bluuebunny/crossref_metadata_2025 huggingface dataset:
Elongation dynamics shape bursty transcription and translation
Authors: Dobrzyński Maciej , Bruggeman Frank J.
Published: February 2009

Cells in isogenic populations may differ substantially in their molecular make up because of the stochastic nature of molecular processes. Stochastic bursts in process activity have a great potential for generating molecular noise. They are characterized by (short) periods of high process activity followed by (long) periods of process silence causing different cells to experience activity periods varying in size, duration, and timing. We present an analytically solvable model of bursts in molecular networks, originally developed for the analysis of telecommunication networks. We define general measures for model-independent characterization of bursts (burst size, significance, and duration) from stochastic time series. Inspired by the discovery of bursts in mRNA and protein production by others, we use those indices to investigate the role of stochastic motion of motor proteins along biopolymer chains in determining burst properties. Collisions between neighboring motor proteins can attenuate bursts introduced at the initiation site on the chain. Pausing of motor proteins can give rise to bursts. We investigate how these effects are modulated by the length of the biopolymer chain and the kinetic properties of motion. We discuss the consequences of those results for transcription and translation.
MicroRNA-219 modulates NMDA receptor-mediated neurobehavioral dysfunction
Authors: Kocerha Jannet , Faghihi Mohammad Ali , Lopez-Toledano Miguel A. , Huang Jia , Ramsey Amy J. , Caron Marc G. , Sales Nicole , Willoughby David , Elmen Joacim , Hansen Henrik F. , Orum Henrik , Kauppinen Sakari , Kenny Paul J. , Wahlestedt Claes
Published: February 2009

N
-methyl-
d
-aspartate (NMDA) glutamate receptors are regulators of fast neurotransmission and synaptic plasticity in the brain. Disruption of NMDA-mediated glutamate signaling has been linked to behavioral deficits displayed in psychiatric disorders such as schizophrenia. Recently, noncoding RNA molecules such as microRNAs (miRNAs) have emerged as critical regulators of neuronal functions. Here we show that pharmacological (dizocilpine) or genetic (NR1 hypomorphism) disruption of NMDA receptor signaling reduces levels of a brain-specific miRNA, miR-219, in the prefrontal cortex (PFC) of mice. Consistent with a role for miR-219 in NMDA receptor signaling, we identify calcium/calmodulin-dependent protein kinase II γ subunit (CaMKIIγ), a component of the NMDA receptor signaling cascade, as a target of miR-219. In vivo inhibition of miR-219 by specific antimiR in the murine brain significantly modulated behavioral responses associated with disrupted NMDA receptor transmission. Furthermore, pretreatment with the antipsychotic drugs haloperidol and clozapine prevented dizocilpine-induced effects on miR-219. Taken together, these data support an integral role for miR-219 in the expression of behavioral aberrations associated with NMDA receptor hypofunction.
Stimulated nuclear translocation of NF-κB and shuttling differentially depend on dynein and the dynactin complex
Authors: Shrum Cynthia K. , DeFrancisco Daniel , Meffert Mollie K.
Published: February 2009

Translocation from the cytoplasm to the nucleus is required for the regulation of gene expression by transcription factors of the nuclear factor kappa B (NF-κB) family. The p65:p50 NF-κB heterodimer that predominates in many cell types can undergo stimulated movement, following degradation of the IκB inhibitor, as well as shuttling in the absence of stimulation with IκB bound. Disruption of the dynactin complex and knockdown of endogenous dynein were used to investigate the nuclear translocation requirements for stimulated and shuttling movement of NF-κB. A differential dependence of these two modes of transport on the dynein molecular motor and dynactin was found. NF-κB used active dynein-dependent transport following stimulation while translocation during shuttling was mediated by a dynein-independent pathway that could be potentiated by dynactin disruption, consistent with a process of facilitated diffusion. Nuclear translocation and activation of NF-κB-dependent gene expression showed a dependence on endogenous dynein in a variety of cell types and in response to diverse activating stimuli, suggesting that dynein-dependent transport of NF-κB may be a conserved mechanism in the NF-κB activation pathway and could represent a potential point of regulation.
Genomic reconstruction of
Shewanella oneidensis
MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization
Authors: Pinchuk Grigory E. , Rodionov Dmitry A. , Yang Chen , Li Xiaoqing , Osterman Andrei L. , Dervyn Etienne , Geydebrekht Oleg V. , Reed Samantha B. , Romine Margaret F. , Collart Frank R. , Scott James H. , Fredrickson Jim K. , Beliaev Alexander S.
Published: February 2009

The ability to use lactate as a sole source of carbon and energy is one of the key metabolic signatures of Shewanellae, a diverse group of dissimilatory metal-reducing bacteria commonly found in aquatic and sedimentary environments. Nonetheless, homology searches failed to recognize orthologs of previously described bacterial
d
- or
l
-lactate oxidizing enzymes (
Escherichia coli
genes
dld
and
lldD
) in any of the 13 analyzed genomes of
Shewanella
spp. By using comparative genomic techniques, we identified a conserved chromosomal gene cluster in
Shewanella oneidensis
MR-1 (locus tag: SO_1522–SO_1518) containing lactate permease and candidate genes for both
d
- and
l
-lactate dehydrogenase enzymes. The predicted
d
-LDH gene (
dld-II
, SO_1521) is a distant homolog of FAD-dependent lactate dehydrogenase from yeast, whereas the predicted
l
-LDH is encoded by 3 genes with previously unknown functions (
lldEGF
, SO_1520–SO_1518). Through a combination of genetic and biochemical techniques, we experimentally confirmed the predicted physiological role of these novel genes in
S. oneidensis
MR-1 and carried out successful functional validation studies in
Escherichia coli
and
Bacillus subtilis
. We conclusively showed that
dld-II
and
lldEFG
encode fully functional
d
-and
l
-LDH enzymes, which catalyze the oxidation of the respective lactate stereoisomers to pyruvate. Notably, the
S. oneidensis
MR-1 LldEFG enzyme is a previously uncharacterized example of a multisubunit lactate oxidase. Comparative analysis of >400 bacterial species revealed the presence of LldEFG and Dld-II in a broad range of diverse species accentuating the potential importance of these previously unknown proteins in microbial metabolism.
Site-specific chemical modification of recombinant proteins produced in mammalian cells by using the genetically encoded aldehyde tag
Authors: Wu Peng , Shui Wenqing , Carlson Brian L. , Hu Nancy , Rabuka David , Lee Julia , Bertozzi Carolyn R.
Published: February 2009

The properties of therapeutic proteins can be enhanced by chemical modification. Methods for site-specific protein conjugation are critical to such efforts. Here, we demonstrate that recombinant proteins expressed in mammalian cells can be site-specifically modified by using a genetically encoded aldehyde tag. We introduced the peptide sequence recognized by the endoplasmic reticulum (ER)-resident formylglycine generating enzyme (FGE), which can be as short as 6 residues, into heterologous proteins expressed in mammalian cells. Cotranslational modification of the proteins by FGE produced products bearing a unique aldehyde group. Proteins bearing this “aldehyde tag” were chemically modified by selective reaction with hydrazide- or aminooxy-functionalized reagents. We applied the technique to site-specific modification of monoclonal antibodies, the fastest growing class of biopharmaceuticals, as well as membrane-associated and cytosolic proteins expressed in mammalian cells.
Different thermal sensitivity of the repair of photodamaged photosynthetic machinery in cultured
Symbiodinium
species
Authors: Takahashi Shunichi , Whitney Spencer M. , Badger Murray R.
Published: February 2009

Coral bleaching caused by heat stress is accompanied by photoinhibition, which occurs under conditions where the rate of photodamage to photosystem II (PSII) exceeds the rate of its repair, in the symbiotic algae (
Symbiodinium
spp.) within corals. However, the mechanism of heat stress-induced photoinhibition in
Symbiodinium
still remains poorly understood. In the present work, we have investigated the effect of elevated temperature on the processes associated with the repair of photodamaged PSII in cultured
Symbiodinium
(OTcH-1 and CS-73). Severe photoinhibition was observed at temperature exceeding 32 °C in
Symbiodinium
CS-73 cells grown at 25–34 °C but not in cultures of the more thermally tolerant
Symbiodinium
OTcH-1. After photoinhibition treatment by strong light, photodamaged PSII was repaired close to initial levels under low light at 25 °C in both OTcH-1 and CS-73. However, the repair was strongly inhibited by increased temperature exceeding 31 °C in CS-73 but only weakly in OTcH-1. We found that inhibition of the repair process in CS-73 is attributed to impairment of both protein synthesis-dependent and -independent repair processes and is at least partially caused by suppression of the de novo synthesis of thylakoid membrane proteins and impairment of the generation of ΔpH across the thylakoid membrane, respectively. Our results suggest that acceleration of photoinhibition by moderate heat stress is attributed primarily to inhibition of the repair of photodamaged PSII and that the photoinhibition sensitivity of
Symbiodinium
to heat stress is determined by the thermal sensitivity of the PSII repair processes.
Calcium-activated nonspecific cation current and synaptic depression promote network-dependent burst oscillations
Authors: Rubin Jonathan E. , Hayes John A. , Mendenhall Jeffrey L. , Del Negro Christopher A.
Published: February 2009

Central pattern generators (CPGs) produce neural-motor rhythms that often depend on specialized cellular or synaptic properties such as pacemaker neurons or alternating phases of synaptic inhibition. Motivated by experimental evidence suggesting that activity in the mammalian respiratory CPG, the preBötzinger complex, does not require either of these components, we present and analyze a mathematical model demonstrating an unconventional mechanism of rhythm generation in which glutamatergic synapses and the short-term depression of excitatory transmission play key rhythmogenic roles. Recurrent synaptic excitation triggers postsynaptic Ca
2+
-activated nonspecific cation current (
I
CAN
) to initiate a network-wide burst. Robust depolarization due to
I
CAN
also causes voltage-dependent spike inactivation, which diminishes recurrent excitation and thus attenuates postsynaptic Ca
2+
accumulation. Consequently, activity-dependent outward currents—produced by Na/K ATPase pumps or other ionic mechanisms—can terminate the burst and cause a transient quiescent state in the network. The recovery of sporadic spiking activity rekindles excitatory interactions and initiates a new cycle. Because synaptic inputs gate postsynaptic burst-generating conductances, this rhythm-generating mechanism represents a new paradigm that can be dubbed a ‘group pacemaker’ in which the basic rhythmogenic unit encompasses a fully interdependent ensemble of synaptic and intrinsic components. This conceptual framework should be considered as an alternative to traditional models when analyzing CPGs for which mechanistic details have not yet been elucidated.
Disruption of the M80-Fe ligation stimulates the translocation of cytochrome
c
to the cytoplasm and nucleus in nonapoptotic cells
Authors: Godoy Luiz C. , Muñoz-Pinedo Cristina , Castro Laura , Cardaci Simone , Schonhoff Christopher M. , King Michael , Tórtora Verónica , Marín Mónica , Miao Qian , Jiang Jian Fei , Kapralov Alexandr , Jemmerson Ronald , Silkstone Gary G. , Patel Jinal N. , Evans James E. , Wilson Michael T. , Green Douglas R. , Kagan Valerian E. , Radi Rafael , Mannick Joan B.
Published: February 2009

Native cytochrome
c
(cyt
c
) has a compact tertiary structure with a hexacoordinated heme iron and functions in electron transport in mitochondria and apoptosis in the cytoplasm. However, the possibility that protein modifications confer additional functions to cyt
c
has not been explored. Disruption of methionine 80 (M80)-Fe ligation of cyt
c
under nitrative stress has been reported. To model this alteration and determine if it confers new properties to cyt
c
, a cyt
c
mutant (M80A) was constitutively expressed in cells. M80A-cyt
c
has increased peroxidase activity and is spontaneously released from mitochondria, translocating to the cytoplasm and nucleus in the absence of apoptosis. Moreover, M80A models endogenously nitrated cyt
c
because nitration of WT-cyt
c
is associated with its translocation to the cytoplasm and nucleus. Further, M80A cyt
c
may up-regulate protective responses to nitrative stress. Our findings raise the possibility that endogenous protein modifications that disrupt the M80-Fe ligation (such as tyrosine nitration) stimulate nuclear translocation and confer new functions to cyt
c
in nonapoptotic cells.
Acute inflammatory proteins constitute the organic matrix of prostatic corpora amylacea and calculi in men with prostate cancer
Authors: Sfanos Karen S. , Wilson Brice A. , De Marzo Angelo M. , Isaacs William B.
Published: February 2009

Corpora amylacea (CA) are a frequent microscopic finding in radical prostatectomy specimens from men undergoing treatment for prostate cancer. Although often observed histologically to be associated with inflammation, the contribution of CA to prostatitis-related symptoms of unknown etiology or to prostate carcinogenesis remains unclear. Prostatic calculi (PC), which potentially represent calcified forms of CA, are less common but can cause urological disease including urinary retention and prostatitis. We conducted a comprehensive compositional analysis of CA/PC to gain insight into their biogenesis. Infrared spectroscopy analysis of calculi collected from 23 patients confirmed a prevalence of calcium phosphate in the form of hydroxyapatite. This result sets PC apart from most urinary stones, which largely are composed of calcium oxalate. Tandem mass spectrometry-based proteomic analysis of CA/PC revealed that lactoferrin is the predominant protein component, a result that was confirmed by Western blot analysis. Other proteins identified, including calprotectin, myeloperoxidase, and α-defensins, are proteins contained in neutrophil granules. Immunohistochemistry (IHC) suggested the source of lactoferrin to be prostate-infiltrating neutrophils as well as inflamed prostate epithelium; however, IHC for calprotectin suggested prostate-infiltrating neutrophils as a major source of the protein, because it was absent from other prostate compartments. This study represents a definitive analysis of the protein composition of prostatic CA and calculi and suggests that acute inflammation has a role in their biogenesis—an intriguing finding, given the prevalence of CA in prostatectomy specimens and the hypothesized role for inflammation in prostate carcinogenesis.
DSCAM functions as a netrin receptor in commissural axon pathfinding
Authors: Liu Guofa , Li Weiquan , Wang Lei , Kar Amar , Guan Kun-Liang , Rao Yi , Wu Jane Y.
Published: February 2009

Down syndrome cell adhesion molecule (DSCAM) is required for axon guidance and dendrite arborization. How DSCAM functions in vertebrates is not well understood. Here we show that DSCAM is expressed on commissural axons and interacts with Netrin-1, a prototypical guidance cue for commissural axons. The knockdown of DSCAM by specific siRNA or blockage of DSCAM signaling by overexpression of a mutant lacking its intracellular domain inhibits netrin-induced axon outgrowth and commissural axon turning in vitro. SiRNA-mediated knockdown of DSCAM in ovo causes defects in commissural axon projection and pathfinding. In transfected cells, DSCAM by itself, in the absence of DCC, is capable of mediating netrin signaling in activating phosphorylation of Fyn and Pak1. These findings demonstrate an essential role of vertebrate DSCAM in axon guidance, indicating that DSCAM functions as a receptor of netrin-1. Our data suggest previously unexpected complexity in receptors that mediate vertebrate netrin signaling.
Aligned carbon nanotubes as polarization-sensitive, molecular near-field detectors
Authors: Cubukcu Ertugrul , Degirmenci Fatih , Kocabas Coskun , Zimmler Mariano A. , Rogers John A. , Capasso Federico
Published: February 2009

Near-field scanning optical microscopes are widely used in imaging of subwavelength features in various material systems and nanostructures. For a variety of applications, polarization-sensitive near-field probes can provide valuable information on the nature and symmetry of the imaged nanoparticles and emitters. Conventional near-field optical microscopy lacks in-plane polarization sensitivity. Here, we use aligned single-wall carbon nanotubes as polarization-sensitive molecular scale probes to image the transverse near-field components of an optical Hertzian dipole antenna. Because of the Raman “antenna effect” in carbon nanotubes, only the near-field components along the nanotube axis are detected. These findings demonstrate that aligned carbon nanotubes can be used as polarization-sensitive near-field detectors.
Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure
Authors: Shtengel Gleb , Galbraith James A. , Galbraith Catherine G. , Lippincott-Schwartz Jennifer , Gillette Jennifer M. , Manley Suliana , Sougrat Rachid , Waterman Clare M. , Kanchanawong Pakorn , Davidson Michael W. , Fetter Richard D. , Hess Harald F.
Published: February 2009

Understanding molecular-scale architecture of cells requires determination of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in molecular specificity or resolution. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal molecular specificity. We demonstrate measurement of the 25-nm microtubule diameter, resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. iPALM thus closes the gap between electron tomography and light microscopy, enabling both molecular specification and resolution of cellular nanoarchitecture.
Ndy1/KDM2B immortalizes mouse embryonic fibroblasts by repressing the
Ink4a
/
Arf
locus
Authors: Tzatsos Alexandros , Pfau Raymond , Kampranis Sotirios C. , Tsichlis Philip N.
Published: February 2009

The histone H3 demethylase Not dead yet-1 (Ndy1/KDM2B) is a physiological inhibitor of senescence. Here, we show that Ndy1 is down-regulated during senescence in mouse embryonic fibroblasts (MEFs) and that it represses the
Ink4a
/
Arf
locus. Ndy1 counteracts the senescence-associated down-regulation of Ezh2, a component of polycomb-repressive complex (PRC) 2, via a JmjC domain-dependent process leading to the global and
Ink4a
/
Arf
locus-specific up-regulation of histone H3K27 trimethylation. The latter promotes the
Ink4a
/
Arf
locus-specific binding of Bmi1, a component of PRC1. Ndy1, which interacts with Ezh2, also binds the
Ink4a
/
Arf
locus and demethylates the locus-associated histone H3K36me2 and histone H3K4me3. The combination of histone modifications driven by Ndy1 interferes with the binding of RNA Polymerase II, resulting in the transcriptional silencing of the
Ink4a
/
Arf
locus and contributing to the Ndy1 immortalization phenotype. Other studies show that, in addition to inhibiting replicative senescence, Ndy1 inhibits Ras oncogene-induced senescence via a similar molecular mechanism.
Identifying essential genes in
Escherichia coli
from a metabolic optimization principle
Authors: Martelli Carlotta , De Martino Andrea , Marinari Enzo , Marsili Matteo , Pérez Castillo Isaac
Published: February 2009

Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable approximation schemes that rely on the stoichiometric data only, because full-scale kinetic approaches are computationally affordable only for small networks (e.g., red blood cells, ≈50 reactions). Methods commonly used are based on finding the stationary flux configurations that satisfy mass-balance conditions for metabolites, often coupling them to local optimization rules (e.g., maximization of biomass production) to reduce the size of the solution space to a single point. Such methods have been widely applied and have proven able to reproduce experimental findings for relatively simple organisms in specific conditions. Here, we define and study a constraint-based model of cellular metabolism where neither mass balance nor flux stationarity are postulated and where the relevant flux configurations optimize the global growth of the system. In the case of
Escherichia coli
, steady flux states are recovered as solutions, although mass-balance conditions are violated for some metabolites, implying a nonzero net production of the latter. Such solutions furthermore turn out to provide the correct statistics of fluxes for the bacterium
E. coli
in different environments and compare well with the available experimental evidence on individual fluxes. Conserved metabolic pools play a key role in determining growth rate and flux variability. Finally, we are able to connect phenomenological gene essentiality with “frozen” fluxes (i.e., fluxes with smaller allowed variability) in
E. coli
metabolism.
B7-H1 (PD-L1) on T cells is required for T-cell-mediated conditioning of dendritic cell maturation
Authors: Talay Oezcan , Shen Ching-Hung , Chen Lieping , Chen Jianzhu
Published: February 2009

Studies have shown that T-cell-dendritic cell (DC) interaction is required for efficient DC maturation. However, the identities of the molecules that mediate the interaction in vivo are largely unknown. Here, we show that maturation of DCs as well as CD8 T-cell responses were impaired in B7-H1-deficient (
B7-H1
−/−
) mice to influenza virus infection. Both defects were restored by transferring B7-H1-expressing naïve T cells into
B7-H1
−/−
mice. Similarly, transferring DCs from wild-type mice or from
RAG1
−/−
mice that had been injected with B7-H1-expressing naïve T cells also restored CD8 T-cell responses in
B7-H1
−/−
mice. These results demonstrate that B7-H1 on naïve T cells is required to condition immature DCs to undergo efficient maturation when they encounter microbial infection. In return, the mature DCs stimulate a robust T-cell reponse against the infecting pathogen.
Impact of a Mandatory Infection Control Education Program on Nosocomial Acquisition of Methicillin-ResistantStaphylococcus aureus
Authors: Lee Todd C. , Moore Christine , Raboud Janet M. , Muller Matthew P. , Green Karen , Tong Agnes , Dhaliwal Jastej , McGeer Allison ,   Mount Sinai Hospital Infection Control Team
Published: February 2009

Objective.

To assess the impact of an institution-wide infection control education program on the rate of transmission of methicillin-resistantStaphylococcus aureus(MRSA).

Design.

Before-and-after study.

Setting.

A 472-bed, urban, university-affiliated hospital.

Intervention.

During the period March-May 2004, all hospital staff completed a mandatory infection control education program, including the receipt of hospital-specific MRSA data and case-based practice with additional precautions.

Outcome Measure.

The rate of nosocomial MRSA acquisition was calculated as the number of cases of nosocomial MRSA acquisition per 100 days that a person with MRSA colonization or infection detected at admission is present in the hospital (“admission MRSA” exposure-days) for 3 time periods: June 2002-February 2003 (before the Toronto outbreak of severe acute respiratory syndrome [SARS]), June 2003-February 2004 (after the outbreak of SARS), and June 2004-February 2005 (after education). A case of nosocomial acquisition of MRSA colonization or infection represented a patient first identified as colonized or infected more than 72 hours after admission or at admission after a previous hospitalization.

Results.

The rate of nosocomial acquisition of MRSA colonization or infection was 8.8 cases per 100 admission MRSA exposure-days for the period before SARS, 3.8 cases per 100 admission MRSA exposure-days for the period after SARS (P< .001 for before SARS vs after SARS), and 1.9 cases per 100 admission MRSA exposure-days for the period after education (P= .02 for after education vs before education). The volume of alcohol-based handrub purchased was apparently stable, with 4,010 L during fiscal year 2003-2004 (April 2003-March 2004) compared with 3,780 L during fiscal year 2004—2005. The observed rate of compliance with hand washing did not change significantly (40.9% during education vs 44.2% after education;P= .23). The total number of patients screened for MRSA colonization was not different in the 3 periods.

Conclusions.

The rate of nosocomial acquisition of MRSA colonization or infection decreased after SARS and was further reduced in association with a hospital-wide education program.
A topological approach to induction theorems in Springer theory
Authors: Treumann David
Published: February 2009

We give a self-contained account of a construction due to Rossmann, which lifts Springer’s action of a Weyl group on the cohomology of a Springer fiber to an action on its homotopy type. We use this construction to produce a generalization of an “induction theorem” of Alvis and Lusztig, which relates the Springer representations attached to a reductive group to those attached to a Levi subgroup. Our generalization applies to more general centralizers and to representations of Weyl groups on modppcohomology.
Estimating mortality from times-at-large: testing accuracy and precision using simulated single tag-recovery data
Authors: McGarvey Richard , Matthews Janet M. , Feenstra John E.
Published: February 2009

McGarvey, R., Matthews, J. M., and Feenstra, J. F. 2009. Estimating mortality from times-at-large: testing accuracy and precision using simulated single tag-recovery data. – ICES Journal of Marine Science, 66: 573–581. Single tag-recovery data are available for many commercial and recreational fish stocks. However, the use of tag-recovery data has been limited by the unknown proportion of tagged recaptured animals that fishers report back to researchers. Tag underreporting causes underestimation bias in commonly applied Petersen-based estimators of fraction harvested. Using simulated data, we tested the claim that estimates of total instantaneous mortality rate (Z) based on mean time-at-large are unbiased by tag non-reporting, and by short-term (type 1) tag shedding and tag-induced mortality. The Chapman time-at-large estimator produced unbiased estimates of Z. Non-reporting and short-term tag losses produced no detectable bias in estimates of Z. Standard errors of the Chapman Z-estimate decreased with , as predicted. Non-constant-Z scenarios of fishery closure and seasonal cycling gave time-at-large Z-estimates that closely approximated the true population time averages when tag releases were spread evenly across time. Ongoing (type 2) tag shedding and tag-induced mortality biased Z-estimates upwards by the respective ongoing loss rates. When tag-recovery experiments are cut short, accurate estimates of Z are provided by Deemer and Votaw's ‘truncated’ estimator, which had wide standard errors for short experimental length, precision becoming acceptable for tag-recovery experiments run longer than approximately two or three times Z−1.
Artificial neural networks for fish-species identification
Authors: Cabreira Ariel G. , Tripode Martín , Madirolas Adrián
Published: February 2009

Cabreira, A. G., Tripode, M., and Madirolas, A. 2009. Artificial neural networks for fish-species identification. – ICES Journal of Marine Science, 66: 1119–1129. Acoustic fish detection is a valuable tool for the continuous monitoring of fish schools. However, changes in species composition or mixed multispecies situations still complicate the analysis of acoustic data. Validation of echo recordings is usually accomplished by trawling, but only at point locations. However, species proportions and size distributions in the catch can be biased because of gear selectivity and fish avoidance. In this paper, techniques involving training and testing of artificial neural networks (ANNs) are applied for the automatic recognition and classification of digital echo recordings of schools in the Southwest Atlantic. Energetic, morphometric, and bathymetric school descriptors were extracted from the echo-recordings as the input for the ANNs. Several pelagic and demersal fish species known to aggregate into schools were considered, including anchovy, rough scad, longtail hoki, sprat, and blue whiting. Different types of ANNs were tested. Best performances were obtained by levelling the input data (number of schools) per species. Correct classification rates up to 96% were obtained, depending on the species, type of network, and the number of school descriptors utilized. Some of these species inhabit areas geographically distant from each other. Hence, the contribution of the school position as a descriptor was investigated. By deleting the geographical location of the schools from the ANN input data, the average performance decreased to some extent but was still satisfactory, proving the networks were able usually to recognize fish species based only on the intrinsic characteristics of the school. The results have encouraged further testing of this method as a useful tool for scrutinizing echograms.
Influences of physical processes on the ecosystem of Jakarta Bay: a coupled physical–ecosystem model experiment
Authors: Koropitan Alan F. , Ikeda Motoyoshi , Damar Ario , Yamanaka Yasuhiro
Published: February 2009

Koropitan, A. F., Ikeda, M., Damar, A., and Yamanaka, Y. 2009. Influences of physical processes on the ecosystem of Jakarta Bay: a coupled physical–ecosystem model experiment. – ICES Journal of Marine Science, 66: 336–348. A coupled physical–ecosystem model is applied to Jakarta Bay to examine the role of physical processes on the ecosystem. The simulated physical processes include tides, river discharge, and monsoon winds. The potential sources of nitrogen to Jakarta Bay are through river inputs and wet deposition flux. The model separates the detritus compartment into pelagic and benthic components, based on cohesive sediment processes. Physical model results agree well with the observed tidal amplitude and phase, as well as tidal currents. The biological model can produce reasonable spatial and temporal patterns in lower trophic level characteristics of the ecosystem in some areas of the bay, although a lack of observed data limits confidence in model predictions. Model results show that the physical processes associated with monsoons produce an intensification of Chl a and nutrient concentrations in the eastern and western parts of the bay during northwest monsoon and southeast monsoon, respectively. The physical and biological characteristics of bay waters are controlled by influxes from offshore; the influence of river discharge is limited to the coastal area. The sensitivity of model predictions to the open boundary, river fluxes, and benthic detritus is discussed.
The Streptococcus equi prophage-encoded protein SEQ2045 is a hyaluronan-specific hyaluronate lyase that is produced during equine infection
Authors: Lindsay Anna-Marie , Zhang Meng , Mitchell Zoe , Holden Matthew T. G. , Waller Andrew S. , Sutcliffe Iain C. , Black Gary W.
Published: February 2009

Streptococcus equi causes equine ‘strangles’. Hyaluronate lyases, which degrade connective tissue hyaluronan and chondroitins, are thought to facilitate streptococcal invasion of the host. However, prophage-encoded hyaluronate lyases are hyaluronan-specific and are thought to be primarily involved in the degradation of the hyaluronan capsule of streptococci during bacteriophage infection. To understand the role of prophage-encoded hyaluronate lyases further, we have biochemically characterized such a hyaluronate lyase, SEQ2045 from S. equi, and have shown that it is produced during equine infection. Prophage-encoded hyaluronan-specific hyaluronate lyases may therefore play a more direct role in disease pathogenesis than previously thought.
Genes involved in the repression of mutacin I production in Streptococcus mutans
Authors: Nguyen Trang , Zhang Zhijun , Huang I-Hsiu , Wu Chenggang , Merritt Justin , Shi Wenyuan , Qi Fengxia
Published: February 2009

Streptococcus mutans is considered a primary pathogen for human dental caries. Its ability to produce a variety of peptide antibiotics called mutacins may play an important role in its invasion and establishment in the dental biofilm. S. mutans strain UA140 produces two types of mutacins, the lantibiotic mutacin I and the non-lantibiotic mutacin IV. In a previous study, we constructed a random insertional-mutation library to screen for genes involved in regulating mutacin I production, and found 25 genes/operons that have a positive effect on mutacin I production. In this study, we continued our previous work to identify genes that are negatively involved in mutacin I production. By using a high-phosphate brain heart infusion agar medium that inhibited mutacin I production of the wild-type, we isolated 77 clones that consistently produced mutacin I under repressive conditions. From the 34 clones for which we were able to obtain a sequence, 17 unique genes were identified. These genes encompass a variety of functional groups, including central metabolism, surface binding and sugar transport, and unknown functions. Some of the 17 mutations were further characterized and shown to increase mutacin gene expression during growth when the gene is usually not expressed in the wild-type. These results further demonstrate an intimate and intricate connection between mutacin production and the overall cellular homeostasis.
The Rhizobium etli RpoH1 and RpoH2 sigma factors are involved in different stress responses
Authors: Martínez-Salazar Jaime M. , Sandoval-Calderón Mario , Guo Xianwu , Castillo-Ramírez Santiago , Reyes Alma , Loza Maria G. , Rivera Javier , Alvarado-Affantranger Xochitl , Sánchez Federico , González Víctor , Dávila Guillermo , Ramírez-Romero Miguel A.
Published: February 2009

The physiological role and transcriptional expression of Rhizobium etli sigma factors rpoH1 and rpoH2 are reported in this work. Both rpoH1 and rpoH2 were able to complement the temperature-sensitive phenotype of an Escherichia coli rpoH mutant. The R. etli rpoH1 mutant was sensitive to heat shock, sodium hypochlorite and hydrogen peroxide, whereas the rpoH2 mutant was sensitive to NaCl and sucrose. The rpoH2 rpoH1 double mutant had increased sensitivity to heat shock and oxidative stress when compared with the rpoH1 single mutant. This suggests that in R. etli, RpoH1 is the main heat-shock sigma factor, but a more complete protective response could be achieved with the participation of RpoH2. Conversely, RpoH2 is involved in osmotic tolerance. In symbiosis with bean plants, the R. etli rpoH1 and rpoH2 rpoH1 mutants still elicited nodule formation, but exhibited reduced nitrogenase activity and bacterial viability in early and late symbiosis compared with nodules produced by rpoH2 mutants and wild-type strains. In addition, nodules formed by R. etli rpoH1 and rpoH2 rpoH1 mutants showed premature senescence. It was also determined that fixNf and fixKf expression was affected in rpoH1 mutants. Both rpoH genes were induced under microaerobic conditions and in the stationary growth phase, but not in response to heat shock. Analysis of the upstream region of rpoH1 revealed a σ
70 and a probable σ
E promoter, whereas in rpoH2, one probable σ
E-dependent promoter was detected. In conclusion, the two RpoH proteins operate under different stress conditions, RpoH1 in heat-shock and oxidative responses, and RpoH2 in osmotic tolerance.
Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis
Authors: Pieper Rembert , Huang Shih-Ting , Robinson Jeffrey M. , Clark David J. , Alami Hamid , Parmar Prashanth P. , Perry Robert D. , Fleischmann Robert D. , Peterson Scott N.
Published: February 2009

Yersinia pestiscells were grownin vitroat 26 and 37 °C, the ambient temperatures of its flea vector and its mammalian hosts, respectively, and subjected to subcellular fractionation. Abundance changes at 26 vs 37 °C were observed for many outer-membrane (OM) proteins. The cell adhesion protein Ail (y1324) and three putative smallβ-barrel OM proteins (y1795, y2167 and y4083) were strongly increased at 37 °C. The Ail/Lom family protein y1682 (OmpX) was strongly increased at 26 °C. Several porins and TonB-dependent receptors, which control small molecule transport through the OM, were also altered in abundance in a temperature-dependent manner. These marked differences in the composition of the OM proteome are probably important for the adaptation ofY. pestisto itsin vivolife stages. Thirteen proteins that appear to be part of an intact type VI secretion system (T6SS) were identified in membrane fractions of stationary-phase cells grown at 26 °C, but not at 37 °C. The corresponding genes are clustered in theY. pestisKIM gene locus y3658–y3677. The proteins y3674 and y3675 were particularly abundant and co-fractionated in aMrrange indicative of participation in a multi-subunit complex. The soluble haemolysin-coregulated protein y3673 was even more abundant. Its release into the extracellular medium was triggered by treatment ofY. pestiscells with trypsin. Proteases and other stress-response-inducing factors may constitute environmental cues resulting in the activation of the T6SS inY. pestis.
Stability and lability of circadian period of gene expression in the cyanobacterium Synechococcus elongatus
Authors: Clerico Eugenia M. , Cassone Vincent M. , Golden Susan S.
Published: February 2009

Molecular aspects of the circadian clock in the cyanobacterium Synechococcus elongatus have been described in great detail. Three-dimensional structures have been determined for the three proteins, KaiA, KaiB and KaiC, that constitute a central oscillator of the clock. Moreover, a temperature-compensated circadian rhythm of KaiC phosphorylation can be reconstituted in vitro with the addition of KaiA, KaiB and ATP. These data suggest a relatively simple circadian system in which a single oscillator provides temporal information for all downstream processes. However, in vivo the situation is more complex, and additional components contribute to the maintenance of a normal period, the resetting of relative phases of circadian oscillations, and the control of rhythms of gene expression. We show here that two well-studied promoters in the S. elongatus genome report different circadian periods of expression under a given set of conditions in wild-type as well as mutant genetic backgrounds. Moreover, the period differs between these promoters with respect to modulation by light intensity, growth phase, and the presence or absence of a promoter-recognition subunit of RNA polymerase. These data contrast sharply with the current clock model in which a single Kai-based oscillator governs circadian period. Overall, these findings suggest that complex interactions among the circadian oscillator, perhaps other oscillators, and other cellular machinery result in a clock that is plastic and sensitive to the environment and to the physiological state of the cell.
Cloning and heterologous expression of a novel ligninolytic peroxidase gene from poroid brown-rot fungus Antrodia cinnamomea
Authors: Huang S. T. , Tzean S. S. , Tsai B. Y. , Hsieh H. J.
Published: February 2009

A novel ligninolytic peroxidase gene (ACLnP) was cloned and characterized from a poroid brown-rot fungus,Antrodia cinnamomea. The genomic DNA of the fungus harboured two copies ofACLnP, with a length of 2111 bp, interlaced with 12 introns, while the full-length cDNA was 1183 bp, with a 66 bp signal peptide and an ORF of 990 bp. The three-dimensional molecular structure model was comparable to that of the versatile peroxidase ofPleurotus eryngii.ACLnPwas cloned into vector pQE31, successfully expressed inEscherichia colistrain M15 under the control of the T5 promoter and produced a non-glycosylated protein of about 38 kDa, pI 5.42. The native and recombinant ACLnP was capable of oxidizing the redox mediator veratryl alcohol, and also decolorized bromophenol blue and 2,6-dimethoxyphenol dyes, implicating a functional extracellular peroxidase activity. The significance of discovering a functionalACLnPgene inA. cinnamomeain terms of wood degradation and colonization capacity in its unique niche is discussed.
Phagocytosis, germination and killing of Bacillus subtilis spores presenting heterologous antigens in human macrophages
Authors: Ceragioli Mara , Cangiano Giuseppina , Esin Semih , Ghelardi Emilia , Ricca Ezio , Senesi Sonia
Published: February 2009

Bacillus subtilis is a Gram-positive spore-bearing bacterium long used as a probiotic product and more recently regarded as an attractive vehicle for delivering heterologous antigens to be used for mucosal vaccination. This report describes the in vitro interaction between human macrophages and B. subtilis spores displaying the tetanus toxin fragment C or the B subunit of the heat-labile toxin of Escherichia coli on their surface in comparison to spores of the parental strain. Recombinant and parental B. subtilis spores were similarly internalized by human macrophages, at a frequency lower than 2.5 %. Inside macrophages, nearly all spores germinated and were killed within 6 h. Using germination-defective spores and inhibiting spore germination inside macrophages, evidence was produced that only germinated spores were killed by human macrophages and that intracellular spore germination was mediated by an alanine-dependent pathway. The germinated spores were killed by macrophages before any round of cell duplication, as estimated by fluorescence microscopy analysis of macrophages infected with spores carrying the gfp gene fused to abrB, a B. subtilis gene shown here to be expressed at the transition between outgrowth and vegetative growth. Monitoring of macrophage infection never revealed cytotoxic effects being exerted by B. subtilis spores. These in vitro data support the hypothesis that B. subtilis spores may potentially be used as a suitable and safe vehicle for administering heterologous antigens to humans.
Amoeba co-culture of soil specimens recovered 33 different bacteria, including four new species and Streptococcus pneumoniae
Authors: Evstigneeva Anna , Raoult Didier , Karpachevskiy Lev , La Scola Bernard
Published: February 2009

Amoeba-resistant bacteria (ARB), such as Legionella spp., are currently regarded as potential human pathogens that live in the natural environment, and thus their habitat is regarded as a reservoir of human pathogens. To detect ARB in human and environmental samples, co-culture with amoebae has been demonstrated to be an efficient tool. However, to date, only water samples from cooling towers and hospital water supplies have been investigated as possible reservoirs of ARB using this procedure. In the present study, we studied the ARB population of 11 diverse soil and sand sources in proximity to human environments; these sources included the university, the station, hospitals, the square, parks and public beaches in the city of Marseilles, France. As a result, a total of 33 different species of ARB were identified. The ability to grow within and/or lyse amoebae was demonstrated, for what is believed to be the first time, for several species; moreover, 20 of the isolates (61 %), including Streptococcus pneumoniae, have been described as human pathogens. However, Legionella spp. were not isolated. Four isolates are likely to be the members of new or uncharacterized genera or species, and their capability to be human pathogens needs to be determined. This preliminary work demonstrates that soils and sands in the vicinity of humans are reservoirs of human pathogenic ARB.
The conserved portion of the putative virulence region contributes to virulence of avian pathogenic Escherichia coli
Authors: Tivendale Kelly A. , Noormohammadi Amir H. , Allen Joanne L. , Browning Glenn F.
Published: February 2009

Colibacillosis is a common systemic disease of worldwide economic importance in poultry, caused byEscherichia coli.E. coliare normally found in the intestines of poultry, but some strains are able to cause extraintestinal disease. Plasmid pVM01 is essential for virulence in avian pathogenicEscherichia coli(APEC) strain E3 in chickens after aerosol exposure and contains the virulence-associated genesiucA,issandtshin distinct regions. The determination of the complete sequence of this plasmid identified many ORFs that were highly similar to genes found in the APEC O1 plasmid, as well as many hypothetical ORFs. Truncated versions of pVM01 were constructed and introduced into avirulent APEC strain E3/2.4 and the pathogenicity of these strains was assessed by aerosol exposure. The function of the region of pVM01 that contains the genes for conjugation was confirmed. Strains carrying the truncated plasmids appeared to be of intermediate virulence compared to the wild-type APEC strain E3. The conserved portion of the putative virulence region was found to contribute to the colonization of and generation of lesions in the air sacs. Both the conserved and variable portions of the putative virulence region were shown to contribute to the colonization of the trachea, but the variable portion of the putative virulence region was not required for the strain to confer a virulent phenotype. These results reveal that deletion of the conserved portion of the putative virulence region, but not the variable portion of the putative virulence region, is associated with a decrease in virulence of APEC.
The Hog1 MAP kinase controls respiratory metabolism in the fungal pathogen Candida albicans
Authors: Alonso-Monge Rebeca , Carvaihlo Sara , Nombela Cesar , Rial Eduardo , Pla Jesús
Published: February 2009

Signal transduction pathways mediated by mitogen-activated protein kinases (MAPKs) play crucial roles in eukaryotic cells. In the pathogenic fungusCandida albicansthe HOG MAPK pathway regulates the response to external stresses (osmotic and oxidative among others) and is involved in morphogenesis and virulence. We show here that the lack of the Hog1 MAPK increases the sensitivity of this fungus to inhibitors of the respiratory chain.hog1mutants also show an enhanced basal respiratory rate compared to parental strains, and higher levels of intracellular reactive oxygen species despite an increased expression of detoxifying enzymes. We also demonstrate that although oxidative phosphorylation is essentially unaffected,hog1mutants have an altered mitochondrial membrane potential. Data indicate thathog1-defective mutants are more dependent on mitochondrial ATP synthesis, probably due to an increased cellular ATP demand. Our results therefore link a MAPK pathway with respiratory metabolism in pathogenic fungi.