bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional square water in the presence of an external electric field
Authors: Girardi M. , Figueiredo W.
Published: September 2006

In this work we study a tridimensional statistical model for the hydrogen-bond (HB) network formed in liquid water in the presence of an external electric field. This model is analogous to the so-called square water, whose ground state gives a good estimate for the residual entropy of the ice. In our case, each water molecule occupies one site of a cubic lattice, and no hole is allowed. The hydrogen atoms of water molecules are disposed at the lines connecting nearest-neighbor sites, in a way that each water can be found in 15 different states. We say that there is a hydrogen bond between two neighboring molecules when only one hydrogen is in the line connecting both molecules. Through Monte Carlo simulations with Metropolis and entropic sampling algorithms, and by exact calculations for small lattices, we determined the dependence of the number of molecules aligned to the field and the number of hydrogen bonds per molecule as a function of temperature and the intensity of the external field. The results for both approaches showed that, different of the two-dimensional case, there is no maximum in the number of HBs as a function of the electric field. However, we observed nonmonotonic behaviors as a function of the temperature of the quantities of interest. We also found the dependence of the entropy on the external electric field at very low temperatures. In this case, the entropy vanishes for the value of the external field for which the contributions to the total energy coming from the HBs and the field become the same.
Therapeutic potential of histamine H3 receptor agonist for the treatment of obesity and diabetes mellitus
Authors: Yoshimoto Ryo , Miyamoto Yasuhisa , Shimamura Ken , Ishihara Akane , Takahashi Kazuhiko , Kotani Hidehito , Chen Airu S. , Chen Howard Y. , MacNeil Douglas J. , Kanatani Akio , Tokita Shigeru
Published: September 2006

Histamine H3 receptors (H3Rs) are located on the presynaptic membranes and cell soma of histamine neurons, where they negatively regulate the synthesis and release of histamine. In addition, H3Rs are also located on nonhistaminergic neurons, acting as heteroreceptors to regulate the releases of other amines such as dopamine, serotonin, and norepinephrine. The present study investigated the effects of H3R ligands on appetite and body-weight regulation by using WT and H3R-deficient mice (H3RKO), because brain histamine plays a pivotal role in energy homeostasis. The results showed that thioperamide, an H3R inverse agonist, increases, whereas imetit, an H3R agonist, decreases appetite and body weight in diet-induced obese (DiO) WT mice. Moreover, in DiO WT mice, but not in DiO H3RKO mice, imetit reduced fat mass, plasma concentrations of leptin and insulin, and hepatic triglyceride content. The anorexigenic effects of imetit were associated with a reduction in histamine release, but a comparable reduction in histamine release with α-fluoromethylhistidine, an inhibitor of histamine synthesis, increased appetite. Moreover, the anorexigenic effects of imetit were independent of the melanocortin system, because imetit comparably reduced appetite in melanocortin 3 and 4 receptor-deficient mice. The results provide roles of H3Rs in energy homeostasis and suggest a therapeutic potential for H3R agonists in the treatment of obesity and diabetes mellitus.
LPS-induced TNF-α factor (LITAF)-deficient mice express reduced LPS-induced cytokine: Evidence for LITAF-dependent LPS signaling pathways
Authors: Tang Xiaoren , Metzger Daniel , Leeman Susan , Amar Salomon
Published: September 2006

Previously we identified a transcription factor, LPS-Induced TNF-α Factor (LITAF), mediating inflammatory cytokine expression in LPS-induced processes. To characterize the role of LITAF
in vivo
, we generated a macrophage-specific LITAF-deficient mouse (macLITAF
−/−
). Our data demonstrate that in macrophages (
i
) several cytokines (such as TNF-α, IL-6, sTNF-RII, and CXCL16) are induced at lower levels in macLITAF
−/−
compared with LITAF
+/+
control macrophages; (
ii
) macLITAF
−/−
mice are more resistant to LPS-induced lethality. To further identify LITAF signaling pathways, we tested mouse TLR-2
−/−
, -4
−/−
, and -9
−/−
and WT peritoneal macrophages exposed to LPS. Using these cells, we now show that LITAF expression can be induced after challenge either with LPS from
Porphyromonas gingivalis
via agonism at TLR-2, or with LPS from
Escherichia coli
via agonism at TLR-4, both requiring functional MyD88. We also show that, in response to LPS, the MyD88-dependent LITAF pathway differs from the NF-κB pathway. Furthermore, using a kinase array, p38α was found to mediate LITAF phosphorylation and the inhibition of p38α with a p38-specific inhibitor (SB203580) blocked LITAF nuclear translocation and reduced LPS-induced TNF-α protein levels. Finally, macLITAF
−/−
macrophages rescued by LITAF cDNA transfection restored levels of TNF-α similar to those observed in WT cells. We conclude that LITAF is an important mediator of the LPS-induced inflammatory response that can be distinguished from NF-κB pathway and that p38α is the specific kinase involved in the pathway linking LPS/MyD88/LITAF to TNF.
Tubulin tyrosination is a major factor affecting the recruitment of CAP-Gly proteins at microtubule plus ends
Authors: Peris Leticia , Thery Manuel , Fauré Julien , Saoudi Yasmina , Lafanechère Laurence , Chilton John K. , Gordon-Weeks Phillip , Galjart Niels , Bornens Michel , Wordeman Linda , Wehland Juergen , Andrieux Annie , Job Didier
Published: September 2006

Tubulin-tyrosine ligase (TTL), the enzyme that catalyzes the addition of a C-terminal tyrosine residue to α-tubulin in the tubulin tyrosination cycle, is involved in tumor progression and has a vital role in neuronal organization. We show that in mammalian fibroblasts, cytoplasmic linker protein (CLIP) 170 and other microtubule plus-end tracking proteins comprising a cytoskeleton-associated protein glycine-rich (CAP-Gly) microtubule binding domain such as CLIP-115 and p150 Glued, localize to the ends of tyrosinated microtubules but not to the ends of detyrosinated microtubules. In vitro, the head domains of CLIP-170 and of p150 Glued bind more efficiently to tyrosinated microtubules than to detyrosinated polymers. In TTL-null fibroblasts, tubulin detyrosination and CAP-Gly protein mislocalization correlate with defects in both spindle positioning during mitosis and cell morphology during interphase. These results indicate that tubulin tyrosination regulates microtubule interactions with CAP-Gly microtubule plus-end tracking proteins and provide explanations for the involvement of TTL in tumor progression and in neuronal organization.
Cell cycle regulators control centrosome elimination during oogenesis in Caenorhabditis elegans
Authors: Kim Dae Young , Roy Richard
Published: September 2006

In many animals, the bipolar spindle of the first zygotic division is established after the contribution of centrioles by the sperm at fertilization. To avoid the formation of a multipolar spindle in the zygote, centrosomes are eliminated during oogenesis in most organisms, although the mechanism of this selective elimination is poorly understood. We show that cki-2, a Caenorhabditis elegans cyclin-dependent kinase (Cdk) inhibitor, is required for their appropriate elimination during oogenesis. In the absence of cki-2, embryos have supernumerary centrosomes and form multipolar spindles that result in severe aneuploidy after anaphase of the first division. Moreover, we demonstrate that this defect can be suppressed by reducing cyclin E or Cdk2 levels. This implies that the proper regulation of a cyclin E–Cdk complex by cki-2 is required for the elimination of the centrosome that occurs before or during oogenesis to ensure the assembly of a bipolar spindle in the C. elegans zygote.
B-1 B lymphocytes require Blimp-1 for immunoglobulin secretion
Authors: Savitsky David , Calame Kathryn
Published: September 2006

B-1 B cells produce circulating natural antibodies that provide “innate-like” protection against bacterial and viral pathogens. They also provide adaptive responses to blood and air-borne pathogens. B lymphocyte–induced maturation protein 1 (Blimp-1) is a transcriptional repressor that is required for the formation of B-2–derived antibody-secreting plasma cells. In this study, we used mice lacking Blimp-1 in the B cell lineage to show that Blimp-1 is not necessary for the formation or self-renewal of B-1 B cells but that Blimp-1 is required for normal immunoglobulin (Ig) secretion by B-1 cells. B-1 cells lacking Blimp-1 do not repress Pax5 mRNA and do not induce X-box binding protein 1, and μ secreted mRNA normally, showing that B-1 and B-2 cells both use a common pathway for Ig secretion. Blimp-1–deficient B-1 B cells are also defective in providing early protection against influenza infection.
Targeted Comparative RNA Interference Analysis Reveals Differential Requirement of Genes Essential for Cell Proliferation
Authors: Machida Yuichi J. , Chen Yuefeng , Machida Yuka , Malhotra Ankit , Sarkar Sukumar , Dutta Anindya
Published: September 2006

Differences in the genetic and epigenetic make up of cell lines have been very useful for dissecting the roles of specific genes in the biology of a cell. Targeted comparative RNAi (TARCOR) analysis uses high throughput RNA interference (RNAi) against a targeted gene set and rigorous quantitation of the phenotype to identify genes with a differential requirement for proliferation between cell lines of different genetic backgrounds. To demonstrate the utility of such an analysis, we examined 257 growth-regulated genes in parallel in a breast epithelial cell line, MCF10A, and a prostate cancer cell line, PC3. Depletion of an unexpectedly high number of genes (25%) differentially affected proliferation of the two cell lines. Knockdown of many genes that spare PC3 (p53−) but inhibit MCF10A (p53+) proliferation induces p53 in MCF10A cells. EBNA1BP2, involved in ribosome biogenesis, is an example of such a gene, with its depletion arresting MCF10A at G1/S in a p53-dependent manner. TARCOR is thus useful for identifying cell type–specific genes and pathways involved in proliferation and also for exploring the heterogeneity of cell lines. In particular, our data emphasize the importance of considering the genetic status, when performing siRNA screens in mammalian cells.
Regression analysis for comparing protein samples with 16O/18O stable-isotope labeled mass spectrometry
Authors: Eckel-Passow J. E. , Oberg A. L. , Therneau T. M. , Mason C. J. , Mahoney D. W. , Johnson K. L. , Olson J. E. , Bergen H. R.
Published: September 2006

Motivation: Using stable isotopes in global proteome scans, labeled molecules from one sample are pooled with unlabeled molecules from another sample and subsequently subjected to mass-spectral analysis. Stable-isotope methodologies make use of the fact that identical molecules of different stable-isotope compositions are differentiated in a mass spectrometer and are represented in a mass spectrum as distinct isotopic clusters with a known mass shift. We describe two multivariable linear regression models for 16O/18O stable-isotope labeled data that jointly model pairs of resolved isotopic clusters from the same peptide and quantify the abundance present in each of the two biological samples while concurrently accounting for peptide-specific incorporation rates of the heavy isotope. The abundance measure for each peptide from the two biological samples is then used in down-stream statistical analyses, e.g. differential expression analysis. Because the multivariable regression models are able to correct for the abundance of the labeled peptide that appear as an unlabeled peptide due to the inability to exchange the natural C-terminal oxygen for the heavy isotope, they are particularly advantageous for a two-step digestion/labeling procedure. We discuss how estimates from the regression model are used to quantify the variability of the estimated abundance measures for the paired samples. Although discussed in the context of 16O/18O stable-isotope labeled data, the multivariable regression models are generalizable to other stable-isotope labeled technologies.

Contact:  eckel@mayo.edu
DUF283 domain of Dicer proteins has a double-stranded RNA-binding fold
Authors: Dlakić Mensur
Published: September 2006

Two RNases, Dicer and Argonaute, are at the heart of the RNA interference (RNAi) molecular machinery responsible for gene silencing. Both RNases contain multiple domains, most of which have been characterized or have functions that can be predicted based on sequence comparisons. However, Dicers of higher eukaryotes contain the domain known as DUF283 which at present has no assigned role. Using sensitive profile–profile comparisons, we detected a divergent double-stranded RNA-binding domain coinciding with the DUF283 of Dicer. This finding has potential implications regarding the mechanistic role of Dicer in RNAi.

Contact:  mdlakic@montana.edu

Supplementary information: Supplementary images are available at Bioinformatics online.
Synthetic biology—putting engineering into biology
Authors: Heinemann Matthias , Panke Sven
Published: September 2006

Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology's system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.

Contact: panke@ipe.mavt.ethz.ch
Reclassification of Gluconacetobacter hansenii strains and proposals of Gluconacetobacter saccharivorans sp. nov. and Gluconacetobacter nataicola sp. nov.
Authors: Lisdiyanti Puspita , Navarro Richard R. , Uchimura Tai , Komagata Kazuo
Published: September 2006

Ten strains previously assigned toAcetobacter hansenii(=Gluconacetobacter hansenii),Acetobacter pasteurianusLMG 1584 and eight reference strains of the genusGluconacetobacterwere reclassified by 16S rRNA gene sequencing, DNA–DNA similarity, DNA base composition and phenotypic characteristics. TheA. hanseniistrains andA. pasteurianusLMG 1584 were included in the cluster of acetic acid bacteria (familyAcetobacteraceae) by 16S rRNA gene sequences. Further, they were separated into seven distinct groups by DNA–DNA similarity. DNA–DNA similarity group I was identified asG. hansenii. DNA–DNA similarity group II was retained asGluconacetobactersp., because DNA–DNA similarity between the strain andGluconacetobacter entaniiLTH 4560Tcould not be determined. This was due to a lack of availability of the type strain from any source. DNA–DNA similarity group III was regarded as a novel species, for which the nameGluconacetobacter saccharivoranssp. nov. (type strain, LMG 1582T=NRIC 0614T) is proposed. DNA–DNA similarity group IV included the type strains ofGluconacetobacter oboediensandGluconacetobacter intermedius, and threeA. hanseniistrains. This group was identified asG. oboediensbecause high values of DNA–DNA similarity were obtained between the type strains andG. oboedienshas priority overG. intermedius. DNA–DNA similarity group V was identified asGluconacetobacter europaeus. DNA–DNA similarity group VI was regarded as a novel species, for which the nameGluconacetobacter nataicolasp. nov. (type strain, LMG 1536T=NRIC 0616T) is proposed. DNA–DNA similarity group VII was reclassified asGluconacetobacter xylinus. The description ofG. hanseniiis emended.
Gracilibacter thermotolerans gen. nov., sp. nov., an anaerobic, thermotolerant bacterium from a constructed wetland receiving acid sulfate water
Authors: Lee Yong-Jin , Romanek Christopher S. , Mills Gary L. , Davis Richard C. , Whitman William B. , Wiegel Juergen
Published: September 2006

An obligatorily anaerobic, thermotolerant, asporogenic bacterium, strain JW/YJL-S1T, was isolated from a sediment sample of a constructed wetland system receiving acid sulfate water (pH 1.6–3.0). Cells of strain JW/YJL-S1T were straight to curved rods 0.2–0.4 μm in diameter and 2.0–7.0 μm in length, and stained Gram-negative. Growth of strain JW/YJL-S1T was observed at 25–54 °C (no growth at or below 20 or at or above 58 °C), with an optimum temperature range for growth of 42.5–46.5 °C. The pH25 °C range for growth was 6.0–8.25 (no growth at or below pH 5.7 or at or above pH 8.5), with optimum growth at pH 6.8–7.75. The salinity range for growth was 0–1.5 % (w/v) NaCl, with an optimum at 0–0.5 %. During growth on glucose the isolate produced acetate, lactate and ethanol as main fermentation end products. The fatty acid composition was dominated by branched-chain compounds: i15 : 0, a15 : 0, i16 : 0 and i17 : 0. The G+C content of the genomic DNA was 42.8 mol% (HPLC). Strain JW/YJL-S1T showed polymorphism of the 16S rRNA gene. Its closest relative was the thermophilic Clostridium thermosuccinogenes DSM 5807T (a member of Clostridium cluster III) (a blastn search revealed Clostridium pascui DSM 10365T to have 92.7 % gene sequence similarity, the highest value). The inferred phylogenetic trees placed strain JW/YJL-S1T between Clostridium clusters I/II and III. Based on the morphological and phylogenetic data presented, JW/YJL-S1T (=DSM 17427T=ATCC BAA-1219T) is proposed as the type strain of a novel species in a new genus, Gracilibacter thermotolerans gen. nov., sp. nov.
Actinomyces ruminicola sp. nov., isolated from cattle rumen
Authors: An Dengdi , Cai Shichun , Dong Xiuzhu
Published: September 2006

Two obligate anaerobic bacterial strains, B71Tand D471, were isolated from cattle rumen. The novel strains were Gram-positive and rod-shaped. The strains hydrolysed xylan and starch, fermented some mono-, di- and oligosaccharides and produced formic, acetic and lactic acids as end products from glucose. Growth of the isolates was observed at 20–55 °C and pH 6.5–9.0. The DNA G+C contents of strains B71Tand D471 were 68.06 and 68.26 mol%, respectively. Although the two novel strains met the genus description forActinomyces, some phenotypic characteristics, such as optimum growth temperature, requirement for O2and the end products of fermentation, distinguished them from previously described members of the genus. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the novel strains belonged to the genusActinomyces(88.3–93.6 % sequence similarity) and formed a distinct line within the clade containingActinomyces bovis. On the basis of these results, a novel species,Actinomyces ruminicolasp. nov., is proposed. The type strain is B71T(=JCM 13352T=CGMCC 1.5030T).
Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil
Authors: Vasilyeva Lina V. , Omelchenko Marina V. , Berestovskaya Yulia Y. , Lysenko Anatolii M. , Abraham Wolf-Rainer , Dedysh Svetlana N. , Zavarzin George A.
Published: September 2006

A Gram-negative, aerobic, heterotrophic, non-pigmented, dimorphic prosthecate bacterium was isolated from tundra wetland soil and designated strain Z-0023T. Cells of this strain had a dimorphic life cycle and developed a non-adhesive stalk at a site not coincident with the centre of the cell pole, a characteristic typical of representatives of the genus Asticcacaulis. A highly distinctive feature of cells of strain Z-0023T was the presence of a conical, bell-shaped sheath when grown at low temperature. This prosthecate bacterium was a psychrotolerant, moderately acidophilic organism capable of growth between 4 and 28 °C (optimum 15–20 °C) and between pH 4.5 and 8.0 (optimum 5.6–6.0). The major phospholipid fatty acid was 18 : 1ω7c and the major phospholipids were phosphatidylglycerols. The G+C content of the DNA was 60.4 mol%. On the basis of 16S rRNA gene sequence similarity, strain Z-0023T was most closely related to Asticcacaulis biprosthecium (98 % similarity), Asticcacaulis taihuensis (98 %) and Asticcacaulis excentricus (95 %). However, low levels of DNA–DNA relatedness to these organisms and a number of distinctive features of the tundra wetland isolate indicated that it represented a novel species of the genus Asticcacaulis, for which the name Asticcacaulis benevestitus sp. nov. is proposed. The type strain is Z-0023T (=DSM 16100T=ATCC BAA-896T).
Hymenobacter rigui sp. nov., isolated from wetland freshwater
Authors: Baik Keun Sik , Seong Chi Nam , Moon Eun Young , Park Yoon-Dong , Yi Hana , Chun Jongsik
Published: September 2006

A non-motile, rod-shaped and pinkish-red-pigmented bacterium, designated strain WPCB131T, was isolated from freshwater of Woopo wetland, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter with sequence similarities of 93.2–95.5 % to known Hymenobacter species. No other taxa in the phylum Bacteroidetes showed more than 90 % sequence similarity to the isolate. Cells were Gram-negative, oxidase-negative and catalase-positive. Optimum growth was observed at pH 6 and 30 °C. The major fatty acids were iso-C15 : 0 (34.8 %), C16 : 1
ω5c (15.0 %), anteiso-C17 : 1 B/iso-C17 : 1 I (14.4 %) and C16 : 1
ω7c/iso-C15 : 0 2-OH (13.8 %). The DNA G+C content of strain WPCB131T was 65 mol%. The isolate could be readily distinguished from other Hymenobacter species using a combination of phenotypic characters. On the basis of the polyphasic evidence presented in this study, it is proposed that strain WPCB131T (=IMSNU 14116T=KCTC 12533T=NBRC 101118T) represents a novel species, Hymenobacter rigui sp. nov.
Rubrivivax benzoatilyticus sp. nov., an aromatic, hydrocarbon-degrading purple betaproteobacterium
Authors: Ramana Ch. V. , Sasikala Ch. , Arunasri K. , Anil Kumar P. , Srinivas T. N. R. , Shivaji S. , Gupta P. , Süling J. , Imhoff J. F.
Published: September 2006

A brown-coloured bacterium was isolated from photoheterotrophic (benzoate) enrichments of flooded paddy soil from Andhra Pradesh, India. On the basis of 16S rRNA gene sequence analysis, strain JA2T was shown to belong to the class Betaproteobacteria, related to Rubrivivax gelatinosus (99 % sequence similarity). Cells of strain JA2T are Gram-negative, motile rods with monopolar single flagella. The strain contained bacteriochlorophyll a and most probably the carotenoids spirilloxanthin and sphaeroidene, but did not have internal membrane structures. Intact cells had absorption maxima at 378, 488, 520, 590, 802 and 884 nm. No growth factors were required. Strain JA2T grew on benzoate, 2-aminobenzoate (anthranilate), 4-aminobenzoate, 4-hydroxybenzoate, phthalate, phenylalanine, trans-cinnamate, benzamide, salicylate, cyclohexanone, cyclohexanol and cyclohexane-2-carboxylate as carbon sources and/or electron donors. The DNA G+C content was 74.9 mol%. Based on DNA–DNA hybridization studies, 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA2T is different from representatives of other photosynthetic species of the Betaproteobacteria and was recognised as representing a novel species, for which the name Rubrivivax benzoatilyticus sp. nov. is proposed. The type strain is JA2T (=ATCC BAA-35T=JCM 13220T=MTCC 7087T).
Paenibacillus gansuensis sp. nov., isolated from desert soil of Gansu Province in China
Authors: Lim Jee-Min , Jeon Che Ok , Lee Jae-Chan , Xu Li-Hua , Jiang Cheng-Lin , Kim Chang-Jin
Published: September 2006

A Gram-positive, endospore-forming, rod-shaped bacterium, designated strain B518T, was isolated from a desert-soil sample from Gansu Province in China. The isolate was strictly aerobic and was motile by means of several flagella. The strain grew optimally at 35–40 °C and at pH 7.0–7.5. The predominant fatty acids of strain B518Twere anteiso-C15 : 0, C16 : 0, anteiso-C17 : 0, iso-C16 : 0and iso-C15 : 0. The G+C content of the genomic DNA was 50 mol% and the predominant quinone was MK-7. Comparative 16S rRNA gene sequence analyses showed that strain B518Tformed a distinct phyletic line within the genusPaenibacillusand was most closely related toPaenibacillus chitinolyticusIFO 15660T, with a 16S rRNA gene sequence similarity of 95.8 %. The levels of 16S rRNA gene sequence similarity with respect to other type strains ofPaenibacillusspecies were below 95.1 %. On the basis of the chemotaxonomic data and molecular properties, strain B518Trepresents a novel species within the genusPaenibacillus, for which the namePaenibacillus gansuensissp. nov. is proposed. The type strain is B518T(=KCTC 3950T=DSM 16968T).
Trichococcus patagoniensis sp. nov., a facultative anaerobe that grows at −5 °C, isolated from penguin guano in Chilean Patagonia
Authors: Pikuta Elena V. , Hoover Richard B. , Bej Asim K. , Marsic Damien , Whitman William B. , Krader Paul E. , Tang Jane
Published: September 2006

A novel, extremely psychrotolerant, facultative anaerobe, strain PmagG1T, was isolated from guano of Magellanic penguins (Spheniscus magellanicus) collected in Chilean Patagonia. Gram-variable, motile cocci with a diameter of 1.3–2.0 μm were observed singularly or in pairs, short chains and irregular conglomerates. Growth occurred within the pH range 6.0–10.0, with optimum growth at pH 8.5. The temperature range for growth of the novel isolate was from −5 to 35 °C, with optimum growth at 28–30 °C. Strain PmagG1Tdid not require NaCl, as growth was observed in the presence of 0–6.5 % NaCl with optimum growth at 0.5 % (w/v). Strain PmagG1Twas a catalase-negative chemo-organoheterotroph that used sugars and some organic acids as substrates. The metabolic end products were lactate, formate, acetate, ethanol and CO2. Strain PmagG1Twas sensitive to ampicillin, tetracycline, chloramphenicol, rifampicin, kanamycin and gentamicin. The G+C content of its genomic DNA was 45.8 mol%. 16S rRNA gene sequence analysis showed 100 % similarity of strain PmagG1TwithTrichococcus collinsiiATCC BAA-296T, but DNA–DNA hybridization between them demonstrated relatedness values of <45±1 %. Another phylogenetically closely related species,Trichococcus pasteurii, showed 99.85 % similarity by 16S rRNA sequencing and DNA–DNA hybridization showed relatedness values of 47±1.5 %. Based on genotypic and phenotypic characteristics, the novel speciesTrichococcus patagoniensissp. nov. is proposed, with strain PmagG1T(=ATCC BAA-756T=JCM 12176T=CIP 108035T) as the type strain.
Actinoplanes liguriensis sp. nov. and Actinoplanes teichomyceticus sp. nov.
Authors: Wink Joachim M. , Kroppenstedt Reiner M. , Schumann Peter , Seibert Gerhard , Stackebrandt Erko
Published: September 2006

The taxonomic status of ‘Actinoplanes liguriae’ A/6353 and ‘Actinoplanes teichomyceticus’ AB8327 was established by using a polyphasic approach. Strains A/6353 and AB8327 form distinct phylogenetic lineages in the 16S rRNA gene tree of members of the genus Actinoplanes and are related moderately and closely to Actinoplanes rectilineatus and Actinoplanes cyaneus, respectively. Morphological, cultural and physiological properties indicated that strains A/6353 and AB8327 represent separate, novel species of the genus Actinoplanes, Actinoplanes liguriensis sp. nov. (type strain A/6353T=FH 2244T=DSM 43865T=ATCC 31048T=BCRC 12121T=CBS 355.75T=IMSNU 22127T=JCM 3250T=KCTC 9536T=KCC A-0250T=NBRC 13997T=NCIMB 12636T=NRRL B-16723T=SANK 62178T) and Actinoplanes teichomyceticus sp. nov. (type strain AB8327T=FH 2149T=DSM 43866T=ATCC 31121T=BCRC 12106T=FERM P-3462T=IMSNU 20043T=IMET 9254T=JCM 3252T=KCC A-0252T=KCTC 9543T=NBRC 13999T=NCIMB 12640T=NRRL B-16726T=SANK 60479T).
Xylanibacter oryzae gen. nov., sp. nov., a novel strictly anaerobic, Gram-negative, xylanolytic bacterium isolated from rice-plant residue in flooded rice-field soil in Japan
Authors: Ueki Atsuko , Akasaka Hiroshi , Suzuki Daisuke , Hattori Satoshi , Ueki Katsuji
Published: September 2006

A strictly anaerobic, xylanolytic bacterium, strain KB3T, isolated from rice-plant residue in flooded anoxic rice-field soil in Japan, was characterized phenotypically and phylogenetically. Cells were Gram-negative, non-motile, non-spore-forming, short to filamentous rods. Growth of the strain was remarkably stimulated by the addition of haemin to the medium. The novel strain utilized various sugars including xylan, xylose, pectin and carboxymethylcellulose and produced acetate, propionate and succinate with a small amount of malate. Propionate production was stimulated by the addition of a B-vitamin mixture or cobalamin to the medium. The novel strain was slightly acidophilic with an optimum pH 5.7–6.2 and the optimum growth temperature was 30 °C. Oxidase, catalase and nitrate-reducing activities were negative. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0 and iso-3-OH C17 : 0. The major respiratory quinones were menaquinones MK-12(H2) and MK-13(H2). The genomic DNA G+C content was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence placed the strain in the phylum Bacteroidetes. The closest related species was Prevotella bivia with a 16S rRNA gene sequence similarity of 89.5 %. Prevotella albensis and Prevotella oulorum were the next closest recognized species with sequence similarities of 89.1 %. Based on a comprehensive examination of the differences in phylogenetic, ecological, physiological and chemotaxonomic characteristics of strain KB3T and those of related species, a novel genus and species, Xylanibacter oryzae gen. nov., sp. nov., is proposed to accommodate strain KB3T. The type strain of the novel species is KB3T (=JCM 13648T=DSM 17970T).
Proposal of Hymenobacter norwichensis sp. nov., classification of ‘Taxeobacter ocellatus’, ‘Taxeobacter gelupurpurascens’ and ‘Taxeobacter chitinovorans’ as Hymenobacter ocellatus sp. nov., Hymenobacter gelipurpurascens sp. nov. and Hymenobacter chitinivorans sp. nov., respectively, and emended description of the genus Hymenobacter Hirsch et al. 1999
Authors: Buczolits Sandra , Denner Ewald B. M. , Kämpfer Peter , Busse Hans-Jürgen
Published: September 2006

Two airborne bacterial isolates, NS/2 and NS/50T, were examined in order to determine their taxonomic position. Their almost complete 16S rRNA gene sequences shared 95.9 % similarity. Sequence comparisons demonstrated that their next relatives are species of the genus Hymenobacter (93.6–95.7 % similarity) and the strains ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T (90.5–96.4 %). Phylogenetic calculations indicated that these five strains together with the three recognized Hymenobacter species form a separate line of descent within the family ‘Flexibacteraceae’. Isolates NS/2 and NS/50T, as well as ‘Taxeobacter chitinovorans’ Txc1T, ‘Taxeobacter gelupurpurascens’ Txg1T and ‘Taxeobacter ocellatus’ Myx 2105T, possessed the characteristics of the genus Hymenobacter, the quinone system menaquinone MK-7 and a polyamine pattern with the major polyamine being sym-homospermidine. Each of the five strains had complex, unique polar lipid profiles, with phosphatidylethanolamine and several unknown aminophospho-, amino-, phospho-, glyco- and polar lipids of which several compounds were also found in established Hymenobacter species. All the strains studied possessed fatty acids characteristic of Hymenobacter species, including major acids iso-C15 : 0, anteiso-C15 : 0, C16 : 1
ω5c, summed feature 3 (C16 : 1
ω7c/iso-C15 : 0 2-OH) and summed feature 4 (iso-C17 : 1 I/anteiso-C17 : 1 B). The five strains could be distinguished from each other and from the three established species of the genus Hymenobacter based on relatively low 16S rRNA gene sequence similarities (<97 %), unique polar lipids and differing fatty acid profiles and physiological characteristics. In conclusion, the description of four novel species of the genus Hymenobacter appears to be justified, for which the names Hymenobacter norwichensis sp. nov. (type strain NS/50T=LMG 21876T=DSM 15439T), Hymenobacter chitinivorans sp. nov. (type strain Txc1T=LMG 21951T=DSM 11115T), Hymenobacter gelipurpurascens sp. nov. (type strain Txg1T=LMG 21873T=DSM 11116T) and Hymenobacter ocellatus sp. nov. (type strain Myx 2105T=Txo1T=LMG 21873T=DSM 11117T) are proposed. For strain NS/2, a description only is provided without proposal of a name because its status as a novel species was not demonstrated unambiguously.
Do the Benefits Justify the Costs? An Evaluation of the ‘Sitter Service’ in Scotland
Authors: Wilson Valerie , Hall Stuart , Davidson Julia
Published: September 2006

This research identified the costs and benefits of the sitter service in Scotland. A ‘sitter service’ is one that provides home‐based childcare outside the hours of 8:00 am to 6:00 pm on weekdays and at weekends to support children of shift workers, single parents/carers and for children who require additional support. Nine sitter services, organised by voluntary or not‐for‐profit organisations in Scotland, were contacted; their costs were compared and the views of sitters and users identified. For very little expenditure, they provided a service that resulted in a range of individual and community benefits. However, the research concludes that most sitter services are hat small scale and piecemeal funding endangers their long‐term viability.
(De)Constructing the Risk Categories in the AIM Assessment Model for Children with Sexually Harmful Behaviour
Authors: Myers Steve
Published: September 2006

This article critically analyses the AIM Assessment Model for children who have sexually harmful behaviour, exploring the underpinning knowledge and the processes involved. The model reflects current trends in the assessment of children, in child welfare and criminal justice services, producing categories of risk that lead to levels of intervention. When subjected to critical review, the knowledge base emerges as partial, contingent and obscured, and the process generates a particular construction of the subject which has consequences for practice. A social constructionist perspective is used to make visible some of the ways in which this knowledge is generated and how this may assist practitioners in considering the relations of power within such protocols.
‘Sticking with your Mates?’ Children's Friendship Trajectories during the Transition from Primary to Secondary School
Authors: Weller Susie
Published: September 2006

For many children, the transition to secondary school is marked by both anxiety and excitement, particularly in relation to friendship. This article draws upon the concept of social capital — the resources individuals and collectives derive from their social networks — in order to understand the significance of change and continuity in children's friendships during a challenging period in their lives. Children's social networks often provide important, but under‐researched resources which aid their progress through the transition. This article presents findings from a three‐year ESRC study exploring children's and parents’ use of social capital during their secondary school transfer.
Modelling the effect of Nile perch predation and harvesting on fisheries dynamics of Lake Victoria
Authors: Mugisha J. Y. T. , Ddumba H.
Published: September 2006

We used a mathematical model to predict and explain the effect of harvesting combined with predation by the Nile perch on Nile tilapia. The model incorporates three developmental stages of each species. The findings show that uncontrolled human exploitation of the stock leads to loss of fish biodiversity in the lake. The results of the study also show that increasing harvesting rate of the mature Nile perch leads to stable stationary states of the system. However, increasing predation rates by Nile perch lead to unstable equilibria.
Living in the shadow of fear: adolescents’ lived experience of depression
Authors: Woodgate Roberta Lynn
Published: September 2006

Aim.  This paper reports a phenomenological study whose aim was to gain an understanding of what it was like to be an adolescent living with depression.

Background.  Depression is a significant mental health problem among adolescents. Identifying the meanings that adolescents assign to their experiences with depression is needed in order to develop interventions that will improve their care and quality of life.

Method.  The study took place in a city in Western Canada. Fourteen adolescents (13·5 to 18 years) diagnosed with depression participated in individual open‐ended interviews and focus group interviews between July 2001 and June 2002. Field notes were recorded. Thematic statements that were representative of the adolescents’ lived experience were isolated from the interviews and field notes. Using all the phrases, sentence clusters and field notes, the data were then reduced until essential and incidental themes emerged.

Findings.  ‘Living in the shadow of fear’ emerged as the essence of the adolescents’ experiences and ultimately defined what it was like to live with depression. The shadow of fear was associated not only with fear of a return of the ‘bad’ feelings related to their depression, but also to fear of not getting help, not surviving the ‘bad’ feelings, and fear of having to do all the ‘hard work’ in overcoming the ‘bad’ feelings. This essence was supported by four themes: ‘containing the shadow of fear’, ‘keeping the self alive’, ‘maintaining a sense of belonging in the world’ and ‘feeling valued as a human being’.

Conclusions.  Adolescents with depression need adequate resources and support throughout the illness trajectory, including those periods when their depression is under control.
Effects of growth hormone and gonadotrophin releasing hormone antagonists on ovarian follicle growth in sheep
Authors: GONZALEZ AÑOVER P. , GONZALEZ‐BULNES A. , VEIGA‐LOPEZ A. , GARCIA‐GARCIA R. M. , MCNEILLY A. S. , ENCINAS T.
Published: September 2006

Our objective was to determine the effects of the administration of growth hormone (GH) alone or plus teverelix, a gonadotrophin releasing hormone antagonist (GnRHa), on follicle development in sheep. Ewes were treated daily for 6 days by the intramuscular route with 15 mg of GH alone (GH group; n = 6) or combined with two subcutaneous doses of GnRHa (1.5 mg) on days 0 and 3 of GH treatment (GH/GnRHa group; n = 6); the control group (n = 6) received similar treatment with saline solution. Plasma follicle stimulating hormone levels were significantly lower in the GH/GnRHa group than in the control (P < 0.001) and GH groups (P < 0.05). The number of follicles ≥2 mm increased to reach significant differences with control (18.7 ± 0.6) on day 4 in GH/GnRHa group (22.7 ± 0.5, P < 0.001) and on day 5 in GH group (20.3 ± 0.4 vs. 17.0 ± 0.6, P < 0.05). These results indicate that GH and GnRHa may be useful for increasing the number of gonadotrophin‐responsive follicles in the ovary. However, follicle function could be affected as both GH and GH/GnRHa groups showed lower plasma inhibin A concentrations than control sheep (90–110 pg/mL vs. 170–185 pg/mL, P < 0.005).
Neurophysiological techniques to assess pain in animals
Authors: MURRELL J. C. , JOHNSON C. B.
Published: September 2006

Neurophysiological techniques are widely applied to animals, both in the search as a monitor for adequacy of anaesthesia, and studies to assess the efficacy of analgesic agents. Laboratory animals have been extensively used in models to investigate pain in man. However a substantial number of studies have also used neurophysiological techniques to increase knowledge of pain in specific animal species, with the aim of improving animal welfare. This review provides an overview of neurophysiological techniques involving the brain that have been used in the assessment of pain in animals. An explanation of the methodology of EEG recording, with particular emphasis on veterinary studies, is given. Neurophysiological models developed to assess pain in different species are described, and their relevance to advancements in animal welfare or best clinical practice indicated.
Effect of ofloxacin on theophylline pharmacokinetics at clinical dosage in dogs
Authors: REGMI N. L. , ABD EL‐ATY A. M. , KUBOTA R. , TOMITA A. , SHIMODA M.
Published: September 2006

We examined the effects of ofloxacin (OFX) and norfloxacin (NFX) on theophylline (TP) pharmacokinetics in dogs. OFX, as a noncompetitive and mechanism‐based inhibitor, and NFX, as a noncompetitive inhibitor, were orally administered (5 mg/kg) for a single dose or multiple doses (12 hourly for 3 days). TP (5 mg/kg, i.v) was injected at 2 h after the final dose of the fluoroquinolones (FQs). The same dose of TP was injected (i.v) 3 weeks before the start of FQs treatment for control. Multiple doses of OFX significantly reduced the total body clearance (ClB) of TP from 0.117 to 0.085 L/h/kg, although a single dose did not change it. Neither a single dose nor multiple doses of NFX changed the TP pharmacokinetics. Plasma NFX concentrations increased after multiple doses. Those of OFX also increased but were still two orders of magnitude below the Kifor noncompetitive inhibition of CYP1A in dogs. Time‐dependent reduction inClBof TP suggests that mechanism‐based inhibition of OFX was the major mode to decreaseClBof TP. The mechanism‐based inhibition may result in substantial inhibition of CYP1A activities in clinical conditions.
Interspecies allometric scaling. Part I: prediction of clearance in large animals
Authors: MAHMOOD I. , MARTINEZ M. , HUNTER R. P.
Published: September 2006

Interspecies scaling is a useful tool for the prediction of pharmacokinetic parameters from animals to humans, and it is often used for estimating a first‐time in human dose. The knowledge of pharmacokinetics in veterinary species is important for dosage selection, particularly in the treatment of large zoo animal species, such as elephants, giant cats and camels, for which pharmacokinetic data are scant. Therefore, the accuracy in clearance predictions in large animal species, with and without the use of correction factors (rule of exponents), and the impact of species selection in the prediction of clearance in large animal species was examined. Based upon this analysis, it was determined that there is a much larger risk of inaccuracies in the clearance estimates in large animal species when compared with that observed for humans. Unlike in humans, for large animal species, correction factors could not be applied because there was no trend between the exponents of simple allometry and the appropriate correction factor for improving our predictions. Nevertheless, we did see an indication that the exponents of simple allometry may alert us as to when the predicted clearance in the large animal may be underestimated or overpredicted. For example, if a large animal is included in the scaling, the predicted clearance in a large animal should be considered overestimated if the exponent of simple allometry is >1.3. Despite the potential for extrapolation error, the reality is that allometric scaling is needed across many veterinary practice situations, and therefore will be used. For this reason, it is important to consider mechanisms for reducing the risk of extrapolation errors that can seriously affect target animal safety, therapeutic response, or the accuracy of withdrawal time predictions.
Late Quaternary history of Hippophaë rhamnoides L. (Elaeagnaceae) inferred from chalcone synthase intron (Chsi) sequences and chloroplast DNA variation
Authors: BARTISH IGOR V. , KADEREIT JOACHIM W. , COMES HANS PETER
Published: September 2006

Fossil pollen records indicate that Hippophaë rhamnoides (Sea Buckthorn) was widespread on late‐ and early postglacial raw soils throughout much of central and northern Europe, but that Early Holocene reforestation restricted populations to northern coastal habitats, or along mountain streams in the Alps, Pyrenees, and Carpathians. We used sequence variation at the nuclear chalcone synthase intron (Chsi), in conjunction with chloroplast DNA–restriction fragment length polymorphism data, to investigate the intraspecific phylogeny, phylogeographic structure, and expansion demographic history of this dioecious and wind‐pollinated shrub at its range‐wide scale in Europe and Asia Minor. Four major Chsi phylogroups of unresolved relationships were identified with estimated divergences ∼172 000 years ago. Large‐scale phylogeographic structures of nuclear and cytoplasmic markers were congruent in identifying (i) southeastern Europe as the most likely source of colonization into central Europe and Scandinavia, and (ii) the area just north of the Alps as a contact zone between populations from the Alps and the east/central European‐Scandinavian lineage. Coalescence‐based analyses (i.e. nested clade analysis and mismatch distributions) of Chsi variation were able to detect at least four major episodes of population growth, all within about the last 40 000 years. In particular, these analyses identified a nearly synchronized timing of population expansions in various parts of the species’ range in central‐eastern Europe/Asia Minor, most likely correlating with the Younger Dryas Stadial (∼13 000–11 600 years ago). It remains to be established whether the phylogeographic history of H. rhamnoides, and particularly its rapid response to the rapid environmental changes of the Younger Dryas cold snap, is unique to the species, or whether it is shared with other cold‐tolerant shrub (or grassland) species known from late‐glacial raw soils in Europe.
Demographic history and population structure of the Antarctic silverfish Pleuragramma antarcticum
Authors: ZANE L. , MARCATO S. , BARGELLONI L. , BORTOLOTTO E. , PAPETTI C. , SIMONATO M. , VAROTTO V. , PATARNELLO T.
Published: September 2006

The Antarctic silverfish Pleuragramma antarcticum (Nototheniidae) is the most abundant pelagic fish inhabiting Antarctic waters. In this study we investigated, through partial sequencing of the D‐loop mitochondrial region, samples collected at four different locations in the Southern Ocean, three in the Atlantic and one in the Pacific sector. Sampling was replicated in two different years at two locations. Sequence analysis showed a remarkably high polymorphism, with 110 haplotypes over the 256 investigated specimens, and about 80% of haplotypes occurring only once. Neutrality tests indicated that all samples were not at mutation–drift equilibrium, and suggested a past population expansion. This result was supported by the presence of a star‐like topology in the D‐loop gene tree, and by results of mismatch distribution. The start of the expansion was dated, using a specifically calibrated clock, between 111 and 126 thousand years ago. This value corresponds to the start of the cooling period that led to the last glaciation peak, and is in close agreement with a recently suggested range expansion for pelagic Antarctic ecosystems. Analysis of molecular variation indicated a small, though highly significant, value of differentiation between samples. This result, together with the lack of association between clades and geographical locations, indicates a weak population structure for the species.