bluuebunny/crossref_metadata_2025 huggingface dataset:
Cost-effectiveness analysis of an alternative tuberculosis management strategy for permanent farm dwellers in South Africa amidst health service contraction
Authors: Clarke Marina , Dick Judy , Bogg Lennart
Published: January 2006

Aim: To establish the cost-effectiveness of lay health workers (LHWs) in conjunction with the current, local tuberculosis (TB) control programme, amidst health service contraction. Method: A cost-effectiveness analysis, comparing direct time costs of the current TB management strategy among permanent farm dwellers, with an intervention, whereby LHWs are involved in TB control activities on farms. Measure of effectiveness was case finding and cure rates of adult new smear-positive (NSP) TB cases, alongside a randomized control trial (RCT): Results: The observed cost reduction to the Boland Health District was 74% per case detected and cured on the intervention farms relative to the control farms. Intervention farms reached 83% successful treatment completion rate, control farms 65%. Although the successful treatment adherence was significantly different (18% letter). The improved case detection and cure rates were not statistically significant (chisquared test). Direct LHW costs are borne by farmers. Farmers were motivated to bear costs by reduced job absenteeism and other positive side-effects. Even without outcome improvements costs per case cured were 59% lower on the intervention farms. Conclusion: TB control has suffered from budget reductions in South Africa. It is critically important to develop cost-effective strategies to reduce the TB burden. Costs to public budgets can be substantially reduced while maintaining or improving case detection and treatment outcomes, by using farm-based LHWs.
Context effects of pictures and words in naming objects, reading words, and generating simple phrases
Authors: Roelofs Ardi
Published: January 2006

In five language production experiments it was examined which aspects of words are activated in memory by context pictures and words. Context pictures yielded Stroop-like and semantic effects on response times when participants generated gender-marked noun phrases in response to written words (Experiment 1A). However, pictures yielded no such effects when participants simply read aloud the noun phrases (Experiment 2). Moreover, pictures yielded a gender congruency effect in generating gender-marked noun phrases in response to the written words (Experiments 3A and 3B). These findings suggest that context pictures activate lemmas (i.e., representations of syntactic properties), which leads to effects only when lemmas are needed to generate a response (i.e., in Experiments 1A, 3A, and 3B, but not in Experiment 2). Context words yielded Stroop-like and semantic effects in picture naming (Experiment 1B). Moreover, words yielded Stroop-like but no semantic effects in reading nouns (Experiment 4) and in generating noun phrases (Experiment 5). These findings suggest that context words activate the lemmas and forms of their names, which leads to semantic effects when lemmas are required for responding (Experiment 1B) but not when only the forms are required (Experiment 4). WEAVER++ simulations of the results are presented.
Visual saliency and semantic incongruency influence eye movements when inspecting pictures
Authors: Underwood Geoffrey , Foulsham Tom
Published: January 2006

Models of low-level saliency predict that when we first look at a photograph our first few eye movements should be made towards visually conspicuous objects. Two experiments investigated this prediction by recording eye fixations while viewers inspected pictures of room interiors that contained objects with known saliency characteristics. Highly salient objects did attract fixations earlier than less conspicuous objects, but only in a task requiring general encoding of the whole picture. When participants were required to detect the presence of a small target, then the visual saliency of nontarget objects did not influence fixations. These results support modifications of the model that take the cognitive override of saliency into account by allowing task demands to reduce the saliency weights of task-irrelevant objects.

The pictures sometimes contained incongruent objects that were taken from other rooms. These objects were used to test the hypothesis that previous reports of the early fixation of congruent objects have not been consistent because the effect depends upon the visual conspicuity of the incongruent object. There was an effect of incongruency in both experiments, with earlier fixation of objects that violated the gist of the scene, but the effect was only apparent for inconspicuous objects, which argues against the hypothesis.
Attention to Arrows: Pointing to a New Direction
Authors: Ristic Jelena , Kingstone Alan
Published: January 2006

It was long believed that central arrows needed to be spatially predictive to produce a shift in spatial attention. Recent evidence indicates, however, that central spatially nonpredictive directional cues, like arrows, will trigger reflexive shifts in attention. We asked what this recent discovery means for past studies that used predictive directional cues such as arrows. Our findings indicate that predictive arrows produce attention effects that greatly exceed the individual or summed effects of reflexive orienting to nonpredictive arrows and volitional orienting to predictive numbers. This suggests that the especially large effect produced by predictive arrows reflects an interaction between reflexive and volitional orienting. Given the broad application of the predictive arrow cueing paradigm in both past and current research, the present data shed new light on a wide range of investigations, from psychophysical studies of basic attention to behavioural and neuroimaging studies of cognition and social development.
Compatibility Effects in Stopping and Response Initiation in a Continuous Tracking Task
Authors: Morein-Zamir Sharon , Nagelkerke Paul , Chua Romeo , Franks Ian , Kingstone Alan
Published: January 2006

Two experiments explored stopping performance using a new stimulus–response compatibility effect spanning action initiation and stopping. Participants tracked a sometimes-moving, sometimes-stationary target by controlling the speed of a response marker via a force sensor. In the compatible condition, participants pressed the sensor in response to the target moving and stopped pressing in response to the target stopping. In the incompatible condition, participants stopped pressing in response to the target moving and initiated pressing in response to the target stopping. Response initiation and stopping were found to be faster under compatible than under incompatible conditions, regardless of whether compatible and incompatible trials were blocked or mixed. These findings indicate that stopping, like response initiation, is influenced by stimulus–response properties such as compatibility. This in turn suggests that stopping is governed by constraints similar to those of other behaviours.
The Distinct Contributions of Age of Acquisition and Word Frequency in Auditory Word Perception
Authors: Smith Philip T. , Turner Judy E. , Brown Penelope A. , Henry Lucy A.
Published: January 2006

We report two studies of the distinct effects that a word's age of acquisition (AoA) and frequency have on the mental lexicon. In the first study, a purely statistical analysis, we show that AoA and frequency are related in different ways to the phonological form and imageability of different words. In the second study, three groups of participants (34 seven-year-olds, 30 ten-year-olds, and 17 adults) took part in an auditory lexical decision task, with stimuli varying in AoA, frequency, length, neighbourhood density, and imageability. The principal result is that the influence of these different variables changes as a function of AoA: Neighbourhood density effects are apparent for early and late AoA words, but not for intermediate AoA, whereas imageability effects are apparent for intermediate AoA words but not for early or late AoA. These results are discussed from the perspective that AoA affects a word's representation, but frequency affects processing biases.
P21-activated kinase 1: convergence point in PDGF- and LPA-stimulated collagen matrix contraction by human fibroblasts
Authors: Rhee Sangmyung , Grinnell Frederick
Published: January 2006

Fibroblast three-dimensional collagen matrix culture provides a tissue-like model that can be used to analyze cell form and function. The physiological agonists platelet-derived growth factor (PDGF) and lysophosphatidic acid (LPA) both stimulate human fibroblasts to contract floating collagen matrices. In this study, we show that the PDGF and LPA signaling pathways required for matrix contraction converge on p21-activated kinase 1 (PAK1) and its downstream effector cofilin1 and that contraction depends on cellular ruffling activity, rather than on the protrusion and retraction of cellular dendritic extensions. We also show that, depending on the agonist, different Rho effectors cooperate with PAK1 to regulate matrix contraction, Rho kinase in the case of PDGF and mDia1 in the case of LPA. These findings establish a unified framework for understanding the cell signaling pathways involved in fibroblast contraction of floating collagen matrices.
Neuronal cotransport of glycine receptor and the scaffold protein gephyrin
Authors: Maas Christoph , Tagnaouti Nadia , Loebrich Sven , Behrend Bardo , Lappe-Siefke Corinna , Kneussel Matthias
Published: January 2006

The dynamics of postsynaptic receptor scaffold formation and remodeling at inhibitory synapses remain largely unknown. Gephyrin, which is a multimeric scaffold protein, interacts with cytoskeletal elements and stabilizes glycine receptors (GlyRs) and individual subtypes of γ-aminobutyric acid A receptors at inhibitory postsynaptic sites. We report intracellular mobility of gephyrin transports packets over time. Gephyrin units enter and exit active synapses within several minutes. In addition to previous reports of GlyR–gephyrin interactions at plasma membranes, we show cosedimentation and coimmunoprecipitation of both proteins from vesicular fractions. Moreover, GlyR and gephyrin are cotransported within neuronal dendrites and further coimmunoprecipitate and colocalize with the dynein motor complex. As a result, the blockade of dynein function or dynein–gephyrin interaction, as well as the depolymerization of microtubules, interferes with retrograde gephyrin recruitment. Our data suggest a GlyR–gephyrin–dynein transport complex and support the concept that gephyrin–motor interactions contribute to the dynamic and activity-dependent rearrangement of postsynaptic GlyRs, a process thought to underlie the regulation of synaptic strength.
Localized recruitment and activation of RhoA underlies dendritic spine morphology in a glutamate receptor–dependent manner
Authors: Schubert Vanessa , Da Silva Jorge Santos , Dotti Carlos G.
Published: January 2006

Actin is the major cytoskeletal source of dendritic spines, which are highly specialized protuberances on the neuronal surface where excitatory synaptic transmission occurs (Harris, K.M., and S.B. Kater. 1994. Annu. Rev. Neurosci. 17:341–371; Yuste, R., and D.W. Tank. 1996. Neuron. 16:701–716). Stimulation of excitatory synapses induces changes in spine shape via localized rearrangements of the actin cytoskeleton (Matus, A. 2000. Science. 290:754–758; Nagerl, U.V., N. Eberhorn, S.B. Cambridge, and T. Bonhoeffer. 2004. Neuron. 44:759–767). However, what remains elusive are the precise molecular mechanisms by which different neurotransmitter receptors forward information to the underlying actin cytoskeleton. We show that in cultured hippocampal neurons as well as in whole brain synaptosomal fractions, RhoA associates with glutamate receptors (GluRs) at the spine plasma membrane. Activation of ionotropic GluRs leads to the detachment of RhoA from these receptors and its recruitment to metabotropic GluRs. Concomitantly, this triggers a local reduction of RhoA activity, which, in turn, inactivates downstream kinase RhoA-specific kinase, resulting in restricted actin instability and dendritic spine collapse. These data provide a direct mechanistic link between neurotransmitter receptor activity and the changes in spine shape that are thought to play a crucial role in synaptic strength.
Asynchronous nuclear division cycles in multinucleated cells
Authors: Gladfelter Amy S. , Hungerbuehler A. Katrin , Philippsen Peter
Published: January 2006

Synchronous mitosis is common in multinucleated cells. We analyzed a unique asynchronous nuclear division cycle in a multinucleated filamentous fungus, Ashbya gossypii. Nuclear pedigree analysis and observation of GFP-labeled spindle pole bodies demonstrated that neighboring nuclei in A. gossypii cells are in different cell cycle stages despite close physical proximity. Neighboring nuclei did not differ significantly in their patterns of cyclin protein localization such that both G1 and mitotic cyclins were present regardless of cell cycle stage, suggesting that the complete destruction of cyclins is not occurring in this system. Indeed, the expression of mitotic cyclin lacking NH2-terminal destruction box sequences did not block cell cycle progression. Cells lacking AgSic1p, a predicted cyclin-dependent kinase (CDK) inhibitor, however, showed aberrant multipolar spindles and fragmented nuclei that are indicative of flawed mitoses. We hypothesize that the continuous cytoplasm in these cells promoted the evolution of a nuclear division cycle in which CDK inhibitors primarily control CDK activity rather than oscillating mitotic cyclin proteins.
Derlin-2 and Derlin-3 are regulated by the mammalian unfolded protein response and are required for ER-associated degradation
Authors: Oda Yukako , Okada Tetsuya , Yoshida Hiderou , Kaufman Randal J. , Nagata Kazuhiro , Mori Kazutoshi
Published: January 2006

Proteins that are unfolded or misfolded in the endoplasmic reticulum (ER) must be refolded or degraded to maintain the homeostasis of the ER. Components of both productive folding and ER-associated degradation (ERAD) mechanisms are known to be up-regulated by the unfolded protein response (UPR). We describe two novel components of mammalian ERAD, Derlin-2 and -3, which show weak homology to Der1p, a transmembrane protein involved in yeast ERAD. Both Derlin-2 and -3 are up-regulated by the UPR, and at least Derlin-2 is a target of the IRE1 branch of the response, which is known to up-regulate ER degradation enhancing α-mannosidase–like protein (EDEM) and EDEM2, receptor-like molecules for misfolded glycoprotein. Overexpression of Derlin-2 or -3 accelerated degradation of misfolded glycoprotein, whereas their knockdown blocked degradation. Derlin-2 and -3 are associated with EDEM and p97, a cytosolic ATPase responsible for extraction of ERAD substrates. These findings indicate that Derlin-2 and -3 provide the missing link between EDEM and p97 in the process of degrading misfolded glycoproteins.
Salamander limb regeneration involves the activation of a multipotent skeletal muscle satellite cell population
Authors: Morrison Jamie I. , Lööf Sara , He Pingping , Simon András
Published: January 2006

In contrast to mammals, salamanders can regenerate complex structures after injury, including entire limbs. A central question is whether the generation of progenitor cells during limb regeneration and mammalian tissue repair occur via separate or overlapping mechanisms. Limb regeneration depends on the formation of a blastema, from which the new appendage develops. Dedifferentiation of stump tissues, such as skeletal muscle, precedes blastema formation, but it was not known whether dedifferentiation involves stem cell activation. We describe a multipotent Pax7+ satellite cell population located within the skeletal muscle of the salamander limb. We demonstrate that skeletal muscle dedifferentiation involves satellite cell activation and that these cells can contribute to new limb tissues. Activation of salamander satellite cells occurs in an analogous manner to how the mammalian myofiber mobilizes stem cells during skeletal muscle tissue repair. Thus, limb regeneration and mammalian tissue repair share common cellular and molecular programs. Our findings also identify satellite cells as potential targets in promoting mammalian blastema formation.
Prostacyclin-IP signaling and prostaglandin E2-EP2/EP4 signaling both mediate joint inflammation in mouse collagen-induced arthritis
Authors: Honda Tetsuya , Segi-Nishida Eri , Miyachi Yoshiki , Narumiya Shuh
Published: January 2006

Prostaglandin (PG)I2 (prostacyclin [PGI]) and PGE2 are abundantly present in the synovial fluid of rheumatoid arthritis (RA) patients. Although the role of PGE2 in RA has been well studied, how much PGI2 contributes to RA is little known. To examine this issue, we backcrossed mice lacking the PGI receptor (IP) to the DBA/1J strain and subjected them to collagen-induced arthritis (CIA). IP-deficient (IP−/−) mice exhibited significant reduction in arthritic scores compared with wild-type (WT) mice, despite anti-collagen antibody production and complement activation similar to WT mice. IP−/− mice also showed significant reduction in contents of proinflammatory cytokines, such as interleukin (IL)-6 in arthritic paws. Consistently, the addition of an IP agonist to cultured synovial fibroblasts significantly enhanced IL-6 production and induced expression of other arthritis-related genes. On the other hand, loss or inhibition of each PGE receptor subtype alone did not affect elicitation of inflammation in CIA. However, a partial but significant suppression of CIA was achieved by the combined inhibition of EP2 and EP4. Our results show significant roles of both PGI2-IP and PGE2-EP2/EP4 signaling in the development of CIA, and suggest that inhibition of PGE2 synthesis alone may not be sufficient for suppression of RA symptoms.
All is not Toll: new pathways in DNA recognition
Authors: Wagner Hermann , Bauer Stefan
Published: January 2006

Immunological defense depends on the ability of the innate immune system to recognize invading microbes as foreign and thus eliminate them. The Toll-like receptors (TLRs) help detect foreign invaders by sensing various pathogen-associated molecules, including microbial RNA and DNA. At present, it is unclear whether and how the immune system distinguishes between microbial and self nucleic acids, as host-derived RNA and DNA also stimulate TLRs. In addition, recent studies have revealed the existence of TLR-independent pathways that are activated in response to microbial and host nucleic acids.
A Na+- and Cl−-activated K+ Channel in the Thick Ascending Limb of Mouse Kidney
Authors: Paulais Marc , Lachheb Sahran , Teulon Jacques
Published: January 2006

This study investigates the presence and properties of Na+-activated K+ (KNa) channels in epithelial renal cells. Using real-time PCR on mouse microdissected nephron segments, we show that Slo2.2 mRNA, which encodes for the KNa channels of excitable cells, is expressed in the medullary and cortical thick ascending limbs of Henle's loop, but not in the other parts of the nephron. Patch-clamp analysis revealed the presence of a high conductance K+ channel in the basolateral membrane of both the medullary and cortical thick ascending limbs. This channel was highly K+ selective (PK/PNa ∼ 20), its conductance ranged from 140 to 180 pS with subconductance levels, and its current/voltage relationship displayed intermediate, Na+-dependent, inward rectification. Internal Na+ and Cl− activated the channel with 50% effective concentrations (EC50) and Hill coefficients (nH) of 30 ± 1 mM and 3.9 ± 0.5 for internal Na+, and 35 ± 10 mM and 1.3 ± 0.25 for internal Cl−. Channel activity was unaltered by internal ATP (2 mM) and by internal pH, but clearly decreased when internal free Ca2+ concentration increased. This is the first demonstration of the presence in the epithelial cell membrane of a functional, Na+-activated, large-conductance K+ channel that closely resembles native KNa channels of excitable cells. This Slo2.2 type, Na+- and Cl−-activated K+ channel is primarily located in the thick ascending limb, a major renal site of transcellular NaCl reabsorption.
Identification of a Disulfide Bridge Linking the Fourth and the Seventh Extracellular Loops of the Na+/Glucose Cotransporter
Authors: Gagnon Dominique G. , Bissonnette Pierre , Lapointe Jean-Yves
Published: January 2006

The Na+/glucose cotransporter (SGLT1) is an archetype for the SLC5 family, which is comprised of Na+-coupled transporters for sugars, myo-inositol, choline, and organic anions. Application of the reducing agent dithriothreitol (DTT, 10 mM) to oocytes expressing human SGLT1 affects the protein's presteady-state currents. Integration of these currents at different membrane potentials (Vm) produces a Q-V curve, whose form was shifted by +25 mV due to DTT. The role of the 15 endogenous cysteine residues was investigated by expressing SGLT1 constructs, each bearing a single mutation for an individual cysteine, in Xenopus oocytes, using two-microelectrode voltage-clamp electrophysiology and fluorescent labeling. 12 of the 15 mutants were functional and could be separated into three distinct groups based on the effect of the mutation on the Q-V curve: four mutants did not perturb the transferred charge, six mutants shifted the Q-V curve towards negative potentials, and two mutants (C255A and C511A) produced a shift in the positive direction that was identical to the shift produced by DTT on the wild-type (wt) SGLT1. The double mutant C255,511A confirms that the effects of each single mutant on the Q-V curve were not additive. With respect to wt SGLT1, the apparent affinities for α-methylglucose (αMG) were increased in a similar manner for the single mutants C255A and C511A, the double mutant C255,511A as well as for wt SGLT1 treated with DTT. When exposed to a maleimide-based fluorescent probe, wt SGLT1 was not significantly labeled but mutants C255A and C511A could be clearly labeled, indicating an accessible cysteine residue. These residues are presumed to be C511 and C255, respectively, as the double mutant C255,511A could not be labeled. These results strongly support the hypothesis that C255 and C511 form a disulfide bridge in human SGLT1 and that this disulfide bridge is involved in the conformational change of the free carrier.
Mini-dystrophin Expression Down-regulates Overactivation of G Protein–mediated IP3 Signaling Pathway in Dystrophin-deficient Muscle Cells
Authors: Balghi Haouaria , Sebille Stéphane , Constantin Bruno , Patri Sylvie , Thoreau Vincent , Mondin Ludivine , Mok Elise , Kitzis Alain , Raymond Guy , Cognard Christian
Published: January 2006

We present here evidence for the enhancement of an inositol 1,4,5-trisphosphate (IP3) mediated calcium signaling pathway in myotubes from dystrophin-deficient cell lines (SolC1(−)) as compared to a cell line from the same origin but transfected with mini-dystrophin (SolD(+)). With confocal microscopy, we demonstrated that calcium rise, induced by the perifusion of a solution containing a high potassium concentration, was higher in SolC1(−) than in SolD(+) myotubes. The analysis of amplitude and kinetics of the calcium increase in SolC1(−) and in SolD(+) myotubes during the exposure with SR Ca2+ channel inhibitors (ryanodine and 2-APB) suggested the presence of two mechanisms of SR calcium release: (1) a fast SR calcium release that depended on ryanodine receptors and (2) a slow SR calcium release mediated by IP3 receptors. Detection analyses of mRNAs (reverse transcriptase [RT]-PCR) and proteins (Western blot and immunolocalization) demonstrated the presence of the three known isoforms of IP3 receptors in both SolC1(−) and SolD(+) myotubes. Furthermore, analysis of the kinetics of the rise in calcium revealed that the slow IP3-dependent release may be increased in the SolC1(−) as compared to the SolD(+), suggesting an inhibitory effect of mini-dystrophin in this signaling pathway. Upon incubation with pertussis toxin (PTX), an inhibitory effect similar to that of the IP3R inhibitor (2-APB) was observed on K+-evoked calcium release. This result suggests the involvement of a Gi protein upstream of the IP3 pathway in these stimulation conditions. A hypothetical model is depicted in which both Gi protein and IP3 production could be involved in K+-evoked calcium release as well as a possible interaction with mini-dystrophin. Our findings demonstrate the existence of a potential relationship between mini-dystrophin and SR calcium release as well as a regulatory role of mini-dystrophin on intracellular signaling.
Bioactive Components of the Traditionally used Mushroom Podaxis pistillaris
Authors: Al-Fatimi M. A. A. , Jülich W.-D. , Jansen R. , Lindequist U.
Published: January 2006

In the course of an ethnobotanical study on fungi used in Yemeni ethnomedicine the fungus Podaxis pistillaris (Podaxales, Podaxaceae, Basidiomycetes) was found to exhibit antibacterial activity against Staphylococcus aureus, Micrococcus flavus, Bacillus subtilis, Proteus mirabilis, Serratia marcescens and Escherichia coli. In the culture medium of P. pistillaris three epidithiodiketopiperazines were identified by activity‐guided isolation. Based on spectral data (NMR, ESI‐MS and DCI‐MS) their identity was established as epicorazine A (1), epicorazine B (2) and epicorazine C (3, antibiotic F 3822), which have not been reported as constituents of P. pistillaris previously. It is assumed that the identified compounds contribute to the antibacterial activity of the extract.
Uniaxial nematic elastomers: constitutive framework and a simple application
Authors: Chen Yi-chao , Fried Eliot
Published: January 2006

Using a geometrical approach to treat the constraints associated with the continuum description of a uniaxial nematic elastomer—that is, a nematic elastomer whose microstructure can be characterized by a single unit vector field, we develop the general constitutive framework for such a material. We also provide a variational formulation of equilibrium and use that formulation to discuss the inflation of a tubular specimen. The analysis demonstrates the existence of a pair of disconnected solution branches. Of these branches, one is stable at low pressure and the other is stable at high pressure. An intermediate regime within which both branches are stable indicates that during loading the specimen may undergo a discontinuous jump from one solution branch to another and thus suggests the possibility of using nematic elastomers for pressure-sensitive optical switches.
Bacillus salarius sp. nov., a halophilic, spore-forming bacterium isolated from a salt lake in China
Authors: Lim Jee-Min , Jeon Che Ok , Lee Sang-Mi , Lee Jae-Chan , Xu Li-Hua , Jiang Cheng-Lin , Kim Chang-Jin
Published: January 2006

A moderately halophilic bacterium, strain BH169T, capable of growing at salinities of 3–20 % (w/v) NaCl was isolated from a saline lake in China. Strain BH169Twas strictly aerobic, short-rod-shaped and non-motile (non-flagellated). Its major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0and iso-C16 : 0. The genomic DNA G+C content was about 43 mol% and the predominant quinone was MK-7. The cell-wall peptidoglycan was of the A1γtype, containingmeso-diaminopimelic acid as the diagnostic diamino acid. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct phylogenetic line within the spore-forming rods of the genusBacillus. The levels of 16S rRNA gene sequence similarity to the type strains ofBacillusspecies were below 93 %. On the basis of phenotypic and molecular properties, strain BH169T(=KCTC 3912T=DSM 16461T) represents the type strain of a novel species within the genusBacillus, for which the nameBacillus salariussp. nov. is proposed.
Pseudovibrio ascidiaceicola sp. nov., isolated from ascidians (sea squirts)
Authors: Fukunaga Yukiyo , Kurahashi Midori , Tanaka Kenji , Yanagi Kensuke , Yokota Akira , Harayama Shigeaki
Published: January 2006

Two bacterial strains, F423T and F10102, were isolated from two ascidians, Polycitor proliferus and Botryllidae sp., respectively, which were collected from a beach on the Boso peninsula in Japan. Cells of both isolates were motile, rod-shaped and formed star-shaped aggregates in the early stage of exponential growth, but were coccoid in stationary growth phase. The results of 16S rRNA gene sequence analysis, fatty acid analysis, DNA–DNA hybridization experiments and physiological and biochemical tests indicated that the two strains were members of a novel species of the genus Pseudovibrio for which the name Pseudovibrio ascidiaceicola sp. nov. is proposed. The type strain is F423T (=NBRC 100514T=IAM 15084T=DSM 16392T=KCTC 12308T).
Marinomonas polaris sp. nov., a psychrohalotolerant strain isolated from coastal sea water off the subantarctic Kerguelen islands
Authors: Gupta Pratima , Chaturvedi Preeti , Pradhan Suman , Delille Daniel , Shivaji Sisinthy
Published: January 2006

Two aerobic, psychrohalotolerant, motile bacterial isolates, CK13T and CK16, isolated from sea-water samples collected off the subantarctic Kerguelen island, were characterized by using a polyphasic taxonomic approach. On the basis of 16S rRNA gene sequence data, the strains were 99·6 % similar and exhibited 93–97 % similarity with the seven recognized species of Marinomonas. The most closely related species were Marinomonas pontica and Marinomonas primoryensis, with 97 and 96 % similarity at the 16S rRNA gene sequence level, respectively. DNA–DNA hybridization values between strain CK13T and M. pontica and M. primoryensis were only 58 and 40 %, respectively. The major fatty acids present in strain CK13T were iso-C16 : 0, C16 : 0, C16 : 1
ω7c and C18 : 1
ω7c. The DNA G+C content of strain CK13T was 41·2 mol%. Phosphatidylethanolamine and phosphatidylglycerol were identified as the predominant phospholipids. All the above characteristics support the affiliation of strain CK13T to the genus Marinomonas. Phylogenetic analysis and phenotypic and genotypic distinctiveness confirmed that strains CK13T and CK16 are members of a novel species of the genus Marinomonas, for which the name Marinomonas polaris sp. nov. is proposed. The type strain is CK13T (=MTCC 6645T=DSM 16579T=JCM 12522T).
Pediococcus stilesii sp. nov., isolated from maize grains
Authors: Franz Charles M. A. P. , Vancanneyt Marc , Vandemeulebroecke Katrien , De Wachter Marjan , Cleenwerck Ilse , Hoste Bart , Schillinger Ulrich , Holzapfel Wilhelm H. , Swings Jean
Published: January 2006

A Gram-positive, coccus-shaped, lactic acid bacterium, strain LMG 23082T, was isolated from steeped maize grains. The organism is homofermentative and producesd- andl-lactic acid from glucose. 16S rRNA gene sequence analysis revealed that the organism belongs to the genusPediococcus, withPediococcus pentosaceusandPediococcus acidilacticias nearest neighbours. Genotypic fingerprinting, whole-cell protein electrophoresis, DNA–DNA hybridizations and physiological and biochemical tests allowed differentiation of strain LMG 23082Tfrom other establishedPediococcusspecies. A remarkable feature was that, unlike other pediococci, this bacterium was capable of growth at pH 9·0. The strain studied represents a novel species for which the namePediococcus stilesiisp. nov. is proposed with the type strain LMG 23082T(=BFE 1652T=FAIR-E 180T=CCUG 51290T), the only currently known isolate of the species.
Burkholderia terrae sp. nov., isolated from a forest soil
Authors: Yang Hee-Chan , Im Wan-Taek , Kim Kwang Kyu , An Dong-Shan , Lee Sung-Taik
Published: January 2006

A Gram-negative, slightly curved rod-shaped bacterium, designated strain KMY02T, was isolated from a forest soil in Daejeon, South Korea. On the basis of 16S rRNA gene sequence similarity, strain KMY02T was shown to belong to the family Burkholderiaceae of the Betaproteobacteria, and to be related most closely to Burkholderia hospita LMG 20598T (98·7 %), Burkholderia caribensis LMG 18531T (98·0 %) and Burkholderia phymatum LMG 21445T (97·4 %). Its phylogenetic distance from all recognized species within the genus Burkholderia was less than 97 %. Chemotaxonomic data [Q-8 as the major ubiquinone; C16 : 0, C17 : 0 cyclo, summed feature 7 (C18 : 1
ω7c/ω9t/ω12t) and C15 : 0 as the major fatty acids] supported the affiliation of strain KMY02T to the genus Burkholderia. The results of DNA–DNA hybridization experiments and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the strain from recognized Burkholderia species. Therefore, KMY02T (=KCTC 12388T=NBRC 100964T) represents the type strain of a novel species, for which the name Burkholderia terrae sp. nov. is proposed.
Novel Neosartorya species isolated from soil in Korea
Authors: Hong Seung-Beom , Cho Hye-Sun , Shin Hyeon-Dong , Frisvad Jens C. , Samson Robert A.
Published: January 2006

Phenotypic and genotypic characters of strains ofNeosartorya spinosaand related taxa were analysed.N. spinosa,Neosartorya botucatensisandNeosartorya paulistensishad identical partialβ-tubulin and calmodulin gene sequences and could not be differentiated on macro- and micro-morphological characteristics, including by scanning electron microscopy. Based on partialβ-tubulin and calmodulin gene sequences and ascospore morphology, two separate groups are distinguished and are proposed as novel species.Neosartorya laciniosasp. nov. has microtuberculate ascospores with two bent crests and two distinct equatorial rings of small projections.Neosartorya coreanasp. nov. has rugose to weak reticulate ascospores with two often bent crests, but without the equatorial rings of small projections. The type strain ofN. laciniosais CBS 117721T(=NRRL 35589T=KACC 41657T) and the type strain ofN. coreanais CBS 117059T(=NRRL 35590T=KACC 41659T).
Thorsellia anophelis gen. nov., sp. nov., a new member of the Gammaproteobacteria
Authors: Kämpfer Peter , Lindh Jenny M. , Terenius Olle , Haghdoost Siamak , Falsen Enevold , Busse Hans-Jürgen , Faye Ingrid
Published: January 2006

A Gram-negative, rod-shaped organism (CCUG 49520T) was isolated from the midgut of the mosquito Anopheles arabiensis. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing <93 % similarity to species of the families Enterobacteriaceae and Vibrionaceae. The quinone system consisted exclusively of ubiquinone Q-8; the polar lipid profile consisted of the major compounds phosphatidylethanolamine and phosphatidylglycerol, a moderate to minor amount of two unknown aminophospholipids, an unknown phospholipid and two unknown polar lipids; the polyamine pattern was characterized by the predominant compound 1,3-diaminopropane and showed some significant differences when compared with members of the Enterobacteriaceae and Vibrionaceae. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic data, strain CCUG 49520T is considered to represent a new genus and species, for which the name Thorsellia anophelis gen. nov., sp. nov. is proposed. The type strain is CCUG 49520T (=CIP 108754T).
Lactobacillus suntoryeus Cachat and Priest 2005 is a later synonym of Lactobacillus helveticus (Orla-Jensen 1919) Bergey et al. 1925 (Approved Lists 1980)
Authors: Naser Sabri M. , Hagen Karen E. , Vancanneyt Marc , Cleenwerck Ilse , Swings Jean , Tompkins Thomas A.
Published: January 2006

Strain R0052, isolated from a North American dairy starter culture, was initially identified as Lactobacillus acidophilus based on phenotypic analyses. However, upon sequencing the 16S rRNA gene, it became clear that the isolate was very highly related to Lactobacillus suntoryeus, Lactobacillus helveticus and Lactobacillus gallinarum, as similarities ranging from 99·3 to 99·8 % were observed. As an initial screening test to investigate the relatedness of strain R0052 and reference strains of L. suntoryeus, L. helveticus and L. gallinarum, the partial sequences for the genes encoding the alpha subunit of ATP synthase (atpA), RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), the translational elongation factor Tu (tuf), a surface-layer protein (slp) and the Hsp60 chaperonins (groEL) were determined and they revealed high relatedness between all of the strains. The determination of the 16S–23S rRNA internally transcribed spacer (ITS) sequences revealed 98·3–100 % similarity between L. suntoryeus and L. helveticus strains. SDS-PAGE of whole-cell proteins did not distinguish between these species. Fluorescent amplified fragment length polymorphism (FAFLP) could distinguish between these taxa, but they still constituted a single cluster within the L. acidophilus group. Finally, DNA–DNA hybridization experiments between strain R0052 and the type strains of L. helveticus and L. suntoryeus yielded reassociation values above 70 % and confirmed that these names are synonyms.
Flavobacterium saliperosum sp. nov., isolated from freshwater lake sediment
Authors: Wang Zhong-Wen , Liu Ying-Hao , Dai Xin , Wang Bao-Jun , Jiang Cheng-Ying , Liu Shuang-Jiang
Published: January 2006

An aerobic, yellow-pigmented, Gram-negative bacterium, designated strain S13T, was isolated from freshwater sediment of Taihu Lake in central China. The taxonomy of strain S13T was studied by using phenotypic and phylogenetic methods. Cells of strain S13T were rod-shaped, non-motile and with a size range of 0·35–0·55×1·5–2·5 μm. The nearly complete 16S rRNA gene of strain S13T was amplified and sequenced. A blast search and phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain S13T was related to members of the genus Flavobacterium, with the highest sequence similarity of 93·8 % to Flavobacterium columnare (ATCC 23463T). Cells contained menaquinone-6 (MK-6) as the major respiratory quinone and the genomic DNA G+C content was 41 mol%. The major fatty acids were iso-C15 : 0 (28·2 %) and iso-C17 : 1
ω9c (19·0 %). It is proposed that S13T (=CGMCC 1.3801T=JCM 13331T) represents the type strain of a novel species, Flavobacterium saliperosum sp. nov.
Trafficking from the bone marrow to the thymus: a prerequisite for thymopoiesis
Authors: Schwarz Benjamin A. , Bhandoola Avinash
Published: January 2006

Summary:  T‐cell development in the thymus requires periodic importation of hematopoietic progenitors from the bone marrow. Such thymus settling progenitors arise from hematopoietic stem cells (HSCs) that are retained in a specific bone marrow microenvironmental niche. Vacation of this niche is required for HSC proliferation and differentiation into downstream progenitors. In order to reach the thymus, progenitors must then be mobilized from bone marrow to blood. Finally, progenitors in blood must settle in the thymus. Here we review signals and molecular interactions that are likely to play a role in trafficking from the bone marrow to the thymus, focusing on how these interactions may regulate which progenitors physiologically contribute to thymopoiesis.
Trafficking on serpentines: molecular insight on how maturating T cells find their winding paths in the thymus
Authors: Mißlitz Ana , Bernhardt Günter , Förster Reinhold
Published: January 2006

Summary:  Maintenance of the peripheral T‐cell pool throughout the life requires uninterrupted generation of T cells. The majority of peripheral T cells are generated in the thymus. However, the thymus does not contain hematopoietic progenitors with unlimited self‐renewing potential, and continuous production of T cells requires importation of such progenitors from the bone marrow into the thymus. Thymus‐homing progenitors enter the thymus and subsequently migrate throughout distinct intrathymic microenvironments while differentiating into mature T cells. At each step of this scheduled journey, developing thymocytes interact intimately with the local stroma, which allow them to proceed to the next stage of their differentiation and maturation program. Undoubtedly, thymocyte/stroma interactions are instrumental for both thymocytes and stroma, because only their ongoing interplay generates and maintains a fully operational thymus, able to guarantee unimpaired T‐cell supply. Therefore, proper T‐cell generation intrinsically involves polarized cell migration during both adult life and embryogenesis when the thymus primordium develops into a functional thymus. The molecular mechanisms controlling cell migration during thymus development and postnatal T‐cell differentiation are beginning to be defined. This review focuses on recent data regarding the role of cell migration in both colonization of the fetal thymus and T‐cell development during postnatal life in mice.
Cyclical mobilization and gated importation of thymocyte progenitors in the adult mouse: evidence for a thymus‐bone marrow feedback loop
Authors: Goldschneider Irving
Published: January 2006

Summary:  It has recently been observed, as in the fetal thymus, that the importation of hematogenous thymocyte progenitors by the adult thymus is a gated phenomenon, whereby saturating numbers of progenitors periodically enter the thymus and occupy a finite number of intrathymic niches. In addition, the mobilization of thymocyte progenitors from the bone marrow appears to be a cyclical process that coincides temporally with the periods of thymic receptivity (open gate). It is proposed that these events are coordinated by a thymus‐bone marrow feedback loop in which a wave of developing triple negative (CD3–CD4–CD8–) thymocytes interacts with stromal cells in the stratified regions of the thymus cortex to sequentially induce the release of diffusible cytokines that regulate the production, mobilization, and recruitment of thymocyte progenitors. The likely components of this feedback loop are described here, as are the properties of the intrathymic vascular gates and niches for thymocyte progenitors. The cyclical production and release of thymocyte progenitors from the bone marrow is placed in the context of a general phenomenon of oscillatory feedback regulation involving all lymphohemopoietic cell lineages. Lastly, the question of whether the gated (as opposed to the continuous) entry of thymocyte progenitors is essential for normal thymocytopoiesis in adult life is discussed.
Progression of regulatory gene expression states in fetal and adult pro‐T‐cell development
Authors: David‐Fung Elizabeth‐Sharon , Yui Mary A. , Morales Marissa , Wang Hua , Taghon Tom , Diamond Rochelle A. , Rothenberg Ellen V.
Published: January 2006

Summary:  Precursors entering the T‐cell developmental pathway traverse a progression of states characterized by distinctive patterns of gene expression. Of particular interest are regulatory genes, which ultimately control the dwell time of cells in each state and establish the mechanisms that propel them forward to subsequent states. Under particular genetic and developmental circumstances, the transitions between these states occur with different timing, and environmental feedbacks may shift the steady‐state accumulations of cells in each state. The fetal transit through pro‐T‐cell stages is faster than in the adult and subject to somewhat different genetic requirements. To explore causes of such variation, this review presents previously unpublished data on differentiation gene activation in pro‐T cells of pre‐T‐cell receptor‐deficient mutant mice and a quantitative comparison of the profiles of transcription factor gene expression in pro‐T‐cell subsets of fetal and adult wildtype mice. Against a background of consistent gene expression, several regulatory genes show marked differences between fetal and adult expression profiles, including those encoding two basic helix‐loop‐helix antagonist Id factors, the Ets family factor SpiB and the Notch target gene Deltex1. The results also reveal global differences in regulatory alterations triggered by the first T‐cell receptor‐dependent selection events in fetal and adult thymopoiesis.
ATM‐dependent DNA damage surveillance in T‐cell development and leukemogenesis: the DSB connection
Authors: Matei Irina R. , Guidos Cynthia J. , Danska Jayne S.
Published: January 2006

Summary:  The immune system is capable of recognizing and eliminating an enormous array of pathogens due to the extremely diverse antigen receptor repertoire of T and B lymphocytes. However, the development of lymphocytes bearing receptors with unique specificities requires the generation of programmed double strand breaks (DSBs) coupled with bursts of proliferation, rendering lymphocytes susceptible to mutations contributing to oncogenic transformation. Consequently, mechanisms responsible for monitoring global genomic integrity must be activated during lymphocyte development to limit the oncogenic potential of antigen receptor locus recombination. Mutations in ATM (ataxia‐telangiectasia mutated), a kinase that coordinates DSB monitoring and the response to DNA damage, result in impaired T‐cell development and predispose to T‐cell leukemia. Here, we review recent evidence providing insight into the mechanisms by which ATM promotes normal lymphocyte development and protects from neoplastic transformation.
Divergence time estimates for major cephalopod groups: evidence from multiple genes
Authors: Strugnell Jan , Jackson Jennifer , Drummond Alexei J. , Cooper Alan
Published: January 2006

This is the first study to use both molecular and fossil data to date the divergence of taxa within the coleoid cephalopods (octopus, squid, cuttlefish). A dataset including sequences from three nuclear and three mitochondrial genes (3415 bp in total) was used to investigate the evolutionary divergences within the group. Divergence time analyses were performed using the Thorne/Kishino method of analysis which allows multiple constraints from the fossil record and permits rates of molecular evolution to vary on different branches of a phylogenetic tree. The data support a Paleozoic origin of the Orders Vampyromorpha, Octopoda and the majority of the extant higher level decapodiform taxa. These estimated divergence times are considerably older than paleontological estimates. The major lineages within the Order Octopoda were estimated to have diverged in the Mesozoic, with a radiation of many taxa around the Cretaceous/Cenozoic boundary. Higher level decapodiform phylogenetic relationships appear to have been obscured due to an ancient diversification of this group.

© The Willi Hennig Society 2006.