , Staschke Kirk , Bulek Katarzyna , Yao Jianhong , Peters Kristi , Oh Keun-Hee , Vandenburg Yvonne , Xiao Hui , Qian Wen , Hamilton Tom , Min Booki , Sen Ganes , Gilmour Raymond , Li Xiaoxia
Published: May 2007

IRAK4 is a member of IL-1 receptor (IL-1R)–associated kinase (IRAK) family and has been shown to play an essential role in Toll-like receptor (TLR)–mediated signaling. We recently generated IRAK4 kinase-inactive knock-in mice to examine the role of kinase activity of IRAK4 in TLR-mediated signaling pathways. The IRAK4 kinase–inactive knock-in mice were completely resistant to lipopolysaccharide (LPS)- and CpG-induced shock, due to impaired TLR-mediated induction of proinflammatory cytokines and chemokines. Although inactivation of IRAK4 kinase activity did not affect the levels of TLR/IL-1R–mediated nuclear factor κB activation, a reduction of LPS-, R848-, and IL-1–mediated mRNA stability contributed to the reduced cytokine and chemokine production in bone marrow–derived macrophages from IRAK4 kinase–inactive knock-in mice. Both TLR7- and TLR9-mediated type I interferon production was abolished in plasmacytoid dendritic cells isolated from IRAK4 knock-in mice. In addition, influenza virus–induced production of interferons in plasmacytoid DCs was also dependent on IRAK4 kinase activity. Collectively, our results indicate that IRAK4 kinase activity plays a critical role in TLR-dependent immune responses.
Recovery from optic neuritis: an ROI-based analysis of LGN and visual cortical areas
Authors: Korsholm Kirsten , Madsen Kristoffer H. , Frederiksen Jette L. , Skimminge Arnold , Lund Torben E.
Published: May 2007

Optic neuritis (ON) is the first clinical manifestation in ∼20% of patients with multiple sclerosis (MS). The inflammation and demyelination of the optic nerve are characterized by symptomatic visual impairment and retrobulbar pain, and associated with decreased visual acuity, decreased colour and contrast sensitivity, delayed visual evoked potentials and visual field defects. Spontaneous recovery of vision typically occurs within weeks or months after onset, depending on the resolution of inflammation, remyelination, restoration of conduction in axons which persist demyelinated and neuronal plasticity in the cortical and subcortical visual pathways. To assess where recovery takes place along the visual pathway, visual activation was studied in the lateral geniculate nucleus (LGN), the main thalamic relay nucleus in the visual pathway and in three areas of the visual cortex: the lateral occipital complexes (LOC), V1 and V2. We conducted a longitudinal functional magnetic resonance imaging (fMRI) study of regions of interest (ROI) of activation in LGN and visual cortex in 19 patients with acute ON at onset, 3 and 6 months from presentation. With fMRI we measured the activation in the ROIs and compared activation during monocular stimulation of the affected and unaffected eye. In the acute phase the activation of LGN during visual stimulation of the affected eye was significantly reduced (P< 0.01) compared to the unaffected eye. This difference in LGN activation between the affected and unaffected eye diminished during recovery, and after 180 days the difference was no longer significant (P = 0.59). The decreased difference during recovery was mainly due to an increase in the fMRI signal when stimulating the affected eye, but included a component of a decreasing fMRI signal from LGN when stimulating the unaffected eye. In LOC, V1 and V2 activation during visual stimulation of the affected eye in the acute phase was significantly reduced (P< 0.01) compared to the unaffected eye, and during recovery the difference diminished with no significant differences left after 180 days. As the pattern of activation in LOC, V1 and V2 resembled the development in LGN we found no evidence of additional cortical adaptive changes. The reduced activation of the LGN to stimulation of the unaffected eye is interpreted as a shift away from early compensatory changes established in the acute phase in LGN and may indicate very early plasticity of the visual pathways.
Red Cabbage (Brassica oleracea) Ameliorates Diabetic Nephropathy in Rats
Authors: Kataya Hazem A. H. , Hamza AlaaEldin A.
Published: April 2007

The protective action against oxidative stress of red cabbage (Brassica oleracea) extract was investigated. Diabetes was induced in male Wistar rats using streptozotocin (60 mg/kg body weight). Throughout the experimental period (60 days), diabetic rats exhibited many symptoms including loss of body weight, hyperglycemia, polyuria, polydipsia, renal enlargement and renal dysfunction. Significant increase in malondialdehyde, a lipid peroxidation marker, was observed in diabetic kidney. This was accompanied by a significant increase in reduced glutathione and superoxide dismutase activity and a decrease in catalase activity and in the total antioxidant capacity of the kidneys. Daily oral ingestion (1 g/kg body weight) of B. oleracea extract for 60 days reversed the adverse effect of diabetes in rats. B. oleracea extract lowered blood glucose levels and restored renal function and body weight loss. In addition, B. oleracea extract attenuated the adverse effect of diabetes on malondialdehyde, glutathione and superoxide dismutase activity as well as catalase activity and total antioxidant capacity of diabetic kidneys. In conclusion, the antioxidant and antihyperglycemic properties of B. oleracea extract may offer a potential therapeutic source for the treatment of diabetes.
Ki‐Energy (Life‐Energy) Stimulates Osteoblastic Cells and Inhibits the Formation of Osteoclast‐Like Cells in Bone Cell Culture Models
Authors: Tsuyoshi Ohnishi S. , Nishino Kozo , Uchiyama Satoshi , Ohnishi Tomoko , Yamaguchi Masayoshi
Published: April 2007

Some practitioners of the Nishino Breathing Method (NBM) were found to have a higher bone density than the average values of age‐ and gender‐matched non‐practitioners. Using bone cell culture models, we investigated a possible mechanism behind this observation. For the study of bone mineralization, we performed the following two experiments using cultured osteoblastic MC3T3‐E1 cells: (i) Kozo Nishino, a Japanese Ki expert, sent Ki‐energy to the cells once for 5 or 10 min after they were seeded in culture dishes in the presence of 10% fetal bovine serum (FBS). They were incubated for 72 h and the cells were counted. The number in the dish with 10‐min Ki‐exposure was significantly greater than that in the control (P < 0.01 with n = 8). We performed a reverse transcription‐polymerase chain reaction (RT–PCR) study using these cells, but the mRNA expressions did not change significantly. (ii) After cells were incubated for 72 h without Ki‐exposure (in the presence of FBS), they were further cultured for 48 h (in the absence of FBS) to promote differentiation. At the beginning of the second culture stage, Ki was applied once for 10 min. After 48 h, RT–PCR was performed. The mRNA expressions which are related to bone mineralization, such as Runx2, α1(I) collagen, alkaline phosphatase and osteocalcin, increased significantly (P < 0.05 and n = 4 for all). For the bone resorption study, we used mouse marrow cultures, which can form osteoclast‐like cells in the presence of (1–34) parathyroid hormone (PTH), and stimulate resorption. We exposed these cells to Ki‐energy twice for the duration of 5 or 10 min on day 0 and day 4. On day 7, the cells were counted. The number of osteoclast‐like cells in dishes with Ki exposure was significantly smaller than those in control dishes (P < 0.05 with n = 5). The difference between 5‐min exposure and 10‐min exposure was not statistically significant. All of our data suggest that the Ki‐effect on osteoporosis should be further explored.
Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of Bacillus fusiformis to Lysinibacillus fusiformis comb. nov. and Bacillus sphaericus to Lysinibacillus sphaericus comb. nov.
Authors: Ahmed Iftikhar , Yokota Akira , Yamazoe Atsushi , Fujiwara Toru
Published: May 2007

Three strains of a spore-forming, Gram-positive, motile, rod-shaped and boron-tolerant bacterium were isolated from soil. The strains, designated 10aT, 11c and 12B, can tolerate 5 % (w/v) NaCl and up to 150 mM boron, but optimal growth was observed without addition of boron or NaCl in Luria–Bertani agar medium. The optimum temperature for growth was 37 °C (range 16–45 °C) and the optimum pH was 7.0–8.0 (range pH 5.5–9.5). A comparative analysis of the 16S rRNA gene sequence demonstrated that the isolated strains were closely related toBacillus fusiformisDSM 2898T(97.2 % similarity) andBacillus sphaericusDSM 28T(96.9 %). DNA–DNA relatedness was greater than 97 % among the isolated strains and 61.1 % withB. fusiformisDSM 2898Tand 43.2 % withB. sphaericusIAM 13420T. The phylogenetic and phenotypic analyses and DNA–DNA relatedness indicated that the three strains belong to the same species, that was characterized by a DNA G+C content of 36.5–37.9 mol%, MK-7 as the predominant menaquinone system and iso-C15 : 0(32 % of the total) as a major cellular fatty acid. In contrast to the type species of the genusBacillus, the strains contained peptidoglycan with lysine, aspartic acid, alanine and glutamic acid. Based on the distinctive peptidoglycan composition, phylogenetic analyses and physiology, the strains are assigned to a novel species within a new genus, for which the nameLysinibacillus boronitoleransgen. nov., sp. nov. is proposed. The type strain ofLysinibacillus boronitoleransis strain 10aT(=DSM 17140T=IAM 15262T=ATCC BAA-1146T). It is also proposed thatBacillus fusiformisandBacillus sphaericusbe transferred to this genus asLysinibacillus fusiformiscomb. nov. andLysinibacillus sphaericuscomb. nov., respectively.
Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples
Authors: Teyssier Corinne , Marchandin Hélène , Jean-Pierre Hélène , Masnou Agnès , Dusart Ghislaine , Jumas-Bilak Estelle
Published: May 2007

Three novel Gram-negative, non-fermenting aerobic bacilli were isolated from human clinical samples. They shared more than 99.8 % of the 16S rRNA gene nucleotide positions. The strains were related to Ochrobactrum intermedium with about 97.48 % 16S rRNA gene sequence similarity. In 16S rRNA gene-, dnaK- and rpoB-based phylogenies, the strains were grouped in a lineage that was distinct from other Ochrobactrum species in the family Brucellaceae. Fatty acid composition, polar lipids, quinone system, DNA–DNA relatedness, genome organization, and physiological and biochemical data differentiated these isolates from recognized species of the genus Ochrobactrum. The three clinical strains therefore represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum pseudintermedium sp. nov., is proposed. The type strain is ADV31T (=CIP 109116T=DSM 17490T). The DNA G+C content of strain ADV31T was 54.5 mol%.
Bacillus decisifrondis sp. nov., isolated from soil underlying decaying leaf foliage
Authors: Zhang Li , Xu Zhihong , Patel Bharat K. C.
Published: May 2007

An aerobic bacterium, designated strain E5HC-32T, was isolated from soil underlying the decaying leaf litter of a slash pine forest located in south east Queensland, Australia. The strictly aerobic, motile rod-shaped cells (0.8–1.6×2.6–4.8 μm) produced subterminal spherical spores which distended the cells. Strain E5HC-32Tgrew optimally in 1 % trypticase soy broth (TSB) at 30 °C (temperature range for growth, 25–40 °C) and a pH of 8.4 (pH growth range, pH 7.1–9.1). Electron microscopic examination of negatively stained cells revealed the presence of peritrichous flagella and thin sections showed the presence of a typical Gram-positive type cell-wall ultrastructure. The strain was catalase-positive and oxidase-negative and metabolized pyruvic acid methyl ester,d-galactonic acid lactone,α-ketobutyric acid,α-ketovaleric acid,l-proline,l-alanine, urocanic acid, inosine, uridine, thymidine, glycerol,α-cyclodextrin,α-d-lactose,d-psicose,d-raffinose,l-rhamnose,d-sorbitol, turanose,cis-aconitic acid,α-hydroxybutyric acid,l-alaninamide and 2-aminoethanol. The G+C content of DNA was 41±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis revealed that strain E5HC-32Twas placed equidistantly as a member of the classBacilli, phylumFirmicutes, withBacillus sphaericusDSM 28TandBacillus odysseyiATCC PTA-4993T(similarity of 93 %). In addition to its significant phylogenetic separation from its nearest relatives, strain E5HC-32Tpossessed phenotypic traits that also suggested that it represented a novel species, for which the nameBacillus decisifrondissp. nov. is proposed. The type strain is E5HC-32T(=JCM 13601T=DSM 17725T).
Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand
Authors: Kwon Soon-Wo , Kim Byung-Yong , Weon Hang-Yeon , Baek Youn-Kyung , Go Seung-Joo
Published: May 2007

A Gram-negative, aerobic bacterium, designated strain HO3-R19T, which was isolated from seashore sand in Pohang city, Korea, was characterized on the basis of a polyphasic taxonomic approach. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain HO3-R19Trepresents a new lineage within theGammaproteobacteria; sequence similarities between strain HO3-R19Tand members of other related genera were less than 93.5 %. Strain HO3-R19Twas also distinguished from related genera based on differences in several phenotypic characteristics. Cells were straight or slightly curved rods and formed white colonies on R2A agar. The major isoprenoid quinone was ubiquinone 8 (Q-8), and predominant cellular fatty acids were iso-C16 : 0, iso-C15 : 0and iso-C17 : 1ω9c. The DNA G+C content of strain HO3-R19Twas 65.0 mol%. Based on physiological, biochemical and chemotaxonomic traits together with results of comparative 16S rRNA sequence analysis, strain HO3-R19Tis considered to represent a novel species in a new genus, for which the nameArenimonas donghaensisgen. nov., sp. nov. is proposed. The type strain ofArenimonas donghaensisis HO3-R19T(=KACC 11381T=DSM 18148T).
Zhihengliuella halotolerans gen. nov., sp. nov., a novel member of the family Micrococcaceae
Authors: Zhang Yu-Qin , Schumann Peter , Yu Li-Yan , Liu Hong-Yu , Zhang Yue-Qin , Xu Li-Hua , Stackebrandt Erko , Jiang Cheng-Lin , Li Wen-Jun
Published: May 2007

The actinobacterial strain YIM 70185Twas isolated from a saline soil sample collected from Qinghai province, north-west China, and subjected to a taxonomic investigation. Phylogenetic analysis based on 16S rRNA gene sequences revealed 93.5–96.4 % similarity to members of related genera in the familyMicrococcaceae. In the phylogenetic dendrogram based on 16S rRNA gene sequence analysis, strain YIM 70185Tformed a separate clade next to the generaMicrococcusandCitricoccuswithin the familyMicrococcaceae. The peptidoglycan type was A4α,l-lys–l-ala–l-Glu. Cell-wall sugars contained glucose and tyvelose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, an unknown phospholipid and an unknown glycolipid. The menaquinones were MK-9, MK-10 and MK-8 (molar ratio 5 : 2 : 1). The major fatty acids were ai-C15 : 0and i-C15 : 0and the DNA G+C content was 66.5 mol%. These chemotaxonomic profiles supported the assignment of strain YIM 70185Tto a novel genus within the familyMicrococcaceae. The nameZhihengliuella halotoleransgen. nov., sp. nov. is proposed. The type strain ofZhihengliuella halotoleransis YIM 70185T(=DSM 17364T=KCTC 19085T).
Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm
Authors: Nedashkovskaya Olga I. , Kim Seung Bum , Shin Dong Sung , Beleneva Irina A. , Mikhailov Valery V.
Published: May 2007

A novel, strictly aerobic, heterotrophic, gliding, Gram-negative, oxidase-, catalase-, β-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6220T, was isolated from seawater and studied by using a polyphasic taxonomic approach. The DNA G+C content of strain KMM 6220T was 59.9 mol%. The predominant fatty acids were iso-C15 : 1, iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1
ω7/iso-C15 : 0 2-OH. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that strain KMM 6220T formed a cluster with the misclassified strains [Flexibacter] aggregans NBRC 15974 and [Flexibacter] tractuosus NBRC 16035 and with the type strains of Reichenbachiella agariperforans and Roseivirga ehrenbergii with levels of similarity of 95.9, 94.4, 92.0 and 91.8 %, respectively. On the basis of its phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, strain KMM 6220T is considered to represent a novel species of a new genus in the phylum Bacteroidetes, for which the name Fulvivirga kasyanovii gen. nov., sp. nov. is proposed. The type strain of the type species is KMM 6220T (=CCTCC AB 206119T=KCTC 12832T).
Bacillus qingdaonensis sp. nov., a moderately haloalkaliphilic bacterium isolated from a crude sea-salt sample collected near Qingdao in eastern China
Authors: Wang Qian-fu , Li Wei , Liu Yan-li , Cao Hai-hua , Li Zhao , Guo Guang-qin
Published: May 2007

A moderately haloalkaliphilic, Gram-positive bacterium, designated as strain CM1T, was isolated from a crude sea-salt sample collected near Qingdao in eastern China. Strain CM1T was found to grow optimally at 37 °C and pH 9.0. It was shown to be aerobic, rod-shaped and capable of growth at salinities of 2.5–20 % (w/v) NaCl (optimum, 12 %). The genomic DNA G+C content was about 48 mol%. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0 and the major isoprenoid quinones were MK-7(H2) and MK-6(H2). Phylogenetic analyses based on 16S rRNA gene sequences revealed that CM1T is a member of the genus Bacillus and has less than 95.2 % gene sequence similarity to the most closely related strain, Bacillus salarius BH169T. Its DNA–DNA reassociation value with respect to B. salarius BH169T was 35.4 %. On the basis of phenotypic and molecular properties, strain CM1T represents a novel Bacillus species, for which the name Bacillus qingdaonensis sp. nov. is proposed. The type strain is CM1T (=CGMCC 1.6134T=JCM 14087T).
Gulbenkiania mobilis gen. nov., sp. nov., isolated from treated municipal wastewater
Authors: Vaz-Moreira Ivone , Nobre M. Fernanda , Nunes Olga C. , Manaia Célia M.
Published: May 2007

A bacterial strain (E4FC31T) isolated from treated municipal wastewater was characterized phenotypically and phylogenetically. Cells were Gram-negative, curved rods with a polar flagellum. The isolate was catalase-, oxidase- and arginine dihydrolase-positive, and able to grow between 15 and 45 °C and between pH 5.5 and 9.0. The predominant fatty acids were C16 : 1/iso-C15 : 02-OH and C16 : 0, the major respiratory quinone was ubiquinone 8 and the G+C content of the genomic DNA was 63 mol%. 16S rRNA gene sequence analysis indicated that strain E4FC31Tbelonged to the classBetaproteobacteriaand was a member of the familyNeisseriaceae. Its closest phylogenetic neighbours wereAquitalea magnusoniiandChromobacterium violaceum(<94 % 16S rRNA gene sequence similarity). Phylogenetic analysis and phenotypic characteristics of strain E4FC31Tsuggest that it represents a novel species of a new genus, for which the nameGulbenkiania mobilisgen. nov., sp. nov. is proposed. The type strain ofGulbenkiania mobilisis E4FC31T(=DSM 18507T=LMG 23770T).
Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan
Authors: Yoon Jaewoo , Yasumoto-Hirose Mina , Katsuta Atsuko , Sekiguchi Hiroshi , Matsuda Satoru , Kasai Hiroaki , Yokota Akira
Published: May 2007

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24T, was isolated from seawater surrounding the hard coralGalaxea fascicularisL., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum ‘Verrucomicrobia’ and shared 84–95 % sequence similarity with cultivated strains of ‘Verrucomicrobia’ subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C14 : 0, C18 : 1ω9cand C18 : 0were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24Trepresents a novel species in a new genus in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the nameCoraliomargarita akajimensisgen. nov., sp. nov. is proposed. The type strain ofCoraliomargarita akajimensisis 04OKA010-24T(=MBIC06463T=IAM 15411T=KCTC 12865T).
Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces
Authors: Hayashi Hidenori , Shibata Kensaku , Sakamoto Mitsuo , Tomita Shinichi , Benno Yoshimi
Published: May 2007

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genusPrevotellaand made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related toPrevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related toPrevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of otherPrevotellaspecies. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35Twere MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species,Prevotella coprisp. nov. andPrevotella stercoreasp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7Tand CB35Twere 45.3 and 48.2 mol%, respectively. The type strains ofP. copriandP. stercoreaare CB7T(=JCM 13464T=DSM 18205T) and CB35T(=JCM 13469T=DSM 18206T), respectively.
Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens
Authors: Sawabe Tomoo , Fujimura Yusuke , Niwa Kentaro , Aono Hideaki
Published: May 2007

Nine alginolytic, facultatively anaerobic, non-motile bacteria were isolated from the guts of the abalonesHaliotis discus discus,H. gigantea,H. madakaandH. rufescens. Phylogenetic analyses based on 16S rRNA gene sequences indicated that these bacteria were closely related toVibrio superstesG3-29T(98.6–99.3 % sequence similarity). DNA–DNA hybridization and phylogenetic analysis based on thegapAgene demonstrated that six strains constituted one bacterial species, two strains represented a second species and one strain represented a third species. The three novel bacterial species were different from all currently known vibrios. The namesVibrio comitanssp. nov. (type strain GHG2-1T=LMG 23416T=NBRC 102076T; DNA G+C content 45.0–48.0 mol%),Vibrio inusitatussp. nov. (type strain RW14T=LMG 23434T=NBRC 102082T; DNA G+C content 43.1–43.7 mol%) andVibrio rarussp. nov. (type strain RW22T=LMG 23674T=NBRC 102084T; DNA G+C content 43.8 mol%) are proposed to encompass these new taxa. Several phenotypic features were revealed that discriminateV. comitans,V. rarusandV. inusitatusfrom otherVibriospecies.
Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses
Authors: Behrendt Undine , Ulrich Andreas , Schumann Peter , Meyer Jean-Marie , Spröer Cathrin
Published: May 2007

The taxonomic position of a group of fluorescent pseudomonad strains isolated from the phyllosphere of grasses was investigated through a polyphasic approach. Riboprinting analysis revealed highly similar patterns for the investigated strains which supported, together with the agreement of many phenotypic characteristics, their affiliation to the same species. A comparison of 16S rRNA gene sequences of strain P 513/18T, a representative strain from the grass isolates, revealed that it was affiliated to the cluster of the ‘Pseudomonas fluorescensgroup’, withPseudomonas costantiniias the closest phylogenetic neighbour. However, DNA–DNA hybridization showed a clear demarcation at the species level between strain P 513/18TandP. costantinii. Furthermore, a comparison of riboprint patterns withPseudomonasspecies clustering next to the novel grass isolates on the basis of 16S rRNA gene sequences supported their separate species status at the phylogenetic level. Based on phenotypic features, the novel isolates could also be differentiated from the other fluorescentPseudomonasspecies that share positive arginine dihydrolase and oxidase reactions. As a consequence of these phenotypic and phylogenetic analyses, the isolates from the grass pyllosphere represent a novel species for which the namePseudomonas luridasp. nov. is proposed. The type strain is P 513/18T(=DSM 15835T=LMG 21995T).
Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern
Authors: Srinivas T. N. R. , Kumar P. Anil , Sasikala Ch. , Ramana Ch. V. , Imhoff J. F.
Published: May 2007

A pink-pigmented, phototrophic, purple nonsulfur bacterium, strain JA173T, was isolated in pure culture from a saltern in Gokarna, India, in a medium containing 2 % (w/v) NaCl. Strain JA173T was a non-motile Gram-negative rod that multiplied by budding. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA173T clusters with the class Alphaproteobacteria; highest sequence similarity (98 %) was to the type strain of Rhodobium orientis and 94 % similarity was observed to the 16S rRNA gene sequence of the type strain of Rhodobium marinum. However, DNA–DNA hybridization with R. orientis DSM 11290T revealed a relatedness value of only 35.1 % with strain JA173T. Strain JA173T contained lamellar internal membranes, bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Strain JA173T had an obligate requirement for NaCl (optimum growth at 2–6 %, w/v) and grew photoheterotrophically with a number of organic compounds as carbon source or electron donor. Photoautotrophic, chemoautotrophic and fermentative growth could not be demonstrated. Yeast extract was required for growth. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and morphological and physiological characteristics, strain JA173T is sufficiently different from other species of the genus Rhodobium to be recognized as a representative of a novel species, Rhodobium gokarnense sp. nov. The type strain is JA173T (=ATCC BAA-1215T=DSM 17935T=JCM 13532T).
Mesorhizobium ciceri biovar biserrulae, a novel biovar nodulating the pasture legume Biserrula pelecinus L.
Authors: Nandasena Kemanthi G. , O'Hara Graham W. , Tiwari Ravi P. , Willlems Anne , Howieson John G.
Published: May 2007

Biserrula pelecinus L. is a pasture legume species that forms a highly specific nitrogen-fixing symbiotic interaction with a group of bacteria that belong to Mesorhizobium. These mesorhizobia have >98.8 % sequence similarity to Mesorhizobium ciceri and Mesorhizobium loti for the 16S rRNA gene (1440 bp) and >99.3 % sequence similarity to M. ciceri for the dnaK gene (300 bp), and strain WSM1271 has 100 % sequence similarity to M. ciceri for GSII (600 bp). Strain WSM1271 had 85 % relatedness to M. ciceri LMG 14989T and 50 % relatedness to M. loti LMG 6125T when DNA–DNA hybridization was performed. WSM1271 also had a similar cellular fatty acid profile to M. ciceri. These results are strong evidence that the Biserrula mesorhizobia and M. ciceri belong to the same group of bacteria. Significant differences were revealed between the Biserrula mesorhizobia and M. ciceri in growth conditions, antibiotic resistance and carbon source utilization. The G+C content of the DNA of WSM1271 was 62.7 mol%, compared to 63–64 mol% for M. ciceri. The Biserrula mesorhizobia contained a plasmid (~500 bp), but the symbiotic genes were detected on a mobile symbiosis island and considerable variation was present in the symbiotic genes of Biserrula mesorhizobia and M. ciceri. There was <78.6 % sequence similarity for nodA and <66.9 % for nifH between Biserrula mesorhizobia and M. ciceri. Moreover, the Biserrula mesorhizobia did not nodulate the legume host of M. ciceri, Cicer arietinum, and M. ciceri did not nodulate B. pelecinus. These significant differences observed between Biserrula mesorhizobia and M. ciceri warrant the proposal of a novel biovar for Biserrula mesorhizobia within M. ciceri. The name Mesorhizobium ciceri biovar biserrulae is proposed, with strain WSM1271 (=LMG 23838=HAMBI 2942) as the reference strain.
Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant
Authors: Yassin A. F. , Shen Fo-Ting , Hupfer H. , Arun A. B. , Lai Wei-An , Rekha P. D. , Young Chiu Chung
Published: May 2007

The taxonomic status of a bacterial isolate from the sludge of a wastewater treatment plant was characterized by using a polyphasic taxonomic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genusGordonia, fatty acids C16 : 0and C18 : 0(found by pyrolysis gas chromatography) and a dihydrogenated menaquinone with nine isoprene units [MK-9(H2)] as the predominant menaquinone. The genus assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that the novel isolate constitutes a hitherto unknown subline within the genusGordonia, displaying 95.9 to 97.6 % gene sequence similarity to the recognized species of the genus. The novel isolate was distinguished from the type strains of phylogenetically related species by using a set of phenotypic features. The genotypic and phenotypic data show that the new strain merits classification as a novel species of the genusGordonia, for which the nameGordonia malaquaesp. nov. is proposed. The type strain is IMMIB WWCC-22T(=DSM 45064T=CCUG 53555T).
Halovivax ruber sp. nov., an extremely halophilic archaeon isolated from Lake Xilinhot, Inner Mongolia, China
Authors: Castillo A. M. , Gutiérrez M. C. , Kamekura M. , Xue Y. , Ma Y. , Cowan D. A. , Jones B. E. , Grant W. D. , Ventosa A.
Published: May 2007

A Gram-negative, pleomorphic, extremely halophilic archaeon, designated strain XH-70T, was isolated from the saline Lake Xilinhot, in Inner Mongolia, China. It formed small (0.9–1.5 mm), red-pigmented, elevated colonies on agar medium. The strain required at least 2.5 M NaCl and 5 mM Mg2+ for growth. The 16S rRNA gene sequence analysis indicated that strain XH-70T belongs to the family Halobacteriaceae, showing 99.5 % similarity to the type strain of Halovivax asiaticus and 94.7 and 94.6 % similarity, respectively, to the type strains of Natronococcus amylolyticus and Natronococcus occultus. Polar lipid analysis supported the placement of strain XH-70T in the genus Halovivax. DNA–DNA hybridization studies (32 % with Halovivax asiaticus CGMCC 1.4248T), as well as biochemical and physiological characterization, allowed strain XH-70T to be differentiated from Halovivax asiaticus. A novel species, Halovivax ruber sp. nov., is therefore proposed to accommodate this strain. The type strain is XH-70T (=CGMCC 1.6204T=DSM 18193T=JCM 13892T).
The status of the species Leifsonia rubra Reddy et al. 2003. Request for an Opinion
Authors: An Sun-Young , Yokota Akira
Published: May 2007

On the basis of 16S rRNA gene sequence analysis, it is ascertained that the type strain ofLeifsonia rubradoes not exist in any established culture collection or with the authors who described this species. Therefore, it cannot be included in any scientific study. It is proposed that the Judicial Commission place the nameLeifsonia rubraon the list of rejected names if a suitable type strain is not found or a neotype is not proposed within two years following the publication of this Request for an Opinion.
Transcription elongation controls cell fate specification in the Drosophila embryo
Authors: Wang Xiaoling , Lee Chanhyo , Gilmour David S. , Gergen J. Peter
Published: May 2007

The simple combinatorial rules for regulation of the sloppy-paired-1 (slp1) gene by the pair-rule transcription factors during early Drosophila embryogenesis offer a unique opportunity to investigate the molecular mechanisms of developmentally regulated transcription repression. We find that the initial repression of slp1 in response to Runt and Fushi-tarazu (Ftz) does not involve chromatin remodeling, or histone modification. Chromatin immunoprecipitation and in vivo footprinting experiments indicate RNA polymerase II (Pol II) initiates transcription in slp1-repressed cells and pauses downstream from the promoter in a complex that includes the negative elongation factor NELF. The finding that NELF also associates with the promoter regions of wingless (wg) and engrailed (en), two other pivotal targets of the pair-rule transcription factors, strongly suggests that developmentally regulated transcriptional elongation is central to the process of cell fate specification during this critical stage of embryonic development.
RDH10 is essential for synthesis of embryonic retinoic acid and is required for limb, craniofacial, and organ development
Authors: Sandell Lisa L. , Sanderson Brian W. , Moiseyev Gennadiy , Johnson Teri , Mushegian Arcady , Young Kendra , Rey Jean-Philippe , Ma Jian-xing , Staehling-Hampton Karen , Trainor Paul A.
Published: May 2007

Regulation of patterning and morphogenesis during embryonic development depends on tissue-specific signaling by retinoic acid (RA), the active form of Vitamin A (retinol). The first enzymatic step in RA synthesis, the oxidation of retinol to retinal, is thought to be carried out by the ubiquitous or overlapping activities of redundant alcohol dehydrogenases. The second oxidation step, the conversion of retinal to RA, is performed by retinaldehyde dehydrogenases. Thus, the specific spatiotemporal distribution of retinoid synthesis is believed to be controlled exclusively at the level of the second oxidation reaction. In an N-ethyl-N-nitrosourea (ENU)-induced forward genetic screen we discovered a new midgestation lethal mouse mutant, called trex, which displays craniofacial, limb, and organ abnormalities. The trex phenotype is caused by a mutation in the short-chain dehydrogenase/reductase, RDH10. Using protein modeling, enzymatic assays, and mutant embryos, we determined that RDH10trex mutant protein lacks the ability to oxidize retinol to retinal, resulting in insufficient RA signaling. Thus, we show that the first oxidative step of Vitamin A metabolism, which is catalyzed in large part by the retinol dehydrogenase RDH10, is critical for the spatiotemporal synthesis of RA. Furthermore, these results identify a new nodal point in RA metabolism during embryogenesis.
Functional cooperation between HP1 and DNMT1 mediates gene silencing
Authors: Smallwood Andrea , Estève Pierre-Olivier , Pradhan Sriharsa , Carey Michael
Published: May 2007

Mammalian euchromatic gene silencing results from the combined repressive effects of histone and DNA methyltransferases. Little is known of the mechanism by which these enzymes cooperate to induce silencing. Here we show that mammalian HP1 family members mediate communication between histone and DNA methyltransferases. In vitro, methylation of histone 3 Lys 9 by G9a creates a binding platform for HP1α, β, and γ. DNMT1 interacts with HP1 resulting in increased DNA methylation on DNA and chromatin templates in vitro. The functional and physical interaction can be recapitulated in vivo. Binding of GAL4-HP1 to a reporter construct is sufficient to induce repression and DNA methylation in DNMT1 wild-type but not DNMT1-null cells. Additionally, silencing of the Survivin gene coincides with recruitment of G9a and HP1 in DNMT1 wild-type but not null cells. We conclude that direct interactions between HP1 and DNMT1 mediate silencing of euchromatic genes.