bluuebunny/crossref_metadata_2025 huggingface dataset:
Cadherin Adhesion Receptors Orient the Mitotic Spindle during Symmetric Cell Division in Mammalian Epithelia
Authors: den Elzen Nicole , Buttery Carmen V. , Maddugoda Madhavi P. , Ren Gang , Yap Alpha S.
Published: June 2009

Oriented cell division is a fundamental determinant of tissue organization. Simple epithelia divide symmetrically in the plane of the monolayer to preserve organ structure during epithelial morphogenesis and tissue turnover. For this to occur, mitotic spindles must be stringently oriented in the Z-axis, thereby establishing the perpendicular division plane between daughter cells. Spatial cues are thought to play important roles in spindle orientation, notably during asymmetric cell division. The molecular nature of the cortical cues that guide the spindle during symmetric cell division, however, is poorly understood. Here we show directly for the first time that cadherin adhesion receptors are required for planar spindle orientation in mammalian epithelia. Importantly, spindle orientation was disrupted without affecting tissue cohesion or epithelial polarity. This suggests that cadherin receptors can serve as cues for spindle orientation during symmetric cell division. We further show that disrupting cadherin function perturbed the cortical localization of APC, a microtubule-interacting protein that was required for planar spindle orientation. Together, these findings establish a novel morphogenetic function for cadherin adhesion receptors to guide spindle orientation during symmetric cell division.
Feldenkrais Method Balance Classes Improve Balance in Older Adults: A Controlled Trial
Authors: Connors Karol A. , Galea Mary P. , Said Catherine M.
Published: June 2009

The objective of this study was to investigate the effects of Feldenkrais Method balance classes on balance and mobility in older adults. This was a prospective non‐randomized controlled study with pre/post measures. The setting for this study was the general community. A convenience sample of 26 community‐dwelling older adults (median age 75 years) attending Feldenkrais Method balance classes formed the Intervention group. Thirty‐seven volunteers were recruited for the Control group (median age 76.5 years). A series of Feldenkrais Method balance classes (the 33312Getting Grounded Gracefully33313 series), two classes per week for 10 weeks, were conducted. Main outcome measures were Activities‐Specific Balance Confidence (ABC) questionnaire, Four Square Step Test (FSST), self‐selected gait speed (using GAITRite instrumented gait mat). At re‐testing, the Intervention group showed significant improvement on all of the measures (ABC, P = .016, FSST, P = .001, gait speed, P < .001). The Control group improved significantly on one measure (FSST, P < .001). Compared to the Control group, the Intervention group made a significant improvement in their ABC score (P = .005), gait speed (P = .017) and FSST time (P = .022). These findings suggest that Feldenkrais Method balance classes may improve mobility and balance in older adults.
Podophyllum hexandrum‐Mediated Survival Protection and Restoration of Other Cellular Injuries in Lethally Irradiated Mice
Authors: Sankhwar Sanghmitra , Gupta Manju Lata , Gupta Vanita , Verma Savita , Suri Krishna Avtar , Devi Memita , Sharma Punita , Khan Ehsan Ahmed , Alam M. Sarwar
Published: June 2009

This study aims at the development of a safe and effective formulation to counter the effects of lethal irradiation. The sub‐fraction (G‐001M), prepared from Podophyllum hexandrum has rendered high degree of survival (>90%) at a dose of 6 mg kg−1 body weight (intramuscular) in lethally irradiated mice. Therapeutic dose of G‐001M, at about 20 times lower concentration than its LD100, has revealed a DRF of 1.62. Comet assay studies in peripheral blood leukocytes have reflected that, treatment of G‐001M before irradiation has significantly reduced DNA tail length (P < .001) and DNA damage score (P < .001), as compared to radiation‐only group. Spleen cell counts in irradiated animals had declined drastically at the very first day of exposure, and the fall continued till the 5th day (P < .001). In the treated irradiated groups, there was a steep reduction in the counts initially, but this phase did not prolong. More than 60% decline in thymocytes of irradiated group animals was registered at 5 h of irradiation when compared with controls, and the fall progressed further downwards with the similar pace till 5th day of exposure (P < .001). At later intervals, thymus was found fully regressed. In G‐001M pre‐treated irradiated groups also, thymocytes decreased till the 5th day but thereafter rejuvenated and within 30 days of treatment the values were close to normal. Current studies have explicitly indicated that, G‐001M in very small doses has not only rendered high survivability in lethally irradiated mice, but also protected their cellular DNA, besides supporting fast replenishment of the immune system.
End-to-end foodweb control of fish production on Georges Bank
Authors: Collie Jeremy S. , Gifford Dian J. , Steele John H.
Published: June 2009

Collie, J. S., Gifford, D. J., and Steele, J. H. 2009. End-to-end foodweb control of fish production on Georges Bank. – ICES Journal of Marine Science, 66: 2223–2232. The ecosystem approach to management requires the productivity of individual fish stocks to be considered in the context of the entire ecosystem. We derive an annual end-to-end budget for the Georges Bank ecosystem, based on data from the GLOBEC programme and fisheries surveys for the years 1993–2002. Scenarios based on this budget describe the consequences of various alterations in the Georges Bank trophic web: reduced nutrient input, increased benthic production, removal of carnivorous plankton, and changes in species dominance within fish guilds. Potential yields of cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) are compared with historical catches and estimates of maximum sustainable yield (MSY) from recent stock assessments. The MSYs of cod and haddock can be met if the fish community is restructured to make them the dominant species in their respective diet-defined guilds. A return to the balance of fish species present in the early 20th century would depend on an increase in the fraction of primary production going to the benthos rather than to plankton. Estimates of energy flux through the Georges Bank trophic web indicate that rebuilding the principal groundfish species to their MSY levels requires restructuring of the fish community and repartitioning of energy within the foodweb.
Predicting Presidential Elections with Equally Weighted Regressors in Fair's Equation and the Fiscal Model
Authors: Cuzán Alfred G. , Bundrick Charles M.
Published: June 2009

Three-decade-old research suggests that although regression coefficients obtained with ordinary least squares (OLS) are optimal for fitting a model to a sample, unless the N over which the model was estimated is large, they are generally not very much superior and frequently inferior to equal weights or unit weights for making predictions in a validating sample. Yet, that research has yet to make an impact on presidential elections forecasting, where models are estimated with fewer than 25 elections, and often no more than 15. In this research note, we apply equal weights to generate out-of-sample and one-step-ahead predictions in two sets of related presidential elections models, Fair's presidential equation and the fiscal model. We find that most of the time, using equal weights coefficients does improve the forecasting performance of both.
Dealing with Weak Instruments: An Application to the Protection for Sale Model
Authors: Gawande Kishore , Li Hui
Published: June 2009

Endogeneity of explanatory variables is now receiving the concern it deserves in the empirical political science literature. Instrumental variables (IVs) estimators, such as two-stage least squares (2SLS), are the primary means for tackling this problem. These estimators solve the endogeneity problem by “instrumenting” the endogenous regressors using exogenous variables (the instruments). In many applications, a problem that the IV approach must overcome is that of weak instruments (WIs), where the instruments only weakly identify the regression coefficients of interest. With WIs, the infinite-sample properties (e.g., consistency) used to justify the use of estimators like 2SLS are on thin ground because these estimators have poor small-sample properties. Specifically, they may suffer from excessive bias and/or Type I error. We highlight the WI problem in the context of empirical testing of “protection for sale” model that predicts the cross-sectional pattern of trade protection as a function of political organization, imports and output. These variables are endogenous. Importantly, the instruments used to solve the endogeneity problem are weak. A method better suited to exact inference with WIs is the limited information maximum likelihood (LIML) estimator. Censoring in the dependent variable in the application requires a nonlinear Tobit LIML estimator.
Differences in the 2nd to 4th digit length ratio in humans reflect shifts along the common allometric line
Authors: Kratochvíl Lukáš , Flegr Jaroslav
Published: June 2009

Ratios often lead to biased conclusions concerning the actual relationships between examined traits and comparisons of the relative size of traits among groups. Therefore, the use of ratios has been abandoned in most comparative studies. However, ratios such as body mass index and waist-to-hip ratio are widely used in evolutionary biology and medicine. One such, the ratio of the 2nd to the 4th finger (2D : 4D), has been the subject of much recent interest in both humans and animals. Most studies agree that 2D : 4D is sexually dimorphic. In men, the 2nd digit tends to be shorter than the 4th, while in women the 2nd digit tends to be of the same size or slightly longer than the 4th. Nevertheless, here we demonstrate that the sexes do not greatly differ in the scaling between the 2nd and 4th digit. Sexual differences in 2D : 4D are mainly caused by the shift along the common allometric line with non-zero intercept, which means 2D : 4D necessarily decreases with increasing finger length, and the fact that men have longer fingers than women. We conclude that previously published results on the 2D : 4D ratio are biased by its covariation with finger length. We strongly recommend regression-based approaches for comparisons of hand shape among different groups.
Pitch then power: limitations to acceleration in quadrupeds
Authors: Williams Sarah B. , Tan Huiling , Usherwood James R. , Wilson Alan M.
Published: June 2009

Rapid acceleration and deceleration are vital for survival in many predator and prey animals and are important attributes of animal and human athletes. Adaptations for acceleration and deceleration are therefore likely to experience strong selective pressures—both natural and artificial. Here, we explore the mechanical and physiological constraints to acceleration. We examined two elite athletes bred and trained for acceleration performance (polo ponies and racing greyhounds), when performing maximal acceleration (and deceleration for ponies) in a competitive setting. We show that maximum acceleration and deceleration ability may be accounted for by two simple limits, one mechanical and one physiological. At low speed, acceleration and deceleration may be limited by the geometric constraints of avoiding net nose-up or tail-up pitching, respectively. At higher speeds, muscle power appears to limit acceleration.
How does breeding system variation modulate sexual antagonism?
Authors: Bedhomme Stéphanie , Bernasconi Giorgina , Koene Joris M. , Lankinen Åsa , Arathi H. S. , Michiels Nico K. , Anthes Nils
Published: June 2009

The study of sexually antagonistic (SA) traits remains largely limited to dioecious (separate sex), mobile animals. However, the occurrence of sexual conflict is restricted neither by breeding system (the mode of sexual reproduction, e.g. dioecy or hermaphroditism) nor by sessility. Here, we synthesize how variation in breeding system can affect the evolution and expression of intra- and inter-locus sexual conflicts in plants and animals. We predict that, in hermaphrodites, SA traits will (i) display lower levels of polymorphism; (ii) respond more quickly to selection; and (iii) involve unique forms of interlocus conflict over sex allocation, mating roles and selfing rates. Explicit modelling and empirical tests in a broader range of breeding systems are necessary to obtain a general understanding of the evolution of SA traits.
Thomas Beddoes and the German psychological tradition
Authors: Vickers Neil
Published: June 2009

This paper considers Thomas Beddoes's role in disseminating German psychological ideas in Britain. It describes the German tradition as inaugurated by Karl Philipp Moritz (1756–93) and considers the chief differences between this tradition and the English one stemming from David Hartley. It is suggested that Beddoes found strong support for his convictions about human interiority in writings by Moritz and his followers. In particular, these enabled him to think about sanity and madness as being continuous with one another (rather than as one another's negation); they helped him locate the signs of madness in ordinary childhood behaviours; they reinforced his suspicions that many so-called nervous disorders were psychically caused; and they supplied him with a conception of unconscious passion. The paper concludes by considering Beddoes's appeal to Shakespeare's plays as a source of clinical knowledge about the nature of insanity, and argues that Beddoes has been overlooked as a crucial source for nineteenth-century psychiatrist-bardologists such as J. Conolly, J. C. Bucknill and H. Maudsley.
On the groundstate energy of tight knots
Authors: Maggioni Francesca , Ricca Renzo L.
Published: June 2009

New results on the groundstate energy of tight, magnetic knots are presented. Magnetic knots are defined as tubular embeddings of the magnetic field in an ideal, perfectly conducting, incompressible fluid. An orthogonal, curvilinear coordinate system is introduced and the magnetic energy is determined by the poloidal and toroidal components of the magnetic field. Standard minimization of the magnetic energy is carried out under the usual assumptions of volume- and flux-preserving flow, with the additional constraints that the tube cross section remains circular and that the knot length (ropelength) is independent from internal field twist (framing). Under these constraints the minimum energy is determined analytically by a new, exact expression, function of ropelength and framing. Groundstate energy levels of tight knots are determined from ropelength data obtained by the SONO tightening algorithm. Results for torus knots are compared with previous work, and the groundstate energy spectrum of the first prime knots — up to 10 crossings — is presented and analysed in detail. These results demonstrate that ropelength and framing determine the spectrum of magnetic knots in tight configuration.
Campbell diagrams of weakly anisotropic flexible rotors
Authors: Kirillov O. N.
Published: June 2009

We consider an axi-symmetric flexible rotor perturbed by dissipative, conservative and non-conservative positional forces originated at the contact with the anisotropic stator. The Campbell diagram of the unperturbed system is a mesh-like structure in the frequency–speed plane with double eigenfrequencies at the nodes. The diagram is convenient for the analysis of the travelling waves in the rotating elastic continuum. Computing sensitivities of the doublets, we find that at every particular node the unfolding of the mesh into the branches of complex eigenvalues in the first approximation is generically determined by only four 2×2 sub-blocks of the perturbing matrix. Selection of the unstable modes that cause self-excited vibrations in the subcritical speed range is governed by the exceptional points at the corners of the singular eigenvalue surfaces—‘double coffee filter’ and ‘viaduct’—which are sharply associated with the crossings of the unperturbed Campbell diagram with the definite symplectic (Krein) signature. The singularities connect the problems of wave propagation in the rotating continua with that of electromagnetic and acoustic wave propagation in non-rotating anisotropic chiral media. As mechanical examples a model of a rotating shaft with two degrees of freedom and a continuous model of a rotating circular string passing through the eyelet are studied in detail.
Analysis of Regge poles for the Schrödinger equation
Authors: Hiscox A. , Brown B. M. , Marletta M.
Published: June 2009

We study the question addressed by Barut and Dilley (
Barut & Dilley 1963
J. Math. Phys
.
4
, 1401–1408) of counting the number of Regge poles for a radial Schrödinger equation. Using the asymptotics of Rudolph Langer, we acquire estimates for the free solutions at infinity for large generalized complex angular momentum |
λ
|. These estimates allow us to calculate the Wronskian of two particular solutions, which is the function whose zeros are the Regge poles, for large |
λ
| in the right-half
λ
-plane. These angular momentum asymptotics are rigorously related to the large-radius asymptotics by generalizing Marianna Shubova’s idea of formulating an integral equation for the solution at infinity. This leads to the proof that for integrable potentials there are only finitely many Regge poles. This should be compared with the ideas of Barut and Dilley, who require that the potential be analytic in the right-half plane with
r
2
V
(
r
) remaining bounded.
The decay of flexural-gravity waves in long sea ice transects
Authors: Vaughan Gareth L. , Bennetts Luke G. , Squire Vernon A.
Published: June 2009

Flexural oscillations of floating sea ice sheets induced by ocean waves travelling at the boundary between the ice and the water below can propagate great distances. But, by virtue of scattering, changes of ice thickness and other properties encountered during the journey affect their passage, notwithstanding attenuation arising from several other naturally occurring agencies. We describe here a two-dimensional model that can simulate wave scattering by long (approx. 50 km) stretches of inelastic sea ice, the goal being to replicate heterogeneity accurately while also assimilating supplementary processes that lead to energy loss in sea ice at scales that are amenable to experimental validation. In work concerned with scattering from solitary or juxtaposed stylized features in the sea ice canopy, reflection and transmission coefficients are commonly used to quantify scattering, but on this occasion, we use the attenuation coefficient as we consider that it provides a more helpful description when dealing with long sequences of adjoining scatterers. Results show that scattering and viscosity both induce exponential decay and we observe three distinct regimes: (i) low period, where scattering dominates, (ii) high period, where viscosity dominates, and (iii) a transition regime. Each regime’s period range depends on the sea ice properties including viscosity, which must be included for the correct identification of decay rate.
Size-dependent alternative male mating tactics in the yellow dung fly,
Scathophaga stercoraria
Authors: Pitnick Scott , Henn Kali R. H. , Maheux Stephen D. , Higginson Dawn M. , Hurtado-Gonzales Jorge L. , Manier Mollie K. , Berben Kirstin S. , Guptill Chase , Uy J. Albert C.
Published: June 2009

Whenever males can monopolize females and/or resources used by females, the opportunity for sexual selection will be great. The greater the variation among males in reproductive success, the greater the intensity of selection on less competitive males to gain matings through alternative tactics. In the yellow dung fly,
Scathophaga stercoraria
, males aggressively compete for access to receptive, gravid females on fresh dung. Larger males are better able to acquire mates and to complete copulation successfully and guard the female throughout oviposition. Here we demonstrate that when an alternative resource is present where females aggregate (i.e. apple pomace, where both sexes come to feed), smaller males will redirect their searching for females from dung to the new substrate. In addition, we identify a class of particularly small males on the alternative substrate that appears never to be present searching for females on or around dung. Smaller males were found to have a mating ‘advantage’ on pomace, in striking contrast to the pattern observed on dung, providing further support for the existence of an alternative male reproductive tactic in this species.
Separate and combined effects of nutrition during juvenile and sexual development on female life-history trajectories: the thrifty phenotype in a cockroach
Authors: Barrett Emma L. B. , Hunt John , Moore Allen J. , Moore Patricia J.
Published: June 2009

We have yet to understand fully how conditions during different periods of development interact to influence life-history structure. Can the negative effects of poor juvenile nutrition be overcome by a good adult diet, or are life-history strategies set by early experience? Here, we tested the influence and interaction of different nutritional quality during juvenile and sexual development on female resource allocation physiology, life history and courtship behaviour in the cockroach,
Nauphoeta cinerea
. Nymphs were raised on either a good-quality or poor-quality diet. After adult eclosion, females were either switched to the opposite diet or remained on their original diet. We assessed mating behaviour and lifetime reproductive success for half of the females from each treatment. We evaluated reproductive investment, somatic investment and resource reallocation from reproduction to the soma via oocyte apoptosis in the remaining females. We found that poor juvenile conditions resulted in a fat phenotype with slow juvenile growth and short reproductive lifespan that could not be retrieved with a change in diet. Good juvenile conditions resulted in the converse, but again fixed, phenotype in adulthood. Thus, juvenile nutrition sets adult patterns of resource allocation.
Brain organization mirrors caste differences, colony founding and nest architecture in paper wasps (Hymenoptera: Vespidae)
Authors: Molina Y. , Harris R. M. , O'Donnell S.
Published: June 2009

The cognitive challenges that social animals face depend on species differences in social organization and may affect mosaic brain evolution. We asked whether the relative size of functionally distinct brain regions corresponds to species differences in social behaviour among paper wasps (Hymenoptera: Vespidae). We measured the volumes of targeted brain regions in eight species of paper wasps. We found species variation in functionally distinct brain regions, which was especially strong in queens. Queens from species with open-comb nests had larger central processing regions dedicated to vision (mushroom body (MB) calyx collars) than those with enclosed nests. Queens from advanced eusocial species (swarm founders), who rely on pheromones in several contexts, had larger antennal lobes than primitively eusocial independent founders. Queens from species with morphologically distinct castes had augmented central processing regions dedicated to antennal input (MB lips) relative to caste monomorphic species. Intraspecific caste differences also varied with mode of colony founding. Independent-founding queens had larger MB collars than their workers. Conversely, workers in swarm-founding species with decentralized colony regulation had larger MB calyx collars and optic lobes than their queens. Our results suggest that brain organization is affected by evolutionary transitions in social interactions and is related to the environmental stimuli group members face.
Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
Authors: Leversen Nils Anders , de Souza Gustavo A. , Målen Hiwa , Prasad Swati , Jonassen Inge , Wiker Harald G.
Published: June 2009

Secreted proteins play an important part in the pathogenicity of Mycobacterium tuberculosis, and are the primary source of vaccine and diagnostic candidates. A majority of these proteins are exported via the signal peptidase I-dependent pathway, and have a signal peptide that is cleaved off during the secretion process. Sequence similarities within signal peptides have spurred the development of several algorithms for predicting their presence as well as the respective cleavage sites. For proteins exported via this pathway, algorithms exist for eukaryotes, and for Gram-negative and Gram-positive bacteria. However, the unique structure of the mycobacterial membrane raises the question of whether the existing algorithms are suitable for predicting signal peptides within mycobacterial proteins. In this work, we have evaluated the performance of nine signal peptide prediction algorithms on a positive validation set, consisting of 57 proteins with a verified signal peptide and cleavage site, and a negative set, consisting of 61 proteins that have an N-terminal sequence that confirms the annotated translational start site. We found the hidden Markov model of SignalP v3.0 to be the best-performing algorithm for predicting the presence of a signal peptide in mycobacterial proteins. It predicted no false positives or false negatives, and predicted a correct cleavage site for 45 of the 57 proteins in the positive set. Based on these results, we used the hidden Markov model of SignalP v3.0 to analyse the 10 available annotated proteomes of mycobacterial species, including annotations of M. tuberculosis H37Rv from the Wellcome Trust Sanger Institute and the J. Craig Venter Institute (JCVI). When excluding proteins with transmembrane regions among the proteins predicted to harbour a signal peptide, we found between 7.8 and 10.5 % of the proteins in the proteomes to be putative secreted proteins. Interestingly, we observed a consistent difference in the percentage of predicted proteins between the Sanger Institute and JCVI. We have determined the most valuable algorithm for predicting signal peptidase I-processed proteins of M. tuberculosis, and used this algorithm to estimate the number of mycobacterial proteins with the potential to be exported via this pathway.
Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC
Authors: Eldholm Vegard , Johnsborg Ola , Haugen Kristine , Ohnstad Hilde Solheim , Håvarstein Leiv Sigve
Published: June 2009

Pneumococci that have developed the competent state kill and lyse non-competent sister cells and members of closely related species during co-cultivation in vitro. The key component in this process, called fratricide, is the product of the late competence gene cbpD. In addition, the peptidoglycan hydrolases LytA and LytC are required for efficient lysis of target cells. Here, we have investigated the relative contribution and possible role of each of the proteins mentioned above. Previous studies have shown that CbpD is produced exclusively by competent cells, whereas LytA and LytC can be provided by the competent attackers as well as the non-competent target cells. By using an improved assay to compare the effect of cis- versus trans-acting LytA and LytC, we were able to show that target cells are lysed much more efficiently when LytA and LytC are provided in cis, i.e. by the target cells themselves. Western analysis demonstrated that considerable amounts of LytC are present in the growth medium. In contrast, we were not able to detect any extracellular LytA. This finding indicates that LytA- and LytC-mediated fratricide represent different processes. In the absence of LytA and LytC, only a tiny fraction of the target cells were lysed, demonstrating that CbpD does not function efficiently on its own. However, in the presence of 1 mM EDTA, the fraction of target cells lysed directly by CbpD increased dramatically, indicating that divalent cations are involved in the regulation of fratricide under natural conditions.
Ferrous iron-binding protein Omb of Salmonella enterica serovar Choleraesuis promotes resistance to hydrophobic antibiotics and contributes to its virulence
Authors: Su Jer-Horng , Chung Yin-Ching , Lee Hsin-Chun , Tseng I-Cheng , Chang Ming-Chung
Published: June 2009

Salmonella enterica serovar Choleraesuis (SC) is an important enteric pathogen that causes serious systemic infections in swine and humans. To identify the genes required for resistance to antimicrobial peptides, we constructed a bank of SC transposon mutants and screened them for hypersensitivity to the cationic peptide polymyxin B. Here we report one isolated polymyxin B-susceptible mutant that also exhibited increased sensitivity toward human neutrophil peptide alpha-defensin 1 (HNP-1) and hydrophobic antibiotics including erythromycin and novobiocin. The mutant had a mutation in an ORF identified as outer membrane β-barrel protein gene omb. The purified recombinant Omb protein was characterized as a ferrous iron-binding protein. The constructed omb isogenic mutant grew more slowly in iron-limiting conditions than the wild-type (WT) parent strain. In addition, compared with the WT strain, the omb mutant exhibited an increase in net negative charge upon the cell surface and was more easily killed by polymyxin B, HNP-1 and hydrophobic antibiotics. The omb gene was transcribed, regardless of the iron content within the growth medium, and the Omb protein appeared exclusively in the outer membrane fraction. Infection experiments demonstrated virulence attenuation when the mutant was administered orally or intraperitoneally to mice. This study indicates that Omb is a previously unrecognized ferrous iron-binding protein. In vivo, Omb may be involved in the acquisition of ferrous iron during the initial stages of SC infection and appears to be an important virulence factor for SC in mice.
Carbohydrate-binding properties of a separately folding protein module from β-1,3-glucanase Lic16A of Clostridium thermocellum
Authors: Dvortsov Igor A. , Lunina Natalia A. , Chekanovskaya Ludmila A. , Schwarz Wolfgang H. , Zverlov Vladimir V. , Velikodvorskaya Galina A.
Published: June 2009

The multi-modular non-cellulosomal endo-1,3(4)-β-glucanase Lic16A from Clostridium thermocellum contains a so-called X module (denoted as CBMX) near the N terminus of the catalytic module (191–426 aa). Melting of X-module-containing recombinant proteins revealed an independent folding of the module. CBMX was isolated and studied as a separate fragment. It was shown to bind to various insoluble polysaccharides, including xylan, pustulan, chitin, chitosan, yeast cell wall glucan, Avicel and bacterial crystalline cellulose. CBMX thus contains a hitherto unknown carbohydrate-binding module (CBM54). It did not bind soluble polysaccharides on which Lic16A is highly active. Ca2+ ions had effects on the binding, e.g. stimulated complex formation with chitosan, which was observed only in the presence of Ca2+. The highest affinity to CBMX was shown for xylan (binding constant K=3.1×104 M−1), yeast cell wall glucan (K=1.4×105 M−1) and chitin (K=3.3.105 M−1 in the presence of Ca2+). Lic16A deletion derivatives lacking CBMX had lower affinity to lichenan and laminarin and a slight decrease in optimum temperature and thermostability. However, the specific activity was not significantly affected.
Mce3R, a TetR-type transcriptional repressor, controls the expression of a regulon involved in lipid metabolism in Mycobacterium tuberculosis
Authors: Santangelo María de la Paz , Klepp Laura , Nuñez-García Javier , Blanco Federico C. , Soria Marcelo , García-Pelayo Maria del Carmen , Bianco María Verónica , Cataldi Angel A. , Golby Paul , Jackson Mary , Gordon Stephen V. , Bigi Fabiana
Published: June 2009

The mce operons constitute four homologous regions in the Mycobacterium tuberculosis genome, each of which has 8–13 ORFs. Although the function of the Mce protein family has not been clearly established, its members are believed to be membrane lipid transporters. Based on functional experiments, we found that the regulator of the mce3 locus, Mce3R, negatively regulates the expression of the Rv1933c–Rv1935c and Rv1936–Rv1941 transcriptional units. These operons are adjacent to one another and divergently transcribed. The predicted functions of most of these genes are related to either lipid metabolism or redox reactions. Bioinformatic analysis of the 5′ UTR sequences of the differentially expressed genes allowed us to define a putative Mce3R motif. Importantly, the Mce3R motif was present six and three times in the mce3R–yrbE3A and Rv1935c–Rv1936 intergenic regions, respectively. Two occurrences of this motif mapped within the two regions of the mce3 operon that were protected by Mce3R in a footprinting analysis, thus indicating that this motif is likely to serve as an operator site for the Mce3R regulator in the promoter. In addition, alterations in the lipid content of M. tuberculosis were detected in the absence of Mce3R. Taken together, these results suggest that Mce3R controls the expression of both the putative transport system encoded in the mce3 operon and the enzymes implicated in the modification of the Mce3-transported substrates.
Expression of the sarA family of genes in different strains of Staphylococcus aureus
Authors: Ballal Anand , Manna Adhar C.
Published: June 2009

Expression of genes involved in the pathogenesis of Staphylococcus aureus is controlled by global regulatory loci, including two-component regulatory systems and transcriptional regulators. The staphylococcal-specific SarA family of transcription regulators control large numbers of target genes involved in virulence, autolysis, biofilm formation, stress responses and metabolic processes, and are recognized as potential therapeutic targets. Expression of some of these important regulators has been examined, mostly in laboratory strains, while the pattern of expression of these genes in other strains, especially clinical isolates, is largely unknown. In this report, a comparative analysis of 10 sarA-family genes was conducted in six different S. aureus strains, including two laboratory (RN6390, SH1000) and four clinical (MW2, Newman, COL and UAMS-1) strains, by Northern and Western blot analyses. Transcription of most of the sarA-family genes showed a strong growth phase-dependence in all strains tested. Among these genes, no difference was observed in expression of the sarA, sarV, sarT and sarU genes, while a major difference was observed in expression of the sarX gene only in strain RN6390. Expression of mgrA, rot, sarZ, sarR and sarS was observed in all strains, but the level of expression varied from strain to strain.
Comparative proteomic analysis of an Aspergillus fumigatus mutant deficient in glucosidase I (AfCwh41)
Authors: Zhang Lei , Feng Deqin , Fang Wenxia , Ouyang Haomiao , Luo Yuanming , Du Ting , Jin Cheng
Published: June 2009

α-Glucosidase I regulates trimming of the terminal α-1,2-glucose residue in the N-glycan processing pathway, which plays an important role in quality control systems in mammalian cells. Previously, we identified the gene encoding α-glucosidase I in the opportunistic human fungal pathogen Aspergillus fumigatus, namely Afcwh41. Deletion of the Afcwh41 gene results in a severe reduction of conidia formation, a temperature-sensitive deficiency of cell wall integrity, and abnormalities of polar growth and septation. An upregulation of the genes encoding Rho-type GTPases was also observed, which suggests activation of the cell wall integrity pathway in the mutant. Using 2D gel analysis, we revealed that the proteins involved in protein assembly, ubiquitin-mediated degradation and actin organization are altered in the ΔAfcwh41 mutant. Evidence was obtained for a defect in the polarized localization of the actin cytoskeleton in the mutant. Our results suggest that blocking of the glucose trimming in A. fumigatus might induce accumulation of misfolded proteins in the endoplasmic reticulum; these misfolded proteins are probably required for cell wall synthesis and thus activate the cell wall integrity pathway, which then causes the abnormal polarity associated with the ΔAfcwh41 mutant.
A family of fibrinogen-binding MSCRAMMs from Enterococcus faecalis
Authors: Sillanpää Jouko , Nallapareddy Sreedhar R. , Houston Janeu , Ganesh Vannakambadi K. , Bourgogne Agathe , Singh Kavindra V. , Murray Barbara E. , Höök Magnus
Published: June 2009

We report that three (EF0089, EF2505 and EF1896, renamed here Fss1, Fss2 and Fss3, respectively, forEnterococcusfaecalissurface protein) of the recently predicted MSCRAMMs (microbial surface components recognizing adhesive matrix molecules) inE. faecalisstrain V583 bind fibrinogen (Fg). Despite an absence of extensive primary sequence homology, the three proteins appear to be related structurally. Within the N-terminal regions of the three enterococcal proteins, we identified pairs of putative IgG-like modules with a high degree of predicted structural similarity to the Fg-binding N2 and N3 domains of the staphylococcal MSCRAMMs ClfA and SdrG. A second N2N3-like segment was predicted in Fss1. Far-UV circular dichroism spectroscopy revealed that all four predicted N2N3-like regions are composed mainly ofβ-sheets with only a minor proportion ofα-helices, which is characteristic of Ig-like folded domains. Three of the four identified enterococcal N2N3-like regions showed potent dose-dependent binding to Fg. However, the specificity of the Fg-binding MSCRAMMs differs, as indicated by far-Western blots, which showed that recombinant segments of the MSCRAMMs bound different Fg polypeptide chains. Enterococci grown in serum-supplemented broth adhere to Fg-coated surfaces, and inactivation in strain OG1RF of the gene encoding Fss2 resulted in reduced adherence, whilst complementation of the mutant restored full Fg adherence. Thus,E. faecaliscontains a family of MSCRAMMs that structurally and functionally resemble the Fg-binding MSCRAMMs of staphylococci.
DNA microarray analysis of global gene regulation by A-factor in Streptomyces griseus
Authors: Hara Hirofumi , Ohnishi Yasuo , Horinouchi Sueharu
Published: June 2009

A-factor (2-isocapryloyl-3R-hydroxymethyl-γ-butyrolactone) is a microbial hormone that triggers morphological differentiation and secondary metabolism in Streptomyces griseus. The effects of A-factor on global gene expression were determined by DNA microarray analysis of transcriptomes obtained with the A-factor-deficient mutant ΔafsA. A-factor was added at a concentration of 25 ng ml−1 to mutant ΔafsA at the middle of the exponential growth phase, and RNA samples were prepared from the cells grown after A-factor addition for a further 5, 15 and 30 min, and 1, 2, 4, 8 and 12 h. The effects of A-factor on transcription of all protein-coding genes of S. griseus were evaluated by comparison of the transcriptomes with those obtained from cells grown in the absence of A-factor. Analysis of variance among the transcriptomes revealed that 477 genes, which were dispersed throughout the chromosome, were differentially expressed during the 12 h after addition of A-factor, when evaluated by specific criteria. Quality threshold clustering analysis with regard to putative polycistronic transcriptional units and levels of upregulation predicted that 152 genes belonging to 74 transcriptional units were probable A-factor-inducible genes. Competitive electrophoretic mobility shift assays using DNA fragments including putative promoter regions of these 74 transcriptional units suggested that AdpA bound 37 regions to activate 72 genes in total. Many of these A-factor-inducible genes encoded proteins of unknown function, suggesting that the A-factor regulatory cascade of S. griseus affects gene expression at a specific time point more profoundly than expected.
Pseudomonas aeruginosa extracellular products inhibit staphylococcal growth, and disrupt established biofilms produced by Staphylococcus epidermidis
Authors: Qin Zhiqiang , Yang Liang , Qu Di , Molin Soeren , Tolker-Nielsen Tim
Published: June 2009

Multiple bacterial species often coexist as communities, and compete for environmental resources. Here, we describe how an opportunistic pathogen,Pseudomonas aeruginosa, uses extracellular products to interact with the nosocomial pathogenStaphylococcus epidermidis.S. epidermidisbiofilms and planktonic cultures were challenged withP. aeruginosasupernatant cultures overnight. Results indicated that quorum-sensing-controlled factors fromP. aeruginosasupernatant inhibitedS. epidermidisgrowth in planktonic cultures. We also found thatP. aeruginosaextracellular products, mainly polysaccharides, disrupted establishedS. epidermidisbiofilms. Cellulase-treatedP. aeruginosasupernatant, and supernatant frompelA,pslFandpelApslBCDmutants, which are deficient in polysaccharide biosynthesis, diminished the disruption ofS. epidermidisbiofilms. In contrast,S. epidermidissupernatant in overnight cultures had no effect on establishedP. aeruginosabiofilms and planktonic growth. These findings reveal thatP. aeruginosaextracellular products are important microbial competition factors that overcome competition withS. epidermidis, and the results may provide clues for the development of a novel strategy for controllingS. epidermidisbiofilms.
Detection of 140 clinically relevant antibiotic-resistance genes in the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to selected antibiotics
Authors: Szczepanowski Rafael , Linke Burkhard , Krahn Irene , Gartemann Karl-Heinz , Gützkow Tim , Eichler Wolfgang , Pühler Alfred , Schlüter Andreas
Published: June 2009

To detect plasmid-borne antibiotic-resistance genes in wastewater treatment plant (WWTP) bacteria, 192 resistance-gene-specific PCR primer pairs were designed and synthesized. Subsequent PCR analyses on total plasmid DNA preparations obtained from bacteria of activated sludge or the WWTP's final effluents led to the identification of, respectively, 140 and 123 different resistance-gene-specific amplicons. The genes detected included aminoglycoside, β-lactam, chloramphenicol, fluoroquinolone, macrolide, rifampicin, tetracycline, trimethoprim and sulfonamide resistance genes as well as multidrug efflux and small multidrug resistance genes. Some of these genes were only recently described from clinical isolates, demonstrating genetic exchange between clinical and WWTP bacteria. Sequencing of selected resistance-gene-specific amplicons confirmed their identity or revealed that the amplicon nucleotide sequence is very similar to a gene closely related to the reference gene used for primer design. These results demonstrate that WWTP bacteria are a reservoir for various resistance genes. Moreover, detection of about 64 % of the 192 reference resistance genes in bacteria obtained from the WWTP's final effluents indicates that these resistance determinants might be further disseminated in habitats downstream of the sewage plant.
Function of the N-terminal region of the phosphate-sensing histidine kinase, SphS, in Synechocystis sp. PCC 6803
Authors: Kimura Satoshi , Shiraiwa Yoshihiro , Suzuki Iwane
Published: June 2009

InSynechocystissp. PCC 6803 the histidine kinase SphS (sll0337) is involved in transcriptional activation of the phosphate (Pi)-acquisition system which includes alkaline phosphatase (AP). The N-terminal region of SphS contains both a hydrophobic region and a Per-Arnt-Sim (PAS) domain. The C-terminal region has a highly conserved transmitter domain. Immunological localization studies on heterologously expressed SphS inEscherichia coliindicate that the hydrophobic region is important for membrane localization. In order to evaluate the function of the N-terminal region of SphS, deletion mutants under the control of the native promoter were analysed forin vivoAP activity. Deletion of the N-terminal hydrophobic region resulted in loss of AP activity under both Pi-deficient and Pi-sufficient conditions. Substitution of the hydrophobic region of SphS with that from the Ni2+-sensing histidine kinase, NrsS, resulted in the same induction characteristics as SphS. Deletion of the PAS domain resulted in the constitutive induction of AP activity regardless of Piavailability. To characterize the PAS domain in more in detail, four amino acid residues conserved in the PAS domain were substituted with Ala. Among the mutants R121A constitutively expressed AP activity, suggesting that R121 is important for the function of the PAS domain. Our observations indicated that the presence of a transmembrane helix in the N-terminal region of SphS is critical for activity and that the PAS domain is involved in perception of Piavailability.
Identification of genes required for Pseudomonas aeruginosa carnitine catabolism
Authors: Wargo Matthew J. , Hogan Deborah A.
Published: June 2009

Carnitine is a quaternary amine compound prevalent in animal tissues, and a potential carbon, nitrogen and energy source for pathogens during infection. Characterization of activities in Pseudomonas aeruginosa cell lysates has previously shown that carnitine is converted to 3-dehydrocarnitine (3-dhc) which is in turn metabolized to glycine betaine (GB), an intermediate metabolite in the catabolism of carnitine to glycine. However, the identities of the enzymes required for carnitine catabolism were not known. We used a genetic screen of the P. aeruginosa PA14 transposon mutant library to identify genes required for growth on carnitine. We identified two genomic regions and their adjacent transcriptional regulators that are required for carnitine catabolism. The PA5388–PA5384 region contains the predicted P. aeruginosa carnitine dehydrogenase homologue along with other genes required for growth on carnitine. The second region identified, PA1999–PA2000, encodes the α and β subunits of a predicted 3-ketoacid CoA-transferase, an enzymic activity hypothesized to be involved in the first step of deacetylation of 3-dhc. Furthermore, we confirmed that an intact GB catabolic pathway is required for growth on carnitine. The PA5389 and PA1998 transcription factors are required for growth on carnitine. PA5389 is required for induction of the PA5388–PA5384 transcripts in response to carnitine, and the PA1999–PA2000 transcripts are induced in a PA1998-dependent manner and induction appears to depend on a carnitine catabolite, possibly 3-dhc. These results provide important insight into elements required for carnitine catabolism in P. aeruginosa and probably in other bacteria.
Lateralized spatial and object memory encoding in entorhinal and perirhinal cortices
Authors: Bellgowan Patrick S.F. , Buffalo Elizabeth A. , Bodurka Jerzy , Martin Alex
Published: June 2009

The perirhinal and entorhinal cortices are critical components of the medial temporal lobe (MTL) declarative memory system. Study of their specific functions using blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI), however, has suffered from severe magnetic susceptibility signal dropout resulting in poor temporal signal-to-noise (tSNR) and thus weak BOLD signal detectability. We have demonstrated that higher spatial resolution in the z-plane leads to improved BOLD fMRI signal quality in the anterior medial temporal lobes when using a 16-element surface coil array at 3 T (Tesla). Using this technique, the present study investigated the roles of the anterior medial temporal lobe, particularly the entorhinal and perirhinal cortices, in both object and spatial memory. Participants viewed a series of fractal images and were instructed to encode either the object's identity or location. Object and spatial recognition memory were tested after 18-sec delays. Both the perirhinal and entorhinal cortices were active during the object and spatial encoding tasks. In both regions, object encoding was biased to the left hemisphere, whereas spatial encoding was biased to the right. A similar hemispheric bias was evident for recognition memory. Recent animal studies suggest functional dissociations among regions of the entorhinal cortex for spatial vs. object processing. Our findings suggest that this process-specific distinction may be expressed in the human brain as a hemispheric division of labor.