bluuebunny/crossref_metadata_2025 huggingface dataset:
Behavioral differences affect passive acoustic detectability of foraging North Atlantic right and humpback whales.
Authors: Parks Susan E. , Wiley David N. , Weinrich Mason T. , Bocconcelli Alessandro
Published: October 2010

Passive acoustic monitoring is commonly used to detect the presence of different species of vocalizing marine mammals. The effectiveness of this monitoring strongly depends on the behavioral traits of the species being studied. Description of specific call parameters, such as duration, frequency range, and intensity, are necessary to identify the species present and to predict the potential range of detectability for a particular monitoring system. The behavioral function of these calls and the rates of sound production related to behavior are also important parameters to consider. In this study, a suction cup archival acoustic recording tag (Dtag) was attached to individual North Atlantic right whales and humpback whales in Massachusetts Bay in April of 2009 and 2010. Acoustic records were reviewed for sounds produced by the tagged whale. Analysis of the acoustic records from tagged individuals revealed a marked difference in vocal behavior, with right whales producing few sounds and humpback whales frequently vocalizing during periods of active foraging as confirmed from surface visual observations. These differences in the vocal behavior have potential implications for the relative acoustic detectability of these two species dependent upon the behavioral state of the individual.
Frequency-dependent echolocation beam pattern of the bottlenose dolphin.
Authors: Starkhammar Josefin , Dankiewicz-Talmadge Lois A. , Houser Dorian S. , Moore Patrick W.
Published: October 2010

Moore and others (2008) previously showed that bottlenose dolphins are capable of beam steering and controlling the vertical and horizontal widths of the echolocation beam. A follow-on study was performed using the same methods as the previous study, but with a younger animal and a higher resolution diamond-shaped hydrophone array for characterizing the beam. The dolphin performed a target detection task while stationed on a biteplate with targets placed up to 34 deg to either the left or right of the dolphin’s longitudinal axis. The dolphin was capable of beam steering more than 28 deg to either side, which is a greater capability than previously reported and which exceeded the geometric coverage of the array. Frequency band-limited beam patterns suggested the presence of two beams, spatially separate from one another and which corresponded to higher and lower frequency energies. The finding is consistent with prior anatomical and acoustic evidence of two echolocation click sound sources in the delphinids. In addition, at low frequencies, a local minimum was observed at the center of the beam. The functional significance of the local minimum, if any, is unknown.
Bat calls while preying: A method for reconstructing the signal emitted by a directional sound source.
Authors: Guarato Francesco , Hallam John
Published: October 2010

Understanding and modeling bat biosonar behavior should take into account what the bat actually emitted while exploring the surrounding environment. Recording of the bat calls could be performed by means of a telemetry system small enough to sit on the bat head, though filtering due to bat directivity affects recordings and not all bat species are able to carry such a device. Instead, remote microphone recordings of the bat calls could be processed by means of a mathematical method that estimates bat head orientation as a first step before calculating the amplitudes of each call for each frequency. This approach considers bat position with respect to each microphone, directivity, and head orientation for compensating microphone recordings of bat calls. The method has been tested in a laboratory environment using data from a Polaroid transducer as sound source: results are presented and discussed. A further improvement of the method is necessary as its performance for call reconstruction strongly depends on correct choice of the sample at which the recorded call is thought to start in each microphone data set.
Rapid and long-lasting adaptation to foreign-accented speech.
Authors: Witteman Marijt J. , Weber Andrea , McQueen James M.
Published: October 2010

In foreign-accented speech, listeners have to handle noticeable deviations from the standard pronunciation of a target language. Three cross-modal priming experiments investigated how short- and long-term experiences with a foreign accent influence word recognition by native listeners. In experiment 1, German-accented words were presented to Dutch listeners who had either extensive or limited prior experience with German-accented Dutch. Accented words either contained a diphthong substitution that deviated acoustically quite largely from the canonical form (huis [hŒys], “house”, pronounced as [hoys]), or that deviated acoustically to a lesser extent (lijst [lst], “list”, pronounced as [lst]). The mispronunciations never created lexical ambiguity in Dutch. While long-term experience facilitated word recognition for both types of substitutions, limited experience facilitated recognition only of words with acoustically smaller deviations. In experiment 2, Dutch listeners with limited experience listened to the German speaker for 4 min before participating in the cross-modal priming experiment. The results showed that speaker-specific learning effects for acoustically large deviations can be obtained already after a brief exposure, as long as the exposure contains evidence of the deviations. Experiment 3 investigates whether these short-term adaptation effects for foreign-accented speech are speaker-independent.
Lexical influences on children's perception of foreign-accented speech.
Authors: Bent Tessa
Published: October 2010

The ability to perceive speech accurately in the face of multiple sources of variability appears to develop during early and middle childhood. However, the cognitive-linguistic skills that underlie these improvements are unknown. Early-middle childhood is a time of rapid development in many areas of cognition and language, including the expansion of the lexicon. Lexical development includes both changes in lexicon size and changes in lexicon structure. Research suggests that as the lexicon grows, the words within the lexicon become more highly specified moving from more holistic representations to more fine-grained, segmental representations. This study tested how the expansion and restructuring of the lexicon are related to the ability to perceive highly variable speech signals. Specifically, the perception of foreign-accented speech — a common, real-world source of speech variability — was tested. The relationship between lexicon size and the perception of lexically easy (i.e., high-frequency words from sparse neighborhoods) and lexically hard (i.e., low-frequency words from dense neighborhoods) foreign-accented words was investigated for 5- and 6-year-old children. [Work supported by NIDCD 1R21DC010021.]
Non-native and second language perception of Spanish vowels by Californian English listeners.
Authors: Vasiliev Polina , Escudero Paola
Published: October 2010

The present study investigates multiple category assimilation in Californian English listeners’ cross-language and L2 perception of Spanish vowels, as produced in Lima and Madrid. In labeling and XAB tasks, monolingual California English listeners as well as beginning and advanced learners of Spanish classified 100 Peruvian and 100 Iberian Spanish tokens in terms of 10 native English vowel categories by choosing from English words containing the vowels. Learners of Spanish also identified the Spanish tokens by choosing from the five Spanish vowels. The stimuli were isolated vowels extracted from nonwords produced by 10 female and 10 male monolingual speakers of Spanish from Lima and Madrid. The vowels were produced in the /fVfe/ context and were embedded in a carrier phrase. The results show that Californian English listeners perceived Spanish vowels from both varieties as more than one native vowel category and that this use of extra L1 categories in L2 perception decreased with experience with Spanish. Furthermore, greater multiple category assimilation to native English categories correlated with lower correct identification of the same vowels in the Spanish task. Therefore, multiple category assimilation may be the cause of the problems that Californian English learners have when perceiving Spanish vowels.
The formation of the perceptual vowel space in monolinguals and simultaneous bilinguals: Insights from a model.
Authors: Molnar Monika , Mayor Julien
Published: October 2010

Recent reports on perception and production of speech segments in simultaneous bilinguals, who acquired both of their languages at the same time-frame (from birth), suggest that they do not always exhibit abilities similar to those of the native monolinguals of the same languages [i.e., Guion (2003); Molnar et al. (2009); Sundara and Polka (2008)] despite the fact that simultaneous bilinguals are native users of both of their languages as well. As opposed to the second language users, who often assimilate the acoustically similar non-native phonetic categories to their native ones, simultaneous bilinguals rather tend to dissimilate the phonetically similar sounds that occur across both languages. In order to understand the mechanism underlying the phonemic category formation of simultaneous bilingual language users across their two languages, an unsupervised formation of the phonetic perceptual space of English-French bilinguals was modeled by training self-organizing maps (SOMs) with vowels from both languages at the same time. The formation of phonetic categories in monolinguals by training SOMs with vowels from French or English only was modeled as well. Differences in the perception of speech segments in the bilingual SOMs with respect to the monolingual SOMs will be discussed and compared to experimental findings.
An acoustic study of [liquid + stop] sequences by native and second-language speakers of English.
Authors: Nearey Terrance M. , Tucker Benjamin V.
Published: October 2010

Since the initial work of Mann [Percept. Psychophys. 28, 407–12, (1980)], numerous studies have used liquid + stop clusters in VCCV frames to investigate context effects of liquids on stop perception. However, acoustical studies of related production data have thus far been very limited. The current study will present results of acoustic analyzes of such utterances sampled from 67 native speakers of English (57 from the Canadian Prairie Provinces) and 44 second language speakers of English from a variety of native language backgrounds. The objectives of this work are, first, to understand the nature of variation and covariation of production patterns across a moderate sample of native speakers; second, to investigate how native language background affects production of these sequences (especially those with phonetic realizations of postvocalic liquids that may be quite different from those of English). A key focus will be nature and magnitude of empirical patterns of covariation in relation to perceptual context effects observed in the literature.
Perception of place-of-articulation contrasts in English word-final consonants by Japanese adult second language learners.
Authors: Ito Kikuyo
Published: October 2010

English word-final consonants are realized differently in connected speech from the same word-final consonants produced in isolation because of coarticulation with the following segment. Identifying word-final stops is challenging for Japanese listeners because of the different phonotactic and syllable structures of their L1. This study investigated the perception by Japanese L2 learners and native English controls of word-final stops /p-t-k/, /b-d-g/, and /m-n-ŋ/ when followed by a word-initial /p/, /t/, or /k/ in sentences spoken in clear and in fast (casual) speech. Stimuli were minimal triplets differing in place of articulation (e.g., sip, sit, and sick), followed by positively, tauntingly, or cautiously. Participants listened to sentences, e.g., He said the word sit positively (or tauntingly, or cautiously), and identified the target words by choosing one of three written options. Japanese listeners had difficulty identifying English word-final oral stops in fast speech (26% errors), whereas they did better when the oral stops were released in clear speech (6% errors). Their difficulty identifying word-final nasals in both conditions (23% errors in clear, 34% errors in fast) reflects a language-specific perceptual pattern affected by the phonological rules of their L1.
Lexical familiarity affects Japanese speakers' perception of /b/ and /v/.
Authors: Nakamura Yusuke , Yoneyama Kiyoko
Published: October 2010

Flege et al. (1996) suggested that a relative familiarity of the words existing as a minimal pair affects the identification of word-initial English /l/ and /r/ by Japanese speakers. This study investigated the influence of relative familiarity on word-initial /b/ and /v/ identification by Japanese ESL speakers. Ten real word-real word minimal pairs and ten real word-nonword minimal pairs, both of which begin with /v/ or /b/, were used. Participants were instructed to identify whether a word-initial consonant was either /v/ or /b/ as quickly and accurately as possible in each trial. Further, relative familiarity of the minimal pairs and subjective familiarity of each word were collected. The identification correctness and reaction time analyzes revealed the following findings. First, relative familiarity affected the identification of /v/ and /b/ more than subjective familiarity did. Second, the percentage of initial-sound identification correctness was higher if the relative familiarity of the word was higher. Third, /b/ was identified more quickly and accurately than /v/. Altogether, this study confirmed that relative familiarity affects the identification of word-initial /b/ and /v/ by Japanese ESL speakers.
Acoustical Society of America Silver Medal in Speech Communication
Authors: Pisoni David B.
Published: October 2010

The Silver Medal is presented to individuals, without age limitation, for contributions to the advancement of science, engineering, or human welfare through the application of acoustic principles, or through research accomplishment in acoustics.
Channeling Death
Authors: Wong Wei
Published: October 2010

Apoptotic cells release ATP and UTP through pannexin 1 to recruit phagocytes that clear them.
Jockeying for the Tip
Authors: Wong Wei
Published: October 2010

The relative abundance of VEGFR determines whether an endothelial cell can successfully compete for the tip cell position in a vascular sprout.
Salmonella
Stealth Bomber
Authors: Ash Caroline
Published: October 2010

Food-poisoning pathogen uses a host enzyme to activate its virulence factors.
Role of Syntaxin 4 in Activity-Dependent Exocytosis and Synaptic Plasticity in Hippocampal Neurons
Authors: Mohanasundaram Ponnuswamy , Shanmugam Muniesh Muthaiyan
Published: October 2010

Exocytosis at syntaxin-4–enriched membrane domains is important for long-term potentiation.
Emergence of
Klebsiella pneumoniae
Coproducing KPC-2 and 16S rRNA Methylase ArmA in Poland
Authors: Zacharczuk Katarzyna , Piekarska Katarzyna , Szych Jolanta , Zawidzka Elwira , Sulikowska Agnieszka , Wardak Sebastian , Jagielski Marek , Gierczyński Rafał
Published: October 2010

A
Klebsiella pneumoniae
epidemic strain that coproduced carbapenemase KPC-2 (
K. pneumoniae
carbapenemase 2) and 16S rRNA methylase ArmA has emerged in Poland. Four nonduplicate isolates from patients in a hospital in Warsaw, Poland, were found to carry the
bla
KPC-2
and
armA
genes on ca. 50-kb and 90-kb plasmids, respectively. Tn
4401
with a 100-bp deletion in the variable region was detected in all the isolates. XbaI pulsed-field gel electrophoresis (PFGE) revealed 93.2% similarity of the isolates. All the isolates were resistant to carbapenems and 4,6-disubstituted 2-deoxystreptamines.
Contribution of Specific Amino Acid Changes in Penicillin Binding Protein 1 to Amoxicillin Resistance in ClinicalHelicobacter pyloriisolates
Authors: Qureshi Nadia N. , Morikis Dimitrios , Schiller Neal L.
Published: October 2010

Amoxicillin is commonly used to treatHelicobacter pylori, a major cause of peptic ulcers, stomach cancer, and B-cell mucosa-associated lymphoid tissue lymphoma. Amoxicillin resistance inH. pyloriis increasing steadily, especially in developing countries, leading to treatment failures. In this study, we characterize the mechanism of amoxicillin resistance in the U.S. clinical isolate B258. Transformation of amoxicillin-susceptible strain 26695 with the penicillin binding protein 1 gene (pbp1) from B258 increased the amoxicillin resistance of 26695 to equal that of B258, while studies using biotinylated amoxicillin showed a decrease in the binding of amoxicillin to the PBP1 of B258. Transformation with 4pbp1fragments, each encompassing several amino acid substitutions, combined with site-directed mutagenesis studies, identified 3 amino acid substitutions in PBP1 of B258 which affected amoxicillin susceptibility (Val 469 Met, Phe 473 Leu, and Ser 543 Arg). Homology modeling showed the spatial orientation of these specific amino acid changes in PBP1 from 26695 and B258. The results of these studies demonstrate that amoxicillin resistance in the clinical U.S. isolate B258 is due solely to an altered PBP1 protein with a lower binding affinity for amoxicillin. Homology modeling analyses using previously identified amino acid substitutions of amoxicillin-resistant PBP1s demonstrate the importance of specific amino acid substitutions in PBP1 that affect the binding of amoxicillin in the putative binding cleft, defining those substitutions deemed most important in amoxicillin resistance.
Recombinant Anthrax Toxin Receptor-Fc Fusion Proteins Produced in Plants Protect Rabbits against Inhalational Anthrax
Authors: Wycoff Keith L. , Belle Archana , Deppe Dorothée , Schaefer Leah , Maclean James M. , Haase Simone , Trilling Anke K. , Liu Shihui , Leppla Stephen H. , Geren Isin N. , Pawlik Jennifer , Peterson Johnny W.
Published: October 2010

Inhalational anthrax, a zoonotic disease caused by the inhalation of
Bacillus anthracis
spores, has a ∼50% fatality rate even when treated with antibiotics. Pathogenesis is dependent on the activity of two toxic noncovalent complexes: edema toxin (EdTx) and lethal toxin (LeTx). Protective antigen (PA), an essential component of both complexes, binds with high affinity to the major receptor mediating the lethality of anthrax toxin
in vivo
, capillary morphogenesis protein 2 (CMG2). Certain antibodies against PA have been shown to protect against anthrax
in vivo
. As an alternative to anti-PA antibodies, we produced a fusion of the extracellular domain of human CMG2 and human IgG Fc, using both transient and stable tobacco plant expression systems. Optimized expression led to the CMG2-Fc fusion protein being produced at high levels: 730 mg/kg fresh leaf weight in
Nicotiana benthamiana
and 65 mg/kg in
N. tabacum
. CMG2-Fc, purified from tobacco plants, fully protected rabbits against a lethal challenge with
B. anthracis
spores at a dose of 2 mg/kg body weight administered at the time of challenge. Treatment with CMG2-Fc did not interfere with the development of the animals' own immunity to anthrax, as treated animals that survived an initial challenge also survived a rechallenge 30 days later. The glycosylation of the Fc (or lack thereof) had no significant effect on the protective potency of CMG2-Fc in rabbits or on its serum half-life, which was about 5 days. Significantly, CMG2-Fc effectively neutralized,
in vitro
, LeTx-containing mutant forms of PA that were not neutralized by anti-PA monoclonal antibodies.
In Vitro
Antibiotic Synergy in Extensively Drug-Resistant
Acinetobacter baumannii
: the Effect of Testing by Time-Kill, Checkerboard, and Etest Methods
Authors: Tan Thean Yen , Lim Tze Peng , Lee Winnie Hui Ling , Sasikala Suranthran , Hsu Li Yang , Kwa Andrea Lay-Hoon
Published: October 2010

This study examined the
in vitro
effects of polymyxin B, tigecycline, and rifampin combinations on 16 isolates of extensively drug-resistant
Acinetobacter baumannii
, including four polymyxin-resistant strains.
In vitro
synergy was demonstrated in 19 (40%) of a possible 48 isolate-antibiotic combinations by time-kill methods, 8 (17%) by checkerboard methods, and only 1 (2%) by Etest methods. There was only slight agreement between Etest and checkerboard methods and no agreement between results obtained by other methods.
Spontaneous Mutations in the
Plasmodium falciparum
Sarcoplasmic/ Endoplasmic Reticulum Ca
2+
-ATPase (PfATP6) Gene among Geographically Widespread Parasite Populations Unexposed to Artemisinin-Based Combination Therapies
Authors: Tanabe Kazuyuki , Zakeri Sedigheh , Palacpac Nirianne Marie Q. , Afsharpad Manada , Randrianarivelojosia Milijaona , Kaneko Akira , Marma Aung Swi Prue , Horii Toshihiro , Mita Toshihiro
Published: October 2010

Recent reports on the decline of the efficacy of artemisinin-based combination therapies (ACTs) indicate a serious threat to malaria control. The endoplasmic/sarcoplasmic reticulum Ca
2+
-ATPase ortholog of
Plasmodium falciparum
(PfSERCA) has been suggested to be the target of artemisinin and its derivatives. It is assumed that continuous artemisinin pressure will affect polymorphism of the PfSERCA gene (
serca
) if the protein is the target. Here, we investigated the polymorphism of
serca
in parasite populations unexposed to ACTs to obtain baseline information for the study of potential artemisinin-driven selection of resistant parasites. Analysis of 656 full-length sequences from 13 parasite populations in Africa, Asia, Oceania, and South America revealed 64 single nucleotide polymorphisms (SNPs), of which 43 were newly identified and 38 resulted in amino acid substitutions. No isolates showed L263E and S769N substitutions, which were reportedly associated with artemisinin resistance. Among the four continents, the number of SNPs was highest in Africa. In Africa, Asia, and Oceania, common SNPs, or those with a minor allele frequency of ≥0.05, were less prevalent, with most SNPs noted to be continent specific, whereas in South America, common SNPs were highly prevalent and often shared with those in Africa. Of 50 amino acid haplotypes observed, only one haplotype (3D7 sequence) was seen in all four continents (64%). Forty-eight haplotypes had frequencies of less than 5%, and 40 haplotypes were continent specific. The geographical difference in the diversity and distribution of
serca
SNPs and haplotypes lays the groundwork for assessing whether some artemisinin resistance-associated mutations and haplotypes are selected by ACTs.
Effects of Engineered Cerium Oxide Nanoparticles on Bacterial Growth and Viability
Authors: Pelletier Dale A. , Suresh Anil K. , Holton Gregory A. , McKeown Catherine K. , Wang Wei , Gu Baohua , Mortensen Ninell P. , Allison David P. , Joy David C. , Allison Martin R. , Brown Steven D. , Phelps Tommy J. , Doktycz Mitchel J.
Published: October 2010

Interest in engineered nanostructures has risen in recent years due to their use in energy conservation strategies and biomedicine. To ensure prudent development and use of nanomaterials, the fate and effects of such engineered structures on the environment should be understood. Interactions of nanomaterials with environmental microorganisms are inevitable, but the general consequences of such interactions remain unclear, due to a lack of standard methods for assessing such interactions. Therefore, we have initiated a multianalytical approach to understand the interactions of synthesized nanoparticles with bacterial systems. These efforts are focused initially on cerium oxide nanoparticles and model bacteria in order to evaluate characterization procedures and the possible fate of such materials in the environment. The growth and viability of the Gram-negative species
Escherichia coli
and
Shewanella oneidensis
, a metal-reducing bacterium, and the Gram-positive species
Bacillus subtilis
were examined relative to cerium oxide particle size, growth media, pH, and dosage. A hydrothermal synthesis approach was used to prepare cerium oxide nanoparticles of defined sizes in order to eliminate complications originating from the use of organic solvents and surfactants. Bactericidal effects were determined from MIC and CFU measurements, disk diffusion tests, and live/dead assays. For
E. coli
and
B. subtilis
, clear strain- and size-dependent inhibition was observed, whereas
S. oneidensis
appeared to be unaffected by the particles. Transmission electron microscopy along with microarray-based transcriptional profiling was used to understand the response mechanism of the bacteria. Use of multiple analytical approaches adds confidence to toxicity assessments, while the use of different bacterial systems highlights the potential wide-ranging effects of nanomaterial interactions in the environment.
Antibiotic Manipulation of Intestinal Microbiota To Identify Microbes Associated with
Campylobacter jejuni
Exclusion in Poultry
Authors: Scupham A. J. , Jones J. A. , Rettedal E. A. , Weber T. E.
Published: October 2010

The ability of various subsets of poultry intestinal microbiota to protect turkeys from colonization by
Campylobacter jejuni
was investigated. Community subsets were generated
in vivo
by inoculation of day-old poults with the cecal contents of a
Campylobacter
-free adult turkey, followed by treatment with one antimicrobial, either virginiamycin, enrofloxacin, neomycin, or vancomycin. The
C. jejuni
loads of the enrofloxacin-, neomycin-, and vancomycin-derived communities were decreased by 1 log, 2 logs, and 4 logs, respectively. Examination of the constituents of the derived communities via the array-based method oligonucleotide fingerprinting of rRNA genes detected a subtype of
Megamonas hypermegale
specific to the
C. jejuni
-suppressive treatments.
Activation of a Silent Fungal Polyketide Biosynthesis Pathway through Regulatory Cross Talk with a Cryptic Nonribosomal Peptide Synthetase Gene Cluster
Authors: Bergmann Sebastian , Funk Alexander N. , Scherlach Kirstin , Schroeckh Volker , Shelest Ekaterina , Horn Uwe , Hertweck Christian , Brakhage Axel A.
Published: October 2010

Filamentous fungi produce numerous natural products that constitute a consistent source of potential drug leads, yet it seems that the majority of natural products are overlooked since most biosynthesis gene clusters are silent under standard cultivation conditions. Screening secondary metabolite genes of the model fungus
Aspergillus nidulans
, we noted a silent gene cluster on chromosome II comprising two nonribosomal peptide synthetase (NRPS) genes,
inpA
and
inpB
, flanked by a regulatory gene that we named
scpR
for secondary metabolism cross-pathway regulator. The induced expression of the
scpR
gene using the promoter of the alcohol dehydrogenase AlcA led to the transcriptional activation of both the endogenous
scpR
gene and the NRPS genes. Surprisingly, metabolic profiling of the supernatant of mycelia overexpressing
scpR
revealed the production of the polyketide asperfuranone. Through transcriptome analysis we found that another silent secondary metabolite gene cluster located on chromosome VIII coding for asperfuranone biosynthesis was specifically induced. Quantitative reverse transcription-PCR proved the transcription not only of the corresponding polyketide synthase (PKS) biosynthesis genes,
afoE
and
afoG
, but also of their activator,
afoA
, under
alcAp
-
scpR
-inducing conditions. To exclude the possibility that the product of the
inp
cluster induced the asperfuranone gene cluster, a strain carrying a deletion of the NRPS gene
inpB
and, in addition, the
alcAp
-
scpR
overexpression cassette was generated. In this strain, under inducing conditions, transcripts of the biosynthesis genes of both the NRPS-containing gene cluster
inp
and the asperfuranone gene cluster except gene
inpB
were detected. Moreover, the existence of the polyketide product asperfuranone indicates that the transcription factor ScpR controls the expression of the asperfuranone biosynthesis gene cluster. This expression as well as the biosynthesis of asperfuranone was abolished after the deletion of the asperfuranone activator gene
afoA
, indicating that ScpR binds to the
afoA
promoter. To the best of our knowledge, this is the first report of regulatory cross talk between two biosynthesis gene clusters located on different chromosomes.
Diversity and Mobility of Integrative and Conjugative Elements in Bovine Isolates of
S
treptococcus
agalactiae
,
S. dysgalactiae
subsp.
dysgalactiae
, and
S. uberis
Authors: Haenni Marisa , Saras Estelle , Bertin Stéphane , Leblond Pierre , Madec Jean-Yves , Payot Sophie
Published: October 2010

Bovine isolates of
S
treptococcus
agalactiae
(
n
= 76),
S
treptococcus
dysgalactiae
subsp.
dysgalactiae
(
n
= 32), and
S
treptococcus
uberis
(
n
= 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for
S. agalactiae
and pulsed-field gel electrophoresis for
S. dysgalactiae
and
S. uberis
. Most of the erythromycin-resistant strains carry an
ermB
gene. Five strains of
S. uberis
that are resistant to lincomycin but susceptible to erythromycin carry the
lin
(B) gene, and one has both
linB
and
lnuD
genes. In contrast to
S. uberis
, most of the
S. agalactiae
and
S. dysgalactiae
tetracycline-resistant isolates carry a
tet
(M) gene. A
tet
(S) gene was also detected in the three species. A Tn
916
-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an
S. agalactiae
strain. Most of the isolates carry an ICE integrated in the
rplL
gene. In addition, half of the
S. agalactiae
isolates have an ICE integrated in a tRNA lysine (tRNA
Lys
) gene. Such an element is also present in 20% of the isolates of
S. dysgalactiae
and
S. uberis
. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.
Occurrence, Survival, and Persistence of Human Adenoviruses and F-Specific RNA Phages in Raw Groundwater
Authors: Ogorzaly Leslie , Bertrand Isabelle , Paris Myriam , Maul Armand , Gantzer Christophe
Published: October 2010

Detection of specific genetic markers can rapidly identify the presence of enteric viruses in groundwater. However, comparison of stability characteristics between genetic and infectivity markers is necessary to better interpret molecular data. Human adenovirus serotype 2 (HAdV2), in conjunction with MS2 phages or GA phages, was spiked into raw groundwater microcosms. Viral stability was periodically assessed by both infectivity and real-time PCR methods. The results of this yearlong study suggest that adenoviruses have the most stable persistence profile and an ability to survive for a long time in groundwater. According to a linear regression model, infectivity reductions of HAdV2 ranged from 0.0076 log
10
/day (4°C) to 0.0279 log
10
/day (20°C) and were significantly lower than those observed for phages. No adenoviral genome degradation was observed at 4°C, and the reduction was estimated at 0.0036 log
10
/day at 20°C. Occurrence study showed that DNA of human adenoviruses could be observed in groundwater from a confined aquifer (7 of the 60 samples were positive by real-time PCR), while no fecal indicators were detected. In agreement with the persistence of genetic markers, the presence of adenoviral DNA in groundwater may be misleading in term of health risk, especially in the absence of information on the infective status.
Agrobacterium tumefaciens
-Mediated Transformation for Investigation of Somatic Recombination in the Fungal Pathogen
Armillaria mellea
Authors: Baumgartner Kendra , Fujiyoshi Phillip , Foster Gary D. , Bailey Andy M.
Published: October 2010

Armillaria root disease is one of the most damaging timber and fruit tree diseases in the world. Despite its economic importance, many basic questions about the biology of the causal fungi,
Armillaria
spp., are unanswered. For example,
Armillaria
undergoes matings between diploid and haploid mycelia, which can result in a recombinant diploid without meiosis. Evidence of such somatic recombination in natural populations suggests that this reproductive mode may affect the pathogen's ecology. Investigations of the mechanisms and adaptive consequences of somatic recombination are, however, hampered by the lack of a method to reliably synthesize somatic recombinants. Here we report the first genetic transformation system for the genus
Armillaria
. We transformed
A. mellea
with selective markers for use in diploid-haploid matings to reliably synthesize somatic recombinants. This was accomplished with
Agrobacterium tumefaciens
carrying pBGgHg, which carries the hygromycin phosphotransferase gene (
hph
).
hph
was integrated into transformants, as evidenced by serial transfer to selective media, PCR, reverse transcription-PCR (RT-PCR), and Southern hybridization. Nuclear and mitochondrial markers were developed to genotype synthesized mycelia. In matings between a wild-type diploid and hygromycin-resistant haploids (transgenic), we identified recombinant, hygromycin-resistant diploids and, additionally, hygromycin-resistant triploids, all with the mitochondrial haplotype of the haploid partner. Our approach created no mycelium in which the haploid nucleus was replaced by the diploid nucleus, the typical outcome of diploid-haploid matings in
Armillaria
. This genetic transformation system, in combination with new markers to track chromosomal and cytoplasmic inheritance in
A. mellea
, will advance research aimed at characterizing the significance of somatic recombination in the ecology of this important fungus.
Biodegradation of a Biocide (Cu-
N
-Cyclohexyldiazenium Dioxide) Component of a Wood Preservative by a Defined Soil Bacterial Community
Authors: Jakobs-Schönwandt Désirée , Mathies Helena , Abraham Wolf-Rainer , Pritzkow Wolfgang , Stephan Ina , Noll Matthias
Published: October 2010

The wood protection industry has refined their products from chrome-, copper-, and arsenate-based wood preservatives toward solely copper-based preservatives in combination with organic biocides. One of these is Cu-HDO, containing the chelation product of copper and
N
-cyclohexyldiazenium dioxide (HDO). In this study, the fate of isotope-labeled (
13
C) and nonlabeled (
12
C) Cu-HDO incorporated in wood sawdust mixed with soil was investigated. HDO concentration was monitored by high-pressure liquid chromatography. The total carbon and the δ
13
C content of respired CO
2
, as well as of the soil-wood-sawdust mixture, were determined with an elemental analyzer-isotopic ratio mass spectrometer. The concentration of HDO decreased significantly after 105 days of incubation, and after 24 days the
13
CO
2
concentration respired from soil increased steadily to a maximum after 64 days of incubation. Phospholipid fatty acid-stable isotope probing (PFA-SIP) analysis revealed that the dominant PFAs C
19:0
d8,9, C
18:0
, C
18:1
ω7, C
18:2
ω6,9, C
17:1
d7,8, C
16:0
, and C
16:1
ω7 were highly enriched in their δ
13
C content. Moreover, RNA-SIP identified members of the phylum
Acidobacteria
and the genera
Phenylobacterium
and
Comamonas
that were assimilating carbon from HDO exclusively. Cu-HDO as part of a wood preservative effectively decreased fungal wood decay and overall microbial respiration from soil. In turn, a defined bacterial community was stimulated that was able to metabolize HDO completely.
Potential of the Melanophore Pigment Response for Detection of Bacterial Toxicity
Authors: Dukovcic Stephanie R. , Hutchison Janine R. , Trempy Janine E.
Published: October 2010

Chromatophore cells have been investigated as potential biodetectors for function-based detection of chemically and biologically toxic substances.
Oncorhynchus tshawytscha
(chinook salmon) melanophores, a chromatophore cell type containing brown pigment, rapidly detect the salmonid pathogens
Aeromonas salmonicida
,
Yersinia ruckeri
, and
Flavobacterium psychrophilum
and the human pathogen
Bacillus cereus
.
Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (
Lactuca
Species) Phyllosphere
Authors: Hunter Paul J. , Hand Paul , Pink David , Whipps John M. , Bending Gary D.
Published: October 2010

Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by
Pseudomonas
species and the
Enterobacteriaceae
family. Significant differences in the relative proportions of genera in the
Enterobacteriaceae
were detected between lettuce accessions. Two such genera (
Erwinia
and
Enterobacter
) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.
Associations between the Presence of Virulence Determinants and the Epidemiology and Ecology of Zoonotic
Escherichia coli
Authors: O'Reilly K. M. , Low J. C. , Denwood M. J. , Gally D. L. , Evans J. , Gunn G. J. , Mellor D. J. , Reid S. W. J. , Matthews L.
Published: October 2010

The severity of human infection with pathogenic
Escherichia coli
depends on two major virulence determinants (
eae
and
stx
) that, respectively, produce intimin and Shiga toxin. In cattle, both may enhance colonization, but whether this increases fitness by enhancing cattle-to-cattle transmission in the field is unknown. In
E. coli
O157, the almost uniform presence of the virulence determinants in cattle isolates prevents comparative analysis. The availability to this study of extensive non-O157
E. coli
data, with much greater diversity in carriage of virulence determinants, provides the opportunity to gain insight into their potential impact on transmission. Dynamic models were used to simulate expected prevalence distributions for serogroups O26 and O103. Transmission parameters were estimated by fitting model outputs to prevalence data from Scottish cattle using a Bayesian Markov chain Monte Carlo (MCMC) approach. Despite similar prevalence distributions for O26 and O103, their transmission dynamics were distinct. Serogroup O26 strains appear well adapted to the cattle host. The dynamics are characterized by a basic reproduction ratio (
R
0
) of >1 (allowing sustained cattle-to-cattle transmission), a relatively low transmission rate from environmental reservoirs, and substantial association with
eae
on transmission. The presence of
stx
2
was associated with reduced transmission. In contrast, serogroup O103 appears better adapted to the noncattle environment, characterized by an
R
0
value of <1 for plausible test sensitivities, a significantly higher transmission rate from noncattle sources than serogroup O26, and an absence of fitness benefits associated with the carriage of
eae
. Thus, the association of
eae
with enhanced transmission depends on the
E. coli
serogroup. Our results suggest that the capacity of
E. coli
strains to derive fitness benefits from virulence determinants influences the prevalence in the cattle population and the ecology and epidemiology of the host organism.
Antiglycation Effects of Carnosine and Other Compounds on the Long-Term Survival of
Escherichia coli
Authors: Pepper Evan D. , Farrell Michael J. , Nord Gary , Finkel Steven E.
Published: October 2010

Glycation, or nonenzymatic glycosylation, is a chemical reaction between reactive carbonyl-containing compounds and biomolecules containing free amino groups. Carbonyl-containing compounds include reducing sugars such as glucose or fructose, carbohydrate-derived compounds such as methylglyoxal and glyoxal, and nonsugars such as polyunsaturated fatty acids. The latter group includes molecules such as proteins, DNA, and amino lipids. Glycation-induced damage to these biomolecules has been shown to be a contributing factor in human disorders such as Alzheimer's disease, atherosclerosis, and cataracts and in diabetic complications. Glycation also affects
Escherichia coli
under standard laboratory conditions, leading to a decline in bacterial population density and long-term survival. Here we have shown that as
E. coli
aged in batch culture, the amount of carboxymethyl lysine, an advanced glycation end product, accumulated over time and that this accumulation was affected by the addition of glucose to the culture medium. The addition of excess glucose or methylglyoxal to the culture medium resulted in a dose-dependent loss of cell viability. We have also demonstrated that glyoxylase enzyme GloA plays a role in cell survival during glycation stress. In addition, we have provided evidence that carnosine, folic acid, and aminoguanidine inhibit glycation in prokaryotes. These agents may also prove to be beneficial to eukaryotes since the chemical processes of glycation are similar in these two domains of life.
Response of Nursery Pigs to a Synbiotic Preparation of Starch and an Anti-Escherichia coliK88 Probiotic
Authors: Krause D. O. , Bhandari S. K. , House J. D. , Nyachoti C. M.
Published: October 2010

Postweaning diarrhea in pigs is frequently caused by enterotoxigenicEscherichia coliK88 (ETEC). The aim of this study was to test the efficacy ofE. coliprobiotics (PRO) in young pigs challenged withE. coliK88. We also tested the synbiotic interaction with raw potato starch (RPS), which can be used as a prebiotic. Forty 17-day-old weaned piglets were randomly assigned to four treatments: treatment 1, positive-control diet (C), no probiotics or RPS but containing in-feed antibiotics; treatment 2, probiotic (PRO), no feed antibiotics plus a 50:50 mixture of probioticE. colistrains UM-2 and UM-7; treatment 3, 14% RPS, no antibiotics (RPS); treatment 4, 14% RPS plus a 50:50 mixture of probioticE. colistrains UM-2 and UM-7, no antibiotics (PRO-RPS). The pigs were challenged with pathogenicE. coliK88 strains on day 7 of the experiment (24-day-old pigs) and euthanized on day 10 of the experiment (35-day-old pigs). Probiotic and pathogenicE. colistrains were enumerated by selective enrichment on antibiotics, and microbial community analysis was conducted using terminal restriction length polymorphism analysis (T-RFLP) of 16S rRNA genes. The combination of raw potato starch and the probiotic had a beneficial effect on piglet growth performance and resulted in a reduction of diarrhea and increased microbial diversity in the gut. We conclude that the use ofE. coliprobiotic strains againstE. coliK88 in the presence of raw potato starch is effective in reducing the negative effects of ETEC in a piglet challenge model.
Construction of a Single-Chain Variable-Fragment Antibody against the Superantigen Staphylococcal Enterotoxin B
Authors: Singh Pawan Kumar , Agrawal Ranu , Kamboj Dev Vrat , Gupta Garima , Boopathi M. , Goel Ajay Kumar , Singh Lokendra
Published: October 2010

Staphylococcal food poisoning (SFP) is one of the most prevalent causes of food-borne illness throughout the world. SFP is caused by 21 different types of staphylococcal enterotoxins produced byStaphylococcus aureus. Among these, staphylococcal enterotoxin B (SEB) is the most potent toxin and is a listed biological warfare (BW) agent. Therefore, development of immunological reagents for detection of SEB is of the utmost importance. High-affinity and specific monoclonal antibodies are being used for detection of SEB, but hybridoma clones tend to lose their antibody-secreting ability over time. This problem can be overcome by the use of recombinant antibodies produced in a bacterial system. In the present investigation, genes from a hybridoma clone encoding monoclonal antibody against SEB were immortalized using antibody phage display technology. A murine phage display library containing single-chain variable-fragment (ScFv) antibody genes was constructed in a pCANTAB 5E phagemid vector. Phage particles displaying ScFv were rescued by reinfection of helper phage followed by four rounds of biopanning for selection of SEB binding ScFv antibody fragments by using phage enzyme-linked immunosorbent assay (ELISA). Soluble SEB-ScFv antibodies were characterized from one of the clones showing high affinity for SEB. The anti-SEB ScFv antibody was highly specific, and its affinity constant was 3.16 nM as determined by surface plasmon resonance (SPR). These results demonstrate that the recombinant antibody constructed by immortalizing the antibody genes from a hybridoma clone is useful for immunodetection of SEB.
Antibiotic-Resistant
Escherichia coli
Bacteria, Including Strains with Genes Encoding the Extended-Spectrum Beta-Lactamase and QnrS, in Waterbirds on the Baltic Sea Coast of Poland
Authors: Literak Ivan , Dolejska Monika , Janoszowska Dagmar , Hrusakova Jolana , Meissner Wlodzimierz , Rzyska Hanna , Bzoma Szymon , Cizek Alois
Published: October 2010

Individual cloacal swabs of mallards (
Anas platyrhynchos
) and of herring gulls (
Larus argentatus
), as well as samples of waterbird feces obtained in 2008 and 2009, were cultivated for
Escherichia coli
. Isolates of
E. coli
were tested for susceptibilities to 12 antimicrobial agents by the disk diffusion method. Moreover, the samples were subcultivated on MacConkey agar (MCA) containing cefotaxime (2 mg liter
−1
) to detect
E. coli
with extended-spectrum beta-lactamase (ESBL) and subsequently on MCA supplemented with ciprofloxacin (0.05 mg liter
−1
) and MCA with nalidixic acid (20 mg liter
−1
) to isolate fluoroquinolone-resistant
E. coli
. PCR was used to detect specific antibiotic resistance genes. We found 9
E. coli
isolates producing ESBL with
bla
genes:
bla
CTX-M-1
(6 isolates),
bla
CTX-M-9
plus
bla
TEM-1b
(1 isolate),
bla
CTX-M-15
plus
bla
OXA-1
(1 isolate), and
bla
SHV-12
(1 isolate). In the isolate with
bla
CTX-M-15
, the gene
aac(6)-Ib-cr
was also detected. The
bla
genes were harbored by transferable plasmids of the IncN and IncI1 groups. Nine quinolone-resistant
E. coli
isolates with
qnrS
genes were found and characterized. The gene
qnrS
was associated with a Tn
3
-like transposon on the IncX1 plasmid together with
bla
TEM-1
in two isolates. The gene
qnrS
was also harbored by conjugative plasmids of the IncN and IncX2 groups. Even if populations of wild birds are not directly influenced by antibiotic practice, we have demonstrated that antibiotic-resistant
E. coli
strains, including strains with various ESBL and
qnrS
genes, are found in the feces of wild birds on the coast of the Baltic Sea in Poland.