bluuebunny/crossref_metadata_2025_split huggingface dataset:
cAMP-independent control of twitching motility inPseudomonas aeruginosa
Authors: Buensuceso Ryan N.C. , Daniel-Ivad Martin , Kilmury Sara L.N. , Harvey Hanjeong , Howell P. Lynne , Burrows Lori L. 
Published: March 2017

ABSTRACTFimV is aPseudomonas aeruginosainner membrane hub protein that modulates levels of the second messenger, cyclic AMP (cAMP), through activation of the adenylate cyclase, CyaB. Although type IVa pilus (T4aP)-dependent twitching motility is modulated by cAMP levels, mutants lacking FimV are twitching impaired, even when exogenous cAMP is provided. Here we further define FimV’s cAMP-dependent and -independent regulation of twitching. We confirmed that the response regulator of the T4aP-associated Chp chemotaxis system, PilG, required both FimV and the CyaB regulator, FimL, to activate CyaB. However, in cAMP-replete backgrounds - lacking the cAMP phosphodiesterase CpdA or the CheY-like protein PilH, or expressing constitutively-active CyaB -pilGandfimVmutants failed to twitch. Both cytoplasmic and periplasmic domains of FimV were important for its cAMP-dependent and -independent roles, while its septal peptidoglycan-targeting LysM motif was required only for twitching motility. Polar localization of the sensor kinase PilS, a key regulator of transcription of the major pilin, was FimV-dependent. However, unlike its homologues in other species that localize flagellar system components, FimV was not required for swimming motility. These data provide further evidence to support FimV’s role as a key hub protein that coordinates the polar localization and function of multiple structural and regulatory proteins involved inP. aeruginosatwitching motility.IMPORTANCEPseudomonas aeruginosais a serious opportunistic pathogen. Type IVa pili (T4aP) are important for its virulence, because they mediate dissemination and invasion via twitching motility, and are involved in surface sensing which modulates pathogenicity via changes in cAMP levels. Here we show that the hub protein FimV and the response regulator of the Chp system, PilG, regulate twitching independently of their roles in modulation of cAMP synthesis. These functions do not require the putative scaffold protein FimL, proposed to link PilG with FimV. PilG may regulate asymmetric functioning of the T4aP system to allow for directional movement, while FimV appears to localize both structural and regulatory elements – including the PilSR two-component system – to cell poles for optimal function.
Molecular basis underlying male sterility in bHLH142 overexpressing rice
Authors: Ko Swee-Suak , Li Min-Jeng , Lin Yi-Jyun , Hsing Hong-Xian , Yang Ting-Ting , Chen Tien-Kuan , Jhong Chung-Min , Ku Maurice Sun-Ben 
Published: March 2017

AbstractDevelopment of stable male sterility lines is essential for efficient hybrid seed production. We previously showed that knockout ofbHLH142in rice (Oryza sativa) causes pollen sterility by interrupting tapetal programmed cell death (PCD). In this study, we demonstrated that overexpression ofbHLH142(OE142) under the control of ubiquitin promoter also leads to male sterility in rice by triggering the premature onset of PCD. Protein of bHLH142 was found to accumulate specifically in the OE142 anthers. Overexpression of bHLH142 induced early expression of several key regulatory transcription factors in pollen development. In particular, the upregulation of EAT1 at the early stage of pollen development promoted premature PCD in the OE142 anthers, while its downregulation at the late stage impaired pollen development by suppressing genes involved in pollen wall biosynthesis, ROS scavenging and PCD. Collectively, these events led to male sterility in OE142. Analyses of related mutants further revealed the hierarchy of these pollen development regulatory genes. Thus, the findings of this study create a new method to generate genic male sterility in rice. Exploitation of this novel functionality ofbHLH142would confer a big advantage to hybrid seed production.HighlightOverexpression ofbHLH142leads to male sterility in transgenic rice due to early onset of tapetal PCD. This study creates a new method to generate male sterility in rice.
Dual RNA-seq reveals no plastic transcriptional response of the coccidian parasiteEimeria falciformisto host immune defenses
Authors: Ehret Totta , Spork Simone , Dieterich Christoph , Lucius Richard , Heitlinger Emanuel 
Published: March 2017

ABSTRACTBackgroundParasites can either respond to differences in immune defenses that exist between individual hosts plastically or, alternatively, follow a genetically canalized (“hard wired”) program of infection. Assuming that large-scale functional plasticity would be discernible in the parasite transcriptome we have performed a dual RNA-seq study of the full lifecycle ofEimeria falciformisusing infected mice with different immune status (e.g. naïve versus immune animals) as models for coccidian infections.ResultsWe compared parasite and host transcriptomes (dual transcriptome) between naïve and challenge infected mice, as well as between immune competent and immune deficient ones. Mice with different immune competence show transcriptional differences as well as differences in parasite reproduction (oocyst shedding). Broad gene categories represented by differently abundant host genes indicate enrichments for immune reaction and tissue repair functions. More specifically, TGF-beta, EGF, TNF and IL-1 and IL-6 are examples of functional annotations represented differently depending on host immune status. Much in contrast, parasite transcriptomes were neither different between Coccidia isolated from immune competent and immune deficient mice, nor between those harvested from naïve and challenge infected mice. Instead, parasite transcriptomes have distinct profiles early and late in infection, characterized largely by biosynthesis or motility associated functional gene groups, respectively. Extracellular sporozoite and oocyst stages showed distinct transcriptional profiles and sporozoite transcriptomes were found enriched for species specific genes and likely pathogenicity factors.ConclusionWe propose that the niche and host-specific parasiteE. falciformisuses a genetically canalized program of infection. This program is likely fixed in an evolutionary process rather than employing phenotypic plasticity to interact with its host. In turn this might (negatively) influence the ability of the parasite to use different host species and (positively or negatively) influence its evolutionary potential for adaptation to different hosts or niches.
Inhibitory engrams in perception and memory
Authors: Barron Helen , Vogels Tim P. , Behrens Timothy , Ramaswami Mani 
Published: March 2017

SUMMARYNervous systems use excitatory cell assemblies or “perceptual engrams” to encode and represent sensory percepts. Similarly, synaptically connected cell assemblies or “memory engrams” are thought to represent memories of past experience. Multiple lines of recent evidence indicate that brain systems also create inhibitory replicas of excitatory engrams with important cognitive functions. Such matched inhibitory engrams may form through homeostatic potentiation of inhibition onto postsynaptic cells that show increased levels of excitation. Inhibitory engrams can reduce behavioral responses to familiar stimuli thereby resulting in behavioral habituation. In addition, by preventing inappropriate activation of excitatory memory engrams, inhibitory engrams can make memories quiescent, stored in a latent form that is available for contextrelevant activation. In neural networks with balanced excitatory and inhibitory engrams, the release of innate responses and recall of associative memories can occur through focussed disinhibition. Understanding mechanisms that regulate the formation and expression of inhibitory engramsin vivomay help not only to explain key features of cognition, but also to provide insight into transdiagnostic traits associated with psychiatric conditions such as autism, schizophrenia and post-traumatic stress disorder (PTSD).
Catalytic properties of RNA polymerases IV and V: accuracy, nucleotide incorporation and rNTP/dNTP discrimination
Authors: Marasco Michelle , Li Weiyi , Lynch Michael , Pikaard Craig S. 
Published: March 2017

AbstractCatalytic subunits of DNA-dependent RNA polymerases of bacteria, archaea and eukaryotes share hundreds of ultra-conserved amino acids. Remarkably, the plant-specific RNA silencing enzymes, Pol IV and Pol V differ from Pols I, II and III at ~140 of these positions, yet remain capable of RNA synthesis. Whether these amino acid changes in Pols IV and V alter their catalytic properties in comparison to Pol II, from which they evolved, is unknown. Here, we show that Pols IV and V differ from one another, and Pol II, in nucleotide incorporation rate, transcriptional accuracy and the ability to discriminate between ribonucleotides and deoxyribonucleotides. Pol IV transcription is notably error-prone, which may be tolerable, or even beneficial, for biosynthesis of siRNAs targeting transposon familiesin trans.By contrast, Pol V exhibits high fidelity transcription, suggesting a need for Pol V transcripts to faithfully reflect the DNA sequence of target loci in order to recruit siRNA-Argonaute protein silencing complexes.
Geographically structured genetic variation in theMedicago lupulina–Ensifermutualism
Authors: Harrison Tia L. , Wood Corlett W. , Heath Katy D. , Stinchcombe John R. 
Published: March 2017

AbstractMutualisms are interspecific interactions affecting the ecology and evolution of species. Patterns of geographic variation in interacting species may play an important role in understanding how variation is maintained in mutualisms, particularly in introduced ranges. One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legumeMedicago lupulinaand two rhizobial species (Ensifer medicaeandE. meliloti),we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions ofE. melilotiin southeastern populations and high proportions ofE. medicaein northwestern populations.Medicago lupulinaand theEnsifergenus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the twoEnsiferspecies was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution betweenM. lupulinaand theEnsifergenus, but not betweenM. lupulinaand eitherEnsiferspecies.
Single molecule, full-length transcript sequencing provides insight into the extreme metabolism of ruby-throated hummingbirdArchilochus colubris
Authors: Workman Rachael E. , Myrka Alexander M. , Tseng Elizabeth , Wong G. William , Welch Kenneth C. , Timp Winston 
Published: March 2017

AbstractHummingbirds can support their high metabolic rates exclusively by oxidizing ingested sugars, which is unsurprising given their sugar-rich nectar diet and use of energetically expensive hovering flight. However, they cannot rely on dietary sugars as a fuel during fasting periods, such as during the night, at first light, or when undertaking long-distance migratory flights, and must instead rely exclusively on onboard lipids. This metabolic flexibility is remarkable both in that the birds can switch between exclusive use of each fuel type within minutes and in thatde novolipogenesis from dietary sugar precursors is the principle way in which fat stores are built, sometimes at exceptionally high rates, such as during the few days prior to a migratory flight. The hummingbird hepatopancreas is the principle location ofde novolipogenesis and likely plays a key role in fuel selection, fuel switching, and glucose homeostasis. Yet understanding how this tissue, and the whole organism, achieves and moderates high rates of energy turnover is hampered by a fundamental lack of information regarding how genes coding for relevant enzymes differ in their sequence, expression, and regulation in these unique animals. To address this knowledge gap, we generated ade novotranscriptome of the hummingbird liver using PacBio full-length cDNA sequencing (Iso-Seq), yielding a total of 8.6Gb of sequencing data, or 2.6M reads from 4 different size fractions. We analyzed data using the SMRTAnalysis v3.1 Iso-Seq pipeline, including classification of reads and clustering of isoforms (ICE) followed by error-correction (Arrow). With COGENT, we clustered different isoforms into gene families to generatede novogene contigs. We performed orthology analysis to identify closely related sequences between our transcriptome and other avian and human gene sets. We also aligned our transcriptome against theCalypte annagenome where possible. Finally, we closely examined homology of critical lipid metabolic genes between our transcriptome data and avian and human genomes. We confirmed high levels of sequence divergence within hummingbird lipogenic enzymes, suggesting a high probability of adaptive divergent function in the hepatic lipogenic pathways. Our results have leveraged cutting-edge technology and a novel bioinformatics pipeline to provide a compelling first direct look at the transcriptome of this incredible organism.
Characterizing US dairy farm income and wealth distributions
Authors: Hadrich Joleen C. , Wolf Christopher A. , Johnson Kamina K. 
Published: March 2017

Purpose
The structural change of the dairy industry has been a long-term process with fewer, larger dairy herds in all regions. The purpose of this paper is to evaluate whether this structural change is leading to less income and wealth equality across dairy farms and how these factors differ across the USA.

Design/methodology/approach
Income and wealth inequality of US dairy farms was estimated by Gini coefficients using data from the 2000 and 2010 ARMS dairy costs and returns data. A population-level quantile regression was estimated at decile increments to determine the factors that affect net farm income (NFI) and net worth (NETW) and if they changed across the time periods.

Findings
Adjusted-Gini coefficients were estimated and indicated that income inequality was greater than wealth inequality across US dairy farms. Results of the quantile regressions confirm regional differences exist with dairy farms in Mountain regions consistently having lower NFI and NETW relative to farms in the Lake States region when factors such as herd size were equal. Life cycle effects were not observed for NFI, but present within NETW estimates across the ten years.

Originality/value
This analysis estimates industry-specific-adjusted Gini coefficients to determine if income and wealth inequality exist.
Agricultural credit risk and the macroeconomy
Authors: Johnson Andrew M. , Boehlje Michael D. , Gunderson Michael A. 
Published: March 2017

Purpose
The purpose of this paper is to explore the linkage between agricultural sector and macroeconomic factors with farm financial health. It considers whether agricultural lenders can more accurately anticipate changes in the credit quality of their portfolios by considering broad economic indicators outside the agriculture sector.

Design/methodology/approach
This paper examines firm, sector, and macroeconomic drivers of probability of default (PD) migrations from a sample of 153 grain farms of actual lender data from Farm Credit Mid-America’s portfolio. A series of ordered logit models are developed.

Findings
Farm-level and sector-level variables have the most significant impact on PD migrations. Equity to asset ratios, working capital to gross farm income ratios, and gross corn income per acre are found to be the most significant drivers of PD migrations. Macroeconomic variables are shown to unreliably forecast PD migrations, suggesting that agricultural lenders should emphasize firm and sector variables over macroeconomic factors in credit risk models.

Originality/value
This paper builds the literature on agricultural credit risk by testing a broader set of sector and macroeconomic variables than previous articles. Also, prior articles measured the direction but not magnitude of PD migrations; the ordered model in the analysis measures both.
Food security and nutrition in an urbanizing world
Authors: Fan Shenggen , Cho Emily EunYoung , Rue Christopher 
Published: March 2017

Purpose
The paper is a synthesis of the 2017 Global Food Policy Report, and the purpose of this paper is to put into perspective the major food policy issues, developments, and decisions of 2016 and highlights challenges and opportunities for 2017.

Design/methodology/approach
The paper presents an overview of recent changes in the global context for food security and nutrition, and synthesizes research findings on major issues that arise in an urbanizing world. Based on its findings, the authors present policy recommendations and areas for future research for food security and nutrition.

Findings
Urbanization is linked with dietary changes to more energy-dense diets, and, the triple burden of malnutrition is increasing, particularly in rapidly urbanizing developing countries. Rural-urban linkages are key to improving food security and nutrition in both rural and urban areas, and traditional agricultural value chains linking farms to cities are undergoing a “quiet revolution.” Governance to enhance food security in the context of rapid urbanization faces various challenges in the institutional, administrative, and political realms, especially for the informal economy in developing countries. To address the unique challenges of urbanization, policies will need to create enabling environments, promote efficient and inclusive value chains, improve governance, and promote tailored programs. Research gaps that need to be filled include better, updated, and disaggregated data on food security and nutrition, as well as an enhanced understanding of enabling environments.

Originality/value
The paper highlights the increasingly relevant issue of rapid urbanization, especially in developing countries, for food security and nutrition, and synthesizes recent research in this area.
Traders’ market power along Indonesian rubber value chains
Authors: Kopp Thomas , Brümmer Bernhard 
Published: March 2017

Purpose
While traders of agricultural products are known to often exercise market power, this power has rarely been quantified for developing countries. The paper aims to discuss this issue.

Design/methodology/approach
In order to derive a measure, the authors estimate the traders’ revenue functions and calculate the marginal value products directly from them. The authors subsequently find the determinants affecting their individual market power.

Findings
Results show that market power at the traders’ level exists and is substantial. This market power is amplified in situations of extreme remoteness, and weakens with increasing market size.

Originality/value
An exceptional data set with detailed information on the business practices of rubber traders in Jambi, Indonesia is employed with an innovative methodology to directly estimate revenue functions.
Looking out or looking up: gender differences in expatriate turnover intentions
Authors: Lee Hyun-Jung , Chua Chei Hwee , Miska Christof , Stahl Günter K. 
Published: March 2017

PurposeWith the steady increase in the number of female expatriates and multinational corporations’ (MNCs’) pressing need for global female talent, understanding the factors that attract and retain female expatriates is urgent. Drawing from the literatures on gender differences in (domestic) labor turnover and gender differences in social networks, the purpose of this paper is to investigate gender differences in expatriates’ turnover intentions.Design/methodology/approachThe authors collected data via a questionnaire survey from an international sample of female (n=164) and male (n=1,509) expatriates who were on a company-sponsored international assignment at the time of completing the survey.FindingsThe findings show that female expatriates’ turnover intentions are mainly explained by satisfaction with company support. In contrast, male expatriates’ turnover intentions are explained by repatriation concerns and perceived gap between within- and outside-company career-advancement opportunities, in addition to satisfaction with company support. The authors did not find any gender differences in the levels of turnover intentionper se.Practical implicationsSince males dominate the expatriate cadre of most companies, existing expatriate retention strategies are likely to be geared toward males. Companies that value and want to retain their female talent need to gain a better understanding of what matters to female expatriates in their decisions to stay or leave the company, and adjust their expatriation and repatriation management strategies accordingly.Originality/valueThe study is one of the first to empirically test the gender differences in expatriate turnover intentions. The authors propose two underlying mechanisms that explain gender differences in expatriate turnover intentions: social integration and career advancement. The findings point to an important new research frontier that focuses on gender differences in the underlying mechanisms of turnover intentions rather than in the level of turnover intentions.
The effectiveness of transformational leadership on empowerment
Authors: Kim Soyeon , Shin Mannsoo 
Published: March 2017

PurposeThe purpose of this paper is to investigate the influence of gender on the effectiveness of transformational leadership. Drawing on role congruity theory, it elucidates the moderating effects of leader gender, subordinate gender, and leader-subordinate gender dyad on the relationship between transformational leadership and psychological empowerment.Design/methodology/approachEmployees of companies in Korea responded to a paper-pencil survey, rating their psychological empowerment and leadership behaviors of their direct leader on a five-point Likert-type scale. The analysis includes 339 responses.FindingsThe results indicate that a leader’s gender has no significant moderating effect on psychological empowerment, but the gender of the subordinate has a significant moderating effect, with male subordinates more strongly influenced by transformational leadership than female subordinates. Notably, the findings show that the effectiveness of transformational leadership is contingent on the leader-subordinate gender dyad. Specifically, transformational leadership has as significant an effect on female leader-male subordinate dyads as on male leader-male subordinate dyads.Research limitations/implicationsThis study contributes to leadership and gender studies in the management field by investigating the effect of gender roles on the effectiveness of transformational leadership. Future research should extend this study and explore whether these findings are generalizable.Practical implicationsThe remarkable finding of the effect of female leadership on employee empowerment suggests organizations should use more female leaders.Originality/valueThis is the first empirical study to shed light on gender issues in relation to transformational leadership in Korea.