bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Robinia pseudoacacia target proteins responsive to Mesorhizobium amphore CCNWGS0123 effector protein NopT
Authors: Luo Yantao , Liu Dongying , Jiao Shuo , Liu Shuang , Wang Xinye , Shen Xihui , Wei Gehong 
Published: August 2020

Abstract
Nodulation outer proteins secreted via type 3 secretion systems are involved in the process of symbiosis between legume plants and rhizobia. To study the function of NopT in symbiosis, we mutated nopT in Mesorhizobium amphore CCNWGS0123 (GS0123), which can nodulate black locust (Robinia pseudoacacia). The nopT mutant induced higher levels of jasmonic acid, salicylic acid, and hydrogen peroxide accumulation in the roots of R. pseudoacacia compared with wild-type GS0123. The ΔnopT mutant induced higher disease-resistant gene expression 72 hours post-inoculation (hpi), whereas GS0123 induced higher disease-resistant gene expression earlier, at 36 hpi. Compared with the nopT mutant, GS0123 induced the up-regulation of most genes at 36 hpi and the down-regulation of most genes at 72 hpi. Proteolytically active NopT_GS0123 induced hypersensitive responses when expressed transiently in tobacco leaves (Nicotiana benthamiana). Two NopT_GS0123 targets in R. pseudoacacia were identified, ATP-citrate synthase alpha chain protein 2 and hypersensitive-induced response protein. Their interactions with NopT_GS0123 triggered resistance by the plant immune system. In conclusion, NopT_GS0123 inhibited the host plant immune system and had minimal effect on nodulation in R. pseudoacacia. Our results reveal the underlying molecular mechanism of NopT function in plant–symbiont interactions.
A 5′ UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation
Authors: Maltby Connor J , Schofield James P R , Houghton Steven D , O’Kelly Ita , Vargas-Caballero Mariana , Deinhardt Katrin , Coldwell Mark J 
Published: August 2020

AbstractRNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators of post-transcriptional mRNA localisation and translation. G4s within some neuronal mRNAs are known to control distal localisation and local translation, contributing to distinct local proteomes that facilitate the synaptic remodelling attributed to normal cellular function. In this study, we characterise the G4 formation of a (GGN)13 repeat found within the 5′ UTR of the potassium 2-pore domain leak channel Task3 mRNA. Biophysical analyses show that this (GGN)13 repeat forms a parallel G4 in vitro exhibiting the stereotypical potassium specificity of G4s, remaining thermostable under physiological ionic conditions. Through mouse brain tissue G4-RNA immunoprecipitation, we further confirm that Task3 mRNA forms a G4 structure in vivo. The G4 is inhibitory to translation of Task3 in vitro and is overcome through activity of a G4-specific helicase DHX36, increasing K+ leak currents and membrane hyperpolarisation in HEK293 cells. Further, we observe that this G4 is fundamental to ensuring delivery of Task3 mRNA to distal primary cortical neurites. It has been shown that aberrant Task3 expression correlates with neuronal dysfunction, we therefore posit that this G4 is important in regulated local expression of Task3 leak channels that maintain K+ leak within neurons.
EXPath 2.0: An Updated Database for Integrating High-Throughput Gene Expression Data with Biological Pathways
Authors: Tseng Kuan-Chieh , Li Guan-Zhen , Hung Yu-Cheng , Chow Chi-Nga , Wu Nai-Yun , Chien Yi-Ying , Zheng Han-Qin , Lee Tzong-Yi , Kuo Po-Li , Chang Song-Bin , Chang Wen-Chi 
Published: August 2020

Abstract
Co-expressed genes tend to have regulatory relationships and participate in similar biological processes. Construction of gene correlation networks from microarray or RNA-seq expression data has been widely applied to study transcriptional regulatory mechanisms and metabolic pathways under specific conditions. Furthermore, since transcription factors (TFs) are critical regulators of gene expression, it is worth investigating TFs on the promoters of co-expressed genes. Although co-expressed genes and their related metabolic pathways can be easily identified from previous resources, such as EXPath and EXPath Tool, this information is not simultaneously available to identify their regulatory TFs. EXPath 2.0 is an updated database for the investigation of regulatory mechanisms in various plant metabolic pathways with 1,881 microarray and 978 RNA-seq samples. There are six significant improvements in EXPath 2.0: (i) the number of species has been extended from three to six to include Arabidopsis, rice, maize, Medicago, soybean and tomato; (ii) gene expression at various developmental stages have been added; (iii) construction of correlation networks according to a group of genes is available; (iv) hierarchical figures of the enriched Gene Ontology (GO) terms are accessible; (v) promoter analysis of genes in a metabolic pathway or correlation network is provided; and (vi) user’s gene expression data can be uploaded and analyzed. Thus, EXPath 2.0 is an updated platform for investigating gene expression profiles and metabolic pathways under specific conditions. It facilitates users to access the regulatory mechanisms of plant biological processes. The new version is available at http://EXPath.itps.ncku.edu.tw.
Eye Rubbing and Transient Corneal Ectasia Detected by Topography in a Pediatric Patient
Authors: Scotto Riccardo , Vagge Aldo , Traverso Carlo E. 
Published: August 2020

Abstract:
We report on a 13-year-old girl undergoing changes in the refraction of her OS associated with eye rubbing. Corneal topography showed a corneal deformation in OS, classified as stage 1 keratoconus according to the Krumeich classification. A significant reduction in eye rubbing led to a normal corneal shape at the 1-year follow-up. Transient and fully reversible corneal ectasia can be caused by eye rubbing in pediatric age. This may have implications when counseling very young patients with eye rubbing.
Custom-Made Cleft Palate Models to Teach V-Y Pushback Palatoplasty
Authors: Hwang Kun 
Published: August 2020

Abstract
We developed custom-made cleft palate (CP) models to teach V-Y pushback palatoplasty, with a focus on design and mucoperiosteal elevation.
A model (23 cm wide, 30 cm long, and 13 cm high) was made using silicone (model 1; M1). On the palate of a skull model, 2 layers of colored rubber clay were applied to represent the superficial oral mucoperiosteum and deep nasal mucosa (model 2; M2). From the greater palatine foramen, threads of dental floss were inserted inside the clay, representing the greater palatine artery. In a workshop, a mouth gag was applied on M1, and participants designed 2-flap palatoplasty and 4-flap palatoplasty. On the palate of M2, incisions were made with a #15 blade. On M2, a mucoperiosteal flap (rubber clay over the hard palate) was elevated using a periosteal elevator, avoiding injury to the dental floss mimicking the greater palatine artery. Six participants were recruited for the workshop and were asked to rate their satisfaction with the outcome on a Likert scale.
For CP design, participants answered that they had learned useful knowledge from this workshop, reflecting a significant improvement (4.0 ± 1.1 for incomplete CP, 4.2 ± 1.2 for complete CP). They became confident in this skill after the workshop (4.2 ± 0.8 for incomplete CP, 3.8 ± 0.8 for complete CP). For cleft mucoperiosteal flap elevation, they likewise learned useful knowledge (4.7 ± 0.5 for incomplete CP, 4.5 ± 0.5 for complete CP) and became confident in this skill (3.8 ± 0.8 for incomplete CP, 4.0 ± 0.6 for complete CP.)
These models can be useful for V-Y pushback palatoplasty training for medical personnel.
Anaphylactic Reaction Rates to Blue Dyes Used for Sentinel Lymph Node Mapping
Authors: Perenyei Miklos , Barber Zoe E. , Gibson John , Hemington-Gorse Sarah , Dobbs Thomas D. 
Published: August 2020

Objective:
The primary objective of this study was to quantify the risk of anaphylaxis to blue dyes used in SLNB for cancer. Secondary outcomes included the identification of factors that may influence this risk.

Summary of Background Data:
Blue dyes are widely used to help identify sentinel lymph nodes in oncological surgery. The rate of severe allergic reactions to blue dyes remains a controversial topic, with the true incidence and influencing factors uncertain.

Methods:
A systematic review and meta-analysis was performed to identify all studies which report on the incidence of severe adverse reactions and anaphylaxis to blue dyes (patent blue, isosulfan blue, methylene blue, and indigo carmine), when used for SLNB. Collected data included cancer and dye type, volume, and method of injection. Incidence was estimated using the arcsine method of statistical analysis.

Results:
One hundred nine studies documenting 94 episodes of anaphylaxis in a total of 61,951 SLNB procedures, resulting in a weighed anaphylaxis rate of 0.061%. SLNB for breast cancer carries an anaphylaxis risk of 0.083%, with the risk markedly lower in melanoma surgery (0.0043%). Low dye volume (<2 mL) and intradermal injection are both associated with lower rates of anaphylaxis (0.031% and 0.0068%). Isosulfan blue seems to be the most anaphylactogenic amongst blue dyes with a rate of 0.16%. There were no reported cases of death in this cohort.

Conclusion:
Anaphylaxis to blue dyes in SLNB is rare. Methylene blue, patent blue, lower dye volumes, and intradermal administration are all associated with a lower incidence of anaphylaxis.
Optimized DNA isolation method for microbiome analysis of human tissues
Authors: Bruggeling Carlijn , Garza Daniel R. , Achouiti Soumia , Mes Wouter , Dutilh Bas E. , Boleij Annemarie 
Published: August 2020

AbstractRecent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, developments in the field of tissue microbiomes have been hampered by the presence of host DNA in isolates which interferes with the analysis of the bacterial content. Here, we present a DNA isolation protocol from tissue samples including reduction of host DNA without distortion of microbial abundance profiles. We evaluated which concentrations of Triton and saponin lyse host cells and leave bacterial cells intact, which was combined with DNAse treatment to deplete released host DNA. We applied our protocol to extract microbial DNA fromex vivoandin vivoacquired human colon biopsies (∼2-5 mm in size) and assessed the relative abundance of bacterial and human DNA by qPCR. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5-fold enrichment of bacterial DNA while preserving the relative abundance ofFirmicutes, Bacteroidetes, γ-ProteobacteriaandActinobacteria. Our protocol combined with shotgun metagenomic sequencing revealed a colon tissue microbiome profile with a Shannon diversity index of 3.2 and an UniFrac distance of 0.54, which is comparable to reported numbers based on amplicon sequencing. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of rigid Gram-positive bacteria without depleting the more sensitive Gram-negative bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.
The cognitive effects of a promised bonus do not depend on dopamine synthesis capacity
Authors: Hofmans Lieke , van den Bosch Ruben , Määttä Jessica I. , Verkes Robbert-Jan , Aarts Esther , Cools Roshan 
Published: August 2020

ABSTRACTReward motivation is known to enhance cognitive control. However, detrimental effects have also been observed, which have been attributed to overdosing of already high baseline dopamine levels by further dopamine increases elicited by reward cues. Aarts et al. (2014) indeed demonstrated, in 14 individuals, that reward effects depended on striatal dopamine synthesis capacity, measured with [18F]FMT-PET: promised reward improved Stroop control in low-dopamine individuals, while impairing it in high-dopamine individuals. Here, we aimed to assess this same effect in 44 new participants, who had previously undergone an [18F]DOPA-PET scan to quantify dopamine synthesis capacity. This sample performed the exact same rewarded Stroop paradigm as in the prior study. However, we did not find any correlation between reward effects on cognitive control and striatal dopamine synthesis capacity. The discrepancy between the current and our previous findings might reflect the use of different radiotracers for indexing dopamine synthesis capacity.STATEMENT OF RELEVANCEReward motivation is generally thought to enhance cognitive control, but paradoxical negative effects of rewards on cognitive control have also been observed. A previous PET study demonstrated that reward effects on Stroop control depended on baseline striatal dopamine synthesis capacity, indexed by uptake of the radiotracer [18F]FMT. The sample size is this study was very small for a between-subject correlational design. Replicating the exact same Stroop paradigm within a larger sample is therefore crucial to robustly establish the mechanistic link between incentive motivation and cognitive control and advancing our understanding of who chokes under pressure and why, a topic of great societal relevance today. The present study did not reveal any correlation between reward effects on cognitive control and striatal dopamine synthesis capacity, indexed with [18F]FDOPA-PET. Future studies might consider putative differential sensitivity of the radiotracer [18F]FMT and [18F]FDOPA, while also addressing other indices of dopamine transmission.
Covering soybean leaves with cellulose nanofiber changes leaf surface hydrophobicity and confers resistance againstPhakopsora pachyrhizi
Authors: Saito Haruka , Yamashita Yuji , Sakata Nanami , Ishiga Takako , Shiraishi Nanami , Usuki Giyu , Nguyen Viet Tru , Yamamura Eiji , Ishiga Yasuhiro 
Published: August 2020

AbstractAsian soybean rust (ASR) caused byPhakopsora pachyrhizi, an obligate biotrophic fungal pathogen, is the most devastating soybean production disease worldwide. Currently, timely fungicide application is the only means to control ASR in the field. We investigated cellulose nanofiber (CNF) application on ASR disease management. CNF-treated leaves showed reduced lesion number afterP. pachyrhiziinoculation compared to control leaves, indicating that covering soybean leaves with CNF confersP. pachyrhiziresistance. We also demonstrated that formation ofP. pachyrhizipre-infection structures including germ-tubes and appressoria, and also gene expression related to these formations, such aschitin synthases(CHSs), were significantly suppressed in CNF-treated soybean leaves compared to control leaves. Moreover, contact angle measurement revealed that CNF converts soybean leaf surface properties from hydrophobic to hydrophilic. These results suggest that CNF can change soybean leaf surface hydrophobicity, conferring resistance againstP. pachyrhizi, based on the reduced expression ofCHSs, as well as reduced formation of pre-infection structures. This is the first study to investigate CNF application to control field disease.
Robust Population Single Neuronal Calcium Signal Extraction Using SCOUT Allows for Longitudinal Analysis of Behavior-associated Neural Ensemble Dynamics
Authors: Johnston Kevin G. , Grieco Steven F. , Yu Zhaoxia , Jin Suoqin , Shen Tong , Crary Rachel , Guzowski John F. , Holmes Todd C. , Nie Qing , Xu Xiangmin 
Published: August 2020

SummaryIn vivocalcium imaging enables simultaneous recording of large neuronal ensembles while engaged in operations such as learning and memory. However, suchin vivooptical recordings are typically subject to motion artifact and background contamination from neurons and blood vessels. Further, population cell tracking across multiple recordings is complicated by non-rigid transformation induced by cell movements and field shifts. We introduce the novel method SCOUT for Single-Cell SpatiOtemporal LongitUdinal Tracking, consisting of two crucial parts: (1) imposition of spatial constraints on neuronal footprints extracted from individual optical recordings to improve ROI selection and eliminate false discoveries, and (2) application of a predictor-corrector, using spatiotemporal correlation of extracted neurons across sessions, for population cell tracking across multiple sessions. SCOUT empirically outperforms current methods for cell extraction and tracking in long-term multi-session imaging experiments across multiple brain regions. Application of this method allows for robust longitudinal analysis of contextual discrimination associated neural ensemble dynamics in the hippocampus up to 60 days.
Autophagy is required for the rejection of self-incompatible pollen in two accessions of transgenicArabidopsis thaliana
Authors: Macgregor Stuart R. , Lee Hyun Kyung , Nelles Hayley , Johnson Daniel C. , Zhang Tong , Ma Chaozhi , Goring Daphne R. 
Published: August 2020

AbstractSuccessful reproduction in the Brassicaceae is mediated by a complex series of interactions between the pollen and the pistil, and some species have an additional layer of regulation with the self-incompatibility trait. While the initial activation of the self-incompatibility pathway by the pollen S-locus protein11/S-locus cysteine-rich peptide and the stigmaSReceptor Kinase is well characterized, the downstream mechanisms causing self-pollen rejection are still not fully understood. In previous studies, we had detected the presence of autophagic bodies with self-incompatible pollinations inArabidopsis lyrataand transgenicA. thalianalines, but it was not known if autophagy was essential for self-pollen rejection. Here, we investigated the requirement of autophagy in this response by crossing mutations in the essentialAUTOPHAGY7(ATG7) orAUTOPHAGY5(ATG5) genes into two different transgenic self-incompatibleA. thalianalines in the Col-0 and C24 accessions. By using these previously characterized transgenic lines that expressA. lyrataandA. halleriself-incompatibility genes, we demonstrated that disrupting autophagy can weaken their self-incompatible responses in the stigma. When theatg7oratg5mutations were present, an increased number of self-incompatible pollen were found to hydrate and form pollen tubes that successfully fertilized the self-incompatible pistils. Additionally, we confirmed the presence of GFP-ATG8a labelled autophagosomes in the stigmatic papillae following self-incompatible pollinations. Together, these findings support the requirement of autophagy in the self-incompatibility response and add to the growing understanding of the cellular events that take place in the stigma to reject self-pollen.One Sentence SummaryIn self-incompatible transgenicArabidopsis thalianalines, autophagy is an integral part of the cellular responses in the stigma to efficiently block fertilization by self-incompatible pollen.
Gene disruption by structural mutations drives selection in US rice breeding over the last century
Authors: Vaughn Justin N. , Korani Walid , Stein Joshua C. , Edwards Jeremy D. , Peterson Daniel G. , Simpson Sheron A. , Youngblood Ramey C. , Grimwood Jane , Ware Doreen H. , McClung Anna M. , Scheffler Brian E. 
Published: August 2020

AbstractThe genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropicaljaponicarice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup,Oryza glaberrima. Supporting prior work, we find substantial genome expansion is thesativabranch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use ofab initioestimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.
Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed inBrassica rapa
Authors: Chakraborty Tania , Kendall Timmy , Grover Jeffrey W. , Mosher Rebecca A. 
Published: August 2020

AbstractBackgroundRNA directed DNA methylation (RdDM) initiates cytosine methylation in all contexts, and maintains asymmetric CHH methylation (where H is any base other than G). Mature plant embryos show one of the highest levels of CHH methylation, and it has been suggested that RdDM is responsible for this hypermethylation. Because loss of RdDM inBrassica rapacauses seed abortion, embryo methylation might play a role in seed development. RdDM is required in the maternal sporophyte, suggesting that small RNAs from the maternal sporophyte might translocate to the developing embryo, triggering DNA methylation that prevents seed abortion. This raises the question whether embryo hypermethylation is autonomously regulated by the embryo itself or influenced by the maternal sporophyte.ResultsHere, we demonstrate thatB. rapaembryos are hypermethylated in both euchromatin and heterochromatin and that this process requires RdDM. Contrary to current models,B. rapaembryo hypermethylation is not correlated with demethylation of the endosperm. We also show that maternal somatic RdDM is not sufficient for global embryo hypermethylation, and we find no compelling evidence for maternal somatic influence over embryo methylation at any locus. Decoupling of maternal and zygotic RdDM leads to successful seed development despite loss of embryo CHH hypermethylation.ConclusionsWe conclude that embryo CHH hypermethylation is conserved, autonomously controlled, and not required for embryo development. Furthermore, maternal somatic RdDM, while required for seed development, does not directly influence embryo methylation patterns.