bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Transcriptional Activator XlnR Regulates Both Xylanolytic and Endoglucanase Gene Expression inAspergillus niger
Authors: van Peij Noël N. M. E. , Gielkens Marco M. C. , de Vries Ronald P. , Visser Jaap , de Graaff Leo H. 
Published: December 2019

ABSTRACTThe expression of genes encoding enzymes involved in xylan degradation and two endoglucanases involved in cellulose degradation was studied at the mRNA level in the filamentous fungusAspergillus niger. A strain with a loss-of-function mutation in thexlnRgene encoding the transcriptional activator XlnR and a strain with multiple copies of this gene were investigated in order to define which genes are controlled by XlnR. The data presented in this paper show that the transcriptional activator XlnR regulates the transcription of thexlnB,xlnC, andxlnDgenes encoding the main xylanolytic enzymes (endoxylanases B and C and β-xylosidase, respectively). Also, the transcription of the genes encoding the accessory enzymes involved in xylan degradation, including α-glucuronidase A, acetylxylan esterase A, arabinoxylan arabinofuranohydrolase A, and feruloyl esterase A, was found to be controlled by XlnR. In addition, XlnR also activates transcription of two endoglucanase-encoding genes,eglAandeglB, indicating that transcriptional regulation by XlnR goes beyond the genes encoding xylanolytic enzymes and includes regulation of two endoglucanase-encoding genes.
Study of Toxin Production by Isolates of
Stachybotrys chartarum
and
Memnoniella echinata
Isolated during a Study of Pulmonary Hemosiderosis in Infants
Authors: Jarvis Bruce B. , Sorenson W. G. , Hintikka Eeva-Liisa , Nikulin Marjo , Zhou Yihong , Jiang Jian , Wang Shengun , Hinkley Simon , Etzel Ruth A. , Dearborn D. 
Published: December 2019

ABSTRACT

A cluster of cases of pulmonary hemosiderosis among infants was reported in Cleveland, Ohio, during 1993 and 1994. These unusual cases appeared only in infants ranging in age from 1 to 8 months and were characterized by pulmonary hemorrhage, which caused the babies to cough up blood. A case-control study identified major home water damage (from plumbing leaks, roof leaks, or flooding) as a risk factor for development of pulmonary hemorrhage in these infants. Because of an interest in the possibility that trichothecene mycotoxins might be involved in this illness, a number of isolates of
Stachybotrys chartarum
were grown in the laboratory on rice, and extracts were prepared and analyzed both for cytotoxicity and for specific toxins. Two isolates of
Memnoniella echinata
, a fungus closely related to
S. chartarum
, were also included in these studies.
S. chartarum
isolates collected from the homes were shown to produce a number of highly toxic compounds, and the profiles of toxic compounds from
M. echinata
were similar; the most notable difference was the fact that the principal metabolites produced by
M. echinata
were griseofulvins.
Ellipsometric Measurement of Bacterial Films at Metal-Electrolyte Interfaces
Authors: Busalmen J. P. , de Sánchez S. R. , Schiffrin D. J. 
Published: December 2019

ABSTRACT

Ellipsometric measurements were used to monitor the formation of a bacterial cell film on polarized metal surfaces (Al-brass and Ti). Under cathodic polarization bacterial attachment was measured from changes in the ellipsometric angles. These were fitted to an effective medium model for a nonabsorbing bacterial film with an effective refractive index (

n
f

) of 1.38 and a thickness (

d
f

) of 160 ± 10 nm. From the optical measurements a surface coverage of 17% was estimated, in agreement with direct microscopic observations. The influence of bacteria on the formation of oxide films was monitored by ellipsometry following the film growth in situ. A strong inhibition of metal oxide film formation was observed, which was assigned to the decrease in oxygen concentration due to the presence of bacteria. It is shown that the irreversible adhesion of bacteria to the surface can be monitored ellipsometrically. Electrophoretic mobility is proposed as one of the factors determining bacterial attachment. The high sensitivity of ellipsometry and its usefulness for the determination of growth of interfacial bacterial films is demonstrated.
Characteristics of Airborne Actinomycete Spores
Authors: Reponen T. A. , Gazenko S. V. , Grinshpun S. A. , Willeke K. , Cole E. C. 
Published: December 2019

ABSTRACT

Airborne actinomycete spores, important contaminants in occupational and residential environments, were studied with respect to their (i) release into the air, (ii) aerodynamic and physical size while airborne, and (iii) survival after collection onto agar with an impactor. Three actinomycete species were selected for the tests to exemplify the three main spore types:
Streptomyces albus
for arthrospores,
Micromonospora halophytica
for aleuriospores, and
Thermoactinomyces vulgaris
for endospores. The results show that the incubation conditions (temperature, time, and nutrients) needed for the development of spores for their release into air are different from the conditions that are needed for colony growth only. Additional drying of
M. halophytica
and
T. vulgaris
cultures was needed before spores could be released from the culture. The aerodynamic sizes of the spores, measured with an aerodynamic particle sizer, ranged from 0.57 (
T. vulgaris
) to 1.28 μm (
M. halophytica
). The physical sizes of the spores, when measured with a microscope and an image analysis system, were found to be smaller than previously reported in the literature. The relative recovery of the spores on agar media ranged from 0.5 (
T. vulgaris
) to 35% (
S. albus
). The results indicate that the culturability of the collected airborne actinomycete spores varies widely and is affected by several variables, such as the species and the sampling flow rate. Therefore, alternatives to commonly used cultivation methods need to be developed for the enumeration of actinomycete spores.
Quantitative and Physiological Analyses of Chloride Dependence of Growth of
Halobacillus halophilus
Authors: Roeßler Markus , Müller Volker 
Published: December 2019

ABSTRACT

A quantitative analysis of the Cl
−
dependence of growth of
Halobacillus halophilus
was performed. Optimal growth rates were obtained at Cl
−
concentrations of between 0.5 and 2.0 M, and the final yield was also strictly dependent on the Cl
−
concentration. Br
−
but not I
−
, SO
4
2−
, NO
2
−
, SO
2
−
, OCN
−
, SCN
−
, BO
2
−
, or BrO
3
−
could substitute for Cl
−
. To analyze the function of chloride, chloride concentration was determined. At low external Cl
−
(Cl
e
−
) concentrations, the growth rate was low and Cl
−
was excluded from the cytoplasm; increasing the Cl
e
−
concentration led to an increase in the growth rate and an energy-dependent uptake of Cl
−
, thus decreasing the Cl
e
−
/internal Cl
i
−
gradient from ≥10 at 0.1 M Cl
e
−
to a nearly constant value of 2 at Cl
e
−
concentrations which allowed optimal growth. Two membrane proteins with apparent molecular masses of 31 and 16 kDa which were identified to be specific for Cl
−
-grown cultures are possible candidates for a chloride uptake system.
Interlaboratory Comparison of Methods To Quantify Microsclerotia of
Verticillium dahliae
in Soil
Authors: Termorshuizen A. J. , Davis J. R. , Gort G. , Harris D. C. , Huisman O. C. , Lazarovits G. , Locke T. , Melero Vara J. M. , Mol L. , Paplomatas E. J. , Platt H. W. , Powelson M. , Rouse D. I. , Rowe R. C. , Tsror L. 
Published: December 2019

ABSTRACT

In a comparison of different methods for estimating
Verticillium dahliae
in soil, 14 soil samples were analyzed in a blinded fashion by 13 research groups in seven countries, using their preferred methods. One group analyzed only four samples. Twelve soil samples were naturally infested, and two had known numbers of microsclerotia of
V. dahliae
added to them. In addition, a control was included to determine whether transport had an effect on the results. Results differed considerably among the research groups. There was a 118-fold difference between the groups with the lowest and highest mean estimates. Results of the other groups were evenly distributed between these extremes. In general, methods based on plating dry soil samples gave higher numbers of
V. dahliae
than did plating of an aqueous soil suspension. Recovery of
V. dahliae
from samples with added microsclerotia varied from 0 to 59%. Most of the variability within each analysis was at the petri dish level. The results indicate the necessity to check the performance of detection assays regularly by comparing recoveries with other laboratories, using a common set of soil samples. We conclude that wet plating assays are less accurate than dry plating assays.
Physiological Activity of
Campylobacter jejuni
Far below the Minimal Growth Temperature
Authors: Hazeleger Wilma C. , Wouters Jeroen A. , Rombouts Frank M. , Abee Tjakko 
Published: December 2019

ABSTRACT

The behavior of
Campylobacter jejuni
at environmental temperatures was examined by determining the physiological activities of this human pathogen. The minimal growth temperatures were found to be 32 and 31°C for strains 104 and ATCC 33560, respectively. Both strains exhibited a sudden decrease in growth rate from the maximum to zero within a few degrees not only near the maximal growth temperature but also near the minimal growth temperature. This could be an indication that a temperature-dependent transition in the structure of a key enzyme(s) or regulatory compound(s) determines the minimal growth temperature. Oxygen consumption, catalase activity, ATP generation, and protein synthesis were observed at temperatures as low as 4°C, indicating that vital cellular processes were still functioning. PCR analysis showed that cold shock protein genes, which play a role in low-temperature adaptation in many bacteria, are not present in
C. jejuni
. The fact that chemotaxis and aerotaxis could be observed at all temperatures shows that the pathogen is able to move to favorable places at environmental temperatures, which may have significant implications for the survival of
C. jejuni
in the environment.
A New Genetic Locus in
Sinorhizobium meliloti
Is Involved in Stachydrine Utilization
Authors: Phillips Donald A. , Sande Eve S. , Vriezen J. A. C. , de Bruijn Frans J. , Le Rudulier Daniel , Joseph Cecillia M. 
Published: December 2019

ABSTRACT

Stachydrine, a betaine released by germinating alfalfa seeds, functions as an inducer of nodulation genes, a catabolite, and an osmoprotectant in
Sinorhizobium meliloti
. Two stachydrine-inducible genes were found in
S. meliloti
1021 by mutation with a Tn
5-luxAB
promoter probe. Both mutant strains (S10 and S11) formed effective alfalfa root nodules, but neither grew on stachydrine as the sole carbon and nitrogen source. When grown in the absence or presence of salt stress, S10 and S11 took up [
14
C]stachydrine as well as wild-type cells did, but neither used stachydrine effectively as an osmoprotectant. In the absence of salt stress, both S10 and S11 took up less [
14
C]proline than wild-type cells did. S10 and S11 appeared to colonize alfalfa roots normally in single-strain tests, but when mixed with the wild-type strain, their rhizosphere counts were reduced more than 50% (
P
≤ 0.01) relative to the wild type. These results suggest that stachydrine catabolism contributes to root colonization. DNA sequence analysis identified the mutated locus in S11 as
putA
, and the
luxAB
fusion in that gene was induced by proline as well as stachydrine. DNA that restored the capacity of mutant S10 to catabolize stachydrine contained a new open reading frame,
stcD
. All data are consistent with the concept that
stcD
codes for an enzyme that produces proline by demethylation of
N
-methylproline, a degradation product of stachydrine.
Relatedness of Strains of
Xanthomonas fragariae
by Restriction Fragment Length Polymorphism, DNA-DNA Reassociation, and Fatty Acid Analyses
Authors: Roberts P. D. , Hodge N. C. , Bouzar H. , Jones J. B. , Stall R. E. , Berger R. D. , Chase A. R. 
Published: December 2019

ABSTRACT

The levels of relatedness of strains of
Xanthomonas fragariae
collected over several years from locations in Canada and the United States were compared by determining fatty acid methyl ester profiles, restriction fragment length polymorphisms (RFLP) based on pulsed-field gel electrophoresis (PFGE) analysis, and DNA-DNA reassociation values. Based on qualitative and quantitative differences in fatty acid profiles, the strains were divided into nine groups and four groups by the MIDI “10% rule” and unweighted pair analysis, respectively. Restriction analysis of genomic DNA by PFGE with two endonucleases (
Xba
I and
Spe
I) revealed four distinct profiles. When a third endonuclease (
Vsp
I) was used, one group was divided into three subgroups. The profile of the American Type Culture Collection type strain differed from the profile of every other strain of
X. fragariae
. Considerable diversity was observed within
X. fragariae
, although the majority of the strains represented a clonal population. The four groups based on fatty acid profiles were similar to the four groups based on RFLP, but neither method related groups to the geographic origins of the strains. The DNA-DNA reassociation values were high for representative strains, providing evidence that all of the strains belong to the same species.
Enzymatic Conversion of Glucose to UDP-4-Keto-6-Deoxyglucose in
Streptomyces
spp
Authors: Liu Song Yu , Rosazza John P. N. 
Published: December 2019

ABSTRACT

All of the 2,6-dideoxy sugars contained within the structure of chromomycin A
3
are derived from
d
-glucose. Enzyme assays were used to confirm the presence of hexokinase, phosphoglucomutase, UDPG pyrophosphorylase (UDPGP), and UDPG oxidoreductase (UDPGO), all of which are involved in the pathway of glucose activation and conversion into 2,6-dideoxyhexoses during chromomycin biosynthesis. Levels of the four enzymes in
Streptomyces
spp. cell extracts were correlated with the production of chromomycins. The pathway of sugar activation in
Streptomyces
spp. involves glucose 6-phosphorylation by hexokinase, isomerization to G-1-P catalyzed by phosphoglucomutase, synthesis of UDPG catalyzed by UDPGP, and formation of UDP-4-keto-6-deoxyglucose by UDPGO.
Purification and Substrate Specificities of Two α-l-Arabinofuranosidases fromAspergillus awamoriIFO 4033
Authors: Kaneko Satoshi , Arimoto Mitsue , Ohba Misako , Kobayashi Hideyuki , Ishii Tadashi , Kusakabe Isao 
Published: December 2019

ABSTRACTα-l-Arabinofuranosidases I and II were purified from the culture filtrate ofAspergillus awamoriIFO 4033 and had molecular weights of 81,000 and 62,000 and pIs of 3.3 and 3.6, respectively. Both enzymes had an optimum pH of 4.0 and an optimum temperature of 60°C and exhibited stability at pH values from 3 to 7 and at temperatures up to 60°C. The enzymes released arabinose fromp-nitrophenyl-α-l-arabinofuranoside,O-α-l-arabinofuranosyl-(1→3)-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose, and arabinose-containing polysaccharides but not fromO-β-d-xylopyranosyl-(1→2)-O-α-l-arabinofuranosyl-(1→3)-O-β-d-xylopyranosyl-(1→4)-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose. α-l-Arabinofuranosidase I also released arabinose fromO-β-d-xylopy-ranosyl-(1→4)-[O-α-l-arabinofuranosyl-(1→3)]-O-β-d-xylopyranosyl-(1→4)-d-xylopyranose. However, α-l-arabinofuranosidase II did not readily catalyze this hydrolysis reaction. α-l-Arabinofuranosidase I hydrolyzed all linkages that can occur between two α-l-arabinofuranosyl residues in the following order: (1→5) linkage > (1→3) linkage > (1→2) linkage. α-l-Arabinofuranosidase II hydrolyzed the linkages in the following order: (1→5) linkage > (1→2) linkage > (1→3) linkage. α-l-Arabinofuranosidase I preferentially hydrolyzed the (1→5) linkage of branched arabinotrisaccharide. On the other hand, α-l-arabinofuranosidase II preferentially hydrolyzed the (1→3) linkage in the same substrate. α-l-Arabinofuranosidase I released arabinose from the nonreducing terminus of arabinan, whereas α-l-arabinofuranosidase II preferentially hydrolyzed the arabinosyl side chain linkage of arabinan.
Comparison of a New
Thiomicrospira
Strain from the Mid-Atlantic Ridge with Known Hydrothermal Vent Isolates
Authors: Wirsen C. O. , Brinkhoff T. , Kuever J. , Muyzer G. , Molyneaux S. , Jannasch H. W. 
Published: December 2019

ABSTRACT

A new autotrophic
Thiomicrospira
strain, MA-3, was isolated from the surface of a polymetal sulfide deposit collected at a Mid-Atlantic Ridge hydrothermal vent site. The DNA homology among three vent isolates,
Thiomicrospira crunogena
,
Thiomicrospira
sp. strain L-12, and
Thiomicrospira
sp. strain MA-3, was 99.3% or higher, grouping them as the same species,
T. crunogena
(type strain, ATCC 35932). The fact that
T. crunogena
and
Thiomicrospira
sp. strain L-12 were isolated from Pacific vent sites demonstrates a cosmopolitan distribution of this species.
Activities of
Bacillus thuringiensis
Insecticidal Crystal Proteins Cyt1Aa and Cyt2Aa against Three Species of Sheep Blowfly
Authors: Chilcott Chris N. , Wigley Peter J. , Broadwell Andrew H. , Park Danny J. , Ellar David J. 
Published: December 2019

ABSTRACT

The toxicity of
Bacillus thuringiensis
Cyt1Aa protein to sheep blowfly larvae depends on its solubilization and proteolytic activation. Cyt1Aa crystals were not toxic. Full-length and trypsin-digested Cyt1Aa proteins were toxic to larvae of three species of sheep blowfly. Neither full-length nor trypsin-digested Cyt2A soluble crystal proteins were toxic.
Use of Phospholipid Fatty Acids and Carbon Source Utilization Patterns To Track Microbial Community Succession in Developing Compost
Authors: Carpenter-Boggs Lynne , Kennedy Ann C. , Reganold John P. 
Published: December 2019

ABSTRACT
Carbon source utilization and phospholipid fatty acid analyses were used to track the rapidly changing microbial community in composting dairy waste. Microbial abilities to utilize common plant sugars increased during composting. Community phospholipid profiles changed significantly over time. Phospholipids suggested the presence of more thermophiles and fewer bacteria with continued compost development.
Evidence for Interspecies Gene Transfer in the Evolution of 2,4-Dichlorophenoxyacetic Acid Degraders
Authors: McGowan Catherine , Fulthorpe Roberta , Wright Alice , Tiedje J. M. 
Published: December 2019

ABSTRACT

Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class
Proteobacteria
. To understand the origin of 2,4-D degradation in this diverse collection, the first gene in the 2,4-D pathway,
tfdA
, was sequenced. The sequences fell into three unique classes found in various members of the beta and gamma subgroups of
Proteobacteria
. None of the α-Proteobacteria yielded
tfdA
PCR products. A comparison of the dendrogram of the
tfdA
genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. Only those strains with
tfdA
sequences highly similar to the
tfdA
sequence of strain JMP134 (
tfdA
class I) transferred all the 2,4-D genes and conferred the 2,4-D degradation phenotype to a
Burkholderia cepacia
recipient.
Substrate Selectivity and Biochemical Properties of 4-Hydroxy-2-Keto-Pentanoic Acid Aldolase from
Escherichia coli
Authors: Pollard John R. , Rialland Delphine , Bugg Timothy D. H. 
Published: December 2019

ABSTRACT

4-Hydroxy-2-keto-pentanoic acid aldolase from
Escherichia coli
was identified as a class I aldolase. The enzyme was found to be highly selective for the acetaldehyde acceptor but would accept α-ketobutyric acid or phenylpyruvic acid in place of the pyruvic acid carbonyl donor.
Oxidation of Morphine to 2,2′-Bimorphine by
Cylindrocarpon didymum
Authors: Stabler Peter J. , Bruce Neil C. 
Published: December 2019

ABSTRACT

The oxidation of morphine by whole-cell suspensions and cell extracts of
Cylindrocarpon didymum
gave rise to the formation of 2,2′-bimorphine. The identity of 2,2′-bimorphine was confirmed by mass spectrometry and
1
H nuclear magnetic resonance spectroscopy.
C. didymum
also displayed activity with the morphine analogs hydromorphone, 6-acetylmorphine, and dihydromorphine, but not codeine or diamorphine, suggesting that a phenolic group at C-3 is essential for activity.
Heat Killing of
Bacillus subtilis
Spores in Water Is Not Due to Oxidative Damage
Authors: Setlow Barbara , Setlow Peter 
Published: December 2019

ABSTRACT

The heat resistance of wild-type spores of
Bacillus subtilis
or spores (termed α
−
β
−
) lacking DNA protective α/β-type small, acid-soluble spore proteins was not altered by anaerobiosis or high concentrations of the free radical scavenging agents ethanethiol and ethanedithiol. Heat-killed wild-type and α
−
β
−
spores exhibited no increase in either protein carbonyl content or oxidized bases in DNA. These data strongly suggest that oxidative damage to spore macromolecules does not contribute significantly to spore killing by heat.
Bacteriophage Diversity in the North Sea
Authors: Wichels Antje , Biel Stefan S. , Gelderblom Hans R. , Brinkhoff Thorsten , Muyzer Gerard , Schütt Christian 
Published: December 2019

ABSTRACT

In recent years interest in bacteriophages in aquatic environments has increased. Electron microscopy studies have revealed high numbers of phage particles (10
4
to 10
7
particles per ml) in the marine environment. However, the ecological role of these bacteriophages is still unknown, and the role of the phages in the control of bacterioplankton by lysis and the potential for gene transfer are disputed. Even the basic questions of the genetic relationships of the phages and the diversity of phage-host systems in aquatic environments have not been answered. We investigated the diversity of 22 phage-host systems after 85 phages were collected at one station near a German island, Helgoland, located in the North Sea. The relationships among the phages were determined by electron microscopy, DNA-DNA hybridization, and host range studies. On the basis of morphology, 11 phages were assigned to the virus family
Myoviridae
, 7 phages were assigned to the family
Siphoviridae
, and 4 phages were assigned to the family
Podoviridae
. DNA-DNA hybridization confirmed that there was no DNA homology between phages belonging to different families. We found that the 22 marine bacteriophages belonged to 13 different species. The host bacteria were differentiated by morphological and physiological tests and by 16S ribosomal DNA sequencing. All of the bacteria were gram negative, facultatively anaerobic, motile, and coccoid. The 16S rRNA sequences of the bacteria exhibited high levels of similarity (98 to 99%) with the sequences of organisms belonging to the genus
Pseudoalteromonas
, which belongs to the γ subdivision of the class
Proteobacteria
.