bluuebunny/crossref_metadata_2025 huggingface dataset:
Sound classification during Seabed Classification Experiment 2017
Authors: Earnhardt Allison N. , Neilsen Tracianne B. , Acree Mason C. , Hodgkiss William , Knobles David P.
Published: June 2021

In ocean acoustics, finding acoustic signals within long recordings is usually time consuming. The need to optimize this process we propose an experiment to discover the optimal acoustic signal classification model using the PyTorch deep learning package. This machine learning algorithm was designed to recognize and classify various sources from an input of spectrograms compiled from raw sound data. In the case of continuous audio files, this model’s purpose is to identify areas of interest for human operators so they don’t need to listen to each hour of the audio files marking down noises as they are heard. Four Convolutional Neural Networks (CNN) with differing numbers of layers took in one minute spectrograms. The most successful of the CNNs acted on time-averaged spectrograms, and resulted in a model which achieved a high degree of accuracy. This machine learning algorithm can help identify underwater sound signal sources, and can more efficiently identify when different signals are present in long audio files. The results of these tests imply that time averaging spectrograms may improve the identification of long term signal sources by a CNN. [ Research supported by the NSF REU program.]
Information content of reflection-coefficient data versus angle and frequency for geoacoustic inversion
Authors: Jiang Yong-Min , Dosso Stan , Holland Charles W. , Dettmer Jan
Published: June 2021

This paper considers the information content of seabed reflection-coefficientdata (as a function of angle and frequency) to resolve fine seabed structure through geoacoustic inversion. During the 2017 Seabed Characterization Experiment conducted on the New England Mud Patch, two types of measurement systems were employed to collect reflection data. One is a bistatic system with bottom-moored hydrophones and an omni-directional towed source, and the other is a towed system that uses the same source and a 15.4 m acoustic array on the same cable (source separation to the closest sensor is ∼ 27 m). Limited by the source–receiver geometry and data quality, the angular coverages of the reflection data for the bistatic and towed systems are ∼25–58° and ∼43–55°, respectively. This study aims to assess the capabilities of these systems to infer sediment structure using simulations over a frequency band of 1–6 kHz. Inversions show that the data simulated for the bistatic system better resolve fine structure of the seabed even with fewer frequency components, while the data for the towed system must include reflections at higher frequencies to get acceptable results. [Work supported by the Office of Naval Research.]
Baleen whale presence in northern Mariana islands in 2015–2017
Authors: Ollier Camille , Wood Megan A. , Oleson Erin M. , Širović Ana
Published: June 2021

Many baleen whale vocalizations are species, and in some cases, population−specific. Although baleen whale occurrence has been studied in different parts of the ocean, little is known about the seasonal distribution of baleen whales in the Western Pacific. Since 2010, more concerted visual and acoustic survey effort has been occurred around a very remote region of the western Pacific Ocean, the Northern Mariana Islands. Passive acoustic data were collected at two locations in the Northern Mariana Islands, Tinian and Saipan, from 2015–2017 and they were analyzed for call characteristics and occurrence of different baleen whale call types from blue whales, fin whales, and Bryde’s whales. There was a clear seasonal pattern in fin whale calls, with peak call detections during winter and spring. Low levels of blue whale calls were detected year-round with peaks in winter (December) and summer (June). Bryde’s whales were detected sporadically at both locations. Moreover, two low-frequency sounds with currently unknown origin were detected, one tonal and one pulsed sound. The former was more common at Tinian and the latter at Saipan. This work enhances our understanding of the species’ vocal repertoire and population structure.
Recent advances in multi-frequency analysis with the boundary element method
Authors: Koji Baydoun Suhaib , Marburg Steffen
Published: June 2021

The boundary element discretization of the acoustic Helmholtz equation yields frequency-dependent linear systems, which require efficient solution strategies for multi-frequency analysis. We briefly review recent advances in this field covering frequency approximation and extraction of coefficient matrices, frequency sampling strategies, iterative solvers for frequency-dependent linear systems and model order reduction techniques.
Substrate deformation regulates DRM2-mediated DNA methylation in plants
Authors: Fang Jian , Leichter Sarah M. , Jiang Jianjun , Biswal Mahamaya , Lu Jiuwei , Zhang Zhi-Min , Ren Wendan , Zhai Jixian , Cui Qiang , Zhong Xuehua , Song Jikui
Published: June 2021

DRM2 induces substrate deformation to underlie its methylation preference for CHH DNA in plants.
Metabolically engineered stem cell–derived exosomes to regulate macrophage heterogeneity in rheumatoid arthritis
Authors: You Dong Gil , Lim Gyeong Taek , Kwon Seunglee , Um Wooram , Oh Byeong Hoon , Song Seok Ho , Lee Jungmi , Jo Dong-Gyu , Cho Yong Woo , Park Jae Hyung
Published: June 2021

Surface engineering of exosomes enhances the therapeutic efficacy of rheumatoid arthritis by macrophage reprogramming.
Ultrahigh specific strength in a magnesium alloy strengthened by spinodal decomposition
Authors: Xin Tongzheng , Zhao Yuhong , Mahjoub Reza , Jiang Jiaxi , Yadav Apurv , Nomoto Keita , Niu Ranming , Tang Song , Ji Fan , Quadir Zakaria , Miskovic David , Daniels John , Xu Wanqiang , Liao Xiaozhou , Chen Long-Qing , Hagihara Koji , Li Xiaoyan , Ringer Simon , Ferry Michael
Published: June 2021

Spinodal decomposition is discovered to be an effective way to strengthen magnesium alloy.
Cis P-tau underlies vascular contribution to cognitive impairment and dementia and can be effectively targeted by immunotherapy in mice
Authors: Qiu Chenxi , Albayram Onder , Kondo Asami , Wang Bin , Kim Nami , Arai Ken , Tsai Cheng-Yu , Bassal Mahmoud A. , Herbert Megan K. , Washida Kazuo , Angeli Peter , Kozono Shingo , Stucky Joseph E. , Baxley Sean , Lin Yu-Min , Sun Yan , Rotenberg Alexander , Caldarone Barbara J. , Bigio Eileen H. , Chen Xiaochun , Tenen Daniel G. , Zeidel Mark , Lo Eng H. , Zhou Xiao Zhen , Lu Kun Ping
Published: June 2021

Reducing brain blood flow induces toxic but druggable cis P-tau that drives progressive neurodegeneration and memory loss in mice.
First exposure to the pandemic H1N1 virus induced broadly neutralizing antibodies targeting hemagglutinin head epitopes
Authors: Guthmiller Jenna J. , Han Julianna , Li Lei , Freyn Alec W. , Liu Sean T. H. , Stovicek Olivia , Stamper Christopher T. , Dugan Haley L. , Tepora Micah E. , Utset Henry A. , Bitar Dalia J. , Hamel Natalie J. , Changrob Siriruk , Zheng Nai-Ying , Huang Min , Krammer Florian , Nachbagauer Raffael , Palese Peter , Ward Andrew B. , Wilson Patrick C.
Published: June 2021

Broadly neutralizing antibodies are critical for protection against both drifted and shifted influenza viruses. Here, we reveal that first exposure to the 2009 pandemic H1N1 influenza virus recalls memory B cells that are specific to the conserved receptor-binding site (RBS) or lateral patch epitopes of the hemagglutinin (HA) head domain. Monoclonal antibodies (mAbs) generated against these epitopes are broadly neutralizing against H1N1 viruses spanning 40 years of viral evolution and provide potent protection in vivo. Lateral patch-targeting antibodies demonstrated near universal binding to H1 viruses, and RBS-binding antibodies commonly cross-reacted with H3N2 viruses and influenza B viruses. Lateral patch-targeting mAbs were restricted to expressing the variable heavy-chain gene VH3-23 with or without the variable kappa-chain gene VK1-33 and often had a Y-x-R motif within the heavy-chain complementarity determining region 3 to make key contacts with HA. Moreover, lateral patch antibodies that used both VH3-23 and VK1-33 maintained neutralizing capability with recent pH1N1 strains that acquired mutations near the lateral patch. RBS-binding mAbs used a diverse repertoire but targeted the RBS epitope similarly and made extensive contacts with the major antigenic site Sb. Together, our data indicate that RBS- and lateral patch-targeting clones are abundant within the human memory B cell pool, and universal vaccine strategies should aim to drive antibodies against both conserved head and stalk epitopes.
Broad-host-range IncP-4 plasmid R1162: effects of deletions and insertions on plasmid maintenance and host range
Authors: Meyer R , Laux R , Boch G , Hinds M , Bayly R , Shapiro J A
Published: June 2021

R1162 is an 8.7-kilobase (kb) broad-host-range replicon encoding resistance to streptomycin and sulfa drugs. In vitro deletion of 1.8-kb DNA between coordinates 3.0 and 5.3 kb did not affect plasmid maintenance, but a Tn1 insertion at coordinate 6.3 kb led to a recessive defect in plasmid maintenance. The only cis-acting region necessary for plasmid replication appears to lie between the Tn1 insertion at coordinate 6.3 kb and a second Tn1 insertion at coordinate 6.5 kb. All R1162 sequences between position 6.5 kb and the EcoRI site at coordinate 8.7/0 kb were dispensible for replication in Escherichia coli and Pseudomonas putida. Plasmids carrying insertions in a variety of restriction sites in an R1162::Tn1 derivative were unstable in P. putida but stable in E. coli. Tn5 insertions in R1162 showed a hot spot at coordinate 7.5 kb. A Tn5 insertion at coordinate 8.2 kb appeared to mark the 3' end of the streptomycin phosphotransferase coding sequence. All R1162::Tn5 derivatives showed specific instability in Pseudomonas strains but not in E. coli. The instability could be relieved by internal deletions of Tn5 sequences. In the haloaromatic-degrading Pseudomonas sp. strain B13, introduction of an unstable R1162::Tn5 plasmid led to loss of ability to utilize m-chlorobenzoate as a growth substrate. Our results showed that alteration of plasmid sequence organization in nonessential regions can result in restriction of plasmid host range.
Mechanisms of appearance of the Pasteur effect in Saccharomyces cerevisiae: inactivation of sugar transport systems
Authors: Lagunas R , Dominguez C , Busturia A , Sáez M J
Published: June 2021

Saccharomyces cerevisiae does not show a noticeable Pasteur effect (activation of sugar catabolism by anaerobiosis) when growing with an excess of sugar and nitrogen source, but it does do so after exhaustion of the nitrogen source in the medium (resting state). We have found that this different behavior of growing and resting S. cerevisiae seems due to differences in the contribution of respiration to catabolism under both states. Growing S. cerevisiae respired only 3 to 20% of the catabolized sugar, depending on the sugar present; the remainder was fermented. In contrast, resting S. cerevisiae respired as much as 25 to 100% of the catabolized sugar. These results suggest that a shift to anaerobiosis would have much greater energetic consequences in resting than in growing S. cerevisiae. In resting S. cerevisiae anaerobiosis would strongly decrease the formation of ATP; as a consequence, various regulatory mechanisms would switch on, producing the observed increase of the rate of glycolysis. The greater significance that respiration reached in resting cells was not due to an increase of the respiratory capacity itself, but to a loss of fermentation which turned respiration into the main catabolic pathway. The main mechanism involved in the loss of fermentation observed during nitrogen starvation was a progressive inactivation of the sugar transport systems that reduced the rate of fermentation to less than 10% of the value observed in growing cells. Inactivation of the sugar transports seems a consequence of the turnover of the sugar carriers whose apparent half-lives were 2 to 7 h.
Phospholipase C (heat-labile hemolysin) of Pseudomonas aeruginosa: purification and preliminary characterization
Authors: Berka R M , Vasil M L
Published: June 2021

Phospholipase C (heat-labile hemolysin) was purified from Pseudomonas aeruginosa culture supernatants to near homogeneity by ammonium sulfate precipitation followed by a novel application of DEAE-Sephacel chromatography. Enzymatic activity remained associated with DEAE-Sephacel even in the presence of 1 M NaCl, but was eluted with a linear gradient of 0 to 5% tetradecyltrimethylammonium bromide. Elution from DEAE-Sephacel was also obtained with 2% lysophosphatidylcholine, and to a lesser extent with 2% phosphorylcholine, but not at all with choline. The enzyme was highly active toward phospholipids possessing substituted ammonium groups (e.g., phosphatidycholine, lysophosphatidylcholine, and sphingomyelin); however, it had little if any activity toward phospholipids lacking substituted ammonium groups (e.g., phosphatidylethanolamine, phosphatidylserine, and phosphaditylglycerol). Collectively, these data suggest that phospholipase C from P. aeruginosa exhibits high affinity for substituted ammonium groups, but requires an additional hydrophobic moiety for optimum binding. The specific activity of the purified enzyme preparation increased 1,900-fold compared with that of culture supernatants. The molecular weight of the phospholipase C was estimated to be 78,000 by both sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Sephacryl S-200 column chromatography and was 76,000 by high-performance size exclusion chromatography. The isoelectric point was 5.5. Amino acid analysis showed that phospholipase C was rich in glycine, serine, threonine, aspartyl, glutamyl, and aromatic amino acids, but was cystine free.
Changes in cell dimensions during amino acid starvation of Escherichia coli
Authors: Grossman N , Ron E Z , Woldringh C L
Published: June 2021

Electron microscopic analysis was used to study cells of Escherichia coli B and K-12 during and after amino acid starvation. The results confirmed our previous conclusion that cell division and initiation of DNA replication occur at a smaller cell volume after amino acid starvation. Although during short starvation periods, the number of constricting cells decreased due to residual division, it appears that during prolonged starvation, cells of E. coli B and K-12 were capable of initiating new constrictions. During amino acid starvation, cell diameter decreased significantly. The decrease was reversed only after two generation times after the resumption of protein synthesis and was larger in magnitude than that previously observed before division (F. J. Trueba and C. L. Woldringh, J. Bacteriol. 142:869-878, 1980). This decrease in cell diameter correlates with synchronization of cell division which has been shown to occur after amino acid starvation.
A decrease in S-adenosylmethionine synthetase activity increases the probability of spontaneous sporulation
Authors: Ochi K , Freese E
Published: June 2021

Starting with a relaxed (relA) strain, mutants with reduced activity of adenosine triphosphate:L-methionine S-adenosyl transferase (EC 2.5.1.6; SAM synthetase) were isolated in Bacillus subtilis. One such mutant (gene symbol metE1) had only 3% of the normal SAM synthetase activity but grew almost as well as the parent strain. Another mutant was isolated (gene symbol spdC1) as being able to sporulate continually at a high frequency; it had one-half the normal SAM synthetase activity at 33 degrees C. Both mutants continually and spontaneously entered spore development at a higher frequency than the parent strain in a medium containing excess glucose, ammonium ions, and phosphate. Sporulation was prevented by a high concentration of SAM (1 mM or more) or by the combination of adenosine and methionine (0.5 mM or more each), both of which are precursors of SAM. In contrast to this continual increase in the spore titer, addition of decoyinine, an inhibitor of GMP synthetase, rapidly initiated massive sporulation. Various amino acid analogs also induced sporulation in the relA strain, the methionine analogs ethionine and selenomethionine being most effective.
Trail following by gliding bacteria
Authors: Burchard R P
Published: June 2021

Slime trails, which are deposited on surfaces by gliding bacteria and which serve as preferential pathways for gliding motility, were tested for the species specificity of their support of movement. Among the pairs of bacteria tested, a variety of gliding bacteria and a flagellated bacterium moved along trails of unrelated species. Thus, the trails did not serve as pheromones. Rather, they may have guided gliding elasticotactically. Some biological implications of this finding are considered.
Effect of silver ions on transport and retention of phosphate by Escherichia coli
Authors: Schreurs W J , Rosenberg H
Published: June 2021

Silver ions inhibited phosphate uptake and exchange in Escherichia coli and caused efflux of accumulated phosphate as well as of mannitol, succinate, glutamine, and proline. The effects of Ag+ were reversed by thiols and, to a lesser extent, by bromide. In the presence of N-ethylmaleimide and several uncouplers, Ag+ failed to cause phosphate efflux, but still inhibited exchange of intracellular and extracellular phosphate, indicating an interaction at more than one site. It is unlikely that Ag+ caused metabolite efflux by acting solely as an uncoupler, as an inhibitor of the respiratory chain, or as a thiol reagent.
Induction of germ tube formation by N-acetyl-D-glucosamine in Candida albicans: uptake of inducer and germinative response
Authors: Mattia E , Carruba G , Angiolella L , Cassone A
Published: June 2021

A number of strains of Candida albicans were tested for germ tube formation after induction by N-acetyl-D-glucosamine (GlcNAc) and other simple (proline, glucose plus glutamine) or complex (serum) compounds. A proportion of strains (high responders) were induced to form germ tubes evolving to true hyphae by GlcNAc alone or by proline or glucose plus glutamine mixture. The majority of strains were low responders because they could be induced only by serum or GlcNAc-serum medium. Two strains were found to be nonresponders: they grew as pseudohyphae in serum. Despite minor quantitative differences, all strains efficiently utilized GlcNAc for growth under the yeast form at 28 degrees C. They also had comparable active, inducible, and constitutive uptake systems for GlcNAc. During germ tube formation in GlcNAc, the inducible uptake system was modulated, as expected from induction and decay of GlcNAc kinase. Uranyl acetate, at a concentration of 0.01 mM, inhibited both GlcNAc uptake and germ tube formation and was reversed by phosphates. Germinating and nongerminating cells differed in the rapidity and extent of GlcNAc incorporation into acid-insoluble and alkali-acid-insoluble cell fractions. During germ tube formation induced by proline, GlcNAc was almost totally incorporated into the acid-insoluble fraction after 60 min. Moreover, hyphal development on induction by either GlcNAc or proline was characterized by an apparent "uncoupling" between protein and polysaccharide metabolism, the ratio between the two main cellular constituents falling from more than 1 to less than 0.5 after 270 min of development. The data suggest that utilization of the inducer for wall synthesis is a determinant of germ tube formation C. albicans but that the nature and extent of inducer uptake is not a key event for this phenomenon to occur.
Aerotactic response of Azospirillum brasilense
Authors: Barak R , Nur I , Okon Y , Henis Y
Published: June 2021

Five strains of Azospirillum brasilense and two of Azospirillum spp., from Israel, responded to self-created and preformed oxygen gradients by forming aerotactic bands in capillary tubes and actively moving toward a specific zone with low dissolved oxygen. Increasing the oxygen concentration in capillaries containing phosphate buffer increased the number of attracted bacteria and decreased band velocity. High O2 concentrations and H2O2 temporarily repulsed the bacteria, causing the formation of a bacterial arc around the capillary mouth. There was no band formation under anaerobic conditions, although the bacteria remained highly motile. Exogenous energy sources were unnecessary for aerotaxis in Azospirillum spp. The addition of oxidizable substrates to the capillary slightly enhanced aerotaxis, possibly by accelerating O2 consumption. Aerotactic band formation was affected by pH, bacterial concentration and age, incubation time, and respiratory inhibitors, but not by the lack of combined nitrogen in the growth medium. It is proposed that aerotaxis plays a role in the capacity of Azospirillum spp. to reach an environment suitable for N2 fixation.
Escherichia coli phenylalanyl-tRNA synthetase operon: transcription studies of wild-type and mutated operons on multicopy plasmids
Authors: Plumbridge J A , Springer M
Published: June 2021

The construction of three lambda bacteriophages containing parts of the structural gene for threonyl-tRNA synthetase, thrS, and those for the two subunits of phenylalanyl-tRNA synthetases, pheS and pheT, is described. These phages were used as hybridization probes to measure the in vivo levels of mRNA specific to these three genes. Plasmid pB1 carries the three genes thrS, pheS, and pheT, and strains carrying the plasmid show enhanced levels of mRNA corresponding to these genes. Although the steady-state levels of threonyl-tRNA synthetase and phenylalanyl-tRNA synthetase produced by the presence of the plasmid differed by a factor of 10, their pulse-labeled mRNA levels were about the same. Mutant derivatives of pB1 were also analyzed. Firstly, a cis-acting insertion located before the structural genes for phenylalanyl-tRNA synthetase caused a major decrease in both pheS and pheT mRNA. Secondly, mutations affecting either structural gene pheS or pheT caused a reduction in the mRNA levels for both pheS and pheT. This observation suggests that autoregulation plays a role in the expression of phenylalanyl-tRNA synthetase.
Identification of pilin pools in the membranes of Pseudomonas aeruginosa
Authors: Watts T H , Worobec E A , Paranchych W
Published: June 2021

The proteins of purified inner and outer membranes obtained from Pseudomonas aeruginosa strains PAK and PAK/2Pfs were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis, transferred to nitrocellulose, and treated with antiserum raised against pure pili. Bound antipilus antibodies were visualized by reaction with 125I-labeled protein A from Staphylococcus aureus. The results showed that there are pools of pilin in both the inner and outer membranes of P. aeruginosa and that the pool size in the multipiliated strain is comparable with that of the wild-type strain.
Molecular cloning of the spo0B sporulation locus in bacteriophage lambda
Authors: Ferrari F A , Lang D , Ferrari E , Hoch J A
Published: June 2021

The stage 0 sporulation locus spo0B has been mapped by transformation between the pheA and spoIVF loci. Analysis of the behavior of alleles of the spo0B locus in trpE26 merodiploid strains indicates that all of the known alleles of this locus comprise a single complementation group. The spoIVF88 mutation was found to reside in a separate complementation group. The chromosomal region surrounding and including the spo0B locus was cloned in the lambda vector Charon 4A. Extensive restriction endonuclease analyses of the inserts in these phage revealed that an EcoRI fragment of DNA of 2.3 kilobases had transforming activity for spo0B mutations. Examination of the physical and genetic maps of the locus suggested that the entire spo0B locus is contained within this fragment. Subcloning of restriction endonuclease fragments of the lambda inserts and transformation analyses allowed assignment of surrounding genetic loci to specific DNA fragments.
Deletion of the Penicillin-Binding Protein 6 Gene of
Escherichia coli
Authors: Broome-Smith Jennifer K. , Spratt Brian G.
Published: June 2021

A strain of
Escherichia coli
with a deletion of the penicillin-binding protein 6 gene (
dacC
) has been constructed. The properties of this strain establish that the complete lack of penicillin-binding protein 6 has no marked effect on the growth of
E. coli
.
Escherichia coli mutants with a temperature-sensitive alcohol dehydrogenase
Authors: Lorowitz W , Clark D
Published: June 2021

Mutants of Escherichia coli resistant to allyl alcohol were selected. Such mutants were found to lack alcohol dehydrogenase. In addition, mutants with temperature-sensitive alcohol dehydrogenase activity were obtained. These mutations, designated adhE, are all located at the previously described adh regulatory locus. Most adhE mutants were also defective in acetaldehyde dehydrogenase activity.
Insertions of transposon Tn5 into ribosomal protein PNA polymerase operons
Authors: Hui I , Maltman K , Little R , Hastrup S , Johnsen M , Fiil N , Dennis P
Published: June 2021

The genetic organization and interrelationships between the two ribosomal protein transcription units (the L11 and L10 operons) from near 89 min on the Escherichia coli chromosome were studied by using insertional mutations generated by the kanamycin-resistant transposable element Tn5. The polar effects of Tn5 insertions on the expression of the L11, L1, L10, and L12 ribosomal protein genes and the beta RNA polymerase subunit gene were examined (i) by the level of beta-galactosidase activity generated from L10-lacZ and beta-lacZ gene fusions, (ii) by direct sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the proteins specified by plasmid ribosomal protein genes in UV-irradiated maxicells, and (iii) by urea-polyacrylamide gel electrophoresis of plasmid- and chromosome-specified L12 protein. The results confirmed the organization of these genes into two transcription units as follows: PL11, rplK (L11), rplA (L1), PL10, rplJ (L10), rplL (L12), rpoB (beta). . .; they also localized the position of the PL10 promoter within an 80-nucleotide region near the end of the L1 gene. The results also support the idea that the translational regulatory proteins for the L11 and L10 operons are L1 and L10, respectively, and that the expression of the L12 gene is closely linked to L10 gene expression.
Fumarate reduction and product formation by the Reiter strain of Treponema phagedenis
Authors: George H A , Smibert R M
Published: June 2021

The catabolic pathways for butyrate, acetate, succinate, and ethanol formation by the Reiter strain of Treponema phagedenis were investigated. Enzyme activities were demonstrated for glucose catabolism to pyruvate by the Embden-Meyerhof-Parnas pathway. Butyrate formation from acetyl-coenzyme A (acetyl-CoA) does not generate ATP by substrate level phosphorylation and involves NAD+-dependent 3-hydroxybutyryl-CoA dehydrogenase and NAD(P)+-independent butyryl-CoA dehydrogenase activities. Butyrate is formed from butyryl-CoA in a CoA transphorase reaction. Phosphate acetyltransferase and acetate kinase activities convert acetyl-CoA to acetate. An NADP+-dependent alcohol dehydrogenase participates in ethanol formation; however, the manner in which acetyl-CoA is reduced to acetaldehyde is unclear. A membrane-associated fumarate reductase was found which utilized reduced ferredoxin or flavin nucleotides as physiological electron donors. Additional electron carriers may also be involved in electron transfer for fumarate reduction. Strains of Treponema denticola, T. vincentii, and T. minutum utilized fumarate without succinate formation, whereas strains of T. phagedenis and T. refringens formed succinate from exogenously supplied fumarate.
Characterization of
Escherichia coli men
Mutants Defective in Conversion of
o
-Succinylbenzoate to 1,4-Dihydroxy-2-Naphthoate
Authors: Shaw Duncan J. , Guest John R. , Meganathan Rangaswamy , Bentley Ronald
Published: June 2021

Four independent menaquinone (vitamin K
2
)-deficient mutants of
Escherichia coli
, blocked in the conversion of
o
-succinylbenzoate (OSB) to 1,4-dihydroxy-2-naphthoate (DHNA), were found to represent two distinct classes. Enzymatic complementation was observed when a cell-free extract of one mutant was mixed with extracts of any of the remaining three mutants. The missing enzymes in the two classes were identified by in vitro complementation with preparations of OSB-coenzyme A (CoA) synthetase or DHNA synthase isolated from
Mycobacterium phlei
. Mutants lacking DHNA synthase (and therefore complementing with
M. phlei
DHNA synthase) were designated
menB
, and the mutant lacking OSB-CoA synthetase (and therefore complementing with
M. phlei
OSB-CoA synthetase) was designated
menE
. The
menB
mutants produced only the spirodilactone form of OSB when extracts were incubated with [2,3-
14
C
2
]OSB, ATP, and CoA; the OSB was unchanged on incubation with an extract from the
menE
mutant under these conditions. Experiments with strains lysogenized by a λ
men
transducing phage (λG68) and transduction studies with phage P1 indicated that the
menB
and
menE
genes form part of a cluster of four genes, controlling the early steps in menaquinone biosynthesis, located at 48.5 min in the
E. coli
linkage map. Evidence was obtained for the clockwise gene order
gyrA
....-B-D, where the asterisk denotes the uncertain position of
menE
relative to
menC
and
menB
. The transducing phage (λG68) contained functional
menB, menC
, and
menE
genes, but only part of the
menD
gene, and it was designated λ
menC B(D)
.
Immunochemical properties of NAD+-linked glycerol dehydrogenases from Escherichia coli and Klebsiella pneumoniae
Authors: Tang J C , Forage R G , Lin E C
Published: June 2021

An NAD+-linked glycerol dehydrogenase hyperproduced by a mutant of Escherichia coli K-12 was found to be immunochemically homologous to a minor glycerol dehydrogenase of unknown physiological function in Klebsiella pneumoniae 1033, but not to the glycerol dehydrogenase of the dha system responsible for anaerobic dissimilation of glycerol or to the 2,3-butanediol dehydrogenase of K. pneumoniae.
DNA primase of plasmid ColIb is involved in conjugal DnA synthesis in donor and recipient bacteria
Authors: Chatfield L K , Orr E , Boulnois G J , Wilkins B M
Published: June 2021

The sog gene of the IncI alpha group plasmid ColIb is known to encode a DNA primase that can substitute for defective host primase in dnaG mutants of Escherichia coli during discontinuous DNA replication. The biological significance of this enzyme was investigated by using sog mutants, constructed from a derivative of ColIb by in vivo recombination of previously defined mutations in a cloned sog gene. The resultant Sog- plasmids failed to specify detectable primase activity and were unable to suppress a dnaG lesion. These mutants were maintained stably in E. coli, implying that the enzyme is not involved in vegetative replication of ColIb. However, the Sog- plasmids were partially transfer deficient in E. coli and Salmonella typhimurium matings, consistent with the hypothesis that the normal physiological role of this enzyme is in conjugation. This was confirmed by measurements of conjugal DNA synthesis. Studies of recipient cells have indicated that plasmid primase is required to initiate efficient synthesis of DNA complementary to the transferred strand, with the protein being supplied by the donor parent and probably transmitted between the mating cells. Primase specified by the dnaG gene of the recipient can substitute partially for the mutant enzyme, thus providing an explanation for the partial transfer proficiency of the mutant plasmids. Conjugal DNA synthesis in dnaB donor cells was deficient in the absence of plasmid primase, implying that the enzyme also initiates synthesis of DNA to replace the transferred material.
Physical mapping of TOL plasmids pWWO and pND2 and various R plasmid-TOL derivatives from Pseudomonas spp
Authors: Lehrbach P R , Ward J , Meulien P , Broda P
Published: June 2021

Analysis of several independently isolated R plasmid-TOL hybrids revealed a wide variation in the amount of TOL DNA they contain. If the formation of the various R plasmid-TOL hybrids involves transposition (which has yet to be rigorously assessed), such transposition does not involve a unique segment of TOL DNA.
Restriction enzyme mapping of the DNA of Streptomyces bacteriophage B alpha and its deletion derivatives
Authors: Ishihara H , Nakano M M , Ogawara H
Published: June 2021

Cleavage analysis of actinophage B alpha DNA was done with several restriction enzymes, and a restriction map of the DNA was determined. The DNA appeared to carry cohesive ends. Deletion mutants of actinophage B alpha were isolated by five cycles of treatment with 15 mM PPi. Both mutants had deletions of 2.5 of 1.8 megadaltons near one end of the genome, and one of them lost the single EcoRI cleavage site.
Glycerol kinase as a substitute for dihydroxyacetone kinase in a mutant of Klebsiella pneumoniae
Authors: Jin R Z , Forage R G , Lin E C
Published: June 2021

With dihydroxyacetone as the sole source of carbon and energy, constitutively synthesized glycerol kinase of the glp system supported aerobic growth of Klebsiella pneumoniae mutants lacking the inducible dihydroxyacetone kinase of the dha system. Glycerol kinase had an apparent Km of 0.01 mM for its physiological substrate and 1 mM for its surrogate substrate. However, the growth rate on dihydroxyacetone of cells relying on glycerol kinase increased with the concentration of the carbon and energy source up to 50 mM, suggesting that permeation is rate limiting.
Colicin M is an inhibitor of murein biosynthesis
Authors: Schaller K , Höltje J V , Braun V
Published: June 2021

Colicin M inhibited the incorporation of DL + meso-2,6-diamino[3,4,5-3H]pimelic acid into the murein (peptidoglycan) of growing cells of Escherichia coli W7 dap lys. The inhibition of the UDP-N-acetylmuramyl pentapeptide-dependent incorporation of UDP-N-acetyl-D-[U-14C]glucosamine into isolated cell envelopes indicated interference with a late step of murein biosynthesis. After the inhibition of murein biosynthesis, cells lysed, and they released lysis products of murein. In vitro, the murein biosynthesis of colicin M-tolerant mutants (tolM) was inhibited by colicin M. Therefore, tolerance is probably conferred by an impaired uptake of an altered fixation close to the target site and not by a mutation of the target itself. Preliminary studies with beta-lactam antibiotics and with mutants in penicillin-binding proteins did not reveal a specific enzymatic step inhibited by colicin M. The unique action among the colicins renders colicin M a potentially useful tool for studying murein biosynthesis.
Assessment of an In-House Enzyme-Linked Immunosorbent Assay and IgG Avidity Test Based on SAG1 and GRA7 Proteins for Discriminating between Acute and Chronic Toxoplasmosis in Humans
Authors: Teimouri Aref , Abbaszadeh Afshar Mohammad Javad , Mohtasebi Sina , Jafarpour Azami Sanaz , Alimi Rasoul , Keshavarz Hossein
Published: June 2021

To improve serodiagnostic methods for diagnosis of acute from chronic toxoplasmosis, an economical in-house enzyme-linked immunosorbent assay (ELISA) for measuring
Toxoplasma
-specific IgG, IgM, and IgG avidity has been developed and assessed based on use of various
Toxoplasma gondii
antigens, including SAG1, GRA7, and a combination of SAG1 and GRA7 (SAG1+GRA7), as well as
Toxoplasma
lysate antigens (TLAs). Performances of in-house IgM, IgG, and IgG avidity assays were compared to those of ELISA commercial kits and VIDAS Toxo IgG avidity.
Oligomeric immunoglobulin A antibody response to rubella virus infection
Authors: Inouye S , Kono R , Takeuchi Y
Published: June 2021

Pooled sera from rubella patients in the early convalescent stage, containing a high titer of hemagglutination-inhibiting (HI) antibody, were treated with protein A-conjugated gel to reduce immunoglobulin G (IgG) antibody and then centrifuged in sucrose gradients. This treatment resulted in the detection of an HI activity peak sedimenting at a rate intermediate between 7S and 19S. In contrast to the 19S antibody, the HI activity of this peak was not abolished by 2-mercaptoethanol, but sedimented at 7S after this treatment. The activity was considered to consist of IgA oligomers, since it was removed by anti-IgA immunosorbent. The appearance of the oligomeric IgA antibody after the infection was then studied using serum samples collected sequentially from five rubella patients. Shortly after the onset of the disease, the HI activity appeared at high titer and thereafter gradually decreased in titer until it could no longer be detected in the sera. The time of its disappearance varied with each patient.
Comparison of continuous and discontinuous counterimmunoelectrophoresis with immunodiffusion in identification of candida antibody using HS antigen
Authors: Marier R , Andriole V T
Published: June 2021

We have compared continuous counterimmunoelectrophoresis (CCIE) and discontinuous counterimmunoelectrophoresis (DCIE) with immunodiffusion (ID) in the identification of Candida albicans antibody using HS antigen. Eighteen sera with a titer of 1/1 to 1/32 1/32 by CCIE were titered by CCIE and ID. Fewer were positive by CCIE and ID (13 of 18 and 9 of 18, respectively). Furthermore, the titers were lower when measured by these two methods in comparison to DCIE (4 of 18 and 3 of 18 sera had titers greather than or equal to 1/8 in comparison with 7 of 18 greater than or equal to 1/8 by DCIE). Finally, DCIE was found to be much faster than CCIE and ID. After 20 min of electrophoresis, 17 of 21 sera were positive by DCIE, whereas none were positive by CCIE. Even after 90 min, only 10 of 21 were positive by CCIE, whereas 4 of 21 were positive by ID. The increased sensitivity and speed of DCIE over CCIE and ID suggest that DCIE is preferable to these other methods in the measurement of candida antibody using HS antigen.
Radioimmunoassay for Quantitation of Antibodies to Alphaviruses with Staphylococcal Protein A
Authors: Jahrling Peter B. , Hesse Richard A. , Metzger Joseph F.
Published: June 2021

A radioimmunoassay (RIA) procedure is described for measuring antibodies to alphaviruses in human and other mammalian sera. The test employed protein Abearing
Staphylococcus aureus
as a solid-phase immunoadsorbent for
3
H-labeled viruses complexed with immunoglobulin G. Using antibodies produced in humans and guinea pigs, the RIA procedure clearly differentiated among antibodies to Venezuelan, western, and eastern equine encephalomyelitis viruses. Sensitivity of the RIA depended on the concentrations of labeled viruses employed. The dilution of serum that effected binding of 50% of the
3
H-labeled virus (determined by probit analysis) was consistently higher than the neutralizing antibody titer determined by a conventional plaque reduction neutralization test using 80% plaque reduction end points. In addition, sera from 73 individuals were screened for seroconversion following live attenuated Venezuelan equine encephalomyelitis virus vaccine (strain TC-83) inoculation, by RIA using a single serum dilution (1:80); results were identical with seroconversions identified by plaque reduction neutralization test. Hyperimmune Venezuelan equine encephalomyelitis virus sera from a number of mammalian species were successfully titrated by RIA; the species tested were human, guinea pig, white rat, rabbit, burro, dog, monkey, sheep, and cotton rat. The protein A-mediated RIA is a rapid, sensitive, specific, and precise serological tool for measuring antibodies to surface antigens of alphaviruses, and should allow the subsequent development of a competitive binding RIA to measure antigenic potency of inactivated alphavirus vaccines.
Occurrence of mycoplasmas in urinary tracts of patients with acute pyelonephritis
Authors: Thomsen A C
Published: June 2021

Mycoplasma hominis was isolated from the upper urinary tract in 7 of 80 patients with acute pyelonephritis and from 0 of 60 patients with noninfectious diseases of the urinary tract, a significant difference. In four cases M. hominis was isolated in pure culture, in one it was isolated together with Ureaplasma urealyticum, and in two it was isolated with bacteria. U. urealyticum was isolated from the upper urinary tract of five patients, all with acute pyelonephritis; this was not significantly different from the control group.
Cerebrospinal fluid lactic acid in diagnosis of meningitis
Authors: Komorowski R A , Farmer S G , Hanson G A , Hause L L
Published: June 2021

Quantitative lactate determinations were performed on cerebrospinal fluids to assess their value in the rapid diagnosis of bacterial and mycotic meningitis and to evaluate their value in assessing the prognosis in these patients. Cerebrospinal fluid lactate concentrations were elevated in all patients with untreated bacterial or fungal meningitis. Lactate concentrations proved very valuable in following patients with mycotic meningitis and in differentiating aseptic from bacterial meningitis. Elevated cerebrospinal fluid lactate is not specific for meningitis. Lactate is also elevated in situations where there is central nervous system ischemia and necrosis and in patients with brain tumors. Lactate concentration is normal in chronic degenerative brain diseases. Thus, the clinical situation must be taken into account when interpreting the lactate concentrations.
Noncultivable viruses and neonatal diarrhea: fifteen-month survey in a newborn special care nursery
Authors: Cameron D J , Bishop R F , Veenstra A A , Barnes G L
Published: June 2021

During a 15-month period of surveillance, diarrhea developed in 257 of 913 babies (28%) admitted within 2 hours of birth to a special care nursery in Melbourne, Australia. Diarrhea was seasonal, affecting a maximum of 43% of babies admitted during one winter month (July) and a minimum of 13% of babies admitted during one summer month (December). Diarrhea was no more frequent nor more severe in babies of very low birth weight or of very early gestational age. Two noncultivable viruses were located by electron microscopy in feces from babies with or without diarrhea. Excretion of a reovirus-like particle (rotavirus, duovirus, human reovirus-like agent, infantile gastroenteritis virus) was temporally related to diarrheal symptoms. Asymptomatic infection with this virus also occurred. A 28-nm virus-like particle was excreted by some babies, but it could not be implicated on epidemiological grounds in the etiology of the diarrhea. Rotavirus infection may be an important cause of endemic diarrhea in nurseries for the newborn. Infection may be difficult to control or eradicate, since it is often asymptomatic and may be influenced by infection in the community at large.
Human infections caused by thiamine- or menadione-requiring Staphylococcus aureus
Authors: Acar J F , Goldstein F W , Lagrange P
Published: June 2021

Stable dwarf forms of Staphylococcus aureus have been identified in clinical specimens as the sole or predominant isolate in eight cases. These organisms have been shown to be menadione or thiamine dependent, i.e., cultivation in the presence of one of these agents has permitted growth of colonies which appear typical of S. aureus. In vitro resistance to aminoglycosides was overcome by cultivation in the presence of menadione or thiamine. Menadione- or thiamine-requiring S. aureus can be considered as causative agents in severe human infections. Special care must be taken if they are to be identified in pathological specimens. Their antibiotic sensitivity testing should be done comparatively on supplemented and nonsupplemented media.
Analysis of antibody assay methods and classes of viral antibodies in serodiagnosis of cytomegalovirus infection
Authors: Cremer N E , Hoffman M , Lennette E H
Published: June 2021

Forty-nine serum pairs with antibody to cytomegalovirus (CMV) were evaluated for rises in antibody titer (greater than or equal to fourfold) by indirect hemagglutination (IHA) and complement fixation (CF), using a freeze-thaw antigen (FT) and a glycine extract antigen (GE). In this sample CF-FT detected more rises in antibody titer than did CF-GE. IHA detected the least number. The apparent reason for stationary antibody titers with CF-GE and IHA was the presence of high antibody titers in the first serum specimen. Separation of immunoglobulin classes of 20 serum pairs by sucrose gradient centrifugation indicated that these antibodies with IHA were of the immunoglobulin M (IgM) class and those with CF-GE were of the IgG class. By separation of immunoglobulin classes, rises in IgG CMV antibody titers were seen with IHA, rises not observed in the whole serum because of high IgM antibody titers in the first serum specimen. Absence of rises in antibody titers with CF-FT was due in part to too early sampling of the second serum specimen (less than 21 days) and in part to an apparent inability of some individuals to respond with antibody reactive with FT antigen. CF-GE and CF-FT antibodies of the IgM class were detected in some sera, usually in specimens collected more than 10 days after the onset of symptoms. Although reactive with CMV antigen, the specificity of these IgM antibodies in relation to rheumatoid factor requires clarification.
Immunoglobulin-specific radioimmunoprecipitation assays for quantitation of nasal secretory antibodies to hemagglutinin of type A influenza viruses
Authors: Kasel J A , Six H R , Oborn C J , Dreesman G R
Published: June 2021

Radioimmunoprecipitation (RIP) assays were developed to selectively quantitate class-specific antibodies to purified hemagglutinins (HA) of type A influenza virus in nasal secretions. Rabbit anti-human secretory piece of immunoglobulin A (IgA) and rabbit anti-human IgG were used as second antibodies. A third antibody, goat anti-rabbit IgG, was incorporated into the system to separate immune complexes formed between iodinated HA, nasal wash test specimen, and second antibody. The utilization of this reagent avoided the need for large quantities of IgA and IgG antibody-negative carrier secretions. Nasal was specimens obtained from 14 adults immunized with an inactivated type A influenza virus vaccine were evaluated by RIP and viral neutralization assays. Significant homologous postvaccination secretory IgA and IgG antibody levels were demonstrable in 13 (93%) of individuals by RIP, whereas only 5 (36%) exhibited rises by viral neutralization tests. Moreover, the geometric mean IgA and IgG antibody levels were at least 20- and 37-fold greater than the neutralizing antibody titer. The pattern of heterologous immunoglobulin-specific antibody responses tended to be similar to those observed with the homologous HA subunit.
Serological classification of Pseudomonas aeruginosa by a slide agglutination test
Authors: Kusama H
Published: June 2021

Serological classification of Pseudomonas aeruginosa by the slide agglutination test with live organisms was studied, based on the O antigen schema adopted by the international expert panel sponsored by the Subcommittee on Pseudomonas and Related Organisms of the International Committee on Systematic Bacteriology. The typing results obtained by the slide test with well-absorbed O sera were identical to those obtained by the conventional tube agglutination test with autoclaved organisms. Most O antigens occur singly; but O2, O5, and O16 occur in four combinations. Antigens O13 and O14 are closely related, as are O7 and O8, and it would be convenient to classify organisms possessing these antigens collectively as O7,8 and O13,14.