bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of
Cryptosporidium
Parasites Based on the Small-Subunit rRNA Gene Locus
Authors: Xiao Lihua , Escalante Lillian , Yang Chunfu , Sulaiman Irshad , Escalante Anannias A. , Montali Richard J. , Fayer Ronald , Lal Altaf A. 
Published: December 2019

ABSTRACT

Biological data support the hypothesis that there are multiple species in the genus
Cryptosporidium
, but a recent analysis of the available genetic data suggested that there is insufficient evidence for species differentiation. In order to resolve the controversy in the taxonomy of this parasite genus, we characterized the small-subunit rRNA genes of
Cryptosporidium parvum
,
Cryptosporidium baileyi
,
Cryptosporidium muris
, and
Cryptosporidium serpentis
and performed a phylogenetic analysis of the genus
Cryptosporidium
. Our study revealed that the genus
Cryptosporidium
contains the phylogenetically distinct species
C. parvum
,
C. muris
,
C. baileyi
, and
C. serpentis
, which is consistent with the biological characteristics and host specificity data. The
Cryptosporidium
species formed two clades, with
C. parvum
and
C. baileyi
belonging to one clade and
C. muris
and
C. serpentis
belonging to the other clade. Within
C. parvum
, human genotype isolates and guinea pig isolates (known as
Cryptosporidium wrairi
) each differed from bovine genotype isolates by the nucleotide sequence in four regions. A
C. muris
isolate from cattle was also different from parasites isolated from a rock hyrax and a Bactrian camel. Minor differences were also detected between
C. serpentis
isolates from snakes and lizards. Based on the genetic information, a species- and strain-specific PCR-restriction fragment length polymorphism diagnostic tool was developed.
The Alkene Monooxygenase from
Xanthobacter
Strain Py2 Is Closely Related to Aromatic Monooxygenases and Catalyzes Aromatic Monohydroxylation of Benzene, Toluene, and Phenol
Authors: Zhou Ning-Yi , Jenkins Alister , Chan Kwo Chion Chan K. N. , Leak David J. 
Published: December 2019

ABSTRACT

The genes encoding the six polypeptide components of the alkene monooxygenase from
Xanthobacter
strain Py2 (Xamo) have been located on a 4.9-kb fragment of chromosomal DNA previously cloned in cosmid pNY2. Sequencing and analysis of the predicted amino acid sequences indicate that the components of Xamo are homologous to those of the aromatic monooxygenases, toluene 2-, 3-, and 4-monooxygenase and benzene monooxygenase, and that the gene order is identical. The genes and predicted polypeptides are
aamA
, encoding the 497-residue oxygenase α-subunit (XamoA);
aamB
, encoding the 88-residue oxygenase γ-subunit (XamoB);
aamC
, encoding the 122-residue ferredoxin (XamoC);
aamD
, encoding the 101-residue coupling or effector protein (XamoD);
aamE
, encoding the 341-residue oxygenase β-subunit (XamoE); and
aamF
, encoding the 327-residue reductase (XamoF). A sequence with >60% concurrence with the consensus sequence of ς
54
(RpoN)-dependent promoters was identified upstream of the
aamA
gene. Detailed comparison of XamoA with the oxygenase α-subunits from aromatic monooxygenases, phenol hydroxylases, methane monooxygenase, and the alkene monooxygenase from
Rhodococcus rhodochrous
B276 showed that, despite the overall similarity to the aromatic monooxygenases, XamoA has some distinctive characteristics of the oxygenases which oxidize aliphatic, and particularly alkene, substrates. On the basis of the similarity between Xamo and the aromatic monooxygenases,
Xanthobacter
strain Py2 was tested and shown to oxidize benzene, toluene, and phenol, while the alkene monooxygenase-negative mutants NZ1 and NZ2 did not. Benzene was oxidized to phenol, which accumulated transiently before being further oxidized. Toluene was oxidized to a mixture of
o
-,
m
-, and
p
-cresols (39.8, 18, and 41.7%, respectively) and a small amount (0.5%) of benzyl alcohol, none of which were further oxidized. In growth studies
Xanthobacter
strain Py2 was found to grow on phenol and catechol but not on benzene or toluene; growth on phenol required a functional alkene monooxygenase. However, there is no evidence of genes encoding steps in the metabolism of catechol in the vicinity of the
aam
gene cluster. This suggests that the inducer specificity of the alkene monooxygenase may have evolved to benefit from the naturally broad substrate specificity of this class of monooxygenase and the ability of the host strain to grow on catechol.
Ferrioxamine-Mediated Iron(III) Utilization bySalmonella enterica
Authors: Kingsley Robert A. , Reissbrodt Rolf , Rabsch Wolfgang , Ketley Julian M. , Tsolis Renée M. , Everest Paul , Dougan Gordon , Bäumler Andreas J. , Roberts Mark , Williams Peter H. 
Published: December 2019

ABSTRACTUtilization of ferrioxamines as sole sources of iron distinguishesSalmonella entericaserotypes Typhimurium and Enteritidis from a number of related species, includingEscherichia coli. Ferrioxamine supplements have therefore been used in preenrichment and selection media to increase the bacterial growth rate while selectivity is maintained. We characterized the determinants involved in utilization of ferrioxamines B, E, and G byS. entericaserotype Typhimurium by performing siderophore cross-feeding bioassays. Transport of all three ferric siderophores across the outer membrane was dependent on the FoxA receptor encoded by the Fur-repressiblefoxAgene. However, only the transport of ferrioxamine G was dependent on the energy-transducing protein TonB, since growth stimulation of atonBstrain by ferrioxamines B and E was observed, albeit at lower efficiencies than in the parental strain. Transport across the inner membrane was dependent on the periplasmic binding protein-dependent ABC transporter complex comprising FhuBCD, as has been reported for other hydroxamate siderophores of enteric bacteria. The distribution of thefoxAgene in the genusSalmonella, as indicated by DNA hybridization studies and correlated with the ability to utilize ferrioxamine E, was restricted to subspecies I, II, and IIIb, and this gene was absent from subspecies IIIa, IV, VI, and VII (formerly subspecies IV) andSalmonella bongori(formerly subspecies V).S. entericaserotype Typhimurium mutants with either a transposon insertion or a defined nonpolar frameshift (+2) mutation in thefoxAgene were not able to utilize any of the three ferrioxamines tested. A strain carrying the nonpolarfoxAmutation exhibited a significantly reduced ability to colonize rabbit ileal loops compared to thefoxA+parent. In addition, afoxAmutant was markedly attenuated in mice inoculated by either the intragastric or intravenous route. Mice inoculated with thefoxAmutant were protected against subsequent challenge by thefoxA+parent strain.
High-Rate Anaerobic Treatment of Wastewater at Low Temperatures
Authors: Lettinga Gatze , Rebac Salih , Parshina Sofia , Nozhevnikova Alla , van Lier Jules B. , Stams Alfons J. M. 
Published: December 2019

ABSTRACTAnaerobic treatment of a volatile fatty acid (VFA) mixture was investigated under psychrophilic (3 to 8°C) conditions in two laboratory-scale expanded granular sludge bed reactor stages in series. The reactor system was seeded with mesophilic methanogenic granular sludge and fed with a mixture of VFAs. Good removal of fatty acids was achieved in the two-stage system. Relative high levels of propionate were present in the effluent of the first stage, but propionate was efficiently removed in the second stage, where a low hydrogen partial pressure and a low acetate concentration were advantageous for propionate oxidation. The specific VFA-degrading activities of the sludge in each of the modules doubled during system operation for 150 days, indicating a good enrichment of methanogens and proton-reducing acetogenic bacteria at such low temperatures. The specific degradation rates of butyrate, propionate, and the VFA mixture amounted to 0.139, 0.110, and 0.214 g of chemical oxygen demand g of volatile suspended solids−1day−1, respectively. The biomass which was obtained after 1.5 years still had a temperature optimum of between 30 and 40°C.
Real-Time Monitoring of
Escherichia coli
O157:H7 Adherence to Beef Carcass Surface Tissues with a Bioluminescent Reporter
Authors: Siragusa Gregory R. , Nawotka Kevin , Spilman Stanley D. , Contag Pamela R. , Contag Christopher H. 
Published: December 2019

ABSTRACT

A method for studying bacteria that are attached to carcass surfaces would eliminate the need for exogenous sampling and would facilitate understanding the interaction of potential human food-borne pathogens with food animal tissue surfaces. We describe such a method in which we used a bioluminescent reporter strain of
Escherichia coli
O157:H7 that was constructed by transformation with plasmid pCGLS1, an expression vector that contains a complete bacterial luciferase (
lux
) operon. Beef carcass surface tissues were inoculated with the bioluminescent strain, and adherent bacteria were visualized in real time by using a sensitive photon-counting camera to obtain in situ images. The reporter strain was found to luminesce from the tissue surfaces whether it was inoculated as a suspension in buffer or as a suspension in a bovine fecal slurry. With this method, areas of tissues inoculated with the reporter strain could be studied without obtaining, excising, homogenizing, and culturing multiple samples from the tissue surface. Use of the complete
lux
operon as the bioluminescent reporter eliminated the need to add exogenous substrate. This allowed detection and quantitation of bacterial inocula and rapid evaluation of adherence of a potential human pathogen to tissue surfaces. Following simple water rinses of inoculated carcass tissues, the attachment duration varied with different carcass surface types. On average, the percent retention of bioluminescent signal from the reporter strain was higher on lean fascia-covered tissue (54%) than on adipose fascia-covered tissue (18%) following water washing of the tissues. Bioluminescence and culture-derived viable bacterial counts were highly correlated (
r
2
= 0.98). Real-time assessment of microbial attachment to this complex menstruum should facilitate evaluation of carcass decontamination procedures and mechanistic studies of microbial contamination of beef carcass tissues.
Genomic Relationships between
Enterococcus faecium
Strains from Different Sources and with Different Antibiotic Resistance Profiles Evaluated by Restriction Endonuclease Analysis of Total Chromosomal DNA Using
Eco
RI and
Pvu
II
Authors: Quednau M. , Ahrné S. , Molin G. 
Published: December 2019

ABSTRACT

Forty-seven
Enterococcus faecium
strains from different sources were evaluated by restriction endonuclease analysis (REA) of total chromosomal DNA. Strains from chicken, pork, and humans were clearly divided into separate clusters, whereas strains from different countries, strains with different antibiotic resistance profiles, or clinical and healthy-subject strains were not.
Different Strategies for Molecular Differentiation of
Mycobacterium bovis
Strains Isolated in Sardinia, Italy
Authors: Sechi Leonardo A. , Leori Guido , Lollai Stefano A. , Duprè Ilaria , Molicotti Paola , Fadda Giovanni , Zanetti Stefania 
Published: December 2019

ABSTRACT

Different genetic markers were used to analyze 22
Mycobacterium bovis
strains isolated from cattle in Sardinia and one human isolate. IS
6110
DNA fingerprinting differentiated the strains into six patterns, whereas with enterobacterial repetitive consensus sequence primers produced seven clusters. PCR ribotyping followed by digestion with
Hae
III and
Pvu
II produced five and seven patterns, respectively. PCR with the (GTG)
5
oligonucleotide primer showed the best discriminatory power, generating eight clusters among the strains analyzed.
Enhanced Degradation of Polyvinyl Alcohol by
Pycnoporus cinnabarinus
after Pretreatment with Fenton’s Reagent
Authors: Larking Daniel M. , Crawford Russell J. , Christie Gregor B. Y. , Lonergan Greg T. 
Published: December 2019

ABSTRACT

Degradation of polyvinyl alcohol (PVA) was investigated by using a combination of chemical treatment with Fenton’s reagent and biological degradation with the white rot fungus
Pycnoporus cinnabarinus
. Inclusion of the chemical pretreatment resulted in greater degradation of PVA than the degradation observed when biological degradation alone was used.
Activation and Inactivation of
Pseudomonas stutzeri
Methylbenzene Catabolism Pathways Mediated by a Transposable Element
Authors: Bolognese Fabrizio , di Lecce Cinzia , Galli Enrica , Barbieri Paola 
Published: December 2019

ABSTRACT

The arrangement of the genes involved in
o
-xylene,
m
-xylene, and
p
-xylene catabolism was investigated in three
Pseudomonas stutzeri
strains: the wild-type strain OX1, which is able to grow on
o
-xylene but not on the
meta
and
para
isomers; the mutant M1, which grows on
m
-xylene and
p
-xylene but is unable to utilize the
ortho
isomer; and the revertant R1, which can utilize all the three isomers of xylene. A 3-kb insertion sequence (IS) termed IS
Ps1
, which inactivates the
m
-xylene and
p
-xylene catabolic pathway in
P. stutzeri
OX1 and the
o
-xylene catabolic genes in
P. stutzeri
M1, was detected. No IS was detected in the corresponding catabolic regions of the
P. stutzeri
R1 genome. IS
Ps1
is present in several copies in the genomes of the three strains. It is flanked by 24-bp imperfect inverted repeats, causes the direct duplication of 8 bp in the target DNA, and seems to be related to the ISL3 family.
Feed Deprivation Affects Crop Environment and Modulates
Salmonella enteritidis
Colonization and Invasion of Leghorn Hens
Authors: Durant Juliet A. , Corrier Donald E. , Byrd J. Allen , Stanker Larry H. , Ricke Steven C. 
Published: December 2019

ABSTRACT

Leghorn hens over 50 weeks of age were assigned to two treatment groups designated as either unmolted controls or molted. A forced molt was induced by a 9-day feed withdrawal, and each hen was challenged orally with 10
5
Salmonella enteritidis
organisms on day 4 of feed withdrawal. On days 4 and 9 of molt, the numbers of lactobacilli and the concentrations of lactate, acetate, propionate, and butyrate, and total volatile fatty acids in the crops decreased while crop pH increased significantly (
P
< 0.05) in the molted hens compared to the controls.
S. enteritidis
crop and cecal colonization, in addition to spleen and liver invasion, increased significantly (
P
< 0.05) in the molted hens compared to the controls. The invasive phenotype of
Salmonella
spp. is complex and requires several virulence genes which are regulated by the transcriptional activator HilA. Samples of the crop contents from the molted and unmolted birds were pooled separately, centrifuged, and filter sterilized. The sterile crop contents were then used to measure the expression of
hilA
. By using a
lacZY
transcriptional fusion to the
hilA
gene in
S. enteritidis
, we found that
hilA
expression was 1.6- to 2.1-fold higher in the crop contents from molted birds than in those from control birds in vitro. The results of the study suggest that the changes in the microenvironment of the crop caused by feed deprivation are important regulators of
S. enteritidis
survival and influence the susceptibility of molted hens to
S. enteritidis
infections. Furthermore, our in vitro results on the expression of
hilA
suggest that the change in crop environment during feed withdrawal has the potential to significantly affect virulence by increasing the expression of genes necessary for intestinal invasion.
Characterization of Six Bacteriophages ofSerratia liquefaciensCP6 Isolated from the Sugar Beet Phytosphere
Authors: Ashelford Kevin E. , Fry John C. , Bailey Mark J. , Jeffries Aaron R. , Day Martin J. 
Published: December 2019

ABSTRACTSix phages (ΦCP6-1 to ΦCP6-6) that are commonly found in the phytosphere of sugar beet (Beta vulgarisvar. Amethyst) were investigated, and their relative impacts on their host (Serratia liquefaciensCP6) were compared. There were fundamental differences between the two most abundant predators of CP6 (ΦCP6-1 and ΦCP6-4). Like ΦCP6-2 and ΦCP6-5, ΦCP6-1 belonged to the familySiphoviridae, while ΦCP6-4 exhibited the morphology of the familyPodoviridae. The other phages were members of the familyMyoviridae. DNA-DNA cross-hybridization revealed that ΦCP6-1 and ΦCP6-4 had little common DNA, although all of the other phages exhibited some genetic similarity. Like ΦCP6-2, ΦCP6-3, and ΦCP6-5, ΦCP6-1 was capable of forming a lysogenic association with its host, while ΦCP6-4 and ΦCP6-6 appeared to be entirely virulent. Single-step growth curve experiments revealed that ΦCP6-4 had a much shorter latent period and a smaller burst size than ΦCP6-1. Also, ΦCP6-1 could transduce a number of host chromosomal markers with transfer frequencies of 2.9 × 10−9to 3.9 × 10−7, whereas ΦCP6-4 could not transduceS. liquefaciensCP6 genes. When viewed in the context of the strikingly different temporal niches of these phages, our data provide an insight into how bacteriophage interactions with their hosts might reflect the natural ecology of bacteriophages. Our data also illustrate how the potential for gene transfer changes over time in an environment that supports several different phages.
Cell-Wall-Bound Proteinase of
Lactobacillus delbrueckii
subsp.
lactis
ACA-DC 178: Characterization and Specificity for β-Casein
Authors: Tsakalidou E. , Anastasiou R. , Vandenberghe I. , van Beeumen J. , Kalantzopoulos G. 
Published: December 2019

ABSTRACT

Lactobacillus delbrueckii
subsp.
lactis
ACA-DC 178, which was isolated from Greek Kasseri cheese, produces a cell-wall-bound proteinase. The proteinase was removed from the cell envelope by washing the cells with a Ca
2+
-free buffer. The crude proteinase extract shows its highest activity at pH 6.0 and 40°C. It is inhibited by phenylmethylsulfonyl fluoride, showing that the enzyme is a serine-type proteinase. Considering the substrate specificity, the enzyme is similar to the lactococcal P
I
-type proteinases, since it hydrolyzes β-casein mainly and α- and κ-caseins to a much lesser extent. The cell-wall-bound proteinase from
L. delbrueckii
subsp.
lactis
ACA-DC 178 liberates four main peptides from β-casein, which have been identified.
Antagonism between Cry1Ac1 and Cyt1A1 Toxins of
Bacillus thuringiensis
Authors: del Rincón-Castro M. Cristina , Barajas-Huerta José , Ibarra Jorge E. 
Published: December 2019

ABSTRACT

Most strains of the insecticidal bacterium
Bacillus thuringiensis
have a combination of different protoxins in their parasporal crystals. Some of the combinations clearly interact synergistically, like the toxins present in
B. thuringiensis
subsp.
israelensis
. In this paper we describe a novel joint activity of toxins from different strains of
B. thuringiensis
. In vitro bioassays in which we used pure, trypsin-activated Cry1Ac1 proteins from
B. thuringiensis
subsp.
kurstaki
, Cyt1A1 from
B. thuringiensis
subsp.
israelensis
, and
Trichoplusia ni
BTI-Tn5B1-4 cells revealed contrasting susceptibility characteristics. The 50% lethal concentrations (LC
50
s) were estimated to be 4,967 of Cry1Ac1 per ml of medium and 11.69 ng of Cyt1A1 per ml of medium. When mixtures of these toxins in different proportions were assayed, eight different LC
50
s were obtained. All of these LC
50
s were significantly higher than the expected LC
50
s of the mixtures. In addition, a series of bioassays were performed with late first-instar larvae of the cabbage looper and pure Cry1Ac1 and Cyt1A1 crystals, as well as two different combinations of the two toxins. The estimated mean LC
50
of Cry1Ac1 was 2.46 ng/cm
2
of diet, while Cyt1A1 crystals exhibited no toxicity, even at very high concentrations. The estimated mean LC
50
s of Cry1Ac1 crystals were 15.69 and 19.05 ng per cm
2
of diet when these crystals were mixed with 100 and 1,000 ng of Cyt1A1 crystals per cm
2
of diet, respectively. These results indicate that there is clear antagonism between the two toxins both in vitro and in vivo. Other joint-action analyses corroborated these results. Although this is the second report of antagonism between
B. thuringiensis
toxins, our evidence is the first evidence of antagonism between toxins from different subspecies of
B. thuringiensis
(
B. thuringiensis
subsp.
kurstaki
and
B. thuringiensis
subsp.
israelensis
) detected both in vivo and in vitro. Some possible explanations for this relationship are discussed.
Occurrence of Choline and Glycine Betaine Uptake and Metabolism in the Family
Rhizobiaceae
and Their Roles in Osmoprotection
Authors: Boncompagni Eric , Østerås Magne , Poggi Marie-Christine , le Rudulier Daniel 
Published: December 2019

ABSTRACT

The role of glycine betaine and choline in osmoprotection of various
Rhizobium
,
Sinorhizobium
,
Mesorhizobium
,
Agrobacterium
, and
Bradyrhizobium
reference strains which display a large variation in salt tolerance was investigated. When externally provided, both compounds enhanced the growth of
Rhizobium tropici
,
Sinorhizobium meliloti
,
Sinorhizobium fredii
,
Rhizobium galegae
,
Agrobacterium tumefaciens
,
Mesorhizobium loti
, and
Mesorhizobium huakuii
, demonstrating their utilization as osmoprotectants. However, both compounds were inefficient for the most salt-sensitive strains, such as
Rhizobium leguminosarum
(all biovars),
Agrobacterium rhizogenes
,
Rhizobium etli
, and
Bradyrhizobium japonicum
. Except for
B. japonicum
, all strains exhibit transport activity for glycine betaine and choline. When the medium osmolarity was raised, choline uptake activity was inhibited, whereas glycine betaine uptake was either increased in
R. leguminosarum
and
S. meliloti
or, more surprisingly, reduced in
R. tropici
,
S. fredii
, and
M. loti
. The transport of glycine betaine was increased by growing the cells in the presence of the substrate. With the exception of
B. japonicum
, all strains were able to use glycine betaine and choline as sole carbon and nitrogen sources. This catabolic function, reported for only a few soil bacteria, could increase competitiveness of rhizobial species in the rhizosphere. Choline dehydrogenase and betaine-aldehyde dehydrogenase activities were present in the cells of all strains with the exception of
M. huakuii
and
B. japonicum
. The main physiological role of glycine betaine in the family
Rhizobiaceae
seems to be as an energy source, while its contribution to osmoprotection is restricted to certain strains.