bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of ATP-dependent phosphofructokinase as a regulatory step in the glycolytic pathway of the actinomycete Streptomyces coelicolor A3(2)
Authors: Alves A M , Euverink G J , Bibb M J , Dijkhuizen L
Published: January 2020

The ATP-dependent phosphofructokinase (ATP-PFK) of Streptomyces coelicolor A3(2) was purified to homogeneity (1,600-fold) and characterized (110 kDa, with a single type of subunit of 40 kDa); it is allosterically inhibited by phosphoenolpyruvate. Cloning of the pfk gene of S. coelicolor A3(2) and analysis of the deduced amino acid sequence (343 amino acids; 36,667 Da) revealed high similarities to the PPi-PFK enzyme from Amycolatopsis methanolica (tetramer, nonallosteric; 70%) and to the allosteric ATP-PFK enzymes from other bacteria, e.g., Escherichia coli (tetramer; 37%) and Bacillus stearothermophilus (tetramer, 41%). Further structural and functional analysis of the two actinomycete PFK enzymes should elucidate the features of these proteins that determine substrate specificity (ATP versus PPi) and allosteric (in)sensitivity.
Epitope regions in the heavy chain of Clostridium botulinum type E neurotoxin recognized by monoclonal antibodies
Authors: Kubota T , Watanabe T , Yokosawa N , Tsuzuki K , Indoh T , Moriishi K , Sanda K , Maki Y , Inoue K , Fujii N
Published: January 2020

Seventeen monoclonal antibodies (MAbs) were previously established against the heavy chain (Hc) of botulinum type E neurotoxin in BALB/c mice immunized with the type E toxoid. Five MAbs (LE15-5, LE34-6, EK19-7, EK21-4, and AE27-9) showed toxin-neutralizing activity in mice. Two of the five MAbs, EK19-7 and EK21-4, recognized the regions located at amino acid positions 731 to 787 and 811 to 897, respectively. One of the remaining three antibodies (LE34-6) reacted with the amino acid sequence VIKAIN, at amino acid positions 663 to 668, closed by the ion channel-forming domain. It is suggested that the ion channel-forming domain may also be associated with the blocking of acetylcholine release. Furthermore, the amino acid sequence YLTHMRD within 30 residues of the C-terminal region of the Hc component seemed to be recognized by LE15-5. It has been reported that the binding domain of the type E toxin is located on the C-terminal half of the Hc component. Therefore, the neutralizing activity of LE15-5 antibody may be attributed to its ability to block the binding of neurotoxin to the receptor of target cells.
Typing Listeria monocytogenes isolates from fish products and human listeriosis cases
Authors: Boerlin P , Boerlin-Petzold F , Bannerman E , Bille J , Jemmi T
Published: January 2020

Seventy-two Listeria monocytogenes isolates originating from 10 different fish products of 12 producers and 47 isolates from human listeriosis cases were typed by serotyping and multilocus enzyme electrophoresis. Seventy-five of these isolates were further subtyped by restriction analysis of genomic DNA with the enzyme XhoI and by pulsed-field gel electrophoresis using the enzymes ApaI and SmaI. The results show that several L. monocytogenes clones identified by multilocus enzyme electrophoresis are frequently found in fish products of different origins. One of these clones is the same as another previously shown to be frequently associated with meat and meat products. The epidemic-associated electrophoretic type 1 was only rarely found in fish products. No association was found between any type of fish product and a particular lineage of L. monocytogenes. Both long-term persistence of a strain and simultaneous presence of several clearly distinct strains in the products of single producers were observed. The comparison of L. monocytogenes isolates from human clinical listeriosis cases in Switzerland and those from imported fish products by use of multilocus enzyme electrophoresis showed that they do not form two clearly distinct lineages but nevertheless belong to two separate populations. None of the 48 subtypes distinguished by the combination of all four typing methods could be found in both populations of human origin and those of fish origin.
Seasonal distributions of dominant 16S rRNA-defined populations in a hot spring microbial mat examined by denaturing gradient gel electrophoresis
Authors: Ferris M J , Ward D M
Published: January 2020

Denaturing gradient gel electrophoresis analysis of PCR-amplified 16S rRNA gene segments was used to examine the distributions of bacterial populations within a hot spring microbial mat (Octopus Spring, Yellowstone National Park). Populations at sites along the thermal gradient of the spring's effluent channel were surveyed at seasonal intervals. No shift in the thermal gradient was detected, and populations at spatially or temperature-defined sites exhibited only slight changes over the annual sampling period. A new cyanobacterial 16S rRNA sequence type was detected at temperatures from 63 to 75 degrees C. A new green nonsulfur bacterium-like sequence type was also detected at temperatures from 53 to 62 degrees C. Genetically unique though closely related cyanobacterial and green nonsulfur bacterium-like populations were successively distributed along the thermal gradient of the Octopus Spring effluent channel. At least two cyanobacterial populations were detected at each site; however, a limited ability to detect some cyanobacterial populations suggests that only dominant populations were observed.
Genetic manipulation of Bacillus methanolicus, a gram-positive, thermotolerant methylotroph
Authors: Cue D , Lam H , Dillingham R L , Hanson R S , Flickinger M C
Published: January 2020

We report the fist genetic transformation system, shuttle vectors, and integrative vectors for the thermotolerant, methylotrophic bacterium Bacillus methanolicus. By using a polyethylene glycol-mediated transformation procedure, we have successfully transformed B. methanolicus with both integrative and multicopy plasmids. For plasmids with a single BmeTI recognition site, dam methylation of plasmid DNA (in vivo or in vitro) was found to enhance transformation efficiency from 7- to 11-fold. Two low-copy-number Escherichia coli-B, methanolicus shuttle plasmids, pDQ507 and pDQ508, are described. pDQ508 caries the replication origin cloned from a 17-kb endogenous B. methanolicus plasmid, pBM1. pDQ507 carries a cloned B. methanolicus DNA fragment, pmr-1, possibly of chromosomal origin, that supports maintenance of pDQ507 as a circular, extrachromosomal DNA molecule. Deletion analysis of pDQ507 indicated two regions required for replication, i.e., a 90-bp AT-rich segment containing a 46-bp imperfect, inverted repeat sequence and a second region 65% homologous to the B. subtilis dpp operon. We also evaluated two E. coli-B. subtilis vectors, pEN1 and pHP13, for use as E. coli-B. methanolicus shuttle vectors. The plasmids pHP13, pDQ507, and pDQ508 were segregationally and structurally stable in B. methanolicus for greater than 60 generations of growth under nonselective conditions; pEN1 was segregationally unstable. Single-stranded plasmid DNA was detected in B. methanolicus transformants carrying either pEN1, pHP13, or pDQ508, suggesting that pDQ508, like the B. subtilis plasmids, is replicated by a rolling-circle mechanism. These studies provide the basic tools for the genetic manipulation of B. methanolicus.
Determination of Binding of Bacillus thuringiensis (delta)-Endotoxin Receptors to Rice Stem Borer Midguts
Authors: Lee M K , Aguda R M , Cohen M B , Gould F L , Dean D H
Published: January 2020

Insecticidal activity and receptor binding properties of Bacillus thuringiensis toxins to yellow and striped rice stem borers (Sciropophaga incertulas and Chilo suppresalis, respectively) were investigated. Yellow stem borer (YSB) was susceptible to Cry1Aa, Cry1Ac, Cry2A, and Cry1C toxins with similar toxicities. To striped stem borer (SSB), Cry1Ac, Cry2A, and Cry1C were more toxic than Cry1Aa toxin. Binding assays were performed with (sup125)I-labeled toxins (Cry1Aa, Cry1Ac, Cry2A, and Cry1C) and brush border membrane vesicles (BBMV) prepared from YSB and SSB midguts. Both Cry1Aa and Cry1Ac toxins showed saturable, high-affinity binding to YSB BBMV. Cry2A and Cry1C toxins bound to YSB BBMV with relatively low binding affinity but with high binding site concentration. To SSB, both Cry1Aa and Cry1Ac exhibited high binding affinity, although these toxins are less toxic than Cry1C and Cry2A. Cry1C and Cry2A toxins bound to SSB BBMV with relatively low binding affinity but with high binding site concentration. Heterologous competition binding assays were performed to investigate the binding site cross-reactivity. The results showed that Cry1Aa and Cry1Ac recognize the same binding site, which is different from the Cry2A or Cry1C binding site in YSB and SSB. These data suggest that development of multitoxin systems in transgenic rice with toxin combinations which recognize different binding sites may be useful in implementing deployment strategies that decrease the rate of pest adaptation to B. thuringiensis toxin-expressing rice varieties.
Development of PCR primers from internal transcribed spacer region 2 for detection of Phytophthora species infecting potatoes
Authors: Tooley P W , Bunyard B A , Carras M M , Hatziloukas E
Published: January 2020

We developed PCR primers and assay methods to detect and differentiate three Phytophthora species which infect potatoes and cause late blight (Phytophthora infestans) and pink rot (P. erythroseptica and P. nicotianae) diseases. Primers based on sequence analysis of internal transcribed spacer region 2 of ribosomal DNA produced PCR products of 456 bp (P. infestans), 136 bp (P. erythroseptica), and 455 bp (P. nicotianae) and were used to detect the pathogens in potato leaf (P. infestans) and tuber (P. infestans, P. erythroseptica, and P. nicotianae) tissue with a sensitivity of 1 to 10 pg of DNA. Leaf and tuber tissue were processed for PCR by a rapid NaOH method as well as a method based on the use of commercially available ion-exchange columns of P. infestans primers and the rapid NaOH extraction method were used to detect late blight in artificially and naturally infected tubers of potato cultivar Red LaSoda. In sampling studies, P. infestans was detected by PCR from artificially infected tubers at 4 days postinoculation, before any visible symptoms were present. The PCR assay and direct tissue extraction methods provide tools which may be used to detect Phytophthora pathogens in potato seedlots and storages and thus limit the transmission and spread of new, aggressive strains of P. infestans in U.S. potato-growing regions.
Polylactide Degradation by an Amycolatopsis sp
Authors: Pranamuda H , Tokiwa Y , Tanaka H
Published: January 2020

By applying the plate count and clear-zone methods, it was confirmed that polylactide (PLA)-degrading microorganisms are sparsely distributed in soil environments. An Amycolatopsis isolate was successfully isolated. Microbial degradation of PLA film was demonstrated; i.e., about 60% of the 100-mg film initially added was degraded by the strain after 14 days of liquid culture.
Sequence analysis and characterization of pOM1, a small cryptic plasmid from Butyrivibrio fibrisolvens, and its use in construction of a new family of cloning vectors for Butyrivibrios
Authors: Hefford M A , Kobayashi Y , Allard S E , Forster R J , Teather R M
Published: January 2020

As a preliminary step in the development of vector systems, we have isolated and begun to characterize small, cryptic plasmids from several strains of the rumen bacterium Butyrivibrio fibrisolvens. We present here the complete nucleotide sequence of Butyrivibrio plasmid pOM1, which was isolated from B. fibrisolvens Bu49. While it is very similar in size to the previously characterized Butyrivibrio plasmids pRJF1 and pRJF2, pOM1 exhibits a restriction pattern which is quite distinct. Analysis of sequence data reveals that pOM1 contains only two open reading frames of significant length (ORF1 and ORF2), both of which are required for self-replication and maintenance. The protein encoded in ORF1 shows homologies with Pre (plasmid recombination enzyme) proteins encoded in plasmids from gram-positive organisms such as Staphylococcus aureus, Streptococcus agalactiae, Lactobacillus plantarum, and Bacillus thuringiensis. The putative translation product of ORF2, on the other hand, resembles Rep (replication) proteins of a different group of gram-positive plasmids, for which the Staphylococcus plasmid pSN2 is a prototype. Unlike the other characterized-Butyrivibrio plasmids, pOM1 appears to replicate via a rolling-circle mechanism. Experimental evidence showing the presence of a single-stranded replication intermediate consistent with this mechanism is presented. pOM1 has been used in the construction of a new Escherichia coli-B. fibrisolvens shuttle vector, pSMerm1, which has been successfully used to introduce a cloned gene into B. fibrisolvens harboring the pRJF1 plasmid.
Silencing MIG1 in Saccharomyces cerevisiae: effects of antisense MIG1 expression and MIG1 gene disruption
Authors: Olsson L , Larsen M E , Rønnow B , Mikkelsen J D , Nielsen J
Published: January 2020

Silencing of MIG1, a transcription factor imposing carbon catabolite repression on invertase, was attempted, either by disrupting the gene or by expressing antisense copies of the gene. The performance of the recombinant strains in bioreactor batch cultivations on sucrose, in the presence of glucose, was compared with that of the wild-type strain under the same conditions. In the delta migI strain, the rate of sucrose utilization was independent (10 mmol/g/h) of the glucose concentration. During the cultivations with the wild-type strain and the antisense strains, two distinct phases were observed. The rates of sucrose hydrolysis were < 1 mmol/g/h and 9 to 10 mmol/g/h in the first and second phases, respectively. Entry into the second cultivation phase was characterized by a decline in glucose concentration below 12 mmol/liter. As expected, disruption of MIG1 resulted in a relief of glucose repression. However, silencing of MIG1 expression was not achieved by expressing antisense MIG1, even though antisense MIG1 RNA was sufficiently stable to be detected. In the wild-type and delta migI strains, the specific growth rate was 0.32 to 0.33 h-1, whereas it was lower in the antisense strains, 0.25 to 0.30 h-1.
Sensitive detection of a novel class of toluene-degrading denitrifiers, Azoarcus tolulyticus, with small-subunit rRNA primers and probes
Authors: Zhou J , Palumbo A V , Tiedje J M
Published: January 2020

Azoarcus tolulyticus is a new class of widely distributed toluene-degrading denitrifiers of potential importance in remediating benzene, toluene, ethylbenzene, and xylene (BTEX)-contaminated environments. To detect these organisms in the environment, 16S rRNA gene-based phylogenetic probes were developed. Two sets of specific PCR amplification primers and two oligonucleotide hybridization probes were designed and tested against both closely and distantly related environmental isolates. All of these primers and probes were specific to the species A. tolulyticus. The sensitivity of the PCR amplification primer sets was evaluated with DNA isolated from A. tolulyticus Tol-4 pure culture and from sterile soils seeded with a known number of Tol-4 and Escherichia coli cells. These primer sets were able to detect 1 fg to 1 pg of template DNA from the pure culture and 1.11 x 10(2) to 1.1 x 10(8) Tol-4 cells per g of soil in the presence of 1.56 x 10(10) E. coli cells. These two PCR amplification primers were also successfully tested at two field sites. The primers identified the A. tolulyticus strains among the toluene-degrading bacteria isolated from a low-O2-high-NO(3)- aquifer at Moffett Field, Calif. Also, the presence of A. tolulyticus was detected in the groundwater samples from a BTEX-contaminated aquifer at an industrial site in Detroit, Mich., which showed anaerobic toluene degradation.
Specificity of an extracellular proteinase from Brevibacterium linens ATCC 9174 on bovine beta-casein
Authors: Rattray F P , Fox P F , Healy A
Published: January 2020

The specificity of the extracellular proteinase from Brevibacterium linens ATCC 9174 on bovine beta-casein was studied. Hydrolysis was monitored over time by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (PAGE) and urea-PAGE. The major pH 4.6-soluble peptides were isolated by high-performance liquid chromatography and identified by N-terminal amino acid sequencing and mass spectrometry. The major sites of hydrolysis were Ser-18-Ser-19, Glu-20-Glu-21, Gln-56-Ser-57, Gln-72-Asn-73, Leu-77-Thr-78, Ala-101-Met-102, Phe-119-Thr-120, Leu-139-Leu-140, Ser-142-Trp-143, His-145-Gln-146, Gln-167-Ser-168, Gln-175-Lys-176, Tyr-180-Pro-181, and Phe-190-Leu-191. The proteinase had a broad specificity for the amino acid residues present at the P1 and P'1 positions but showed a preference for hydrophobic residues at the P2, P3, P4, P'2, P'3, and P'4 positions.
Stabilization of lignin peroxidases in white rot fungi by tryptophan
Authors: Collins P J , Field J A , Teunissen P , Dobson A D
Published: January 2020

Supplementation of various cultures of white rot fungi with tryptophan was found to have a large stimulatory effect on lignin peroxidase activity levels. This enhancement was greater than that observed in the presence of the lignin peroxidase recycling agent veratryl alcohol. Using reverse transcription-PCR, we found that tryptophan does not act to induce lignin peroxidase expression at the level of gene transcription. Instead, the activity enhancement observed is likely to result from the protective effect of tryptophan against H2O2 inactivation. In experiments using a partially purified lignin peroxidase preparation, tryptophan and its derivative indole were determined to function in the same way as veratryl alcohol in converting compound II, an oxidized form of lignin peroxidase, to ferric enzyme, thereby completing the catalytic cycle. Furthermore, tryptophan was found to be a better substrate for lignin peroxidase than veratryl alcohol. Inclusion of either tryptophan or indole enhanced the oxidation of the azo dyes methyl orange and Eriochrome blue black. Stimulation of azo dye oxidations by veratryl alcohol has previously been shown to be due to its enzyme recycling function. Our data allow us to propose that tryptophan stabilizes lignin peroxidase by acting as a reductant for the enzyme.
Use of commercial enzyme immunoassays and immunomagnetic separation systems for detecting Escherichia coli O157 in bovine fecal samples
Authors: Chapman P A , Malo A T , Siddons C A , Harkin M
Published: January 2020

A commercial enzyme immunoassay (EIA) (E. coli O157 Visual Immunoassay; Tecra Diagnostics) performed on enrichment cultures in modified Escherichia coli broth (mECn) was compared with immunomagnetic separation (IMS) (Dynabeads anti-E. coli O157; Dynal) performed on enrichment cultures in modified buffered peptone water (BPW-VCC) for the detection of E. coli O157 in bovine fecal samples. Tests on fecal suspensions inoculated with each of 12 different strains of E. coli O157 showed that both the EIA and IMS methods were 10- to 100-fold more sensitive than direct culture or enrichment subculture methods for detection of the organism. EIA and IMS were then compared for detection of E. coli O157 in bovine rectal swabs. For confirmation of positive EIA tests, a commercial system (Immunocapture System [ICS]; Tecra Diagnostics) was compared with IMS; both were performed on mECn enrichment cultures. Of 200 rectal swabs examined, 17 gave positive results in the EIA which were confirmed by both confirmation systems, 2 gave positive results in the EIA which were confirmed by IMS but not by ICS, and 1 gave a positive result in the EIA which was confirmed by ICS but not by IMS. Of these 20, 15 were also positive by the BPW-VCC-IMS culture system; a further 3 samples were positive by this culture system but gave a negative result in the EIA. Eight samples were negative by the BPW-VCC-IMS culture system but gave a positive result in the EIA which could not be confirmed by either confirmation system. Further examination of the eight unconfirmed EIA-positive samples yielded sorbitol-fermenting E. coli O157 from three samples. Of the remaining five cultures, four were positive in an EIA for verocytotoxins (VT) and two were positive in a cell culture assay for VT1. The remaining 170 samples were negative by both EIA and BPW-VCC-IMS. The Tecra EIA and IMS are both technically simple and sensitive methods for detecting E. coli O157 in bovine fecal samples. There was no statistically significant difference between the numbers of positives detected by the different assays (P = 0.29).
Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola Bay
Authors: Parveen S , Murphree R L , Edmiston L , Kaspar C W , Portier K M , Tamplin M L
Published: January 2020

A total of 765 Escherichia coli isolates from point and nonpoint sources were collected from the Apalachicola National Estuarine Research Reserve, and their multiple-antibiotic-resistance (MAR) profiles were determined with 10 antibiotics. E. coli isolates from point sources showed significantly greater resistance (P < 0.05) to antibiotics and higher MAR indices than isolates from nonpoint sources. Specifically, 65 different resistance patterns were observed among point source isolates, compared to 32 among nonpoint source isolates. Examples of this contrast in MAR profiles included percentages of isolates with resistance to chlortetracycline-sulfathiazole of 33.7% and to chlortetracycline-penicillin G-sulfathiazole of 14.5% for point source isolates versus 15.4 and 1.7%, respectively, for nonpoint source isolates. MAR profile homology, based on coefficient similarity, showed that isolates from point sources were markedly more diverse than isolates from nonpoint sources. Seven clusters were observed among point source isolates, with a coefficient value of approximately 1.8. In contrast, only four clusters were observed among nonpoint source isolates. Covariance matrices of data displayed six very distinct foci representing nonpoint source E. coli isolates. Importantly, E. coli isolates obtained directly from human and animal feces also clustered among point and nonpoint sources, respectively. We conclude that E. coli MAR profiles were associated with point and nonpoint sources of pollution within Apalachicola Bay and that this method may be useful in facilitating management of other estuaries.
Cultivation of Escherichia coli with mixtures of 3-phenylpropionic acid and glucose: steady-state growth kinetics
Authors: Kovárová K , Käch A , Zehnder A J , Egli T
Published: January 2020

The fate of pollutants in the environment is affected by the presence of easily degradable carbon sources. As a step towards understanding these complex interactions, a model system was explored: the degradation of mixtures of glucose (i.e., an easily degradable substrate) and 3-phenylpropionic acid (3ppa) (a model pollutant) by Escherichia coli ML 30 was studied systematically in carbon-limited continuous culture. The two substrates were always consumed simultaneously regardless of the dilution rate applied. Even at dilution rates higher than the maximum specific growth rate for 3ppa (0.35 +/- 0.05 h-1), the two carbon substrates were utilized together. When cells were grown at a constant dilution rate with different mixtures of 3ppa and glucose, in which 3ppa contributed between 5 and 90% of carbon substrate in the feed medium, the steady-state concentrations of 3ppa and glucose were approximately proportional to the ratio of the two substrates in the feed medium. When cells were cultivated at different dilution rates with a 1:1 mixture (based on carbon) of glucose and 3ppa, an overall maximum specific growth rate of 0.90 +/- 0.05 h-1 and a Monod substrate saturation constant for 3ppa (Ks) of 600 to 700 micrograms liter-1, similar to that measured during growth with 3ppa alone, fitted the experimentally determined steady-state 3ppa concentrations. However, due to the highly differing substrate affinity constants for 3ppa and glucose (Ks approximately 30 to 70 micrograms liter-1), the total steady-state carbon concentration in the culture at a constant dilution rate was determined mainly by the steady-state 3ppa carbon concentration, and it increased with increasing proportions of 3ppa in the feed medium.
Metabolism and Energetics of Lactococcus lactis during Growth in Complex or Synthetic Media
Authors: Novak L , Cocaign-Bousquet M , Lindley N D , Loubiere P
Published: January 2020

When Lactococcus lactis was grown in various complex or synthetic media, the fermentation of glucose remained homolactic whatever the medium used, with a global carbon balance of about 87%. Moreover, the nitrogen balance was not equilibrated, indicating that some amino acids led to the production of unknown nitrogen-containing carbon compounds while part of the glucose might contribute to anabolic pathways. In minimal medium containing six amino acids, a high concentration of serine was deaminated to pyruvate. This did not occur in more complete media, suggesting the presence of a regulation of this phenomenon by an amino acid. Ammonia produced during serine consumption was partly reconsumed after serine exhaustion. The values for biomass yield and biomass yield relative to ATP (Y(infATP)), the maximal growth rate, the specific rate of glucose consumption, and the corresponding rate of ATP synthesis all increased with the complexity of the medium, amino acid composition having the most pronounced effect. The Y(infATP) values were shown to range from 6.6 to 17.6 g of biomass(middot)mol of ATP(sup-1) on minimal and complex media.
Metabolism of Melamine by Klebsiella terragena
Authors: Shelton D R , Karns J S , McCarty G W , Durham D R
Published: January 2020

Experiments were conducted to determine the pathway of melamine metabolism by Klebsiella terragena (strain DRS-1) and the effect of added NH(inf4)(sup+) on the rates and extent of melamine metabolism. In the absence of added NH(inf4)(sup+), 1 mM melamine was metabolized concomitantly with growth. Ammeline, ammelide, cyanuric acid, and NH(inf4)(sup+) accumulated transiently in the culture medium to maximal concentrations of 0.012 mM, 0.39 mM, trace levels, and 0.61 mM, respectively. In separate incubations, in which cells were grown on either ammeline or ammelide (in the absence of NH(inf4)(sup+)), ammeline was metabolized without a lag while ammelide metabolism was observed only after 3 h. In the presence of 6 mM added NH(inf4)(sup+) (enriched with 5% (sup15)N), ammeline, ammelide, and cyanuric acid accumulated transiently to maximal concentrations of 0.002 mM, 0.47 mM, and trace levels, respectively, indicating that the added NH(inf4)(sup+) had little effect on the relative rates of triazine metabolism. These data suggest that the primary mode of melamine metabolism by K. terragena is hydrolytic, resulting in successive deaminations of the triazine ring. Use of (sup15)N-enriched NH(inf4)(sup+) allowed estimates of rates of triazine-N mineralization and assimilation of NH(inf4)(sup+)-N versus triazine-N into biomass. A decrease in the percent (sup15)N in the external NH(inf4)(sup+) pool, in conjunction with the accumulation of ammelide and/or triazine-derived NH(inf4)(sup+) in the culture medium, suggests that the initial reactions in the melamine metabolic pathway may occur outside the cytoplasmic membrane.
Development of the FUN-1 family of fluorescent probes for vacuole labeling and viability testing of yeasts
Authors: Millard P J , Roth B L , Thi H P , Yue S T , Haugland R P
Published: January 2020

A new family of fluorescent probes has been developed for assessing the viability and metabolic activity of yeasts. This class of halogenated unsymmetric cyanine dyes is exemplified by the FUN-1 [2-chloro-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)- methylidene)-1-phenylquinolinium iodide] stain, a membrane-permeant nucleic acid-binding dye that has been found to give rise to cylindrical intravacuolar structures (CIVS) in Saccharomyces cerevisiae. Biochemical processing of the dye by active yeasts yielded CIVS that were markedly red shifted in fluorescence emission and therefore spectrally distinct from the nucleic acid-bound form of the dye. The formation of CIVS occurred under both aerobic and anaerobic conditions and was highly temperature dependent. Treatment of yeasts with the nonmetabolizable glucose analog 2-deoxy-D-glucose reduced cellular ATP levels approximately 6-fold and completely inhibited CIVS formation. Under aerobic conditions, the formation of CIVS was abrogated by the cytochrome oxidase inhibitors azide and cyanide; however, the H+ transport uncoupler carbonyl cyanide m-chlorophenylhydrazone inhibited CIVS formation under both aerobic and anaerobic conditions. Depletion of cellular thiols, including glutathione, with millimolar concentrations of N-ethylmaleimide, iodoacetamide, or allyl alcohol completely inhibited CIVS production. Marked reduction in the formation of CIVS by ethacrynic acid and sulfobromophthalein, inhibitors of glutathione S-transferase, suggested that dye processing can involve enzyme-mediated formation of glutathione conjugates. The conversion of FUN-1 by S. cerevisiae was studied quantitatively by using several techniques, including fluorometry, flow cytometry, and wide-field and confocal laser scanning fluorescence microscopy.
In Vitro Interactions of Asian Freshwater Clam (Corbicula fluminea) Hemocytes and Cryptosporidium parvum Oocysts
Authors: Graczyk T K , Fayer R , Cranfield M R , Conn D B
Published: January 2020

Corbicula fluminea hemocytes phagocytosed infectious oocysts of Cryptosporidium parvum in vitro. After 15, 30, 60, 90, and 120 min of incubation, averages of 35.8, 58.0, 69.7, 77.7, and 81.6% of the oocysts were phagocytosed by 24.3, 70.0, 78.5, 87.3, and 93.0% of the hemocytes, respectively. A single clam can retain by phagocytosis an average of 1.84 x 10(sup6) oocysts per ml of hemolymph. C. fluminea bivalves can serve as biological indicators of contamination of wastewaters and agricultural drainages with Cryptosporidium.
Isolation and Metabolic Characterization of a Pseudomonas stutzeri Mutant Able To Grow on the Three Isomers of Xylene
Authors: Di L , Accarino M , Bolognese F , Galli E , Barbieri P
Published: January 2020

From an o-xylene-degrading Pseudomonas stutzeri strain (OX1), we previously isolated mutant M1, which had acquired the ability to grow on m-xylene and p-xylene but lost the ability to utilize the ortho isomer. From M1 cultures we have now isolated a revertant strain (R1) which grows on o-xylene and retains the ability to grow with the meta and para isomers regardless of the selective pressure applied. In P. stutzeri R1, o-xylene is degraded through two successive monooxygenations of the aromatic ring, while m-xylene and p-xylene catabolism proceeds through the progressive oxidation of a methyl substituent, although unquantifiable amounts of these two substrates are transformed into the corresponding dimethylphenols, which are not utilized for further growth. The two catabolic pathways are inducible by all three xylene isomers.
PCR primers to amplify 16S rRNA genes from cyanobacteria
Authors: Nübel U , Garcia-Pichel F , Muyzer G
Published: January 2020

We developed and tested a set of oligonucleotide primers for the specific amplification of 16S rRNA gene segments from cyanobacteria and plastids by PCR. PCR products were recovered from all cultures of cyanobacteria and diatoms that were checked but not from other bacteria and archaea. Gene segments selectively retrieved from cyanobacteria and diatoms in unialgal but nonaxenic cultures and from cyanobionts in lichens could be directly sequenced. In the context of growing sequence databases, this procedure allows rapid and phylogenetically meaningful identification without pure cultures or molecular cloning. We demonstrate the use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities.
Bacterial transformations of naphthothiophenes
Authors: Kropp K G , Andersson J T , Fedorak P M
Published: January 2020

Naphthothiophenes are minor components of fossil fuels, and they can enter the environment from oil spills. Naphtho[2,1-b]thiophene, naphtho[2,3-b]thiophene, and 1-methylnaphtho[2,1-b]thiophene were synthesized and used in biodegradation studies with 1-methylnaphthalene (1-MN)-degrading Pseudomonas strains W1, F, and BT1. Cultures were incubated with one of the naphthothiophenes with or without 1-MN, acidified, and extracted with CH(inf2)Cl(inf2). The extracts were analyzed by gas chromatography with flame photometric and mass detectors to characterize sulfur-containing metabolites and with an atomic emission detector for quantification. Only strain W1 was able to grow on naphtho[2,1-b]thiophene, but strains F and BT1 cometabolized this compound if 1-MN was present. 1-MN was required by all three strains to metabolize naphtho[2,3-b]thiophene, which was more resistant to biodegradation than the [2,1-b] isomer. Two metabolites of naphtho [2,1-b]thiophene were purified, analyzed by (sup1)H nuclear magnetic resonance spectroscopy, and found to be 4-hydroxybenzothiophene-5-carboxylic acid (metabolite I) and 5-hydroxybenzothiophene-4-carboxylic acid (metabolite II). In cultures of strain W1 grown for 7 days on 52 (mu)mol of naphtho[2,1-b]thiophene, >84% of the substrate was degraded and metabolites I and II accounted for 19 and 9%, respectively, of the original amount of naphtho[2,1-b]thiophene. When 1-MN was present, strain W1 degraded >97% of the naphtho[2,1-b]thiophene and similar amounts of metabolite II were produced, but metabolite I did not accumulate. 1-MN was shown to promote the further degradation of metabolite I, but not of metabolite II, by strain W1. Thus, 1-MN enhanced the biodegradation of naphtho[2,1-b]thiophene. Approximately 70% of the 1-methylnaphtho [2,1-b]thiophene added to cultures of strain W1 with 1-MN was recovered as 4-hydroxy-3-methylbenzothiophene-5-carboxylic acid, the 3-methyl analog of metabolite I. The methyl substitution hindered further metabolism of 3-methyl-metabolite I even in the presence of 1-MN. Cometabolism of naphtho[2,3-b]thiophene yielded two products that were tentatively identified as 5-hydroxybenzothiophene-6-carboxylic and 6-hydroxybenzothiophene-5-carboxylic acids.
Influence of sulfur oxyanions on reductive dehalogenation activities in Desulfomonile tiedjei
Authors: Townsend G T , Suflita J M
Published: January 2020

The inhibition of aryl reductive dehalogenation reactions by sulfur oxyanions has been demonstrated in environmental samples, dehalogenating enrichments, and the sulfate-reducing bacterium Desulfomonile tiedjei; however, this phenomenon is not well understood. We examined the effects of sulfate, sulfite, and thiosulfate on reductive dehalogenation in the model microorganism D. tiedjei and found separate mechanisms of inhibition due to these oxyanions under growth versus nongrowth conditions. Dehalogenation activity was greatly reduced in extracts of cells grown in the presence of both 3-chlorobenzoate, the substrate or inducer for the aryl dehalogenation activity, and either sulfate, sulfite, or thiosulfate, indicating that sulfur oxyanions repress the requisite enzymes. In extracts of fully induced cells, thiosulfate and sulfite, but not sulfate, were potent inhibitors of aryl dehalogenation activity even in membrane fractions lacking the cytoplasmically located sulfur oxyanion reductase. These results suggest that under growth conditions, sulfur oxyanions serve as preferred electron acceptors and negatively influence dehalogenation activity in D. tiedjei by regulating the amount of active aryl dehalogenase in cells. Additionally, in vitro inhibition by sulfur oxyanions is due to the interaction of the reactive species with enzymes involved in dehalogenation and need not involve competition between two respiratory processes for reducing equivalents. Sulfur oxyanions also inhibited tetrachloroethylene dehalogenation by the same mechanisms, further indicating that chloroethylenes are fortuitously dehalogenated by the aryl dehalogenase. The commonly observed inhibition of reductive dehalogenation reactions under sulfate-reducing conditions may be due to similar regulation mechanisms in other dehalogenating microorganisms that contain multiple respiratory activities.
Diversity of the ribulose bisphosphate carboxylase/oxygenase form I gene (rbcL) in natural phytoplankton communities
Authors: Pichard S L , Campbell L , Paul J H
Published: January 2020

The phytoplankton of the world's oceans play an integral part in global carbon cycling and food webs by conversion of carbon dioxide into organic carbon. They accomplish this task through the action of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Here we have investigated the phylogenetic diversity in the form I rbcL locus in natural phytoplankton communities of the open ocean and representative clones of marine autotrophic picoplankton by mRNA or DNA amplification and sequencing of a 480 to 483 bp internal fragment of this gene. Five gene sequences were recovered from nucleic acids of natural phytoplankton communities of the Gulf of Mexico. The rbcL genes of two Prochlorococcus isolates and one Synechococcus strain (WH8007) were also sequenced. Sequences were aligned with the database of rbcL genes and subjected to both neighbor-joining and parsimony analyses. The five sequences from the natural phytoplankton community spanned nearly the entire diversity of characterized form I rbcL genes, with some sequences closely related to isolates such as Synechococcus and Prochlorococcus (forms IA and I) and prymnesiophyte algae (form ID), while other sequences were deeply rooted. Unexpectedly, the deep euphotic zone contained an organism that possesses a transcriptionally active rbcL gene closely related to that of a recently characterized manganese-oxidizing bacterium, suggesting that such chemoautotrophs may contribute to the diversity of carbon-fixing organisms in the marine euphotic zone.
Characterization of superoxide dismutase in Streptococcus thermophilus
Authors: Chang S K , Hassan H M
Published: January 2020

Streptococcus thermophilus AO54 possesses a single manganese-containing superoxide dismutase (MnSOD). The enzyme was found to be insensitive to cyanide or to a modified H2O2 treatment. The enzyme is expressed in a growth-phase-dependent fashion, increasing three- to fourfold upon entry into stationary phase. The specific activity for MnSOD was the same under anaerobic or aerobic conditions and was not induced by the presence of paraquat under aerobic conditions.
Cross-regulation of toluene monooxygenases by the transcriptional activators TbmR and TbuT
Authors: Leahy J G , Johnson G R , Olsen R H
Published: January 2020

The toluene-3-monooxygenase from Burkholderia pickettii PKO1 and the toluene/benzene-2-monooxygenase from Burkholderia (Pseudomonas) sp. strain JS150 are distinct enzymes which differ not only in catalytic specificity and substrate range but also in the arrangement and sequence of the genes within the operons that encode the enzymes, tbuA1UBVA2C and tbmABCDEF, respectively. In the present study, we examined the transcriptional activation of the PtbuA1 and PtbmA promoters by their cognate regulators, TbuT and TbmR. TbmR and TbuT each exhibited activation of both PtbmA and PtbuA1, with toluene, benzene, and chlorobenzene serving as strong effectors. These results strongly suggest that TbmR is an NtrC-like regulator which is functionally homologous to TbuT, and they provide evidence for the evolutionary "recruitment" of the same or a similar type of regulator for both monooxygenase pathways.
Elevated Candida antigen titers are associated with neutrophil dysfunction after injury
Authors: Sweeney J F , Rosemurgy A S , Wei S , Djeu J Y
Published: January 2020

This study was undertaken to determine if impaired neutrophil (polymorphonuclear leukocytes [PMNL]) function is associated with an elevated Candida antigen titer after injury. PMNL from eight severely injured adults with Candida antigen titers of > or = 1:4 (titer positive) were evaluated for the ability to inhibit growth of Candida albicans in vitro by using a [3H]glucose incorporation assay. PMNL from eight severely injured adults with titers of < 1:4 (titer negative) and from eight healthy volunteers were studied for comparison. PMNL from the titer-positive patients had suppressed ability to inhibit C. albicans growth compared with PMNL from titer-negative patients and healthy volunteers. In vitro, PMNL function against C. albicans could be augmented significantly by cytokines. Granulocyte macrophage-colony-stimulating factor was most potent at augmenting function, followed by interleukin-8 and gamma interferon. Injured patients with elevated candida antigen titers have impaired PMNL function against C. albicans, and this function can be restored by cytokines.
Comparison of three commercially available assays for detection of varicella-zoster virus antibody
Authors: Martins T B , Jaskowski T D , Schroder C , Streeter B , Hill H R
Published: January 2020

Three commercially available diagnostic assays for the detection of antibodies to varicella-zoster virus were evaluated to determine which would be the most suitable for our clinical laboratory. Three different methods were examined: an enzyme-linked immunosorbent assay (ELISA), latex agglutination (LA), and an indirect fluorescent-antibody technique. For the 141 serum specimens tested, the ELISA had an agreement of 90.1% and LA had an agreement of 92.2% with the indirect immunofluorescent-antibody technique. The ELISA had a lower sensitivity (85.6%) than LA (100.0%), but suffered from a low specificity (78.4%) compared with the ELISA (98.0%).
Spontaneous lymphocyte proliferation in human T-cell lymphotropic virus type I (HTLV-I) and HTLV-II infection: T-cell subset responses and their relationships to the presence of provirus and viral antigen production
Authors: Prince H E , York J , Golding J , Owen S M , Lal R B
Published: January 2020

Spontaneous lymphocyte proliferation (SLP) during in vitro culture of mononuclear cells (MCs) characterizes over half of asymptomatic individuals infected with human T-cell lymphotropic virus type I (HTLV-I) or HTLV-II. Both CD4 and CD8 T-cell subsets within MC cultures are activated during SLP, as judged by high-density CD25 (CD25bright) expression; it is unclear, however, whether both cell subsets can directly undergo SLP. In the present investigation, the SLP capacities of purified CD8 and CD4 cells were examined in subjects infected with HTLV-I (n = 19) or HTLV-II (n = 54) in relation to the SLP status of MCs from each subject. No increase in SLP was observed for CD8 or CD4 cells from SLP-negative (SLP-) HTLV-infected subjects, whereas robust SLP characterized CD8 cells from all SLP-positive (SLP+) individuals, regardless of HTLV type. In contrast, SLP+ CD4 cells characterized only 23% (7 of 31) of HTLV-II+ SLP+ individuals, whereas SLP+ CD4 cells characterized 100% of HTLV-I+ SLP+ individuals. In cocultures of HTLV-II+ SLP+ CD8 cells and autologous SLP- CD4 cells, sizable proportions of both CD8 cells and CD4 cells coexpressed CD25bright, suggesting that SLP- CD4 cells were activated in the presence of SLP+ CD8 cells. PCR analysis for tax sequences detected provirus in most CD4- and CD8-cell preparations from HTLV-seropositive individuals, regardless of type and the SLP status of cell subsets. To determine whether SLP was associated with activation of viral genes, levels of HTLV-I and HTLV-II core antigen (Ag) in supernatants were measured. Viral Ag production and SLP responses were significantly correlated for both CD4 and CD8 cells in both HTLV-I and HTLV-II infections. However, inhibition of CD8- or CD4-cell SLP by cyclosporin A or anti-Tac (anti-CD25) did not reduce Ag production, indicating that Ag production is not coupled to SLP. These findings show that CD4 cells from SLP+ HTLV-I+ and SLP+ HTLV-II+ individuals differ in SLP capacity, that the absence of SLP does not indicate a lack of infection, and that production of viral Ag is associated with, but not dependent on, SLP.
Use of fixed autologous stimulator cells to correctly present human immunodeficiency virus type 1 viral peptides to nonhuman primate lymphocytes in proliferation and cytotoxic T-lymphocyte assays
Authors: Munroe K J , Anderson C A , Wu J Y , Wyand M S , Newman G W , Newman M J
Published: January 2020

Autologous, virus-transformed lymphoblastoid cell lines were established by using peripheral blood lymphocytes from rhesus monkeys that were previously immunized with recombinant human immunodeficiency virus type 1 strain IIIB glycoprotein 160. These autologous cell lines were used to present human immunodeficiency virus type 1 viral antigens in a processed and cell-associated manner to T lymphocytes. This was accomplished by either infecting the cells with recombinant vaccinia viruses or pulsing them with synthetic peptides and then subjecting them to a mild fixation step with glutaraldehyde. Fixed antigen-presenting cells were then used as stimulator cells in vitro to measure cell-mediated immune responses. Both the vaccinia virus-infected and peptide-pulsed autologous cells stimulated antigen-specific cellular proliferative responses. The magnitude of the responses correlated with the immunization histories of the animals and other measures of immunity, such as antibody titers. Autologous vaccinia virus-infected cells were also capable of inducing the in vitro maturation of CD4+ and CD8+ precursor cytotoxic T lymphocytes into antigen-specific mature cytotoxic T lymphocytes. The use of stimulator cells to present viral peptides in a cell-associated manner appeared to be a very sensitive and versatile manner in which to measure cell-mediated immune responses with peripheral blood lymphocytes from nonhuman primates. It is likely that a similar approach will function with peripheral blood lymphocytes from humans.
Molecular basis for serological cross-reactivity between enteroviruses
Authors: Samuelson A , Forsgren M , Johansson B , Wahren B , Sällberg M
Published: January 2020

The recognition sites for human antibodies which are cross-reactive between different types of enteroviruses were determined and characterized. Serum samples obtained from 58 patients with culture-confirmed enteroviral infections were analyzed in enzyme immunoassays against two sets of overlapping synthetic peptides covering residues 31 to 96 of poliovirus 1 VP1 (Mahoney strain) and residues 31 to 148 of coxsackievirus B1 VP1 (position based on alignment with poliovirus 1 VP1, Mahoney strain). A major antigenic region eliciting cross-reactive antibodies could be located to residues 37 to 51 of VP1. Furthermore, a single peptide covering residues 42 to 55 almost completely inhibited the binding of human antibodies to heat-inactivated enteroviruses, indicating that residues 42 to 55 of VP1 contain a major region eliciting cross-reactive antibodies. By using peptide analogs in which each residue within positions 42 to 55 of VP1 was sequentially substituted by Ala or Gly, we were able to determine the most essential residues for human antibody binding in 38 of the convalescent-phase patient serum samples. In a majority of the serum samples, the most essential residues for antibody binding were found to be Pro-42, Ala-43, Leu-44, Thr-45, Ala-46, Glu-48, Thr-49, and Gly-50. All of these residues are conserved, according to known enterovirus sequences, with the divergent echovirus 22 excepted. In conclusion, we could demonstrate that the essential residues for binding of cross-reactive antibodies are well conserved within the enterovirus family. These findings provide a molecular basis for the observed antibody cross-reactivity within the enterovirus group.