bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors
Authors: Hohmann Ulrich , Santiago Julia , Nicolet Joël , Olsson Vilde , Spiga Fabio M. , Hothorn Ludwig A. , Butenko Melinka A. , Hothorn Michael
Published: March 2018

Significance

Plants contain a unique family of membrane receptors, which are different from the ones found in bacteria and animals. These proteins are able to sense very different signals, such as steroid molecules, peptides, and proteins at the cell surface using a spiral-shaped ligand binding domain. Ligand binding allows the receptor to engage with a smaller coreceptor kinase, which is shared among different receptors. Here it is analyzed how one coreceptor protein can contribute to the sensing of two different ligands involved in plant growth and organ abscission and to activation of their cognate receptors.
Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia
Authors: Valdiosera Cristina , Günther Torsten , Vera-Rodríguez Juan Carlos , Ureña Irene , Iriarte Eneko , Rodríguez-Varela Ricardo , Simões Luciana G. , Martínez-Sánchez Rafael M. , Svensson Emma M. , Malmström Helena , Rodríguez Laura , Bermúdez de Castro José-María , Carbonell Eudald , Alday Alfonso , Hernández Vera José Antonio , Götherström Anders , Carretero José-Miguel , Arsuaga Juan Luis , Smith Colin I. , Jakobsson Mattias
Published: March 2018

Significance

The gene pool of modern Europeans was shaped through prehistoric migrations that reached the Western Mediterranean last. Obtaining biomolecular data has been challenging due to poor preservation related to adverse climatic conditions in this region. Here, we study the impact of prehistoric (Neolithic–Bronze Age) migrations in Iberia by analyzing genomic and dietary data, demonstrating that farming practices were introduced by a population genetically distinct from the first farmers in central and northern Europe. After recovering from a founder bottleneck, these first farmers mixed with local hunter-gatherers. Finally, post-Neolithic migrations had a much smaller impact on the Iberian gene pool than they had in other parts of Europe. Stable isotope analysis reveals a homogenous terrestrial diet throughout this period.
Human diets drive range expansion of megafauna-dispersed fruit species
Authors: van Zonneveld Maarten , Larranaga Nerea , Blonder Benjamin , Coradin Lidio , Hormaza José I. , Hunter Danny
Published: March 2018

Significance

Neotropical fruit species once dispersed by megafauna have regained relevance for diversifying human diets to address malnutrition. Little is known about the historic interactions between humans and these fruit species. We quantified the human role in modifying distribution ranges of Neotropical fruit species by comparing the distribution of fruit species that have been part of both human and megafauna diets with fruit species that were exclusively part of megafauna diets. Our results show that human food usage has expanded the distribution of species that would otherwise have suffered range contraction after extinction of megafauna. Our analyses help in identifying range segments of fruit species that may hold key genetic diversity to sustain food systems and to maintain critical ecosystem functions.
Structural changes of TasA in biofilm formation of
Bacillus subtilis
Authors: Diehl Anne , Roske Yvette , Ball Linda , Chowdhury Anup , Hiller Matthias , Molière Noel , Kramer Regina , Stöppler Daniel , Worth Catherine L. , Schlegel Brigitte , Leidert Martina , Cremer Nils , Erdmann Natalja , Lopez Daniel , Stephanowitz Heike , Krause Eberhard , van Rossum Barth-Jan , Schmieder Peter , Heinemann Udo , Turgay Kürşad , Akbey Ümit , Oschkinat Hartmut
Published: March 2018

Significance

Understanding the formation and structure of protective bacterial biofilms will help to design and identify antimicrobial strategies. Our experiments with the secreted major biofilm protein TasA characterize on a molecular level in vivo the transition of a folded protein into protease-resistant biofilm-stabilizing fibrils. Such conformational changes from a globular state into fibrillar structures are so far not seen for other biofilm-forming proteins. In this context, TasA can serve as a model system to study functional fibril formation from a globular state.
Complex electrophysiological remodeling in postinfarction ischemic heart failure
Authors: Hegyi Bence , Bossuyt Julie , Griffiths Leigh G. , Shimkunas Rafael , Coulibaly Zana , Jian Zhong , Grimsrud Kristin N. , Sondergaard Claus S. , Ginsburg Kenneth S. , Chiamvimonvat Nipavan , Belardinelli Luiz , Varró András , Papp Julius G. , Pollesello Piero , Levijoki Jouko , Izu Leighton T. , Boyd W. Douglas , Bányász Tamás , Bers Donald M. , Chen-Izu Ye
Published: March 2018

Significance

Cardiac arrhythmias often occur in heart failure (HF) patients, but drug therapies using selective ion channel blockers have failed clinical trials and effective drug therapies remain elusive. Here we systematically study the major ionic currents during the cardiac action potential (AP) and arrhythmogenic Ca
2+
release in postinfarction HF. We found that changes in any individual current are relatively small, and alone could mislead as to consequences. However, differential changes in multiple currents integrate to shorten AP in the infarct border zone but prolong AP in the remote zone, increasing AP repolarization inhomogeneity. Our findings help explain why single channel-blocker therapy may fail, and highlight the need to understand the integrated changes of ionic currents in treating arrhythmias in HF.
Archaeal acetoacetyl-CoA thiolase/HMG-CoA synthase complex channels the intermediate via a fused CoA-binding site
Authors: Vögeli Bastian , Engilberge Sylvain , Girard Eric , Riobé François , Maury Olivier , Erb Tobias J. , Shima Seigo , Wagner Tristan
Published: March 2018

Significance

Mevalonate is a building block of archaeal lipids. Three enzymes are involved in its biosynthesis: acetoacetyl-CoA thiolase (thiolase), 3-hydroxy-3-methylglutaryl (HMG)-CoA synthase (HMGCS), and HMG-CoA reductase. The thiolase reaction is highly endergonic, which means that archaea have to find a way to overcome this low-flux bottleneck. Our work revealed the presence of a thiolase/HMGCS complex, which directly couples the endergonic thiolase reaction to the exergonic HMGCS reaction. An unexpected third protein spatially connects the thiolase and HMGCS. Strikingly, these two enzymes share the same substrate-binding site. Genomic information indicated that the presence of a thiolase/HMGCS complex is common in most of archaea and many bacteria. Such a natural intermediate-channeling system could lead to new strategies to improve biotechnological mevalonate synthesis.
Noncatalytic aspartate at the exonuclease domain of proofreading DNA polymerases regulates both degradative and synthetic activities
Authors: del Prado Alicia , Franco-Echevarría Elsa , González Beatriz , Blanco Luis , Salas Margarita , de Vega Miguel
Published: March 2018

Significance

Replicative DNA polymerases (DNAPs) combine two processes to ensure the extremely faithful synthesis of DNA, nucleotide selectivity, and editing of misinserted nucleotides by a 3′-5′ exonuclease activity. The 3′-5′ exonuclease activity is governed by four universally conserved aspartate residues that coordinate the two metal ions responsible for the hydrolysis of the last phosphodiester bond of the primer strand. In this work, we have identified an additional conserved aspartate residue that establishes multiple interactions with residues responsible for the exonucleolysis and for the forward movement of the DNAP along the DNA after inserting a nucleotide, acting as a master organizer for the processive intramolecular proofreading of polymerization errors.
Rapid growth of the US wildland-urban interface raises wildfire risk
Authors: Radeloff Volker C. , Helmers David P. , Kramer H. Anu , Mockrin Miranda H. , Alexandre Patricia M. , Bar-Massada Avi , Butsic Van , Hawbaker Todd J. , Martinuzzi Sebastián , Syphard Alexandra D. , Stewart Susan I.
Published: March 2018

Significance

When houses are built close to forests or other types of natural vegetation, they pose two problems related to wildfires. First, there will be more wildfires due to human ignitions. Second, wildfires that occur will pose a greater risk to lives and homes, they will be hard to fight, and letting natural fires burn becomes impossible. We examined the number of houses that have been built since 1990 in the United States in or near natural vegetation, in an area known as the wildland-urban interface (WUI), and found that a large number of houses have been built there. Approximately one in three houses and one in ten hectares are now in the WUI. These WUI growth trends will exacerbate wildfire problems in the future.
Disinhibition of CA1 pyramidal cells by low-dose ketamine and other antagonists with rapid antidepressant efficacy
Authors: Widman Allie J. , McMahon Lori L.
Published: March 2018

Significance

Ketamine is an NMDA receptor (NMDAR) antagonist that alleviates depressive symptoms in patients with treatment-resistant depression within hours of administering a single dose. However, psychoactive side effects limit its use. Understanding the mechanism underlying ketamine’s antidepressant effect is crucial in identifying targets for novel therapeutics with fewer side effects. Here, we report ketamine enhances excitability of pyramidal cells indirectly by reducing synaptic GABAergic inhibition, thus causing disinhibition. Additionally, we investigated whether other NMDAR antagonists and the muscarinic acetylcholine receptor antagonist scopolamine shared this disinhibition mechanism. Our results show that only those antagonists with antidepressant efficacy in humans disinhibit pyramidal cells at a clinically relevant concentration, supporting the concept that disinhibition is likely involved in the antidepressant effect of these antagonists.
Deletion of dopamine D
2
receptors from parvalbumin interneurons in mouse causes schizophrenia-like phenotypes
Authors: Tomasella Eugenia , Bechelli Lucila , Ogando Mora Belén , Mininni Camilo , Di Guilmi Mariano N. , De Fino Fernanda , Zanutto Silvano , Elgoyhen Ana Belén , Marin-Burgin Antonia , Gelman Diego M.
Published: March 2018

Significance

Schizophrenia and bipolar disorder are psychiatric syndromes with a significant social and economic burden that share a common symptom, psychosis, attributed to excessive dopamine release. Despite years of intensive research, the causes of these devastating diseases are still unknown. In this work, a mouse line with a selective deletion of the molecular target of antipsychotics, dopamine D
2
receptors, from the most affected neuron subtype in patients, parvalbumin interneurons, results in animals with schizophrenia-like phenotypes and resistance to the broadly used antipsychotic aripiprazole. Therefore, this genetic dissection provides clues about the intrinsic molecular mechanism leading to a dysregulated dopamine system and the development of psychiatric conditions like schizophrenia, bringing opportunities to develop diagnostic and treatment approaches.
Geospatial analysis of near-term potential for carbon-negative bioenergy in the United States
Authors: Baik Ejeong , Sanchez Daniel L. , Turner Peter A. , Mach Katharine J. , Field Christopher B. , Benson Sally M.
Published: March 2018

Significance

Bioenergy with carbon capture and storage (BECCS) is widely utilized in ambitious climate mitigation scenarios as a negative-emissions technology. However, the future technical potential of BECCS remains uncertain. Two significant deployment barriers that have largely been overlooked by previous studies are the suitability of existing storage sites and the availability of transportation of biomass and/or CO
2
. This study assesses the near-term deployment potential of BECCS in the United States in the absence of long-distance transportation networks. Considering these constraints, 30% of the projected available 2020 biomass resources can be utilized for BECCS, yielding a negative-emissions potential of 100 Mt CO
2
⋅y
−1
. The analysis further pinpoints areas with colocated resources that could be prioritized for near-term deployment of BECCS.
Direct observation of ultrafast large-scale dynamics of an enzyme under turnover conditions
Authors: Aviram Haim Yuval , Pirchi Menahem , Mazal Hisham , Barak Yoav , Riven Inbal , Haran Gilad
Published: March 2018

Significance

The potential effect of conformational dynamics of enzymes on their chemical steps has been intensely debated recently. We use single-molecule FRET experiments on adenylate kinase (AK) to shed new light on this question. AK closes its domains to bring its two substrate close together for reaction. We show that domain closure takes only microseconds to complete, which is two orders of magnitude faster than the chemical reaction. Nevertheless, active-site mutants that reduce the rate of domain closure also reduce the reaction rate, suggesting a connection between the two phenomena. We propose that ultrafast domain closure is used by enzymes as a mechanism to optimize mutual orientation of substrates, a novel mode of coupling between conformational dynamics and catalysis.
Regional pest suppression associated with widespread Bt maize adoption benefits vegetable growers
Authors: Dively Galen P. , Venugopal P. Dilip , Bean Dick , Whalen Joanne , Holmstrom Kristian , Kuhar Thomas P. , Doughty Hélène B. , Patton Terry , Cissel William , Hutchison William D.
Published: March 2018

Significance

Area-wide
Bacillus thuringiensis
(Bt) adoption suppresses pests regionally, with declines expanding beyond the planted Bt crops into other non-Bt crop fields. The offsite benefits to vegetable crops from such pest suppression have not been documented. We show that widespread Bt field corn adoption is strongly associated with marked decreases in the number of recommended insecticidal applications, insecticides applied, and damage to vegetable crops in the United States. These positive impacts to growers, including organic producers, in the agricultural landscape expands on known ecological effects of Bt adoption.
Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response
Authors: Gao Xinghua , Cao Qiuhua , Cheng Yan , Zhao Dandan , Wang Zhuo , Yang Hongbao , Wu Qijin , You Linjun , Wang Yue , Lin Yanting , Li Xianjing , Wang Yun , Bian Jin-Song , Sun Dongdong , Kong Lingyi , Birnbaumer Lutz , Yang Yong
Published: March 2018

Significance

Stress cannot be avoided in the present competitive world, and chronic stress is associated with detrimental effects on physical health, including the progression of inflammatory bowel disease (IBD). However, the mechanisms behind it are less clearly understood. This study showed that chronic stress disturbed gut microbiota, thereby triggering immune system response and facilitating dextran sulfate sodium-induced colitis. Results also showed stress-deficient expression of mucin-2 and lysozyme, which may contribute to the disorder of gut microbiota. This study adds to our understanding of interactions between microbiota and host and provides the basis for future clinical studies of microbiota manipulation and transplantation and the development of new therapeutic strategies for depression or IBD.
Psychopaths fail to automatically take the perspective of others
Authors: Drayton Lindsey A. , Santos Laurie R. , Baskin-Sommers Arielle
Published: March 2018

Significance

Psychopathic individuals behave in callous and antisocial ways that suggest that these individuals fail to consider what others are thinking (i.e., theory of mind). However, most empirical studies of psychopathy find that, despite their behavior, psychopathic individuals have an intact theory of mind: they successfully predict other’s perspectives. Here, we show that psychopathic individuals have a previously unobserved cognitive deficit that might explain their pattern of destructive and antisocial behavior. We report that psychopathic individuals fail to automatically take the perspective of others, but can deliberately take the perspective of others. These findings suggest that psychopathic individuals have the ability to take the perspective of others but lack the propensity to do so.
EF-Tu and EF-G are activated by allosteric effects
Authors: Mondal Dibyendu , Warshel Arieh
Published: March 2018

Significance

The mechanism of activation of GTPases is a problem of general interest, but despite major effort this issue has not been fully resolved in the case of EF-Tu and EF-G. The open questions include the discrimination between two-water (2W) and one-water (1W) mechanisms and the importance of the allosteric contribution in the activation process. Here, we revisit the above questions by comparing simulations of both EF-Tu and EF-G, as well as by analyzing mutational effects. It is found that both the 2W and 1W mechanisms are possible, but in either case, the activation is an allosteric effect. We also conclude that the allosteric activation is common to other GTPases.
Transcriptome landscape of a bacterial pathogen under plant immunity
Authors: Nobori Tatsuya , Velásquez André C. , Wu Jingni , Kvitko Brian H. , Kremer James M. , Wang Yiming , He Sheng Yang , Tsuda Kenichi
Published: March 2018

Significance

Plants have evolved a powerful innate immune system to defend against microbial pathogens. Despite extensive studies, how plant immunity ultimately inhibits bacterial pathogen growth is largely unknown, due to difficulties in profiling bacterial responses
in planta
. In this study, we established two methods for
in planta
bacterial transcriptome analysis using RNA sequencing. By analyzing 27 combinations of plant immunity mutants and
Pseudomonas syringae
strains, we succeeded in the identification of specific bacterial transcriptomic signatures that are influenced by plant immune activation. In addition, we found that overexpression of an immune-responsive
P. syringae
sigma factor gene involved in iron regulation could partially counter bacterial growth restriction during plant immunity. This study illuminates the enigmatic mechanisms of bacterial growth inhibition by plant immunity.
DEC2 modulates orexin expression and regulates sleep
Authors: Hirano Arisa , Hsu Pei-Ken , Zhang Luoying , Xing Lijuan , McMahon Thomas , Yamazaki Maya , Ptáček Louis J. , Fu Ying-Hui
Published: March 2018

Significance

Sleep is essential for healthy aging, and most people need approximately 8–8-1/2 hours of sleep per night to feel good and to function optimally. We previously reported a proline-to-arginine mutation in DEC2 that leads to a life-long decrease in daily sleep need. We found that the expression of an important sleep-relevant gene,
orexin
, was increased in the DEC2 mutant mice. Further investigation revealed that DEC2 is a transcriptional repressor for orexin expression, and that mutant DEC2 exerts less repressor activity than WT-DEC2, resulting in increased orexin expression. This study represents the first step toward understanding the underlying molecular mechanism through which DEC2 modulates sleep.
Creativity and Incentives
Authors: Charness Gary , Grieco Daniela
Published: March 2018

Creativity is a complex and multidimensional phenomenon with tremendous economic importance. A crucial question for economists and for firms is the interplay of incentives and creativity. We present experiments where subjects face creativity tasks where, in one case, ex ante goals and constraints are imposed on their answers (“closed” tasks), and in the other case no restrictions apply (“open” tasks). The effect of tournament incentives on creativity is then tested. Our experimental findings provide striking evidence that financial incentives in the form of tournament competition affect creativity in “closed” (constrained) tasks, but do not facilitate creativity in “open” (unconstrained) tasks, whereas being ranked relative to one's peers is an effective nonmonetary incentive with both types of tasks. We develop a structural model that allows for subjects’ heterogeneity in being affected by the openness of the task, and then use the structural model to not only estimate creative output in tournaments but also to predict creative output in two counterfactual incentive schemes: piece rate and target bonus.
Spatial extinction date estimation: a novel method for reconstructing spatiotemporal patterns of extinction and identifying potential zones of rediscovery
Authors: Carlson Colin J. , Burgio Kevin R. , Dallas Tad A. , Bond Alexander L.
Published: March 2018

The estimation of extinction dates from limited and incomplete sighting records is a key challenge in conservation (when experts are uncertain whether a species has gone extinct) and historical ecology (when the date and mechanism of extinction is controversial).

We introduce a spatially-explicit method of interpolating extinction date estimators, allowing users to estimate spatiotemporal surfaces of population persistence from georeferenced sighting data of variable quality.

We present the R package spatExtinct, which produces spatially-explicit extinction date surfaces from geolocated sightings, including options for custom randomization schemes to improve accuracy with limited datasets. We use simulations to illustrate the sensitivity of the method to parameterization, and apply the method to identify potential areas where Bachman’s warbler (Vermivora bachmanii) might be rediscovered.

Our method, and the spatExtinct package, has the potential to help describe and differentiate different drivers of extinction for historical datasets, and could be used to identify possible regions of population persistence for species with an uncertain extinction status, improving on non-spatial or imprecise methods that are currently in use.
Genetic variation in Pan species is shaped by demographic history and underlies lineage-specific functions
Authors: Han Sojung , Andrés Aida M. , Marques-Bonet Tomas , Kuhlwilm Martin
Published: March 2018

Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but they show distinct behavioral and physiological differences, particularly regarding female reproduction. Despite their recent rapid decline, the demographic histories of the two species have been different during the past one to two million years, likely having an impact on their genomic diversity. Here, we analyze the inferred functional consequences of genetic variation across 69 individuals, making use of the most complete dataset of genomic variation in the Pan clade to date. We test to which extent the demographic history influences the efficacy of purifying selection in these species. We find that small historical effective population sizes (Ne) correlate not only with small genetic diversity, but also with more homozygous deleterious alleles, and an increased proportion of deleterious changes at low frequencies. Furthermore, we exploit the catalog of deleterious protein-coding changes on each lineage to investigate the putative genetic basis for phenotypic differences between chimpanzees and bonobos. We show that bonobo-specific non-synonymous changes are enriched in genes related to age at menarche in humans, suggesting that the prominent physiological differences in the female reproductive system between chimpanzees and bonobos might be explained, in part, by putatively adaptive changes on the bonobo lineage.
Predictive entrainment of natural speech through two fronto-motor top-down channels
Authors: Park Hyojin , Thut Gregor , Gross Joachim
Published: March 2018

Natural communication between interlocutors is enabled by the ability to predict upcoming speech in a given context. Previously we showed that these predictions rely on a fronto-motor top-down control of low-frequency oscillations in auditory-temporal brain areas that track intelligible speech. However, a comprehensive spatio-temporal characterisation of this effect is still missing. Here, we applied transfer entropy to source-localised MEG data during continuous speech perception. First, at low frequencies (1-4 Hz, brain delta phase to speech delta phase), predictive effects start in left fronto-motor regions and progress to right temporal regions. Second, at higher frequencies (14-18 Hz, brain beta power to speech delta phase), predictive patterns show a transition from left inferior frontal gyrus via left precentral gyrus to left primary auditory areas. Our results suggest a progression of prediction processes from higher-order to early sensory areas in at least two different frequency channels.
Polyamines support myogenesis by facilitating myoblast migration
Authors: Brenner Shirley , Feiler Yulia , Kahana Chaim
Published: March 2018

The regeneration of the muscle tissue relies on the differentiation of myoblasts into myocytes, to create myotubes and myofibers. Disruption of key events in this process may interfere with the correct formation or repair of muscle tissue. Polyamines, ubiquitous polycations that are essential for fundamental cellular processes, were demonstrated necessary for myogenesis; however, the mechanism by which polyamines contribute to this process has not yet been deciphered. In the present study, we examined the effect of polyamine depletion on the muscle regeneration model of C2C12myoblasts. Our results reveal a requirement for polyamines at the very beginning of the muscle differentiation process. Myogenesis is accompanied by polyamine synthesis, even though the myoblasts contain high levels of polyamines at the moment of induction. Polyamine depletion at the time of induction, or inability to synthesize more polyamines during the first 24 hours of the process, inhibited myogenesis. Polyamine depletion inhibited the expression of all tested myogenic markers (Pax7, MyoD, Myogenin, Myf5 and Myosin heavy chain), as well as the cells migration and fusion abilities. Real time PCR analysis revealed two key early activation and migration factors, HGF and Annexin A1.
Molecular Dynamics Simulations of the FtsZ mutant G105S
Authors: Muthukumar Vidyalakshmi C
Published: March 2018

In our previous studies we simulated FtsZ monomer and dimer in different nucleotide binding states. In our simulations, we had used theE.coliFtsZ homology model including the FtsZ Intrinsically Disordered Region (IDR). Our simulations revealed that FtsZ dynamics involves a key stage in which GTP binds to monomeric FtsZ and opens its nucleotide binding site which in turn favours polymerization. During dimerization, the C-terminal of the top monomer rotates considerably towards the bottom monomer. Such a rotation of the C-terminal domain leads to capture of the nucleotide by its N-terminal domain. In this study we simulate the FtsZ G105S mutant to see if it may have ATPase activity which was reported in a previous study.
A morphological and molecular analysis of the species diversity of the cichlid genus Petrochromis from Lake Tanganyika (Teleostei: Cichlidae)
Authors: Mattsson Carl
Published: March 2018

A taxonomic revision of the cichlid fish genus Petrochromis endemic to Lake Tanganyika. All recognized taxa are herein described, one subspecies is given species status and five new species, viz. P. calliris, P. daidali, P. heffalumpus, P. lisachisme and P. paucispinis, are presented. P. calliris is described from 6 specimens from Cape Mpimbwe, and distinguished primarily by having a high number of both gill rakers on the lower limb of the first gill arch and vertebrae. P. daidali is described from 18 specimens from Cape Mpimbwe, Kansombo and Nkwazi point, and distinguished primarily by males having a labyrinth-like pattern on the head. P. heffalumpus is described from 7 specimens from Cape Mpimbwe, and distinguished primarily by its great size. P. lisachisme is described from 12 specimens from Cape Mpimbwe and Lyamembe, and distinguished primarily by having a high number of dorsal spines. P. paucispinis is described from 4 specimens from Halembe, and distinguished primarily by having a low number of dorsal spines. A revised key to Petrochromis is included. A phylogenetic tree hypothesis of the genus, based on molecular (mitochondrial cytochrome b and d-loop) and morphological results show that jaw position and number of vertebrae are important diagnostic characters. Analyses suggest that the “ancestral Petrochromis” might have looked something like P. orthognathus.
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
Authors: Choi Kyuha , Zhao Xiaohui , Tock Andrew J. , Lambing Christophe , Underwood Charles J. , Hardcastle Thomas J. , Serra Heïdi , Kim Juhyun , Cho Hyun Seob , Kim Jaeil , Ziolkowski Piotr A. , Yelina Nataliya E. , Hwang Ildoo , Martienssen Robert A. , Henderson Ian R.
Published: March 2018

Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis thaliana SPO11-1-oligonucleotides. SPO11-1-oligos are elevated in gene promoters, terminators, and introns, which is driven by AT-sequence richness that excludes nucleosomes and allows SPO11-1 access. A positive relationship was observed between SPO11-1-oligos and crossovers genome-wide, although fine-scale correlations were weaker. This may reflect the influence of interhomolog polymorphism on crossover formation, downstream from DSB formation. Although H3K4me3 is enriched in proximity to SPO11-1-oligo hotspots at gene 5′ ends, H3K4me3 levels do not correlate with DSBs. Repetitive transposons are thought to be recombination silenced during meiosis, to prevent nonallelic interactions and genome instability. Unexpectedly, we found high SPO11-1-oligo levels in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. High SPO11-1-oligo transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin in SPO11-1-oligo distributions. Epigenetic activation of meiotic DSBs in proximity to centromeres and transposons occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription, and H3K4me3. Together, our work reveals a complex relationship between chromatin and meiotic DSBs within A. thaliana genes and transposons, with significance for the diversity and evolution of plant genomes.
Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
Authors: Underwood Charles J. , Choi Kyuha , Lambing Christophe , Zhao Xiaohui , Serra Heïdi , Borges Filipe , Simorowski Joe , Ernst Evan , Jacob Yannick , Henderson Ian R. , Martienssen Robert A.
Published: March 2018

Eukaryotic centromeres contain the kinetochore, which connects chromosomes to the spindle allowing segregation. During meiosis, centromeres are suppressed for inter-homolog crossover, as recombination in these regions can cause chromosome missegregation and aneuploidy. Plant centromeres are surrounded by transposon-dense pericentromeric heterochromatin that is epigenetically silenced by histone 3 lysine 9 dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation pathways, for example, via mutation of the H3K9 methyltransferase genes KYP/SUVH4 SUVH5 SUVH6, or the CHG DNA methyltransferase gene CMT3, increases meiotic recombination in proximity to the centromeres. Using immunocytological detection of MLH1 foci and genotyping by sequencing of recombinant plants, we observe that H3K9me2 and non-CG DNA methylation pathway mutants show increased pericentromeric crossovers. Increased pericentromeric recombination in H3K9me2/non-CG mutants occurs in hybrid and inbred backgrounds and likely involves contributions from both the interfering and noninterfering crossover repair pathways. We also show that meiotic DNA double-strand breaks (DSBs) increase in H3K9me2/non-CG mutants within the pericentromeres, via purification and sequencing of SPO11-1-oligonucleotides. Therefore, H3K9me2 and non-CG DNA methylation exert a repressive effect on both meiotic DSB and crossover formation in plant pericentromeric heterochromatin. Our results may account for selection of enhancer trap Dissociation (Ds) transposons into the CMT3 gene by recombination with proximal transposon launch-pads.
Beyond the borders of the local
Authors: Runesson Ulla , Lövström Anna , Hellquist Björn
Published: March 2018

Purpose

The purpose of this paper is to present how experiences gained from a theory-informed lesson study – learning study (LrS) – in regard to a specific learning goal can be shared and used by other teachers in new contexts.

Design/methodology/approach

A group of teachers worked together in a cyclic, iterative process of planning, evaluating and revising teaching. The aim was to provide possibilities for grade 2 and 3 students to become familiar with negative numbers. The teacher group came to the conclusion that the students needed to be able to differentiate some aspects of negative numbers. The conjecture was put to the test in a follow-up study (FS) with five new teachers and eight classes. One lesson was taught based on the empirical findings in the LrS.

Findings

The results suggest that teachers’ collaborative work has possibilities to produce knowledge about critical aspects of learning that can be communicated and adopted in new contexts. The teachers in the FS were able to make sense of the results from LrS and incorporate the critical aspects in their teaching in a way that enhanced students’ learning.

Originality/value

It is demonstrated that teacher collaboration in LrS can create knowledge that goes beyond the border of the local context.
The potential of Lesson Study project as a tool for dealing with dilemmas in university teaching
Authors: Calvo Adelina , Braga Blanco Gloria María , Fueyo Aquilina
Published: March 2018

Purpose

The purpose of this paper is to demonstrate the potential of Lesson Study (LS) as a tool for dealing with dilemmas in university teaching.

Design/methodology/approach

This paper is the result of a LS project which was developed over two academic years (2015-2016 and 2016-2017) in the Faculties of Education and Teacher Training at the Universities of Cantabria and Oviedo (Spain). The research asked the question “How can better learning be achieved?” The starting point for the research methodology was the identification and analysis of teaching dilemmas. The whole process was based on the triangulation of perspectives through the collection of data using techniques such as peer observation, focus groups, interviews, and the writing of the Teacher’s final report. The methodology the authors used was inspired by the Student Voice “movement.”

Findings

The findings show that the potential of LS methodology for professional development in higher education is very promising, enabling teachers to deal with the questions raised by practice collaboratively, broaden their professional knowledge, introduce improvements, and establish new ways of understanding the teaching profession based on a collegial approach.

Originality/value

LS methodology is beginning to be known in Spain. Developments have only taken place very recently and there are still few experiences within the university context. It is not common practice for teaching in higher education to become a public space for reflection and research breaking from the traditional isolation between teachers and incorporating the voices of students.
Reporting sexual violence on mental health wards
Authors: Foley Marian , Cummins Ian
Published: March 2018

Purpose

The purpose of this paper is to report the findings of a scoping study that explored the extent of recorded sexual violence perpetrated on inpatients on mental health (MH) units.

Design/methodology/approach

A Freedom of Information Act (FOI) request was sent to 45 police forces. The FOI asked for the number of recorded offences of rape and sexual assault by penetration for the five years 2010-2015. Following the responses from the police, a similar FOI request was sent to MH trusts.

Findings

There were significant variations in the way that both police forces and MH trusts approached the recording of this information.

Research limitations/implications

The research highlights variation and inadequacy of current recording practices in relation to sexual offences committed against inpatients on MH units.

Practical implications

There needs to be more consistent systems of recording of allegations of sexual assault and responses to them by agencies. In the trust recording of these incidents, it is recommended that a specific category of sexual violence is created. On a national level, the Office for National Statistics should produce a national data set that records the number of rapes that are committed in MH inpatient units.

Originality/value

This paper highlights the “gap” of information in relation to recorded rape and may indicate that complainants with a history of mental illness are less likely to have their allegation recorded as a crime.
The impact of personal income tax rates on the employment decisions of small businesses
Authors: Grace Kathleen
Published: March 2018

Purpose

Small businesses file taxes in accordance with the personal income tax code because they are considered flow-through entities. Thus, personal income tax reforms directly affect the incentives small business owners face regarding employment and operations. The paper aims to discuss these issues.

Design/methodology/approach

The authors use the changes in personal income tax rates during the 1993 and 2001-2003 reforms and micro-level data to estimate the effect of statutory tax rate changes on small business employment decisions.

Findings

The authors add two contributions to the current literature: first, the author allow for intertemporal tax planning and second, the author allow the firm’s decision to employ labor to be correlated with the firm’s wage bill decision. Estimation of a Heckman selection model for wage bills shows that the probability that a business will employ labor is 1.18 percent higher when current tax rates increase by one percentage point and 0.70 percent lower when future rates are expected to increase by one percentage point. Among firms that already employ labor, the median wage bill elasticity with respect to current tax rates is −0.64. These estimates are larger than those reported in previous research because my model includes future taxes and allows for correlation between the firm’s employment and wage bill decisions. Omitting the intertemporal tax responses biases the estimates of previous researchers upwards, whereas assuming the two firm decisions are independent biases estimates towards zero.

Originality/value

This paper has been cited in publications published in Journal of Entrepreneurship and Public Policy.
Heuristic evaluation of e-dictionaries
Authors: Ball Liezl H. , Bothma Theo J.D.
Published: March 2018

Purpose

The purpose of this paper is to discuss the heuristic evaluations of five e-dictionaries according to the criteria developed by Ball and Bothma (2018). E-dictionaries are increasingly making use of modern information technology to create advanced information tools. It is necessary to ensure that these new products are still usable. Heuristic evaluation is a usability evaluation method used to evaluate the usability of a product.

Design/methodology/approach

Five e-dictionaries were evaluated through heuristic evaluation. This method requires an evaluator to evaluate a product by using a set of criteria or guidelines.

Findings

Various usability issues, as well as good features of e-dictionaries, could be identified through these evaluations, and are discussed under the categories of content, information architecture, navigation, access (searching and browsing), help, customisation and use of other innovative technologies.

Originality/value

Through the evaluations in this study, the criteria could be validated and an example of how the criteria can be used to evaluate e-dictionaries could be presented.
Below‐ground processes control the success of an invasive seaweed
Authors: Gribben Paul E. , Thomas Torsten , Pusceddu Antonio , Bonechi Lisa , Bianchelli Silvia , Buschi Emanuela , Nielsen Shaun , Ravaglioli Chiara , Bulleri Fabio
Published: March 2018

Whilst the successful establishment and spread of invasive species can be determined by above‐ground processes, results are often equivocal. Emergent research, mostly from terrestrial ecosystems, demonstrates that below‐ground processes (nutrient cycling, chemical properties) under microbial control can mediate interactions between native and invasive plants. Because microbes can control similar sediment properties in marine ecosystem that influence plant fitness, we argue that below‐ground properties should also exert strong control interactions between native and invasive marine macrophytes.

We coupled surveys of microbial communities and chemistry of sediments collected from an invasive alga (Caulerpa cylindracea), a native competitor (the seagrass Posidonia oceanica) and unvegetated sediments with a large field experiment, in which we manipulated the presence/absence of the canopies of both species to determine the effects of above‐ and below‐ground processes on the success of C. cylindracea.

Posidonia oceanica and C. cylindracea sediments have microbial communities and predicted metabolic process that reflect aerobic and anaerobic conditions, respectively. Moreover, the nutritional quantity of organic matter was higher, but quality lower in C. cylindracea sediments compared to the two native habitats. The growth of C. cylindracea fragments was equally low in the presence or absence of a P. oceanica canopy, whereas the growth of C. cylindracea was higher in the canopy removed vs. present treatment, possibly because, in the absence of a C. cylindracea canopy, fragments are released from intraspecific competition for resources.

Synthesis. Sediment/soil processes are increasingly recognized as important drivers of the success and hence impacts of invasive plants. We extended this theory to marine ecosystems and suggest biotic resistance to invasion may not always be attributable to intact canopies, but may also result from indirect effects of native macrophytes on sediment quality and microbial processes. This information may, in part, resolve why above‐ground interactions do not always explain invasive plant success and thus can be used to develop better informed management strategies.
Peer‐mediated intervention to improve play skills in children with autism spectrum disorder: A feasibility study
Authors: Kent Cally , Cordier Reinie , Joosten Annette , Wilkes‐Gillan Sarah , Bundy Anita
Published: March 2018

Background/aim

Children with autism spectrum disorder (ASD) frequently demonstrate impaired play skills and poor quality social interactions compared to typically developing peers. Complex interventions to improve play skills should be investigated with randomised control trials (RCT) where possible to support evidence‐based practice for occupational therapists. Prior to a RCT, multiple feasibility studies are recommended to identify barriers to the trial. The aim of this study is to adapt a complex intervention to improve play skills in children with ASD and investigate the feasibility of conducting a RCT.

Methods

Participants were 10 children with ASD paired with typically developing playmates chosen by their families. Pairs attended 10 intervention sessions involving video modelling, therapist‐ and peer‐mediation and free play. Participant numbers needed for future investigation of effectiveness were calculated and time and cost considerations were reviewed. The Test of Playfulness (ToP) was the primary outcome measure; both parent‐ and child‐report outcome measures were evaluated for appropriateness.

Results

To determine effectiveness of the intervention 34 pairs in both control and intervention groups will be needed to conduct a RCT over an 18‐month timeframe. ToP scores showed a positive, but not statistically significant trend from pre‐ to post‐intervention. These improvements were maintained at follow‐up in both clinic and home environments. The Piers‐Harris 2 and the Parent Relationship Questionnaire were identified as appropriate secondary outcome measures; additional parent‐ and teacher‐report outcome measures are recommended for the RCT.

Conclusion

A RCT to investigate effectiveness of this intervention for improving play skills of children with ASD and their playmates are feasible.
The impact of a Role Emerging Placement while a student occupational therapist, on subsequent qualified employability, practice and career path
Authors: Thew Miranda , Thomas Yvonne , Briggs Michelle
Published: March 2018

Background

Although Role Emerging Placements (REP) are now a common feature in pre‐registration occupational therapy curricula, there is a need to expand the understanding of the impact of this experience on employability, practice and career path of qualified occupational therapists.

Method

A case finding online survey was used to create a purposive sample for Thematic Analysis of semi‐structured interviews with practising occupational therapists from one UK Masters’ level pre‐registration occupational therapy program.

Results

The case finding survey (n = 19) led to recruitment of six participants to be interviewed. The qualitative findings reflected the impact of a REP experience on occupational therapists’ employability, practice and career path. The complementary features of the more traditional placement and the role emergent type of placement were considered as being useful and beneficial to qualified practice regardless of setting. However, the REP additionally, had an internal and outward impact. Internally, the therapist gains a passion for occupation‐focussed practice and builds confidence to promote both self and the profession. Outwardly, the therapist can offer extra skills in qualified practice, particularly in innovative service development and delivery, thereby offering added value for employability.

Conclusion

A REP experience as an occupational therapy student, can develop additional skills for qualified professional practice than traditional practice placements alone. The impact of such a placement matches with the ‘Generation Y’ traits of young adults who are now starting to emerge into training and the work place, translates well into a variety of working environments and lasts into career development. The placement model of occupation‐focussed project development and the less apprentice style learning of a REP may be influential, and could be a suitable model within traditional placements.