bluuebunny/crossref_metadata_2025 huggingface dataset:
Silicon Alleviates Changes in the Source-Sink Relationship of Wheat Plants Infected by Pyricularia oryzae
Authors: Araújo Marcela Uli Peixoto , Rios Jonas Alberto , Silva Ernesto Ticiano , Rodrigues Fabrício Ávila
Published: February 2019

Blast, caused by Pyricularia oryzae, has become a devastating disease on wheat in several countries worldwide. Growers need alternative methods for blast management, and silicon (Si) stands out for its potential to decrease the intensity of important diseases in several crops. This study investigated the effect of Si on improving photoassimilate production on flag leaves of wheat plants and their partitioning to spikes in a scenario where blast symptoms decreased as a result of potentiation of defense mechanisms by Si. Wheat plants (cultivar BRS Guamirim) were grown in hydroponic culture with 0 or 2 mM Si and inoculated with P. oryzae at 10 days after anthesis. The Si concentration on flag leaves and spikes of Si-supplied plants increased and resulted in lower blast symptoms. High concentrations of total soluble phenols and lignin-thioglycolic acid derivatives and greater peroxidase, polyphenoloxidase, phenylalanine ammonia-lyase, β-1,3-glucanase, and chitinase activity occurred on flag leaves and spikes of Si-supplied plants and increased their resistance to blast. The concentration of photosynthetic pigments decreased and the photosynthetic performance of infected flag leaves and spikes from plants not supplied with Si was impaired for chlorophyll a fluorescence parameters including maximal photosystem II quantum efficiency, fraction of energy absorbed used in photochemistry, quantum yield of nonregulated energy dissipation, and quantum yield of regulated energy dissipation. The concentration of soluble sugars was lower on infected flag leaves and spikes from plants not supplied with Si, whereas the hexose-to-sucrose ratio increased on infected flag leaves. Sucrose-phosphate synthase activity was lower and acid invertase activity was higher on flag leaves and spikes of plants not supplied with Si, respectively, compared with Si-supplied plants. The starch concentration on spikes of Si-supplied plants increased. In conclusion, Si showed a beneficial effect in improving the source-sink relationship of infected flag leaves and spikes by preserving alterations in assimilate production and partitioning during the grain filling process.
Extracranial Internal Carotid Aneurysm in a 10-Year-Old Boy Diagnosed via Ultrasound
Authors: Sosa Philip A. , Matar Phillip , Gross Isabel T.
Published: February 2019

Background

Extracranial carotid aneurysms in children are extremely rare but carry a high mortality and morbidity. For pediatric patients, they are often complications of pharyngeal infections and surgical trauma but can also arise from congenital and inflammatory diseases. They have a wide range of presentation from an asymptomatic mass to a rapidly fatal hemorrhage.

Case

A 10-year-old boy presented to the emergency department with complaints of a neck mass and residual cough from a recent upper respiratory infection. Ultrasound revealed a carotid aneurysm that was further characterized by magnetic resonance angiography as a 3-cm aneurysm of the internal carotid artery. The patient was taken for surgery where he underwent resection and placement of an interposition graft. The procedure was well tolerated and the boy recovered fully.

Discussion

Carotid aneurysms in children can present with 1 or more of the following: a pulsatile neck mass, hematemesis, epistaxis, neurologic symptoms, and symptoms of airway compression. Although ultrasound is the preferred initial test, the choice of additional imaging for further characterization will depend most on the patient age, hemodynamic stability, airway status, and availability of pediatric anesthesia. Hemodynamic and neurologic status should be monitored closely, and clinicians must also be prepared for a potentially complicated airway. Surgery is indicated for children owing to high risk of neurologic complications.

Conclusions

Although these lesions are rare, it is crucial that physicians recognize when there is a need for further evaluation so that these children have the most favorable outcomes possible.
Comparison of three different eye-tracking tasks for distinguishing autistic from typically developing children and autistic symptom severity
Authors: Kou Juan , Le Jiao , Fu Meina , Lan Chunmei , Chen Zhuo , Li Qin , Zhao Weihua , Xu Lei , Becker Benjamin , Kendrick Keith M
Published: February 2019

Altered patterns of visual social attention preference detected using eye-tracking and a variety of different paradigms are increasingly proposed as sensitive biomarkers for autism spectrum disorder. However, few eye tracking studies have compared the relative efficacy of different paradigms to discriminate between autistic compared with typically developing children and their sensitivity to specific symptoms. To target this issue, the current study used three common eye tracking protocols contrasting social versus non-social stimuli in young (2-7 years old) Chinese autistic (n = 35) and typically developing (n = 34) children matched for age and gender. Protocols included dancing people vs. dynamic geometrical images, biological motion (dynamic light point walking human or cat) vs. non-biological motion (scrambled controls) and child playing with toy vs. toy alone. Although all three paradigms differentiated autistic and typically developing children, the dancing people versus dynamic geometry pattern paradigm was the most effective, with autistic children showing marked reductions in visual preference for dancing people and correspondingly increased one for geometric patterns. Furthermore, this altered visual preference in autistic children was correlated with the ADOS social affect score and had the highest discrimination accuracy. Our results therefore indicate that decreased visual preference for dynamic social stimuli may be the most effective visual attention-based paradigm for use as a biomarker for autism in Chinese children. Clinical trial ID: NCT03286621 (clinicaltrials.gov); Clinical trial name: Development of Eye-tracking Based Markers for Autism in Young Children.

Lay summary

Eye-tracking measures may be useful in aiding diagnosis and treatment of autism, although it is unclear which specific tasks are optimal. Here we compare the ability of three different social eye-gaze tasks to discriminate between autistic and typically developing young Chinese children and their sensitivity to specific autistic symptoms. Our results show that a dynamic task comparing visual preference for social (individuals dancing) versus geometric patterns is the most effective both for diagnosing autism and sensitivity to its social affect symptoms.
Who Bears the Burden of Long-Lived Molecular Biology Databases?
Authors: Imker Heidi J.
Published: February 2019

In the early 1990s the life sciences quickly adopted online databases to facilitate wide-spread dissemination and use of scientific data. From 1991, the journalNucleic Acids Researchhas published an annual Database Issue dedicated to articles describing molecular biology databases. Analysis of these articles reveals a set of long-lived databases which have now remained available for more than 15 years. Given the pervasive challenge of sustaining community resources, these databases provide an opportunity to examine what factors contribute to persistence by addressing two questions 1) which organizations fund these long-lived databases? and 2) which organizations maintain these long-lived databases? Funding and operating organizations for 67 databases were determined through review of Database Issue articles. The results reveal a diverse set of contributing organizations with financial and operational support spread across six categories: academic, consortium/collective, government, industry, philanthropic, and society/association. The majority of databases reported support from more than one funding organization, of which government organizations were most common source of funds. Operational responsibilities were more distributed, with academic organizations serving as the most common hosts. Although overall there is evidence of diversification, the most acknowledged funding and operating organizations contribute to disproportionately large percentages of the long-lived databases investigated here.
Sex and area differences in the association between adiposity and lipid profile in Malawi
Authors: Soares Ana Luiza G , Banda Louis , Amberbir Alemayehu , Jaffar Shabbar , Musicha Crispin , Price Alison , Nyrienda Moffat J , Lawlor Deborah A , Crampin Amelia C
Published: February 2019

Background

Evidence from high-income countries shows that higher adiposity results in an adverse lipid profile, but it is unclear whether this association is similar in Sub-Saharan African (SSA) populations. This study aimed to assess the association between total and central adiposity measures and lipid profile in Malawi, exploring differences by sex and area of residence (rural/urban).

Methods

Data from 12,847 rural and 12,096 urban Malawian residents were used. The associations of body mass index (BMI) and waist-hip ratio (WHR) with fasting lipids (total cholesterol (TC), low density lipoprotein-cholesterol (LDL-C), high density lipoprote in-cholesterol (HDL-C) and triglycerides (TG)) were assessed by area and sex.

Results

A great proportion of adults have high BMI and WHR, and this was associated with adverse lipid profiles; higher BMI and WHR were linearly associated with increased TC, LDL-C and TG and reduced HDL-C. BMI was more strongly related to fasting lipids than was WHR. The associations of adiposity with adverse lipid profile were stronger in urban compared with rural residents.

Conclusions

The consistent associations observed of higher adiposity with adverse lipid profiles in females and males living in rural and urban areas of Malawi highlight the emerging adverse cardio-metabolic epidemic in this poor population. Our findings underline the potential utility of BMI in estimating cardiovascular risk and highlight the need for greater investment to understand the long-term health outcomes of obesity and adverse lipid profiles and the extent to which lifestyle changes and treatments effectively prevent and modify adverse cardio-metabolic outcomes.

Key messages

Higher body mass index (BMI) and waist to hip ratio (WHR) are associated with increased total cholesterol (TC), low density lipoprotein-cholesterol (LDL-C) and triglycerides (TG) and reduced high density lipoprotein-cholesterol (HDL-C) in a large sub-Saharan African population.

Total adiposity is more strongly associated with adverse lipid profile than central adiposity.

Despite the higher BMI and the less favourable lipid profile in urban residents, stronger associations between BMI and TC, LDL-C and TG are observed in rural than urban residents.
Rabies-induced behavioural changes are key to rabies persistence in dog populations: investigation using a network-based model
Authors: Brookes Victoria J. , Dürr Salome , Ward Michael P.
Published: February 2019

Canine-rabies was endemic pre-urbanisation, yet little is known about how it persists in small populations of dogs typically seen in rural and remote regions. Our objectives were to simulate rabies outbreaks in such populations (50—90 dogs) using a network-based model, and investigate the influence of rabies-induced behavioural changes.

Such changes – increased bite frequency and either roaming or paralysis that increased the number or duration of contacts, respectively – were essential for disease propagation. Spread occurred in approximately 50% of model simulations and in these, a very low case rates (2.0—2.6 cases/month) over long durations (95% range 20—473 days) were predicted. Consequently, disease detection is a challenge, risking human infection and spread to other communities via dog movements. Even with 70% pre-emptive vaccination, spread occurred in >30% of model simulations (in these, median case rate was 1.5/month with 95% range of 15—275 days duration).

We conclude that the social disruption caused by rabies-induced behavioural change is the key to explaining how rabies persists in small populations of dogs. We predict that vaccination of substantially greater than the recommended 70% of dog populations is required to prevent rabies emergence in currently free rural areas.
Temporal Trends without Seasonal Effects on Gestational Diabetes Incidence Relate to Reductions in Indices of Insulin Secretion: The Cambridge Baby Growth Study
Authors: Petry Clive J. , Fisher Benjamin G. , Ong Ken K. , Hughes Ieuan A. , Acerini Carlo L. , Dunger David B.
Published: February 2019

Aims

The incidence of gestational diabetes has been reported to have risen over the first decade of this century. Some studies have also found it to vary with seasons of the year. We therefore investigated temporal and seasonal trends on gestational diabetes incidence in a single centre cohort study from Cambridge, U.K., and attempted to explain trends using associations with risk factors.

Materials and Methods

Using a cosinor model we tested whether there were both temporal and seasonal trends in gestational diabetes incidence in 1,074 women recruited to the Cambridge Baby Growth Study in 2001-2009 who underwent oral glucose tolerance tests around week 28 of pregnancy. We also undertook risk factor analyses.

Results

There was a temporal increase in gestational diabetes incidence over the course of recruitment to this study (p=2.1×10−3) but no seasonal effect (p=0.7). HOMA B (p=3.0×10−3; n=1,049) and the insulin disposition index (p=3.0×10−3; n=1,000) showed negative temporal trends. There was no negative association with HOMA S. Risk factor analyses showed a concomitant temporal slight increase in the index of multiple deprivation (p=4.6×10−10, n=1,068). This index was positively associated with HOMA B (p=6.1×10−5, n=955) but not directly with gestational diabetes (p=0.6, n=1,032), HOMA S (p=0.2, n=955) or the insulin disposition index (p=0.4, n=955).

Conclusions

In this population there were temporal but not seasonal increases in gestational diabetes incidence between the years 2001 and 2009, which appeared to be related more to reductions in insulin secretion than sensitivity. Possible mediators of this link include confounding factors related to deprivation.
Genetic Diversity and Phylogenetic Relationships of Annual and PerennialGlycineSpecies
Authors: Hwang Eun-Young , Wei He , Schroeder Steven G. , Fickus Edward W. , Quigley Charles V. , Elia Patrick , Costa Larissa , Araya Susan , Ferreira Marcio Elias , Cregan Perry B. , Song Qijian
Published: February 2019

We estimated average genetic diversity of twoGlycineannual and six perennial species based upon 76 orthologous gene sets and performed phylogenetic analysis, divergence analysis and tests for departure from neutrality of the eight species using 52 orthologous gene sets. In addition, 367 orthologous gene sets were used to estimate the relationships of 11G. canescensaccessions. Among the perennials,G. canescensshowed the highest nucleotide diversity and the other perennials exceptG. tomentellahad higher nucleotide diversity than the two annuals. Phylogenetic analysis of theGlycineshowed a similar genome grouping with the previous report exceptG. cyrtolobaandG. stenophitaformed a sister clade in the study. Divergence analysis supported the phylogenetic relationships,G. falcatawas the most divergent fromG. max, followed byG. cyrtoloba,G. syndetika,G. tomentellaD3,G. stenophitaandG. canescens. Neutrality selection tests within species showed that most genes were subjected to a recent directional selection due to a selective sweep or rapid population expansion. Although most gene sequence had negative and significant Tajima’s D, the sequences were homogeneous in the levels of polymorphism and divergence betweenG. maxand otherGlycinespecies based on the HKA test, thus,Glycineperennials may have experienced very similar evolutionary selection as inferred by trans-specific mutation analysis. The greater genetic diversity of most perennialGlycinespecies and their origins from the warmer and drier climates of Australia suggested the perennials as potential sources of heat and drought resistance that will be of value in the face of climate change.
IFNγ induces epigenetic programming of human T-bethiB cells and promotes TLR7/8 and IL-21 induced differentiation
Authors: Zumaquero Esther , Stone Sara L. , Scharer Christopher D. , Jenks Scott A. , Nellore Anoma , Mousseau Betty , Rosal-Vela Antonio , Botta Davide , Bradley John E. , Wojciechowski Wojciech , Ptacek Travis , Danila Maria I. , Edberg Jeffrey C. , Bridges S. Louis , Kimberly Robert P. , Chatham W. Winn , Schoeb Trenton R. , Rosenberg Alexander , Boss Jeremy M. , Sanz Ignacio , Lund Frances E.
Published: February 2019

Although B cells expressing the IFNγR or the IFNγ-inducible transcription factor T-bet drive autoimmunity in Systemic Lupus Erythematosus (SLE)-prone mouse models, the role for IFNγ signaling in human antibody responses is unknown. We show that elevated levels of IFNγ in SLE patients correlate with expansion of the T-bet expressing IgDnegCD27negCD11c+CXCR5neg(DN2) pre-antibody secreting cell (pre-ASC) subset. We demonstrate that naïve B cells form T-bethipre-ASCs following stimulation with either Th1 cells or with IFNγ, IL-2, anti-Ig and TLR7/8 ligand and that IL-21 dependent ASC formation is significantly enhanced by IFNγ or IFNγ-producing T cells. IFNγ promotes ASC development by synergizing with IL-2 and TLR7/8 ligands to induce genome-wide epigenetic reprogramming of B cells, which results in increased chromatin accessibility surrounding IRF4 and BLIMP1 binding motifs and epigenetic remodeling ofIL21RandPRDM1loci. Finally, we show that IFNγ signals poise B cells to differentiate by increasing their responsiveness to IL-21.
A lipid-structured model for macrophage populations in atherosclerotic plaques
Authors: Ford Hugh Z. , Byrne Helen M. , Myerscough Mary R.
Published: February 2019

Atherosclerosis is a chronic inflammatory disease driven by the accumulation of pro-inflammatory, lipid-loaded macrophages at sites inside artery walls. These accumulations lead to the development of atherosclerotic plaques. The rupture of plaques that contain lipid-rich necrotic cores can trigger heart attacks and strokes via occlusion of blood vessels. We construct and analyse a system of partial integro-differential equations that model lipid accumulation by macrophages, including generating apoptotic cells and a necrotic core. The model includes the following cell behaviours: recruitment of macrophages into the plaque; macrophage ingestion of low density lipoproteins LDL and of apoptotic cells and necrotic material; lipid offloading to high density lipoproteins (HDL); macrophage emigration; and macrophage apoptosis and necrosis of apoptotic cells. With this model, we study how changes in parameters predict the characteristic features of plaque pathology. In particular, we find the qualitative form of lipid distribution across the macrophage population and show that high lipid loads can occur in the absence of LDL ingestion. We also demonstrate the importance of macrophage emigration in the model in mitigating and resolving inflammation and plaque lipid accumulation.

Contributions

HZF: conceptualisation, formal analysis, investigation, methodology, visualisation, writing— original draft preparation, writing—review and editing.

HMB: conceptualisation, funding acquisition, methodology, project administration, resources, supervision, writing—review and editing.

MRM: conceptualisation, funding acquisition, methodology, project administration, resources, supervision, writing—original draft, writing—review and editing.
Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density
Authors: Li Mao , Klein Laura L. , Duncan Keith E. , Jiang Ni , Londo Jason P. , Miller Allison J. , Topp Christopher N.
Published: February 2019

We characterized grapevine inflorescence architecture (the rachis and all branches without berries) to describe variation among 10 wild Vitis species, assess phylogenetic signals underlying inflorescence architecture traits, and interpret this variation in the context of breeding objectives.

Three-dimensional X-ray tomography scans of grapevine inflorescences were used to measure geometric traits and inflorescence topology using persistent homology, a mathematical approach that can comprehensively measure and compare shapes. We simulated potential space available for berry growth within a given inflorescence architecture by evaluating expanding spheres attached to pedicels, referred to as “berry potential.” Lastly, we performed phylogenetic analysis and mapped trait variation.

We detected wide variation in inflorescence architecture features among Vitis species. Hierarchical clustering and correlation analyses revealed relationships among traits. Multivariate analyses identify traits contributing the most to variation and distinguish between species with high accuracy. Phylogenetic analyses revealed 12 morphological traits with strong phylogenetic signal.

Morphometric analysis uncovered novel differences in inflorescence architecture among clades and between Vitis species. Cluster density is an important trait for assessing crop quality and forecasting yield; analyses presented here can be used to tease apart subtle, heritable features and environmental influences on this major agronomic trait.
Programming conventional electron microscopes for solving ultrahigh-resolution structures of small and macro-molecules
Authors: zhou Heng , Luo Feng , Luo Zhipu , Li Dan , Liu Cong , Li Xueming
Published: February 2019

Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lacking of automated data collection method. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ~0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED, and demonstrates the capability of the low-end 120kV microscope with a CCD camera in solving ultra-high resolution structures of both organic compound and biological macromolecules.
mRNA adenosine methylase (MTA) deposits m6A on pri-miRNAs to modulate miRNA biogenesis in Arabidopsis thaliana
Authors: Bhat Susheel Sagar , Bielewicz Dawid , Grzelak Natalia , Gulanicz Tomasz , Bodi Zsuzsanna , Szewc Lukasz , Bajczyk Mateusz , Dolata Jakub , Smolinski Dariusz J. , Fray Rupert G. , Jarmolowski Artur , Szweykowska-Kulinska Zofia
Published: February 2019

m6A, one of the most abundant mRNA modifications, has been associated with various metabolic processes in plants. Here we show that m6A also plays a role in miRNA biogenesis in Arabidopsis thaliana. Significant reductions in plant m6A/MTA levels results in lower accumulation of miRNAs whereas pri-miRNA levels tend to be higher in such plants. m6A-IP Seq and MTA-GFP RIP were used to show that many pri-miRNAs are m6A methylated and are bound by MTA, further demonstrating that pri-miRNAs can also be substrates for m6A methylation by MTA. We report that MTA interacts with RNA Pol II, supporting the assumption that m6A methylation is a co-transcriptional process, and also identify TGH, a known miRNA biogenesis related protein, as a novel protein that interacts with MTA. Finally, reduced levels of miR393b may partially explain the strong auxin insensitivity seen in Arabidopsis plants with reduced m6A levels.
Factors that influence scientific productivity from different countries: A causal approach through multiple regression using panel data
Authors: Lancho-Barrantes Bárbara S. , Ceballos Héctor G. , Cantú-Ortiz Francisco J.
Published: February 2019

The main purpose of the economic expenditure of countries in research and development is to achieve higher levels of scientific findings within research ecosystems, which in turn could generate better living standards for society. Therefore, the collection of scientific production constitutes a faithful image of the capacity, trajectory and scientific depth assignable to each country. The intention of this article is to contribute to the understanding of the factors that certainly influence in the scientific production and how could be improved. In order to achieve this challenge, we select a sample of 19 countries considered partners in science and technology. On the one hand we download social and economic variables (gross domestic expenditure on R&D (GERD) as a percentage of gross domestic product (GDP) and researchers in full-time equivalent (FTE)) and on the other hand variables related to scientific results (total scientific production, scientific production by subject areas and by different institutions, without overlook the citations received as an impact measure) all this data within a 17-year time window. Through a causal model with multiple linear regression using panel data, the experiment confirms that two independent (or explanatory) variables of five selected explain the amount of scientific production by 98% for the countries analyzed. An important conclusion that we highlight stays the importance of checking for compliance of statistical assumptions when using multiple regression in research studies. As a result, we built a reliable predictive model to analyze scenarios in which the increase in any of the independent variables causes a positive effect on scientific production. This model allows decision maker to make comparison among countries and helps in the formulation of future plans on national scientific policies.
A semi-parametric Bayesian approach, iSBA, for differential expression analysis of RNA-seq data
Authors: Bi Ran , Liu Peng
Published: February 2019

RNA sequencing (RNA-seq) technologies have been popularly applied to study gene expression in recent years. Identifying differentially expressed (DE) genes across treatments is one of the major steps in RNA-seq data analysis. Most differential expression analysis methods rely on parametric assumptions, and it is not guaranteed that these assumptions are appropriate for real data analysis. In this paper, we develop a semi-parametric Bayesian approach for differential expression analysis. More specifically, we model the RNA-seq count data with a Poisson-Gamma mixture model, and propose a Bayesian mixture modeling procedure with a Dirichlet process as the prior model for the distribution of fold changes between the two treatment means. We develop Markov chain Monte Carlo (MCMC) posterior simulation using Metropolis Hastings algorithm to generate posterior samples for differential expression analysis while controlling false discovery rate. Simulation results demonstrate that our proposed method outperforms other popular methods used for detecting DE genes.
PRH1 mediates ARF7-LBD dependent auxin signaling to regulate lateral root development inArabidopsis thaliana
Authors: Zhang Feng , Tao Wenqing , Sun Ruiqi , Wang Junxia , Li Cuiling , Kong Xiangpei , Tian Huiyu , Ding Zhaojun
Published: February 2019

The development of lateral roots inArabidopsis thalianais strongly dependent on signaling directed by the AUXIN RESPONSE FACTOR7 (ARF7), which in turn activates LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors (LBD16,18,29and33). Here, the product ofPRH1,aPR-1homolog annotated previously as encoding a pathogen-responsive protein, was identified as a target of ARF7-mediated auxin signaling and also as participating in the development of lateral roots.PRH1was shown to be strongly induced by auxin treatment, and plants lacking a functional copy ofPRH1formed fewer lateral roots. The transcription ofPRH1was controlled by the binding of both ARF7 and LBDs to its promoter region. An interaction was detected between PRH1 and GATA23, a protein which regulates cell identity in lateral root founder cells.

Author Summary

InArabidopsis thalianaAUXIN RESPONSE FACTOR7 (ARF7)-mediated auxin signaling plays a key role in lateral roots (LRs) development. TheLATERAL ORGAN BOUNDARIES DOMAIN (LBD)transcription factors (LBD16,18,29and33) act downstream of ARF7-mediated auxin signaling to control LRs formation. Here, thePR-1homologPRH1was identified as a novel target of both ARF7 and LBDs (especially the LBD29) during auxin induced LRs formation, as both ARF7 and LBDs were able to bind to thePRH1promoter. More interestingly, PRH1 has a physical interaction with GATA23, which has been also reported to be up-regulated by auxin and influences LR formation through its regulation of LR founder cell identity. Whether the interaction between GATA23 and PRH1 affects the stability and/or the activity of either (or both) of these proteins remains an issue to be explored. This study provides improves new insights about how auxin regulates lateral root development.
Rapid and scalable in vitro production of single-stranded DNA
Authors: Minev Dionis , Guerra Richard , Kishi Jocelyn Y. , Smith Cory , Krieg Elisha , Said Khaled , Hornick Amanda , Sasaki Hiroshi M. , Filsinger Gabriel , Beliveau Brian J. , Yin Peng , Church George M. , Shih William M.
Published: February 2019

We present a rapid, scalable, user-friendly method for in vitro production of high-purity single-stranded DNA (ssDNA) ranging from 89–3315 nucleotides in length. PCR with a forward primer bearing a methanol-responsive polymer generates a tagged amplicon that enables selective precipitation of the modified strand under denaturing conditions. We demonstrate that the recovered ssDNA can be used for CRISPR/Cas9 homology-directed repair in human cells, DNA-origami folding, and fluorescent in situ hybridization.
The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanisms
Authors: Garvin Alexander J. , Walker Alexandra K. , Densham Ruth M. , Chauhan Anoop Singh , Stone Helen R. , Mackay Hannah L. , Jamshad Mohammed , Starowicz Katarzyna , Daza-Martin Manuel , Ronson George E. , Lanz Alexander J. , Beesley James F. , Morris Joanna R.
Published: February 2019

SUMOylation (small ubiquitin-like modifier) in the DNA double-strand break (DSB) response regulates recruitment, activity, and clearance of repair factors. However, our understanding of a role for deSUMOylation in this process is limited. Here we identify different mechanistic roles for deSUMOylation in homologous recombination (HR) and nonhomologous end joining (NHEJ) through the investigation of the deSUMOylase SENP2. We found that regulated deSUMOylation of MDC1 prevents excessive SUMOylation and its RNF4-VCP mediated clearance from DSBs, thereby promoting NHEJ. In contrast, we show that HR is differentially sensitive to SUMO availability and SENP2 activity is needed to provide SUMO. SENP2 is amplified as part of the chromosome 3q amplification in many cancers. Increased SENP2 expression prolongs MDC1 focus retention and increases NHEJ and radioresistance. Collectively, our data reveal that deSUMOylation differentially primes cells for responding to DSBs and demonstrates the ability of SENP2 to tune DSB repair responses.
Cohesin occupancy and composition at enhancers and promoters are linked to DNA replication origin proximity in Drosophila
Authors: Pherson Michelle , Misulovin Ziva , Gause Maria , Dorsett Dale
Published: February 2019

Cohesin consists of the SMC1-SMC3-Rad21 tripartite ring and the SA protein that interacts with Rad21. The Nipped-B protein loads cohesin topologically around chromosomes to mediate sister chromatid cohesion and facilitate long-range control of gene transcription. It is largely unknown how Nipped-B and cohesin associate specifically with gene promoters and transcriptional enhancers, or how sister chromatid cohesion is established. Here, we use genome-wide chromatin immunoprecipitation in Drosophila cells to show that SA and the Fs(1)h (BRD4) BET domain protein help recruit Nipped-B and cohesin to enhancers and DNA replication origins, whereas the MED30 subunit of the Mediator complex directs Nipped-B and Vtd in Drosophila (also known as Rad21) to promoters. All enhancers and their neighboring promoters are close to DNA replication origins and bind SA with proportional levels of cohesin subunits. Most promoters are far from origins and lack SA but bind Nipped-B and Rad21 with subproportional amounts of SMC1, indicating that they bind cohesin rings only part of the time. Genetic data show that Nipped-B and Rad21 function together with Fs(1)h to facilitate Drosophila development. These findings show that Nipped-B and cohesin are differentially targeted to enhancers and promoters, and suggest models for how SA and DNA replication help establish sister chromatid cohesion and facilitate enhancer–promoter communication. They indicate that SA is not an obligatory cohesin subunit but a factor that controls cohesin location on chromosomes.
The Macromolecular Femtosecond Crystallography Instrument at the Linac Coherent Light Source
Authors: Sierra Raymond G. , Batyuk Alexander , Sun Zhibin , Aquila Andrew , Hunter Mark S. , Lane Thomas J. , Liang Mengning , Yoon Chun Hong , Alonso-Mori Roberto , Armenta Rebecca , Castagna Jean-Charles , Hollenbeck Michael , Osier Ted O. , Hayes Matt , Aldrich Jeff , Curtis Robin , Koglin Jason E. , Rendahl Theodore , Rodriguez Evan , Carbajo Sergio , Guillet Serge , Paul Rob , Hart Philip , Nakahara Kazutaka , Carini Gabriella , DeMirci Hasan , Dao E. Han , Hayes Brandon M. , Rao Yashas P. , Chollet Matthieu , Feng Yiping , Fuller Franklin D. , Kupitz Christopher , Sato Takahiro , Seaberg Matthew H. , Song Sanghoon , van Driel Tim B. , Yavas Hasan , Zhu Diling , Cohen Aina E. , Wakatsuki Soichi , Boutet Sébastien
Published: February 2019

The Macromolecular Femtosecond Crystallography (MFX) instrument at the Linac Coherent Light Source (LCLS) is the seventh and newest instrument at the world's first hard X-ray free-electron laser. It was designed with a primary focus on structural biology, employing the ultrafast pulses of X-rays from LCLS at atmospheric conditions to overcome radiation damage limitations in biological measurements. It is also capable of performing various time-resolved measurements. The MFX design consists of a versatile base system capable of supporting multiple methods, techniques and experimental endstations. The primary techniques supported are forward scattering and crystallography, with capabilities for various spectroscopic methods and time-resolved measurements. The location of the MFX instrument allows for utilization of multiplexing methods, increasing user access to LCLS by running multiple experiments simultaneously.
Ethyl 2-(4-benzyl-3-methyl-6-oxo-1,6-dihydropyridazin-1-yl)acetate: crystal structure and Hirshfeld surface analysis
Authors: Zaoui Younes , Ramli Youssef , Taoufik Jamal , Mague Joel T. , Jotani Mukesh M. , Tiekink Edward R. T. , Ansar M'hammed
Published: February 2019

The title compound, C16H18N2O3, is constructed about a central oxopyridazinyl ring (r.m.s. deviation = 0.0047 Å), which is connected to an ethylacetate group at the N atom closest to the carbonyl group, and benzyl and methyl groups second furthest and furthest from the carbonyl group, respectively. An approximately orthogonal relationship exists between the oxopyridazinyl ring and the best plane through the ethylacetate group [dihedral angle = 77.48 (3)°]; the latter lies to one side of the central plane [the Nr—Nr—Cm—Cc (r = ring, m = methylene, c = carbonyl) torsion angle being 104.34 (9)°]. In the crystal, both H atoms of the N-bound methylene group form methylene-C—H...O(ring carbonyl) or N(pyridazinyl) interactions, resulting in the formation of a supramolecular tape along the a-axis direction. The tapes are assembled into a three-dimensional architecture by methyl- and phenyl-C—H...O(ring carbonyl) and phenyl-C—H...O(ester carbonyl) interactions. The analysis of the calculated Hirshfeld surface indicates the dominance of H...H contacts to the overall surface (i.e. 52.2%). Reflecting other identified points of contact between molecules noted above, O...H/H...O (23.3%), C...H/H...C (14.7%) and N...H/H...N (6.6%) contacts also make significant contributions to the surface.
Mortality versus survival in drought‐affected Aleppo pine forest depends on the extent of rock cover and soil stoniness
Authors: Preisler Yakir , Tatarinov Fyodor , Grünzweig José M. , Bert Didier , Ogée Jérôme , Wingate Lisa , Rotenberg Eyal , Rohatyn Shani , Her Nir , Moshe Itzhak , Klein Tamir , Yakir Dan
Published: February 2019

Drought‐related tree mortality had become a widespread phenomenon in forests around the globe. This process leading to these events and its complexity is not fully understood. Trees in the dry timberline are exposed to ongoing drought, and the available water for transpiration in the soil can determine their survival chances.

Recent drought years led to 5%–10% mortality in the semi‐arid pine forest of Yatir (Israel). The distribution of dead trees was, however, highly heterogeneous with parts of the forest showing >80% dead trees (D plots) and others with mostly live trees (L plots). At the tree level, visible stress was associated with low pre‐dawn leaf water potential at the dry season (−2.8 MPa vs. −2.3 MPa in non‐stressed trees), shorter needles (5.5 vs. 7.7 mm) and lower chlorophyll content (0.6 vs. 1 mg/g dw). Trends in tree‐ring widths reflected differences in stress intensity (30% narrower rings in stressed compared with unstressed trees), which could be identified 15–20 years prior to mortality.

At the plot scale, no differences in topography, soil type, tree age or stand density could explain the mortality difference between the D and L plots. It could only be explained by the higher surface rock cover and in stoniness across the soil profile in the L plots. Simple bucket model simulations using the site’s long‐term hydrological data supported the idea that these differences could result in higher soil water concentration (m3/m3) in the L plots and extend the time above wilting point by several months across the long dry season.

Accounting for subsurface heterogeneity may therefore critical to assessing stand‐level response to drought and projecting tree survival, and can be used in management strategies in regions undergoing drying climate trends.

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Grassland plants show no relationship between leaf drought tolerance and soil moisture affinity, but rapidly adjust to changes in soil moisture
Authors: Májeková Maria , Martínková Jana , Hájek Tomáš
Published: February 2019

Assessing drought tolerance and the ability of plants to adjust to changes in available water resources is crucial for understanding current and future distributions of plant species. While turgor loss point (πtlp) has been recognized as a direct determinant of drought tolerance in woody plants, information on it for grassland species is largely missing.

We first validated a rapid method to estimate πtlp for grassland species, using osmometry measurements (πtlp‐osm) of osmotic potential at full hydration (πo‐osm), originally proposed for woody species. We confirmed that πo‐osm was tightly positively related to πtlp measured by the classic pressure–volume curve (πtlp‐pv). Cell wall elasticity was not important in the maintenance of turgor and neither specific leaf area nor leaf dry matter content influenced πtlp.

We then studied the relationship between πtlp‐osm measured under controlled conditions and species’ soil moisture affinity (Ellenberg indicator values) in 40 diverse grassland species from the full range of soil moisture conditions found in temperate grasslands. On a subset of 12 species, we studied the adjustment in πtlp‐osm to drought stress and recovery from drought.

We hypothesized that dry grassland species are better adapted to drier conditions by having comparatively higher leaf drought tolerance (more negative πtlp) and a better ability to adjust to acute drought stress.

We found that πtlp‐osm was unrelated to species’ soil moisture affinity. However, all species developed higher leaf drought tolerance by decreasing πtlp‐osm after seven weeks of drought stress. After only one week of recovery, all species reduced the leaf drought tolerance back to the πtlp‐osm level comparable with non‐stressed plants.

Our results considerably extend the relationship between πo‐osm and πtlp, originally defined for woody species, and thus propose a yet unexploited direct method for assessing leaf drought tolerance via turgor loss point in herbaceous species. However, the lack of relationship between πtlp and soil moisture affinity suggests that, unlike in woody plants, leaf‐level drought tolerance in grassland plants does not fully translate into whole‐plant drought resistance, suggesting an importance of other drought resistance strategies.

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Transparency reduces predator detection in mimetic clearwing butterflies
Authors: Arias Mónica , Mappes Johanna , Desbois Charlotte , Gordon Swanne , McClure Melanie , Elias Marianne , Nokelainen Ossi , Gomez Doris
Published: February 2019

Predation is an important selective pressure, and some prey have evolved conspicuous warning signals that advertise unpalatability (i.e., aposematism) as an antipredator defence. Conspicuous colour patterns have been shown effective as warning signals, by promoting predator learning and memory. Unexpectedly, some butterfly species from the unpalatable tribe Ithomiini possess transparent wings, a feature rare on land but common in water, known to reduce predator detection.

We tested whether transparency of butterfly wings was associated with decreased detectability by predators, by comparing four butterfly species exhibiting different degrees of transparency, ranging from fully opaque to largely transparent. We tested our prediction using both wild birds and humans in behavioural experiments. Vision modelling predicted butterfly detectability to be similar for these two predator types.

In concordance with predictions, the most transparent species were almost never found first and were detected less often than the opaque species by both birds and humans, suggesting that transparency enhances crypsis. However, humans were able to learn to better detect the more transparent species over time.

Our study demonstrates for the first time that transparency on land likely decreases detectability by visual predators.

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JumpDetector: An automated monitoring equipment for the locomotion of jumping insects
Authors: Zhou Feng , Kang Le , Wang Xian‐Hui
Published: February 2019

Continuous jumping behavior, a kind of endurance locomotion, plays important roles in insect ecological adaption and survival. However, the methods used for the efficient evaluation of insect jumping behavior remain largely lacking. Here, we developed a locomotion detection system named JumpDetector with automatic trajectory tracking and data analysis to evaluate the jumping of insects. This automated system exhibits more accurate, efficient, and adjustable performance than manual methods. By using this automatic system, we characterized a gradually declining pattern of continuous jumping behavior in 4th‐instar nymphs of the migratory locust. We found that locusts in their gregarious phase outperformed locusts in their solitary phase in the endurance jumping locomotion. Therefore, the JumpDetector could be widely used in jumping behavior and endurance locomotion measurement.
Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488
Authors: Hernández‐Arriaga Ana M. , del Cerro Carlos , Urbina Leire , Eceiza Arantxa , Corcuera Mª Angeles , Retegi Aloña , Auxiliadora Prieto M.
Published: February 2019

Komagataeibacter medellinensis ID13488 (formerly Gluconacetobacter medellinensis ID13488) is able to produce crystalline bacterial cellulose (BC) under high acidic growth conditions. These abilities make this strain desirable for industrial BC production from acidic residues (e.g. wastes generated from cider production). To explore the molecular bases of the BC biosynthesis in this bacterium, the genome has been sequenced revealing a sequence of 3.4 Mb containing three putative plasmids of 38.1 kb (pKM01), 4.3 kb (pKM02) and 3.3 Kb (pKM03). Genome comparison analyses of K. medellinensis ID13488 with other cellulose‐producing related strains resulted in the identification of the bcs genes involved in the cellulose biosynthesis. Genes arrangement and composition of four bcs clusters (bcs1, bcs2, bcs3 and bcs4) was studied by RT‐PCR, and their organization in four operons transcribed as four independent polycistronic mRNAs was determined. qRT‐PCR experiments demonstrated that mostly bcs1 and bcs4 are expressed under BC production conditions, suggesting that these operons direct the synthesis of BC. Genomic differences with the close related strain K. medellinensis NBRC 3288 unable to produce BC were also described and discussed.
Comparison of genomic landscapes of large cell neuroendocrine carcinoma, small cell lung carcinoma, and large cell carcinoma
Authors: Zhou Zhen , Zhu Lei , Niu Xiaomin , Shen Shengping , Zhao Yi , Zhang Jie , Ye Junyi , Han‐Zhang Han , Liu Junjun , Liu Chenglin , Lu Shun
Published: February 2019

Background

The classification of large cell neuroendocrine carcinoma (LCNEC) has generated considerable debate and has been revised since its recognition as a separate entity. Although it shares clinical features with small cell lung carcinoma (SCLC) and was classified with SCLC in the 2015 World Health Organization classification system, numerous studies have revealed inferior treatment outcomes of LCNEC when it was treated as SCLC. Because the incidence of LCNEC is rare, its mutational landscape has not been comprehensively interrogated.

Methods

We performed capture‐based ultra‐deep targeted sequencing on tumor samples of LCNEC, large cell carcinoma (LCC), and SCLC to elucidate its biological relationship with these subtypes and to identify potentially targetable molecular alterations.

Results

Our data revealed a molecular signature, consisting of RUNX1, ERBB4, BRCA1, and EPHA3, that is distinctively mutated in LCNEC. A majority (60%) of LCNEC patients harbored copy number variations (CNVs). Interestingly, there were no common CNVs shared among the three subtypes: NFкBIA amplification was shared between LCNEC and LCC, while AKT2 amplification was shared between LCNEC and SCLC. Furthermore, genetic alterations in the PI3K/AKT/mTOR pathway were enriched in all three subtypes.

Conclusion

Despite the histological and/or morphological similarities among LCNEC, LCC, and SCLC, our data revealed a molecular signature, consisting of RUNX1, ERBB4, BRCA1, and EPHA3, that is distinctively mutated in LCNEC, which has the potential to be used as a panel of biomarkers to distinguish LCNEC from a molecular perspective. Furthermore, the molecular distinction among the three subtypes can also be reflected from CNV events.