scholarly journals Dynamics of the Linuron HydrolaselibAGene Pool Size in Response to Linuron Application and Environmental Perturbations in Agricultural Soil and On-Farm Biopurification Systems

2012 ◽  
Vol 78 (8) ◽  
pp. 2783-2789 ◽  
Author(s):  
Karolien Bers ◽  
Kristel Sniegowski ◽  
René De Mot ◽  
Dirk Springael
Keyword(s):  
Agricultural Soil ◽  
Environmental Changes ◽  
Gene Encoding ◽  
Soil Microcosms ◽  
Content Type ◽  
Environmental Perturbations ◽  
Biopurification System ◽  
Reported Data ◽  
On Farm ◽  
Biopurification Systems

ABSTRACTlibA, a gene encoding a novel type of linuron hydrolase, was recently identified in the linuron-mineralizingVariovoraxsp. strain SRS16. In order to assess the contribution oflibAto linuron degradation in environmental settings,libAabundance was monitored in response to the application of linuron and to environmental perturbations in agricultural soil microcosms and microcosms simulating the matrix of on-farm biopurification systems.libAnumbers were measured by real-time PCR and linked to reported data ofVariovoraxcommunity composition and linuron mineralization capacity. In the soil microcosms and one biopurification system setup,libAnumbers responded to the application of linuron and environmental changes in congruency with the modulation of linuron mineralization capacity and the occurrence of a particularVariovoraxphylotype (phylotype A). However, in another biopurification system setup, no such correlations were found. Our data suggest that in the simulated environmental settings, the occurrence oflibAcan be linked to the linuron mineralization capacity and thatlibAis primarily hosted byVariovoraxphylotype A strains. However, the results also suggest that, apart fromlibA, other, as-yet-unknown isofunctional genes play an important role in linuron mineralization in the environment.

scholarly journals Functional Redundancy of Linuron Degradation in Microbial Communities in Agricultural Soil and Biopurification Systems

2016 ◽  
Vol 82 (9) ◽  
pp. 2843-2853 ◽  
Author(s):  
Benjamin Horemans ◽  
Karolien Bers ◽  
Erick Ruiz Romero ◽  
Eva Pose Juan ◽  
Vincent Dunon ◽  
...  
Keyword(s):  
Agricultural Soil ◽  
Bacterial Consortium ◽  
Bacterial Degradation ◽  
Catabolic Gene ◽  
Bacterial Populations ◽  
Content Type ◽  
Respective Contribution ◽  
On Farm ◽  
Biopurification Systems

ABSTRACTThe abundance oflibA, encoding a hydrolase that initiates linuron degradation in the linuron-metabolizingVariovoraxsp. strain SRS16, was previously found to correlate well with linuron mineralization, but not in all tested environments. Recently, an alternative linuron hydrolase, HylA, was identified inVariovoraxsp. strain WDL1, a strain that initiates linuron degradation in a linuron-mineralizing commensal bacterial consortium. The discovery of alternative linuron hydrolases poses questions about the respective contribution and competitive character ofhylA- andlibA-carrying bacteria as well as the role of linuron-mineralizing consortia versus single strains in linuron-exposed settings. Therefore, dynamics ofhylAas well asdcaQas a marker for downstream catabolic functions involved in linuron mineralization, in response to linuron treatment in agricultural soil and on-farm biopurification systems (BPS), were compared with previously reportedlibAdynamics. The results suggest that (i) organisms containing eitherlibAorhylAcontribute simultaneously to linuron biodegradation in the same environment, albeit to various extents, (ii) environmental linuron mineralization depends on multispecies bacterial food webs, and (iii) initiation of linuron mineralization can be governed by currently unidentified enzymes.IMPORTANCEA limited set of different isofunctional catabolic gene functions is known for the bacterial degradation of the phenylurea herbicide linuron, but the role of this redundancy in linuron degradation in environmental settings is not known. In this study, the simultaneous involvement of bacteria carrying one of two isofunctional linuron hydrolysis genes in the degradation of linuron was shown in agricultural soil and on-farm biopurification systems, as was the involvement of other bacterial populations that mineralize the downstream metabolites of linuron hydrolysis. This study illustrates the importance of the synergistic metabolism of pesticides in environmental settings.

scholarly journals Robust Linuron Degradation in On-Farm Biopurification Systems Exposed to Sequential Environmental Changes

2011 ◽  
Vol 77 (18) ◽  
pp. 6614-6621 ◽  
Author(s):  
Kristel Sniegowski ◽  
Karolien Bers ◽  
Jaak Ryckeboer ◽  
Peter Jaeken ◽  
Pieter Spanoghe ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Environmental Changes ◽  
Drought Period ◽  
Content Type ◽  
Pesticide Mixture ◽  
Operation Conditions ◽  
Severe Effect ◽  
Favorable Conditions ◽  
On Farm ◽  
Biopurification Systems

ABSTRACTOn-farm biopurification systems (BPS) treat pesticide-contaminated wastewater of farms through biodegradation. Adding pesticide-primed soil has been shown to be beneficial for the establishment of pesticide-degrading populations in BPS. However, no data exist on the response of pesticide-degrading microbiota, either endogenous or introduced with pesticide-primed soil, when BPS are exposed to expected less favorable environmental conditions like cold periods, drought periods, and periods without a pesticide supply. Therefore, the response of microbiota mineralizing the herbicide linuron in BPS microcosm setups inoculated either with a linuron-primed soil or a nonprimed soil to a sequence of such less favorable conditions was examined. A period without linuron supply or a drought period reduced the size of the linuron-mineralizing community in both setups. The most severe effect was recorded for the setup containing nonprimed soil, in which stopping the linuron supply decreased the linuron degradation capacity to nondetectable levels. In both systems, linuron mineralization rapidly reestablished after conventional operation conditions were restored. A cold period and feeding with a pesticide mixture did not affect linuron mineralization. The changes in the linuron-mineralizing capacity in microcosms containing primed soil were associated with the dynamics of a particularVariovoraxphylotype that previously had been associated with linuron mineralization. This study suggests that the pesticide-mineralizing community in BPS is robust in stress situations imposed by changes in environmental conditions expected to occur on farms. Moreover, it suggests that, in cases where effects do occur, recovery is rapid after restoring conventional operation conditions.

scholarly journals PacBio Amplicon Sequencing Method To Measure Pilin Antigenic Variation Frequencies of Neisseria gonorrhoeae

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Egon A. Ozer ◽  
Lauren L. Prister ◽  
Shaohui Yin ◽  
Billy H. Ward ◽  
Stanimir Ivanov ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Antigenic Variation ◽  
Amplicon Sequencing ◽  
Common Mechanism ◽  
Macrophage Infection ◽  
Gene Encoding ◽  
Transmitted Infection ◽  
Variable Regions ◽  
Content Type ◽  
Strain Fa1090

ABSTRACT Gene diversification is a common mechanism pathogens use to alter surface structures to aid in immune avoidance. Neisseria gonorrhoeae uses a gene conversion-based diversification system to alter the primary sequence of the gene encoding the major subunit of the pilus, pilE. Antigenic variation occurs when one of the nonexpressed 19 silent copies donates part of its DNA sequence to pilE. We have developed a method using Pacific Biosciences (PacBio) amplicon sequencing and custom software to determine pilin antigenic variation frequencies. The program analyzes 37 variable regions across the strain FA1090 1-81-S2 pilE gene and can be modified to determine sequence variation from other starting pilE sequences or other diversity generation systems. Using this method, we measured pilin antigenic variation frequencies for various derivatives of strain FA1090 and showed we can also analyze pilin antigenic variation frequencies during macrophage infection. IMPORTANCE Diversity generation systems are used by many unicellular organism to provide subpopulations of cell with different properties that are available when needed. We have developed a method using the PacBio DNA sequencing technology and a custom computer program to analyze the pilin antigenic variation system of the organism that is the sole cause of the sexually transmitted infection, gonorrhea.

From Ossau and Iraty to PDO Ossau-Iraty

2019 ◽  
Vol 121 (12) ◽  
pp. 3062-3075 ◽  
Author(s):  
Morgane Millet
Keyword(s):  
Local Development ◽  
Qualitative Interviews ◽  
Pasture Production ◽  
Content Type ◽  
Farm Production ◽  
Protected Designation Of Origin ◽  
Summer Pasture ◽  
On Farm ◽  
Term Analysis

Purpose The purpose of this paper is to understand how a geographical indication (GI) is built through time and how its (non)appropriation by local producers shapes it. The reciprocity of such process is also considered: how the creation of a GI changes local relationships between producers, within the GI and out of it? The case of Ossau-Iraty is relevant: in south-west of France, this protected designation of origin (PDO) has been based on two distinct regions: Bearn (Ossau) and Pays Basque (Iraty). Since then, most producers of Bearn have rejected this PDO. Design/methodology/approach The author adopts a diachronic perspective: the trajectory of the local dairy ewe sector is described, focusing on the trajectory of on-farm cheese makers from Bearn and Pays Basque and the trajectory of Ossau-Iraty. Based on different methods (qualitative interviews and archive research), this paper aims at analyzing the interactions within such heterogeneous networks. Findings When the PDO was created (1980), the opposition between producers of Bearn and Pays Basque was based on strong senses of place, which would be translated in a different perception of tradition: to Bearn producers, PDO Ossau-Iraty would be an industrial cheese, in which they did not recognize their product and themselves. With time, the producers who have been involved in the PDO worked on its specifications. The recognition of symbolic practices such as on-farm production or Summer pasture production, the recognition of differences between Basque cheese and Bearn cheese are changes that contribute to the evolution of perceptions within the local producers’ community. The author observes a recent convergence between Basque producers and Bearn producers, as their distinct products share common and strong qualifications within PDO Ossau-Iraty that contribute to their respective valorization. However, it seems to occur at an institutional level and the adhesion of the local producers might still be at stakes. Research limitations/implications A statistical study could reinforce the author’s exploratory and historical research. Furthermore, it would have been relevant to take local inhabitants and local consumers into account, as they have participated in the products’ qualifications as well. Originality/value A long-term analysis (40 years) contributes to better understand how cheeses are valorized and how such process is based on controversial processes. It contributes to root GIs into local histories, which are nor as consensual neither as uniform as we would primarily think, and to identity levers for sustainable local development.

scholarly journals Defects in Mitochondrial and Peroxisomal β-Oxidation Influence Virulence in the Maize Pathogen Ustilago maydis

2012 ◽  
Vol 11 (8) ◽  
pp. 1055-1066 ◽  
Author(s):  
Matthias Kretschmer ◽  
Jana Klose ◽  
James W. Kronstad
Keyword(s):  
Ustilago Maydis ◽  
Short Chain Fatty Acids ◽  
Phytopathogenic Fungi ◽  
Metabolic Adaptation ◽  
In Planta ◽  
Gene Encoding ◽  
Disease Symptoms ◽  
Content Type ◽  
C Terminus ◽  
Fungal Phytopathogens

ABSTRACTAn understanding of metabolic adaptation during the colonization of plants by phytopathogenic fungi is critical for developing strategies to protect crops. Lipids are abundant in plant tissues, and fungal phytopathogens in the phylum basidiomycota possess both peroxisomal and mitochondrial β-oxidation pathways to utilize this potential carbon source. Previously, we demonstrated a role for the peroxisomal β-oxidation enzyme Mfe2 in the filamentous growth, virulence, and sporulation of the maize pathogenUstilago maydis. However,mfe2mutants still caused disease symptoms, thus prompting a more detailed investigation of β-oxidation. We now demonstrate that a defect in thehad1gene encoding hydroxyacyl coenzyme A dehydrogenase for mitochondrial β-oxidation also influences virulence, although its paralog,had2, makes only a minor contribution. Additionally, we identified a gene encoding a polypeptide with similarity to the C terminus of Mfe2 and designated it Mfe2b; this gene makes a contribution to virulence only in the background of anmfe2Δ mutant. We also show that short-chain fatty acids induce cell death inU. maydisand that a block in β-oxidation leads to toxicity, likely because of the accumulation of toxic intermediates. Overall, this study reveals that β-oxidation has a complex influence on the formation of disease symptoms byU. maydisthat includes potential metabolic contributions to proliferationin plantaand an effect on virulence-related morphogenesis.

Credit constraints and labour allocation decisions in rural Burkina Faso

2017 ◽  
Vol 77 (2) ◽  
pp. 257-274 ◽  
Author(s):  
Mohamed Porgo ◽  
John K.M. Kuwornu ◽  
Pam Zahonogo ◽  
John Baptist D. Jatoe ◽  
Irene S. Egyir
Keyword(s):  
Burkina Faso ◽  
Agricultural Production ◽  
Credit Constraints ◽  
Probit Model ◽  
Multinomial Logit Model ◽  
Farm Households ◽  
Content Type ◽  
Labour Market Participation ◽  
On Farm ◽  
Allocation Decisions

Purpose Credit is central in labour allocation decisions in smallholder agriculture in developing countries. The purpose of this paper is to analyse the effect of credit constraints on farm households’ labour allocation decisions in rural Burkina Faso. Design/methodology/approach The study used a direct elicitation approach of credit constraints and applied a farm household model to categorize households into four labour market participation regimes. A joint estimation of both the multinomial logit model and probit model was applied on survey data from Burkina Faso to assess the effect of credit constraint on the probability of choosing one of the four alternatives. Findings The results of the probit model showed that households’ endowment of livestock, access to news, and membership to an farmer-based organization were factors lowering the probability of being credit constrained in rural Burkina Faso. The multinomial logit model results showed that credit constraints negatively influenced the likelihood of a farm household to use hired labour in agricultural production and perhaps more importantly it induces farm households to hire out labour off farm. The results also showed that the other components of household characteristics and farm attributes are important factors determining the relative probability of selecting a particular labour market participation regime. Social implications Facilitating access to credit in rural Burkina Faso can encourage farm households to use hired labour in agricultural production and thereby positively impacting farm productivity and relieving unemployment pressures. Originality/value In order to identify the effect of credit constraints on farm households’ labour decisions, this study examined farm households’ decisions of hiring on-farm labour, supplying labour off-farm or simultaneously hiring on-farm labour and supplying family labour off-farm under credit constraints using the direct elicitation approach of credit constraints. To the best of the authors’ knowledge, this study is the first to examine this problem in Burkina Faso.

scholarly journals Heterologous Expression of Lysergic Acid and Novel Ergot Alkaloids in Aspergillus fumigatus

2014 ◽  
Vol 80 (20) ◽  
pp. 6465-6472 ◽  
Author(s):  
Sarah L. Robinson ◽  
Daniel G. Panaccione
Keyword(s):  
Aspergillus Fumigatus ◽  
Candidate Genes ◽  
Mass Spectra ◽  
Ergot Alkaloids ◽  
Lysergic Acid ◽  
Precursor Feeding ◽  
Gene Encoding ◽  
Content Type ◽  
Multiple Reactions ◽  
Important Pathway

ABSTRACTDifferent lineages of fungi produce distinct classes of ergot alkaloids. Lysergic acid-derived ergot alkaloids produced by fungi in the Clavicipitaceae are particularly important in agriculture and medicine. The pathway to lysergic acid is partly elucidated, but the gene encoding the enzyme that oxidizes the intermediate agroclavine is unknown. We investigated two candidate agroclavine oxidase genes from the fungusEpichloë festucaevar.lolii×Epichloë typhinaisolate Lp1 (henceforth referred to asEpichloësp. Lp1), which produces lysergic acid-derived ergot alkaloids. Candidate geneseasHandcloAwere expressed in a mutant strain of the moldAspergillus fumigatus, which typically produces a subclass of ergot alkaloids not derived from agroclavine or lysergic acid. Candidate genes were coexpressed with theEpichloësp. Lp1 allele ofeasA, which encodes an enzyme that catalyzed the synthesis of agroclavine from anA. fumigatusintermediate; the agroclavine then served as the substrate for the candidate agroclavine oxidases. Strains expressingeasAandcloAfromEpichloësp. Lp1 produced lysergic acid from agroclavine, a process requiring a cumulative six-electron oxidation and a double-bond isomerization. Strains that accumulated excess agroclavine (as a result ofEpichloësp. Lp1easAexpression in the absence ofcloA) metabolized it into two novel ergot alkaloids for which provisional structures were proposed on the basis of mass spectra and precursor feeding studies. Our data indicate that CloA catalyzes multiple reactions to produce lysergic acid from agroclavine and that combining genes from different ergot alkaloid pathways provides an effective strategy to engineer important pathway molecules and novel ergot alkaloids.

The impact of executives’ perceptions of environmental threats and organizational slack on innovation strategies

2016 ◽  
Vol 7 (2) ◽  
pp. 216-230 ◽  
Author(s):  
Chengyuan Wang ◽  
Biao Luo ◽  
Yong Liu ◽  
Zhengyun Wei
Keyword(s):  
Cognitive Theory ◽  
Environmental Changes ◽  
Ordinary Least Squares ◽  
Organizational Slack ◽  
Least Squares Regression ◽  
Content Type ◽  
Environmental Threats ◽  
Innovation Strategies ◽  
The Impact ◽  
The Relationship

Purpose The paper aims to study the relationship between executives’ perceptions of environmental threats and innovation strategies and investigate the moderating effect of contextual factor (i.e. organizational slack) on such relations. It proposes a dualistic relationship between executives’ perceptions of environmental threats and innovation strategies, in which different perceptions of environmental threats will lead to corresponding innovation strategies, and dyadic organizational slack can promote such processes. Design/methodology/approach The paper is based on a survey with 163 valid questionnaires, which were all completed by executives. Hierarchical ordinary least-squares regression analysis is used to test the hypotheses proposed in this paper. Findings The paper provides empirical insights about that executives tend to choose exploratory innovation when they perceive environmental changes as likely loss threats, yet adopt exploitative innovation when perceiving control-reducing threats. Furthermore, unabsorbed slack (e.g. financial redundancy) positively moderates both relationships, while absorbed slack (e.g. operational redundancy) merely positively influences the relationship between the perception of control-reducing threats and exploitative innovation. Originality/value The paper bridges the gap between organizational innovation and cognitive theory by proposing a dualistic relationship between executives’ perceptions of environmental threats and innovation strategies. The paper further enriches innovation studies by jointly considering both subjective and objective influence factors of innovation and argues that organizational slack can moderate such dualistic relationship.

scholarly journals Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes

2016 ◽  
Vol 55 (3) ◽  
pp. 844-858 ◽  
Author(s):  
Per Sikora ◽  
Sofia Andersson ◽  
Jadwiga Winiecka-Krusnell ◽  
Björn Hallström ◽  
Cecilia Alsmark ◽  
...  
Keyword(s):  
Parasite Burden ◽  
Genomic Variation ◽  
Loss Of Function ◽  
Oocyst Wall ◽  
Gene Encoding ◽  
Cryptosporidium Hominis ◽  
Content Type ◽  
Successful Isolation ◽  
Target Dna ◽  
Stool Samples

ABSTRACTIn order to improve genotyping and epidemiological analysis ofCryptosporidiumspp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 differentCryptosporidium hominispatient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17× and 490× coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encodingCryptosporidiumoocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to theCryptosporidium parvumreference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in theC. hoministree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencingCryptosporidiumdirectly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes ofCryptosporidiumfrom human fecal samples, while alluding to the potential for a higher degree of genotyping withinCryptosporidiumepidemiology.

The role of organizational learning in soft regulation of workplace gender equality

2017 ◽  
Vol 39 (3) ◽  
pp. 317-334 ◽  
Author(s):  
Johanna Macneil ◽  
Ziheng Liu
Keyword(s):  
Organizational Learning ◽  
Gender Equality ◽  
Significant Shift ◽  
Policy And Practice ◽  
Content Type ◽  
Large Organization ◽  
Regulatory Processes ◽  
Responsible Government ◽  
Reported Data

Purpose The purpose of this paper is to explain progress, or the lack of it, in achieving workplace gender equality goals prescribed by affirmative action regulation by using concepts from soft regulation and organizational learning. Design/methodology/approach The research design is a longitudinal study (2002-2012) of a critical case, that of a single large organization in the male-dominated steel manufacturing, distribution and mining industries. The case focusses on the evidence about organizational learning to be found in that organization’s reports to government on its activities to promote workplace gender equality. Findings While other factors play a role, the apparent failure of the soft regulation to generate a significant shift in gender equality outcomes may also be attributed to ineffective organizational learning, demonstrated by the absence of systematic reflection within the organization on how to improve workplace gender equality, and the lack of firm targets and external benchmarking. Research limitations/implications Self-reported data may be overstated or incomplete. More research is needed to confirm the nature of the specific learning processes occurring within organizations. Practical implications Absent the advent of hard sanctions in workplace gender equality regulation, the responsible government agencies may find it valuable to focus on ways to encourage target organizations to develop competence in organizational learning. Social implications More effective gender equality regulation may change organizational policy and practice and improve work opportunities for women. Originality/value Rather than concluding that the only alternative, when soft regulation is unsuccessful, is hard regulation, this paper shifts the focus to ways that soft regulatory processes might be improved to strengthen their effect.

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