bluuebunny/crossref_metadata_2025 huggingface dataset:
Acute Impacts of Different Types of Exercise on Circulating α-Klotho Protein Levels
Authors: Iturriaga Tamara , Yvert Thomas , Sanchez-Lorente Isabel M. , Diez-Vega Ignacio , Fernandez-Elias Valentin E. , Sanchez-Barroso Lara , Dominguez-Balmaseda Diego , Larrosa Mar , Perez-Ruiz Margarita , Santiago Catalina
Published: September 2021

Introduction: Elevated plasma α-klotho (αKl) protects against several ageing phenotypes and has been proposed as a biomarker of a good prognosis for different diseases. The beneficial health effects of elevated plasma levels of soluble αKl (SαKl) have been likened to the positive effects of exercise on ageing and chronic disease progression. It has also been established that molecular responses and adaptations differ according to exercise dose. The aim of this study is to compare the acute SαKl response to different exercise interventions, cardiorespiratory, and strength exercise in healthy, physically active men and to examine the behavior of SαKl 72h after acute strength exercise.

Methods: In this quasi-experimental study, plasma SαKl was measured before and after a cardiorespiratory exercise session (CR) in 43 men, and strength exercise session (ST) in 39 men. The behavior of SαKl was also examined 24, 48, and 72h after ST.

Results: Significant differences (time×group) were detected in SαKl levels (p=0.001; d=0.86) between CR and ST. After the ST intervention, SαKl behavior varied significantly (p=0.009; d=0.663) in that levels dropped between pre- and post-exercises (p=0.025; d=0.756) and were also significantly higher compared to pre ST values at 24h (p=0.033; d=0.717) and at 48h (p=0.015; d=0.827).

Conclusions: SαKl levels increased in response to a single bout of cardiorespiratory exercise; while they decreased immediately after strength exercise, levels were elevated after 24h indicating different klotho protein responses to different forms of exercise.
Exploring the Association Between Genetic Polymorphisms in Genes Involved in Craniofacial Development and Isolated Tooth Agenesis
Authors: Küchler Erika Calvano , Reis Caio Luiz Bitencourt , Silva-Sousa Alice Corrêa , Marañón-Vásquez Guido Artemio , Matsumoto Mirian Aiko Nakane , Sebastiani Aline , Scariot Rafaela , Paddenberg Eva , Proff Peter , Kirschneck Christian
Published: September 2021

Tooth agenesis is a common congenital anomaly in humans and is more common in oral cleft patients than in the general population. Many previous studies suggested that oral cleft and tooth agenesis share a similar genetic background. Therefore, this study explored the association between isolated tooth agenesis and genetic polymorphisms in genes that are crucial for craniofacial and tooth development. Panoramic radiographs, anamnesis, and genomic DNA from 273 patients were included. Patients were classified as tooth agenesis present, when at least one permanent tooth was congenitally missing. Patients with syndromes and oral cleft were excluded. Only unrelated patients were included. The genetic polymorphisms in BMP2 (rs235768 and rs1005464), BMP4 (rs17563), RUNX2 (rs59983488 and rs1200425), and SMAD6 (rs3934908 and rs2119261) were genotyped by real-time polymerase chain reaction. Genotype and allele distributions were compared between the tooth agenesis phenotypes and controls by Chi-square test. Haplotype and diplotype analysis were also performed, in addition to multivariate analysis (alpha of 0.05). A total of 86 tooth agenesis cases and 187 controls were evaluated. For the rs235768 in BMP2, patients carrying TT genotype have higher chance to present tooth agenesis [p < 0.001; prevalence ratio (PR) = 8.29; 95% confidence interval (CI) = 4.26–16.10]. The TT genotype in rs3934908 (SMAD6) was associated with higher chance to present third molar agenesis (p = 0.023; PR = 3.25; 95% CI = 1.17–8.99). BMP2 was also associated in haplotype and diplotype analysis with tooth agenesis. In conclusion, genetic polymorphisms in BMP2 and SMAD6 were associated with isolated tooth agenesis.
Harnessing Inflammation Resolution in Arthritis: Current Understanding of Specialized Pro-resolving Lipid Mediators’ Contribution to Arthritis Physiopathology and Future Perspectives
Authors: Zaninelli Tiago H. , Fattori Victor , Verri Waldiceu A.
Published: September 2021

The concept behind the resolution of inflammation has changed in the past decades from a passive to an active process, which reflects in novel avenues to understand and control inflammation-driven diseases. The time-dependent and active process of resolution phase is orchestrated by the endogenous biosynthesis of specialized pro-resolving lipid mediators (SPMs). Inflammation and its resolution are two forces in rheumatic diseases that affect millions of people worldwide with pain as the most common experienced symptom. The pathophysiological role of SPMs in arthritis has been demonstrated in pre-clinical and clinical studies (no clinical trials yet), which highlight their active orchestration of disease control. The endogenous roles of SPMs also give rise to the opportunity of envisaging these molecules as novel candidates to improve the life quality of rhematic diseases patients. Herein, we discuss the current understanding of SPMs endogenous roles in arthritis as pro-resolutive, protective, and immunoresolvent lipids.
Estimation of Subglottal Pressure, Vocal Fold Collision Pressure, and Intrinsic Laryngeal Muscle Activation From Neck-Surface Vibration Using a Neural Network Framework and a Voice Production Model
Authors: Ibarra Emiro J. , Parra Jesús A. , Alzamendi Gabriel A. , Cortés Juan P. , Espinoza Víctor M. , Mehta Daryush D. , Hillman Robert E. , Zañartu Matías
Published: September 2021

The ambulatory assessment of vocal function can be significantly enhanced by having access to physiologically based features that describe underlying pathophysiological mechanisms in individuals with voice disorders. This type of enhancement can improve methods for the prevention, diagnosis, and treatment of behaviorally based voice disorders. Unfortunately, the direct measurement of important vocal features such as subglottal pressure, vocal fold collision pressure, and laryngeal muscle activation is impractical in laboratory and ambulatory settings. In this study, we introduce a method to estimate these features during phonation from a neck-surface vibration signal through a framework that integrates a physiologically relevant model of voice production and machine learning tools. The signal from a neck-surface accelerometer is first processed using subglottal impedance-based inverse filtering to yield an estimate of the unsteady glottal airflow. Seven aerodynamic and acoustic features are extracted from the neck surface accelerometer and an optional microphone signal. A neural network architecture is selected to provide a mapping between the seven input features and subglottal pressure, vocal fold collision pressure, and cricothyroid and thyroarytenoid muscle activation. This non-linear mapping is trained solely with 13,000 Monte Carlo simulations of a voice production model that utilizes a symmetric triangular body-cover model of the vocal folds. The performance of the method was compared against laboratory data from synchronous recordings of oral airflow, intraoral pressure, microphone, and neck-surface vibration in 79 vocally healthy female participants uttering consecutive /pæ/ syllable strings at comfortable, loud, and soft levels. The mean absolute error and root-mean-square error for estimating the mean subglottal pressure were 191 Pa (1.95 cm H2O) and 243 Pa (2.48 cm H2O), respectively, which are comparable with previous studies but with the key advantage of not requiring subject-specific training and yielding more output measures. The validation of vocal fold collision pressure and laryngeal muscle activation was performed with synthetic values as reference. These initial results provide valuable insight for further vocal fold model refinement and constitute a proof of concept that the proposed machine learning method is a feasible option for providing physiologically relevant measures for laboratory and ambulatory assessment of vocal function.
Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines
Authors: Callet Thérèse , Dupont-Nivet Mathilde , Danion Morgane , Burel Christine , Cluzeaud Marianne , Surget Anne , Aguirre Pierre , Kerneis Thierry , Labbé Laurent , Panserat Stephane , Quillet Edwige , Geurden Inge , Skiba-Cassy Sandrine , Médale Françoise
Published: September 2021

Within the context of a growing aquaculture production coupled with a plateau of the production in the main components of aquafeeds (fish oil and fishmeal), recent studies have typically focused on replacing these feedstuffs with terrestrial plant ingredients for cultured carnivorous aquatic species, such as rainbow trout (Oncorhynchus mykiss). Substitution rates without adverse effects have, however, reached their limit. One potential way forward would be to take advantage of the genetic variability that exists in the salmonid population. However, to date, little is known about the underlying molecular mechanisms responsible for this genetic variability. The aim of the present research was to understand why some genotypes are better able to utilize plant-based diets devoid of marine resources. In this regard, three isogenic lines of rainbow trout (R23h, AB1h, and A22h), with similar growth when fed marine resources-based diets and which differ greatly in their responses to a plant-based diet, were fed with either a complete plant-based diet (V diet) or a marine resources-based diet (M diet) since first-feeding. Fish traits and the hepatic transcriptome of these three genotypes were compared after 5 months of feeding. First, differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but instead due to differences in feed efficiency. The comparison of transcriptome profiles revealed 575 (R23h vs. AB1h), 1,770 (R23h vs. A22h), and 2,973 (AB1h vs. A22h) probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, R23h and AB1h fish, which were the least affected by the V diet, exhibited the highest growth. These results demonstrate that these fish were able to maintain a high level of energy production and protein synthesis. Moreover, these genotypes were also able to activate pathways linked to lipid and cholesterol metabolisms, such as the biosynthesis of long-chain polyunsaturated fatty acids. Finally, as previously, immunity seems to also play an important role in the ability of fish to use the V diet, and further studies are needed to understand the mechanisms by which immunity interacts with growth.
Effective Antidepressant Chronotherapeutics (Sleep Deprivation and Light Therapy) Normalize the IL-1β:IL-1ra Ratio in Bipolar Depression
Authors: Benedetti Francesco , Dallaspezia Sara , Melloni Elisa Maria Teresa , Lorenzi Cristina , Zanardi Raffaella , Barbini Barbara , Colombo Cristina
Published: September 2021

Background

Mood disorders associate with peripheral markers of low-grade inflammation, among which circulating levels of interleukin-1β (IL-1β) consistently predict diagnosis and poor outcomes. Antidepressant chronotherapeutics (total sleep deprivation and light therapy, TSD+LT) prompts response in drug-resistant bipolar depression, but its effect on peripheral inflammation were never assessed. Here we explored the effects of TSD+LT on IL-1β signaling.

Methods

We studied the ratio between IL-1β and its receptor antagonist (IL-1β:IL1ra) in 33 healthy participants, and in 26 inpatients with a major depressive episode in course of Bipolar Disorder, before and after treatment with three cycles of repeated TSD+LT, interspersed with sleep recovery nights, administered during 1 week. Treatment effects of mood and on IL-1β:IL1ra were analyzed in the context of the Generalized Linear Model (GLM).

Results

At baseline, patients had higher IL-1β, IL1ra, and IL-1β:IL1ra than controls. Treatment significantly decreased IL-1β:IL1ra, by decreasing IL-1β and increasing IL1ra, the effect being proportional to baseline levels and normalizing values. Patients with higher baseline levels showed the highest decrease in IL-1β:IL-1ra, which associated with the immediate antidepressant response at the first cycle; while patients with lower baseline values showed negligible changes in the IL-1β:IL-1ra, unrelated to treatment response.

Conclusion

We observed a parallel change of inflammatory biomarkers and severity of depression after chronotherapeutics, suggesting that a reduction in inflammation associated with depression could contribute to the mechanism of action of TSD+LT, and warranting interest for controlled studies addressing the role of inflammation in the recovery from bipolar depression.
Applications of Multi-Omics Technologies for Crop Improvement
Authors: Yang Yaodong , Saand Mumtaz Ali , Huang Liyun , Abdelaal Walid Badawy , Zhang Jun , Wu Yi , Li Jing , Sirohi Muzafar Hussain , Wang Fuyou
Published: September 2021

Multiple “omics” approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivumL.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgareL.), maize (Zea maysL.), millet (Setaria italicaL.), cotton (Gossypium hirsutumL.),Medicago truncatula, and rice (Oryza sativaL.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the “phenotype to genotype” and “genotype to phenotype” concept. Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.
The Coevolution of RuBisCO, Photorespiration, and Carbon Concentrating Mechanisms in Higher Plants
Authors: Cummins Peter L.
Published: September 2021

Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO) is the carbon-fixing enzyme present in most photosynthetic organisms, converting CO2 into organic matter. Globally, photosynthetic efficiency in terrestrial plants has become increasingly challenged in recent decades due to a rapid increase in atmospheric CO2 and associated changes toward warmer and dryer environments. Well adapted for these new climatic conditions, the C4 photosynthetic pathway utilizes carbon concentrating mechanisms to increase CO2 concentrations surrounding RuBisCO, suppressing photorespiration from the oxygenase catalyzed reaction with O2. The energy efficiency of C3 photosynthesis, from which the C4 pathway evolved, is thought to rely critically on an uninterrupted supply of chloroplast CO2. Part of the homeostatic mechanism that maintains this constancy of supply involves the CO2 produced as a byproduct of photorespiration in a negative feedback loop. Analyzing the database of RuBisCO kinetic parameters, we suggest that in genera (Flaveria and Panicum) for which both C3 and C4 examples are available, the C4 pathway evolved only from C3 ancestors possessing much lower than the average carboxylase specificity relative to that of the oxygenase reaction (SC/O=SC/SO), and hence, the higher CO2 levels required for development of the photorespiratory CO2 pump (C2 photosynthesis) essential in the initial stages of C4 evolution, while in the later stage (final optimization phase in the Flaveria model) increased CO2 turnover may have occurred, which would have been supported by the higher CO2 levels. Otherwise, C4 RuBisCO kinetic traits remain little changed from the ancestral C3 species. At the opposite end of the spectrum, C3 plants (from Limonium) with higher than average SC/O, which may be associated with the ability of increased CO2, relative to O2, affinity to offset reduced photorespiration and chloroplast CO2 levels, can tolerate high stress environments. It is suggested that, instead of inherently constrained by its kinetic mechanism, RuBisCO possesses the extensive kinetic plasticity necessary for adaptation to changes in photorespiration that occur in the homeostatic regulation of CO2 supply under a broad range of abiotic environmental conditions.
In planta Activity of the Novel Copper Product HA + Cu(II) Based on a Biocompatible Drug Delivery System on Vine Physiology and Trials for the Control of Botryosphaeria Dieback
Authors: Mondello Vincenzo , Fernandez Olivier , Guise Jean-François , Trotel-Aziz Patricia , Fontaine Florence
Published: September 2021

The growing concerns on human and environment health are forcing the plant protection industry toward the formulation of more eco-sustainable plant protection products (PPP), both efficient and innovative in their approach to disease control. A large number of these innovative formulations now rely on a combination of pathogens antagonistic properties and stimulation of natural plant defense to pathogens. The formulation HA + Cu(II), in which copper is delivered to the plants by the drug-delivery molecule hydroxyapatite (HA), was found efficient against the grapevine pathogens Plasmopara viticola and Phaeoacremonium minimum and able to induce the host-plant defense system. We investigated the HA + Cu(II) impacts on grapevine physiology, both in uninfected and when infected by the Botryosphaeria dieback agents Diplodia seriata and Neofusicoccum parvum. This study of plant physiology and disease impact were addressed to evaluate both the HA + Cu(II) potential as a plant defense elicitor and its possible and future use as PPP in vineyard. Our results showed that HA + Cu(II) induced several key-defense genes without negatively affecting plant growth and photosynthetic activity. In addition, fungistatic effect on the two Botryosphaeriaceae at the in planta tested concentrations is reported. Altogether, our results obtained under controlled conditions fully support the potential of HA + Cu(II) as a promising PPP toward grapevine trunk diseases in vineyard.
Effect of Root and Mycelia on Fine Root Decomposition and Release of Carbon and Nitrogen Under Artemisia halodendron in a Semi-arid Sandy Grassland in China
Authors: Liu Xinping , Luo Yongqing , Cheng Li , Hu Hongjiao , Wang Youhan , Du Zhong
Published: September 2021

Plant fine root turnover is a continuous process both spatially and temporally, and fine root decomposition is affected by many biotic and abiotic factors. However, the effect of the living roots and the associated mycorrhizal fungal mycelia on fine root decomposition remains unclear. The objective of this study is to explore the influence of these biotic factors on fine root decomposition in a semi-arid ecosystem. In this study, we investigated the effect of fine roots and mycelia on fine root decomposition of a pioneer shrub (Artemisia halodendron) in Horqin sandy land, northeast China, by the ingrowth core method combined with the litterbag method. Litterbags were installed in cores. Results showed that core a allowed the growth of both fine roots and mycelia (treatment R + M), core b only allowed the growth of mycelia (treatment M), and in core c the fine root and mycelia growth were restricted and only bulk soil was present (treatment S). These findings suggest that the process of root decomposition was significantly affected by the living roots and mycelia, and carbon (C) and nitrogen (N) concentration dynamics during root decomposition differed among treatments. Mycelia significantly stimulated the mass loss and C and N release during root decomposition. Treatment R + M significantly stimulated the accumulation of soil total C, total N, and organic N under litterbags. The mycelia significantly stimulated the accumulation of the inorganic N (ammonium-N and nitrate-N) but the presence of fine roots weakened nitrate-N accumulation. The presence of living roots and associated mycelia strongly affected the process of root decomposition and matter release in the litter-soil system. The results of this study should strengthen the understanding of root-soil interactions.
Detection of Parietaria Mottle Virus by RT-qPCR: An Emerging Virus Native of Mediterranean Area That Undermine Tomato and Pepper Production in Southern Italy
Authors: Panno Stefano , Caruso Andrea Giovanni , Bertacca Sofia , Matić Slavica , Davino Salvatore , Parrella Giuseppe
Published: September 2021

Parietaria mottle virus (PMoV) is considered an emerging virus in many countries of the Mediterranean basin, especially on tomato and pepper crops. Symptoms on tomato leaves and fruits can be easily confused with those induced by cucumber mosaic virus (CMV) with necrogenic satellite RNA (CMV-satRNA), tomato spotted wilt virus (TSWV) or tomato mosaic virus (ToMV). Mixed infection of these viruses has been also reported in some tomato cultivars, with an increase in the complexity of the symptoms and severity of the disease. Although a specific serum and riboprobes have been produced, nowadays no sensitive diagnostic methods are available for the rapid PMoV detection. Here, we have developed a RT-qPCR assay with the aim to establish a more sensitive and specific method for PMoV detection. Specific primers and TaqMan probe were designed and in silico tested with all PMoV isolates available in GenBank. Moreover, this method was evaluated on tomato naturally infected samples from Sicily region (Italy). Results obtained showed that the RT-qPCR assay developed in this work is extremely sensitive, in fact, it is able to detect as few as 10 PMoV RNA copies in tomato total RNA; moreover, it will be a particularly valuable tool for early detection of PMoV. Furthermore, the analyzes on field samples show how this pathogen is increasingly present in tomato crops in the last years, helping to undermine the Italian horticultural sector.
Five OsS40 Family Members Are Identified as Senescence-Related Genes in Rice by Reverse Genetics Approach
Authors: Habiba  , Xu Jiaxuan , Gad Ahmed G. , Luo Yuling , Fan Chunlan , Uddin Junaite Bin Gias , ul Ain Noor , Huang Chengxin , Zhang Yu , Miao Ying , Zheng Xiangzi
Published: September 2021

A total of 16OsS40genes ofOryza sativawere identified in our previous work, but their functions remain unclear. In this study, 13OsS40members were knocked out using the CRISPR/cas9 gene-editing technology. After screening phenotype characterization of CRISPR/Cas9 mutants compared to WT, fiveoss40smutants exhibited a stay-green phenotype at 30 days after heading. Moreover, increased grain size and grain weight occurred in theoss40-1, oss40-12, andoss40-14lines, while declined grain weight appeared in theoss40-7andoss40-13mutants. The transcript levels of several senescence-associated genes (SAGs), chlorophyll degradation-related genes (CDGs), as well as WRKY members were differentially decreased in the five stay-greenoss40smutants compared to WT. Fiveoss40mutants also exhibited a stay-green phenotype when the detached leaves were incubated under darkness for 4 days.OsSWEET4andOsSWEET1bwere significantly upregulated, whileOsSWEET1aandOsSWEET13were significantly downregulated in bothoss40-7andoss40-14compared to WT. Furthermore, these fiveOsS40displayed strong transcriptional activation activity and were located in the nucleus. Most of theOsS40genes were downregulated in theoss40-1, oss40-7, andoss40-12mutants, but upregulated in theoss40-13andoss40-14mutants, indicating coordinated regulation amongOsS40members. These results suggest thatOsS40-1, OsS40-7, OsS40-12, OsS40-13, andOsS40-14are senescence-associated genes, involved in the senescence and carbon allocation network by modulating otherOsS40members,SWEETmember genes, and senescence-related gene expression.
Wood Anatomy of Douglas-Fir in Eastern Arizona and Its Relationship With Pacific Basin Climate
Authors: Balanzategui Daniel , Nordhauß Henry , Heinrich Ingo , Biondi Franco , Miley Nicholas , Hurley Alexander G. , Ziaco Emanuele
Published: September 2021

Dendroclimatic reconstructions, which are a well-known tool for extending records of climatic variability, have recently been expanded by using wood anatomical parameters. However, the relationships between wood cellular structures and large-scale climatic patterns, such as El Niño-Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO), are still not completely understood, hindering the potential for wood anatomy as a paleoclimatic proxy. To better understand the teleconnection between regional and local climate processes in the western United States, our main objective was to assess the value of these emerging tree-ring parameters for reconstructing climate dynamics. Using Confocal Laser Scanning Microscopy, we measured cell lumen diameter and cell wall thickness (CWT) for the period 1966 to 2015 in five Douglas-firs [Pseudotsuga menziesii (Mirb.) Franco] from two sites in eastern Arizona (United States). Dendroclimatic analysis was performed using chronologies developed for 10 equally distributed sectors of the ring and daily climatic records to identify the strongest climatic signal for each sector. We found that lumen diameter in the first ring sector was sensitive to previous fall–winter temperature (September 25th to January 23rd), while a precipitation signal (October 27th to February 13th) persisted for the entire first half of the ring. The lack of synchronous patterns between trees for CWT prevented conducting meaningful climate-response analysis for that anatomical parameter. Time series of lumen diameter showed an anti-phase relationship with the Southern Oscillation Index (a proxy for ENSO) at 10 to 14year periodicity and particularly in 1980–2005, suggesting that chronologies of wood anatomical parameters respond to multidecadal variability of regional climatic modes. Our findings demonstrate the potential of cell structural characteristics of southwestern United States conifers for reconstructing past climatic variability, while also improving our understanding of how large-scale ocean–atmosphere interactions impact local hydroclimatic patterns.
The Toughest Material in the Plant Kingdom: An Update on Sporopollenin
Authors: Grienenberger Etienne , Quilichini Teagen D.
Published: September 2021

The extreme chemical and physical recalcitrance of sporopollenin deems this biopolymer among the most resilient organic materials on Earth. As the primary material fortifying spore and pollen cell walls, sporopollenin is touted as a critical innovation in the progression of plant life to a terrestrial setting. Although crucial for its protective role in plant reproduction, the inert nature of sporopollenin has challenged efforts to determine its composition for decades. Revised structural, chemical, and genetic experimentation efforts have produced dramatic advances in elucidating the molecular structure of this biopolymer and the mechanisms of its synthesis. Bypassing many of the challenges with material fragmentation and solubilization, insights from functional characterizations of sporopollenin biogenesis in planta, and in vitro, through a gene-targeted approach suggest a backbone of polyhydroxylated polyketide-based subunits and remarkable conservation of biochemical pathways for sporopollenin biosynthesis across the plant kingdom. Recent optimization of solid-state NMR and targeted degradation methods for sporopollenin analysis confirms polyhydroxylated α-pyrone subunits, as well as hydroxylated aliphatic units, and unique cross-linkage heterogeneity. We examine the cross-disciplinary efforts to solve the sporopollenin composition puzzle and illustrate a working model of sporopollenin’s molecular structure and biosynthesis. Emerging controversies and remaining knowledge gaps are discussed, including the degree of aromaticity, cross-linkage profiles, and extent of chemical conservation of sporopollenin among land plants. The recent developments in sporopollenin research present diverse opportunities for harnessing the extraordinary properties of this abundant and stable biomaterial for sustainable microcapsule applications and synthetic material designs.
A Life Cycle for Modeling Biology at Different Scales
Authors: Harline Kate , Martínez-Gómez Jesús , Specht Chelsea D. , Roeder Adrienne H. K.
Published: September 2021

Modeling has become a popular tool for inquiry and discovery across biological disciplines. Models allow biologists to probe complex questions and to guide experimentation. Modeling literacy among biologists, however, has not always kept pace with the rise in popularity of these techniques and the relevant advances in modeling theory. The result is a lack of understanding that inhibits communication and ultimately, progress in data gathering and analysis. In an effort to help bridge this gap, we present a blueprint that will empower biologists to interrogate and apply models in their field. We demonstrate the applicability of this blueprint in two case studies from distinct subdisciplines of biology; developmental-biomechanics and evolutionary biology. The models used in these fields vary from summarizing dynamical mechanisms to making statistical inferences, demonstrating the breadth of the utility of models to explore biological phenomena.
Leaf Shedding and Non-Stomatal Limitations of Photosynthesis Mitigate Hydraulic Conductance Losses in Scots Pine Saplings During Severe Drought Stress
Authors: Nadal-Sala Daniel , Grote Rüdiger , Birami Benjamin , Knüver Timo , Rehschuh Romy , Schwarz Selina , Ruehr Nadine K.
Published: September 2021

During drought, trees reduce water loss and hydraulic failure by closing their stomata, which also limits photosynthesis. Under severe drought stress, other acclimation mechanisms are trigged to further reduce transpiration to prevent irreversible conductance loss. Here, we investigate two of them: the reversible impacts on the photosynthetic apparatus, lumped as non-stomatal limitations (NSL) of photosynthesis, and the irreversible effect of premature leaf shedding. We integrate NSL and leaf shedding with a state-of-the-art tree hydraulic simulation model (SOX+) and parameterize them with example field measurements to demonstrate the stress-mitigating impact of these processes. We measured xylem vulnerability, transpiration, and leaf litter fall dynamics in Pinus sylvestris (L.) saplings grown for 54 days under severe dry-down. The observations showed that, once transpiration stopped, the rate of leaf shedding strongly increased until about 30% of leaf area was lost on average. We trained the SOX+ model with the observations and simulated changes in root-to-canopy conductance with and without including NSL and leaf shedding. Accounting for NSL improved model representation of transpiration, while model projections about root-to-canopy conductance loss were reduced by an overall 6%. Together, NSL and observed leaf shedding reduced projected losses in conductance by about 13%. In summary, the results highlight the importance of other than purely stomatal conductance-driven adjustments of drought resistance in Scots pine. Accounting for acclimation responses to drought, such as morphological (leaf shedding) and physiological (NSL) adjustments, has the potential to improve tree hydraulic simulation models, particularly when applied in predicting drought-induced tree mortality.
Cold-Triggered Induction of ROS- and Raffinose Metabolism in Freezing-Sensitive Taproot Tissue of Sugar Beet
Authors: Keller Isabel , Müdsam Christina , Rodrigues C. Martins , Kischka Dominik , Zierer Wolfgang , Sonnewald Uwe , Harms Karsten , Czarnecki Olaf , Fiedler-Wiechers Karin , Koch Wolfgang , Neuhaus H. Ekkehard , Ludewig Frank , Pommerrenig Benjamin
Published: September 2021

Sugar beet (Beta vulgaris subsp. vulgaris) is the exclusive source of sugar in the form of sucrose in temperate climate zones. Sugar beet is grown there as an annual crop from spring to autumn because of the damaging effect of freezing temperatures to taproot tissue. A collection of hybrid and non-hybrid sugar beet cultivars was tested for winter survival rates and freezing tolerance. Three genotypes with either low or high winter survival rates were selected for detailed study of their response to frost. These genotypes differed in the severity of frost injury in a defined inner region in the upper part of the taproot, the so-called pith. We aimed to elucidate genotype- and tissue-dependent molecular processes during freezing and combined analyses of sugar beet anatomy and physiology with transcriptomic and metabolite profiles of leaf and taproot tissues at low temperatures. Freezing temperatures induced strong downregulation of photosynthesis in leaves, generation of reactive oxygen species (ROS), and ROS-related gene expression in taproots. Simultaneously, expression of genes involved in raffinose metabolism, as well as concentrations of raffinose and its intermediates, increased markedly in both leaf and taproot tissue at low temperatures. The accumulation of raffinose in the pith tissue correlated with freezing tolerance of the three genotypes. We discuss a protective role for raffinose and its precursors against freezing damage of sugar beet taproot tissue.
A Deep Learning-Based Method for Automatic Assessment of Stomatal Index in Wheat Microscopic Images of Leaf Epidermis
Authors: Zhu Chuancheng , Hu Yusong , Mao Hude , Li Shumin , Li Fangfang , Zhao Congyuan , Luo Lin , Liu Weizhen , Yuan Xiaohui
Published: September 2021

The stomatal index of the leaf is the ratio of the number of stomata to the total number of stomata and epidermal cells. Comparing with the stomatal density, the stomatal index is relatively constant in environmental conditions and the age of the leaf and, therefore, of diagnostic characteristics for a given genotype or species. Traditional assessment methods involve manual counting of the number of stomata and epidermal cells in microphotographs, which is labor-intensive and time-consuming. Although several automatic measurement algorithms of stomatal density have been proposed, no stomatal index pipelines are currently available. The main aim of this research is to develop an automated stomatal index measurement pipeline. The proposed method employed Faster regions with convolutional neural networks (R-CNN) and U-Net and image-processing techniques to count stomata and epidermal cells, and subsequently calculate the stomatal index. To improve the labeling speed, a semi-automatic strategy was employed for epidermal cell annotation in each micrograph. Benchmarking the pipeline on 1,000 microscopic images of leaf epidermis in the wheat dataset (Triticum aestivum L.), the average counting accuracies of 98.03 and 95.03% for stomata and epidermal cells, respectively, and the final measurement accuracy of the stomatal index of 95.35% was achieved. R2 values between automatic and manual measurement of stomata, epidermal cells, and stomatal index were 0.995, 0.983, and 0.895, respectively. The average running time (ART) for the entire pipeline could be as short as 0.32 s per microphotograph. The proposed pipeline also achieved a good transferability on the other families of the plant using transfer learning, with the mean counting accuracies of 94.36 and 91.13% for stomata and epidermal cells and the stomatal index accuracy of 89.38% in seven families of the plant. The pipeline is an automatic, rapid, and accurate tool for the stomatal index measurement, enabling high-throughput phenotyping, and facilitating further understanding of the stomatal and epidermal development for the plant physiology community. To the best of our knowledge, this is the first deep learning-based microphotograph analysis pipeline for stomatal index assessment.
Data Management and Modeling in Plant Biology
Authors: Krantz Maria , Zimmer David , Adler Stephan O. , Kitashova Anastasia , Klipp Edda , Mühlhaus Timo , Nägele Thomas
Published: September 2021

The study of plant-environment interactions is a multidisciplinary research field. With the emergence of quantitative large-scale and high-throughput techniques, amount and dimensionality of experimental data have strongly increased. Appropriate strategies for data storage, management, and evaluation are needed to make efficient use of experimental findings. Computational approaches of data mining are essential for deriving statistical trends and signatures contained in data matrices. Although, current biology is challenged by high data dimensionality in general, this is particularly true for plant biology. Plants as sessile organisms have to cope with environmental fluctuations. This typically results in strong dynamics of metabolite and protein concentrations which are often challenging to quantify. Summarizing experimental output results in complex data arrays, which need computational statistics and numerical methods for building quantitative models. Experimental findings need to be combined by computational models to gain a mechanistic understanding of plant metabolism. For this, bioinformatics and mathematics need to be combined with experimental setups in physiology, biochemistry, and molecular biology. This review presents and discusses concepts at the interface of experiment and computation, which are likely to shape current and future plant biology. Finally, this interface is discussed with regard to its capabilities and limitations to develop a quantitative model of plant-environment interactions.
Genome-Wide Identification, Evolution, and Expression Analysis of LBD Transcription Factor Family in Bread Wheat (Triticum aestivum L.)
Authors: Wang Zhenyu , Zhang Ruoyu , Cheng Yue , Lei Pengzheng , Song Weining , Zheng Weijun , Nie Xiaojun
Published: September 2021

The lateral organ boundaries domain (LBD) genes, as the plant-specific transcription factor family, play a crucial role in controlling plant architecture and stress tolerance. Although it has been thoroughly characterized in many species, the LBD family was not well studied in wheat. Here, the wheat LBD family was systematically investigated through an in silico genome-wide search method. A total of 90 wheat LBD genes (TaLBDs) were identified, which were classified into class I containing seven subfamilies, and class II containing two subfamilies. Exon–intron structure, conserved protein motif, and cis-regulatory elements analysis showed that the members in the same subfamily shared similar gene structure organizations, supporting the classification. Furthermore, the expression patterns of these TaLBDs in different types of tissues and under diverse stresses were identified through public RNA-seq data analysis, and the regulation networks of TaLBDs involved were predicted. Finally, the expression levels of 12 TaLBDs were validated by quantitative PCR (qPCR) analysis and the homoeologous genes showed differential expression. Additionally, the genetic diversity of TaLBDs in the landrace population showed slightly higher than that of the genetically improved germplasm population while obvious asymmetry at the subgenome level. This study not only provided the potential targets for further functional analysis but also contributed to better understand the roles of LBD genes in regulating development and stress tolerance in wheat and beyond.
Integrated Genomic Analyses From Low-Depth Sequencing Help Resolve Phylogenetic Incongruence in the Bamboos (Poaceae: Bambusoideae)
Authors: Chalopin Domitille , Clark Lynn G. , Wysocki William P. , Park Minkyu , Duvall Melvin R. , Bennetzen Jeffrey L.
Published: September 2021

The bamboos (Bambusoideae, Poaceae) comprise a major grass lineage with a complex evolutionary history involving ancient hybridization and allopolyploidy. About 1700 described species are classified into three tribes, Olyreae (herbaceous bamboos), Bambuseae (tropical woody bamboos), and Arundinarieae (temperate woody bamboos). Nuclear analyses strongly support monophyly of the woody tribes, whereas plastome analyses strongly support paraphyly, with Bambuseae sister to Olyreae. Our objectives were to clarify the origin(s) of the woody bamboo tribes and resolve the nuclear vs. plastid conflict using genomic tools. For the first time, plastid and nuclear genomic information from the same bamboo species were combined in a single study. We sampled 51 species of bamboos representing the three tribes, estimated their genome sizes and generated low-depth sample sequence data, from which plastomes were assembled and nuclear repeats were analyzed. The distribution of repeat families was found to agree with nuclear gene phylogenies, but also provides novel insights into nuclear evolutionary history. We infer two early, independent hybridization events, one between an Olyreae ancestor and a woody ancestor giving rise to the two Bambuseae lineages, and another between two woody ancestors giving rise to the Arundinarieae. Retention of the Olyreae plastome associated with differential dominance of nuclear genomes and subsequent diploidization in some lineages explains the paraphyly observed in plastome phylogenetic estimations. We confirm ancient hybridization and allopolyploidy in the origins of the extant woody bamboo lineages and propose biased fractionation and diploidization as important factors in their evolution.
Improving Quantitative Traits in Self-Pollinated Crops Using Simulation-Based Selection With Minimal Crossing
Authors: Sekine Daisuke , Tsuda Mai , Yabe Shiori , Shimizu Takehiko , Machita Kayo , Saruta Masayasu , Yamada Tetsuya , Ishimoto Masao , Iwata Hiroyoshi , Kaga Akito
Published: September 2021

Genomic selection and marker-assisted recurrent selection have been applied to improve quantitative traits in many cross-pollinated crops. However, such selection is not feasible in self-pollinated crops owing to laborious crossing procedures. In this study, we developed a simulation-based selection strategy that makes use of a trait prediction model based on genomic information to predict the phenotype of the progeny for all possible crossing combinations. These predictions are then used to select the best cross combinations for the selection of the given trait. In our simulated experiment, using a biparental initial population with a heritability set to 0.3, 0.6, or 1.0 and the number of quantitative trait loci set to 30 or 100, the genetic gain of the proposed strategy was higher or equal to that of conventional recurrent selection method in the early selection cycles, although the number of cross combinations of the proposed strategy was considerably reduced in each cycle. Moreover, this strategy was demonstrated to increase or decrease seed protein content in soybean recombinant inbred lines using SNP markers. Information on 29 genomic regions associated with seed protein content was used to construct the prediction model and conduct simulation. After two selection cycles, the selected progeny had significantly higher or lower seed protein contents than those from the initial population. These results suggest that our strategy is effective in obtaining superior progeny over a short period with minimal crossing and has the potential to efficiently improve the target quantitative traits in self-pollinated crops.
Discovery of the REN11 Locus From Vitis aestivalis for Stable Resistance to Grapevine Powdery Mildew in a Family Segregating for Several Unstable and Tissue-Specific Quantitative Resistance Loci
Authors: Karn Avinash , Zou Cheng , Brooks Siraprapa , Fresnedo-Ramírez Jonathan , Gabler Franka , Sun Qi , Ramming David , Naegele Rachel , Ledbetter Craig , Cadle-Davidson Lance
Published: September 2021

Race-specific resistance loci, whether having qualitative or quantitative effects, present plant-breeding challenges for phenotypic selection and deciding which loci to select or stack with other resistance loci for improved durability. Previously, resistance to grapevine powdery mildew (GPM, caused by Erysiphe necator) was predicted to be conferred by at least three race-specific loci in the mapping family B37-28 × C56-11 segregating for GPM resistance from Vitis aestivalis. In this study, 9 years of vineyard GPM disease severity ratings plus a greenhouse and laboratory assays were genetically mapped, using a rhAmpSeq core genome marker platform with 2,000 local haplotype markers. A new qualitative resistance locus, named REN11, on the chromosome (Chr) 15 was found to be effective in nearly all (11 of 12) vineyard environments on leaves, rachis, berries, and most of the time (7 of 12) stems. REN11 was independently validated in a pseudo-testcross with the grandparent source of resistance, “Tamiami.” Five other loci significantly predicted GPM severity on leaves in only one or two environments, which could indicate race-specific resistance or their roles in different timepoints in epidemic progress. Loci on Chr 8 and 9 reproducibly predicted disease severity on stems but not on other tissues and had additive effects with REN11 on the stems. The rhAmpSeq local haplotype sequences published in this study for REN11 and Chr 8 and 9 stem quantitative trait locus (QTL) can be used directly for marker-assisted selection or converted to SNP assays. In screening for REN11 in a diversity panel of 20,651 vines representing the diversity of Vitis, this rhAmpSeq haplotype had a false positive rate of 0.034% or less. The effects of the other foliar resistance loci detected in this study seem too unstable for genetic improvement regardless of quantitative effect size, whether due to race specificity or other environmental variables.
Examining the Relationships Among Concealment Tendencies, Illness Attitudes, Belief in a Just World, and Cognitive Flexibility
Authors: Cha Kyung Hwan , Jin Hua , Ha Jung Hee , Jue Juliet
Published: September 2021

The purpose of this study was to verify the relationships among concealment tendencies, illness attitudes, belief in a just world, and cognitive flexibility. The participants were 418 Korean and 400 Chinese adults. We conducted correlational analysis, structural equation modeling, and verification of mediating effects. We found that cognitive flexibility–control factor fully mediated the relationship between concealment tendencies and illness attitudes for Korean participants and partially mediated the relationship for Chinese participants. The relationship between concealment tendencies and cognitive flexibility–alternatives factor differed across participants’ country of origin. For Chinese participants, cognitive flexibility–alternatives fully mediated the relationship between concealment tendencies and belief in a just world. These differences might stem from the countries’ different social systems, values, and attitudes. Finally, we discuss this study’s implications and limitations.