bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Bacteroidales Microbial Source Tracking To Monitor Fecal Contamination in Fresh Produce Production
Authors: Ravaliya Kruti , Gentry-Shields Jennifer , Garcia Santos , Heredia Norma , Fabiszewski de Aceituno Anna , Bartz Faith E. , Leon Juan S. , Jaykus Lee-Ann 
Published: November 2013

ABSTRACT

In recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. Most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. Microbial source tracking (MST) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. This study investigated the utility of an MST method based on
Bacteroidales
16S rRNA gene sequences as a means of identifying potential fecal contamination, and its source, in the fresh produce production environment. The method was applied to rinses of fresh produce, source and irrigation waters, and harvester hand rinses collected over the course of 1 year from nine farms (growing tomatoes, jalapeño peppers, and cantaloupe) in Northern Mexico. Of 174 samples, 39% were positive for a universal
Bacteroidales
marker (AllBac), including 66% of samples from cantaloupe farms (3.6 log
10
genome equivalence copies [GEC]/100 ml), 31% of samples from tomato farms (1.7 log
10
GEC/100 ml), and 18% of samples from jalapeño farms (1.5 log
10
GEC/100 ml). Of 68 AllBac-positive samples, 46% were positive for one of three human-specific markers, and none were positive for a bovine-specific marker. There was no statistically significant correlation between
Bacteroidales
and generic
Escherichia coli
across all samples. This study provides evidence that
Bacteroidales
markers may serve as alternative indicators for fecal contamination in fresh produce production, allowing for determination of both general contamination and that derived from the human host.
PhaM Is the Physiological Activator of Poly(3-Hydroxybutyrate) (PHB) Synthase (PhaC1) in Ralstonia eutropha
Authors: Pfeiffer Daniel , Jendrossek Dieter 
Published: November 2013

ABSTRACT

Poly(3-hydroxybutyrate) (PHB) synthase (PhaC1) is the key enzyme of PHB synthesis in
Ralstonia eutropha
and other PHB-accumulating bacteria and catalyzes the polymerization of 3-hydroxybutyryl-CoA to PHB. Activity assays of
R. eutropha
PHB synthase are characterized by the presence of lag phases and by low specific activity. It is assumed that the lag phase is caused by the time necessary to convert the inactive PhaC1 monomer into the active dimeric form by an unknown priming process. The lag phase can be reduced by addition of nonionic detergents such as hecameg [6-
O
-(
N
-heptyl-carbamoyl)-methyl-α-
d
-glucopyranoside], which apparently accelerates the formation of PhaC1 dimers. We identified the PHB granule-associated protein (PGAP) PhaM as the natural primer (activator) of PHB synthase activity. PhaM was recently discovered as a novel type of PGAP with multiple functions in PHB metabolism. Addition of PhaM to PHB synthase assays resulted in immediate polymerization of 3HB coenzyme A with high specific activity and without a significant lag phase. The effect of PhaM on (i) PhaC1 activity, (ii) oligomerization of PhaC1, (iii) complex formation with PhaC1, and (iv) PHB granule formation
in vitro
and
in vivo
was shown by cross-linking experiments of purified proteins (PhaM, PhaC1) with glutardialdehyde, by size exclusion chromatography, and by fluorescence microscopic detection of
de novo
-synthesized PHB granules.
Newly Cultured Bacteria with Broad Diversity Isolated from Eight-Week Continuous Culture Enrichments of Cow Feces on Complex Polysaccharides
Authors: Ziemer Cherie J. 
Published: November 2013

ABSTRACT

One of the functions of the mammalian large intestinal microbiota is the fermentation of plant cell wall components. In ruminant animals, the majority of their nutrients are obtained via pregastric fermentation; however, up to 20% can be recovered from microbial fermentation in the large intestine. Eight-week continuous culture enrichments of cattle feces with cellulose and xylan-pectin were used to isolate bacteria from this community. A total of 459 bacterial isolates were classified phylogenetically using 16S rRNA gene sequencing. Six phyla were represented:
Firmicutes
(51.9%),
Bacteroidetes
(30.9%),
Proteobacteria
(11.1%),
Actinobacteria
(3.5%),
Synergistetes
(1.5%), and
Fusobacteria
(1.1%). The majority of bacterial isolates had <98.5% identity to cultured bacteria with sequences in the Ribosomal Database Project and thus represent new species and/or genera. Within the
Firmicutes
isolates, most were classified in the families
Lachnospiraceae
,
Ruminococcaceae
,
Erysipelotrichaceae
, and
Clostridiaceae
I. The majority of the
Bacteroidetes
were most closely related to
Bacteroides thetaiotaomicron
,
B. ovatus
, and
B. xylanisolvens
and members of the
Porphyromonadaceae
family. Many of the
Firmicutes
and
Bacteroidetes
isolates were related to species demonstrated to possess enzymes which ferment plant cell wall components; the others were hypothesized to cross-feed these bacteria. The microbial communities that arose in these enrichment cultures had broad bacterial diversity. With over 98% of the isolates not represented as previously cultured, there are new opportunities to study the genomic and metabolic capacities of these members of the complex intestinal microbiota.
Phenotypic Effect of “Candidatus Rickettsiella viridis,” a Facultative Symbiont of the Pea Aphid (Acyrthosiphon pisum), and Its Interaction with a Coexisting Symbiont
Authors: Tsuchida Tsutomu , Koga Ryuichi , Fujiwara Akiko , Fukatsu Takema 
Published: November 2013

ABSTRACT

A gammaproteobacterial facultative symbiont of the genus
Rickettsiella
was recently identified in the pea aphid,
Acyrthosiphon pisum
. Infection with this symbiont altered the color of the aphid body from red to green, potentially affecting the host's ecological characteristics, such as attractiveness to different natural enemies. In European populations of
A. pisum
, the majority of
Rickettsiella
-infected aphids also harbor another facultative symbiont, of the genus
Hamiltonella
. We investigated this
Rickettsiella
symbiont for its interactions with the coinfecting
Hamiltonella
symbiont, its phenotypic effects on
A. pisum
with and without
Hamiltonella
coinfection, and its infection prevalence in
A. pisum
populations. Histological analyses revealed that coinfecting
Rickettsiella
and
Hamiltonella
exhibited overlapping localizations in secondary bacteriocytes, sheath cells, and hemolymph, while
Rickettsiella
-specific localization was found in oenocytes.
Rickettsiella
infections consistently altered hosts' body color from red to green, where the greenish hue was affected by both host and symbiont genotypes.
Rickettsiella
-
Hamiltonella
coinfections also changed red aphids to green; this greenish hue tended to be enhanced by
Hamiltonella
coinfection. With different host genotypes,
Rickettsiella
infection exhibited either weakly beneficial or nearly neutral effects on host fitness, whereas
Hamiltonella
infection and
Rickettsiella
-
Hamiltonella
coinfection had negative effects. Despite considerable frequencies of
Rickettsiella
infection in European and North American
A. pisum
populations, no
Rickettsiella
infection was detected among 1,093 insects collected from 14 sites in Japan. On the basis of these results, we discuss possible mechanisms for the interaction of
Rickettsiella
with other facultative symbionts, their effects on their hosts' phenotypes, and their persistence in natural host populations. We propose the designation “
Candidatus
Rickettsiella viridis” for the symbiont.
Polycyclic Aromatic Hydrocarbon Degradation of Phytoplankton-Associated Arenibacter spp. and Description of Arenibacter algicola sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium
Authors: Gutierrez Tony , Rhodes Glenn , Mishamandani Sara , Berry David , Whitman William B. , Nichols Peter D. , Semple Kirk T. , Aitken Michael D. 
Published: November 2013

ABSTRACT

Pyrosequencing of the bacterial community associated with a cosmopolitan marine diatom during enrichment with crude oil revealed several
Arenibacter
phylotypes, of which one (OTU-202) had become significantly enriched by the oil. Since members of the genus
Arenibacter
have not been previously shown to degrade hydrocarbons, we attempted to isolate a representative strain of this genus in order to directly investigate its hydrocarbon-degrading potential. Based on 16S rRNA sequencing, one isolate (designated strain TG409
T
) exhibited >99% sequence identity to three type strains of this genus. On the basis of phenotypic and genotypic characteristics, strain TG409
T
represents a novel species in the genus
Arenibacter
, for which the name
Arenibacter algicola
sp. nov. is proposed. We reveal for the first time that polycyclic aromatic hydrocarbon (PAH) degradation is a shared phenotype among members of this genus, indicating that it could be used as a taxonomic marker for this genus. Kinetic data for PAH mineralization rates showed that naphthalene was preferred to phenanthrene, and its mineralization was significantly enhanced in the presence of glass wool (a surrogate for diatom cell surfaces). During enrichment on hydrocarbons, strain TG409
T
emulsified
n
-tetradecane and crude oil, and cells were found to be preferentially attached to oil droplets, indicating an ability by the strain to express cell surface amphiphilic substances (biosurfactants or bioemulsifiers) as a possible strategy to increase the bioavailability of hydrocarbons. This work adds to our growing knowledge on the diversity of bacterial genera in the ocean contributing to the degradation of oil contaminants and of hydrocarbon-degrading bacteria found living in association with marine eukaryotic phytoplankton.
Rumen Methanogenic Genotypes Differ in Abundance According to Host Residual Feed Intake Phenotype and Diet Type
Authors: Carberry CIara A. , Waters Sinead M. , Kenny David A. , Creevey Christopher J. 
Published: November 2013

ABSTRACT

Methane is an undesirable end product of rumen fermentative activity because of associated environmental impacts and reduced host feed efficiency. Our study characterized the rumen microbial methanogenic community in beef cattle divergently selected for phenotypic residual feed intake (RFI) while offered a high-forage (HF) diet followed by a low-forage (LF) diet. Rumen fluid was collected from 14 high-RFI (HRFI) and 14 low-RFI (LRFI) animals at the end of both dietary periods. 16S rRNA gene clone libraries were used, and methanogen-specific tag-encoded pyrosequencing was carried out on the samples. We found that
Methanobrevibacter
spp. are the dominant methanogens in the rumen, with
Methanobrevibacter smithii
being the most abundant species. Differences in the abundance of
Methanobrevibacter smithii
and
Methanosphaera stadtmanae
genotypes were detected in the rumen of animals offered the LF compared to the HF diet while the abundance of
Methanobrevibacter smithii
genotypes was different between HRFI and LRFI animals irrespective of diet. Our results demonstrate that while a core group of methanogen operational taxonomic units (OTUs) exist across diet and phenotype, significant differences were observed in the distribution of genotypes within those OTUs. These changes in genotype abundance may contribute to the observed differences in methane emissions between efficient and inefficient animals.
Substrate Promiscuity: AglB, the Archaeal Oligosaccharyltransferase, Can Process a Variety of Lipid-Linked Glycans
Authors: Cohen-Rosenzweig Chen , Guan Ziqiang , Shaanan Boaz , Eichler Jerry 
Published: November 2013

ABSTRACT

Across evolution, N-glycosylation involves oligosaccharyltransferases that transfer lipid-linked glycans to selected Asn residues of target proteins. While these enzymes catalyze similar reactions in each domain, differences exist in terms of the chemical composition, length and degree of phosphorylation of the lipid glycan carrier, the sugar linking the glycan to the lipid carrier, and the composition and structure of the transferred glycan. To gain insight into how oligosaccharyltransferases cope with such substrate diversity, the present study analyzed the archaeal oligosaccharyltransferase AglB from four haloarchaeal species. Accordingly, it was shown that despite processing distinct lipid-linked glycans in their native hosts, AglB from
Haloarcula marismortui
,
Halobacterium salinarum
, and
Haloferax mediterranei
could readily replace their counterpart from
Haloferax volcanii
when introduced into
Hfx. volcanii
cells deleted of
aglB
. As the four enzymes show significant sequence and apparently structural homology, it appears that the functional similarity of the four AglB proteins reflects the relaxed substrate specificity of these enzymes. Such demonstration of AglB substrate promiscuity is important not only for better understanding of N-glycosylation in
Archaea
and elsewhere but also for efforts aimed at transforming
Hfx. volcanii
into a glycoengineering platform.
Biochemical and Structural Studies of NADH-Dependent FabG Used To Increase the Bacterial Production of Fatty Acids under Anaerobic Conditions
Authors: Javidpour Pouya , Pereira Jose H. , Goh Ee-Been , McAndrew Ryan P. , Ma Suzanne M. , Friedland Gregory D. , Keasling Jay D. , Chhabra Swapnil R. , Adams Paul D. , Beller Harry R. 
Published: November 2013

ABSTRACT

Major efforts in bioenergy research have focused on producing fuels that can directly replace petroleum-derived gasoline and diesel fuel through metabolic engineering of microbial fatty acid biosynthetic pathways. Typically, growth and pathway induction are conducted under aerobic conditions, but for operational efficiency in an industrial context, anaerobic culture conditions would be preferred to obviate the need to maintain specific dissolved oxygen concentrations and to maximize the proportion of reducing equivalents directed to biofuel biosynthesis rather than ATP production. A major concern with fermentative growth conditions is elevated NADH levels, which can adversely affect cell physiology. The purpose of this study was to identify homologs of
Escherichia coli
FabG, an essential reductase involved in fatty acid biosynthesis, that display a higher preference for NADH than for NADPH as a cofactor. Four potential NADH-dependent FabG variants were identified through bioinformatic analyses supported by crystallographic structure determination (1.3- to 2.0-Å resolution).
In vitro
assays of cofactor (NADH/NADPH) preference in the four variants showed up to ∼35-fold preference for NADH, which was observed with the
Cupriavidus taiwanensis
FabG variant. In addition, FabG homologs were overexpressed in fatty acid- and methyl ketone-overproducing
E. coli
host strains under anaerobic conditions, and the
C. taiwanensis
variant led to a 60% higher free fatty acid titer and 75% higher methyl ketone titer relative to the titers of the control strains. With further engineering, this work could serve as a starting point for establishing a microbial host strain for production of fatty acid-derived biofuels (e.g., methyl ketones) under anaerobic conditions.
Improved Short-Sequence-Repeat Genotyping of Mycobacterium avium subsp. paratuberculosis by Using Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Ahlstrom Christina , Barkema Herman W. , De Buck Jeroen 
Published: November 2013

ABSTRACT

Accurate sequence analysis of mononucleotide repeat regions is difficult, complicating the use of short sequence repeats (SSRs) as a tool for bacterial strain discrimination. Although multiple SSR loci in the genome of
Mycobacterium avium
subsp.
paratuberculosis
allow genotyping of
M. avium
subsp.
paratuberculosis
isolates with high discriminatory power, further characterization of the most discriminatory loci is limited due to inherent difficulties in sequencing mononucleotide repeats. Here, a method was evaluated using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) as an alternative to Sanger sequencing to further differentiate the dominant mycobacterial interspersed repetitive-unit (MIRU)–variable-number tandem-repeat (VNTR)
M. avium
subsp.
paratuberculosis
type (
n
= 37) in Canadian dairy herds by targeting a highly discriminatory mononucleotide SSR locus. First, PCR-amplified DNA was digested with two restriction enzymes to yield a sufficiently small fragment containing the SSR locus. Second, MALDI-TOF MS was performed to identify the mass, and thus repeat length, of the target. Sufficiently intense, discriminating spectra were obtained to determine repeat lengths up to 15, an improvement over the limit of 11 using traditional sequencing techniques. Comparison to synthetic oligonucleotides and Sanger sequencing results confirmed a valid and reproducible assay that increased discrimination of the dominant
M. avium
subsp.
paratuberculosis
MIRU-VNTR type. Thus, MALDI-TOF MS was a reliable, fast, and automatable technique to accurately resolve
M. avium
subsp.
paratuberculosis
genotypes based on SSRs.
Type IV Pilus Biogenesis, Twitching Motility, and DNA Uptake in Thermus thermophilus: Discrete Roles of Antagonistic ATPases PilF, PilT1, and PilT2
Authors: Salzer Ralf , Joos Friederike , Averhoff Beate 
Published: November 2013

ABSTRACT

Natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species.
Thermus thermophilus
HB27 has emerged as the leading model organism for studies of DNA transporters in thermophilic bacteria. Recently, we identified a zinc-binding polymerization nucleoside triphosphatase (NTPase), PilF, which is essential for the transport of DNA through the outer membrane. Here, we present genetic evidence that PilF is also essential for the biogenesis of pili. One of the most challenging questions was whether
T. thermophilus
has any depolymerization NTPase acting as a counterplayer of PilF. We identified two depolymerization NTPases, PilT1 (TTC1621) and PilT2 (TTC1415), both of which are required for type IV pilus (T4P)-mediated twitching motility and adhesion but dispensable for natural transformation. This suggests that T4P dynamics are not required for natural transformation. The latter finding is consistent with our suggestion that in
T. thermophilus
, T4P and natural transformation are linked but distinct systems.
Diversity in Robustness of Lactococcus lactis Strains during Heat Stress, Oxidative Stress, and Spray Drying Stress
Authors: Dijkstra Annereinou R. , Setyawati Meily C. , Bayjanov Jumamurat R. , Alkema Wynand , van Hijum Sacha A. F. T. , Bron Peter A. , Hugenholtz Jeroen 
Published: November 2013

ABSTRACT

In this study we tested 39
Lactococcus lactis
strains isolated from diverse habitats for their robustness under heat and oxidative stress, demonstrating high diversity in survival (up to 4 log units). Strains with an
L. lactis
subsp.
lactis
phenotype generally displayed more-robust phenotypes than strains with an
L. lactis
subsp.
cremoris
phenotype, whereas the habitat from which the strains had been isolated did not appear to influence stress survival. Comparison of the stress survival phenotypes with already available comparative genomic data sets revealed that the absence or presence of specific genes, including genes encoding a GntR family transcriptional regulator, a manganese ABC transporter permease, a cellobiose phosphotransferase system (PTS) component, the FtsY protein, and hypothetical proteins, was associated with heat or oxidative stress survival. Finally, 14 selected strains also displayed diversity in survival after spray drying, ranging from 20% survival for the most robust strains, which appears acceptable for industrial application, to 0.1% survival for the least-tolerant strains. The high and low levels of survival upon spray drying correlated clearly with the combined robustness under heat and oxidative stress. These results demonstrate the relevance of screening culture collections for robustness under heat and oxidative stress on top of the typical screening for acidifying and flavor-forming properties.
Distinct Roles of a Mitogen-Activated Protein Kinase in Cytokinesis between Different Life Cycle Forms of Trypanosoma brucei
Authors: Wei Ying , Li Ziyin 
Published: November 2013

ABSTRACT

Mitogen-activated protein kinase (MAPK) modules are evolutionarily conserved signaling cascades that function in response to the environment and play crucial roles in intracellular signal transduction in eukaryotes. The involvement of a MAP kinase in regulating cytokinesis in yeast, animals, and plants has been reported, but the requirement for a MAP kinase for cytokinesis in the early-branching protozoa is not documented. Here, we show that a MAP kinase homolog (TbMAPK6) from
Trypanosoma brucei
plays distinct roles in cytokinesis in two life cycle forms of
T. brucei
. TbMAPK6 is distributed throughout the cytosol in the procyclic form but is localized in both the cytosol and the nucleus in the bloodstream form. RNA interference (RNAi) of TbMAPK6 results in moderate growth inhibition in the procyclic form but severe growth defects and rapid cell death in the bloodstream form. Moreover, TbMAPK6 appears to be implicated in furrow ingression and cytokinesis completion in the procyclic form but is essential for cytokinesis initiation in the bloodstream form. Despite the distinct defects in cytokinesis in the two forms, RNAi of TbMAPK6 also caused defective basal body duplication/segregation in a small cell population in both life cycle forms. Altogether, our results demonstrate the involvement of the TbMAPK6-mediated pathway in regulating cytokinesis in trypanosomes and suggest distinct roles of TbMAPK6 in cytokinesis between different life cycle stages of
T. brucei
.
Gene Network and Proteomic Analyses of Cardiac Responses to Pathological and Physiological Stress
Authors: Drozdov Ignat , Didangelos Athanasios , Yin Xiaoke , Zampetaki Anna , Abonnenc Mélanie , Murdoch Colin , Zhang Min , Ouzounis Christos A. , Mayr Manuel , Tsoka Sophia , Shah Ajay M. 
Published: November 2013

Background—
The molecular mechanisms underlying similarities and differences between physiological and pathological left ventricular hypertrophy (LVH) are of intense interest. Most previous work involved targeted analysis of individual signaling pathways or screening of transcriptomic profiles. We developed a network biology approach using genomic and proteomic data to study the molecular patterns that distinguish pathological and physiological LVH.

Methods and Results—
A network-based analysis using graph theory methods was undertaken on 127 genome-wide expression arrays of in vivo murine LVH. This revealed phenotype-specific pathological and physiological gene coexpression networks. Despite >1650 common genes in the 2 networks, network structure is significantly different. This is largely because of rewiring of genes that are differentially coexpressed in the 2 networks; this novel concept of differential wiring was further validated experimentally. Functional analysis of the rewired network revealed several distinct cellular pathways and gene sets. Deeper exploration was undertaken by targeted proteomic analysis of mitochondrial, myofilament, and extracellular subproteomes in pathological LVH. A notable finding was that mRNA–protein correlation was greater at the cellular pathway level than for individual loci.

Conclusions—

This first combined gene network and proteomic analysis of LVH reveals novel insights into the integrated pathomechanisms that distinguish pathological versus physiological phenotypes. In particular, we identify differential gene wiring as a major distinguishing feature of these phenotypes. This approach provides a platform for the investigation of potentially novel pathways in LVH and offers a freely accessible protocol (
http://sites.google.com/site/cardionetworks
) for similar analyses in other cardiovascular diseases.