bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of evolocumab on the progression of intraplaque neovascularization of the carotid based on contrast-enhanced ultrasonography (EPIC study): A prospective single-arm, open-label study
Authors: Chen Ju , Zhao Faming , Lei Chengbin , Qi Tianjun , Xue Xin , Meng Yuan , Zhang Wenzhong , Zhang Hui , Wang Jian , Zhu Haijun , Cheng Cheng , Wang Qilei , Bi Chenglong , Song Beibei , Jin Chengwei , Niu Qiang , An Fengshuang , Li Bin , Huo Xiaoguang , Zhao Yunhe , Li Bo
Published: January 2023

Background and Purpose: The aim of this study was to explore the effect of half a year of evolocumab plus moderate-intensity statin treatment on carotid intraplaque neovascularization (IPN) and blood lipid levels.

Methods: A total of 31 patients with 33 carotid plaques who received evolocumab plus statin treatment were included. Blood lipid levels, B-mode ultrasound and contrast-enhanced ultrasonography (CEUS) at baseline and after half a year of evolocumab plus statin therapy were collected. The area under the curve (AUC) reflected the total amount of acoustic developer entering the plaque or lumen within the 180 s measurement period. The enhanced intensity reflected the peak blood flow intensity during the monitoring period, and the contrast agent area reflected the area of vessels in the plaques.

Results: Except for high-density lipoprotein cholesterol (HDL-c), all other lipid indices decreased. Compared with baseline, low-density lipoprotein cholesterol (LDL-c) decreased by approximately 57% (p < 0.001); total cholesterol (TC) decreased by approximately 34% (p < 0.001); small dense low-density lipoprotein (sd-LDL) decreased by approximately 52% (p < 0.001); and HDL-c increased by approximately 20% (p < 0.001). B-mode ultrasonography showed that the length and thickness of the plaque and the hypoechoic area ratio were reduced (p < 0.05). The plaque area, calcified area ratio, and lumen cross-sectional area changed little (p > 0.05). CEUS revealed that the area under the curve of plaque/lumen [AUC (P/L)] decreased from 0.27 ± 0.13 to 0.19 ± 0.11 (p < 0.001). The enhanced intensity ratio of plaque/lumen [intensity ratio (P/L)] decreased from 0.37 ± 0.16 to 0.31 ± 0.14 (p = 0.009). The contrast agent area in plaque/area of plaque decreased from 19.20 ± 13.23 to 12.66 ± 9.59 (p = 0.003). The neovascularization score decreased from 2.64 ± 0.54 to 2.06 ± 0.86 (p < 0.001). Subgroup analysis based on statin duration (<6 months and ≥6 months) showed that there was no significant difference in the AUC (P/L) or intensity ratio (P/L) at baseline or after half a year of evolocumab treatment.

Conclusion: This study found that evolocumab combined with moderate-intensity statins significantly improved the blood lipid profile and reduced carotid IPN.

Clinical Trial Registration:https://www.clinicaltrials.gov; identifier: NCT04423406.
Foundational concepts in person-machine teaming
Authors: Greenberg Ariel M. , Marble Julie L.
Published: January 2023

As we enter an age where the behavior and capabilities of artificial intelligence and autonomous system technologies become ever more sophisticated, cooperation, collaboration, and teaming between people and these machines is rising to the forefront of critical research areas. People engage socially with almost everything with which they interact. However, unlike animals, machines do not share the experiential aspects of sociality. Experiential robotics identifies the need to develop machines that not only learn from their own experience, but can learn from the experience of people in interactions, wherein these experiences are primarily social. In this paper, we argue, therefore, for the need to place experiential considerations in interaction, cooperation, and teaming as the basis of the design and engineering of person-machine teams. We first explore the importance of semantics in driving engineering approaches to robot development. Then, we examine differences in the usage of relevant terms like trust and ethics between engineering and social science approaches to lay out implications for the development of autonomous, experiential systems.
Ideal nodal net phonons in Pn3¯m type Ag2O
Authors: Li Yang
Published: January 2023

The topological phonon state is a new field that has sparked much interest. Weyl phonons in FeSi, for example, have been theoretically proposed and experimentally identified. In this work, via the first-principle calculation, we prove the ideal nodal net phonons exist in a realistic material Ag2O with Pn3¯m type structure. With the help of the Berry phase calculations, we find that the nodal net phonons in Ag2O are topologically non-trivial. The phononic surface states are visible, which benefits the experimental detections. The results in this work contribute to the material realization of topological nodal net phonons. The author hopes the experimental verification of the novel topological phonons can be performed in the following investigations.
Seasonal analysis of match load in professional soccer players: An observational cohort study of a Swiss U18, U21 and first team
Authors: Ammann Linda , Altmann Stefan , Ruf Ludwig , Sperlich Billy
Published: January 2023

The aim of this study was to quantify and compare various external match load measures in three age groups and leagues in male soccer (U18 in highest league of their age group vs U21 in fourth highest league vs first team in highest league). In this retrospective observational cohort study accelerations, decelerations, absolute and relative high-speed running as well as sprint distance, dynamic stress load, explosive distance, high intensity bursts total distance, high metabolic load (HML) distance, speed intensity, total distance, total time, and total loading were assessed in 416 individual player matches of 59 players. All these external load measures showed large inter-individual variability. At a group level, one-way ANOVAs or Kruskal–Wallis tests revealed statistically significant differences between the three teams for all measures analyzed (all p < 0.05), except accelerations. The first team displayed statistically significant higher dynamic stress load, explosive distance, HML distance, speed intensity, total distance and total loading compared to the two youth teams (all p < 0.05). The U18 featured statistically significant higher number of decelerations, absolute and relative high-speed running distance, high metabolic load distance, speed intensity, relative sprint distance, total distance, and total time than the U21, while for U21 higher dynamic stress load was observed than for U18 (all p < 0.05). Based on our data we conclude a routinely monitoring of match loads of different age groups and competitive settings to be required to 1) provide an indication of what players need to be prepared for, 2) track the athletic and match evolution, and 3) individually tailor training programs allowing players to fulfill the short- and long-term sport-specific requirements.
Bioinformatics analysis combined with clinical sample screening reveals that leptin may be a biomarker of preeclampsia
Authors: Wang Yajuan , Bai Xuening , Guo Xin , Gao Xiaoli , Chen Yuanyuan , Li Huanrong , Fan Wenjun , Han Cha
Published: January 2023

Introduction: Preeclampsia (PE) is a gestational hypertensive disease with unclear pathogenesis. This study aimed to identify the genes that play an important role in determining the pathogenesis of PE using bioinformatics analysis and fundamental researches.

Materials and methods: Datasets from the Gene Expression Omnibus (GEO) database were used to screen for differentially expressed genes (DEGs). The NCBI, SangerBox, and other databases were used to analyze the functions of the DEGs. Targetscan7, miRWalk, ENCORI, DIANA TOOLS, CircBank databases, and the Cytoscape tool were used to construct the lncRNA/circRNA-miRNA- LEP network. SRAMP, RPISeq, RBPsuite, and catRPAID were used to analyze the RNA modifications of LEP. Immune cell infiltration was analyzed using the dataset GSE75010. Placental tissues from normal pregnant women and PE patients were collected, screened for gene expression using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting. The results were further verified in HTR-8/SVneo cell line hypoxia model and PE mouse model.

Results: Our analyses revealed that LEP was significantly upregulated in eight datasets. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses indicated that LEP was involved in the JAK/STAT signaling pathway, angiogenesis, and placental development. Immune cell infiltration analysis showed that M1 and M2 macrophages differed between normal pregnancies and those in PE patients. A competing endogenous RNA (ceRNA) network was constructed, and proteins interacting with LEP were identified. RNA modification sites of LEP were also identified. Finally, the overexpression of LEP in PE was confirmed in clinical samples, HTR-8/SVneo cell line and PE mouse model.

Conclusion: Our results indicate that LEP overexpression is associated with PE and may be a potential diagnostic marker and therapeutic target.
Twelve weeks of a diet and exercise intervention alters the acute bone response to exercise in adolescent females with overweight/obesity
Authors: Kurgan Nigel , Skelly Lauren E. , Ludwa Izabella A. , Klentrou Panagiota , Josse Andrea R.
Published: January 2023

Introduction: Exercise and consumption of dairy foods have been shown to improve bone mineralization. However, little is known about the magnitude and timing of their synergistic effects on markers and regulators of bone metabolism in response to acute exercise in adolescent females with obesity, a population susceptible to altered bone metabolism and mineral properties. This study examined the influence of twelve weeks of exercise training and nutritional counselling on the bone biochemical marker response to acute exercise and whether higher dairy consumption could further influence the response.

Methods: Thirty adolescent females (14.3 ± 2.0 years) with overweight/obesity (OW/OB) completed a 12-week lifestyle modification intervention involving exercise training and nutritional counselling. Participants were randomized into two groups: higher dairy intake (RDa; 4 servings/day; n = 14) or low dairy intake (LDa; 0-2 servings/d; n = 16). Participants performed one bout of plyometric exercise (5 circuits; 120 jumps) both pre- and post-intervention. Blood samples were taken at rest, 5 min and 1 h post-exercise. Serum sclerostin, osteocalcin (OC), osteoprotegerin (OPG), receptor activator nuclear factor kappa B ligand (RANKL), and C-terminal telopeptide of type 1 collagen (βCTX) concentrations were measured.

Results: While there was an overall increase in sclerostin pre-intervention from pre to 5 min post-exercise (+11% p = 0.04), this response was significantly decreased post-intervention (−25%, p = 0.03) independent of dairy intake. The OPG:RANKL ratio was unresponsive to acute exercise pre-intervention but increased 1 h post-exercise (+2.6 AU; p < 0.001) post-intervention. Dairy intake did not further influence these absolute responses. However, after the 12-week intervention, the RDa group showed a decrease in the relative RANKL post-exercise response (−21.9%; p < 0.01), leading to a consistent increase in the relative OPG:RANKL ratio response, which was not the case in the LDa group. There was no influence of the intervention or dairy product intake on OC, OPG, or βCTX responses to acute exercise (p > 0.05).

Conclusion: A lifestyle modification intervention involving exercise training blunts the increase in sclerostin and can augment the increase in OPG:RANKL ratio to acute exercise in adolescent females with OW/OB, while dairy product consumption did not further influence these responses.
Effect of the 3q26-coding oncogene SEC62 as a potential prognostic marker in patients with ovarian neoplasia
Authors: Radosa Julia C. , Kasoha Mariz , Schilz Anne-Christine , Takacs Zoltan F. , Kaya Askin , Radosa Marc P. , Linxweiler Barbara , Linxweiler Maximilian , Bohle Rainer M. , Wagner Mathias , Wagenpfeil Gudrun , Solomayer Erich-Franz , Zimmermann Julia S. M.
Published: January 2023

With approximately 220,000 newly diagnosed cases per year, ovarian cancer is among the most frequently occurring cancers among women and the second leading cause of death from gynecological malignancies worldwide. About 70% of these cancers are diagnosed in advanced stages (FIGO IIB–IV), with a 5-year survival rate of 20–30%. Due to the poor prognosis of this disease, research has focused on its pathogenesis and the identification of prognostic factors. One possible approach for the identification of biological markers is the identification of tumor entity-specific genetic “driver mutations”. One such mutation is 3q26 amplification in the tumor driver SEC62, which has been identified as relevant to the pathogenesis of ovarian cancer. This study was conducted to investigate the role of SEC62 in ovarian malignancies. Patients with ovarian neoplasias (borderline tumors of the ovary and ovarian cancer) who were treated between January 2007 and April 2019 at the Department of Gynecology and Obstetrics, Saarland University Hospital, were included in this retrospective study. SEC62 expression in tumor tissue samples taken during clinical treatment was assessed immunohistochemically, with the calculation of immunoreactivity scores according to Remmele and Stegner, Pathologe, 1987, 8, 138–140. Correlations of SEC62 expression with the TNM stage, histological subtype, tumor entity, and oncological outcomes (progression-free and overall survival) were examined. The sample comprised 167 patients (123 with ovarian cancer and 44 with borderline tumors of the ovary) with a median age of 60 (range, 15–87) years. At the time of diagnosis, 77 (46%) cases were FIGO stage III. All tissue slides showed SEC62 overexpression in tumor cells and no SEC62 expression in other cells. Median immunoreactivity scores were 8 (range, 2–12) for ovarian cancer and 9 (range, 4–12) for borderline tumors of the ovary. Patients with borderline tumors of the ovary as well as patients with ovarian cancer and an immunoreactive score (IRS) ≤ 9 showed an improved overall survival compared to those presenting with an IRS score >9 (p = 0.03). SEC62 seems to be a prognostic biomarker for the overall survival of patients with ovarian malignancies.
Placental treatment with insulin-like growth factor 1 via nanoparticle differentially impacts vascular remodeling factors in guinea pig sub-placenta/decidua
Authors: Davenport Baylea N. , Jones Helen N. , Wilson Rebecca L.
Published: January 2023

Clinically, fetal growth restriction (FGR) is only detectable in later gestation, despite pathophysiological establishment likely earlier in pregnancy. Additionally, there are no effective in utero treatment options for FGR. We have developed a nanoparticle to deliver human insulin-like 1 growth factor (hIGF-1) in a trophoblast-specific manner which results in increased expression of hIGF-1. IGF-1 signaling in the placenta regulates multiple developmental processes including trophoblast invasion and maternal vascular remodeling, both of which can be diminished in the FGR placenta. We aimed to determine the effects of short-term hIGF-1 nanoparticle treatment on sub-placenta/decidua trophoblast signaling mechanisms in FGR and under normal growth conditions. Using the guinea pig maternal nutrient restriction (MNR) model of FGR, ultrasound-guided, intra-placenta injections of hIGF-1 nanoparticle were performed at gestational day 30–33, and dams sacrificed 5 days later. Sub-placenta/decidua tissue was separated from placenta for further analyses. Western blot was used to analyze protein expression of ERK/AKT/mTOR signaling proteins (phospho-Erk (pERK), phospho-Akt (pAKT), raptor, rictor and deptor). qPCR was used to analyze gene expression of vascular/remodeling factors [vascular endothelial growth factor (Vegf), placenta growth factor (Pgf), platelet-derived growth factor (Pdgf)) and tight junction/adhesion proteins (claudin 5 (Cldn5), p-glycoprotein (Abcb1), occludin (Ocln) and tight junction protein 1 (Zo1)]. MNR reduced expression of pERK, PdgfB and Cldn5, and increased expression of Ocln and Zo1 in the sub-placenta/decidua. In MNR + hIGF1 nanoparticle sub-placenta/decidua, expression of PdgfB, Ocln and Zo1 was normalized, whilst pAkt, VegfB, Vegf receptor 1 and PdgfB receptor were increased compared to MNR. In contrast, hIGF-1 nanoparticle treatment of normal placentas reduced expression of pERK, raptor and increased expression of the mTOR inhibitor deptor. This was associated with reduced expression of VegfA, Plgf, and PdgfB. Here we have shown that the impact of hIGF-1 nanoparticle treatment is dependent on pregnancy environment. Under MNR/FGR, hIGF-1 nanoparticle treatment triggers increased expression of growth factors and normalization of EMT factors. However, under normal conditions, the response of the placenta is to decrease AKT/mTOR signaling and growth factor expression to achieve homeostasis.
Characteristics of the postural stability of the lower limb in different visual states of undergraduate students with moderate myopia
Authors: Huang Zhaoxin , Xiao Xiaofei
Published: January 2023

Objective: To explore the characteristics of lower limb postural stability in undergraduates with moderate myopia in three different visual states.

Methods: Twenty male undergraduate students were recruited to complete respectively the static and dynamic postural stability tests under eyes-closed, myopia (taking off their glasses immediately) and corrected vision conditions. A three-dimensional force platform (Bertec, United States) was used to test static postural stability, which calculated the total path length of the Center of Pressure (COP), path length in the antero-posterior (A/P) and medio-lateral (M/L) directions, COP area, SampleEntropy (SampEn), and low-, medium-, and high-frequency spectrum energies. Dynamic postural stability was tested using the Y-balance test, and the Y-balance test scores were calculated. The Vicon three-dimensional motion capture system (Oxford, United Kingdom) measured the maximum flexion angles of the ankle, knee, and hip joints. The electromyography (EMG) root mean square (RMS) and integral EMG (iEMG) of the tibialis anterior and lateral gastrocnemius of the lower extremity were simultaneously measured using wireless surface electromyography (Noraxon, United States).

Results: The SampEn-A/P and SampEn-M/L of corrected vision state higher than myopia and eyes-closed states, and myopia state larger than eyes-closed state (χ2 = 51.631, p < .001). The original and standard scores of the anterior, postero-medial and comprehensive values of the three visual states had significant differences (F = 32.125, p < .001). The original and standard values of postero-lateral corrected vision and myopia were larger than those of eyes-closed states (F = 37.972, p < .001). The maximum flexion angles of the ankle and knee joints were in the following order: corrected vision, myopia and eyes-closed (F = 10.93, p < .001). The iEMG and RMS had significant differences in the three different states (χ2 = 12.700, p < .001) in the all directions of YBT.

Conclusion: Compared with corrected vision, the stability of static posture in the state of myopia was decreased, and the postural regularity was more regular. The dynamic postural stability in the state of myopia was also lower than that corrected vision, and the activation and work of ankle muscles were also increased.
Epigenetic regulation in premature ovarian failure: A literature review
Authors: Wang Jing , Sun Xiguang , Yang Zongxing , Li Sijie , Wang Yufeng , Ren Ruoxue , Liu Ziyue , Yu Dehai
Published: January 2023

Premature ovarian failure (POF), or premature ovarian insufficiency (POI), is a multifactorial and heterogeneous disease characterized by amenorrhea, decreased estrogen levels and increased female gonadotropin levels. The incidence of POF is increasing annually, and POF has become one of the main causes of infertility in women of childbearing age. The etiology and pathogenesis of POF are complex and have not yet been clearly elucidated. In addition to genetic factors, an increasing number of studies have revealed that epigenetic changes play an important role in the occurrence and development of POF. However, we found that very few papers have summarized epigenetic variations in POF, and a systematic analysis of this topic is therefore necessary. In this article, by reviewing and analyzing the most relevant literature in this research field, we expound on the relationship between DNA methylation, histone modification and non-coding RNA expression and the development of POF. We also analyzed how environmental factors affect POF through epigenetic modulation. Additionally, we discuss potential epigenetic biomarkers and epigenetic treatment targets for POF. We anticipate that our paper may provide new therapeutic clues for improving ovarian function and maintaining fertility in POF patients.
Comprehensive identification and analysis of circRNAs during hickory (Carya cathayensis Sarg.) flower bud differentiation
Authors: Jin Hongmiao , Yang Zhengfu , Luo Jia , Li Caiyun , Chen Junhao , Lim Kean-Jin , Wang Zhengjia
Published: January 2023

Flower bud differentiation represents a crucial transition from vegetative growth to reproductive development. Carya cathayensis (hickory) is an important economic species in China, with a long juvenile period that hinders its commercial development. In recent years, circular RNAs (circRNAs) have been widely studied and identified as sponges for miRNA regulation of mRNA expression. However, little is known regarding the role of circRNAs in flower buds. In this study, we sequenced circRNAs at three developmental stages (undifferentiated, differentiating, and fully differentiated) in both female and male buds. A total of 6,931 circRNAs were identified in the three developmental stages and 4,449 and 2,209 circRNAs were differentially expressed in female and male buds, respectively. Gene ontology demonstrated that many circRNA host genes participated in various processes, for example, cellular and intracellular pH regulation. Function annotation identified 46 differentially expressed circRNAs involved in flowering regulation, with 28 circRNAs found only in female buds, 4 found only in male buds, and 11 found in both female and male buds. A circRNA-miRNA-mRNA network was predicted based on 13 flowering-related circRNAs and their seven putative interacting miRNAs to describe the regulatory mechanism. Our preliminary results demonstrated a potential involvement of circRNA in bud differentiation. They provided a preliminary theoretical basis for how circRNA might participate in flower development in hickory, perhaps in woody plants.
Phenotypic diversity and distinctiveness of the Belltall garlic landrace
Authors: Casals Joan , Rivera Ana , Campo Sonia , Aymerich Ernest , Isern Helena , Fenero Daniel , Garriga Alba , Palou Anna , Monfort Amparo , Howad Werner , Rodríguez Miguel Ángel , Riu Marc , Roig-Villanova Irma
Published: January 2023

Among the Mediterranean horticultural landraces, garlic is one of the crops most threatened by genetic erosion. Due to its sexual sterility and to the incidence of seed-borne diseases, historical varieties have been widely replaced by commercial cultivars. In Catalonia, despite the historical relevance of the crop, solely the Belltall garlic landrace is cultivated for commercial purposes. To assess the genotypic and phenotypic diversity within the Belltall garlic, we evaluated sixteen local accessions and five recognized traditional and modern varieties as controls. Genetic analysis with SSR and InDel markers showed low genetic diversity within the Belltall population, grouping modern and traditional varieties separately. Farmers and consumers were involved in the definition of the landrace ideotype and classified the materials by means of projective mapping. Scant phenotypic diversity was found within the Belltall landrace, which is characterized by its color profile and the small size of bulb and cloves. The Belltall landrace grown outside its area of origin lost the distinctive quality signals that differentiate the landrace from the commercial cultivars (clove appearance), indicating that the high quality of the landrace is under genotype-by-environment effects (i.e. local adaptation). Moreover, the size of the Belltall sowing clove had a strong effect on the harvested bulb size. Our research represents a case study for the description of the variability within garlic landraces and an approach to quantify the phenomenon of local adaptation that currently drives their conservation.
Single-cell transcriptome sequencing atlas of cassava tuberous root
Authors: Song Jinjia , Fan Benji , Shao Xiaodie , Zang Yuwei , Wang Dayong , Min Yi
Published: January 2023

Introduction

Single-cell transcriptome sequencing (ScRNA-seq) has emerged as an effective method for examining cell differentiation and development. In non-model plants, it hasn't been employed very much, especially in sink organs that are abundant in secondary metabolites.

Results

In this study, we sequenced the single-cell transcriptomes at two developmental phases of cassava tuberous roots using the technology known as 10x Genomics (S1, S2). In total, 14,566 cells were grouped into 15 different cell types, primarily based on the marker genes of model plants known to exist. In the pseudotime study, the cell differentiation trajectory was defined, and the difference in gene expression between the two stages on the pseudotime axis was compared. The differentiation process of the vascular tissue and cerebral tissue was identified by the trajectory. We discovered the rare cell type known as the casparian strip via the use of up-regulated genes and pseudotime analysis, and we explained how it differentiates from endodermis. The successful creation of a protoplast isolation technique for organs rich in starch was also described in our study.

Discussion

Together, we created the first high-resolution single-cell transcriptome atlas of cassava tuberous roots, which made significant advancements in our understanding of how these roots differentiate and develop.
Uninterrupted embryonic growth leading to viviparous propagule formation in woody mangrove
Authors: Zhou Xiaoxuan , Weng Yulin , Su Wenyue , Ye Congting , Qu Haidong , Li Qingshun Quinn
Published: January 2023

Vivipary is a rare sexual reproduction phenomenon where embryos germinate directly on the maternal plants. However, it is a common genetic event of woody mangroves in the Rhizophoraceae family. The ecological benefits of vivipary in mangroves include the nurturing of seedlings in harsh coastal and saline environments, but the genetic and molecular mechanisms of vivipary remain unclear. Here we investigate the viviparous embryo development and germination processes in mangrove Kandelia obovata by a transcriptomic approach. Many key biological pathways and functional genes were enriched in different tissues and stages, contributing to vivipary. Reduced production of abscisic acid set a non-dormant condition for the embryo to germinate directly. Genes involved in the metabolism of and response to other phytohormones (gibberellic acid, brassinosteroids, cytokinin, and auxin) are expressed precociously in the axis of non-vivipary stages, thus promoting the embryo to grow through the seed coat. Network analysis of these genes identified the central regulatory roles of LEC1 and FUS3, which maintain embryo identity in Arabidopsis. Moreover, photosynthesis related pathways were significantly up-regulated in viviparous embryos, and substance transporter genes were highly expressed in the seed coat, suggesting a partial self-provision and maternal nursing. We conclude that the viviparous phenomenon is a combinatorial result of precocious loss of dormancy and enhanced germination potential during viviparous seed development. These results shed light on the relationship between seed development and germination, where the continual growth of the embryo replaces a biphasic phenomenon until a mature propagule is established.
N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence
Authors: Rudy Elżbieta , Grabsztunowicz Magda , Arasimowicz-Jelonek Magdalena , Tanwar Umesh Kumar , Maciorowska Julia , Sobieszczuk-Nowicka Ewa
Published: January 2023

Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m6A editing is believed to be a promising strategy. As a reaction to environmental changes, m6A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m6A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m6A modification of RNA in plants seems to be compelling.
Nutrient deficiency effects on root architecture and root-to-shoot ratio in arable crops
Authors: Lopez Gina , Ahmadi Seyed Hamid , Amelung Wulf , Athmann Miriam , Ewert Frank , Gaiser Thomas , Gocke Martina I. , Kautz Timo , Postma Johannes , Rachmilevitch Shimon , Schaaf Gabriel , Schnepf Andrea , Stoschus Alixandrine , Watt Michelle , Yu Peng , Seidel Sabine Julia
Published: January 2023

Plant root traits play a crucial role in resource acquisition and crop performance when soil nutrient availability is low. However, the respective trait responses are complex, particularly at the field scale, and poorly understood due to difficulties in root phenotyping monitoring, inaccurate sampling, and environmental conditions. Here, we conducted a systematic review and meta-analysis of 50 field studies to identify the effects of nitrogen (N), phosphorous (P), or potassium (K) deficiencies on the root systems of common crops. Root length and biomass were generally reduced, while root length per shoot biomass was enhanced under N and P deficiency. Root length decreased by 9% under N deficiency and by 14% under P deficiency, while root biomass was reduced by 7% in N-deficient and by 25% in P-deficient soils. Root length per shoot biomass increased by 33% in N deficient and 51% in P deficient soils. The root-to-shoot ratio was often enhanced (44%) under N-poor conditions, but no consistent response of the root-to-shoot ratio to P-deficiency was found. Only a few K-deficiency studies suited our approach and, in those cases, no differences in morphological traits were reported. We encountered the following drawbacks when performing this analysis: limited number of root traits investigated at field scale, differences in the timing and severity of nutrient deficiencies, missing data (e.g., soil nutrient status and time of stress), and the impact of other conditions in the field. Nevertheless, our analysis indicates that, in general, nutrient deficiencies increased the root-length-to-shoot-biomass ratios of crops, with impacts decreasing in the order deficient P > deficient N > deficient K. Our review resolved inconsistencies that were often found in the individual field experiments, and led to a better understanding of the physiological mechanisms underlying root plasticity in fields with low nutrient availability.
A pleiotropic QTL increased economic water use efficiency in bread wheat (Triticum aestivum L.)
Authors: Hui Jian , Bai Haibo , Lyu Xuelian , Ma Sishuang , Chen Xiaojun , Li Shuhua
Published: January 2023

Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2BNingchun 27, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2BNingchun 4 tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.
The effects of ectomycorrhizal and saprotropic fungi on soil nitrogen mineralization differ from those of arbuscular and ericoid mycorrhizal fungi on the eastern Qinghai-Tibetan Plateau
Authors: Zhang Miaomiao , Liu Shun , Cao Xiangwen , Chen Miao , Chen Jian , Xu Gexi , Shi Zuomin
Published: January 2023

Interactions between soil fungi and soil environmental factors regulate soil nitrogen (N) mineralization rates on the eastern Qinghai-Tibetan Plateau. Some studies have also illuminated differences in soil N mineralization rate based on different mycorrhizal forests, but the associated effect of soil fungal functional guilds and soil environmental factors underlying this process are not well-understood. Three primary forests respectively dominated by Abies fargesii var. faxoniana (ectomycorrhizal, EcM), Cupressus chengiana (arbuscular mycorrhizal, AM) and Rhododendron phaeochrysum (ericoid mycorrhizal, ErM) trees were selected in this area. Meanwhile, soil net N mineralization rate, soil fungal composition and soil enzyme activity among these three mycorrhizal forests were studied. Our results showed that there were significant differences in the seasonal variation of soil net N mineralization rates among three mycorrhizal forests. Soil net N mineralization rate in the AM forest was faster. EcM fungi and saprotroph are the main functional guilds in these three mycorrhizal forests. Meanwhile, the relative abundances of soil fungal functional guilds, soil temperature and soil peroxidase activity could explain 85.0% in the difference of soil net ammonification rate among three mycorrhizal forests. In addition, soil temperature, soil water-filled pore space and soil ammonium content play a central role in controlling the differing soil net nitrification rate among three mycorrhizal forests. Our results suggest differences in soil net mineralization among different mycorrhizal forest types are driven mainly by soil net ammonification. Soil fungal functional guilds and temperature regulate the rate of soil net ammonification by modulating soil peroxidase activity.
Identification of quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight in soybean [Glycine max (L.) Merr.]
Authors: Kumar Rahul , Saini Manisha , Taku Meniari , Debbarma Pulak , Mahto Rohit Kumar , Ramlal Ayyagari , Sharma Deepshikha , Rajendran Ambika , Pandey Renu , Gaikwad Kishor , Lal S. K. , Talukdar Akshay
Published: January 2023

Seed size and shape are important traits determining yield and quality in soybean. Seed size and shape are also desirable for specialty soy foods like tofu, natto, miso, and edamame. In order to find stable quantitative trait loci (QTLs) and candidate genes for seed shape and 100-seed weight, the current study used vegetable type and seed soybean-derived F2 and F2:3 mapping populations. A total of 42 QTLs were mapped, which were dispersed across 13 chromosomes. Of these, seven were determined to be stable QTLs and five of them were major QTLs, namely qSL-10-1, qSW-4-1, qSV-4-1, qSLW-10-1, and qSLH-10-1. Thirteen of the 42 QTLs detected in the current study were found at known loci, while the remaining 29 were discovered for the first time. Out of these 29 novel QTLs, 17 were major QTLs. Based on Protein Analysis Through Evolutionary Relationships (PANTHER), gene annotation information, and literature search, 66 genes within seven stable QTLs were predicted to be possible candidate genes that might regulate seed shape and seed weight in soybean. The current study identified the key candidate genes and quantitative trait loci (QTLs) controlling soybean seed shape and weight, and these results will be very helpful in marker-assisted breeding for developing soybean varieties with improved seed weight and desired seed shape.
A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea
Authors: Xu Xiuming , Shen Yingjia , Zhang Yuchen , Li Qianying , Wang Wenqing , Chen Luzhen , Chen Guangcheng , Ng Wei Lun , Islam Md Nazrul , Punnarak Porntep , Zheng Hailei , Zhu Xueyi
Published: January 2023

In 2003, Kandelia obovata was identified as a new mangrove species differentiated from Kandelia candel. However, little is known about their chloroplast (cp) genome differences and their possible ecological significance. In this study, 25 whole cp genomes, with seven samples of K. candel from Malaysia, Thailand, and Bangladesh and 18 samples of K. obovata from China, were sequenced for comparison. The cp genomes of both species encoded 128 genes, namely 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes, but the cp genome size of K. obovata was ~2 kb larger than that of K. candle due to the presence of more and longer repeat sequences. Of these, tandem repeats and simple sequence repeats exhibited great differences. Principal component analysis based on indels, and phylogenetic tree analyses constructed with homologous protein genes from the single-copy genes, as well as 38 homologous pair genes among 13 mangrove species, gave strong support to the separation of the two species within the Kandelia genus. Homologous genes ndhD and atpA showed intraspecific consistency and interspecific differences. Molecular dynamics simulations of their corresponding proteins, NAD(P)H dehydrogenase chain 4 (NDH-D) and ATP synthase subunit alpha (ATP-A), predicted them to be significantly different in the functions of photosynthetic electron transport and ATP generation in the two species. These results suggest that the energy requirement was a pivotal factor in their adaptation to differential environments geographically separated by the South China Sea. Our results also provide clues for future research on their physiological and molecular adaptation mechanisms to light and temperature.
Biocontrol of Meloidogyne spp. in Solanum lycopersicum using a dual combination of Bacillus strains
Authors: Díaz-Manzano Fernando Evaristo , Amora Deisy X. , Martínez-Gómez Ángela , Moelbak Lars , Escobar Carolina
Published: January 2023

Root-knot nematodes (RKNs, Meloidogyne spp.) are obligate plant parasites that constitute a significant pest for agriculture worldwide. They penetrate the plant roots, reducing the uptake of water and nutrients, causing a significant impact on crop yield. One alternative on focus now for nematode management is biological control. Rhizobacteria within the Bacillus genus show multiple modes of action against plant-parasitic nematodes (PPNs) that can act alone or in combination. In this context, we evaluated a dual-strain bacteria combination (B. paralicheniformi FMCH001 and B. subtilis FMCH002) to reduce nematode infection in tomato plants. We evaluated mortality of larvae from Meloidogyne javanica in vitro, as well as eggs hatching after the treatment. Atraction, penetration, establishment, and reproduction assays in vitro or in pots in tomato plants infected with M. javanica and treated/ untreated with the dual-strain bacteria combination were also performed. Additionally, morphometric parameters comparing giant cells size from galls of treated and untreated plants by using confocal microscopy were also measured. The results showed that this combination of strains has nematicidal properties in the pre-infection phase by decreasing the egg-hatching, juvenile survival, and attractiveness to the roots. Furthermore, nematode establishment, gall formation, and, remarkably, giant cell development was severely impaired after the bacterial treatment, suggesting interference with morphogenetic mechanisms induced by the nematode during GCs development within the plant. Nematode reproduction in tomato plants was reduced independently of the application mode in soil, before or after bacterial treatment. The dual-strain combination was also effective against other PPNs (i.e. Pratylenchus spp.) and in different crops (soybean). Therefore, combining B. paralicheniformis FMCH001 and B. subtilis FMCH002 is an efficient agent for the biological control of Meloidogyne spp. by interfering with different stages of the nematode cycle as a result of multiple modes of action.
Comparative expression analysis in three Brassicaceae species revealed compensatory changes of the underlying gene regulatory network
Authors: Pietsch Jessica , Deneer Anna , Fleck Christian , Hülskamp Martin
Published: January 2023

Trichomes are regularly distributed on the leaves of Arabidopsis thaliana. The gene regulatory network underlying trichome patterning involves more than 15 genes. However, it is possible to explain patterning with only five components. This raises the questions about the function of the additional components and the identification of the core network. In this study, we compare the relative expression of all patterning genes in A. thaliana, A. alpina and C. hirsuta by qPCR analysis and use mathematical modelling to determine the relative importance of patterning genes. As the involved proteins exhibit evolutionary conserved differential complex formation, we reasoned that the genes belonging to the core network should exhibit similar expression ratios in different species. However, we find several striking differences of the relative expression levels. Our analysis of how the network can cope with such differences revealed relevant parameters that we use to predict the relevant molecular adaptations in the three species.
Response of soil bacterial community to alpine wetland degradation in arid Central Asia
Authors: Abulaizi Maidinuer , Chen Mo , Yang Zailei , Hu Yang , Zhu Xinping , Jia Hongtao
Published: January 2023

A large number of studies have reported the importance of bacterial communities in ecosystems and their responses to soil degradation, but the response mechanism in arid alpine wetlands is still unclear. Here, the non-degraded (ND), slightly degraded (SD), and heavily degraded (HD) regions of Bayinbuluk alpine wetland were used to analyzed the diversity, structure and function of bacterial communities in three degraded wetlands using 16S rRNA. The results showed that with the increase of degradation degree, the content of soil moisture (SM) and available nitrogen (AN) decreased significantly, plant species richness and total vegetation coverage decreased significantly, Cyperaceae (Cy) coverage decreased significantly, and Gramineae (Gr) coverage increased significantly. Degradation did not significantly affect the diversity of the bacterial community, but changed the relative abundance of the community structure. Degradation significantly increased the relative abundance of Actinobacteria (ND: 3.95%; SD: 7.27%; HD: 23.97%) and Gemmatimonadetes (ND: 0.39%; SD: 2.17%; HD: 10.78%), while significantly reducing the relative abundance of Chloroflexi (ND: 13.92%; SD: 8.68%; HD: 3.55%) and Nitrospirae (ND: 6.18%; SD: 0.45%; HD: 2.32%). Degradation significantly reduced some of the potential functions in the bacterial community associated with the carbon (C), nitrogen (N) and sulfur (S) cycles, such as hydrocarbon degradation (ND: 25.00%; SD: 1.74%; HD: 6.59%), such as aerobic ammonia oxidation (ND: 5.96%; SD: 22.82%; HD: 4.55%), and dark sulfide oxidation (ND: 32.68%; SD: 0.37%; HD: 0.28%). Distance-based redundancy analysis (db-RDA) results showed that the bacteria community was significantly related to the TC (total carbon) and Gr (P < 0.05). The results of linear discriminant analysis effect size (LEfSe) analysis indicate significant enrichments of Alphaproteobacteria and Sphingomonas in the HD area. The vegetation communities and soil nutrients changed significantly with increasing soil degradation levels, and Sphingomonas could be used as potential biomarker of degraded alpine wetlands.
Development of the Reading Comprehension Strategies Questionnaire (RCSQ) for late elementary school students
Authors: Bogaert Rielke , Merchie Emmelien , Rosseel Yves , Van Keer Hilde
Published: January 2023

Late elementary education constitutes a critical period in the development of reading comprehension strategies, a key competence in today’s society. However, to date, appropriate measurements to map late elementary students’ reading strategies are lacking. In this respect, the present article first describes the development and validation of the 26-item reading comprehension strategies questionnaire (RCSQ). To this aim, exploratory (sample 1: n = 1585 students) and confirmatory (sample 2: n = 1585 students) factor analyses were conducted. These analyses resulted in the RCSQ, consisting of five subscales: (1) overt cognitive reading strategies, (2) covert cognitive reading strategies, (3) monitoring, and (4) evaluating. For non-native and bilingual students, a fifth subscale ‘using home language in view of comprehending texts’ emerged. Second, multilevel analyses were performed to explore individual differences in late elementary students’ reading comprehension strategy use. Implications for practice and future research are discussed.