bluuebunny/crossref_metadata_2025_split huggingface dataset:
RWP‐RK domain‐containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis
Authors: Tedeschi Francesca , Rizzo Paride , Rutten Twan , Altschmied Lothar , Bäumlein Helmut 
Published: November 2016

Summary

The formation of gametes is a prerequisite for any sexually reproducing organism in order to complete its life cycle. In plants, female gametes are formed in a multicellular tissue, the female gametophyte or embryo sac. Although the events leading to the formation of the female gametophyte have been morphologically characterized, the molecular control of embryo sac development remains elusive.

We used single and double mutants as well as cell‐specific marker lines to characterize a novel class of gene regulators in Arabidopsis thaliana, the RWP‐RK domain‐containing (RKD) transcription factors. Morphological and histological analyses were conducted using confocal laser scanning and differential interference contrast microscopy. Gene expression and transcriptome analyses were performed using quantitative reverse transcription−PCR and RNA sequencing, respectively.

Our results showed that RKD genes are expressed during distinct stages of embryo sac development. Morphological analysis of the mutants revealed severe distortions in gametophyte polarity and cell differentiation. Transcriptome analysis revealed changes in the expression of several gametophyte‐specific gene families (RKD2 and RKD3) and ovule development‐specific genes (RKD3), and identified pleiotropic effects on phytohormone pathways (RKD5).

Our data provide novel insight into the regulatory control of female gametophyte development. RKDs are involved in the control of cell differentiation and are required for normal gametophytic development.
Re‐annotation, improved large‐scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus
Authors: Cormier Alexandre , Avia Komlan , Sterck Lieven , Derrien Thomas , Wucher Valentin , Andres Gwendoline , Monsoor Misharl , Godfroy Olivier , Lipinska Agnieszka , Perrineau Marie‐Mathilde , Van De Peer Yves , Hitte Christophe , Corre Erwan , Coelho Susana M. , Cock J. Mark 
Published: November 2016

Summary

The genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles.

We present a complete structural and functional reannotation of the Ectocarpus genome.

The large‐scale assembly of the Ectocarpus genome was significantly improved and genome‐wide gene re‐annotation using extensive RNA‐seq data improved the structure of 11 108 existing protein‐coding genes and added 2030 new loci. A genome‐wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism‐based markers was developed for genetic analyses. These resources are available through an updated and improved genome database.

This study significantly improves the utility of the Ectocarpus genome as a high‐quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.
The diatom Phaeodactylum tricornutum adjusts nonphotochemical fluorescence quenching capacity in response to dynamic light via fine‐tuned Lhcx and xanthophyll cycle pigment synthesis
Authors: Lepetit Bernard , Gélin Gautier , Lepetit Mariana , Sturm Sabine , Vugrinec Sascha , Rogato Alessandra , Kroth Peter G. , Falciatore Angela , Lavaud Johann 
Published: November 2016

Summary

Diatoms contain a highly flexible capacity to dissipate excessively absorbed light by nonphotochemical fluorescence quenching (NPQ) based on the light‐induced conversion of diadinoxanthin (Dd) into diatoxanthin (Dt) and the presence of Lhcx proteins. Their NPQ fine regulation on the molecular level upon a shift to dynamic light conditions is unknown.

We investigated the regulation of Dd + Dt amount, Lhcx gene and protein synthesis and NPQ capacity in the diatom Phaeodactylum tricornutum after a change from continuous low light to 3 d of sine (SL) or fluctuating (FL) light conditions. Four P. tricornutum strains with different NPQ capacities due to different expression of Lhcx1 were included.

All strains responded to dynamic light comparably, independently of initial NPQ capacity. During SL, NPQ capacity was strongly enhanced due to a gradual increase of Lhcx2 and Dd + Dt amount. During FL, cells enhanced their NPQ capacity on the first day due to increased Dd + Dt, Lhcx2 and Lhcx3; already by the second day light acclimation was accomplished. While quenching efficiency of Dt was strongly lowered during SL conditions, it remained high throughout the whole FL exposure.

Our results highlight a more balanced and cost‐effective photoacclimation strategy of P. tricornutum under FL than under SL conditions.
H+‐pyrophosphatase IbVP1 promotes efficient iron use in sweet potato [Ipomoea batatas (L.) Lam.]
Authors: Fan Weijuan , Wang Hongxia , Wu Yinliang , Yang Nan , Yang Jun , Zhang Peng 
Published: November 2016

SummaryIron (Fe) deficiency is one of the most common micronutrient deficiencies limiting crop production globally, especially in arid regions because of decreased availability of iron in alkaline soils. Sweet potato [Ipomoea batatas (L.) Lam.] grows well in arid regions and is tolerant to Fe deficiency. Here, we report that the transcription of type I H+‐pyrophosphatase (H+‐PPase) gene IbVP1 in sweet potato plants was strongly induced by Fe deficiency and auxin in hydroponics, improving Fe acquisition via increased rhizosphere acidification and auxin regulation. When overexpressed, transgenic plants show higher pyrophosphate hydrolysis and plasma membrane H+‐ATPase activity compared with the wild type, leading to increased rhizosphere acidification. The IbVP1‐overexpressing plants showed better growth, including enlarged root systems, under Fe‐sufficient or Fe‐deficient conditions. Increased ferric precipitation and ferric chelate reductase activity in the roots of transgenic lines indicate improved iron uptake, which is also confirmed by increased Fe content and up‐regulation of Fe uptake genes, e.g. FRO2, IRT1 and FIT. Carbohydrate metabolism is significantly affected in the transgenic lines, showing increased sugar and starch content associated with the increased expression of AGPase and SUT1 genes and the decrease in β‐amylase gene expression. Improved antioxidant capacities were also detected in the transgenic plants, which showed reduced H2O2 accumulation associated with up‐regulated ROS‐scavenging activity. Therefore, H+‐PPase plays a key role in the response to Fe deficiency by sweet potato and effectively improves the Fe acquisition by overexpressing IbVP1 in crops cultivated in micronutrient‐deficient soils.
Kinase gene fusions in defined subsets of melanoma
Authors: Turner Jacqueline , Couts Kasey , Sheren Jamie , Saichaemchan Siriwimon , Ariyawutyakorn Witthawat , Avolio Izabela , Cabral Ethan , Glogowska Magdelena , Amato Carol , Robinson Steven , Hintzsche Jennifer , Applegate Allison , Seelenfreund Eric , Gonzalez Rita , Wells Keith , Bagby Stacey , Tentler John , Tan Aik‐Choon , Wisell Joshua , Varella‐Garcia Marileila , Robinson William 
Published: November 2016

SummaryGenomic rearrangements resulting in activating kinase fusions have been increasingly described in a number of cancers including malignant melanoma, but their frequency in specific melanoma subtypes has not been reported. We used break‐apart fluorescence in situ hybridization (FISH) to identify genomic rearrangements in tissues from 59 patients with various types of malignant melanoma including acral lentiginous, mucosal, superficial spreading, and nodular. We identified four genomic rearrangements involving the genes BRAF, RET, and ROS1. Of these, three were confirmed by Immunohistochemistry (IHC) or sequencing and one was found to be an ARMC10‐BRAF fusion that has not been previously reported in melanoma. These fusions occurred in different subtypes of melanoma but all in tumors lacking known driver mutations. Our data suggest gene fusions are more common than previously thought and should be further explored particularly in melanomas lacking known driver mutations.
Skin microtopography as a measure of photoaging and risk of squamous cell carcinoma of the skin in a US population
Authors: Kuklinski Lawrence Fitzgerald , Zens Michael Scot , Perry Ann E. , Green Adele C. , Karagas Margaret R. 
Published: November 2016

SummaryBackgroundSkin microtopography as a measure of photoaging is a noninvasive approach to measuring chronic ultraviolet radiation exposure and reflects the degree of dermal elastosis in populations of European descent in the subtropics. Less is known about the utility of this approach in populations at different latitudes, and whether it relates to skin cancer risk.MethodsA population‐based case–control study of 342 squamous cell carcinoma (SCC) cases and 331 age‐ and gender‐matched controls were evaluated for histologic evidence of solar damage and severity of photoaging based on microtopography on a six‐grade scale. Odds ratios (OR) for SCC associated with degree of photoaging were estimated using logistic regression analysis adjusted for potentially confounding factors.ResultsAfter adjustment for known risk factors, SCC was associated with increasing photoaging grade (OR = 1.7, 95% CI = 0.9–3.0 for severe photoaging; OR = 2.8, 95% CI = 1.6–5.0 for very severe photoaging). Associations remained among those with actinic keratosis (OR = 3.4, 95% CI = 0.9–12.4 for severe photoaging, OR = 5.7, 95% CI = 1.7–19.6 for very severe photoaging).LimitationsThere was limited statistical power, particularly for subgroup analyses.ConclusionOur findings provide further evidence of microtopography as an independent, objective indicator of risk of SCC.
Mixed pollen load and late‐acting self‐incompatibility flexibility in Adenocalymma peregrinum (Miers) L.G. Lohmann (Bignonieae: Bignoniaceae)
Authors: Duarte M. O. , Mendes‐Rodrigues C. , Alves M. F. , Oliveira P. E. , Sampaio D. S. 
Published: November 2016

Abstract

Mixed cross and self‐pollen load on the stigma (mixed pollination) of species with late‐acting self‐incompatibility system (LSI) can lead to self‐fertilized seed production. This “cryptic self‐fertility” may allow selfed seedling development in species otherwise largely self‐sterile. Our aims were to check if mixed pollinations would lead to fruit set in LSI Adenocalymma peregrinum, and test for evidence of early‐acting inbreeding depression in putative selfed seeds from mixed pollinations.

Experimental pollinations were carried out in a natural population. Fruit and seed set from self‐, cross and mixed pollinations were analysed. Further germination tests were carried out for the seeds obtained from treatments.

Our results confirm self‐incompatibility, and fruit set from cross‐pollinations was three‐fold that from mixed pollinations. This low fruit set in mixed pollinations is most likely due to a greater number of self‐ than cross‐fertilized ovules, which promotes LSI action and pistil abortion. Likewise, higher percentage of empty seeds in surviving fruits from mixed pollinations compared with cross‐pollinations is probably due to ovule discounting caused by self‐fertilization. Moreover, germinability of seeds with developed embryos was lower in fruits from mixed than from cross‐pollinations, and the non‐viable seeds from mixed pollinations showed one‐third of the mass of those from cross‐pollinations.

The great number of empty seeds, lower germinability, lower mass of non‐viable seeds, and higher variation in seed mass distribution in mixed pollinations, strongly suggests early‐acing inbreeding depression in putative selfed seeds. In this sense, LSI and inbreeding depression acting together probably constrain self‐fertilized seedling establishment in A. peregrinum.
The insect vector Cacopsylla picta vertically transmits the bacterium ‘Candidatus Phytoplasma mali’ to its progeny
Authors: Mittelberger C. , Obkircher L. , Oettl S. , Oppedisano T. , Pedrazzoli F. , Panassiti B. , Kerschbamer C. , Anfora G. , Janik K. 
Published: November 2016

The phloem‐sucking psyllid Cacopsylla picta plays an important role in transmitting the bacterium ‘Candidatus Phytoplasma mali’, the agent associated with apple proliferation disease. The psyllid can ingest ‘Ca. Phytoplasma mali’ from infected apple trees and spread the bacterium by subsequently feeding on uninfected trees. Until now, this has been the most important method of ‘Ca. Phytoplasma mali’ transmission. The aim of this study was to investigate whether infected C. picta are able to transmit ‘Ca. Phytoplasma mali’ directly to their progeny. This method of transmission would allow the bacteria to bypass a time‐consuming reproductive cycle in the host plant. Furthermore, this would cause a high number of infected F1 individuals in the vector population. To address this question, eggs, nymphs and adults derived from infected overwintering adults of C. picta were reared on non‐infected apple saplings and subsequently tested for the presence of ‘Ca. Phytoplasma mali’. In this study it was shown for the first time that infected C. picta individuals transmit ‘Ca. Phytoplasma mali’ to their eggs, nymphs and F1 adults, thus providing the basis for a more detailed understanding of ‘Ca. Phytoplasma mali’ transmission by C. picta.
Thep-filter: Multilayer False Discovery Rate Control for Grouped Hypotheses
Authors: Barber Rina Foygel , Ramdas Aaditya 
Published: November 2016

SummaryIn many practical applications of multiple testing, there are natural ways to partition the hypotheses into groups by using the structural, spatial or temporal relatedness of the hypotheses, and this prior knowledge is not used in the classical Benjamini–Hochberg procedure for controlling the false discovery rate (FDR). When one can define (possibly several) such partitions, it may be desirable to control the group FDR simultaneously for all partitions (as special cases, the ‘finest’ partition divides the n hypotheses into n groups of one hypothesis each, and this corresponds to controlling the usual notion of FDR, whereas the ‘coarsest’ partition puts all n hypotheses into a single group, and this corresponds to testing the global null hypothesis). We introduce the p-filter, which takes as input a list of n p-values and M ⩾ 1 partitions of hypotheses, and produces as output a list of n or fewer discoveries such that the group FDR is provably simultaneously controlled for all partitions. Importantly, since the partitions are arbitrary, our procedure can also handle multiple partitions which are non-hierarchical. The p-filter generalizes two classical procedures—when M = 1, choosing the finest partition into n singletons, we exactly recover the Benjamini–Hochberg procedure, whereas, choosing instead the coarsest partition with a single group of size n, we exactly recover the Simes test for the global null hypothesis. We verify our findings with simulations that show how this technique can not only lead to the aforementioned multilayer FDR control but also lead to improved precision of rejected hypotheses. We present some illustrative results from an application to a neuroscience problem with functional magnetic resonance imaging data, where hypotheses are explicitly grouped according to predefined regions of interest in the brain, thus allowing the scientist to employ field-specific prior knowledge explicitly and flexibly.
Mesozoic climates and oceans – a tribute to Hugh Jenkyns and Helmut Weissert
Authors: Robinson Stuart A. , Heimhofer Ulrich , Hesselbo Stephen P. , Petrizzo Maria Rose 
Published: November 2016

AbstractThe study of past greenhouse climate intervals in Earth history, such as the Mesozoic, is an important, relevant and dynamic area of research for many sedimentary geologists, geochemists, palaeontologists and climate modellers. The Mesozoic sedimentary record provides key insights into the mechanics of how the Earth system works under warmer conditions, providing examples of natural climate change and perturbations to ocean chemistry, including anoxia, that are of societal relevance for understanding and contextualizing ongoing and future environmental problems. Furthermore, the deposition of widespread organic‐carbon‐rich sediments (‘black shales’) during the Mesozoic means that this is an era of considerable economic interest. In July 2015, an international group of geoscientists attended a workshop in Ascona, Switzerland, to discuss all aspects of the Mesozoic world and to celebrate the four‐decade‐long contributions made by Hugh Jenkyns (University of Oxford) and Helmut Weissert (ETH Zürich) to our understanding of this fascinating era in Earth history. This volume of Sedimentology arose from that meeting and contains papers inspired by (and co‐authored by!) Hugh and Helmi. Here, a brief introduction to the volume is provided that reviews aspects of Hugh and Helmi's major achievements; contextualizes the papers of the Thematic Issue; and discusses some of the outstanding questions and areas for future research.
Non‐invasive evaluation of skin tension lines with elastic waves
Authors: Deroy C. , Destrade M. , Mc Alinden A. , Ní Annaidh A. 
Published: November 2016

BackgroundSince their discovery by Karl Langer in the 19th Century, Skin Tension Lines (STLs) have been used by surgeons to decide the location and orientation of an incision. Although these lines are patient‐specific, most surgeons rely on generic maps to determine their orientation. Beyond the imprecise pinch test, there remains no accepted method for determining STLs in vivo.Methods(i) The speed of an elastic motion travelling radially on the skin of canine cadavers was measured with a commercial device called the Reviscometer®. (ii) Similar to the original experiments conducted by Karl Langer, circular excisions were made on the skin and the geometric changes to the resulting wounds and excised samples were used to determine the orientation of STLs.ResultsA marked anisotropy in the speed of the elastic wave travelling radially was observed. The orientation of the fastest wave was found to correlate with the orientation of the elongated wound (P<0.001, R2=74%). Similarly, the orientation of fastest wave was the same for both in vivo and excised isolated samples, indicating that the STLs have a structural basis. Resulting wounds expanded by an average area of 9% (+16% along STL and −10% across) while excised skin shrunk by an average area of 33% (23% along STL and 10% across).ConclusionElastic surface wave propagation has been validated experimentally as a robust method for determining the orientation of STLs non‐destructively and non‐invasively. This study has implications for the identification of STLs and for the prediction of skin tension levels, both important factors in both human and veterinary reconstructive surgery.
Patterning corrosion‐susceptible metallic alloys for digital image correlation in a scanning electron microscope
Authors: Githens A. , Daly S. 
Published: November 2016

AbstractWe investigate the self‐assembly of gold nanoparticles on the surface of magnesium functionalized with 3‐(aminopropyl)trimethoxysilane or 3‐(mercaptopropyl)trimethoxysilane. These nanoparticles served as a speckle pattern for high magnification deformation tracking via digital image correlation combined with scanning electron microscopy. Controlling the pH of the gold nanoparticle suspension to a specific basicity passivated corrosion in magnesium and in three of its alloys to enable proper nanoparticle bonding and self‐assembly. Magnesium was used as a model material as it is particularly difficult to modify for self‐assembly because of its propensity to quickly form a thick oxide, hydroxide, and carbonate layer in the presence of oxygen, water, and carbon dioxide, respectively. Moreover, it corrodes in acidic and slightly basic solutions, further complicating the self‐assembly process. Due to these difficulties, the successful self‐assembly of nanoparticles on magnesium has not previously been reported, to the best of the authors' knowledge. This technique is potentially amendable to other corrosion‐susceptible materials. Gold nanoparticles were self‐assembled in a uniformly dispersed random distribution on pure cast magnesium, cast AM60 (Mg‐6Al‐0.5Mn), rolled WE43 (Mg‐4Y‐3Nd/Gd), and extruded ZE20 (Mg‐2Zn‐0.2Ce).
Cognitive Analysis of Educational Games: The Number Game
Authors: van der Maas Han L. J. , Nyamsuren Enkhbold 
Published: November 2016

AbstractWe analyze the cognitive strategies underlying performance in the Number task, a Math game that requires both arithmetic fluency and mathematical creativity. In this game all elements in a set of numbers (for instance, 2, 5, 9) have to be used precisely once to create a target number (for instance, 27) with basic arithmetic operations (solution: [5−2] × 9). We argue that some instances of this game are NP complete, by showing its relation to the well‐known Partition problem. We propose heuristics based on the distinction in forward and backward reasoning. The Number Game is part of Math Garden, a popular online educational platform for practicing and monitoring math skills using innovations in computerized adaptive testing. These educational games generate enormous amounts of rich data on children's cognitive development. We found converging evidence for the use of forward proximity heuristics in the data of Math Garden, consisting of more than 20 million answers to 1,700 items. Item difficulties and the structure of correct answers were analyzed.
High‐throughput physiological phenotyping and screening system for the characterization of plant–environment interactions
Authors: Halperin Ofer , Gebremedhin Alem , Wallach Rony , Moshelion Menachem 
Published: November 2016

SummaryWe present a simple and effective high‐throughput experimental platform for simultaneous and continuous monitoring of water relations in the soil–plant–atmosphere continuum of numerous plants under dynamic environmental conditions. This system provides a simultaneously measured, detailed physiological response profile for each plant in the array, over time periods ranging from a few minutes to the entire growing season, under normal, stress and recovery conditions and at any phenological stage. Three probes for each pot in the array and a specially designed algorithm enable detailed water‐relations characterization of whole‐plant transpiration, biomass gain, stomatal conductance and root flux. They also enable quantitative calculation of the whole plant water‐use efficiency and relative water content at high resolution under dynamic soil and atmospheric conditions. The system has no moving parts and can fit into many growing environments. A screening of 65 introgression lines of a wild tomato species (Solanum pennellii) crossed with cultivated tomato (S. lycopersicum), using our system and conventional gas‐exchange tools, confirmed the accuracy of the system as well as its diagnostic capabilities. The use of this high‐throughput diagnostic screening method is discussed in light of the gaps in our understanding of the genetic regulation of whole‐plant performance, particularly under abiotic stress.