bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis and comparisons of gene expression changes in patient- derived neurons from ROHHAD, CCHS, and PWS
Authors: Victor A. Kaitlyn , Hedgecock Tayler , Donaldson Martin , Johnson Daniel , Rand Casey M. , Weese-Mayer Debra E. , Reiter Lawrence T.
Published: May 2023

Background

Rapid-onset obesity with hypothalamic dysfunction, hypoventilation, and autonomic dysregulation (ROHHAD) syndrome is an ultra-rare neurocristopathy with no known genetic or environmental etiology. Rapid-onset obesity over a 3–12 month period with onset between ages 1.5–7 years of age is followed by an unfolding constellation of symptoms including severe hypoventilation that can lead to cardiorespiratory arrest in previously healthy children if not identified early and intervention provided. Congenital Central Hypoventilation syndrome (CCHS) and Prader-Willi syndrome (PWS) have overlapping clinical features with ROHHAD and known genetic etiologies. Here we compare patient neurons from three pediatric syndromes (ROHHAD, CCHS, and PWS) and neurotypical control subjects to identify molecular overlap that may explain the clinical similarities.

Methods

Dental pulp stem cells (DPSC) from neurotypical control, ROHHAD, and CCHS subjects were differentiated into neuronal cultures for RNA sequencing (RNAseq). Differential expression analysis identified transcripts variably regulated in ROHHAD and CCHS vs. neurotypical control neurons. In addition, we used previously published PWS transcript data to compare both groups to PWS patient-derived DPSC neurons. Enrichment analysis was performed on RNAseq data and downstream protein expression analysis was performed using immunoblotting.

Results

We identified three transcripts differentially regulated in all three syndromes vs. neurotypical control subjects. Gene ontology analysis on the ROHHAD dataset revealed enrichments in several molecular pathways that may contribute to disease pathology. Importantly, we found 58 transcripts differentially expressed in both ROHHAD and CCHS patient neurons vs. control neurons. Finally, we validated transcript level changes in expression of ADORA2A, a gene encoding for an adenosine receptor, at the protein level in CCHS neurons and found variable, although significant, changes in ROHHAD neurons.

Conclusions

The molecular overlap between CCHS and ROHHAD neurons suggests that the clinical phenotypes in these syndromes likely arise from or affect similar transcriptional pathways. Further, gene ontology analysis identified enrichments in ATPase transmembrane transporters, acetylglucosaminyltransferases, and phagocytic vesicle membrane proteins that may contribute to the ROHHAD phenotype. Finally, our data imply that the rapid-onset obesity seen in both ROHHAD and PWS likely arise from different molecular mechanisms. The data presented here describes important preliminary findings that warrant further validation.
CircRNA-miRNA-VEGFA: an important pathway to regulate cancer pathogenesis
Authors: Zhang Lei , Zhang Yuan , Li Xin , Gao Huijuan , Chen Xiatian , Li Peifeng
Published: May 2023

Cancers, especially malignant tumors, contribute to high global mortality rates, resulting in great economic burden to society. Many factors are associated with cancer pathogenesis, including vascular endothelial growth factor-A (VEGFA) and circular RNAs (circRNA). VEGFA is a pivotal regulator of vascular development such as angiogenesis, which is an important process in cancer development. CircRNAs have covalently closed structures, making them highly stable. CircRNAs are widely distributed and participate in many physiological and pathological processes, including modulating cancer pathogenesis. CircRNAs act as transcriptional regulators of parental genes, microRNA (miRNA)/RNA binding protein (RBP) sponges, protein templates. CircRNAs mainly function via binding to miRNAs. CircRNAs have been shown to influence different diseases such as coronary artery diseases and cancers by regulating VEGFA levels via binding to miRNAs. In this paper, we explored the origin and functional pathways of VEGFA, reviewed the current understanding of circRNA properties and action mechanisms, and summarized the role of circRNAs in regulating VEGFA during cancer pathogenesis.
Mitochondrial dysfunction-targeting therapeutics of natural products in Parkinson’s disease
Authors: He Ting , Lin Xiaoyan , Su Anping , Zhang Yujie , Xing Zhichao , Mi Li , Wei Tao , Li Zhihui , Wu Wenshuang
Published: May 2023

Parkinson’s disease (PD), the second most common neurodegenerative disease worldwide, often occurs in middle-aged and elderly individuals. The pathogenesis of PD is complex and includes mitochondrial dysfunction, and oxidative stress. Recently, natural products with multiple structures and their bioactive components have become one of the most important resources for small molecule PD drug research targeting mitochondrial dysfunction. Multiple lines of studies have proven that natural products display ameliorative benefits in PD treatment by regulating mitochondrial dysfunction. Therefore, a comprehensive search of recent published articles between 2012 and 2022 in PubMed, Web of Science, Elesvier, Wliey and Springer was carried out, focusing on original publications related to natural products against PD by restoring mitochondrial dysfunction. This paper presented the mechanisms of various kinds of natural products on PD-related mitochondrial dysfunction regulation and provided evidence that natural products are promising to be developed as drugs for PD therapeutics.
In vitro evaluation of the neuroprotective potential of Olea dioica against Aβ peptide-induced toxicity in human neuroblastoma SH-SY5Y cells
Authors: Kenchappa Pratap G. , Karthik Yalpi , Vijendra Poornima D. , Hallur Raghavendra L. S. , Khandagale Ajay S. , Pandurangan Ashok K. , Jayanna Sathisha G. , Alshehri Mohammed Ali , Alasmari Abdulrahman , Sayed Samy , Shantaram Manjula , Mushtaq Muntazir
Published: May 2023

Alzheimer’s disease (AD) is a type of neurodegenerative disease, associated with the hastening of ROS, acetylcholinesterase (AChE) activity, and amyloid β peptides plaques in the brain. The limitations and side effects of existing synthetic drugs incline toward natural sources. In the present communication active principles of methanolic extract of Olea dioica Roxb, leaves are explored as an antioxidant, AChE inhibitor, and anti-amyloidogenic. Furthermore, neuroprotection against the amyloid beta-peptide has been studied. The bioactive principles were identified by GC-MS and LC-MS and further subjected to antioxidant (DPPH and FRAP) and neuroprotection (AChE inhibition, ThT binding, and MTT assay, DCFH-DA and lipid peroxidation (LPO) assay using neuroblastoma (SHSY-5Y) cell lines) assays. Methanolic extract of O. dioica Roxb, leaves was found to contain polyphenols and flavonoids. In vitro assays exhibited potential antioxidant and anti-AChE (˃50%) activities. ThT binding assay indicated protection against amyloid-beta aggregation. MTT assay, Aβ1-40 (10 µM) with extract increase the cell viability (˃50%) and showed significant cytotoxicity to SHSY-5Y cells. ROS level (˃25%) significantly decreased in the Aβ1-40 (10 µM) + extract (15 and 20 μM/mL) and LPO assay (˃50%) suggesting prevention of cell damage. Results advocate that O. dioica leaves are a good source of antioxidants, anti-AChE, and anti-amyloidogenic compounds which may be further evaluated as a natural medicine for the treatment of AD.
Traditional Chinese medicine for heart failure with preserved ejection fraction: clinical evidence and potential mechanisms
Authors: Fan Yujian , Yang Zhihua , Wang Lin , Liu Yangxi , Song Yulong , Liu Yu , Wang Xianliang , Zhao Zhiqiang , Mao Jingyuan
Published: May 2023

Heart failure with preserved ejection fraction accounts for a large proportion of heart failure, and it is closely related to a high hospitalization rate and high mortality rate of cardiovascular disease. Although the methods and means of modern medical treatment of HFpEF are becoming increasingly abundant, they still cannot fully meet the clinical needs of HFpEF patients. Traditional Chinese medicine is an important complementary strategy for the treatment of diseases in modern medicine, and it has been widely used in clinical research on HFpEF in recent years. This article reviews the current situation of HFpEF management, the evolution of guidelines, the clinical evidence and the mechanism of TCM in the treatment of HFpEF. The purpose of this study is to explore the application of TCM for HFpEF, to further improve the clinical symptoms and prognosis of patients and to provide a reference for the diagnosis and treatment of the disease.
Antidepressant-like activity of a brain penetrant HCN channel inhibitor in mice
Authors: Pinares-Garcia Paulo , Spyrou James , McKenzie Chaseley E. , Forster Ian C. , Soh Ming S. , Mohamed Syazwan Erlina , Atif Mohammed , Reid Christopher A.
Published: May 2023

Changes in Hyperpolarization-Activated Cyclic Nucleotide-Gated (HCN) channel function have been linked to depressive-like traits, making them potential drug targets. However, there is currently no peer-reviewed data supporting the use of a small molecule modulator of HCN channels in depression treatment. Org 34167, a benzisoxazole derivative, has been patented for the treatment of depression and progressed to Phase I trials. In the current study, we analysed the biophysical effects of Org 34167 on HCN channels in stably transfected human embryonic kidney 293 (HEK293) cells and mouse layer V neurons using patch-clamp electrophysiology, and we utilised three high-throughput screens for depressive-like behaviour to assess the activity of Org 34167 in mice. The impact of Org 34167 on locomotion and coordination were measured by performing rotarod and ledged beam tests. Org 34167 is a broad-spectrum inhibitor of HCN channels, slowing activation and causing a hyperpolarising shift in voltage-dependence of activation. It also reduced Ih-mediated sag in mouse neurons. Org 34167 (0.5 mg/kg) reduced marble burying and increased the time spent mobile in the Porsolt swim and tail suspension tests in both male and female BALB/c mice, suggesting reduced depressive-like behaviour. Although no adverse effects were seen at 0.5 mg/kg, an increase in dose to 1 mg/kg resulted in visible tremors and impaired locomotion and coordination. These data support the premise that HCN channels are valid targets for anti-depressive drugs albeit with a narrow therapeutic index. Drugs with higher HCN subtype selectivity are needed to establish if a wider therapeutic window can be obtained.
Diagnostic and therapeutic value of P2Y12R in epilepsy
Authors: Chen Xiang , Wang Qi , Yang Jie , Zhang Li , Liu Ting-Ting , Liu Jun , Deng Bin-Lu , Liu Jie
Published: May 2023

There lacks biomarkers in current epilepsy diagnosis, and epilepsy is thus exposed to inadequate treatment, making it necessarily important to conduct search on new biomarkers and drug targets. The P2Y12 receptor is primarily expressed on microglia in the central nervous system, and acts as intrinsic immune cells in the central nervous system mediating neuroinflammation. In previous studies, P2Y12R in epilepsy has been found capable of controlling neuroinflammation and regulating neurogenesis as well as immature neuronal projections, and its expression is altered. P2Y12R is involved in microglia inhibition of neuronal activity and timely termination of seizures in acute seizures. In status epilepticus, the failure of P2Y12R in the process of “brake buffering” may not terminate the neuronal hyperexcitability timely. In chronic epilepsy, neuroinflammation causes seizures, which can in turn induce neuroinflammation, while on the other hand, neuroinflammation leads to neurogenesis, thereby causing abnormal neuronal discharges that give rise to seizures. In this case, targeting P2Y12R may be a novel strategy for the treatment of epilepsy. The detection of P2Y12R and its expression changes can contribute to the diagnosis of epilepsy. Meanwhile, the P2Y12R single-nucleotide polymorphism is associated with epilepsy susceptibility and endowed with the potential to individualize epilepsy diagnosis. To this end, functions of P2Y12R in the central nervous system were hereby reviewed, the effects of P2Y12R in epilepsy were explored, and the potential of P2Y12R in the diagnosis and treatment of epilepsy was further demonstrated.
Modeling semiconducting silicene nanostrips: electronics and THz plasmons
Authors: Tene Talia , Guevara Marco , Borja Myrian , Mendoza Salazar María José , Palacios Robalino María de Lourdes , Vacacela Gomez Cristian , Bellucci Stefano
Published: May 2023

Silicene nanostrips (SiNSs) have garnered significant attention due to their remarkable physical properties, making them an ideal candidate for numerous electronics and plasmonics applications. Their compatibility with current semiconductor technology further enhances their potential. This study aims to investigate the electronic and plasmonic properties of SiNSs with a minimum width of 100 nm using a semi-analytical model that utilizes the carrier velocity of silicene. The carrier velocity was calculated using density functional computations and refined through the GW approximation. Our results reveal that SiNSs with widths ranging from 100 to 500 nm exhibit small bandgaps within the range of a few meV, specifically ranging from 30 to 6 meV, respectively. Furthermore, all the nanostrips analyzed in this study exhibit a q-like plasmon dispersion within the THz regime (≤ 35 THz). By varying the experimental setup or the geometric factors of the nanostrips, the associated plasmon THz frequency can be manipulated, resulting in an increase or decrease in frequency or a shift to larger momentum values. Our study serves as a fundamental starting point and a source of inspiration for future experiments, providing a foundation for confirming the results presented in this study.
Heliknoton in a film of cubic chiral magnet
Authors: Kuchkin Vladyslav M. , Kiselev Nikolai S. , Rybakov Filipp N. , Lobanov Igor S. , Blügel Stefan , Uzdin Valery M.
Published: May 2023

Cubic chiral magnets exhibit a remarkable diversity of two-dimensional topological magnetic textures, including skyrmions. However, the experimental confirmation of topological states localized in all three spatial dimensions remains challenging. In this paper, we investigate a three-dimensional topological state called a heliknoton, which is a hopfion embedded into a helix or conic background. We explore the range of parameters at which the heliknoton can be stabilized under realistic conditions using micromagnetic modeling, harmonic transition state theory, and stochastic spin dynamics simulations. We present theoretical Lorentz TEM images of the heliknoton, which can be used for experimental comparison. Additionally, we discuss the stability of the heliknoton at finite temperatures and the mechanism of its collapse. Our study offers a pathway for future experimental investigations of three-dimensional topological solitons in magnetic crystals.
Understanding development of jugular bulb stenosis in vein of galen malformations: identifying metrics of complex flow dynamics in the cerebral venous vasculature of infants
Authors: Hadad Sara , Rangwala Shivani D. , Stout Jeffrey N. , Mut Fernando , Orbach Darren B. , Cebral Juan R. , See Alfred P.
Published: May 2023

Introduction: Computational fluid dynamics (CFD) assess biological systems based on specific boundary conditions. We propose modeling more advanced hemodynamic metrics, such as core line length (CL) and critical points which characterize complexity of flow in the context of cerebral vasculature, and specifically cerebral veins during the physiologically evolving early neonatal state of vein of Galen malformations (VOGM). CFD has not been applied to the study of arteriovenous shunting in Vein of Galen Malformations but could help illustrate the pathophysiology of this malformation.

Methods: Three neonatal patients with VOGM at Boston Children’s Hospital met inclusion criteria for this study. Structural MRI data was segmented to generate a mesh of the VOGM and venous outflow. Boundary condition flow velocity was derived from PC-MR sequences with arterial and venous dual velocity encoding. The mesh and boundary conditions were applied to model the cerebral venous flow. We computed flow variables including mean wall shear stress (WSSmean), mean OSI, CL, and the mean number of critical points (nCrPointsmean) for each patient specific model. A critical point is defined as the location where the shear stress vector field is zero (stationary point) and can be used to describe complexity of flow.

Results: The division of flow into the left and right venous outflow was comparable between PC-MR and CFD modeling. A high complexity recirculating flow pattern observed on PC-MR was also identified on CFD modeling. Regions of similar WSSmean and OSImean (<1.3 fold) in the left and right venous outflow channels of a single patient have several-fold magnitude difference in higher order hemodynamic metrics (> 3.3 fold CL, > 1.7 fold nCrPointsmean). Specifically, the side which developed JBS in each model had greater nCrPointsmean compared to the jugular bulb with no stenosis (VOGM1: 4.49 vs. 2.53, VOGM2: 1.94 vs. 0, VOGM3: 1 vs. 0). Biologically, these regions had subsequently divergent development, with increased complexity of flow associating with venous stenosis.

Discussion: Advanced metrics of flow complexity identified in computational models may reflect observed flow phenomena not fully characterized by primary or secondary hemodynamic parameters. These advanced metrics may indicate physiological states that impact development of jugular bulb stenosis in VOGM.
The role of the microcirculation and integrative cardiovascular physiology in the pathogenesis of ICU-acquired weakness
Authors: Mendelson Asher A. , Erickson Dustin , Villar Rodrigo
Published: May 2023

Skeletal muscle dysfunction after critical illness, defined as ICU-acquired weakness (ICU-AW), is a complex and multifactorial syndrome that contributes significantly to long-term morbidity and reduced quality of life for ICU survivors and caregivers. Historically, research in this field has focused on pathological changes within the muscle itself, without much consideration for their in vivo physiological environment. Skeletal muscle has the widest range of oxygen metabolism of any organ, and regulation of oxygen supply with tissue demand is a fundamental requirement for locomotion and muscle function. During exercise, this process is exquisitely controlled and coordinated by the cardiovascular, respiratory, and autonomic systems, and also within the skeletal muscle microcirculation and mitochondria as the terminal site of oxygen exchange and utilization. This review highlights the potential contribution of the microcirculation and integrative cardiovascular physiology to the pathogenesis of ICU-AW. An overview of skeletal muscle microvascular structure and function is provided, as well as our understanding of microvascular dysfunction during the acute phase of critical illness; whether microvascular dysfunction persists after ICU discharge is currently not known. Molecular mechanisms that regulate crosstalk between endothelial cells and myocytes are discussed, including the role of the microcirculation in skeletal muscle atrophy, oxidative stress, and satellite cell biology. The concept of integrated control of oxygen delivery and utilization during exercise is introduced, with evidence of physiological dysfunction throughout the oxygen delivery pathway - from mouth to mitochondria - causing reduced exercise capacity in patients with chronic disease (e.g., heart failure, COPD). We suggest that objective and perceived weakness after critical illness represents a physiological failure of oxygen supply-demand matching - both globally throughout the body and locally within skeletal muscle. Lastly, we highlight the value of standardized cardiopulmonary exercise testing protocols for evaluating fitness in ICU survivors, and the application of near-infrared spectroscopy for directly measuring skeletal muscle oxygenation, representing potential advancements in ICU-AW research and rehabilitation.
DynamicSleepNet: a multi-exit neural network with adaptive inference time for sleep stage classification
Authors: Wenjian Wang , Qian Xiao , Jun Xue , Zhikun Hu
Published: May 2023

Sleep is an essential human physiological behavior, and the quality of sleep directly affects a person’s physical and mental state. In clinical medicine, sleep stage is an important basis for doctors to diagnose and treat sleep disorders. The traditional method of classifying sleep stages requires sleep experts to classify them manually, and the whole process is time-consuming and laborious. In recent years, with the help of deep learning, automatic sleep stage classification has made great progress, especially networks using multi-modal electrophysiological signals, which have greatly improved in terms of accuracy. However, we found that the existing multimodal networks have a large number of redundant calculations in the process of using multiple electrophysiological signals, and the networks become heavier due to the use of multiple signals, and difficult to be used in small devices. To solve these two problems, this paper proposes DynamicSleepNet, a network that can maximize the use of multiple electrophysiological signals and can dynamically adjust between accuracy and efficiency. DynamicSleepNet consists of three effective feature extraction modules (EFEMs) and three classifier modules, each EFEM is connected to a classifier. Each EFEM is able to extract signal features while making the effective features more prominent and the invalid features are suppressed. The samples processed by the EFEM are given to the corresponding classifier for classification, and if the classifier considers the uncertainty of the sample to be below the threshold we set, the sample can be output early without going through the whole network. We validated our model on four datasets. The results show that the highest accuracy of our model outperforms all baselines. With accuracy close to baselines, our model is faster than the baselines by a factor of several to several tens, and the number of parameters of the model is lower or close. The implementation code is available at: https://github.com/Quinella7291/A-Multi-exit-Neural-Network-with-Adaptive-Inference-Time-for-Sleep-Stage-Classification/.
Ultrasonic evaluation of metoclopramide’s effect on gastric motility in emergency trauma patients
Authors: Lin Huan , He Jing-Jing , Cai Zhi-Shi , Lu Zhi-Wei , Lin Zhi-Jian , Lin Xian-Zhong , Huang Qiao-Wen
Published: May 2023

Objective: The present study aimed to use bedside ultrasound to evaluate the effects of metoclopramide on gastric motility in patients being treated for trauma in the emergency department.

Methods: Fifty patients underwent an ultrasound immediately after attending the emergency department of Zhang Zhou Hospital due to trauma. The patients were randomly divided into two groups: a metoclopramide group (group M, n = 25) and a normal saline group (group S, n = 25). The cross-sectional area (CSA) of the gastric antrum was measured at 0, 30, 60, 90, and 120 min (T = time). The gastric emptying rate (GER, GER=−AareaTn/AareaTn−30−1×100), GER/min (GER divided by the corresponding interval time), gastric content properties, Perlas grade at different time points, T120 gastric volume (GV), and GV per unit of body weight (GV/W) were evaluated. The risk of vomiting, reflux/aspiration, and type of anesthetic treatment were also evaluated.

Results: The differences between the two groups in the CSA of the gastric antrum at each time point were statistically significant (p < 0.001). The CSAs of the gastric antrum in group M were lower than those in group S, and the greatest difference between the two groups occurred at T30 (p < 0.001). The differences between the two groups in GER and GER/min were also statistically significant (p < 0.001); those differences in group M were higher than those in group S, and the greatest differences between the two groups occurred at T30 (p < 0.001). There were no obvious change trends in the properties of the gastric contents and the Perlas grades in either group, and the differences between the two groups were not statistically significant (p = 0.97). The differences between the two groups in the GV and GV/W at T120 were statistically significant (p < 0.001), as was the risk of reflux and aspiration at T120 (p < 0.001).

Conclusion: When metoclopramide was used in satiated emergency trauma patients, it accelerated gastric emptying within 30 min and reduced the risk of accidental reflux. However, a normal gastric emptying level was not achieved, which can be attributed to the delaying effect of trauma on gastric emptying.
Transcriptional regulations of pollen tube reception are associated with the fertility of the ginger species Zingiber zerumbet and Zingiber corallinum
Authors: Liang Shan , Hu Ming-li , Lin Hao-chuan , He Han-jun , Ning Xi-ping , Peng Pei-pei , Lu Guo-hui , Sun Shu-lan , Wang Xiao-jing , Wang Ying-qiang , Wu Hong
Published: May 2023

Zingiber zerumbet and Zingiber corallinum are economically valuable species in the genus Zingiber. While Z. corallinum is sexually active, Z. zerumbet adopts clonal propagation, although it has the potential for sexual reproduction. It is unclear so far at which step during the sexual reproduction of Z. zerumbet inhibition occurs, and what are the regulatory mechanisms underlying this inhibition. Here, by comparing with the fertile species Z. corallinum using microscopy-based methods, we show that rare differences were observed in Z. zerumbet up to the point when the pollen tubes invaded the ovules. However, a significantly higher percentage of ovules still contained intact pollen tubes 24 h after pollination, suggesting pollen tube rupture was impaired in this species. Further RNA-seq analysis generated accordant results, showing that the transcription of ANX and FER, as well as genes for the partners in the same complexes (e.g., BUPS and LRE, respectively), and those putative peptide signals (e.g., RALF34), were timely activated in Z. corallinum, which ensured the pollen tubes being able to grow, reorient to ovules, and receipt by embryo sacs. In Z. zerumbet, genes for these complexes were cooperatively suppressed, which would result in the maintenance of PT integrity due to the disruption of RALF34-ANX/BUPS signaling in PT and the failure of PT reception by an active synergid due to the insufficiency of the synergid-harbored FER/LRE complex. Taking the results from the cytological and RNA-seq studies together, a model is proposed to illustrate the possible regulation mechanisms in Z. zerumbet and Z. corallinum, in which the regulations for pollen tube rupture and reception are proposed as the barrier for sexual reproduction in Z. zerumbet.
Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye
Authors: Kaya Hilal Betul , Dilli Yıldız , Oncu-Oner Tulay , Ünal Akay
Published: May 2023

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high‐density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r2 was between 0.45 and 0.2 and became flat when r2 was 0.05. The average LD decay for the entire genome was 30 kb when r2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.
Intelligent reprogramming of wheat for enhancement of fungal and nematode disease resistance using advanced molecular techniques
Authors: Jabran Muhammad , Ali Muhammad Amjad , Zahoor Adil , Muhae-Ud-Din Ghulam , Liu Taiguo , Chen Wanquan , Gao Li
Published: May 2023

Wheat (Triticum aestivum L.) diseases are major factors responsible for substantial yield losses worldwide, which affect global food security. For a long time, plant breeders have been struggling to improve wheat resistance against major diseases by selection and conventional breeding techniques. Therefore, this review was conducted to shed light on various gaps in the available literature and to reveal the most promising criteria for disease resistance in wheat. However, novel techniques for molecular breeding in the past few decades have been very fruitful for developing broad-spectrum disease resistance and other important traits in wheat. Many types of molecular markers such as SCAR, RAPD, SSR, SSLP, RFLP, SNP, and DArT, etc., have been reported for resistance against wheat pathogens. This article summarizes various insightful molecular markers involved in wheat improvement for resistance to major diseases through diverse breeding programs. Moreover, this review highlights the applications of marker assisted selection (MAS), quantitative trait loci (QTL), genome wide association studies (GWAS) and the CRISPR/Cas-9 system for developing disease resistance against most important wheat diseases. We also reviewed all reported mapped QTLs for bunts, rusts, smuts, and nematode diseases of wheat. Furthermore, we have also proposed how the CRISPR/Cas-9 system and GWAS can assist breeders in the future for the genetic improvement of wheat. If these molecular approaches are used successfully in the future, they can be a significant step toward expanding food production in wheat crops.
Mining of long non-coding RNAs with target genes in response to rust based on full-length transcriptome in Kentucky bluegrass
Authors: Zhao Xueying , Sun Xiaoyang , Chen Yang , Wu Hanfu , Liu Yujiao , Jiang Yiwei , Xie Fuchun , Chen Yajun
Published: May 2023

Kentucky bluegrass (Poa pratensis L.) is an eminent turfgrass species with a complex genome, but it is sensitive to rust (Puccinia striiformis). The molecular mechanisms of Kentucky bluegrass in response to rust still remain unclear. This study aimed to elucidate differentially expressed lncRNAs (DELs) and genes (DEGs) for rust resistance based on the full-length transcriptome. First, we used single-molecule real-time sequencing technology to generate the full-length transcriptome of Kentucky bluegrass. A total of 33,541 unigenes with an average read length of 2,233 bp were obtained, which contained 220 lncRNAs and 1,604 transcription factors. Then, the comparative transcriptome between the mock-inoculated leaves and rust-infected leaves was analyzed using the full-length transcriptome as a reference genome. A total of 105 DELs were identified in response to rust infection. A total of 15,711 DEGs were detected (8,278 upregulated genes, 7,433 downregulated genes) and were enriched in plant hormone signal transduction and plant–pathogen interaction pathways. Additionally, through co-location and expression analysis, it was found that lncRNA56517, lncRNA53468, and lncRNA40596 were highly expressed in infected plants and upregulated the expression of target genes AUX/IAA, RPM1, and RPS2, respectively; meanwhile, lncRNA25980 decreased the expression level of target gene EIN3 after infection. The results suggest that these DEGs and DELs are important candidates for potentially breeding the rust-resistant Kentucky bluegrass.
The MADS-box gene EjAGL15 positively regulates lignin deposition in the flesh of loquat fruit during its storage
Authors: Ge Hang , Xu Hongxia , Li Xiaoying , Chen Junwei
Published: May 2023

Introduction

Lignification of fruit flesh is a common physiological disorder that occurs during post-harvest storage, resulting in the deterioration of fruit quality. Lignin deposition in loquat fruit flesh occurs due to chilling injury or senescence, at temperatures around 0°C or 20°C, respectively. Despite extensive research on the molecular mechanisms underlying chilling-induced lignification, the key genes responsible for the lignification process during senescence in loquat fruit remain unknown. MADS-box genes, an evolutionarily conserved transcription factor family, have been suggested to play a role in regulating senescence. However, it is still unclear whether MADS-box genes can regulate the lignin deposition that arises from fruit senescence.

Methods

Both senescence- and chilling-induced flesh lignification were simulated by applying temperature treatments on loquat fruits. The flesh lignin content during the storage was measured. Transcriptomic, quantitative reverse transcription PCR and correlation analysis were employed to identify key MADS-box genes that may be involved in flesh lignification. The Dual-luciferase assay was utilized to identify the potential interactions between MADS-box members and genes in phenylpropanoid pathway.

Results and Discussion

The lignin content of the flesh samples treated at 20°C or 0°C increased during storage, but at different rates. Results from transcriptome analysis, quantitative reverse transcription PCR, and correlation analysis led us to identify a senescence-specific MADS-box gene, EjAGL15, which correlated positively with the variation in lignin content of loquat fruit. Luciferase assay results confirmed that EjAGL15 activated multiple lignin biosynthesis-related genes. Our findings suggest that EjAGL15 functions as a positive regulator of senescence-induced flesh lignification in loquat fruit.
The spatiotemporal profile of Dendrobium huoshanense and functional identification of bHLH genes under exogenous MeJA using comparative transcriptomics and genomics
Authors: He Xiaomei , Zhang Wenwu , Sabir Irfan Ali , Jiao Chunyan , Li Guohui , Wang Yan , Zhu Fucheng , Dai Jun , Liu Longyun , Chen Cunwu , Zhang Yingyu , Song Cheng
Published: May 2023

Introduction

Alkaloids are one of the main medicinal components of Dendrobium species. Dendrobium alkaloids are mainly composed of terpene alkaloids. Jasmonic acid (JA) induce the biosynthesis of such alkaloids, mainly by enhancing the expression of JA-responsive genes to increase plant resistance and increase the content of alkaloids. Many JA-responsive genes are the target genes of bHLH transcription factors (TFs), especially the MYC2 transcription factor.

Methods

In this study, the differentially expressed genes involved in the JA signaling pathway were screened out from Dendrobium huoshanense using comparative transcriptomics approaches, revealing the critical roles of basic helix-loop-helix (bHLH) family, particularly the MYC2 subfamily.

Results and discussion

Microsynteny-based comparative genomics demonstrated that whole genome duplication (WGD) and segmental duplication events drove bHLH genes expansion and functional divergence. Tandem duplication accelerated the generation of bHLH paralogs. Multiple sequence alignments showed that all bHLH proteins included bHLH-zip and ACT-like conserved domains. The MYC2 subfamily had a typical bHLH-MYC_N domain. The phylogenetic tree revealed the classification and putative roles of bHLHs. The analysis of cis-acting elements revealed that promoter of the majority of bHLH genes contain multiple regulatory elements relevant to light response, hormone responses, and abiotic stresses, and the bHLH genes could be activated by binding these elements. The expression profiling and qRT-PCR results indicated that bHLH subgroups IIIe and IIId may have an antagonistic role in JA-mediated expression of stress-related genes. DhbHLH20 and DhbHLH21 were considered to be the positive regulators in the early response of JA signaling, while DhbHLH24 and DhbHLH25 might be the negative regulators. Our findings may provide a practical reference for the functional study of DhbHLH genes and the regulation of secondary metabolites.
Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration
Authors: Jha Uday Chand , Nayyar Harsh , Chattopadhyay Anirudha , Beena Radha , Lone Ajaz A. , Naik Yogesh Dashrath , Thudi Mahendar , Prasad Pagadala Venkata Vara , Gupta Sanjeev , Dixit Girish Prasad , Siddique Kadambot H. M.
Published: May 2023

Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and ‘omics’ approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.
Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping
Authors: Xu Shanbin , Cui Jingnan , Cao Hu , Liang Shaoming , Ma Tianze , Liu Hualong , Wang Jingguo , Yang Luomiao , Xin Wei , Jia Yan , Zou Detang , Zheng Hongliang
Published: May 2023

Background

Salinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage.

Results

We used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene.

Conclusion

Based on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.
A genome-wide association study of freezing tolerance in red clover (Trifolium pratense L.) germplasm of European origin
Authors: Zanotto Stefano , Ruttink Tom , Pégard Marie , Skøt Leif , Grieder Christoph , Kölliker Roland , Ergon Åshild
Published: May 2023

Improvement of persistency is an important breeding goal in red clover (Trifolium pratense L.). In areas with cold winters, lack of persistency is often due to poor winter survival, of which low freezing tolerance (FT) is an important component. We conducted a genome wide association study (GWAS) to identify loci associated with freezing tolerance in a collection of 393 red clover accessions, mostly of European origin, and performed analyses of linkage disequilibrium and inbreeding. Accessions were genotyped as pools of individuals using genotyping-by-sequencing (pool-GBS), generating both single nucleotide polymorphism (SNP) and haplotype allele frequency data at accession level. Linkage disequilibrium was determined as a squared partial correlation between the allele frequencies of pairs of SNPs and found to decay at extremely short distances (< 1 kb). The level of inbreeding, inferred from the diagonal elements of a genomic relationship matrix, varied considerably between different groups of accessions, with the strongest inbreeding found among ecotypes from Iberia and Great Britain, and the least found among landraces. Considerable variation in FT was found, with LT50-values (temperature at which 50% of the plants are killed) ranging from -6.0°C to -11.5°C. SNP and haplotype-based GWAS identified eight and six loci significantly associated with FT (of which only one was shared), explaining 30% and 26% of the phenotypic variation, respectively. Ten of the loci were found within or at a short distance (<0.5 kb) from genes possibly involved in mechanisms affecting FT. These include a caffeoyl shikimate esterase, an inositol transporter, and other genes involved in signaling, transport, lignin synthesis and amino acid or carbohydrate metabolism. This study paves the way for a better understanding of the genetic control of FT and for the development of molecular tools for the improvement of this trait in red clover through genomics assisted breeding.
Psychodynamic university counseling: which factors predict psychological functioning after intervention?
Authors: Speranza Anna Maria , Franchini Costanza , Quintigliano Maria , Andreassi Silvia , Morelli Mara , Cerolini Silvia , Petrocchi Chiara , Fortunato Alexandro
Published: May 2023

Introduction

University counseling centers represent important resources for personal development, and students are increasingly turning to them for help. The present study aimed at, first, evaluating changing in psychological functioning before and after a university counseling intervention and, second, exploring which psychological variables predicted the intervention outcome.

Methods

For this purpose, 122 students who attended university counseling services were administered measures to assess personality traits, and measures to assess state variables - intended as contextual, rather than stable, alterations in functioning - such as anxiety, hopelessness and depression. Several Linear Mixed Models were performed to measure the differences between OQ-45 scores before and after the intervention (one for each OQ dimension and OQ total score); then, two steps of multiple regression analyses were performed.

Results

Significative reductions between pre-test and post-test OQ-45 scores were found, highlighting increased levels of well-being; personality traits seem not to be predictive of the intervention outcome, while state variables significantly contribute to the psychological wellbeing improvement after counseling intervention.

Discussion

Our findings highlight the importance of paying attention to the role of affective difficulties in predicting the counseling effectiveness.
Coaching and talent development in esports: a theoretical framework and suggestions for future research
Authors: Bubna Kabir , Trotter Michael Geoffrey , Watson Matthew , Polman Remco
Published: May 2023

Esports is a growing phenomenon that is capturing the attention of individuals worldwide, and has grown to provide professional and lucrative careers for those who reach the upper echelons. One question that arises, is how esports athletes develop the necessary skills required to improve and compete. This perspective piece opens the door to skill acquisition within esports and how research through an ecological approach can benefit researchers and practitioners as they understand the various perception-action couplings and decision-making challenges faced by esports athletes. We will identify and discuss what constraints look like in esports, the role of affordances, and theorize the implementation of a constraints-led approach in contrasting esports genres. As esports is technology-heavy in nature and generally sedentary, the use of eye-tracking technology is argued to represent an effective method to better understand perceptual attunement between individuals and teams. Future research into skill acquisition in esports is needed to develop a clearer picture of what makes the greatest esports player so great, and how newer players can be developed effectively.