bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional changes in deep dorsal horn interneurons following spinal cord injury are enhanced with different durations of exercise training
Authors: Rank M. M. , Flynn J. R. , Battistuzzo C. R. , Galea M. P. , Callister R. , Callister R. J. 
Published: October 2014

Key points
Exercise training after spinal cord injury (SCI) enhances collateral sprouting from axons near the injury and is thought to promote intraspinal circuit reorganisation that effectively bridges the SCI. The effects of exercise training, and its duration, on interneurons in these de novo intraspinal circuits are poorly understood.
In an adult mouse hemisection model of SCI, we used whole‐cell patch‐clamp electrophysiology to examine changes in the intrinsic and synaptic properties of deep dorsal horn interneurons in the vicinity of a SCI in response to the injury, and after 3 and 6 weeks of treadmill exercise training.
SCI alone exerted powerful effects on the intrinsic and synaptic properties of interneurons near the lesion.
Importantly, synaptic activity, both local and descending, was preferentially enhanced by exercise training, suggesting that exercise promotes synaptic plasticity in spinal cord interneurons that are ideally placed to form new intraspinal circuits after SCI.
AbstractFollowing incomplete spinal cord injury (SCI), collaterals sprout from intact and injured axons in the vicinity of the lesion. These sprouts are thought to form new synaptic contacts that effectively bypass the lesion epicentre and contribute to improved functional recovery. Such anatomical changes are known to be enhanced by exercise training; however, the mechanisms underlying exercise‐mediated plasticity are poorly understood. Specifically, we do not know how SCI alone or SCI combined with exercise alters the intrinsic and synaptic properties of interneurons in the vicinity of a SCI. Here we use a hemisection model of incomplete SCI in adult mice and whole‐cell patch‐clamp recording in a horizontal spinal cord slice preparation to examine the functional properties of deep dorsal horn (DDH) interneurons located in the vicinity of a SCI following 3 or 6 weeks of treadmill exercise training. We examined the functional properties of local and descending excitatory synaptic connections by recording spontaneous excitatory postsynaptic currents (sEPSCs) and responses to dorsal column stimulation, respectively. We find that SCI in untrained animals exerts powerful effects on intrinsic, and especially, synaptic properties of DDH interneurons. Plasticity in intrinsic properties was most prominent at 3 weeks post SCI, whereas synaptic plasticity was greatest at 6 weeks post injury. Exercise training did not markedly affect intrinsic membrane properties; however, local and descending excitatory synaptic drive were enhanced by 3 and 6 weeks of training. These results suggest exercise promotes synaptic plasticity in spinal cord interneurons that are ideally placed to form new intraspinal circuits after SCI.
Comparisons of Ectomycorrhizal Colonization of Transgenic American Chestnut with Those of the Wild Type, a Conventionally Bred Hybrid, and Related Fagaceae Species
Authors: D'Amico Katherine M. , Horton Thomas R. , Maynard Charles A. , Stehman Stephen V. , Oakes Allison D. , Powell William A. 
Published: October 2014

ABSTRACTAmerican chestnut (Castanea dentata[Marsh.] Borkh.) dominated the eastern forests of North America, serving as a keystone species both ecologically and economically until the introduction of the chestnut blight,Cryphonectria parasitica, functionally eradicated the species. Restoration efforts include genetic transformation utilizing genes such as oxalate oxidase to produce potentially blight-resistant chestnut trees that could be released back into the native range. However, before such a release can be undertaken, it is necessary to assess nontarget impacts. Since oxalate oxidase is meant to combat a fungal pathogen, we are particularly interested in potential impacts of this transgene on beneficial fungi. This study compares ectomycorrhizal fungal colonization on a transgenic American chestnut clone expressing enhanced blight resistance to a wild-type American chestnut, a conventionally bred American-Chinese hybrid chestnut, and other Fagaceae species. A greenhouse bioassay used soil from two field sites with different soil types and land use histories. The number of colonized root tips was counted, and fungal species were identified using morphology, restriction fragment length polymorphism (RFLP), and DNA sequencing. Results showed that total ectomycorrhizal colonization varied more by soil type than by tree species. Individual fungal species varied in their colonization rates, but there were no significant differences between colonization on transgenic and wild-type chestnuts. This study shows that the oxalate oxidase gene can increase resistance againstCryphonectria parasiticawithout changing the colonization rate for ectomycorrhizal species. These findings will be crucial for a potential deregulation of blight-resistant American chestnuts containing the oxalate oxidase gene.
Embedded Biofilm, a New Biofilm Model Based on the Embedded Growth of Bacteria
Authors: Jung Yong-Gyun , Choi Jungil , Kim Soo-Kyoung , Lee Joon-Hee , Kwon Sunghoon 
Published: October 2014

ABSTRACT
A variety of systems have been developed to study biofilm formation. However, most systems are based on the surface-attached growth of microbes under shear stress. In this study, we designed a microfluidic channel device, called a microfluidic agarose channel (MAC), and found that microbial cells in the MAC system formed an embedded cell aggregative structure (ECAS). ECASs were generated from the embedded growth of bacterial cells in an agarose matrix and better mimicked the clinical environment of biofilms formed within mucus or host tissue under shear-free conditions. ECASs were developed with the production of extracellular polymeric substances (EPS), the most important feature of biofilms, and eventually burst to release planktonic cells, which resembles the full developmental cycle of biofilms. Chemical and genetic effects have also confirmed that ECASs are a type of biofilm. Unlike the conventional biofilms formed in the flow cell model system, this embedded-type biofilm completes the developmental cycle in only 9 to 12 h and can easily be observed with ordinary microscopes. We suggest that ECASs are a type of biofilm and that the MAC is a system for observing biofilm formation.
Evidence for Extraintestinal Growth of Bacteroidales Originating from Poultry Litter
Authors: Weidhaas Jennifer , Mantha Sirisha , Hair Elliott , Nayak Bina , Harwood Valerie J. 
Published: October 2014

ABSTRACT

Water quality monitoring techniques that target microorganisms in the order
Bacteroidales
are potential alternatives to conventional methods for detection of fecal indicator bacteria.
Bacteroidales
and members of the genus
Bacteroides
have been the focus of microbial source tracking (MST) investigations for discriminating sources of fecal pollution (e.g., human or cattle feces) in environmental waters. For accurate source apportionment to occur, one needs to understand both the abundance of
Bacteroides
in host feces and the survival of these host-associated microbial markers after deposition in the environment. Studies were undertaken to evaluate the abundance, persistence, and potential for growth of
Bacteroidales
originating from poultry litter under oxic and anoxic environmental conditions.
Bacteroidales
abundance, as determined by quantitative PCR (qPCR) with GenBac primers and probe, increased 2 to 5 log gene copies ml
−1
and 2 log gene copies g litter
−1
under most conditions during incubation of poultry litter in a variety of laboratory microcosm and field mesocosm studies. DNA sequencing of the
Bacteroidales
organisms in the litter identified taxa with sequences corresponding exactly to the GenBac primer and probe sequences and that were closely related to
Bacteroides uniformis
,
B. ovatus
, and
B. vulgatus
. These results suggest that MST studies using qPCR methods targeting
Bacteroidales
in watersheds that are affected by poultry litter should be interpreted cautiously. Growth of
Bacteroidales
originating from poultry litter in environmental waters may occur while
Bacteroidales
growth from other fecal sources declines, thus confounding the interpretation of MST results.
Distribution of Human-Specific Bacteroidales and Fecal Indicator Bacteria in an Urban Watershed Impacted by Sewage Pollution, Determined Using RNA- and DNA-Based Quantitative PCR Assays
Authors: Kapoor Vikram , Pitkänen Tarja , Ryu Hodon , Elk Michael , Wendell David , Santo Domingo Jorge W. 
Published: October 2014

ABSTRACT

The identification of fecal pollution sources is commonly carried out using DNA-based methods. However, there is evidence that DNA can be associated with dead cells or present as “naked DNA” in the environment. Furthermore, it has been shown that rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) assays can be more sensitive than rRNA gene-based qPCR assays since metabolically active cells usually contain higher numbers of ribosomes than quiescent cells. To this end, we compared the detection frequency of host-specific markers and fecal bacteria using RNA-based RT-qPCR and DNA-based qPCR methods for water samples collected in sites impacted by combined sewer overflows. As a group, fecal bacteria were more frequently detected in most sites using RNA-based methods. Specifically, 8, 87, and 85% of the samples positive for general enterococci,
Enterococcus faecalis
, and
Enterococcus faecium
markers, respectively, were detected using RT-qPCR, but not with the qPCR assay counterpart. On average, two human-specific
Bacteroidales
markers were not detected when using DNA in 12% of the samples, while they were positive for all samples when using RNA (cDNA) as the template. Moreover, signal intensity was up to three orders of magnitude higher in RT-qPCR assays than in qPCR assays. The human-specific
Bacteroidales
markers exhibited moderate correlation with conventional fecal indicators using RT-qPCR results, suggesting the persistence of nonhuman sources of fecal pollution or the presence of false-positive signals. In general, the results from this study suggest that RNA-based assays can increase the detection sensitivity of fecal bacteria in urban watersheds impacted with human fecal sources.
Identification of
ypqP
as a New Bacillus subtilis Biofilm Determinant That Mediates the Protection of Staphylococcus aureus against Antimicrobial Agents in Mixed-Species Communities
Authors: Sanchez-Vizuete Pilar , Le Coq Dominique , Bridier Arnaud , Herry Jean-Marie , Aymerich Stéphane , Briandet Romain 
Published: October 2014

ABSTRACT

In most habitats, microbial life is organized in biofilms, three-dimensional edifices sustained by extracellular polymeric substances that enable bacteria to resist harsh and changing environments. Under multispecies conditions, bacteria can benefit from the polymers produced by other species (“public goods”), thus improving their survival under toxic conditions. A recent study showed that a
Bacillus subtilis
hospital isolate (NDmed) was able to protect
Staphylococcus aureus
from biocide action in multispecies biofilms. In this work, we identified
ypqP
, a gene whose product is required in NDmed for thick-biofilm formation on submerged surfaces and for resistance to two biocides widely used in hospitals. NDmed and
S. aureus
formed mixed biofilms, and both their spatial arrangement and pathogen protection were mediated by YpqP. Functional
ypqP
is present in other natural
B. subtilis
biofilm-forming isolates. However, the gene is disrupted by the SPβ prophage in the weak submerged-biofilm-forming strains NCIB3610 and 168, which are both less resistant than NDmed to the biocides tested. Furthermore, in a 168 laboratory strain cured of the SPβ prophage, the reestablishment of a functional
ypqP
gene led to increased thickness and resistance to biocides of the associated biofilms. We therefore propose that YpqP is a new and important determinant of
B. subtilis
surface biofilm architecture, protection against exposure to toxic compounds, and social behavior in bacterial communities.
Response of Bacterioplankton Communities to Cadmium Exposure in Coastal Water Microcosms with High Temporal Variability
Authors: Wang Kai , Zhang Demin , Xiong Jinbo , Chen Xinxin , Zheng Jialai , Hu Changju , Yang Yina , Zhu Jianlin 
Published: October 2014

ABSTRACT

Multiple anthropogenic disturbances to bacterial diversity have been investigated in coastal ecosystems, in which temporal variability in the bacterioplankton community has been considered a ubiquitous process. However, far less is known about the temporal dynamics of a bacterioplankton community responding to pollution disturbances such as toxic metals. We used coastal water microcosms perturbed with 0, 10, 100, and 1,000 μg liter
−1
of cadmium (Cd) for 2 weeks to investigate temporal variability, Cd-induced patterns, and their interaction in the coastal bacterioplankton community and to reveal whether the bacterial community structure would reflect the Cd gradient in a temporally varying system. Our results showed that the bacterioplankton community structure shifted along the Cd gradient consistently after a 4-day incubation, although it exhibited some resistance to Cd at low concentration (10 μg liter
−1
). A process akin to an arms race between temporal variability and Cd exposure was observed, and the temporal variability overwhelmed Cd-induced patterns in the bacterial community. The temporal succession of the bacterial community was correlated with pH, dissolved oxygen, NO
3
−
-N, NO
2
−
-N, PO
4
3−
-P, dissolved organic carbon, and chlorophyll
a
, and each of these parameters contributed more to community variance than Cd did. However, elevated Cd levels did decrease the temporal turnover rate of community. Furthermore, key taxa, affiliated to the families
Flavobacteriaceae
,
Rhodobacteraceae
,
Erythrobacteraceae
,
Piscirickettsiaceae
, and
Alteromonadaceae
, showed a high frequency of being associated with Cd levels during 2 weeks. This study provides direct evidence that specific Cd-induced patterns in bacterioplankton communities exist in highly varying manipulated coastal systems. Future investigations on an ecosystem scale across longer temporal scales are needed to validate the observed pattern.
Thermoadaptation-Directed Enzyme Evolution in an Error-Prone Thermophile Derived from Geobacillus kaustophilus HTA426
Authors: Suzuki Hirokazu , Kobayashi Jyumpei , Wada Keisuke , Furukawa Megumi , Doi Katsumi 
Published: October 2014

ABSTRACT

Thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. In this study, we constructed an error-prone strain of the thermophile
Geobacillus kaustophilus
HTA426 and investigated thermoadaptation-directed enzyme evolution using the strain. A mutation frequency assay using the antibiotics rifampin and streptomycin revealed that
G. kaustophilus
had substantially higher mutability than
Escherichia coli
and
Bacillus subtilis
. The predominant mutations in
G. kaustophilus
were A · T→G · C and C · G→T · A transitions, implying that the high mutability of
G. kaustophilus
was attributable in part to high-temperature-associated DNA damage during growth. Among the genes that may be involved in DNA repair in
G. kaustophilus
, deletions of the
mutSL
,
mutY
,
ung
, and
mfd
genes markedly enhanced mutability. These genes were subsequently deleted to construct an error-prone thermophile that showed much higher (700- to 9,000-fold) mutability than the parent strain. The error-prone strain was auxotrophic for uracil owing to the fact that the strain was deficient in the intrinsic
pyrF
gene. Although the strain harboring
Bacillus subtilis
pyrF
was also essentially auxotrophic, cells became prototrophic after 2 days of culture under uracil starvation, generating
B. subtilis
PyrF variants with an enhanced half-denaturation temperature of >10°C. These data suggest that this error-prone strain is a promising host for thermoadaptation-directed evolution to generate thermostable variants from thermolabile enzymes.
amoA
Gene Abundances and Nitrification Potential Rates Suggest that Benthic Ammonia-Oxidizing Bacteria and Not Archaea Dominate N Cycling in the Colne Estuary, United Kingdom
Authors: Li Jialin , Nedwell David B. , Beddow Jessica , Dumbrell Alex J. , McKew Boyd A. , Thorpe Emma L. , Whitby Corinne 
Published: October 2014

ABSTRACT

Nitrification, mediated by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), is important in global nitrogen cycling. In estuaries where gradients of salinity and ammonia concentrations occur, there may be differential selections for ammonia-oxidizer populations. The aim of this study was to examine the activity, abundance, and diversity of AOA and AOB in surface oxic sediments of a highly nutrified estuary that exhibits gradients of salinity and ammonium. AOB and AOA communities were investigated by measuring ammonia monooxygenase (
amoA
) gene abundance and nitrification potentials both spatially and temporally. Nitrification potentials differed along the estuary and over time, with the greatest nitrification potentials occurring mid-estuary (8.2 μmol N grams dry weight [gdw]
−1
day
−1
in June, increasing to 37.4 μmol N gdw
−1
day
−1
in January). At the estuary head, the nitrification potential was 4.3 μmol N gdw
−1
day
−1
in June, increasing to 11.7 μmol N gdw
−1
day
−1
in January. At the estuary head and mouth, nitrification potentials fluctuated throughout the year. AOB
amoA
gene abundances were significantly greater (by 100-fold) than those of AOA both spatially and temporally.
Nitrosomonas
spp. were detected along the estuary by denaturing gradient gel electrophoresis (DGGE) band sequence analysis. In conclusion, AOB dominated over AOA in the estuarine sediments, with the ratio of AOB/AOA
amoA
gene abundance increasing from the upper (freshwater) to lower (marine) regions of the Colne estuary. These findings suggest that in this nutrified estuary, AOB (possibly
Nitrosomonas
spp.) were of major significance in nitrification.
Transcriptional Activation of Multiple Operons Involved in
para
-Nitrophenol Degradation by Pseudomonas sp. Strain WBC-3
Authors: Zhang Wen-Mao , Zhang Jun-Jie , Jiang Xuan , Chao Hongjun , Zhou Ning-Yi 
Published: October 2014

ABSTRACT

Pseudomonas
sp. strain WBC-3 utilizes
para
-nitrophenol (PNP) as a sole carbon and energy source. The genes involved in PNP degradation are organized in the following three operons:
pnpA
,
pnpB
, and
pnpCDEFG
. How the expression of the genes is regulated is unknown. In this study, an LysR-type transcriptional regulator (LTTR) is identified to activate the expression of the genes in response to the specific inducer PNP. While the LTTR coding gene
pnpR
was found to be not physically linked to any of the three catabolic operons, it was shown to be essential for the growth of strain WBC-3 on PNP. Furthermore, PnpR positively regulated its own expression, which is different from the function of classical LTTRs. A regulatory binding site (RBS) with a 17-bp imperfect palindromic sequence (GTT-N
11
-AAC) was identified in all
pnpA
,
pnpB
,
pnpC
, and
pnpR
promoters. Through electrophoretic mobility shift assays and mutagenic analyses, this motif was proven to be necessary for PnpR binding. This consensus motif is centered at positions approximately −55 bp relative to the four transcriptional start sites (TSSs). RBS integrity was required for both high-affinity PnpR binding and transcriptional activation of
pnpA
,
pnpB
, and
pnpR
. However, this integrity was essential only for high-affinity PnpR binding to the promoter of
pnpCDEFG
and not for its activation. Intriguingly, unlike other LTTRs studied, no changes in lengths of the PnpR binding regions of the
pnpA
and
pnpB
promoters were observed after the addition of the inducer PNP in DNase I footprinting.
Discovery of a Conjugative Megaplasmid in Bifidobacterium breve
Authors: Bottacini Francesca , O'Connell Motherway Mary , Casey Eoghan , McDonnell Brian , Mahony Jennifer , Ventura Marco , van Sinderen Douwe 
Published: October 2014

ABSTRACT

Bifidobacterium breve
is a common and sometimes very abundant inhabitant of the human gut. Genome sequencing of
B. breve
JCM 7017 revealed the presence of an extrachromosomal element, designated pMP7017 consisting of >190 kb, thus representing the first reported bifidobacterial megaplasmid.
In silico
characterization of this element revealed several genomic features supporting a stable establishment of the megaplasmid in its host, illustrated by predicted CRISPR-Cas functions that are known to protect the host against intrusion of foreign DNA. Interestingly, pMP7017 is also predicted to encode a conjugative DNA transfer apparatus and, consistent with this notion, we demonstrate here the conjugal transfer of pMP7017 to representative strains of
B. breve
and
B. longum
subsp.
longum
. We also demonstrate the presence of a megaplasmid with homology to pMP7017 in three
B. longum
subsp.
longum
strains.
Nationwide Surveillance Study of Clostridium difficile in Australian Neonatal Pigs Shows High Prevalence and Heterogeneity of PCR Ribotypes
Authors: Knight Daniel R. , Squire Michele M. , Riley Thomas V. 
Published: October 2014

ABSTRACT

Clostridium difficile
is an important enteric pathogen of humans and the cause of diarrhea and enteritis in neonatal pigs. Outside Australia, prevalence in piglets can be up to 73%, with a single PCR ribotype (RT), 078, predominating. We investigated the prevalence and genotype of
C. difficile
in Australian pig herds. Rectal swabs (
n
= 229) were collected from piglets aged <7 days from 21 farms across Australia. Selective culture for
C. difficile
was performed and isolates characterized by PCR for toxin genes and PCR ribotyping.
C. difficile
was isolated from 52% of samples by direct culture on chromogenic agar and 67% by enrichment culture (
P
= 0.001). No association between
C. difficile
recovery or genotype and diarrheic status of either farm or piglets was found. The majority (87%; 130/154) of isolates were toxigenic. Typing revealed 23 different RTs, several of which are known to cause disease in humans, including RT014, which was isolated most commonly (23%; 36/154). RT078 was not detected. This study shows that colonization of Australian neonatal piglets with
C. difficile
is widespread in the herds sampled.