bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternative treatment of fungal infections: Synergy with non‐antifungal agents
Authors: Rossato Luana , Camargo dos Santos Marielle , Vitale Roxana G. , de Hoog Sybren , Ishida Kelly
Published: October 2020

Fungal infections are responsible for high mortality rates in immunocompromised and high‐risk surgical patients. Therapy failures during the last decades due to increasing multidrug resistance demand innovative strategies for novel and effective antifungal drugs. Synergistic combinations of antifungals with non‐antifungal agents highlight a pragmatic strategy to reduce the development of drug resistance and potentially repurpose known compounds with other functions to bypass costly and time‐consuming novel drug development.
Atypical macroglossia caused by multiple myeloma‐associated systemic amyloidosis with severe lingual movement disorder and tongue sclerosis
Authors: Murakami Yumi , Watanabe Genya , Yuki Tsubasa , Sugaya Ryo , Harigae Souske , Nakamura Takaaki , Kawasaki Emiko , Tsukita Kenichi , Watanabe Mai , Harashima Shogo , Suzuki Hiroyoshi , Suzuki Yasushi
Published: October 2020

A 70‐year‐old man presented with dysphagia and difficulty in moving the tongue. Macroscopic findings showed features resembling mild tongue atrophy. We suspected a neurodegenerative disease which causes tongue atrophy such as amyotrophic lateral sclerosis. A needle electromyogram showed a strong resistance from the tongue owing to its hardness. Detection of Bence Jones protein κ type M protein in the serum led to a diagnosis of multiple myeloma‐associated light‐chain (κ) type amyloidosis. Thus, in patients with a rugose‐textured and uneven tongue mimicking atrophy, macroglossia caused by amyloidosis should be considered by examining the tongue hardness.
Interior design: how plant pathogens optimize their living conditions
Authors: Meisrimler Claudia‐Nicole , Allan Claudia , Eccersall Sophie , Morris Richard J
Published: October 2020

Pathogens use effectors to suppress host defence mechanisms, promote the derivation of nutrients, and facilitate infection within the host plant. Much is now known about effectors that target biotic pathways, particularly those that interfere with plant innate immunity. By contrast, an understanding of how effectors manipulate nonimmunity pathways is only beginning to emerge. Here, we focus on exciting new insights into effectors that target abiotic stress adaptation pathways, tampering with key functions within the plant to promote colonization. We critically assess the role of various signalling agents in linking different pathways upon perturbation by pathogen effectors. Additionally, this review provides a summary of currently known bacterial, fungal, and oomycete pathogen effectors that induce biotic and abiotic stress responses in the plant, as a first step towards establishing a comprehensive picture for linking effector targets to pathogenic lifestyles.
An increase in xylem embolism resistance of grapevine leaves during the growing season is coordinated with stomatal regulation, turgor loss point and intervessel pit membranes
Authors: Sorek Yonatan , Greenstein Smadar , Netzer Yishai , Shtein Ilana , Jansen Steven , Hochberg Uri
Published: October 2020

Although xylem embolism resistance is traditionally considered as static, we hypothesized that in grapevine (Vitis vinifera) leaf xylem becomes more embolism‐resistant over the growing season.

We evaluated xylem architecture, turgor loss point (ΨTLP) and water potentials leading to 25% of maximal stomatal conductance (gs25) or 50% embolism in the leaf xylem (P50) in three irrigation treatments and at three time points during the growing season, while separating the effects of leaf age and time of season.

Hydraulic traits acclimated over the growing season in a coordinated manner. Without irrigation, ΨTLP, gs25, and P50 decreased between late May and late August by 0.95, 0.77 and 0.71 MPa, respectively. A seasonal shift in P50 occurred even in mature leaves, while irrigation had only a mild effect (< 0.2 MPa) on P50. Vessel size and pit membrane thickness were also seasonally dynamic, providing a plausible explanation for the shift in P50.

Our findings provide clear evidence that grapevines can modify their hydraulic traits along a growing season to allow lower xylem water potential, without compromising gas exchange, leaf turgor or xylem integrity. Seasonal changes should be considered when modeling ecosystem vulnerability to drought or comparing datasets acquired at different phenological stages.
Influence of surgical technique and timing of primary repair on interarch relationship in UCLP: A randomized clinical trial
Authors: Ozawa Terumi Okada , Dutka Jeniffer de Cassia Rillo , Garib Daniela , Lauris Rita C. M. C. , Almeida Araci Malagodi , Brosco Telma Vidotto de Sousa , Lauris José Roberto P. , Dolce Calogero , Pegoraro‐Krook Maria Inês
Published: October 2020

Objective

To compare dental arch relationships in children with unilateral cleft lip and palate (UCLP) between two surgical techniques for repair of cleft lip/palate and two ages of palate repair.

Settings and Sample

Dental models were taken for a group of 448 subjects at a mean age of 7 years and were evaluated by means of the Goslon Yardstick. The patients studied consisted of an initial group of 673 infants with complete UCLP randomized into 8 study groups according to lip repair procedures (Millard versus Spina techniques); palate repair procedures (von Langenbeck versus Furlow techniques); and palate repair timing (early: 9 to 12 months versus late: 15‐18 months).

Methods

Four surgeons performed all surgeries. Dependent variables included the following: lip repair technique, palate repair technique, age at time of palate repair and surgeon; with sex as an independent variable. The data were analysed using a general linear model (P < .05).

Results

There were no significant differences for occlusal index scores as a function of lip or palate surgical technique, palatal repair timing and sex. Significant differences were found for occlusal index scores as a function of the surgeon.

Conclusion

Dental arch relationships were not influenced by lip and palatal repair techniques or patient age at palatal repair. The surgeon was the major factor that influenced the dental arch relationship outcome.
Subtypes of acute and chronic temporomandibular disorders: Their relation to psychological and sleep impairments
Authors: Cao Ye , Yap Adrian Ujin , Lei Jie , Zhang Min‐Juan , Fu Kai‐Yuan
Published: October 2020

Objectives

To determine the differences in psychological states and sleep quality in patients with various temporomandibular disorder (TMD) subtypes, and to ascertain the relationships between TMD duration with psychological and sleep impairments.

Methods

A total of 830 TMD patients were recruited categorized into pain‐related (PT), intra‐articular (IT), and combined (CT) TMD groups. Each group was further divided into acute and chronic subtypes. The Depression, Anxiety, and Stress Scales‐21 (DASS‐21), and Pittsburgh Sleep Quality Index (PSQI) were used to assess emotional states and sleep problems.

Results

Although chronic TMDs generally had higher levels of anxiety, depression, stress, and sleep impairments than acute TMDs, significant differences were only observed for the PT group. Ranking of the mean depression, anxiety, and stress scores was as follows: acute TMDs: CT > PT > IT; chronic TMDs: PT > CT > IT. For both acute and chronic TMDs, the ranking of mean PSQI global and component scores was PT ≥ CT ≥ IT. Logistic regression analyses indicated that stress (ORs = 4.40) and depression (ORs = 2.82) increased the risks of chronic pain‐related TMDs (p < .05).

Conclusions

Chronic pain‐related TMDs are associated with high levels of psychological distress and poorer sleep, while chronic intra‐articular TMDs are not. Stress and depression increased the probability of chronic pain‐related TMDs.
Support for increased cardiovascular risk in non‐segmental vitiligo among Egyptians: A hospital‐based, case–control study
Authors: Azzazi Yousra , Mostafa Wedad Z. , Sayed Khadiga S. , Alhelf Maha , Safwat Miriam , Mahrous Ayman , El Lawindi Mona , Ragab Nanis
Published: October 2020

Background

Data have been accumulating in the past few years that identify vitiligo as a disorder with systemic implications.

Results and methods

In this hospital‐based, cross‐sectional, case–control study, 50 patients with non‐segmental vitiligo and 50 age‐ and sex‐matched controls underwent analysis of serum lipid profile, oxidative stress biomarkers and carotid duplex. Hydrogen peroxide (H2O2) and malondialdehyde (MDA) were significantly higher in patients than controls (p‐value < .001, <.001, respectively); on the other hand, total antioxidant capacity (TAC) was significantly lower in patients than controls (p‐value = .001). A significantly higher percentage of patients had hypercholesterolemia and borderline high, high or very high levels of LDL‐C, compared to controls (p‐value = .001 and .001, respectively). Atherosclerotic plaques and increased common carotid intima media thickness were significantly detected in patients versus controls.

Discussion

Results of the present study suggest that a subset of patients with vitiligo are at a higher risk of developing dyslipidemia and atherosclerosis, which might increase their future risk for the development of cardiovascular disease. Confirmation of these findings would subsequently influence investigative and the treatment strategies in the management plan of vitiligo patients in the near future.

Significance

Vitiligo patients might be at a higher risk of developing dyslipidemia and atherosclerosis, which might increase their risk for the development of cardiovascular disease necessitating prophylactic measures to improve prognosis. Our results might influence the investigative and treatment strategies in the management plan of vitiligo patients in the near future.
The structure and function of the mouse tyrosinase locus
Authors: Seruggia Davide , Josa Santiago , Fernández Almudena , Montoliu Lluis
Published: October 2020

Tyr is the mouse gene that encodes tyrosinase, an enzyme that triggers the first and rate‐limiting step in the biosynthesis of melanin. Mutations in Tyr might result in non‐functional Tyr protein and, consequently, loss of pigment production. This is a rare genetic condition, known as albinism, described for most animal species and one of the most obvious and simple phenotypes to investigate in model organisms. Mutations in the orthologous human TYR gene are associated with oculocutaneous albinism type 1 (OCA1). Over the last thirty years, the mouse Tyr locus has been studied as a paradigm for how genes and expression domains are organized and regulated in mammalian genomes. This review summarizes the major findings and experimental strategies used, from the production of conventional transgenic mice to the latest CRISPR‐Cas9 genome‐edited animals. The main conclusion inferred from all of these studies, which extends beyond the analysis of the mouse Tyr locus, is the relevance of analyzing non‐coding regulatory DNA elements in their natural chromosomal environment, and not only as randomly inserted transgenes. Further, the identification of evolutionary conserved regulatory sequences might highlight new vulnerable sites in the human TYR gene, whose mutations could also be associated with albinism.
Prediction, management, and prognosis of mixed chimerism after hematopoietic stem cell transplantation in transfusion‐dependent pediatric thalassemia patients
Authors: Chen Han , Li Xin‐yu , Zhan Li‐ping , Fang Jian‐pei , Huang Ke , Li Yang , Weng Wen‐jun , Xu Lv‐hong , Xu Hong‐gui , Zhou Dun‐hua
Published: October 2020

Background

Early‐onset mixed chimerism (MC) with a high proportion of residual host cells is considered a signal of graft rejection in patients undergoing allogenic hematopoietic stem cell transplantation for transfusion‐dependent thalassemia. In order to prevent graft rejection and minimize the risk of treatment‐related graft‐versus‐host disease (GVHD), we established a hierarchical management system based on chimerism analysis.

Method

This retrospective study provides a comprehensive review of the characteristics, interventions, and outcomes of the 38 patients who developed MC after transplantation among the 144 pediatric thalassemia patients between July 2007 and January 2019 at our center.

Results

A sibling donor, a blood type‐matched donor, conditioning regimens without fludarabine, and transplants containing <10 × 108 total nucleated cells/kg were identified to be associated with the development of MC. Among the 38 patients developing MC, only four patients rejected the grafts. The response rate to donor lymphocyte infusion (DLI, only for patients receiving sibling donor transplantation) and cytokine immunomodulation without DLI was 70.6% and 42.9%, respectively. Patients that developed GVHD after DLI or cytokine therapy had a more significant increase in donor cell chimerism (16%, range 0%‐35%) than those without (8.5%, range −21% to 40%, P = .049). However, even when treatment‐related GVHD was included, patients with MC had a lower cumulative incidence of total acute GVHD than patients with complete donor chimerism (29.2% vs 48.0%, P = .030).

Conclusions

Interventions based on chimerism analysis were effective in preventing graft rejection and did not increase treatment‐related GVHD in thalassemia patients with MC.
Allogeneic hematopoietic stem cell transplantation from sibling and unrelated donors in pediatric patients with sickle cell disease—A single center experience
Authors: Kogel Friederike , Hakimeh Dani , Sodani Pietro , Lang Peter , Kühl Jörn‐Sven , Hundsdoerfer Patrick , Künkele Annette , Eggert Angelika , Oevermann Lena , Schulte Johannes H.
Published: October 2020

HSCT is curative in SCD. Patients with HLA‐identical sibling donor have an excellent outcome ranging from 90%‐100% overall and event‐free survival. However, due to the lack of matched sibling donors this option is out of reach for 70% of patients with SCD. The pool of potential donors needs to be extended. Transplantations from HLA‐matched unrelated donors were reported to be less successful with shorter event‐free survival and higher incidences of complications including graft‐vs‐host disease, especially in patients with advanced stage SCD. Here we report transplantation outcomes for 25 children with SCD transplanted using HLA‐matched grafts from related or unrelated donors. Overall survival was 100% with no severe (grade III‐IV) graft‐vs‐host disease and a 12% rejection rate. Mixed donor chimerisms only occurred in transplantations from siblings, while transplantations from unrelated donors resulted in either complete donor chimerism or rejection. Despite the small patient number, overall and disease‐free survival for unrelated donor transplantations is excellent in this cohort. The advanced disease state, higher alloreactive effect and stronger immunosuppression in unrelated donor transplantations raises patient risk, for which possible solutions could be found in optimization of transplant preparation, graft manipulation or haploidentical transplantation using T cell receptor α/β‐depleted grafts.
Effectiveness of Photobiomodulation as an Adjunct to Nonsurgical Periodontal Therapy in the Management of Periodontitis‐ A Systematic Review of in vivo Human Studies
Authors: Dalvi Snehal , Benedicenti Stefano , Hanna Reem
Published: October 2020

Photobiomodulation therapy (PBMT) has anti‐inflammatory, analgesic and regenerative properties. This systematic review aimed to critically appraise the published data of in vivo human randomized clinical trials (RCTs), and present a comprehensive overview of the efficacy of PBMT, as an adjunct to the nonsurgical periodontal therapy (NSPT) in the management of periodontitis. The systematic review protocol is registered in the Prospective Register Of Systematic Reviews (PROSPERO) (www.crd.york.ac.uk/PROSPERO/; ref CRD 42020169108). With the help of the appropriate key words, structured electronic and manual search strategies were applied to gather the relevant published data on in vivo human RCTs based on this topic. Seventeen papers that met the eligibility criteria were included in this review and subjected to a qualitative assessment. Current evidence lacks adequate information regarding the photobiomodulation (PBM) dosimetry, which is fundamental in establishing a standardized and replicable protocol for future researches. Furthermore, substantial discrepancies in the study methodology and a high risk of bias, arising from the majority of the included papers, abet to the inferior quality of these studies. Ultimately, there is an urgent necessity to conduct further well‐designed RCTs in order to determine the effectiveness of PBMT, if any, by taking into consideration the abovementioned confounding factors.
Melatonin as a regulatory hub of plant hormone levels and action in stress situations
Authors: Arnao M. B. , Hernández‐Ruiz J.
Published: October 2020

Melatonin, a molecule first discovered in animal tissues, plays an important role in multiple physiological responses as a possible plant master regulator. It mediates responses to different types of stress, both biotic and abiotic. Melatonin reduces the negative effects associated with stressors, improving the plant response by increasing plant stress tolerance. When plants respond to stress situations, they use up a large amount of plant resources through a set of perfectly synchronized actions. Responses mediated by melatonin use the plant’s hormones to, after adequate modulation, counteract and overcome the negative action of the stressor. In this paper, we review melatonin–plant hormone relationships. Factors that trigger the stress response and the central role of melatonin are analysed. An extensive analysis of current studies shows that melatonin modulates the metabolism of plant hormones (biosynthesis and catabolism), the rise or fall in their endogenous levels, the regulation of signalling elements and how melatonin affects the final response of auxin, gibberellins, cytokinins, abscisic acid, ethylene, salicylic acid, jasmonates, brassinosteroids, polyamines and strigolactones. Lastly, a general overview of melatonin’s actions and its regulatory role at a global level is provided and proposals for future research are made.
Cracking Sex Trafficking: Data Analysis, Pattern Recognition, and Path Prediction
Authors: Keskin Burcu B. , Bott Gregory J. , Freeman Nickolas K.
Published: October 2020

Human trafficking, the exploitation of humans for monetary gain or benefit, is a widespread humanitarian issue that is typically sub‐classified into labor and sex trafficking. In the last decade, sex traffickers have used online classified advertisements to advertise sexual services. Although these advertisements are visible to the general public and law enforcement, the volume of ads, the frequency with which their posting locale changes, and the use of obfuscation tactics make it difficult for law enforcement agencies to react. Existing products for law enforcement focus on identifying, tracking, and correlating individual activity by performing deep searches for specific information against a database of historical posts. While this deep search capability is useful for investigating specific cases, it overlooks higher‐level patterns that exist in ads. Using a website that has been linked to several sex trafficking‐related arrests, we demonstrate a framework for harvesting, linking, and detecting these patterns in a dataset comprised of more than 10 million advertisements targeting US cities. Our framework combines information systems and operations research concepts to identify groups of posts based on text, phone numbers, and pictures; determine circuits associated with post groups, and predict future movements using four different methods. Our description of the framework and comparison of the grouping and prediction methods provide insights that can assist law enforcement agencies to combat individuals/organizations involved in illicit sexual activities, including sex trafficking, proactively. Also, this demonstration provides researchers interested in developing advanced interdiction models targeting illicit sexual activities with a clear picture regarding available data formats.
Investigating the effector suite profile of Australian Fusarium oxysporum isolates from agricultural and natural ecosystems
Authors: Achari Saidi R. , Kaur Jatinder K. , Mann Ross C. , Sawbridge Tim , Summerell Brett A. , Edwards Jacqueline
Published: October 2020

Pathogenic and putatively nonpathogenic isolates of Fusarium oxysporum are ubiquitously present in soils. Pathogenic isolates designated as formae speciales are very host specific. The genes that determine host‐specific pathogenicity may be expected to be similar between strains within a forma specialis. Three different pathways were used for mining putative effectors from 85 assembled genome sequences representing isolates from the agricultural and natural ecosystems. A total of 436 putative effectors were identified, of which 115 were present in all the isolates. The presence–absence phylogeny showed some clustering of isolates based on the ecosystems, while some clustered with isolates from different ecosystems. Isolates from the agricultural and natural ecosystems shared 358 putative effectors. Agricultural isolates had 78 unique putative effectors, while isolates from the natural ecosystems had no unique effectors. Isolates from the natural ecosystems had effectors that have previously been confirmed with virulence functions in other filamentous fungi, suggesting that the natural ecosystems may be acting as a reservoir for pathogenic isolates awaiting compatible hosts. They also possessed putative effectors with domains involved in polysaccharide degradation. The putative effectors in the natural ecosystem isolates may be important for both parasitic and ecological fitness. Further analysis of the three characterized ff. sp.—lycopersici, niveum, and pisi—revealed high conservation in the pathogenicity mechanism in F. oxysporum. However, each strain had unique putative effectors, which may be responsible for host specificity.
Service Design and Citizen Satisfaction with E‐Government Services: A Multidimensional Perspective
Authors: Chan Frank K. Y. , Thong James Y. L. , Brown Susan A. , Venkatesh Viswanath
Published: October 2020

This research examines the relationship between service design and citizen satisfaction with e‐government services. Based on a multidimensional conceptualization of service, we define three key service perceptions, each comprising different design characteristics, that jointly influence perceived service quality and citizen satisfaction with e‐government services. The service perceptions and their corresponding design characteristics are: (1) perceptions of a core service—accuracy, completeness, self‐service capability, and convenience; (2) perceptions of facilitating services—accessibility, privacy protection, security protection, and user support; and (3) perceptions of supporting services—personalization capability and transparency. We tested our research model using data from a two‐stage survey of 3,065 users of three e‐government services. The results showed that all design characteristics contributed to their respective service perceptions that influenced perceived service quality that in turn influenced citizen satisfaction. The finding of a three‐way interaction among the service perceptions supported their complementary role in influencing perceived service quality.
Quasi-Stationary Monte Carlo and The Scale Algorithm
Authors: Pollock Murray , Fearnhead Paul , Johansen Adam M. , Roberts Gareth O.
Published: October 2020

This paper introduces a class of Monte Carlo algorithms which are based on the simulation of a Markov process whose quasi-stationary distribution coincides with a distribution of interest. This differs fundamentally from, say, current Markov chain Monte Carlo methods which simulate a Markov chain whose stationary distribution is the target. We show how to approximate distributions of interest by carefully combining sequential Monte Carlo methods with methodology for the exact simulation of diffusions. The methodology introduced here is particularly promising in that it is applicable to the same class of problems as gradient-based Markov chain Monte Carlo algorithms but entirely circumvents the need to conduct Metropolis–Hastings type accept–reject steps while retaining exactness: the paper gives theoretical guarantees ensuring that the algorithm has the correct limiting target distribution. Furthermore, this methodology is highly amenable to ‘big data’ problems. By employing a modification to existing naive subsampling and control variate techniques it is possible to obtain an algorithm which is still exact but has sublinear iterative cost as a function of data size.
Covid‐19, Economic Growth and South African Fiscal Policy
Authors: Burger Philippe , Calitz Estian
Published: October 2020

Following years of fast‐rising debt levels, we show that the Covid‐19 crisis worsened an already deteriorating fiscal position in South Africa. To restore fiscal sustainability in the aftermath of the crisis some commentators argue that higher government expenditure will grow GDP sufficiently to stabilise the debt/GDP ratio. We reject this, showing that although a real increase in expenditure stimulates economic growth (a short‐run, once‐off effect), the public expenditure/GDP ratio exceeds the level at which an increase in the ratio positively impacts growth. We then explore the past efforts of government to maintain or restore fiscal sustainability by estimating a fiscal reaction function using a Markov‐switching model. Following the impact of the Covid‐19 crisis on the budget, we subsequently establish the deficit, expenditure and revenue adjustments that the government will have to make to restore fiscal sustainability. Finally, we consider the merits of introducing a debt ceiling.
Evaluating strange forecasts: The curious case of football match scorelines
Authors: Reade J. James , Singleton Carl , Brown Alasdair
Published: October 2020

This study analyses point forecasts of exact scoreline outcomes for football matches in the English Premier League. These forecasts were made for distinct competitions and originally judged differently. We compare these with implied probability forecasts using bookmaker odds and a crowd of tipsters, as well as point and probability forecasts generated from a statistical model. From evaluating these sources and types of forecast, using various methods, we argue that regression encompassing is the most appropriate way to compare point and probability forecasts, and find that both these types of forecasts for football match scorelines generally add information to one another.
Perceived burdensomeness is a curvilinear, short‐term predictor of suicide ideation in a community sample of adults
Authors: Crosby Eric S. , Zuromski Kelly L. , Witte Tracy K.
Published: October 2020

Objective

Our primary aim was to test the Interpersonal Theory of Suicide's synergy hypothesis (i.e., the interaction between perceived burdensomeness and thwarted belongingness) in the proximal prediction of suicide ideation, while accounting for quadratic effects.

Method

We used MTurk to recruit participants (N = 478) with a lifetime history of suicidal thoughts and behaviors; they completed two batteries of self‐report questionnaires three days apart.

Results

Contrary to the synergy hypothesis, only suicide ideation and the quadratic effect of perceived burdensomeness at Time 1 were significant predictors of suicide ideation at Time 2. The quadratic effect of perceived burdensomeness indicated a u‐shaped function, whereby scores at or above the 80th percentile on perceived burdensomeness at Time 1 had increasingly strong, positive associations with suicide ideation at Time 2, while scores under the 80th percentile were not predictive of suicide ideation at Time 2. Also, thwarted belongingness and suicide ideation at Time 1 were significant predictors of perceived burdensomeness at Time 2.

Conclusions

These findings add to a growing literature that does not support the synergy hypothesis and suggests the importance of including nonlinear terms when examining the Interpersonal Theory of Suicide's constructs.
Marginal nitrate leaching around the recommended nitrogen fertilizer rate in winter cereals
Authors: Vogeler Iris , Thomsen Ingrid Kaag , Jensen Johannes L. , Hansen Elly Møller
Published: October 2020

Optimum nitrogen (N) fertilization, which aims for high productivity while minimizing N losses to the environment, requires a better understanding of the N leaching behaviour around the recommended N rate. A study was conducted with increasing N fertilization levels over 3 years (2016–2019) with early and timely sown winter cereals (rye and wheat) at two sites in Denmark with different climatic conditions. For winter rye N fertilizer application rates ranged from 0 to 258 kg N ha‒1, and for winter wheat from 0 to 300 kg ha‒1. Grain yields did not respond much to the N application above the recommended rate. Nitrate (NO3) leaching was very low in the first period, but increased in the second and third period. The effect of a potential N carry‐over on marginal N leaching (defined as the additional N leaching per unit of additional N fertilizer applied) is large. Under early sown winter rye, marginal N leaching is reduced from 36 to 14 kg N ha‒1 in the third period following N fertilization of the recommended rate of 170 kg N ha‒1 when carry‐over was accounted for, and under the timely sown winter rye from 68 to 24 kg N ha‒1. Our results show that marginal N leaching around the recommended rate is almost linear at the study site, when carry‐over is accounted for. Thus, the use of precision agriculture, with lower fertilization application rates to areas with high residual soil N, is less effective compared with sites, which have an exponential leaching behaviour.
The previously missing c. 2.9 Ga high‐K continental crust in West Gondwana revealed in Northeast Brazil
Authors: Ferreira Alanielson C. D. , Dantas Elton L. , Fuck Reinhardt A.
Published: October 2020

2.9 Ga is an uncommon magmatic age in Archean evolution worldwide, especially in West Gondwana. We identified so far unknown 2.97–2.92 Ga high‐K calc‐alkaline magmatism in the Borborema Province, northeast Brazil. It appears to indicate that the transition to high‐K magmas occurred before c. 2.7 Ga in Earth's history. The 2.9 Ga protoliths were reworked and progressively changed composition to 2.65 Ga and 2.25 Ga higher‐K granites in early magmatic arcs. Therefore, despite several reworking events from the Archean to Proterozoic times, these rare relicts of K‐rich magmatism indicate that reworking of felsic components was significant for the growth and differentiation of continental crust from c. 2.9 Ga onwards in West Gondwana.
Phytochrome B and PCH1 protein dynamics store night temperature information
Authors: Murcia Germán , Enderle Beatrix , Hiltbrunner Andreas , Casal Jorge J.
Published: October 2020

Plants experience temperature fluctuations during the course of the daily cycle, and although stem growth responds rapidly to these changes we largely ignore whether there is a short‐term memory of previous conditions. Here we show that nighttime temperatures affect the growth of the hypocotyl of Arabidopsis thaliana seedlings not only during the night but also during the subsequent photoperiod. Active phytochrome B (phyB) represses nighttime growth and warm temperatures reduce active phyB via thermal reversion. The function of PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1) is to stabilise active phyB in nuclear bodies but, surprisingly, warmth reduces PCH1 gene expression and PCH1 stability. When phyB was active at the beginning of the night, warm night temperatures enhanced the levels of nuclear phyB and reduced hypocotyl growth rate during the following day. However, when end‐of‐day far‐red light minimised phyB activity, warm night temperatures reduced the levels of nuclear phyB and enhanced the hypocotyl growth rate during the following day. This complex growth pattern was absent in the phyB mutant. We propose that temperature‐induced changes in the levels of PCH1 and in the size of the physiologically relevant nuclear pool of phyB amplify the impact of phyB‐mediated temperature sensing.
In vivo imaging of tagged mRNA in plant tissues using the bacterial transcriptional antiterminator BglG
Authors: Peña Eduardo J. , Robles Luna Gabriel , Heinlein Manfred
Published: October 2020

RNA transport and localization represent important post‐transcriptional mechanisms to determine the subcellular localization of protein synthesis. Plants have the capacity to transport messenger (m)RNA molecules beyond the cell boundaries through plasmodesmata and over long distances in the phloem. RNA viruses exploit these transport pathways to disseminate their infections and represent important model systems to investigate RNA transport in plants. Here, we present an in vivo plant RNA‐labeling system based on the Escherichia coli RNA‐binding protein BglG. Using the detection of RNA in mobile RNA particles formed by viral movement protein (MP) as a model, we demonstrate the efficiency and specificity of mRNA detection by the BglG system as compared with MS2 and λN systems. Our observations show that MP mRNA is specifically associated with MP in mobile MP particles but hardly with MP localized at plasmodesmata. MP mRNA is clearly absent from MP accumulating along microtubules. We show that the in vivo BglG labeling of the MP particles depends on the presence of the BglG‐binding stem–loop aptamers within the MP mRNA and that the aptamers enhance the coprecipitation of BglG by MP, thus demonstrating the presence of an MP:MP mRNA complex. The BglG system also allowed us to monitor the cell‐to‐cell transport of the MP mRNA, thus linking the observation of mobile MP mRNA granules with intercellular MP mRNA transport. Given its specificity demonstrated here, the BglG system may be widely applicable for studying mRNA transport and localization in plants.
Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes
Authors: Liu Beibei , Iwata‐Otsubo Aiko , Yang Diya , Baker Robert L. , Liang Chun , Jackson Scott A. , Liu Shengyi , Ma Jianxin , Zhao Meixia
Published: October 2020

In comparison with retrotransposons, DNA transposons make up a smaller proportion of most plant genomes. However, these elements are often proximal to genes to affect gene expression depending on the activity of the transposons, which is largely reflected by the activity of the transposase genes. Here, we show that three AT‐rich introns were retained in the TNP2‐like transposase genes of the Bot1 (Brassica oleracea transposon 1) CACTA transposable elements in Brassica oleracea, but were lost in the majority of the Bot1 elements in Brassica rapa. A recent burst of transposition of Bot1 was observed in B. oleracea, but not in B. rapa. This burst of transposition is likely related to the activity of the TNP2‐like transposase genes as the expression values of the transposase genes were higher in B. oleracea than in B. rapa. In addition, distinct populations of small RNAs (21, 22 and 24 nt) were detected from the Bot1 elements in B. oleracea, but the vast majority of the small RNAs from the Bot1 elements in B. rapa are 24 nt in length. We hypothesize that the different activity of the TNP2‐like transposase genes is likely associated with the three introns, and intron loss is likely reverse transcriptase mediated. Furthermore, we propose that the Bot1 family is currently undergoing silencing in B. oleracea, but has already been silenced in B. rapa. Taken together, our data provide new insights into the differentiation of transposons and their role in the asymmetric evolution of these two closely related Brassica species.
Structural determinants for NF‐Y subunit organization and NF‐Y/DNA association in plants
Authors: Chaves‐Sanjuan Antonio , Gnesutta Nerina , Gobbini Andrea , Martignago Damiano , Bernardini Andrea , Fornara Fabio , Mantovani Roberto , Nardini Marco
Published: October 2020

NF‐Y transcription factor comprises three subunits: NF‐YA, NF‐YB and NF‐YC. NF‐YB and NF‐YC dimerize through their histone fold domain (HFD), which can bind DNA in a non‐sequence‐specific fashion while serving as a scaffold for NF‐YA trimerization. Upon trimerization, NF‐YA specifically recognizes the CCAAT box sequence on promoters and enhancers. In plants, each NF‐Y subunit is encoded by several genes giving rise to hundreds of potential heterotrimeric combinations. In addition, plant NF‐YBs and NF‐YCs interact with other protein partners to recognize a plethora of genomic motifs, as the CCT protein family that binds CORE sites. The NF‐Y subunit organization and its DNA‐binding properties, together with the NF‐Y HFD capacity to adapt different protein modules, represent plant‐specific features that play a key role in development, growth and reproduction. Despite their relevance, these features are still poorly understood at the molecular level. Here, we present the structures of Arabidopsis and rice NF‐YB/NF‐YC dimers, and of an Arabidopsis NF‐Y trimer in complex with the FT CCAAT box, together with biochemical data on NF‐Y mutants. The dimeric structures identify the key residues for NF‐Y HFD stabilization. The NF‐Y/DNA structure and the mutation experiments shed light on HFD trimerization interface properties and the NF‐YA sequence appetite for the bases flanking the CCAAT motif. These data explain the logic of plant NF‐Y gene expansion: the trimerization adaptability and the flexible DNA‐binding rules serve the scopes of accommodating the large number of NF‐YAs, CCTs and possibly other NF‐Y HFD binding partners and a diverse audience of genomic motifs.
Cytochrome P450 CYP81A10v7 in Lolium rigidum confers metabolic resistance to herbicides across at least five modes of action
Authors: Han Heping , Yu Qin , Beffa Roland , González Susana , Maiwald Frank , Wang Jian , Powles Stephen B.
Published: October 2020

Rapid and widespread evolution of multiple herbicide resistance in global weed species endowed by increased capacity to metabolize (degrade) herbicides (metabolic resistance) is a great threat to herbicide sustainability and global food production. Metabolic resistance in the economically damaging crop weed species Lolium rigidum is well known but a molecular understanding has been lacking. We purified a metabolic resistant (R) subset from a field evolved R L. rigidum population. The R, the herbicide susceptible (S) and derived F2 populations were used for candidate herbicide resistance gene discovery by RNA sequencing. A P450 gene CYP81A10v7 was identified with higher expression in R vs. S plants. Transgenic rice overexpressing this Lolium CYP81A10v7 gene became highly resistant to acetyl‐coenzyme A carboxylase‐ and acetolactate synthase‐inhibiting herbicides (diclofop‐methyl, tralkoxydim, chlorsulfuron) and moderately resistant to hydroxyphenylpyruvate dioxygenase‐inhibiting herbicide (mesotrione), photosystem II‐inhibiting herbicides (atrazine and chlorotoluron) and the tubulin‐inhibiting herbicide trifluralin. This wide cross‐resistance profile to many dissimilar herbicides in CYP81A10v7 transgenic rice generally reflects what is evident in the R L. rigidum. This report clearly showed that a single P450 gene in a cross‐pollinated weed species L. rigidum confers resistance to herbicides of at least five modes of action across seven herbicide chemistries.
Targeted gene disruption of ATP synthases 6‐1 and 6‐2 in the mitochondrial genome of Arabidopsis thaliana by mitoTALENs
Authors: Arimura Shin‐ichi , Ayabe Hiroki , Sugaya Hajime , Okuno Miki , Tamura Yoshiko , Tsuruta Yu , Watari Yuta , Yanase Shungo , Yamauchi Takaki , Itoh Takehiko , Toyoda Atsushi , Takanashi Hideki , Tsutsumi Nobuhiro
Published: October 2020

We recently achieved targeted disruptions of cytoplasmic male sterility (CMS)‐associated genes in the mitochondrial genomes of rice and rapeseed by using mitochondria‐targeted transcription activator‐like effector nucleases (mitoTALENs). It was the first report of stable and heritable targeted gene modification of plant mitochondrial genomes. Here, we attempted to use mitoTALENs to disrupt two mitochondrial genes in the model plant Arabidopsis thaliana(Arabidopsis) using three different promoters and two types of TALENs. The targets were the two isoforms of the ATP synthase subunit 6 gene, atp6‐1 and atp6‐2. Each of these genes was successfully deleted and the mitochondrial genomes were recovered in a homoplasmic state. The nuclear genome also has a copy of atp6‐1, and we were able to confirm that it was the mitochondrial gene and not the nuclear pseudogene that was knocked out. Among the three mitoTALEN promoters tried, the RPS5A promoter was the most effective. Conventional mitoTALENs were more effective than single‐molecule mito‐compactTALENs. Targeted mitochondrial gene deletion was achieved by crossing as well as by floral‐dip transformation to introduce the mitoTALEN constructs into the nucleus. The gene disruptions were caused by large (kb‐size) deletions. The ends of the remaining sequences were connected to distant loci, mostly by illegitimate homologous recombinations between repeats.
Coordinated regulation of starch synthesis in maize endosperm by microRNAs and DNA methylation
Authors: Hu Yufeng , Li Yangping , Weng Jianfeng , Liu Hanmei , Yu Guowu , Liu Yinghong , Xiao Qianlin , Huang Huanhuan , Wang Yongbin , wei Bin , Cao Yao , Xie Ying , Long Tiandan , Li Hui , Zhang Junjie , Li Xinhai , Huang Yubi
Published: October 2020

Starch synthesis is an essential feature of crop filling, but knowledge of the molecular mechanisms regulating the expression of starch synthesis genes (SSGs) is currently limited to transcription factors (TFs). Here, we obtained transcriptome, small RNAome, and DNA methylome data from maize (Zea mays) endosperms during multiple developmental stages and established a regulatory network atlas of starch synthesis. Transcriptome analysis showed a sharp transition at 9–10 days after pollination, when genes involved in starch and sucrose metabolism are upregulated and starch accumulates rapidly. Expression pattern analysis established a comprehensive network between SSGs and TFs. During maize endosperm development, the miRNAs with preferential repression of the expression of TFs, particularly the TFs regulating SSG expression, were extensively downregulated. Specifically, ZmMYB138 and ZmMYB115 affected the transcriptional activities of Du1/Wx and Ae1/Bt2 genes at their respective promoter regions. Remarkably, the two TFs were negatively regulated by the copious expression of Zma‐miR159k‐3p at the post‐transcriptional level. This suggests that miRNAs are important regulators of starch synthesis. Moreover, with the exclusion of the TFs, the expression of both SSGs and miRNAs was globally regulated by DNA methylation. Altogether, the present results (i) establish the regulatory functions of miRNAs and DNA methylation in starch synthesis and (ii) indicate that DNA methylation functions as a master switch.
A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR
Authors: Ko Dae Kwan , Brandizzi Federica
Published: October 2020

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large‐scale systems‐level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high‐throughput enhanced yeast one‐hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis‐regulatory elements (CREs) in ER stress‐responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription‐regulatory mechanisms in the stress responses and crop improvement.
SCAR: The high‐prevalence antigen 013.008 in the Scianna blood group system
Authors: Srivastava Kshitij , Albasri Jasem , Alsuhaibani Omar M. , Aljasem Hassan A. , Bueno Marina U. , Antonacci Tania , Branch Donald R. , Denomme Gregory A. , Flegel Willy A.
Published: October 2020

Background

The Scianna (SC) blood group system comprises seven antigens. They reside on the erythroblast membrane‐associated glycoprotein (ERMAP). The ERMAP and RHCE genes are juxtaposed to each other on chromosome 1. We report a novel SC antigen.

Study Design and Methods

Blood samples came from a patient and his two sisters in Saudi Arabia. To investigate the antibody specificity we used the column agglutination technique and soluble recombinant ERMAP protein. The significance of anti‐SCAR was evaluated by the transfusion history and a monocyte monolayer assay. We determined the genomic sequence of ERMAP and RHCE genes.

Results

The patientʼs serum showed an antibody of titer 8 against a high‐prevalence antigen. The soluble recombinant ERMAP protein inhibited the antibody. The propositus genotyped homozygous for an ERMAP:c.424C>G variant, for which his sisters were heterozygous. The c.424C>G variant occurred in the SC*01 allele in one haplotype with the RHCE*03 (RHCE*cE) allele. No signs of hemolysis occurred following an incompatible blood transfusion. The monocyte monolayer assay was negative.

Conclusions

We characterized a high‐prevalence antigen, with the proposed name “SCAR,” which is the eighth antigen of the Scianna blood group system (proposed designation 013.008). Individuals homozygous for ERMAP:p.(Gln142Glu) protein variant can produce anti‐SCAR. Although we did not observe any sign of hemolysis at this time, the anti‐SCAR prompted a change of the treatment regimen. A review of the known reports indicated that all SC alloantibodies of sufficient titer should be considered capable of causing hemolysis.