bluuebunny/crossref_metadata_2025_split huggingface dataset:
BeyondResponsive Regulation: The expanding role of non‐state actors in the regulatory process
Authors: Grabosky Peter 
Published: June 2012

AbstractThis comment extends the vision ofResponsive Regulationby noting subsequent developments in regulatory pluralism, in particular those occurring under private auspices. The apparent weakening or withdrawal of state regulatory institutions has inspired considerable regulatory activity on the part of non‐state actors. In addition, the concurrent growth and pervasiveness of digital technology have greatly facilitated the involvement of individual citizens in non‐state regulatory activity. However, the full implications of what might be called “wiki‐regulation” remain to be seen. The risks that accompany private regulation may include the lack of accountability of non‐state regulatory actors, and the possibility of their failure. There is also a risk that with the increasing salience of what Vogel calls “civil regulation,” state regulatory institutions may atrophy, or fail to develop at all.
Autonomic nervous system modulation affects the inflammatory immune response in mice with acute Chagas disease
Authors: Machado Marcus Paulo Ribeiro , Rocha Aletheia Moraes , de Oliveira Lucas Felipe , de Cuba Marília Beatriz , de Oliveira Loss Igor , Castellano Lucio Roberto , Silva Marcus Vinicius , Machado Juliana Reis , Nascentes Gabriel Antonio Nogueira , Paiva Luciano Henrique , Savino Wilson , Junior Virmondes Rodrigues , Brum Patricia Chakur , Prado Vania Ferreira , Prado Marco Antonio Maximo , Silva Eliane Lages , Montano Nicola , Ramirez Luis Eduardo , Dias da Silva Valdo Jose 
Published: June 2012

The aim of the present study was to evaluate the effects of changes to the autonomic nervous system in mice during the acute phase of Chagas disease, which is an infection caused by the parasite Trypanosoma cruzi. The following types of mice were inoculated with T. cruzi (CHG): wild‐type (WT) and vesicular acetylcholine transporter knockdown (KDVAChT) C57BL/6j mice; wild‐type non‐treated (NT) FVB mice; FVB mice treated with pyridostigmine bromide (PYR) or salbutamol (SALB); and β2‐adrenergic receptor knockout (KOβ2) FVB mice. During infection and at 18–21 days after infection (acute phase), the survival curves, parasitaemia, electrocardiograms, heart rate variability, autonomic tonus and histopathology of the animals were evaluated. Negative control groups were matched for age, genetic background and treatment. The KDVAChT‐CHG mice exhibited a significant shift in the electrocardiographic, autonomic and histopathological profiles towards a greater inflammatory immune response that was associated with a reduction in blood and tissue parasitism. In contrast, the CHG‐PYR mice manifested reduced myocardial inflammation and lower blood and tissue parasitism. Similar results were observed in CHG‐SALB animals. Unexpectedly, the KOβ2‐CHG mice exhibited less myocardial inflammation and higher blood and tissue parasitism, which were associated with reduced mortality. These findings could have been due to the increase in vagal tone observed in the KOβ2 mice, which rendered them more similar to the CHG‐PYR animals. In conclusion, our results indicate a marked immunomodulatory role for the parasympathetic and sympathetic autonomic nervous systems, which inhibit both the inflammatory immune response and parasite clearance during the acute phase of experimental Chagas heart disease in mice.
Time course of hepatic gluconeogenesis during hindlimb suspension unloading
Authors: Bederman Ilya R. , Chandramouli Visvanathan , Sandlers Yana , Henderson Leigh , Cabrera Marco E. 
Published: June 2012

New Findings
What is the central question of this study?The rate of liver gluconeogenesis during hindlimb suspension unloading has not been determined.
What is the main finding and its importance?Hepatic gluconeogenesis is significantly increased under conditions of hindlimb suspension unloading, which simulates the muscular atrophy occurring during spaceflight. This finding supports earlier hypothesis. This metabolic shift in the living animal warrants further study.
The goal of this work was to determine the time‐dependent changes in fractional hepatic gluconeogenesis (GNG) during conditions of hindlimb suspension unloading (HSU), a ‘ground‐based’ method for inducing muscular atrophy to simulate space flight. We hypothesized that GNG would increase in HSU conditions as a result of metabolic shifts in the liver and skeletal muscle. A significant and progressive atrophy was observed in the soleus (30, 47 and 55%) and gastrocnemius muscles (0, 15 and 17%) after 3, 7 and 14 days of HSU, respectively. Fractional hepatic GNG was determined following the incorporation of deuterium from deuterated water (2H2O) into C–H bonds of newly synthesized glucose after an 8 h fast. Enrichment of plasma glucose with 2H was measured using the classic method of Landau et al. (the ‘hexamethylenetetramine (HMT) method’), based on specific 2H labelling of glucose carbons, and the novel method of Chacko et al. (‘average method’), based on the assumption of equal 2H enrichment on all glucose carbons (except C2). After 3 days of HSU, fractional GNG was significantly elevated in the HSU group, as determined by either method (∼13%, P < 0.05). After 7 and 14 days of HSU, gluconeogenesis was not significantly different. Both analytical methods yielded similar time‐dependent trends in gluconeogenic rates, but GNG values determined using the average method were consistently lower (∼30%) than those found by the HMT method. To compare and validate the average method against the HMT method further, we starved animals for 13 h to allow for hepatic GNG to contribute 100% to endogenous glucose production. The HMT method yielded 100% GNG, while the average method yielded GNG of ∼70%. As both methods used the same values of precursor enrichment, we postulated that the underestimation of gluconeogenic rate was as a result of differences in the measurements of product enrichment (2H labelling of plasma glucose). This could be explained by the following factors: (i) loss of deuterium via exchange between acetate and glucose; (ii) interference caused by fragment m/z 169, representing multiple isobaric species; and (iii) interference from other sugars at m/z 169. In conclusion, HSU caused a time‐dependent increase in hepatic gluconeogenesis, irrespective of the analytical methods used.
Comparative Survey of Rumen Microbial Communities and Metabolites across One Caprine and Three Bovine Groups, Using Bar-Coded Pyrosequencing and
1
H Nuclear Magnetic Resonance Spectroscopy
Authors: Lee Hyo Jung , Jung Ji Young , Oh Young Kyoon , Lee Sang-Suk , Madsen Eugene L. , Jeon Che Ok 
Published: June 2012

ABSTRACT

Pyrosequencing of 16S rRNA genes (targeting
Bacteria
and
Archaea
) and
1
H nuclear magnetic resonance were applied to investigate the rumen microbiota and metabolites of Hanwoo steers in the growth stage (HGS), Hanwoo steers in the late fattening stage (HFS), Holstein-Friesian dairy cattle (HDC), and Korean native goats (KNG) in the late fattening stage. This was a two-part investigation. We began by comparing metabolites and microbiota of Hanwoo steers at two stages of husbandry. Statistical comparisons of metabolites and microbial communities showed no significant differences between HFS and HGS (differing by a dietary shift at 24 months and age [67 months versus 12 months]). We then augmented the study by extending the investigation to HDC and KNG. Overall, pyrosequencing of 16S rRNA genes showed that the rumens had highly diverse microbial communities containing many previously undescribed microorganisms. Bioinformatic analysis revealed that the bacterial sequences were predominantly affiliated with four phyla—
Bacteroidetes
,
Firmicutes
,
Fibrobacteres
, and
Proteobacteria
—in all ruminants. However, interestingly, the bacterial reads belonging to
Fibrobacteres
were present at a very low abundance (<0.1%) in KNG. Archaeal community analysis showed that almost all of these reads fell into a clade related to, but distinct from, known cultivated methanogens. Statistical analyses showed that the microbial communities and metabolites of KNG were clearly distinct from those of other ruminants. In addition, bacterial communities and metabolite profiles of HGS and HDC, fed similar diets, were distinctive. Our data indicate that bovine host breeds override diet as the key factor that determines bacterial community and metabolite profiles in the rumen.
Quorum Sensing in the Context of Food Microbiology
Authors: Skandamis Panagiotis N. , Nychas George-John E. 
Published: June 2012

ABSTRACTFood spoilage may be defined as a process that renders a product undesirable or unacceptable for consumption and is the outcome of the biochemical activity of a microbial community that eventually dominates according to the prevailing ecological determinants. Although limited information are reported, this activity has been attributed to quorum sensing (QS). Consequently, the potential role of cell-to-cell communication in food spoilage and food safety should be more extensively elucidated. Such information would be helpful in designing approaches for manipulating these communication systems, thereby reducing or preventing, for instance, spoilage reactions or even controlling the expression of virulence factors. Due to the many reports in the literature on the fundamental features of QS, e.g., chemistry and definitions of QS compounds, in this minireview, we only allude to the types and chemistry of QS signaling moleculesper seand to the (bioassay-based) methods of their detection and quantification, avoiding extensive documentation. Conversely, we attempt to provide insights into (i) the role of QS in food spoilage, (ii) the factors that may quench the activity of QS in foods and review the potential QS inhibitors that might “mislead” the bacterial coordination of spoilage activities and thus may be used as biopreservatives, and (iii) the future experimental approaches that need to be undertaken in order to explore the “gray” or “black” areas of QS, increase our understanding of how QS affects microbial behavior in foods, and assist in finding answers as to how we can exploit QS for the benefit of food preservation and food safety.
Reduction of Photoautotrophic Productivity in the Cyanobacterium Synechocystis sp. Strain PCC 6803 by Phycobilisome Antenna Truncation
Authors: Page Lawrence E. , Liberton Michelle , Pakrasi Himadri B. 
Published: June 2012

ABSTRACT

Truncation of the algal light-harvesting antenna is expected to enhance photosynthetic productivity. The wild type and three mutant strains of
Synechocystis
sp. strain 6803 with a progressively smaller phycobilisome antenna were examined under different light and CO
2
conditions. Surprisingly, such antenna truncation resulted in decreased whole-culture productivity for this cyanobacterium.
Relationship between Enterococcal Levels and Sediment Biofilms at Recreational Beaches in South Florida
Authors: Piggot Alan M. , Klaus James S. , Johnson Sara , Phillips Matthew C. , Solo-Gabriele Helena M. 
Published: June 2012

ABSTRACT
Enterococci, recommended at the U.S. federal level for monitoring water quality at marine recreational beaches, have been found to reside and grow within beach sands. However, the environmental and ecological factors affecting enterococcal persistence remain poorly understood, making it difficult to determine levels of fecal pollution and assess human health risks. Here we document the presence of enterococci associated with beach sediment biofilms at eight south Florida recreational beaches. Enterococcal levels were highest in supratidal sands, where they displayed a nonlinear, unimodal relationship with extracellular polymeric secretions (EPS), the primary component of biofilms. Enterococcal levels peaked at intermediate levels of EPS, suggesting that biofilms may promote the survival of enterococci but also inhibit enterococci as the biofilm develops within beach sands. Analysis of bacterial community profiles determined by terminal restriction fragment length polymorphisms showed the bacterial communities of supratidal sediments to be significantly different from intertidal and subtidal communities; however, no differences were observed in bacterial community compositions associated with different EPS concentrations. Our results suggest that supratidal sands are a microbiologically unique environment favorable for the incorporation and persistence of enterococci within beach sediment biofilms.
Quantification of Diatom Gene Expression in the Sea by Selecting Uniformly Transcribed mRNA as the Basis for Normalization
Authors: Kang Lee-Kuo , Tsui Feng-Hsiu , Chang Jeng 
Published: June 2012

ABSTRACT

To quantify gene expressions by quantitative reverse transcription-PCR (Q-RT-PCR) in natural diatom assemblages, it is necessary to seek a biomass reference specific to the target species. Two housekeeping genes,
TBP
(encoding the TATA box-binding protein) and
EFL
(encoding the translation elongation factor-like protein), were evaluated as candidates for reference genes in Q-RT-PCR assays. Transcript levels of
TBP
and
EFL
were relatively stable under various test conditions including growth stages, light-dark cycle phases, and nutrient stresses in
Skeletonema costatum
and
Chaetoceros affinis
, and
TBP
expression was more stable than that of
EFL
. Next, the sequence diversity of diatom assemblages was evaluated by obtaining 32
EFL
and 29
TBP
homologous gene fragments from the East China Sea (ECS). Based on sequence alignments,
EFL
and
TBP
primer sets were designed for
Chaetoceros
and
Skeletonema
groups in the ECS. An evaluation of primer specificity and PCR efficiency indicated that the
EFL
primer sets performed better. To demonstrate the applicability of
EFL
primer sets in the ECS, they were employed to measure mRNA levels of the FcpB (fucoxanthin-chlorophyll protein) gene in diatoms. The results correctly revealed prominent diel variations in
FcpB
expression and confirmed
EFL
as a good reference gene.
Identification and Biochemical Evidence of a Medium-Chain-Length Polyhydroxyalkanoate Depolymerase in the Bdellovibrio bacteriovorus Predatory Hydrolytic Arsenal
Authors: Martínez Virginia , de la Peña Fernando , García-Hidalgo Javier , de la Mata Isabel , García José Luis , Prieto María Auxiliadora 
Published: June 2012

ABSTRACT

The obligate predator
Bdellovibrio bacteriovorus
HD100 shows a large set of proteases and other hydrolases as part of its hydrolytic arsenal needed for its predatory life cycle. We present genetic and biochemical evidence that open reading frame (ORF) Bd3709 of
B. bacteriovorus
HD100 encodes a novel medium-chain-length polyhydroxyalkanoate (mcl-PHA) depolymerase (PhaZ
Bd
). The primary structure of PhaZ
Bd
suggests that this enzyme belongs to the α/β-hydrolase fold family and has a typical serine hydrolase catalytic triad (serine-histidine-aspartic acid) in agreement with other PHA depolymerases and lipases. PhaZ
Bd
has been extracellularly produced using different hypersecretor Tol-pal mutants of
Escherichia coli
and
Pseudomonas putida
as recombinant hosts. The recombinant PhaZ
Bd
has been characterized, and its biochemical properties have been compared to those of other PHA depolymerases. The enzyme behaves as a serine hydrolase that is inhibited by phenylmethylsulfonyl fluoride. It is also affected by the reducing agent dithiothreitol and nonionic detergents like Tween 80. PhaZ
Bd
is an endoexohydrolase that cleaves both large and small PHA molecules, producing mainly dimers but also monomers and trimers. The enzyme specifically degrades mcl-PHA and is inactive toward short-chain-length polyhydroxyalkanoates (scl-PHA) like polyhydroxybutyrate (PHB). These studies shed light on the potentiality of these predators as sources of new biocatalysts, such as an mcl-PHA depolymerase, for the production of enantiopure hydroxyalkanoic acids and oligomers as building blocks for the synthesis of biobased polymers.
Dual-Serotype Biofilm Formation by Shiga Toxin-Producing Escherichia coli O157:H7 and O26:H11 Strains
Authors: Wang Rong , Kalchayanand Norasak , Bono James L. , Schmidt John W. , Bosilevac Joseph M. 
Published: June 2012

ABSTRACT

Escherichia coli
O26:H11 strains were able to outgrow O157:H7 companion strains in planktonic and biofilm phases and also to effectively compete with precolonized O157:H7 cells to establish themselves in mixed biofilms.
E. coli
O157:H7 strains were unable to displace preformed O26:H11 biofilms. Therefore,
E. coli
O26:H11 remains a potential risk in food safety.
Determination of Whether Quorum Quenching Is a Common Activity in Marine Bacteria by Analysis of Cultivable Bacteria and Metagenomic Sequences
Authors: Romero Manuel , Martin-Cuadrado Ana-Belen , Otero Ana 
Published: June 2012

ABSTRACTThe abundance of quorum quenching (QQ) activity was evaluated in cultivable bacteria obtained from oceanic and estuarine seawater and compared with the frequency of QQ enzyme sequences in the available marine metagenomic collections. The possible role of the high QQ activity found among marine bacteria is discussed.
The TetR-Type Transcriptional Repressor RolR from Corynebacterium glutamicum Regulates Resorcinol Catabolism by Binding to a Unique Operator,
rolO
Authors: Li Tang , Zhao Kexin , Huang Yan , Li Defeng , Jiang Cheng-Ying , Zhou Nan , Fan Zheng , Liu Shuang-Jiang 
Published: June 2012

ABSTRACT

The
rol
(designated for
r
esorcin
ol
) gene cluster
rolRHMD
is involved in resorcinol catabolism in
Corynebacterium glutamicum
, and RolR is the TetR-type regulator. In this study, we investigated how RolR regulated the transcription of the
rol
genes in
C. glutamicum
. The transcription start sites and promoters of
rolR
and
rolHMD
were identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that RolR negatively regulated the transcription of
rolHMD
and of its own gene. Further, a 29-bp operator
rolO
was located at the intergenic region of
rolR
and
rolHMD
and was identified as the sole binding site for RolR. It contained two overlapping inverted repeats and they were essential for RolR-binding. The binding of RolR to
rolO
was affected by resorcinol and hydroxyquinol, which are the starting compounds of resorcinol catabolic pathway. These two compounds were able to dissociate RolR-
rolO
complex, thus releasing RolR from the complex and derepressing the transcription of
rol
genes in
C. glutamicum
. It is proposed that the binding of RolR to its operator
rolO
blocks the transcription of
rolHMD
and of its own gene, thus negatively regulated resorcinol degradation in
C. glutamicum
.
Prophage Carriage and Diversity within Clinically Relevant Strains of Clostridium difficile
Authors: Shan Jinyu , Patel Krusha V. , Hickenbotham Peter T. , Nale Janet Y. , Hargreaves Katherine R. , Clokie Martha R. J. 
Published: June 2012

ABSTRACT

Prophages are encoded in most genomes of sequenced
Clostridium difficile
strains. They are key components of the mobile genetic elements and, as such, are likely to influence the biology of their host strains. The majority of these phages are not amenable to propagation, and therefore the development of a molecular marker is a useful tool with which to establish the extent and diversity of
C. difficile
prophage carriage within clinical strains. To design markers, several candidate genes were analyzed including structural and holin genes. The holin gene is the only gene present in all sequenced phage genomes, conserved at both terminals, with a variable mid-section. This allowed us to design two sets of degenerate PCR primers specific to
C. difficile
myoviruses and siphoviruses. Subsequent PCR analysis of 16 clinical
C. difficile
ribotypes showed that 15 of them are myovirus positive, and 2 of them are also siphovirus positive. Antibiotic induction and transmission electron microscope analysis confirmed the molecular prediction of myoviruses and/or siphovirus presence. Phylogenetic analysis of the holin sequences identified three groups of
C. difficile
phages, two within the myoviruses and a divergent siphovirus group. The marker also produced tight groups within temperate phages that infect other taxa, including
Clostridium perfringens
,
Clostridium botulinum
, and
Bacillus
spp., which suggests the potential application of the holin gene to study prophage carriage in other bacteria. This study reveals the high incidence of prophage carriage in clinically relevant strains of
C. difficile
and correlates the molecular data to the morphological observation.
Fratricide Is Essential for Efficient Gene Transfer between Pneumococci in Biofilms
Authors: Wei Hua , Håvarstein Leiv Sigve 
Published: June 2012

ABSTRACT

Streptococcus pneumoniae
and a number of commensal streptococcal species are competent for natural genetic transformation. The natural habitat of these bacteria is multispecies biofilms in the human oral cavity and nasopharynx. Studies investigating lateral transfer of virulence and antibiotic resistance determinants among streptococci have shown that interspecies as well as intraspecies gene exchange takes place in these environments. We have previously shown that the action of a competence-specific murein hydrolase termed CbpD strongly increases the rate of gene transfer between pneumococci grown in liquid cultures. CbpD is the key component of a bacteriolytic mechanism termed the fratricide mechanism. It is secreted by competent pneumococci and mediates the release of donor DNA from sensitive streptococci present in the same environment. However, in nature, gene exchange between streptococci takes place in biofilms and not in liquid cultures. In the present study, we therefore investigated whether CbpD affects the rate of gene transfer in laboratory-grown biofilms. Our results show that the fratricide mechanism has a strong positive impact on intrabiofilm gene exchange, indicating that it is important for active acquisition of homologous donor DNA under natural conditions. Furthermore, we found that competent biofilm cells of
S. pneumoniae
acquire a Nov
r
marker much more efficiently from neighboring cells than from the growth medium. Efficient lysis of target cells requires that CbpD act in conjunction with the murein hydrolase LytC. In contrast, the major autolysin LytA does not seem to be important for fratricide-mediated gene exchange in a biofilm environment.
Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates
Authors: Bengtson Per , Sterngren Anna E. , Rousk Johannes 
Published: June 2012

ABSTRACT
Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.