bluuebunny/crossref_metadata_2025 huggingface dataset:
Performance of the transverse acoustic variability experiment horizontal line array.
Authors: Goldstein David J. , Mignerey Peter C.
Published: March 2010

The transverse acoustic variability experiment was designed to study the impact of shallow-water environmental fluctuations on acoustic coherence in the horizontal plane, transverse to the direction of propagation. The experiment was conducted during August 2008 in the East China Sea. A critical component to the success of the experiment was a two-segment 96-channel horizontal line array, moored on the sea floor at an approximate depth of 80 m. An analysis of the performance of this array is presented, including pulse arrival time statistics, beam patterns, gains, and signal-to-noise ratio. Methods used to determine the relative positions of array hydrophones are also discussed. [Work supported by the Office of Naval Research. We thank the staff at KORDI and the crews aboard the R/V Eardo and Sunjin for their assistance and bountiful hospitality.]
Characterizing water column variability and its impact on underwater acoustic propagation.
Authors: Becker Kyle M. , Ballard Megan S.
Published: March 2010

During the Shallow Water Experiment 2006 (SW06), a low-frequency acoustic source was towed out and back along radials from a receiver array located at the origin. Measurements were made along three radials, separated by 45 deg, with each track repeatedly traversed over a period of 6–10 h. Concurrently with the acoustic measurements, the water column sound speed field was estimated both along the source track and at the receiver location. The objective was to fully characterize the environment in the water column over the acoustic path during transmissions. In this way, variability in the acoustic field measured along the repeated tracks could be associated with variability in the water column. The variability in the water column, measured independently at the source and at the receiver, is examined and related to variability observed in the acoustic fields. Spatial and temporal variability is characterized on transect-to-transect, radial-to-radial, and day-to-day basis. Over 3 days, variability in the water column could be attributed to thermohaline intrusions, linear and non-linear internal waves, as well as mesoscale variability. This talk will focus on the requirements for characterizing these features and understanding their impact on acoustic propagation and prediction. [Work supported by ONR.]
Propagation of low-frequency sound through densely sampled internal waves.
Authors: Ballard Megan S. , Becker Kyle M.
Published: March 2010

It is well known that nonlinear internal gravity waves can have a significant effect on acoustic propagation. In particular, horizontal refraction and ducting of sound can occur when the acoustic propagation path is aligned with fronts of internal waves. Additionally, more complicated effects are associated with internal waves that are curved and/or truncated. In this talk, observations of internal waves measured on the New Jersey shelf area of the north Atlantic and their effects on the acoustic field are presented. During the experiment, a low-frequency source broadcasting continuous tone was towed repeatedly out and back along radials with respect to a VLA. The ship’s track was oriented parallel to the shelf break so that the acoustic propagation path was roughly aligned with internal waves propagating up the shelf. Internal waves were measured at the location of the receivers by temperature sensors on the VLA, at the location of the source by a towed CTD chain, as well as by a cluster of 16 environmental moorings located adjacent to experiment site. The high-spatial sampling of the environment allows for identification of range-varying features of internal waves.
Horizontal reflection of a low-frequency sound signal from a moving nonlinear internal wave front.
Authors: Badiey M. , Lynch J. F. , Lin Y.-T. , Katsnelson B. G.
Published: March 2010

Simultaneous measurements of acoustical and internal waves are reported while an internal wave approaches an acoustic track during the SW06 experiment. The incoming internal wave packet acts as a moving layer reflecting and refracting acoustic waves in the horizontal plane. The mechanism of this interaction is shown in received acoustic data on a vertical hydrophone array using a modal approach. It is shown that the wave front of internal waves behaves as selective filter, depending on the mode number and frequency of the broadband signal. In other words the reflection coefficient in horizontal plane depends on mode number and frequency. Experimental data analysis shows good agreement with the theory. [Work supported by ONR 321OA.]
Relationship between cavitation, rapid loss of echogenicity, and drug release from echogenic liposomes.
Authors: Radhakrishnan Kirthi , Kopechek Jonathan A. , Haworth Kevin J. , Huang Shaoling , McPherson David D. , Holland Christy K.
Published: March 2010

Echogenic liposomes (ELIPs), encapsulating air and drug, are being developed for use as vesicles for ultrasound-mediated drug release. Both calcein and a thrombolytic drug have been encapsulated in ELIP and released with 6-MHz color Doppler ultrasound in an in vitro flow system. To elucidate the role of stable or inertial cavitation in loss of echogenicity and drug release, ELIPs were insonified with 6-MHz pulsed Doppler ultrasound within the same flow system. A 10-MHz focused passive cavitation detector (PCD) was placed confocally with the pulsed Doppler sample volume. B-mode images and PCD signals were recorded during ELIP infusion (5 ml/min) and exposed to pulsed Doppler over a range of peak rarefactional pressure amplitudes (0–1.4 MPa) at two pulse repetition frequencies (1250 and 2500 Hz). The mean digital intensities were calculated on each image within two regions of interest placed upstream and downstream of the Doppler sample volume. The thresholds for rapid loss of echogenicity were ascertained from six B-mode images acquired over 30 s. These thresholds were compared to stable and inertial cavitation thresholds. The implications of these data on the mechanism of rapid liberation of gas and drug release will be discussed. [Work supported by the NIH R01 HL059586 and NIH R01 HL7400]
Combined ultrasonic and video-microscopic characterization of ultrasound contrast agents in a flow phantom.
Authors: Chitnis Parag V. , Lee Paul , Mamou Jonathan , Dayton Paul A. , Ketterling Jeffrey A.
Published: March 2010

A high-frequency ultrasound pulse-echo system has been combined with a video microscope system for characterizing the response of two types of ultrasound contrast agents (UCAs). A focused-flow phantom was constructed using a glass micropipette (inner diameter 30 μm) mounted vertically in a test tank. The UCA solution was pumped using a syringe pump at a constant flow rate of 40 μl/min. A high-speed CCD camera operating at 10 000 frames/s with an exposure time of 4 μs was used to capture backlit images of individual UCAs. The camera was equipped with a 100× water-immersion objective with a field-of-view of 70×70 μm. A 40-MHz, focused transducer was aligned at the micropipette and used in pulse-echo mode to sonicate individual UCAs and receive the corresponding radio-frequency backscatter signals. The UCAs were subjected to ultrasound at varying incident-pressure levels (0.8–3 MPa) and pulse durations (10, 15, and 20 cycles). Echo signals from individual UCAs were windowed and spectra were calculated. The magnitude of the fundamental (40-MHz) backscatter was observed to increase monotonically with UCA diameter. Correlation between the magnitude of the sub-harmonic (20-MHz) response of UCAs and their size was investigated. [Work supported by NIH EB006372.]
Quantification of endothelial cell transfection as a function of permeability with targeted ultrasound contrast agents.
Authors: Anastasiadis Pavlos , Allen John S.
Published: March 2010

Gene and drug delivery have shown to be enhanced by the localized destruction of ultrasound contrast agents (UCAs). Moreover, deoxyribonucleic acid (DNA) is rapidly degraded by serum DNases following its injection into the bloodstream, and several studies have shown that DNA may be protected from such DNases if it is conjugated onto the shell of UCAs. The optimal acoustic parameters for transfection and delivery are not well understood. Likewise, the real-time monitoring of the related cell membrane permeability changes has only been recently attempted for these applications. This study evaluates the endothelial cell-to-cell and cell-to-substrate gaps with the electric cell-substrate impedance sensing system (ECIS, Applied BioPhysics, Troy, NY). ECIS can detect in real-time the nanometer order changes of cell-to-cell and cell-to-substrate distances separately. Targeted UCAs were conjugated with plasmid vectors and subject to ultrasound insonification, while continuous measurements of the electrical resistance across the endothelial monolayers were conducted in real-time for the determination of membrane permeability changes. The achieved transfection rate is investigated over a range of acoustic parameters. [This work was supported by the National Institutes of Health Grants NIH 2 P20 RR016453-05A1 and NIH 2 G12 RR0030161-21.]
Audio visual scene analysis using spherical arrays and cameras.
Authors: O’Donovan Adam , Duraiswami Ramani , Zotkin Dmitry , Gumerov Nail
Published: March 2010

While audition and vision are used together by living beings to make sense of the world, the observation of the world using machines in applications such as surveillance and robotics has proceeded largely separately. We describe the use of spherical microphone arrays as “audio cameras” and spherical array of video cameras as a tool to perform multi-modal scene analysis that attempts to answer questions such as “Who?,”, “What?,” “Where?,” and “Why?.” Signal processing algorithms to identify the number of people and their identities and to isolate and dereverberate their speech using multi-modal processing will be described. The use of graphics processor based signal processing allows for real-time implementation of these algorithms. [Work supported by ONR.]
Aspects of participation in the Science and Human Rights Coalition of the AAAS (American Association for the Advancement of Science): Working groups and internal outreach.
Authors: Anderson Clinton W.
Published: March 2010

The goal of Dr. Anderson’s presentation is to inform ASA members about two practical aspects of participation in the AAAS Science and Human Rights Coalition: Participation in the working groups that are at the core of the Coalition’s activities and outreach by coalition member representatives internally within their organizations. The speaker will briefly introduce the missions and modes of operation of the five working groups that are currently active within the Coalition and focus more extensively on the operations and objectives of the Service to the Scientific Community Working Group. Based on the action plan of the Service to the Scientific Community Working Group and his own experience as an organization member representative for the American Psychological Association, the speaker will to explore ways in which ASA members might work to increase awareness and appreciation of human rights issues and alternatives within the ASA; to increase capacity of the ASA to address human rights issues through a variety of means, including the application of acoustical tools and techniques; and to increase engagement of ASA in human rights activities.
The role of science in the human rights movement.
Authors: Rubenstein Leonard
Published: March 2010

“Scientists have contributed valuably in making human rights a reality for all. Notable scientific contributions to human rights include the forensic exhumation of mass graves, the use of DNA evidence to identify victims of mass killings, the introduction of information management techniques to illuminate large-scale human rights violations, and, more recently, the use of satellite imagery to document the destruction of communities in remote locations.” [Rubenstein and Younis 2008)]. As a human rights lawyer and a consumer of science, Mr. Rubenstein will discuss the contributions of science to human rights challenges, and the importance of the scientific community becoming a constituency for human rights. He will address head-on some of the greatest misconceptions about human rights work, including the charge that it is too “political” as well as steps needed to assure that scientific work undertaken with human rights organizations and is conducted consistent with scientific traditions of impartiality and independent inquiry. Finally, he will demonstrate how the AAAS Science and Human Rights Coalition can be used as a vehicle for the application of scientific skills, to reinforce the commitment, and to amplify the voices of scientists working toward the realization of human rights for all.
A study on nonlinear ultrasonic waves in bubbly media: One and two-dimensional numerical experiments.
Authors: Christian Vanhille , Cleofé Campos-Pozuelo
Published: March 2010

Nonlinear ultrasonic waves are studied in bubbly media, typically liquids with gas bubbles. The acoustic behavior is modeled by a differential system which couples the acoustic pressure and the nonlinear dynamic of the bubbles. The differential equations are solved by means of a numerical model that gives the acoustic pressure and bubble volume variation as time traces (SNOW-BL code) in two configurations: one and two dimensions. Results are shown for one-dimensional progressive and standing waves as well as for two-dimensional progressive waves, with or without focus. Experiments are carried out with bubbles evenly distributed or forming clouds, for example, in the pre-focal zone. [This work is part of the research project DPI2008-01429.]
Application of matched asymptotic expansions to the analysis of compressional bone conduction.
Authors: Chhan David , Thompson Charles
Published: March 2010

In this work, we will investigate the compressional mode of bone conduction and its effect on the displacement of the cochlear partition. We will use the method of matched asymptotic expansions to obtain the velocity of the partition. In this mode of bone conduction, the cochlea is compressed alternatively due to an applied vibratory force. Velocity difference between the oval and round windows is shown to be critical in determining the amplitude of the partition motion. From this physical process, we will analytically derive equations that will be used to solve for the velocity of the cochlear partition due to the compressional velocity on the cochlear shell.
Observing chartacteristic frequency shifts using chirp-evoked otoacoustic emissions.
Authors: Shaheen Luke , Epstein Michael , Silva Ikaro
Published: March 2010

Otoacoustic emissions (OAEs) are often used to assess the integrity of specific regions of the cochlea. There is, however, evidence that the frequency that causes maximal response for a particular cochlear region shifts toward lower frequencies at high-stimulus levels. Therefore, OAE-based assessments of cochlear activity over a wide range of levels may need to take into account these shifts. The present study employed two experiments in order to confirm and characterize the extent to which this shift in cochlear excitation as a function of level can be observed in OAEs. In the first experiment, chirp-evoked otoacoustic emissions (ChOAEs) were used to track changes in the frequency spectra of each listener. The results showed a shift toward low frequencies in the spectral peak of ChOAE response in a majority of listeners (−9.1% average shift). This shift was then confirmed using a single-listener measurement of tone-burst otoacoustic emission input/output functions measured at three different frequencies. These results support the contention that it may be necessary to vary stimulus frequency to take the cochlear excitation shift into account when making assessments of the cochlear activity at a particular location across a wide range of levels.
Influence of hair bundle configuration on biomimetic hair sensor sensitivity.
Authors: Liu Shuangqin , White Robert
Published: March 2010

Hair cells are the sensory receptors of the auditory system. When the stereocilia (hair buddles) sitting on top of the hair cells are stimulated, a current flows through the hair cell transducing mechanical stimuli into electrical response. For the outer hair cell (OHC), the hair bundles are stimulated by displacement of the tectorial membrane relative to the reticular lamina. For the inner hair cell (IHC), the hair bundles are stimulated by force due to motion of the fluid around the hair bundle. In addition, OHC and IHC hair bundles are shaped differently. In this paper, biomimetic micromachined hair sensors are designed, fabricated, and tested to investigate how the configurations of the hair bundles affect the sensitivity of the hair sensor. These hair sensors use a capacitive scheme and have different hair configurations including the W and U shape representing OHC and IHC hair bundles. Computational results achieved to date indicate that sensitivity can be strongly affected by the placement of the engineered hair bundles. Microfabrication and experimental work are ongoing.
Spatiotemporal coding of signals in the auditory periphery.
Authors: Kumaresan Ramdas , Peddinti Vijay , Cariani Peter
Published: March 2010

Signal representation in the cochlea is often thought to involve either rate-place profiles or purely temporal, interspike interval codes. Spatio-temporal coding strategies based on phase-locking, cochlear delays, and coincidence detectors have also been proposed [Loeb et al., Biol. Cybern. (1983); K. & Shamma, J. Acoust. Soc. Am. 107 (2000); and Carney et al., Acoustica 88, 334–337 (2002)]. In this view, spatiotemporal patterns of spikes locked to relative phases of the traveling wave at specific cochlear places at a given time can convey information about a tone. We propose a general mathematical basis for using such spatial phase/amplitude patterns along the frequency axis to represent an arbitrary (approximately) time and bandwidth-limited signal. We posit that the spatial pattern of phases and amplitudes corresponds to locations at which (real and/or imaginary parts of) the Fourier transform of the signal crosses certain levels (e.g., zero level). Given these locations, we show that we can accurately reconstruct the original signal by solving a simple eigenvalue problem. Using this approach, we propose an analysis/synthesis algorithm to represent speech-like signals. We conjecture that a generalized representation of the forms of signals can be inferred from spatial, cross-CF patterns of phase relations present in the auditory nerve. [Work supported by AFSOR FA9550-09-1-0119.]
On the acoustics of emotion in speech: Desperately seeking a standard.
Authors: Schuller Bjoern
Published: March 2010

Researchers concerned with automatic recognition of human emotion in speech have proposed a considerable variety of segmental and supra-segmental acoustic descriptors. These range from prosodic characteristics to voice quality to acoustic correlates of articulation and represent unequal degrees of perceptual elaboration. Recently, evidence has been reported from first comparisons on multiple speech databases that spectral and cepstral characteristics have the greatest potential for the task [B. Schuller et al., Linguistic Insights 97, 285–307 (2009)]. Yet, novel acoustic correlates are constantly proposed, as the question of the optimal representation remains disputed. The task of evaluating suggested correlates is non-trivial, as no agreed “standard” set and method of assessment exists, and inter-corpus substantiation is usually lacking. Such substantiation is particularly difficult owing to the divergence of models employed for the ground-truth description of emotion. To ease this challenge, using the potency-arousal-valence space as the predominant means for mapping information stemming from diverse speech resources, including acted and spontaneous speech with variable and fixed phonetic content on well-defined binary tasks is proposed. Among the various options for automatic classification, a method combining static and dynamic features representing pitch, intensity, duration, voice quality, and cepstral attributes is recommended.
Green’s function for the scattered field near the surface of a dissipative elastic medium.
Authors: Zabolotskaya Evgenia A. , Ilinskii Yurii A. , Hamilton Mark F.
Published: March 2010

The problem of scattering in bounded elastic media is relevant to medical ultrasound imaging and detection of buried objects. A method was developed that takes into account the propagation of longitudinal, shear, and Rayleigh waves in an elastic medium. The approach is based on solving the inhomogeneous momentum equation for the Green’s function. The forcing function is modified to accommodate different kinds of excitation that are important for shear wave imaging and seismic wave generation. The solution for the Green’s function is presented as a Fourier integral, and coefficients in the Fourier expansion are calculated by applying boundary conditions on the solid surface and matching conditions in the plane parallel to the surface that contains the source. The method permits the scattered bulk and surface waves to be distinguished from one another. The Green’s function has been presented previously in both the frequency and time domains for a lossless medium. The model is generalized here for elastic media with losses. Besides reducing the amplitude of the response, losses also impair ability to distinguish between the bulk and surface modes of propagation. [Work supported by NIH DK070618.]
R. Bruce Lindsay Award
Authors: Gee Kent L.
Published: March 2010

The R. Bruce Lindsay Award (formerly the Biennial Award) is presented in the Spring to a member of the Society who is under 35 years of age on 1 January of the year of the Award and who, during a period of two or more years immediately preceding the award, has been active in the affairs of the Society and has contributed substantially, through published papers, to the advancement of theoretical or applied acoustics, or both. The award was presented biennially until 1986. It is now an annual award.
von Békésy Medal
Authors: Rhode William S.
Published: March 2010

The von Békésy Medal is presented to individuals, irrespective of nationality, age, or society affiliation, who have made outstanding contributions to the area of psychological or physiological acoustics as evidenced by publication of research results in professional journals or by other accomplishments in the fields.
Regulation of
Zap70
Expression During Thymocyte Development Enables Temporal Separation of CD4 and CD8 Repertoire Selection at Different Signaling Thresholds
Authors: Saini Manoj , Sinclair Charles , Marshall Daniel , Tolaini Mauro , Sakaguchi Shimon , Seddon Benedict
Published: March 2010

Regulated expression of
Zap70
determines whether thymocytes develop into CD4
+
or CD8
+
T cells.
Puberty Impairs Plasticity
Authors: Stern Peter
Published: March 2010

Learning incapacity observed during puberty is related to receptor location in the hippocampus.
Source, Sensor, Channel
Authors: Gough Nancy R.
Published: March 2010

A complex containing a calcium channel, a calcium sensor, and a potassium channel regulates neuronal excitability.
Combined Antibacterial and Anti-Inflammatory Activity of a Cationic Disubstituted Dexamethasone-Spermine Conjugate
Authors: Bucki Robert , Leszczyńska Katarzyna , Byfield Fitzroy J. , Fein David E. , Won Esther , Cruz Katrina , Namiot Andrzej , Kułakowska Alina , Namiot Zbigniew , Savage Paul B. , Diamond Scott L. , Janmey Paul A.
Published: March 2010

The rising number of antibiotic-resistant bacterial strains represents an emerging health problem that has motivated efforts to develop new antibacterial agents. Endogenous cationic antibacterial peptides (CAPs) that are produced in tissues exposed to the external environment are one model for the design of novel antibacterial compounds. Here, we report evidence that disubstituted dexamethasone-spermine (D2S), a cationic corticosteroid derivative initially identified as a by-product of synthesis of dexamethasone-spermine (DS) for the purpose of improving cellular gene delivery, functions as an antibacterial peptide-mimicking molecule. This moiety exhibits bacterial killing activity against clinical isolates of
Staphylococcus aureus
,
Pseudomonas aeruginosa
present in cystic fibrosis (CF) sputa, and
Pseudomonas aeruginosa
biofilm. Although compromised in the presence of plasma, D2S antibacterial activity resists the proteolytic activity of pepsin and is maintained in ascites, cerebrospinal fluid, saliva, and bronchoalveolar lavage (BAL) fluid. D2S also enhances
S. aureus
susceptibility to antibiotics, such as amoxicillin (AMC), tetracycline (T), and amikacin (AN). Inhibition of interleukin-6 (IL-6) and IL-8 release from lipopolysaccharide (LPS)- or lipoteichoic acid (LTA)-treated neutrophils in the presence of D2S suggests that this molecule might also prevent systemic inflammation caused by bacterial wall products. D2S-mediated translocation of green fluorescent protein (GFP)-labeled glucocorticoid receptor (GR) in bovine aorta endothelial cells (BAECs) suggests that some of its anti-inflammatory activities involve engagement of glucocorticoid receptors. The combined antibacterial and anti-inflammatory activities of D2S suggest its potential as an alternative to natural CAPs in the prevention and treatment of some bacterial infections.
Fine-Tuning Synthesis ofYersinia pestisLcrV from Runaway-Like Replication Balanced-Lethal Plasmid in aSalmonella entericaSerovar Typhimurium Vaccine Induces Protection against a LethalY. pestisChallenge in Mice
Authors: Torres-Escobar Ascención , Juárez-Rodríguez María Dolores , Gunn Bronwyn M. , Branger Christine G. , Tinge Steven A. , Curtiss Roy
Published: March 2010

A balanced-lethal plasmid expression system that switches from low-copy-number to runaway-like high-copy-number replication (pYA4534) was constructed for the regulated delayedin vivosynthesis of heterologous antigens by vaccine strains. This is an antibiotic resistance-free maintenance system containing theasdAgene (essential for peptidoglycan synthesis) as a selectable marker to complement the lethal chromosomal ΔasdAallele in live recombinant attenuatedSalmonellavaccines (RASVs) such asSalmonella entericaserovar Typhimurium strain χ9447. pYA4534 harbors two origins of replication, pSC101 and pUC (low and high copy numbers, respectively). The pUC replication origin is controlled by a genetic switch formed by the operator/promoter of the P22crogene (O/Pcro) (PR), which is negatively regulated by an arabinose-inducible P22c2gene located on both the plasmid and the chromosome (araCPBADc2). The absence of arabinose, which is unavailablein vivo, triggers replication to a high-copy-number plasmid state. To validate these vector attributes, theYersinia pestisvirulence antigen LcrV was used to develop a vaccine against plague. AnlcrVsequence encoding amino acids 131 to 326 (LcrV196) was optimized for expression inSalmonella, flanked with nucleotide sequences encoding the signal peptide (SS) and the carboxy-terminal domain (CT) of β-lactamase, and cloned into pYA4534 under the control of the Ptrcpromoter to generate plasmid pYA4535. Our results indicate that the liveSalmonellavaccine strain χ9447 harboring pYA4535 efficiently stimulated a mixed Th1/Th2 immune response that protected mice against lethal challenge withY. pestisstrain CO92 introduced through either the intranasal or subcutaneous route.
Association of Pathogen Strain-Specific Gene Transcription and Transmission Efficiency Phenotype ofAnaplasma marginale
Authors: Agnes Joseph T. , Herndon David , Ueti Massaro W. , Ramabu Solomon S. , Evans Marc , Brayton Kelly A. , Palmer Guy H.
Published: March 2010

Efficient transmission of pathogens by an arthropod vector is influenced by the ability of the pathogen to replicate and develop infectiousness within the arthropod host. While the basic life cycle of development within and transmission from the arthropod vector are known for many bacterial and protozoan pathogens, the determinants of transmission efficiency are largely unknown and represent a significant gap in our knowledge. The St. Maries strain ofAnaplasma marginaleis a high-transmission-efficiency strain that replicates to a high titer in the tick salivary gland and can be transmitted by <10 ticks. In contrast,A. marginalesubsp.centrale(Israel vaccine strain) has an identical life cycle but replicates to a significantly lower level in the salivary gland, with transmission requiring >30-fold more ticks. We hypothesized that strain-specific genes expressed in the tick salivary gland at the time of transmission are linked to the differences in the transmission efficiency phenotype. Using both annotation-dependent and -independent analyses of the complete genome sequences, we identified 58 strain-specific genes. These genes most likely represent divergence from common ancestral genes in one or both strains based on analysis of synteny and lack of statistical support for acquisition as islands by lateral gene transfer. Twenty of the St. Maries strain-specific genes and 16 of the strain-specific genes in the Israel strain were transcribed in the tick salivary gland at the time of transmission. Although associated with the transmission phenotype, the expression levels of strain-specific genes were equal to or less than the expression levels in infected erythrocytes in the mammalian host, suggesting that function is not limited to salivary gland colonization.
Genome Sequencing of Recent Clinical
Chlamydia trachomatis
Strains Identifies Loci Associated with Tissue Tropism and Regions of Apparent Recombination
Authors: Jeffrey Brendan M. , Suchland Robert J. , Quinn Kelsey L. , Davidson John R. , Stamm Walter E. , Rockey Daniel D.
Published: March 2010

The human pathogen
Chlamydia trachomatis
exists as multiple serovariants that have distinct organotropisms for different tissue sites. Culture and epidemiologic data have demonstrated that serovar G is more prevalent, while serovar E is less prevalent, for rectal isolates from men having sex with men (MSM). The relative prevalence of these serovars is the opposite for isolates from female cervical infections. In contrast, the prevalence of serovar J isolates is approximately the same at the different tissue sites, and these isolates are the only C-class strains that are routinely cultured from MSM populations. These correlations led us to hypothesize that polymorphisms in open reading frame (ORF) sequences correlate with the different tissue tropisms of these serovars. To explore this possibility, we sequenced and compared the genomes of clinical anorectal and cervical isolates belonging to serovars E, G, and J and compared these genomes with each other, as well as with a set of previously sequenced genomes. We then used PCR- and restriction digestion-based genotyping assays performed with a large collection of recent clinical isolates to show that polymorphisms in ORFs CT144, CT154, and CT326 were highly associated with rectal tropism in serovar G isolates and that polymorphisms in CT869 and CT870 were associated with tissue tropism across all serovars tested. The genome sequences collected were also used to identify regions of likely recombination in recent clinical strains. This work demonstrated that whole-genome sequencing along with comparative genomics is an effective approach for discovering variable loci in
Chlamydia
spp. that are associated with clinical presentation.
Distinct Physiologic and Inflammatory Responses Elicited in Baboons after Challenge with Shiga Toxin Type 1 or 2 from Enterohemorrhagic
Escherichia coli
Authors: Stearns-Kurosawa D. J. , Collins Valta , Freeman Scott , Tesh Vernon L. , Kurosawa Shinichiro
Published: March 2010

Shiga toxin-producing
Escherichia coli
is a principal source of regional outbreaks of bloody diarrhea and hemolytic-uremic syndrome in the United States and worldwide. Primary bacterial virulence factors are Shiga toxin types 1 and 2 (Stx1 and Stx2), and we performed parallel analyses of the pathophysiologies elicited by the toxins in nonhuman primate models to identify shared and unique consequences of the toxemias. After a single intravenous challenge with purified Stx1 or Stx2, baboons (
Papio
) developed thrombocytopenia, anemia, and acute renal failure with loss of glomerular function, in a dose-dependent manner. Differences in the timing and magnitude of physiologic responses were observed between the toxins. The animals were more sensitive to Stx2, with mortality at lower doses, but Stx2-induced renal injury and mortality were delayed 2 to 3 days compared to those after Stx1 challenge. Multiplex analyses of plasma inflammatory cytokines revealed similarities (macrophage chemoattractant protein 1 [MCP-1] and tumor necrosis factor alpha [TNF-α]) and differences (interleukin-6 [IL-6] and granulocyte colony-stimulating factor [G-CSF]) elicited by the toxins with respect to the mediator induced and timing of the responses. Neither toxin induced detectable levels of plasma TNF-α. To our knowledge, this is the first time that the
in vivo
consequences of the toxins have been compared in a parallel and reproducible manner in nonhuman primates, and the data show similarities to patient observations. The availability of experimental nonhuman primate models for Stx toxemias provides a reproducible platform for testing antitoxin compounds and immunotherapeutics with outcome criteria that have clinical meaning.
A comparison of polypeptides from the wheat bunt fungi Tilletia laevis, T. tritici, and T. controversa
Authors: Kawchuk L. M. , Kim W. K. , Nielsen J.
Published: March 2010

Phenol-soluble polypeptides were extracted from teliospores of six races of each of Tilletia laevis and T. tritici, and eight collections of T. controversa. The polypeptides were separated by two-dimensional isoelectric focusing – polyacrylamide gel electrophoresis and the resulting patterns compared. Although the races and collections had the morphological and physiological features of their respective species and possessed different combinations of virulence genes, they all gave similar polypeptide patterns. There were 359 polypeptides common to all 20 races and collections. Another 56 polypeptides were found in only some races and collections, but none of these variable polypeptides were species specific, i.e., found in every race or collection of one species but absent from every race or collection of one or both of the other species. Therefore, no polypeptide could be correlated to a morphological or physiological feature typical of any one species. Furthermore, no correlation was found between the polypeptides and virulence. However, previous studies on interspecific hybridization, the overlap in spore morphology and germination requirements, and the high number of common polypeptides and absence of species-specific polypeptides demonstrated here prove a closer genetic relationship among the three fungi than is indicated by their current taxonomic designation. It is, therefore, proposed to treat them as varieties of one species: T. tritici var. laevis, T. tritici var. tritici, and T. tritici var. controversa.
Presence and absence of large inverted repeats in the mitochondrial DNA of Hyphochytriomycetes
Authors: McNabb Sally A. , Eros Ronald W. , Klassen Glen R.
Published: March 2010

Physical maps of the mitochondrial DNA (mtDNA) of Hyphochytrium catenoides and Rhizidiomyces apophysatus were constructed. Hyphochytrium catenoides has a 54-kb (kilobase pair) circular mtDNA with an inverted repeat of 13.5–14.5 kb which contains the large ribosomal RNA gene at one extreme of the inverted repeat, adjacent to the small unique region. Genome complexity (genome size minus one arm of the inverted repeat) is 39.5–40.5 kb, identical with the average value for Oomycetes. Rhizidiomyces apophysatus has a 50-kb circular mtDNA with no inverted repeat. No obvious alignment of the two maps is possible. The occurrence of a typical inverted repeat in a group of fungi closely related to the Oomycetes indicates that the character is ancestral for the Oomycetes and that its modification or loss within the Oomycetes can be treated as a derived character for the purpose of phylogenetic analysis.
Patterned fens of western Labrador and adjacent Quebec: phytosociology, water chemistry, landform features, and dynamics of surface patterns
Authors: Foster David R. , King George A. , Santelmann Mary V.
Published: March 2010

The landforms, vegetation, water chemistry, and stratigraphy of four patterned fens (aapamires) in western Labrador and adjacent Quebec are described in a study investigating the origin and characteristics of surface patterns on northern peatlands. Phytosociological analysis by the relevé approach, in conjunction with analysis by TWINSPAN, is used to describe 11 floristic noda. The vegetational patterns are largely controlled by depth to the water table. Mire landforms discussed in detail include ice-push ridges, flarks and pools, peat ridges, and mire-margin hummocks. Water chemistry is typical of minerotrophic conditions, with pH ranging from 4.4 to 6.7 and calcium concentrations from 20 to 430 μiequiv. L−1. The water chemistry, vegetation, and landforms on the mires are compared with other studies from Labrador and circumboreal regions. Stratigraphic results and field observations support the theory that surface patterns on the mire develop slowly through the interplay of biological and hydrological processes, specifically differential rate of peat accumulation controlled by vegetation type and depth to water table. Pool formation apparently involves four steps: (i) gradual differentiation of shallow flarks on previously undifferentiated mire surface; (ii) expansion and deepening of flarks and development of ridges due to differential peat accumulation; (iii) degradation of flark vegetation into mud bottoms and open-water pools; and (iv) coalescence, continued expansion, and deepening of open-water areas. Hydrological controls over the rate and extent of pool formation are discussed as a probable explanation of the geographical distribution of patterned mires.
A survey of nitrogen fixation (acetylene reduction) associated with Typha in Minnesota
Authors: Eckardt Nancy A. , Biesboer David D.
Published: March 2010

The acetylene-reduction technique was used on soil–root cores to examine the three species of Typha (Typhaceae) found in Minnesota for differences in rates of nitrogen fixation by associated rhizosphere diazotrophs. In 20 cattail stands sampled in 1985, Typha angustifolia showed a tendency for lower acetylene-reduction activity per ramet, with an average of 2.9 μmol∙ramer−1∙d−1, than T. latifolia and T. ×glauca, with averages of 6.5 and 7.1 μmol∙ramet−1∙d−', respectively. Regression analysis showed no significant differences in these values due to the variability within as well as between stands, and fixation rates were uncorrelated with the pH, soil percent carbon, and soil moisture of the study stands. In 1986, in situ assays of soil–root cores of ramets of T. angustifolia and T. latifolia from adjacent monospecific stands produced average acetylene-reduction rates of 1.4 for T. angustifolia and 1.8 μmol∙ramet−1∙d−1 for T. latifolia, with a substantial reduction in variability within stands over the 1985 data. It is estimated that, contrary to previously published reports, populations of Typha may receive as little as 1–2% of their annual nitrogen requirement from nitrogen fixation.
Variation in growth within and among families of Douglas-fir through a single season
Authors: Banerjee Satindranath , Maze Jack
Published: March 2010

In a study examining the multivariate nature of main stem and branch growth in Pseudotsuga menziesii (Mirb.) Franco, major generalizations from previous studies of ovule development were corroborated. The characteristic increase of individual variable values through time was associated with (i) increases in variation as expressed after both uni- and multi-variate analyses and (ii) changes in variable intercorrelations (= correlation structure). We interpret variation as estimating the number of different states available to a developing system and covariation among traits as a mathematical measure of the organization or integration of the measured plant parts. Together, increases in variation and changes in correlation structure with development reflect increasing complexity in biological systems concomitant with the increase in information expressed in such a system. This change in complexity has been related to the second law of thermodynamics in open (nonequilibrium) systems through recent theoretical developments. Furthermore, this study assesses the effectiveness of known genetic structure in accounting for variation between groups of individuals. Our results attribute the majority of the variation to differences within, rather than among, full-sib families. As well, these families differ in both variable variance and covariance. These results are not consistent with common assumptions in quantitative genetics.
Surface proteinaceous fibrils (fimbriae) on filamentous fungi
Authors: Gardiner R. B. , Day A. W.
Published: March 2010

Proteinaceous fibrils (fimbriae) of 4–10 nm diam. have been described in several lower eukaryotes, including yeast-like fungi and certain algae. Antibodies prepared against the fimbriae of Ustilago violacea cross react with antigens present on the surface of these same organisms. In this paper we extend these observations to a diverse group of filamentous fungi, representing the major groups. These fungi also produce surface fibrils of 6–10 nm diam. and have surface antigens that cross react with the antibodies of U. violacea fimbriae. We conclude that surface proteins of a conserved type are common in the lower eukaryotes and that these may be manifested as surface fibrils of 4–10 nm diam. In some organisms these are extruded as numerous very long fimbriae (up to 30 μm); in others they may remain largely embedded in the wall or appear as a short fringe or as sparse longer fibrils.
Scanning electron microscopy of the sporosorus in Polymyxa betae (Plasmodiophoromycetes)
Authors: Clafardini G. , Marotta B.
Published: March 2010

Results are reported for observations of sporosori of Polymyxa betae Keskin made with the scanning electron microscope on sugar-beet roots. Sporosori were extracted from the host cells 15, 20, and 30 days after inoculation, purified, and observed with the scanning electron microscope. The morphology of sporosori differs, depending on their stage of maturation. Immature resting spores (cysts) are polyhedral and characterized by a wall rich in folds that converge towards the upper portion in six ridges arranged regularly in a spoke fashion. During maturation the walls of the individual resting spores unfold and come into direct contact with each other. Towards the end of maturation the resting spores become rounded and, after their walls split, germination takes place. After germination the sporosori still conserve their structure as a result of the effect of a cementing substance that keeps the walls united. Details are given of the system used to extract and purify the sporosori for observation using the scanning electron microscope.
The germination of Potamogeton pectinatus tubers: environmental control by temperature and light
Authors: Madsen John D. , Adams Michael S.
Published: March 2010

The effects of temperature and light intensity on Potamogeton pectinatus L. tuber germination were investigated in two laboratory experiments. The hypothesis tested was that the initiation of biomass development in the stream is dependent on the temperature regulation of tuber germination. Overwintering tubers were used to eliminate the effects of preconditioning. Low temperature significantly inhibited germination and growth. In addition, germination and growth were significantly higher in the light than in the dark. However, light intensity in the experimental range had no significant effect on tuber germination or early growth.
The effects of desiccation rate on enzyme and protein-synthesis dynamics in the desiccation-tolerant pteridophyte Selaginella lepidophylla
Authors: Eickmeier William G.
Published: March 2010

The effects of desiccation rate on enzyme and protein-synthesis dynamics in the desiccation-tolerant pteridophyte Selaginella lepidophylla (Hook. & Grev.) Spring were examined in the laboratory. Detached, hydrated fronds were desiccated at four rates ranging from 5 to 150 h to frond curling at a water content of 0.35 g H2O∙g dry weight−1. Activities of 10 carbohydrate metabolism enzymes were determined following extraction from both desiccated and rehydrated fronds. Rehydration protein-synthesis rate was determined by the rate of [35S]methionine incorporation and the protein-synthesis profile was examined with a dual-isotope, [3H]leucine and [14C]leucine incoporation and electrophoresis technique. Rate of desiccation significantly affected the conservation and (or) rehydration activity increases of four enzymes; intermediate desiccation rates generally maximized enzyme activity. Desiccation rate did not affect protein-synthesis rate late in rehydration but did appear to affect the nature of proteins synthesized relative to control patterns over a full 24-h recovery period. These results help explain why whole-plant photosynthetic recovery in S. lepidophylla is fastest after intermediate desiccation (ca. 50–100 h to frond curling), but they also indicate that the species is tolerant of a wide range of desiccation rates.
Vegetation patterns in James Bay coastal marshes. II. Effects of hydrology on salinity and vegetation
Authors: Price Jonathan S. , Ewing Kern , Woo Ming-ko , Kershaw Kenneth A.
Published: March 2010

The vegetation of a coastal marsh in southern James Bay was examined in reference to the salinity and hydrological processes. Regional hydrologic influences related to the freshwater budget of James Bay reduce the local salinity so that the vegetation typifies that of a fresh to brackish marsh system, in contrast to the Hudson Bay salt marshes reported in the literature. Thus species that thrive in areas of higher salinity have only limited occurrence at the study site. Infrequent tidal inundation of low salinity bay water diminishes surface salinity, which is primarily controlled by the interaction of marsh hydrology with fossil salt diffusing upward from postglacial deposits. The soil water salinity increases with depth and distance inland. However, local hydrologic gradients near raised beach ridges and incised stream channels affect surface runoff and groundwater recharge and discharge, producing further distinct spatial variations in salinity. These processes thus control the distribution of saline water in the rooting zone and hence the patterns of vegetation.
Reflections on the life, work, and times of Vladimir Joseph Krajina
Authors: Wali Mohan K.
Published: March 2010

A distinguished teacher, botanist, ecologist, and conservationist, Professor Vladimir Joseph Krajina has made major contributions to basic ecology and to the understanding of Canada's natural environment. He has fostered an enviable rigor in the conduct of ecological studies. Combining a unique blend of European and North American ecological approaches to the study of ecosystems, his original synthesis using a biogeoclimatic classification of the ecosystems of British Columbia is now followed both in the classroom and in natural resource management. As a teacher, he has left a strong legacy to ecology through his many students. His achievements in conservation, through the establishment of 117 ecological reserves in British Columbia, devoted solely to ecological research by law, are legendary.