bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weed tolerance in soybean: a direct selection system
Authors: Horneburg Bernd , Seiffert Sabrina , Schmidt Jennifer , Messmer Monika M. , Wilbois Klaus‐Peter 
Published: March 2017

AbstractWeed competition can severely reduce soybean (Glycine max (L.) Merr.) yields, particularly in organic systems. An efficient screening and breeding approach is needed to increase breeding progress for weed tolerance. This study sought to (i) establish a system for direct selection of competitive genotypes, (ii) evaluate genotypic differences in weed tolerance among six early‐maturing genotypes and (iii) assess the contribution of selected morphological traits to weed tolerance. A direct selection system providing two different levels of weed competition through all development stages of a soybean crop was developed, using mixtures of selected crop species as sown competitors. Two resulting mixtures induced intermediate (<30%) and strong (>50%) yield reduction, respectively. This selection system can be applied in screening and breeding programmes to facilitate breeding for weed tolerance. No significant difference in weed tolerance was detected between six soybean genotypes of maturity groups 000 to 00. Morphological traits that might influence competitive ability, for example light absorption, leaf area and lateral shoots, were assessed, and their potential for indirect selection for weed tolerance is discussed.
The host background of rice influences the resistance expression of a three genes pyramid (xa5 + xa13 + Xa21) to bacterial blight (Xanthomonas oryzae pv. oryzae) pathotypes of Indian mainland and Bay islands
Authors: Sakthivel Krishnan , Gautam Raj K. , Manigundan Kaari , Singh Reena , Ramalingam Jegadeesan , Laha Gouri S. , Kumar Aundy , Velazhahan Rethinasamy 
Published: March 2017

AbstractBacterial blight (BB) is a major disease of rice for which host resistance is the only effective solution. The three genes pyramid xa5 + xa13 + Xa21 is recently the most utilized combination for developing resistant varieties through marker‐assisted breeding. Our study was carried out to elicit the detailed response of twenty lines possessing these three genes in five genetic backgrounds to twelve diverse BB pathotypes in India. The lines developed from ADT 47 variety showed incomplete resistance to most of the pathotypes, whereas susceptibility varied from 8.3% to 16.6% in ADT 43 and IR24, respectively. However, in IMP ASD16/60 and Improved Samba Mahsuri, complete resistance against all pathotypes was observed. The overall results confirmed that genetic background plays crucial role for the effective expression of xa5 + xa13 + Xa21 combination. Molecular studies did not reveal correlation between origin of pathotypes and their virulence potential. It is suggested to deploy Improved Samba Mahsuri, IMP ASD 16/60 and AD1306 varieties in the bacterial blight prone areas or use them as donors for realizing wider and durable resistance.
The use of genetic, manual and chemical methods to control pollination in vegetable hybrid seed production: a review
Authors: Colombo Noemí , Galmarini Claudio Rómulo 
Published: March 2017

AbstractProduction of hybrid varieties of vegetable crops is currently a desired breeding goal, due to their remarkable agronomic performance and to the possibility of intellectual property protection. However, efficient hybrid production requires a careful pollination control to guarantee the hybrid nature of F1seed. Several technologies ranging from manual emasculation to genetic transformation are used to inhibit pollen production in mother plants. In this review, we examine the principles underlying strategies like genetically determined systems (genic male sterility, cytoplasmic–genic male sterility, self‐incompatibility) and other methods (manual emasculation, chemical‐hybridizing agents) in different species, considering the benefits and drawbacks of their adoption. Finally, we present the current state of the art for vegetable hybrid seed production.
Enhanced growth of halophyte plants in biochar‐amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation
Authors: Zheng Hao , Wang Xiao , Chen Lei , Wang Zhenyu , Xia Yang , Zhang Yipeng , Wang Hefang , Luo Xianxiang , Xing Baoshan 
Published: March 2017

AbstractSoil health is essential and irreplaceable for plant growth and global food production, which has been threatened by climate change and soil degradation. Degraded coastal soils are urgently required to reclaim using new sustainable technologies. Interest in applying biochar to improve soil health and promote crop yield has rapidly increased because of its multiple benefits. However, effects of biochar addition on the saline–sodic coastal soil health and halophyte growth were poorly understood. Response of two halophytes, Sesbania (Sesbania cannabina) and Seashore mallow (Kosteletzkya virginica), to the individual or co‐application of biochar and inorganic fertilizer into a coastal soil was investigated using a 52 d pot experiment. The biochar alone or co‐application stimulated the plant growth (germination, root development, and biomass), primarily attributed to the enhanced nutrient availability from the biochar‐improved soil health. Additionally, the promoted microbial activities and bacterial community shift towards the beneficial taxa (e.g. Pseudomonas and Bacillus) in the rhizosphere also contributed to the enhanced plant growth and biomass. Our findings showed the promising significance because biochar added at an optimal level (≤5%) could be a feasible option to reclaim the degraded coastal soil, enhance plant growth and production, and increase soil health and food security.
Expression of defence‐related genes in stems and leaves of resistant and susceptible field pea (Pisum sativum) during infection by Phoma koolunga
Authors: Tran H. S. , You M. P. , Barbetti M. J. 
Published: March 2017

The differential expression of 13 defence‐related genes during Phoma koolunga infection of stems and leaves of susceptible versus resistant field pea (Pisum sativum) was determined using qRT‐PCR. Expression, in terms of relative mRNA level ratios, of genes encoding ferredoxin NADP oxidoreductase, 6a‐hydroxymaackiain methyltransferase (hmm6), chalcone synthase (PSCHS3) and ascorbate peroxidase in leaves and stems differed during 6–72 hours post‐inoculation (hpi) and reflected known host resistance levels in leaves versus stems. In comparison to the susceptible genotype, at 24, 48 and 72 hpi, two genes, hmm6 (122.43‐, 206.99‐ and 32.25‐fold, respectively) and PSCHS3 (175.00‐, 250.13‐ and 216.24‐fold, respectively), were strongly up‐regulated in leaves of the resistant genotype, highlighting that resistance against P. koolunga in field pea is governed by the early synthesis of pisatin. At 24 hpi, leaves infected by P. koolunga showed clear differences in expression of target genes. For example, the gene encoding a precursor of the defensin ‘disease resistance response protein 39’ was substantially down‐regulated in leaves of both the susceptible and the resistant genotypes inoculated with P. koolunga. This contrasts with other studies on another pea black spot pathogen, Didymella pinodes, where this same gene is strongly up‐regulated in leaves of resistant and susceptible genotypes. The current study provides the first understanding of defence‐related genes involved in the resistance against P. koolunga, opening novel avenues to engineer new field pea cultivars with improved leaf and stem black spot disease resistance as the basis for developing more effective and sustainable management strategies.
Quantile Spectral Analysis for Locally Stationary Time Series
Authors: Birr Stefan , Volgushev Stanislav , Kley Tobias , Dette Holger , Hallin Marc 
Published: March 2017

SummaryClassical spectral methods are subject to two fundamental limitations: they can account only for covariance-related serial dependences, and they require second-order stationarity. Much attention has been devoted lately to quantile-based spectral methods that go beyond covariance-based serial dependence features. At the same time, covariance-based methods relaxing stationarity into much weaker local stationarity conditions have been developed for a variety of time series models. Here, we combine those two approaches by proposing quantile-based spectral methods for locally stationary processes. We therefore introduce a time varying version of the copula spectra that have been recently proposed in the literature, along with a suitable local lag window estimator. We propose a new definition of local strict stationarity that allows us to handle completely general non-linear processes without any moment assumptions, thus accommodating our quantile-based concepts and methods. We establish a central limit theorem for the new estimators and illustrate the power of the proposed methodology by means of a simulation study. Moreover, in two empirical studies (namely of the Standard & Poor's 500 series and a temperature data set recorded in Hohenpeissenberg), we demonstrate that the new approach detects important variations in serial dependence structures both across time and across quantiles. Such variations remain completely undetected and are actually undetectable, via classical covariance-based spectral methods.
Ultra‐light extensometer for the assessment of the mechanical properties of the human skin in vivo
Authors: Jacquet E. , Joly S. , Chambert J. , Rekik K. , Sandoz P. 
Published: March 2017

Background/purpose:This paper aims to present an ultra‐light extensometer device dedicated to the mechanical characterization of the human skin in vivo.MethodsThe device developed was conceived to be non‐invasive, to work without any stand and to perform various uniaxial tensile tests with either effort or displacement control. We also use specific guarding tabs to make in vivo extension tests analogous to traction tests.ResultsForce‐displacement curves are derived from the data provided by the device's sensors. The latter are converted into stress‐strain curves thanks to complementary measurements of the skin thickness. We present typical experimental data and results that demonstrate the device ability to built stress‐strain curves characteristic of the human skin behavior. An additional imaging unit records a sequence of images of the solicited skin area for further calculations of the displacement fields by digital image correlation.ConclusionThe analysis of the displacement and deformation fields validates the guarding tab efficiency and the capacity of the device to characterize the mechanical behavior of the human skin in vivo.
The role played by oxidative stress in evoking the exercise pressor reflex in health and simulated peripheral artery disease
Authors: Harms Jonathan E. , Kuczmarski J. Matthew , Kim Joyce S. , Thomas Gail D. , Kaufman Marc P. 
Published: March 2017

Key points
Ligating the femoral artery of a rat for 72 h, a model for peripheral artery disease, causes an exaggerated exercise pressor reflex in response to muscle contraction.
Likewise, the hindlimb muscles of rats with ligated femoral arteries show increased levels of reactive oxygen species.
Infusion of tiron, a superoxide scavenger, attenuated the exaggerated pressor reflex and reduced reactive oxygen species production in rats with ligated femoral arteries.
Conversely, we found no effect of tiron infusion on the pressor reflex in rats with patent femoral arteries.
These results suggest a role of reactive oxygen species with respect to causing the exaggerated pressor response to contraction seen in rats with ligated arteries and peripheral artery disease.
AbstractContraction of muscle evokes the exercise pressor reflex (EPR), which is expressed partly by increases in heart rate and arterial pressure. Patients with peripheral artery disease (PAD) show an exaggerated EPR, sometimes report pain when walking and are at risk for cardiac arrthymias. Previous research suggested that reactive oxygen species (ROS) mediate the exaggerated EPR associated with PAD. To examine the effects of ROS on the EPR, we infused a superoxide scavenger, tiron, into the superficial epigastric artery of decerebrated rats. In some, we simulated PAD by ligating a femoral artery for 72 h before the experiment. The peak EPR in ‘ligated’ rats during saline infusion averaged 31 ± 4 mmHg, whereas the peak EPR in these rats during tiron infusion averaged 13 ± 2 mmHg (n = 12; P < 0.001); the attenuating effect of tiron on the EPR was partly reversed when saline was reinfused into the superficial epigastric artery (21 ± 2 mmHg; P < 0.01 vs. tiron). The peak EPR in ‘ligated’ rats was also attenuated (n = 7; P < 0.01) by infusion of gp91ds‐tat, a peptide that blocks the activity of NAD(P)H oxidase. Tiron infusion had no effect on the EPR in rats with patent femoral arteries (n = 9). Western blots showed that the triceps surae muscles of ‘ligated’ rats expressed more Nox2 and p67phox, which are components of NADPH oxidase, compared to triceps surae muscles of ‘freely perfused’ rats. Tiron added to muscle homogenates reduced ROS production in vitro. The results of the present study provide further evidence indicating that ROS mediates the exaggeration of EPR in rats with simulated PAD.
Efficient Hepatitis C Virus Genotype 1b Core-NS5A Recombinants Permit Efficacy Testing of Protease and NS5A Inhibitors
Authors: Pham Long V. , Ramirez Santseharay , Carlsen Thomas H. R. , Li Yi-Ping , Gottwein Judith M. , Bukh Jens 
Published: March 2017

ABSTRACT

Hepatitis C virus (HCV) strains belong to seven genotypes with numerous subtypes that respond differently to antiviral therapies. Genotype 1, and primarily subtype 1b, is the most prevalent genotype worldwide. The development of recombinant HCV infectious cell culture systems for different variants, permitted by the high replication capacity of strain JFH1 (genotype 2a), has advanced efficacy and resistance testing of antivirals. However, efficient infectious JFH1-based cell cultures of subtype 1b are limited and comprise only the 5′ untranslated region (5′UTR)-NS2, NS4A, or NS5A regions. Importantly, it has not been possible to develop efficient 1b infectious systems expressing the NS3/4A protease, an important target of direct-acting antivirals. We developed efficient infectious JFH1-based cultures with genotype 1b core-NS5A sequences of strains DH1, Con1, and J4 by using previously identified HCV cell culture adaptive substitutions A1226G, R1496L, and Q1773H. These viruses spread efficiently in Huh7.5 cells by acquiring additional adaptive substitutions, and final recombinants yielded peak supernatant infectivity titers of 4 to 5 log
10
focus-forming units (FFU)/ml. We subsequently succeeded in adapting a JFH1-based 5′UTR-NS5A DH1 recombinant to efficient growth in cell culture. We evaluated the efficacy of clinically relevant NS3/4A protease and NS5A inhibitors against the novel genotype 1b viruses, as well as against previously developed 1a viruses. The inhibitors were efficient against all tested genotype 1 viruses, with NS5A inhibitors showing half-maximal effective concentrations several orders of magnitude lower than NS3/4A protease inhibitors. In summary, the developed HCV genotype 1b culture systems represent valuable tools for assessing the efficacy of various classes of antivirals and for other virological studies requiring genotype 1b infectious viruses.
Mechanisms of Vesicular Stomatitis Virus Inactivation by Protoporphyrin IX, Zinc-Protoporphyrin IX, and Mesoporphyrin IX
Authors: Cruz-Oliveira Christine , Almeida Andreza F. , Freire João M. , Caruso Marjolly B. , Morando Maria A. , Ferreira Vivian N. S. , Assunção-Miranda Iranaia , Gomes Andre M. O. , Castanho Miguel A. R. B. , Da Poian Andrea T. 
Published: March 2017

ABSTRACT

Virus resistance to antiviral therapies is an increasing concern that makes the development of broad-spectrum antiviral drugs urgent. Targeting of the viral envelope, a component shared by a large number of viruses, emerges as a promising strategy to overcome this problem. Natural and synthetic porphyrins are good candidates for antiviral development due to their relative hydrophobicity and pro-oxidant character. In the present work, we characterized the antiviral activities of protoprophyrin IX (PPIX), Zn-protoporphyrin IX (ZnPPIX), and mesoporphyrin IX (MPIX) against vesicular stomatitis virus (VSV) and evaluated the mechanisms involved in this activity. Treatment of VSV with PPIX, ZnPPIX, and MPIX promoted dose-dependent virus inactivation, which was potentiated by porphyrin photoactivation. All three porphyrins inserted into lipid vesicles and disturbed the viral membrane organization. In addition, the porphyrins also affected viral proteins, inducing VSV glycoprotein cross-linking, which was enhanced by porphyrin photoactivation. Virus incubation with sodium azide and α-tocopherol partially protected VSV from inactivation by porphyrins, suggesting that singlet oxygen (
1
O
2
) was the main reactive oxygen species produced by photoactivation of these molecules. Furthermore,
1
O
2
was detected by 9,10-dimethylanthracene oxidation in photoactivated porphyrin samples, reinforcing this hypothesis. These results reveal the potential therapeutic application of PPIX, ZnPPIX, and MPIX as good models for broad antiviral drug design.
Clofazimine-Containing Regimen for the Treatment of Mycobacterium abscessus Lung Disease
Authors: Yang Bumhee , Jhun Byung Woo , Moon Seong Mi , Lee Hyun , Park Hye Yun , Jeon Kyeongman , Kim Dae Hun , Kim Su-Young , Shin Sung Jae , Daley Charles L. , Koh Won-Jung 
Published: March 2017

ABSTRACT

Patients with lung disease caused by
Mycobacterium abscessus
subsp.
abscessus
(here
M. abscessus
) typically have poor treatment outcomes. Although clofazimine (CFZ) has been increasingly used in the treatment of
M. abscessus
lung disease in clinical practice, there are no reported data on its effectiveness for this disease. This study sought to evaluate the clinical efficacy of a CFZ-containing regimen for the treatment of
M. abscessus
lung disease. We performed a retrospective review of the medical records of 42 patients with
M. abscessus
lung disease who were treated with CFZ-containing regimens between November 2013 and January 2015. CFZ was administered in combination with other antibiotics as an initial antibiotic regimen in 15 (36%) patients (initial treatment group), and it was added to an existing antibiotic regimen for refractory
M. abscessus
lung disease in 27 (64%) patients (salvage treatment group). Overall, there was an 81% treatment response rate based on symptoms and a 31% response rate based on radiographic findings. Conversion to culture-negative sputum samples was achieved in 10 (24%) patients after CFZ-containing antibiotic treatment, and during treatment, there were significant decreases in the positivity of semiquantitative sputum cultures for acid-fast bacilli in both the initial (
P
= 0.018) and salvage (
P
= 0.001) treatment groups. Our study suggests that CFZ-containing regimens may improve treatment outcomes in patients with
M. abscessus
lung disease and that a prospective evaluation of CFZ in
M. abscessus
lung disease is warranted.
Pharmacokinetics and Tolerance of the Phage Endolysin-Based Candidate Drug SAL200 after a Single Intravenous Administration among Healthy Volunteers
Authors: Jun Soo Youn , Jang In Jin , Yoon Seonghae , Jang Kyungho , Yu Kyung-Sang , Cho Joo Youn , Seong Moon-Woo , Jung Gi Mo , Yoon Seong Jun , Kang Sang Hyeon 
Published: March 2017

ABSTRACT

This study was a phase 1, single-center, randomized, double-blind, placebo-controlled, single-dosing, and dose-escalating study of intravenous SAL200. It is a new candidate drug for the treatment of antibiotic-resistant staphylococcal infections based on a recombinant form of the phage endolysin SAL-1. The study evaluated the pharmacokinetics, pharmacodynamics, and tolerance among healthy male volunteers after the intravenous infusion of single ascending doses of SAL200 (0.1, 0.3, 1, 3, and 10 mg/kg of body weight). SAL200 was well tolerated, and no serious adverse events (AEs) were observed in this clinical study. Most AEs were mild, self-limiting, and transient. The AEs reported in more than three participants were fatigue, rigors, headache, and myalgia. No clinically significant values with respect to the findings of clinical chemistry, hematology, and coagulation analyses, urinalysis, vital signs, and physical examinations were observed, and no notable trends in our electrocardiogram (ECG) results for any tested dose were noticed. A greater-than-dose-proportional increase with regard to systemic exposure and the maximum serum concentration was observed when the SAL200 dose was increased from 0.1 mg/kg to 10 mg/kg. This investigation constitutes the first-in-human phase 1 study of an intravenously administered, phage endolysin-based drug. (This study has been registered at ClinicalTrials.gov under identifier NCT01855048 and at the Clinical Research Information Service [
https://cris.nih.go.kr/cris/
] under identifier KCT0000968.).
Examination of Enterococcus faecalis Toxin-Antitoxin System Toxin Fst Function Utilizing a Pheromone-Inducible Expression Vector with Tight Repression and Broad Dynamic Range
Authors: Weaver Keith E. , Chen Yuqing , Miiller Elly M. , Johnson Jake N. , Dangler Alex A. , Manias Dawn A. , Clem Aaron M. , Schjodt Daniel J. , Dunny Gary M. 
Published: March 2017

ABSTRACT

Tools for regulated gene expression in
Enterococcus faecalis
are extremely limited. In this report, we describe the construction of an expression vector for
E. faecalis
, designated pCIE, utilizing the P
Q
pheromone-responsive promoter of plasmid pCF10. We demonstrate that this promoter is tightly repressed, responds to nanogram quantities of the peptide pheromone, and has a large dynamic range. To demonstrate its utility, the promoter was used to control expression of the toxic peptides of two
par
family toxin-antitoxin (TA) loci present in
E. faecalis
,
par
pAD1
of the pAD1 plasmid and
par
EF0409
located on the
E. faecalis
chromosome. The results demonstrated differences in the modes of regulation of toxin expression and in the effects of toxins of these two related systems. We anticipate that this vector will be useful for further investigation of
par
TA system function as well as the regulated expression of other genes in
E. faecalis
.

IMPORTANCE
E. faecalis
is an important nosocomial pathogen and a model organism for examination of the genetics and physiology of Gram-positive cocci. While numerous genetic tools have been generated for the manipulation of this organism, vectors for the regulated expression of cloned genes remain limited by high background expression and the use of inducers with undesirable effects on the cell. Here we demonstrate that the P
Q
pheromone-responsive promoter is repressed tightly enough to allow cloning of TA system toxins and evaluate their effects at very low induction levels. This tool will allow us to more fully examine TA system function in
E. faecalis
and to further elucidate its potential roles in cell physiology.