bluuebunny/crossref_metadata_2025 huggingface dataset:
A summary of behavioral measures of cochlear gain and gain reduction in listeners with normal hearing or minimal cochlear hearing loss
Authors: Strickland Elizabeth A. , Skaggs Miranda , Hopkins Anna , Mielnicki Nicole , Salloom William B. , Morris Hayley , Holt Alexis
Published: June 2021

This study examined the relationship between cochlear hearing loss and psychoacoustic measures related to cochlear function. Listeners’ audiometric thresholds for long tones ranged from well within the clinically normal range to just above this range. Where thresholds were elevated, other clinical tests were consistent with a cochlear origin. Because the medial olivocochlear reflex decreases cochlear gain in response to sound, measures were made with short stimuli. Signal frequencies were from 1 to 8 kHz. One point on the lower leg of the input/output function was measured by finding threshold masker level for a masker almost one octave below the signal frequency needed to mask a signal at 5 dB SL. Gain reduction was estimated by presenting a pink broadband noise precursor before the signal and masker and measuring the change in signal threshold as a function of precursor level. Previous studies with listeners with normal hearing have shown that gain reduction begins at a low precursor level and grows compressively as the precursor level is increased. In the present study, the estimate of gain reduction decreased as quiet threshold increased, but was not solely determined by the amount of gain. [Work supported by NIH(NIDCD)R01 DC008327 (EAS) and NIH(NIDCD) T32 DC016853 (WBS).]
Conducting speech perception experiments remotely: Some tools, successes, and challenges
Authors: Theodore Rachel M.
Published: June 2021

The use of remote (i.e., web-based) data collection for psycholinguistics research has proliferated in recent years, reflecting the emergence of new tools for promoting high-quality data collection beyond the traditional laboratory environment. This is particularly true this past year, demonstrating one way that the pandemic has transformed research in the short-term. In the long-term, remote approaches will remain a powerful tool in the domain of psycholinguistics, in part because they help (1) promote diversity among participant samples and (2) increase feasibility of the new best practices for promoting reproducibility of research (e.g., larger sample sizes, in-house replications, assessing generalization to novel stimulus sets). However, embracing remote data collection is not without its challenges, especially for speech perception researchers who require some degree of control over the listening environment and participants’ linguistic background. In this talk, I will describe tools, successes, and challenges related to our experiences in conducting remote speech perception experiments for a variety of phenomena (e.g., categorical perception, perceptual learning, talker adaptation, Ganong effect), tasks (e.g., phonetic identification, lexical decision, talker discrimination, transcription), and dependent measures (e.g., reaction time, accuracy, sensitivity, psychometric response functions).
Reaching from afar: Pitfalls and promises of online auditory testing
Authors: Shafiro Valeriy , Li Yan
Published: June 2021

Online testing of speech perception and auditory abilities over the Internet can be a cost-effective and efficient way to collect data. It eliminates travel requirements, provides flexibility in scheduling tests, and enables broader and safer outreach to potential participants. However, online testing also involves considerable risks to data quality and integrity stemming from multiple factors, which are often difficult to control. These include access to an appropriate testing environment, availability of broadband Internet connection, and adequate computing and audio equipment. Participants also need to have a sufficient level of computer literacy and engagement. In recent years, several approaches and software applications have been used for online data collection. Selection of a specific approach involves a careful balancing of its strengths and weaknesses, based on the goals of a specific study. This presentation will describe one such approach that led to the development of Basic Auditory Skills Evaluation (BASE) battery. The battery was designed for comprehensive online assessment in adults with cochlear implants and has been recently extended to examine speech perception in other populations. The presentation will describe some applications of BASE battery, discuss the advantages and disadvantages of using this approach to online auditory testing, and review initial findings.
Voices of lockdown: Using self-recorded lockdown diaries to investigate phonetic change in Edinburgh and the Lothians
Authors: Markl Nina , Hall-Lew Lauren , Cowie Claire , Lai Catherine , Joseph McNulty Stephen
Published: June 2021

The Lothian Diary Project is an interdisciplinary research project inviting residents of the Lothians region of Scotland to contribute self-recorded audio and video diaries about their experiences of the COVID-19 pandemic. We present a brief case study, highlighting sociophonetic features of Scottish English which have been undergoing change in the recent years.
Designing a covariance matrix tapered beamformer that is universal over notch width
Authors: Erdim Savas , Buck John R.
Published: June 2021

Universal adaptive beamformers (UABFs) combine classic adaptive beamformers with ensemble methods from machine learning to design new beamformers whose asymptotic performance rivals the performance of the best beamformer in a set. The UABF array weights blend a weighted average of the competing beamformer array weights based on past performance using the softmax function. This model averaging approach avoids a difficult model selection problem by hedging performance across a family of models rather than committing to a single model. This talk presents a UABF which blends covariance matrix tapers (CMT). The CMT technique creates broader notches in beampatterns for environments with moving interferers. Interferers moving with high bearing rates cross resolution cells faster and violate the stationarity solution of the minimum variance distortionless response (MVDR) beamformer. The performance of the CMT depends on the chosen notch width. The UABF adapts to find the blend of CMT notch widths that best balances the interferer output power with white noise gain. We present simulation results illustrating the benefits of the UABF approach for CMT in the presence of moving interferers. [Work supported by ONR 321US.]
A personal perspective and journey through DEI and STEM
Authors: Gates Sylvester James
Published: June 2021

Abdus Salam, a 1979 Nobel Prize recipient in Physics, once told the speaker there was a possibility of “Jazz in Physics” coming into existence when the field became more diverse. This presentation will present a personal interpretation and story on the meaning of this “puzzling” comment and how it led to a citation by the Supreme Court of the United States. Q&A will follow presentation
Experience with coupled spaces: From theory to practice
Authors: Sü Gül Zühre
Published: June 2021

It has been more than a couple of decades since the interest in coupled volume systems started to grow rapidly among researchers. Basically, due to their increasingly popular applications in music halls for providing a rich acoustical environment either to fulfill the competing criteria of clarity and reverberance or simply to tune the auditoriums for multi-functional use. A lifelong experience with coupled spaces is the main motivation behind this paper. The journey starts with further developing the theoretical knowledge through scale model experiments. The results of which are utilized to observe the effects of the aperture size and shape on non-exponential sound energy decay by applying Bayesian analysis. The investigations have continued by field tests of real-size architectural monuments, specifically, worship spaces with multi-volume and domed typology. The relation of non-exponential energy decay and architectural parameters, for different scenarios or original uses of historical buildings, are searched through energy flow decays by applying the diffusion equation model. Simultaneously, all of these findings from academic research have been a source to produce acoustical design solutions for either small sized recording studios or large-scale multi-purpose auditoria in landmark buildings, all of which are briefly exemplified within this study.
Simulation of coupled volume acoustics with coupled volume scattering delay network models
Authors: Atalay Timuçin B. , Sü Gül Zühre , De Sena Enzo , Cvetkovic Zoran , Hacıhabiboğlu Hüseyin
Published: June 2021

Simulation of the acoustics of coupled rooms is an important problem not only in architectural acoustics but also in immersive audio applications that require acoustic simulation at interactive rates. Requirements for such applications are less demanding for accuracy but more demanding for computational cost. Scattering delay network (SDN) is a real-time, interactive room acoustics simulator for cuboid rooms. SDN affords an exact simulation of first-order early reflections, a gracefully degrading simulation of second and higher-order specular reflections and an accurate simulation of the statistical properties of the late reverberation. We propose coupled-volume SDN (CV-SDN) as an extension of the SDN model to simulate acoustics of coupled volumes. The proposed model retains the desirable characteristics of the original SDN model while allowing the simulation of double-slope decays with direct control over the simulated aperture size. The double-slope characteristics of room impulse responses simulated with CV-SDN agree well with those of measured impulse responses from a scale model and state-of-the-art room acoustics simulation software.
Electronic Architecture solves acoustical problems with coupled volumes that cannot be easily remedied using architectural treatments
Authors: Barbar Steve
Published: June 2021

There are a multitude of venues throughout the world supporting music and performing arts with architecture that incorporates coupled volumes. It may be a large balcony—or seating under a large balcony—loge or under loge seating, box seats, or opera boxes. One of the most common coupled volumes in such venues is the performance stage. When that stage is outdoors, another set of challenges arises. In worship spaces, this can be a “platform” for musicians with a choir loft, or a chancel with choir and organ, or a bimah. For many years, we have been successfully employing Electronic Architecture to solve acoustical problems that are all but impossible to resolve with architectural treatments alone. In this presentation, we will describe solutions implemented in several venues that substantially improve the listening experience.
Acoustic holograms for thalamic focusing through the temporal-bone window
Authors: Andrés Diana , Jiménez Noé , Camarena Francisco
Published: June 2021

In this work, we numerically investigate the performance of acoustic holograms created using k-space simulations and a phase-conjugation method at 650 kHz to simultaneously target both thalami through the temporal bone window compared to a curved transducer. Furthermore, we calculate how a misalignment of the acoustic hologram and the skull could affect the resulting acoustic image in terms of focus pressure and treated volume. Our results show that transtemporal acoustic holograms are a robust method to improve focus quality and to enhance sonicated volumes on target deep-brain even under small misallocations of the therapeutic ultrasound device that can be used for highly selective and low-cost blood-brain barrier opening and neuromodulation applications.
Engulfed targeted microbubbles: Sonoporation from within theendothelial cell
Authors: Kooiman Klazina , Beekers Inés , Langeveld Simone A.G. , Meijlink Bram , van der Steen Antonius F. W. , de Jong Nico , Verweij Martin D.
Published: June 2021

Targeted microbubbles are currently regarded as objects attached to the outside of the endothelial cell membrane; nonetheless our study shows that microbubbles targeted to the angiogenic biomarker αvβ3 were fully engulfed by the human umbilical vein endothelial cells, while those targeted to the endothelial biomarker CD31 varied from partially to fully engulfed and non-targeted and IgG1? control-targeted microbubbles were not engulfed at all. The engulfed microbubbles had lower excursion amplitudes than non-engulfed microbubbles and the sonoporation threshold was lower for the engulfed αvβ3-targeted microbubbles than for all other microbubble types investigated, suggesting they can augment the receptiveness to sonoporation from within the cell.
Metabolic shock wave after acoustically-mediated blood-brain barrier opening: Investigations of CSF and serum metabolomes
Authors: Presset Antoine , Bodart Sylvie , Lefevre Antoine , Millet Anaïs , Oujagir Edward , Bouakaz Ayache , Emond Patrick , Escoffre Jean-Michel , Nadal-Desbarats Lydie
Published: June 2021

In this study, rats' right striata were exposed to microbubble-assisted ultrasound in order to open the BBB. This work aimed to investigate the metabolic consequences of this process on rat's serum and cerebrospinal fluid using the 1H-NMR spectroscopy study. The biochemical analysis of CSF and serum metabolomes indicated significant changes in several metabolic pathways related to alternative sources of cellular energetic metabolism, immediately and up to 48 h after the BBB opening. These findings could highlight the implication of hypoxia-associated processes into the BBB opening or the modulation of neurotransmission.
Bovine tendon atomization
Authors: Smallcomb Molly , Simon Julianna C.
Published: June 2021

Thus far, histotripsy has not successfully fractionated tendon tissues, possibly due to bubbles being of insufficient size to create a pressure-release interface. In this study, a planar tissue-air interface was treated with histotripsy to create a micro-fountain and atomization; particulates ejected from the tendon sample were collected and analyzed histologically to determine whether tissue fractionation was achieved. [Work supported by NSF GRFP DGE1255832 and NIH NIBIB EB027886.]
The impact of temperature and humidity variations on the resulting frequencies of metal flue pipes in pipe-organs: An analytical model
Authors: Domenighini Piergiovanni
Published: June 2021

Pipe organs are probably the biggest existing instruments. Apart from positive organs that wheels can move, pipe organs remain in the same place where they have been installed and become parts of the buildings architecture that host them. Churches are the main venues for these instruments due to their important role in the liturgy. Unfortunately, these buildings, usually characterized by huge volumes, are hardly air-conditioned except during events, and temperature and humidity variations affect the pipes' sound. An analytical model has been developed for metal flue pipes to analyse the entity of the emitted-frequency variations. Temperature and humidity affect the dimensions of the pipe as well as air density and sound’s velocity. The model involved plane wave mode and air-jet analysis dynamics depending on the temperature and humidity of the flowed air. Thermo-viscous effect of air flowing into the pipe is also considered. Results have been compared to the spectral analysis of a metal flue pipe of an existing pipe organ located inside a church. Conclusions gather the differences between the results and explain the open opportunities for this research.
Improved steelpan pitch detection through audio feature extraction and machine learning
Authors: Malloy Colin
Published: June 2021

The steelpan, a significant musical instrument invented in the mid-20th century, is a harmonically complex system making fundamental pitch detection a difficult task. Initial experiments using state-of-the-art pitch detection algorithms have shown significant difficulties in detecting the pitch of individual steelpan notes. This paper presents a method of improved pitch detection accuracy by combining music information retrieval techniques with machine learning algorithms. An audio sample set consisting of thousands of steelpan notes from ten different tenor steelpans is used to quantitatively evaluate the proposed methodology. Low-level audio features are extracted from the audio samples and used to train a machine learning algorithm which identifies the salient features for pitch estimation. This method’s performance is measured against the current state-of-the-art pitch detection methods, pYIN (a probabilistic autocorrelation method) and CRéPE (a convolutional neural network-based method), showing improved performance at steelpan pitch detection. The machine learning model developed for this paper using this methodology is focused on the tenor steelpan but is intended to lead to a more generalized model for pitch detection of all types of steelpans.
Perception experiments to try on your friends
Authors: Freeman Valerie
Published: June 2021

This talk presents hands-on activities to give intermediate students experience conducting phonological perception experiments and deepen their grasp of categorical consonant perception. It focuses on two assignments in which students gather categorical perception responses from friends, graph them to reveal crossover points, form hypotheses about contributing cues, and apply Praat measurement skills to test them. In the first, students and naïve friends respond to online phoneme identification and discrimination tasks involving a synthesized /ba-da-ga/ continuum varying only in formant transitions. They tally and graph the pooled responses, identify crossover points, and answer interpretation questions. In the second task, students and friends identify words on a bad-bat continuum varying only in vowel length. They hypothesize which phonetic features might distinguish the words, then measure them in Praat to discover that vowel length cues final consonant voicing, not voice onset time as learned in previous lessons. These activities have been used successfully in an advanced introduction to speech science for speech-language pathology undergraduates with an introductory English phonetics prerequisite. They form many students’ first experience conducting experiments, and the hypothesis, deduction, and interpretation portions stretch their critical thinking skills.
Effects of acoustic nonlinearity on through-tissue communication performance
Authors: Tabak Gizem , Oelze Michael L. , Singer Andrew C.
Published: June 2021

Wide signal bandwidth and high signal amplitude, which are desirable properties to achieve high data rates with linear communication systems, may cause performance degradation in through-tissue communication applications because of acoustic nonlinearity. In this talk, I will quantify the effects of acoustic nonlinearity on data rates and achievable bit error rates in a simulated through-tissue communication system.
Wide-angle PE for a moving medium
Authors: Keith Wilson D.
Published: June 2021

How to easily convert a NAPE (narrow-angle parabolic equation) code to an accurate WAPE (wide-angle parabolic equation) code for a moving medium.
Randomized Informational Intervention and Adult Park Use and Park-Based Physical Activity in Low-Income, Racially Diverse Urban Neighborhoods
Authors: Wexler Noah , Fan Yingling , Das Kirti V. , French Simone
Published: June 2021

Background: Neighborhood parks are important locations to encourage and stimulate physical activity (PA) among the urban population. This study aims to evaluate the impact of an informational intervention on adult park use and PA behaviors in 3 low-income, racially diverse urban neighborhoods in Minneapolis, MN. Method: The study employed a household-level randomized controlled trial and collected baseline and follow-up data from 171 participants. Within each neighborhood, participants were randomized to an informational intervention or to a no-intervention comparison. Intervention households received monthly, neighborhood-specific newsletters about park-based PA opportunities, park program brochures, trail maps, and activity guides. Results: The average treatment effect of the newsletter intervention was positive yet moderated by respondent age. For a 20-year-old resident, treatment was associated with 0.97 (P < .05) additional park visits and 31.24 (P < .05) additional minutes of park-based PA over a 3-day recall period. For 40-year-old respondents, these positive effects are smaller at 0.36 (P < .05) additional visits and 4.66 (P < .05) additional minutes, respectively. Conclusions: An intervention to increase awareness about park-based PA opportunities and benefits increased self-reported park visits and in-park PA among adults who lived in low-income, racially diverse neighborhoods.
Rebalancing expression of HMGB1 redox isoforms to counteract muscular dystrophy
Authors: Careccia Giorgia , Saclier Marielle , Tirone Mario , Ruggieri Elena , Principi Elisa , Raffaghello Lizzia , Torchio Silvia , Recchia Deborah , Canepari Monica , Gorzanelli Andrea , Ferrara Michele , Castellani Patrizia , Rubartelli Anna , Rovere-Querini Patrizia , Casalgrandi Maura , Preti Alessandro , Lorenzetti Isabella , Bruno Claudio , Bottinelli Roberto , Brunelli Silvia , Previtali Stefano Carlo , Bianchi Marco Emilio , Messina Graziella , Vénéreau Emilie
Published: June 2021

The redox-sensitive HMGB1 protein is a functional link between oxidative stress and persistent inflammation in muscular dystrophies.
A nanofibrous encapsulation device for safe delivery of insulin-producing cells to treat type 1 diabetes
Authors: Wang Xi , Maxwell Kristina G. , Wang Kai , Bowers Daniel T. , Flanders James A. , Liu Wanjun , Wang Long-Hai , Liu Qingsheng , Liu Chengyang , Naji Ali , Wang Yong , Wang Bo , Chen Jing , Ernst Alexander U. , Melero-Martin Juan M. , Millman Jeffrey R. , Ma Minglin
Published: June 2021

A nanofibrous cell encapsulation device containing rodent/human islets or human stem cell–derived β cells treats diabetes in rodents.
The brain penetrant PPARγ agonist leriglitazone restores multiple altered pathways in models of X-linked adrenoleukodystrophy
Authors: Rodríguez-Pascau Laura , Vilalta Anna , Cerrada Marc , Traver Estefania , Forss-Petter Sonja , Weinhofer Isabelle , Bauer Jan , Kemp Stephan , Pina Guillem , Pascual Sílvia , Meya Uwe , Musolino Patricia L. , Berger Johannes , Martinell Marc , Pizcueta Pilar
Published: June 2021

Leriglitazone reduces pathologically activated microglia and protects neurons, astrocytes, and oligodendrocytes in experimental models of X-ALD.
Exogenous dTMP utilization by a novel tup mutant of Saccharomyces cerevisiae
Authors: Bisson L F , Thorner J
Published: June 2021

The rate and extent of entry of dTMP were measured in strains of Saccharomyces cerevisiae carrying two new tup mutations (tup5 and tup7) and most of the other tup mutations which have been reported previously by others. The tup7 mutation allowed dramatically greater accumulation of dTMP than any of the other mutations tested. Specific labeling of DNA by [CH3-3H]dTMP, fate of the dTMP pool inside of the cells, and degradation of the dTMP in the culture medium were investigated in strains carrying the tup7 mutation. The extracellular dTMP was not appreciably degraded, and that accumulated intracellularly was readily phosphorylated to dTDP and dTTP. Under optimum labeling conditions, 60 to 80% of the total thymidylate residues in newly synthesized DNA were derived from the exogenously provided dTMP, even in the absence of a block in de novo dTMP biosynthesis. An apparent Km for entry of 2 mM dTMP was found. The tup7 mutation increased permeability to dTMP (and some other 5'-mononucleotides), but did not affect uptake of nucleosides and purine and pyrimidine bases. Uptake of dTMP could be almost completely inhibited by moderate concentrations of Pi. These findings and other observations suggest that entry of dTMP in strains carrying the tup7 mutation is mediated by a permease whose function in normal cells is the transport of Pi.
Membrane-DNA attachment sites in Streptococcus faecalis cells grown at different rates
Authors: Parks L C , Rigney D , Daneo-Moore L , Higgins M L
Published: June 2021

The M-band technique was used to assess the number of attachment points of DNA to the cell membrane of Streptococcus faecalis grown at three different rates. Cells were X irradiated in liquid nitrogen and then analyzed simultaneously for the introduction of double-strand breaks into the chromosome and the degree of removal of DNA from the cell membrane (M band). Consideration of the data from these experiments and of the topology of the bacterial chromosome resulted in a reevaluation of former quantitative models. Our results are consistent with a semiquantitative model in which the bacterial chromosome is organized around a core structure. We interpret our data to mean that the core is attached to the membrane and that the complexity of the core changes more drastically with growth rate than does the number of membrane-DNA attachment points. An alternative model in which RNA hybridizes with DNA containing single- and double-strand breaks is also discussed. In any event, the complexity of these interactions precludes a reliable estimate of the number of membrane-DNA attachment sites.
Helper plasmid cloning in Streptococcus sanguis: cloning of a tetracycline resistance determinant from the Streptococcus mutans chromosome
Authors: Tobian J A , Macrina F L
Published: June 2021

A model system for testing the helper plasmid cloning system of Gryczan et al. (Mol. Gen. Genet. 177:459-467, 1980) was devised for the Streptococcus sanguis (Challis) host-vector system. In this system, linearized pVA736 plasmid efficiently transformed an S. sanguis (Challis) host containing a homologous plasmid, pVA380-1, but did not transform a plasmidless host or a host containing a nonhomologous plasmid, pVA380. In addition, whereas monomeric circular pVA736 transformed a plasmidless host with two-hit kinetics, it transformed a pVA380-1-containing host with one-hit kinetics. This helper plasmid cloning system was used to isolate two HindIII fragments (5.0 megadaltons [Mdal] and 1.9 Mdal in size) from the chromosome of Streptococcus mutans V825 which conferred high-level tetracycline resistance. One tetracycline-resistant clone was examined and found to contain three plasmids which were sized and designated pVA868 (9.0 Mdal), pVA869 (9.5 Mdal), and pVA870 (9.8 Mdal). Results of Southern blot hybridization and restriction endonuclease digestion confirmed that all three chimeras were composed of two HindIII fragments of the S. mutans V825 chromosome, as well as a large portion, varying in size for each chimera, of the 2.8 Mdal cloning vector, pVA380-1. Incompatibility observed between pVA380-1 and each of the chimeras indicated that replication of the chimeras was governed by the pVA380-1 replicative origin. Southern blotting experiments revealed that the chimeras hybridized to Tn916, providing the first evidence that transposon-related genes of enteric streptococcal origin are disseminated among oral streptococci.
Glyceride-cysteine lipoproteins and secretion by Gram-positive bacteria
Authors: Nielsen J B , Lampen J O
Published: June 2021

The membrane penicillinases of Bacillus licheniformis and Bacillus cereus are lipoproteins with N-terminal glyceride thioether modification identical to that of the Escherichia coli outer membrane lipoprotein. They are readily labeled with [3H]palmitate present during exponential growth. At the same time, a few other proteins in each organism become labeled and can be detected by fluorography after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total membrane proteins. We distinguish these proteins from the O-acyl proteolipids by demonstrating the formation of glyceryl cysteine sulfone after performic acid oxidation and hydrolysis of the protein. By this criterion, B. licheniformis and B. cereus contain sets of lipoproteins larger in average molecular weight than that of E. coli. Members of the sets probably are under a variety of physiological controls, as indicated by widely differing relative labeling intensity in different media. The set in B. licheniformis shares with membrane penicillinase a sensitivity to release from protoplasts by mild trypsin treatment, which suggests similar orientation on the outside of the membrane. At least one protein is the membrane-bound partner of an extracellular hydrophilic protein, the pair being related as membrane and exopenicillinases are. We propose that the lipoproteins of gram-positive organisms are the functional equivalent of periplasmic proteins in E. coli and other gram-negative bacteria, prevented from release by anchorage to the membrane rather than by a selectively impermeable outer membrane.
Cloning and identification of the product of the dnaE gene of Escherichia coli
Authors: Welch M M , McHenry C S
Published: June 2021

We successively subcloned the dnaE gene of Escherichia coli into pBR322, resulting in a plasmid that contains 4.6 kilobases of E. coli DNA. This plasmid can complement a dnaE temperature-sensitive mutation. A restriction map of the dnaE gene and the surrounding 10.7-kilobase region of the E. coli chromosome was determined. A unique HindIII restriction endonuclease site within the cloned segment of DNA was identified as a site required for expression of the dnaE gene. By using the maxicell plasmid-directed protein synthesizing system, we demonstrated that dnaE codes for the alpha subunit of DNA polymerase III.
Degradation of 3-phenylbutyric acid by Pseudomonas sp
Authors: Sariaslani F S , Sudmeier J L , Focht D D
Published: June 2021

Pseudomonas sp. isolated by selective culture with 3-phenylbutyrate (3-PB) as the sole carbon source metabolized the compound through two different pathways by initial oxidation of the benzene ring and by initial oxidation of the side chain. During early exponential growth, a catechol substance identified as 3-(2,3-dihydroxyphenyl)butyrate (2,3-DHPB) and its meta-cleavage product 2-hydroxy-7-methyl-6-oxononadioic-2,4-dienoic acid were produced. These products disappeared during late exponential growth, and considerable amounts of 2,3-DHPB reacted to form brownish polymeric substances. The catechol intermediate 2,3-DHPB could not be isolated, but cell-free extracts were able only to oxidize 3-(2,3-dihydroxyphenyl)propionate of all dihydroxy aromatic acids tested. Moreover, a reaction product caused by dehydration of 2,3-DHPB on silica gel was isolated and identified by spectral analysis as (--)-8-hydroxy-4-methyl-3,4-dihydrocoumarin. 3-Phenylpropionate and a hydroxycinnamate were found in supernatants of cultures grown on 3-PB; phenylacetate and benzoate were found in supernatants of cultures grown on 3-phenylpropionate; and phenylacetate was found in cultures grown on cinnamate. Cells grown on 3-PB rapidly oxidized 3-phenylpropionate, cinnamate, catechol, and 3-(2,3-dihydroxyphenyl)propionate, whereas 2-phenylpropionate, 2,3-dihydroxycinnamate, benzoate, phenylacetate, and salicylate were oxidized at much slower rates. Phenylsuccinate was not utilized for growth nor was it oxidized by washed cell suspensions grown on 3-PB. However, dual axenic cultures of Pseudomonas acidovorans and Klebsiella pneumoniae, which could not grow on phenylsuccinate alone, could grow syntrophically and produced the same metabolites found during catabolism of 3-PB by Pseudomonas sp. Washed cell suspensions of dual axenic cultures also immediately oxidized phenylsuccinate, 3-phenylpropionate, cinnamate, phenylacetate, and benzoate.
Nickel in the catalytically active hydrogenase of Alcaligenes eutrophus
Authors: Friedrich C G , Schneider K , Friedrich B
Published: June 2021

Nickel is a constituent of soluble and particulate hydrogenase of Alcaligenes eutrophus. Incorporation of 63Ni2+ revealed that almost the total nickel taken up by the cells was bound to the protein. Chromatography of a crude extract on diethylaminoethyl cellulose demonstrated an association of 63Ni2+ with soluble and particulate hydrogenase, supported by further analysis like polyacrylamide gel electrophoresis. Unspecific binding of 63Ni2+ to the protein was excluded by comparison with a mutant extract free of hydrogenase protein. X-ray fluorescence analysis of the homogeneous soluble hydrogenase indicated the presence of 2 mol of nickel per mol of enzyme, whereas the amount of nickel determined by incorporation of 63Ni2+ was calculated to be approximately 1 mol/mol of enzyme. Cells grown under nickel limitation contained catalytically inactive, but serologically active, soluble and particulate hydrogenase. The immunochemical reactions were only partially identical with the enzyme from nickel-cultivated cells indicating a structural modification of the proteins in the absence of nickel. It is concluded that nickel is essential for the catalytic activity of hydrogenase and not involved as a regulatory component in the synthesis of this enzyme.
Electron transport components involved in hydrogen oxidation in free-living Rhizobium japonicum
Authors: O'Brian M R , Maier R J
Published: June 2021

Membranes from free-living Rhizobium japonicum were isolated to study electron transport components involved in H2 oxidation. The H2/O2 uptake rate ratio in membranes was approximately 2. The electron transport inhibitors antimycin A, cyanide, azide, hydroxylamine, and 2-n-heptyl-4-hydroxyquinoline-N-oxide (HQNO) inhibited H2 uptake and H2-dependent O2 uptake significantly. H2-reduced minus O2-oxidized absorption difference spectra revealed peaks at 551.5, 560, and 603 nm, indicating the involvement of cytochromes c, b, and a-a3, respectively. H2-dependent cytochrome reduction was completely inhibited in the presence of 0.15 mM HQNO. This inhibition was relieved by the addition of 0.1 mM menadione. Evidence is presented for the involvement of two b-type cytochromes in H2 oxidation. One b-type cytochrome was not reduced by ascorbate and had an absorption peak at 560 nm. The reduction of this cytochrome by H2 was not inhibited by cyanide. A second b-type cytochrome, cytochrome b', was not reduced by H2 in the presence of cyanide. This cytochrome had an absorption peak at 558 nm. Carbon monoxide difference spectra with H2 as reductant provided evidence for the involvement of cytochrome o as well as cytochrome a3 in H2 oxidation. H2 uptake activity in cell-free extracts was inhibited by UV light irradiation. Most of the activity of the UV-treated extracts was restored with the addition of ubiquinone. The restored activity was inhibited by cyanide. A branched electron transport pathway from H2 to O2 is proposed.
DNA-binding vesicles released from the surface of a competence-deficient mutant of Haemophilus influenzae
Authors: Concino M F , Goodgal S H
Published: June 2021

Haemophilus influenzae com-51, a mutant deficient in DNA uptake, produces an extracellular DNA-binding activity. The activity was specific for Haemophilus DNA and was isolated from cell-free competence medium after incubation for 100 to 130 min. Initial steps in the purification procedure resulted in the loss of detectable binding activity, but activity was restored by the addition of a nonionic detergent. The active fractions contained vesicles derived from the outer membrane of the cells. The vesicles were produced only under conditions that normally lead to competence development. The lack of competence of com-51 cells was not due to loss of protein synthesis in M-IV competence medium or to competition of extracellular protein for exogenous DNA. Results suggest that the inability of cells to bind DNA was due in part to the loss of DNA receptors that are released into the medium in membrane fragments.
Induction of coordinated movement of Myxococcus xanthus cells
Authors: Shimkets L J , Kaiser D
Published: June 2021

Rhythmically advancing waves of cells, called ripples, arise spontaneously during the aggregation of Myxococcus xanthus into fruiting bodies. Extracts prepared by washing rippling cells contain a substance that will induce quiescent cells to ripple. Three lines of evidence indicate that murein (peptidoglycan) is the ripple-inducing substance in the extracts. First, ripple-inducing activity is associated with the cell envelope of sonically disrupted M. xanthus cells. Second, whole cells, cell extracts, or purified murein from a variety of different bacteria are capable of inducing ripples. In contrast, extracts prepared from Methanobacterium spp. which contain pseudomurein instead of typical bacterial murein fail to induce ripples. Third, four components of M. xanthus murein, N-acetylglucosamine, N-acetylmuramic acid, diaminopimelate, and D-alanine, are able to induce ripples. Ripples produced by aggregating cells have a wavelength of 45 micrometers and a maximum velocity of 2 micrometers/min. Both of the multigene systems that control gliding motility appear to be required for rippling, and all known mutations at the spoC locus eliminate both rippling and sporulation.
Lateral mobility of membrane-bound antibodies on the surface of Acholeplasma laidlawii: evidence for virus-induced cell fusion in a procaryote
Authors: Haberer K , Frösch D
Published: June 2021

Dynamic processes on the membrane of the procaryotic cell Acholeplasma laidlawii have been studied by means of immunoelectron microscopy. Colloidal gold-labeled anti-A. laidlawii antibodies were used as electron-dense markers. This method allowed the demonstration of temperature-dependent lateral mobility of membrane-bound immunoglobulins. By using two different sizes of gold grains to differentiate cells from two different cell populations, virus-induced fusion of procaryotic cells could be shown for the first time.
Plasmolysis during the division cycle of Escherichia coli
Authors: Olijhoek A J , Van Eden C G , Trueba F J , Pas E , Nanninga N
Published: June 2021

Cells of Escherichia coli were plasmolyzed with sucrose. They were classified according to length by way of electron micrographs taken from samples prepared by agar filtration. The percentage of plasmolyzed cells increased about two- and threefold between mean cell sizes of newborn and separating cells. However, dividing cells were less frequently plasmolyzed than nondividing cells of the same length class. Analysis of cell halves (prospective daughters) in dividing cells showed that they behaved as independent cellular units with respect to plasmolysis. The results indicate that compressibility of the protoplast (given a certain plasmolysis space) is inversely related to cell size. That a dividing cell does not react as one osmotic compartment to osmotic stress may suggest that cell size-dependent strength of the cell membrane-cell wall association, rather than variation in turgor, plays a role during the cell division cycle.
Rhizobium japonicum mutants defective in symbiotic nitrogen fixation
Authors: Noel K D , Stacey G , Tandon S R , Silver L E , Brill W J
Published: June 2021

Rhizobium japonicum strains 3I1b110 and 61A76 were mutagenized to obtain 25 independently derived mutants that produced soybean nodules defective in nitrogen fixation, as assayed by acetylene reduction. The proteins of both the bacterial and the plant portions of the nodules were analyzed by two-dimensional polyacrylamide gel electrophoresis. All of the mutants had lower-than-normal levels of the nitrogenase components, and all but four contained a prominent bacteroid protein not observed in wild-type bacteroids. Experiments with bacteria grown ex planta suggested that this protein was derepressed by the absence of ammonia. Nitrogenase component II of one mutant was altered in isoelectric point. The soluble plant fraction of the nodules of seven mutants had very low levels of heme, yet the nodules of five of these seven mutants contained the polypeptide of leghemoglobin. Thus, the synthesis of the globin may not be coupled to the content of available heme in soybean nodules. The nodules of the other two of these seven mutants lacked not only leghemoglobin but most of the other normal plant and bacteroid proteins. Ultrastructural examination of nodules formed by these two mutants indicated normal ramification of infection threads but suggested a problem in subsequent survival of the bacteria and their release from the infection threads.
Expression in Escherichia coli of a staphylococcal gene for resistance to macrolide, lincosamide, and streptogramin type B antibiotics
Authors: Hardy K , Haefeli C
Published: June 2021

Plasmid pBD9, which comprises two plasmids from Staphylococcus aureus, pE194 and pUB110, was joined to plasmid pBR322 by in vitro recombination to form plasmid pKH80. The ermC gene of plasmid pE194 confers inducible resistance to macrolide, lincosamide, and streptogramin type B antibiotics. When pKH80 was transferred to Escherichia coli K-12, the bacteria became resistant to several of these antibodies.
Evolutionary divergence of the Citrobacter freundii tryptophan operon regulatory region: comparison with other enteric bacteria
Authors: Blumenberg M , Yanofsky C
Published: June 2021

The regulatory region of the trp operon of Citrobacter freundii was sequenced and compared with the corresponding regions of other enteric bacteria. Significant differences were noted in the promoter region. These differences are presumably responsible for the weak expression of the cloned trp operon in Escherichia coli. The presumed operator region, although nonfunctional in E. coli, has dyad symmetry, but the sequence of the symmetrical region differs appreciably from those of operators that can be regulated by the E. coli trp repressor. The sequence of the trp leader region of C. freundii resembles that of other enteric bacteria, suggesting that the C. freundii operon is also regulated by attenuation. Comparison of the sequence of the initial portion of trpE with the homologous regions of E. coli and Salmonella typhimurium indicates that the three organisms probably are evolutionary equidistant.
Nitrogen fixation system of tungsten-resistant mutants of Azotobacter vinelandii
Authors: Riddle G D , Simonson J G , Hales B J , Braymer H D
Published: June 2021

Mutants of Azotobacter vinelandii ATCC 12837 were isolated which could fix N2 in the presence of high tungsten concentrations. The most studied of these mutants (WD2) grew well in N-free modified Burk broth containing 10 mM W, whereas the wild type would not grow in this medium. WD2 would also grow in Burk N-free broth at about the same rate as the wild type. WD2 in broth containing W exhibited 22% of the whole cell acetylene reduction activity of the wild type in broth containing Mo and showed a lowered affinity for acetylene. Two-dimensional gel electrophoresis experiments showed that N2-fixing cells of WD2 from broth containing W or Mo did not produce significant amounts of component I of native nitrogenase protein. Electron spin resonance spectra of whole cells and cell-free extracts of WD2 from broth containing W lacked any trace of the g = 3.6 resonance associated with FeMoCo.
Characterization of eight beta-lactamases of Gram-negative bacteria
Authors: Sawai T , Kanno M , Tsukamoto K
Published: June 2021

Eight kinds of beta-lactamases produced by gram-negative bacteria were characterized by the following properties: molecular weight, isoelectric point, pH optimum, molecular activity, immunochemical reactivity, and kinetic parameters with respect to twelve kinds of common beta-lactam antibiotics. These beta-lactamases included two types of penicillinases mediated by R plasmids and six kinds of species-specific cephalosporinases. To determine a reliable value of the kinetic parameter, Km, we introduced a continuous and acidimetric assay method of beta-lactamase activity with a pH stat.
Suppression of the ssb-1 and ssb-113 mutations of Escherichia coli by a wild-type rep gene, NaCl, and glucose
Authors: Tessman E S , Peterson P K
Published: June 2021

The ssb-1 mutation confers severe temperature sensitivity and UV sensitivity on many strains of Escherichia coli K-12 and C, including strain C1412. However, ssb-1 confers only slight temperature sensitivity and slight UV sensitivity on strain C1a, suggesting that strain C1a contains extragenic suppressors of ssb-1. We found that introduction of the wild-type rep gene from C1a into strain C1412 ssb-1 gave strong suppression of temperature sensitivity and moderate suppression of UV sensitivity. Also, the C1a rep+ gene mildly suppressed the temperature sensitivity conferred by the ssb-113 mutation, formerly called lexC113. Suppression of the C1412 ssb-1 growth defect by C1a rep+ rendered the cells Gro- for phi X174. In contrast to the positive suppression of ssb-1 and ssb-113 by a wild-type rep gene, mutant rep alleles enhanced the severity of the ssb-1 defect, with several C1a ssb-1 double mutants being either more temperature sensitive or more UV sensitive than C1a ssb-1, depending on which mutant rep allele was used. As a control, the same rep alleles in combination with a dnaB mutation gave an allele-independent increase in temperature sensitivity. Our results on suppression of ssb-1 by rep and on the role of the genetic background in this suppression suggested that the rep and ssb proteins interact to form a subcomplex of the total DNA replication complex and that this subcomplex has some function in repair. The effects of NaCl and glucose on suppression of both the temperature sensitivity and the UV sensitivity conferred by ssb-1 and ssb-113 are described. The degree of suppression of temperature sensitivity by salt or glucose was dependent on the source of the wild-type rep allele, as well as on the genetic background.
Kinetic analysis of N-acylphosphatidylserine accumulation and implications for membrane assembly in Rhodopseudomonas sphaeroides
Authors: Cain B D , Donohue T J , Kaplan S
Published: June 2021

The accumulation of N-acylphosphatidylserine (NAPS) in response to the inclusion of Tris in the growth medium of Rhodopseudomonas sphaeroides strain M29-5 has been examined. In the accompanying paper (Donohue et al., J. Bacteriol. 152:000--000, 1982), we show that in response to Tris, NAPS accumulated to as much as 40% of the total cellular phospholipid content. NAPS accumulation began immediately upon addition of Tris and was reflected as an abrupt 12-fold increase in the apparent rate of NAPS accumulation. We suggest that Tris altered the flow of metabolites through a preexisting and previously unknown metabolic pathway. NAPS accumulation ceased immediately upon the removal of Tris; however, accumulated NAPS remained largely metabolically stable. Importantly, under conditions in which NAPS was not accumulated, the intracytoplasmic membrane was shown to be virtually devoid of newly synthesized NAPS. The significance of this observation is discussed in terms of its physiological implications on phospholipid transfer and membrane biogenesis in R. sphaeroides.
Enzymes of agmatine degradation and the control of their synthesis in Streptococcus faecalis
Authors: Simon J P , Stalon V
Published: June 2021

Streptococcus faecalis ATCC 11700 uses agmatine as its sole energy source for growth. Agmatine deiminase and putrescine carbamoyltransferase are coinduced by growth on agmatine. Glucose and arginine were found to exert catabolite repression on the agmatine deiminase pathway. Four mutants unable to utilize agmatine as an energy source, isolated from the wild-type strain, exhibited three distinct phenotypes. Two of these strains showed essentially no agmatine deiminase, one mutant showed negligible activity of putrescine carbamoyltransferase, and one mutant was defective in both activities. Two carbamate kinases are present in S. faecalis, one belonging to the arginine deiminase pathway, the other being induced by growth on agmatine. These two enzymes have the same molecular weight, 82,000, and seem quite different in size from the kinases isolated from other streptococci.