bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi‐stemming and size enhance survival of dominant tree species in a frequently typhoon‐disturbed forest
Authors: Su Sheng‐Hsin , Guan Biing T. , Chang‐Yang Chia‐Hao , Sun I‐Fang , Wang Hsiang‐Hua , Hsieh Chang‐Fu 
Published: January 2020

AbstractQuestionsQuantifying tree species persistence through recurrent disturbances is of crucial importance for understanding forest dynamics in typhoon‐prone regions. We ask the following: (a) What are the major determinants of dominant tree survival in frequently typhoon‐disturbed forests? (b) Are survival determinants different between small and large trees?LocationA subtropical old‐growth forest located in Fushan, Taiwan (24°45′34″N, 121°33′58″E), with frequent typhoon disturbances.MethodsData were from three consecutive censuses of a 25‐ha permanent forest plot that censused trees ≥1 cm in diameter every five years. The survival of three dominant tree species was modeled using generalized additive model and boosted trees with abiotic and biotic predictors. We evaluated model performance using validation data obtained from the two available census intervals.ResultsModel validations showed that multi‐stemming and tree size enhanced the survival of large and small trees, respectively. For the most dominant species, multi‐stemming had a consistently positive effect on survival irrespective of diameter classes. Abiotic factors and conspecific density had little effect on tree survival. Furthermore, evaluating model performance based on the data used in the model construction (i.e., training data) overestimated the predictive ability of survival models.ConclusionsWe showed that the survival determinants for the three most dominant species at Fushan changed from tree size for small trees to multi‐stemming for large trees. The results suggest that the dominant species in this frequently typhoon‐disturbed forest have the stature and architectural traits to persist, and thereby maintain their dominance and shape the forest physiognomy. Our approach illustrates how datasets from different census periods can be used in model validation to better assess model performance.
Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)
Authors: Myers Edward A. , McKelvy Alexander D. , Burbrink Frank T. 
Published: January 2020

AbstractThe southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species‐specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
The Lon‐2 protease of Borrelia burgdorferi is critical for infection in the mammalian host
Authors: Mason Charlotte , Thompson Christina , Ouyang Zhiming 
Published: January 2020

AbstractBorrelia burgdorferi encodes a functional homolog of canonical Lon protease termed Lon‐2. To date, the contribution of Lon‐2 to B. burgdorferi fitness and infection remains unexplored. Herein, we showed that expression of lon‐2 was highly induced during animal infection, suggesting that Lon‐2 is important for B. burgdorferi infection. We further generated a lon‐2 deletion mutant. Compared with that of wild‐type (WT) strain, the infectivity of the mutant was severely attenuated in a murine infection model. Although no growth defect was observed for the mutant in normal BSK‐II medium, resistance of the lon‐2 mutant to osmotic stress was markedly reduced. In addition, when exposed to tert‐Butyl hydroperoxide, survival of the lon‐2 mutant was impaired. In addition, we found that the protein levels of RpoS and RpoS‐dependent OspC were decreased in the mutant. All these phenotypes were restored to WT or near‐WT levels when lon‐2 mutation was complemented in cis. Taken together, these results demonstrate that Lon‐2 is critical for B. burgdorferi to establish infection and to cope with environmental stresses. This study provides a foundation for further uncovering the direct link between the dual roles of Lon‐2 in protein quality control and bacterial pathogenesis.
Targeting of proteins to the twin‐arginine translocation pathway
Authors: Palmer Tracy , Stansfeld Phillip J. 
Published: January 2020

AbstractThe twin‐arginine protein transport (Tat pathway) is found in prokaryotes and plant organelles and transports folded proteins across membranes. Targeting of substrates to the Tat system is mediated by the presence of an N‐terminal signal sequence containing a highly conserved twin‐arginine motif. The Tat machinery comprises membrane proteins from the TatA and TatC families. Assembly of the Tat translocon is dynamic and is triggered by the interaction of a Tat substrate with the Tat receptor complex. This review will summarise recent advances in our understanding of Tat transport, focusing in particular on the roles played by Tat signal peptides in protein targeting and translocation.
TubZIP28, a novel bZIP family transcription factor from Triticum urartu, and TabZIP28, its homologue from Triticum aestivum, enhance starch synthesis in wheat
Authors: Song Yanhong , Luo Guangbin , Shen Lisha , Yu Kang , Yang Wenlong , Li Xin , Sun Jiazhu , Zhan Kehui , Cui Dangqun , Liu Dongcheng , Zhang Aimin 
Published: January 2020

Summary

Starch in wheat grain provides humans with carbohydrates and influences the quality of wheaten food. However, no transcriptional regulator of starch synthesis has been identified first in common wheat (Triticum aestivum) due to the complex genome.

Here, a novel basic leucine zipper (bZIP) family transcription factor TubZIP28 was found to be preferentially expressed in the endosperm throughout grain‐filling stages in Triticum urartu, the A genome donor of common wheat.

When TubZIP28 was overexpressed in common wheat, the total starch content increased by c. 4%, which contributed to c. 5% increase in the thousand kernel weight. The grain weight per plant of overexpression wheat was also elevated by c. 9%. Both in vitro and in vivo assays showed that TubZIP28 bound to the promoter of cytosolic AGPase and enhanced both the transcription and activity of the latter. Knockout of the homologue TabZIP28 in common wheat resulted in declines of both the transcription and activity of cytosolic AGPase in developing endosperms and c. 4% reduction of the total starch in mature grains.

To the best of our knowledge, TubZIP28 and TabZIP28 are transcriptional activators of starch synthesis first identified in wheat, and they could be superior targets to improve the starch content and yield potential of wheat.
Leaf carbon and water status control stomatal and nonstomatal limitations of photosynthesis in trees
Authors: Salmon Yann , Lintunen Anna , Dayet Alexia , Chan Tommy , Dewar Roderick , Vesala Timo , Hölttä Teemu 
Published: January 2020

Summary

Photosynthetic rate is concurrently limited by stomatal limitations and nonstomatal limitations (NSLs). However, the controls on NSLs to photosynthesis and their coordination with stomatal control on different timescales remain poorly understood. According to a recent optimization hypothesis, NSLs depend on leaf osmotic or water status and are coordinated with stomatal control so as to maximize leaf photosynthesis.

Drought and notching experiments were conducted on Pinus sylvestris, Picea abies, Betula Pendula and Populus tremula seedlings in glasshouse conditions to study the dependence of NSLs on leaf osmotic and water status, and their coordination with stomatal control, on timescales of minutes and weeks, to test the assumptions and predictions of the optimization hypothesis.

Both NSLs and stomatal conductance followed power‐law functions of leaf osmotic concentration and leaf water potential. Moreover, stomatal conductance was proportional to the square root of soil‐to‐leaf hydraulic conductance, as predicted by the optimization hypothesis.

Though the detailed mechanisms underlying the dependence of NSLs on leaf osmotic or water status lie outside the scope of this study, our results support the hypothesis that NSLs and stomatal control are coordinated to maximize leaf photosynthesis and allow the effect of NSLs to be included in models of tree gas‐exchange.
Host and pathogen autophagy are central to the inducible local defences and systemic response of the giant kelp Macrocystis pyrifera against the oomycete pathogen Anisolpidium ectocarpii
Authors: Murúa Pedro , Müller Dieter G. , Etemadi Mohammad , van West Pieter , Gachon Claire M. M. 
Published: January 2020

Summary

Kelps are key primary producers of cold and temperate marine coastal ecosystems and exhibit systemic defences against pathogens. Yet, the cellular mechanisms underpinning their immunity remain to be elucidated.

We investigated the time course of infection of the kelp Macrocystis pyrifera by the oomycete Anisolpidium ectocarpii using TEM, in vivo autophagy markers and autophagy inhibitors.

Over several infection cycles, A. ectocarpii undergoes sequential physiological shifts sensitive to autophagy inhibitors. Initially lipid‐rich, pathogen thalli become increasingly lipid‐depleted; they subsequently tend to become entirely abortive, irrespective of their lipid content. Moreover, infected algal cells mount local defences and can directly eliminate the pathogen by xenophagy. Finally, autophagy‐dependent plastid recycling is induced in uninfected host cells.

We demonstrate the existence of local, inducible autophagic processes both in the pathogen and infected host cells, which result in the restriction of pathogen propagation. We also show the existence of a systemic algal response mediated by autophagy. We propose a working model accounting for all our observations, whereby the outcome of the algal–pathogen interaction (i.e. completion or not of the pathogen life cycle) is dictated by the induction, and possibly the mutual hijacking, of the host and pathogen autophagy machineries.
Moving on up – controlling internode growth
Authors: McKim Sarah M. 
Published: January 2020

SummaryPlant reproductive success depends on making fertile flowers but also upon developing appropriate shoot internodes that optimally arrange and support the flowering shoot. Compared to floral morphogenesis, we understand little about the networks directing internode growth during flowering. However, new studies reveal that long‐range signals, local factors, and age‐dependent micoRNA‐networks are all important to harmonize internode morphogenesis with shoot development. Some of the same players modulate symplastic transport to seasonally regulate internode growth in perennial species. Exploring possible hierarchical control amongst symplastic continuity, age, systemic signals and local regulators during internode morphogenesis will help elucidate the mechanisms coordinating axial growth with the wider plant body.
Auxin canalization and vascular tissue formation by TIR1/AFB‐mediated auxin signaling in Arabidopsis
Authors: Mazur Ewa , Kulik Ivan , Hajný Jakub , Friml Jiří 
Published: January 2020

Summary

Plant survival depends on vascular tissues, which originate in a self‐organizing manner as strands of cells co‐directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited.

In the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application.

Our methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN‐dependent auxin transport and nuclear, TIR1/AFB‐mediated auxin signaling. We also show that leaf venation and auxin‐mediated PIN repolarization in the root require TIR1/AFB signaling.

Further studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.
Changes in physical activity, diet, and body weight across the education and employment transitions of early adulthood: A systematic review and meta‐analysis
Authors: Winpenny Eleanor M. , Smith Miranda , Penney Tarra , Foubister Campbell , Guagliano Justin M. , Love Rebecca , Clifford Astbury Chloe , van Sluijs Esther M.F. , Corder Kirsten 
Published: January 2020

SummaryEarly adulthood is a time when individuals go through important life transitions, such as moving from high school into higher education or employment, but the impact of these life transitions on changes in body weight, diet, and physical activity is not known. We searched six electronic databases to July 2019 for longitudinal observational studies providing data on adiposity, diet, and/or physical activity across education or employment transitions in young people aged between 15 and 35 years. We found 19 studies, of which 17 assessed changes in physical activity, three body weight, and five diet or eating behaviours. Meta‐analysis (n=9) found that leaving high school was associated with a decrease of −7.04 (95% CI, −11.26, −2.82) min/day of moderate‐to‐vigorous physical activity. Three studies reported increases in body weight on leaving high school. A small number of studies suggested decreases in diet quality on leaving high school (n=2/4 papers) and leaving university (n=1) but not on starting employment (n=1). Studies suggested no change in physical activity on leaving university (n=4) but decreases in physical activity on starting employment (n=2/3). The transition of leaving high school is an important time to support individuals to prevent decreases in physical activity and gains in body weight.
Mechanical stimulation in Brachypodium distachyon: Implications for fitness, productivity, and cell wall properties
Authors: Gladala‐Kostarz Agnieszka , Doonan John H. , Bosch Maurice 
Published: January 2020

AbstractMechanical stimulation, including exposure to wind, is a common environmental variable for plants. However, knowledge about the morphogenetic response of the grasses (Poaceae) to mechanical stimulation and impact on relevant agronomic traits is very limited. Two natural accessions of Brachypodium distachyon were exposed to wind and mechanical treatments. We surveyed a wide range of stem‐related traits to determine the effect of the two treatments on plant growth, development, and stem biomass properties. Both treatments induced significant quantitative changes across multiple scales, from the whole plant down to cellular level. The two treatments resulted in shorter stems, reduced biomass, increased tissue rigidity, delayed flowering, and reduced seed yield in both accessions. Among changes in cell wall‐related features, a substantial increase in lignin content and pectin methylesterase activity was most notable. Mechanical stimulation also reduced the enzymatic sugar release from the cell wall, thus increasing biomass recalcitrance. Notably, treatments had a distinct and opposite effect on vascular bundle area in the two accessions, suggesting genetic variation in modulating these responses to mechanical stimulation. Our findings highlight that exposure of grasses to mechanical stimulation is a relevant environmental factor affecting multiple traits important for their utilization in food, feed, and bioenergy applications.
An efficient genetic test flow for multiple congenital anomalies and intellectual disability
Authors: Yokoi Takayuki , Enomoto Yumi , Tsurusaki Yoshinori , Harada Noriaki , Saito Toshiyuki , Nagai Jun‐ichi , Naruto Takuya , Kurosawa Kenji 
Published: January 2020

AbstractBackgroundGenetic testing has enabled the diagnosis of multiple congenital anomalies and/or intellectual disabilities. However, because of the phenotypic variability in these disorders, selection of an appropriate genetic test can be difficult and complex. For clinical examination, particularly in clinical facilities, a simple and standardized system is needed.MethodsWe compared microarray comparative genomic hybridization and clinical exome sequencing with regard to diagnostic yield, cost, and time required to reach a definitive diagnosis. After first performing G‐banding for 200 patients with multiple congenital anomalies and/or intellectual disability, as a subsequent genetic test, microarray and clinical exome sequencing were compared with regard to diagnostic yield, cost, and time required.ResultsThere was no obvious difference in the diagnostic rate between the two methods; however, clinical exome sequencing was superior in terms of cost and time. In addition, clinical exome sequencing could sufficiently identify copy number variants, and even smaller copy number variants could be identified.ConclusionsClinical exome sequencing should be implemented earlier as a genetic test for undiagnosed patients with multiple congenital anomalies and/or intellectual disabilities. Our results can be used to establish inspection methods in clinical facilities.
Wheat diseases on the prairies: A Canadian story
Authors: Aboukhaddour Reem , Fetch Thomas , McCallum Brent D. , Harding Michael W. , Beres Brian L. , Graf Robert J. 
Published: January 2020

AbstractCanada is one of the largest wheat producers in the world, and wheat is grown over an area spanning most of the southern latitudes, with the prairie region (provinces of Saskatchewan, Alberta, and Manitoba) being the main producer. Several pathogens and pests attack wheat, but at present fusarium head blight (FHB), stripe rust, and leaf spots are the most damaging diseases to wheat production in Canada. Historically, smuts, stem rust, and leaf rust caused major crop losses in Canada and can still pose serious threat if management practices are relaxed. Cropping practices used by Canadian farmers to grow and harvest wheat over the last century have influenced disease development and pathogen biology, affecting the severity, incidence, and prevalence of crop diseases over time. Changes such as reduced tillage coincide with emergence of residue‐borne diseases, such as FHB and leaf spots, while the deployment of resistant cultivars and increased fungicide use has resulted in the reduction of common bunt, stem, and leaf rust. This review will discuss the influence of long‐term cropping practices, alone or in combination, on the biology, emergence, and prevalence of wheat diseases in Canada over the last century.
A new standard area diagram set for assessment of severity of soybean rust improves accuracy of estimates and optimizes resource use
Authors: Franceschi Vinicius T. , Alves Kaique S. , Mazaro Sergio M. , Godoy Cláudia V. , Duarte Henrique S. S. , Del Ponte Emerson M. 
Published: January 2020

AbstractSoybean rust (SBR), caused by Phakopsora pachyrhizi, is the most important yield‐damaging fungal disease of soybean due to severe reduction in healthy leaf area and acceleration of leaf fall. In experimental research, SBR severity is estimated visually aided/trained by a standard area diagram (SAD) developed and validated during the mid‐2000s (Old SAD). In this study, we propose a new SAD set for SBR with six true‐colour diagrams following linear increments (c. 15% increments) amended with four additional diagrams at low (<10%) severities, totalling 10 diagrams (0.2%, 1%, 3%, 5%, 10%, 25%, 40%, 55%, 70%, and 84%). For evaluation, 37 raters were split into two groups. Each assessed severity in a 50‐image sample (0.25%–84%), first unaided and then using either the Old SAD or the New SAD. Accuracy, precision, and reliability of estimates improved significantly relative to unaided estimates only when aided by the New SAD (accuracy >0.95). Low precision (<0.78) and a trend of underestimation with an increase in severity were the main issues with the Old SAD, which did not differ from unaided estimates. Simulation to evaluate the impact of the errors by different methods on hypothesis tests, showed that the new SAD was more powerful for detecting the smallest difference in mean control (e.g., 70% vs. 65% disease reduction) than the Old SAD; the latter required a 2‐fold increase in sample size to achieve the same power. There is a need to improve some SADs, taking advantage of new knowledge and technology to increase accuracy of the estimates, and to optimize both resource use efficiency and management decisions.
Identifying the position of the compacted layer by measuring soil penetration resistance in a dryland farming region in Northeast China
Authors: Zhuo Zhiqing , Xing An , Cao Meng , Li Yong , Zhao Yunze , Guo Xiaoli , Huang Yuanfang 
Published: January 2020

AbstractTopsoil is disturbed by ploughing, the effects of infiltration, the movement of fine particles from the topsoil to the subsoil, and direct pressure from agriculture machinery, all creating an abrupt delineation in the form of a compacted layer with very low permeability. Spatial variability of soil properties, such as soil structure and penetration resistance (PR), can help identify the compacted layer. However, there are no quantitative methods to describe this layer. In this study,PRwas used to survey different soil types. A Mann–Kendall (M‐K) test ofPRdata was used to identify the presence and position of the compacted layer in a dryland farming region of Northeast China. Our results demonstrated thatPRwas mainly affected by bulk density and soil water content. Compared with the topsoil,PRwas more significantly affected by water content in deeper soil layers. An M‐K test of thePRcurve can provide a more reliable and objective assessment of the thickness of the plough layer and location of the compacted layer than field observation. Our data indicated that there was a compacted layer in the soil profile in the study areas and the spatial variability of the compacted layer was heterogeneous. The plough layer was shallow, and the compacted layer was thicker in areas with frequent use of agricultural machinery. Moreover, frequent use of agricultural machinery resulted in aPRof the plough and compacted layers that was greater than that in other areas. Information on identifying the position and thickness of the compacted layer and the factors influencing their spatial distribution can be used to create effective soil management options and improve conditions for the development of plant roots in dryland farming regions.