bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of service number on conception rate in Japanese Black cattle
Authors: Irikura N , Uematsu M , Kitahara G , Osawa T , Sasaki Y 
Published: August 2017

ContentsThe conception rate (CR) of Japanese Black cattle has been decreasing since 1990. The objectives of this study were to compare CR by artificial insemination (AI) number, and to assess the interaction between AI number and possible factors related to CR in Japanese Black cattle. Records of 11,182 AI records for 6,741 heifers and 61,302 AI records for 13,139 cows on 977 farms were analysed. The average CR of heifers was 47.0%, and CR at the first, second and third AI was higher than at the fourth or subsequent AI (p < 0.05). The average CR of cows was 47.8%, and their CR at first and second AI was higher than the fourth or subsequent AI (p < 0.05). Data analysis with CR as the dependent variable revealed significant interactions of AI number with interval from calving to first AI and AI season. Cows first serviced at ≤48 days post‐partum had lower CR than those at ≥90 days at first AI (p < 0.05), but the interval from calving to first AI did not affect CR at second AI. Cows serviced in the autumn had a higher CR at first AI than those serviced in the spring and winter (p < 0.05); however, there was no seasonal difference in CR at the second AI. In summary, CR began to decrease from the fourth AI in heifers and the third AI in cows. The AI season and the interval from calving to first AI significantly affected CR only at the first AI.
Small Domain Estimation of Business Statistics by Using Multivariate Skew Normal Models
Authors: Ferrante Maria Rosaria , Pacei Silvia 
Published: August 2017

SummarySmall domain business statistics are becoming important for better planning business policies. We focus on the estimation of the averages of value added and labour cost in small domains. To take into account the positive skewness in the distribution of outcomes and the correlation between them, we propose a bivariate skew normal small area model. Estimates are obtained from real survey data. The performance of the estimator proposed is evaluated on the basis of both survey data and a synthetic firm population. Results show that the model proposed increases the estimates’ reliability and that the estimates obtained make it possible to perform detailed regional economic studies.
Heritability estimates of endurance‐related phenotypes: A systematic review and meta‐analysis
Authors: Miyamoto‐Mikami E. , Zempo H. , Fuku N. , Kikuchi N. , Miyachi M. , Murakami H. 
Published: August 2017

The aim of this study was to clarify heritability estimates for endurance‐related phenotypes and the underlying factors affecting these estimates. A systematic literature search was conducted for studies reporting heritability estimates of endurance‐related phenotypes using the PubMed database (up to 30 September 2016). Studies that estimated the heritability of maximal oxygen uptake (), submaximal endurance phenotypes, and endurance performance were selected. The weighted mean heritability for endurance‐related phenotypes was calculated using a random‐effects model. A total of 15 studies were selected via a systematic review. Meta‐analysis revealed that the weighted means of the heritability of absolute values and those adjusted for body weight and for fat‐free mass were 0.68 (95% CI: 0.59‐0.77), 0.56 (95% CI: 0.47‐0.65), and 0.44 (95% CI: 0.13‐0.75), respectively. There was a significant difference in the weighted means of the heritability of across these different adjustment methods (P < .05). Moreover, there was evidence of statistical heterogeneity in the heritability estimates among studies. Meta‐regression analysis revealed that sex could partially explain the heterogeneity in the heritability estimates adjusted by body weight. For submaximal endurance phenotypes and endurance performance, the weighted mean heritabilities were 0.49 (95% CI: 0.33‐0.65) and 0.53 (95% CI: 0.27‐0.78), respectively. There was statistically significant heterogeneity in the heritability estimates reported among the studies, and we could not identify the specific factors explaining the heterogeneity. Although existing studies indicate that genetic factors account for 44%‐68% of the variability in endurance‐related phenotypes, further studies are necessary to clarify these values.
Removal of Soluble Strontium via Incorporation into Biogenic Carbonate Minerals by Halophilic Bacterium Bacillus sp. Strain TK2d in a Highly Saline Solution
Authors: Horiike Takumi , Dotsuta Yuma , Nakano Yuriko , Ochiai Asumi , Utsunomiya Satoshi , Ohnuki Toshihiko , Yamashita Mitsuo 
Published: August 2017

ABSTRACT

Radioactive strontium (
90
Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant after a nuclear accident. Since the removal of
90
Sr using general adsorbents (e.g., zeolite) is not efficient at high salinity, a suitable alternative immobilization method is necessary. Therefore, we incorporated soluble Sr into biogenic carbonate minerals generated by urease-producing microorganisms from a saline solution. An isolate,
Bacillus
sp. strain TK2d, from marine sediment removed >99% of Sr after contact for 4 days in a saline solution (1.0 × 10
−3
mol liter
−1
of Sr, 10% marine broth, and 3% [wt/vol] NaCl). Transmission electron microscopy and energy-dispersive X-ray spectroscopy showed that Sr and Ca accumulated as phosphate minerals inside the cells and adsorbed at the cell surface at 2 days of cultivation, and then carbonate minerals containing Sr and Ca developed outside the cells after 2 days. Energy-dispersive spectroscopy revealed that Sr, but not Mg, was present in the carbonate minerals even after 8 days. X-ray absorption fine-structure analyses showed that a portion of the soluble Sr changed its chemical state to strontianite (SrCO
3
) in biogenic carbonate minerals. These results indicated that soluble Sr was selectively solidified into biogenic carbonate minerals by the TK2d strain in highly saline environments.

IMPORTANCE
Radioactive nuclides (
134
Cs,
137
Cs, and
90
Sr) leaked into saline environments, including the ocean, from the Fukushima Daiichi Nuclear Power Plant accident. Since the removal of
90
Sr using general adsorbents, such as zeolite, is not efficient at high salinity, a suitable alternative immobilization method is necessary. Utilizing the known concept that radioactive
90
Sr is incorporated into bones by biomineralization, we got the idea of removing
90
Sr via incorporation into biominerals. In this study, we revealed the ability of the isolated ureolytic bacterium to remove Sr under high-salinity conditions and the mechanism of Sr incorporation into biogenic calcium carbonate over a longer duration. These findings indicated the mechanism of the biomineralization by the urease-producing bacterium and the possibility of the biomineralization application for a new purification method for
90
Sr in highly saline environments.
Antibiofilm Effect of Poly(Vinyl Alcohol-
co
-Ethylene) Halamine Film against Listeria innocua and Escherichia coli O157:H7
Authors: Cossu Andrea , Si Yang , Sun Gang , Nitin Nitin 
Published: August 2017

ABSTRACT

Bacterial biofilm formation is linked to several infections and foodborne disease outbreaks. To address this challenge, there is an unmet need to develop rechargeable antimicrobial materials that can provide continuous sanitation of contact surfaces, especially in the food industry. This study was aimed at evaluating a novel rechargeable antimicrobial polymer formed using poly(vinyl alcohol-
co
-ethylene) (PVA-
co
-PE) with halamine functionality to prevent biofilm formation with repeated exposure to high loads of bacteria and organic content and also to aid in inactivation of preformed biofilms upon contact with this novel material. The antibiofilm activity of this rechargeable antimicrobial material was evaluated using a combination of fluorescence and scanning electron microscopy techniques and biofilm metabolic activity analyses. The results determined on the basis of imaging and metabolic activity measurements demonstrated that halamine-functionalized polymer films significantly reduced
Listeria innocua
and
Escherichia coli
O157:H7 biofilm formation. This novel polymeric material maintained its antibiofilm activity with repeated cycles of extended exposure to high levels of bacterial load. These polymeric films were recharged using bleach and cleaned using mechanical sonication after each cycle of extended incubation with bacteria. Halamine-functionalized polymeric material also exhibited significant antibacterial activity against preformed biofilms on a model surface. In summary, our results demonstrate the potential of this antimicrobial material to provide continuous sanitation of surfaces and applications for inactivating preformed biofilms without extensive use of resources, including water and heat. This polymeric material may be used as a replacement for existing polymeric materials or as a coating on diverse materials.

IMPORTANCE
Conventional sanitizers can have limited efficacy in inactivating biofilms in areas with limited accessibility and buildup of organic biomass. Furthermore, none of the current approaches provide continuous sanitation of surfaces. There is a significant unmet need to develop and validate materials that can prevent biofilm formation as well as inactivate preformed biofilms. In this study, the efficacy of a copolymer film containing
N
-halamine against biofilms of
L. innocua
and
E. coli
O157:H7 was evaluated. The polymer film showed strong inhibitory activity against pregrown biofilm or prevented the growth of a new biofilm. The polymer film also maintained its antibiofilm activity after multiple cycles of exposure to high titers of bacterial load with recharging of the polymer film using bleach at intermediate steps between the cycles. Overall, the results demonstrate the potential of a novel antimicrobial material to inhibit and treat biofilms in food industry applications.
Evidence for Borrelia bavariensis Infections of Ixodes uriae within Seabird Colonies of the North Atlantic Ocean
Authors: Munro Hannah J. , Ogden Nicholas H. , Lindsay L. Robbin , Robertson Gregory J. , Whitney Hugh , Lang Andrew S. 
Published: August 2017

ABSTRACTThe first report of members of the spirochete genusBorreliain the seabird tick,Ixodes uriae, and seabird colonies occurred during the early 1990s. Since then,Borreliaspp. have been detected in these ticks and seabird colonies around the world. To date, the primary species detected has beenBorrelia garinii, with rare occurrences ofBorrelia burgdorferisensu strictoandBorrelia lusitaniae.During our research onBorreliaandI. uriaein seabird colonies of Newfoundland and Labrador, Canada, we have identifiedBorreliabavariensisinI. uriae. To our knowledge,B. bavariensishas previously been found only in the Eurasian tick speciesIxodes persulcatusandIxodes ricinus, and it was believed to be a rodent-specificBorreliaecotype. We foundB. bavariensiswithinI. uriaefrom three seabird colonies over three calendar years. We also reanalyzedB. gariniisequences collected fromI. uriaefrom Eurasian seabird colonies and determined that sequences from two Russian seabird colonies likely also representB. bavariensis. The CanadianB. bavariensissequences fromI. uriaeanalyzed in this study cluster with previously described sequences from Asia. Overall, this is an important discovery that illustrates and expands the range of hosts and vectors forB. bavariensis, and it raises questions regarding the possible mechanisms of pathogen dispersal from Asia to North America.IMPORTANCETo our knowledge, this is the first documentation ofB. bavariensisoutside Eurasia. Additionally, the bacterium was found in a marine ecosystem involving the seabird tickI. uriaeand its associated seabird hosts. This indicates that the epizootiology ofB. bavariensistransmission is much different from what had been described, with this species previously believed to be a rodent-specific ecotype, and it indicates that this pathogen is established, or establishing, much more widely.
Transient MutS-Based Hypermutation System for Adaptive Evolution of Lactobacillus casei to Low pH
Authors: Overbeck Tom J. , Welker Dennis L. , Hughes Joanne E. , Steele James L. , Broadbent Jeff R. 
Published: August 2017

ABSTRACT

This study explored transient inactivation of the gene encoding the DNA mismatch repair enzyme MutS as a tool for adaptive evolution of
Lactobacillus casei
. MutS deletion derivatives of
L. casei
12A and ATCC 334 were constructed and subjected to a 100-day adaptive evolution process to increase lactic acid resistance at low pH. Wild-type parental strains were also subjected to this treatment. At the end of the process, the Δ
mutS
lesion was repaired in representative
L. casei
12A and ATCC 334 Δ
mutS
mutant isolates. Growth studies in broth at pH 4.0 (titrated with lactic acid) showed that all four adapted strains grew more rapidly, to higher cell densities, and produced significantly more lactic acid than untreated wild-type cells. However, the adapted Δ
mutS
derivative mutants showed the greatest increases in growth and lactic acid production. Further characterization of the
L. casei
12A-adapted Δ
mutS
derivative revealed that it had a significantly smaller cell volume, a rougher cell surface, and significantly better survival at pH 2.5 than parental
L. casei
12A. Genome sequence analysis confirmed that transient
mutS
inactivation decreased DNA replication fidelity in both
L. casei
strains, and it identified genetic changes that might contribute to the lactic acid-resistant phenotypes of adapted cells. Targeted inactivation of three genes that had acquired nonsense mutations in the adapted
L. casei
12A Δ
mutS
mutant derivative showed that NADH dehydrogenase (
ndh
), phosphate transport ATP-binding protein PstB (
pstB
), and two-component signal transduction system (TCS) quorum-sensing histidine protein kinase (
hpk
) genes act in combination to increase lactic acid resistance in
L. casei
12A.

IMPORTANCE
Adaptive evolution has been applied to microorganisms to increase industrially desirable phenotypes, including acid resistance. We developed a method to increase the adaptability of
Lactobacillus casei
12A and ATCC 334 through transient inactivation of the DNA mismatch repair enzyme MutS. Here, we show this method was effective in increasing the resistance of
L. casei
to lactic acid at low pH. Additionally, we identified three genes that contribute to increased acid resistance in
L. casei
12A. These results provide valuable insight on methods to enhance an organism's fitness to complex phenotypes through adaptive evolution and targeted gene inactivation.
Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis
Authors: Komiya Dai , Hori Akane , Ishida Takuya , Igarashi Kiyohiko , Samejima Masahiro , Koseki Takuya , Fushinobu Shinya 
Published: August 2017

ABSTRACT

Acetyl xylan esterase (AXE) catalyzes the hydrolysis of the acetyl bonds present in plant cell wall polysaccharides. Here, we determined the crystal structure of AXE from
Aspergillus luchuensis
(
Al
AXEA), providing the three-dimensional structure of an enzyme in the Esterase_phb family.
Al
AXEA shares its core α/β-hydrolase fold structure with esterases in other families, but it has an extended central β-sheet at both its ends and an extra loop. Structural comparison with a ferulic acid esterase (FAE) from
Aspergillus niger
indicated that
Al
AXEA has a conserved catalytic machinery: a catalytic triad (Ser119, His259, and Asp202) and an oxyanion hole (Cys40 and Ser120). Near the catalytic triad of
A
lAXEA, two aromatic residues (Tyr39 and Trp160) form small pockets at both sides. Homology models of fungal FAEs in the same Esterase_phb family have wide pockets at the corresponding sites because they have residues with smaller side chains (Pro, Ser, and Gly). Mutants with site-directed mutations at Tyr39 showed a substrate specificity similar to that of the wild-type enzyme, whereas those with mutations at Trp160 acquired an expanded substrate specificity. Interestingly, the Trp160 mutants acquired weak but significant type B-like FAE activity. Moreover, the engineered enzymes exhibited ferulic acid-releasing activity from wheat arabinoxylan.

IMPORTANCE
Hemicelluloses in the plant cell wall are often decorated by acetyl and ferulic acid groups. Therefore, complete and efficient degradation of plant polysaccharides requires the enzymes for cleaving the side chains of the polymer. Since the Esterase_phb family contains a wide array of fungal FAEs and AXEs from fungi and bacteria, our study will provide a structural basis for the molecular mechanism of these industrially relevant enzymes in biopolymer degradation. The structure of the Esterase_phb family also provides information for bacterial polyhydroxyalkanoate depolymerases that are involved in biodegradation of thermoplastic polymers.
Ornithine Decarboxylase-Mediated Production of Putrescine Influences Ganoderic Acid Biosynthesis by Regulating Reactive Oxygen Species in Ganoderma lucidum
Authors: Wu Chen-Gao , Tian Jia-Long , Liu Rui , Cao Peng-Fei , Zhang Tian-Jun , Ren Ang , Shi Liang , Zhao Ming-Wen 
Published: August 2017

ABSTRACT

Putrescine is an important polyamine that participates in a variety of stress responses. Ornithine decarboxylase (ODC) is a key enzyme that catalyzes the biosynthesis of putrescine. A homolog of the gene encoding ODC was cloned from
Ganoderma lucidum
. In the
ODC
-silenced strains, the transcript levels of the
ODC
gene and the putrescine content were significantly decreased. The
ODC
-silenced strains were more sensitive to oxidative stress. The content of ganoderic acid was increased by approximately 43 to 46% in the
ODC
-silenced strains. The content of ganoderic acid could be recovered after the addition of exogenous putrescine. Additionally, the content of reactive oxygen species (ROS) was significantly increased by approximately 1.3-fold in the
ODC
-silenced strains. The ROS content was significantly reduced after the addition of exogenous putrescine. The gene transcript levels and the activities of four major antioxidant enzymes were measured to further explore the effect of putrescine on the intracellular ROS levels. Further studies showed that the effect of the ODC-mediated production of putrescine on ROS might be a factor influencing the biosynthesis of ganoderic acid. Our study reports the role of putrescine in large basidiomycetes, providing a basis for future studies of the physiological functions of putrescine in microbes.

IMPORTANCE
It is well known that ODC and the ODC-mediated production of putrescine play an important role in resisting various environmental stresses, but there are few reports regarding the mechanisms underlying the effect of putrescine on secondary metabolism in microorganisms, particularly in fungi.
G. lucidum
is gradually becoming a model organism for studying environmental regulation and metabolism. In this study, a homolog of the gene encoding ODC was cloned in
Ganoderma lucidum
. We found that the transcript level of the
ODC
gene and the content of putrescine were significantly decreased in the
ODC
-silenced strains. The content of ganoderic acid was significantly increased in the
ODC
-silenced strains. Further studies showed that the effect of the ODC-mediated production of putrescine on ROS might be a factor influencing the biosynthesis of ganoderic acid. Our study reports the role of putrescine in large basidiomycetes, providing a basis for future studies of the physiological functions of putrescine in microbes.
Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation
Authors: Barney Brett M. , Plunkett Mary H. , Natarajan Velmurugan , Mus Florence , Knutson Carolann M. , Peters John W. 
Published: August 2017

ABSTRACT

Biological nitrogen fixation is accomplished by a diverse group of organisms known as diazotrophs and requires the function of the complex metalloenzyme nitrogenase. Nitrogenase and many of the accessory proteins required for proper cofactor biosynthesis and incorporation into the enzyme have been characterized, but a complete picture of the reaction mechanism and key cellular changes that accompany biological nitrogen fixation remain to be fully elucidated. Studies have revealed that specific disruptions of the antiactivator-encoding gene
nifL
result in the deregulation of the
nif
transcriptional activator NifA in the nitrogen-fixing bacterium
Azotobacter vinelandii
, triggering the production of extracellular ammonium levels approaching 30 mM during the stationary phase of growth. In this work, we have characterized the global patterns of gene expression of this high-ammonium-releasing phenotype. The findings reported here indicated that cultures of this high-ammonium-accumulating strain may experience metal limitation when grown using standard Burk's medium, which could be amended by increasing the molybdenum levels to further increase the ammonium yield. In addition, elevated levels of nitrogenase gene transcription are not accompanied by a corresponding dramatic increase in hydrogenase gene transcription levels or hydrogen uptake rates. Of the three potential electron donor systems for nitrogenase, only the
rnf1
gene cluster showed a transcriptional correlation to the increased yield of ammonium. Our results also highlight several additional genes that may play a role in supporting elevated ammonium production in this aerobic nitrogen-fixing model bacterium.

IMPORTANCE
The transcriptional differences found during stationary-phase ammonium accumulation show a strong contrast between the deregulated (
nifL
-disrupted) and wild-type strains and what was previously reported for the wild-type strain under exponential-phase growth conditions. These results demonstrate that further improvement of the ammonium yield in this nitrogenase-deregulated strain can be obtained by increasing the amount of available molybdenum in the medium. These results also indicate a potential preference for one of two ATP synthases present in
A. vinelandii
as well as a prominent role for the membrane-bound hydrogenase over the soluble hydrogenase in hydrogen gas recycling. These results should inform future studies aimed at elucidating the important features of this phenotype and at maximizing ammonium production by this strain.