bluuebunny/crossref_metadata_2025 huggingface dataset:
Long COVID Classification: Findings from a Clustering Analysis in the Predi-COVID Cohort Study
Authors: Fischer Aurélie , Badier Nolwenn , Zhang Lu , Elbéji Abir , Wilmes Paul , Oustric Pauline , Benoy Charles , Ollert Markus , Fagherazzi Guy
Published: November 2022

The increasing number of people living with Long COVID requires the development of more personalized care; currently, limited treatment options and rehabilitation programs adapted to the variety of Long COVID presentations are available. Our objective was to design an easy-to-use Long COVID classification to help stratify people with Long COVID. Individual characteristics and a detailed set of 62 self-reported persisting symptoms together with quality of life indexes 12 months after initial COVID-19 infection were collected in a cohort of SARS-CoV-2 infected people in Luxembourg. A hierarchical ascendant classification (HAC) was used to identify clusters of people. We identified three patterns of Long COVID symptoms with a gradient in disease severity. Cluster-Mild encompassed almost 50% of the study population and was composed of participants with less severe initial infection, fewer comorbidities, and fewer persisting symptoms (mean = 2.9). Cluster-Moderate was characterized by a mean of 11 persisting symptoms and poor sleep and respiratory quality of life. Compared to the other clusters, Cluster-Severe was characterized by a higher proportion of women and smokers with a higher number of Long COVID symptoms, in particular vascular, urinary, and skin symptoms. Our study evidenced that Long COVID can be stratified into three subcategories in terms of severity. If replicated in other populations, this simple classification will help clinicians improve the care of people with Long COVID.
Study of Anthropometry, Range of Motion, and Muscle Strength of Individuals with Spinal Cord Injury or Amputation for the Design of a Driver’s Seat in Large Agricultural Equipment
Authors: Park Yeongjeong , Yoo Soyoung , Kim Hyunjoong , Choi Jungkab , Son Byungchang , Yook Juhye
Published: November 2022

This study aims to check and compare the anthropometry, range of motion, and upper limb muscle strength of individuals with spinal cord injury or amputation in order to design a driver’s seat in a large farming machine for them to operate. We analyzed previous studies and derived 24 measurement items essential for designing the driver’s seat. For data collection, we recruited 78 people with spinal cord injury and 46 people with amputation. The collected data were classified into 5th, 25th, 50th, 75th, and 95th percentile groups by disability type and gender, before conducting a comparative analysis. For an in-depth analysis, we performed an independent t-test on the samples to compare the individuals with spinal cord injury and the individuals with amputation in terms of disability type and gender. The results showed statistical differences as follows. In the same disability category, male subjects surpassed female subjects. In the same gender category, individuals with amputation surpassed individuals with spinal cord injury. Based on this study’s data and analysis, large farming machines can be designed by reflecting the characteristics of a wide variety of disability types.
Recovery following Orthognathic Surgery Procedures—A Pilot Study
Authors: Dinu Cristian , Manea Avram , Tomoiagă Denisa , Băciuț Mihaela , Almășan Oana , Mitre Andrei Otto , Barbur Ioan , Hedeșiu Mihaela , Armencea Gabriel , Opriș Horia , Stoia Sebastian , Tamaș Tiberiu , Băciuț Grigore , Onișor Florin , Bran Simion
Published: November 2022

This study aims at evaluating and categorizing patients’ objective and subjective postoperative recovery symptoms after bimaxillary orthognathic surgery assigning the healing process. The patients were monitored throughout the recovery process, and their symptoms were managed. A prospective, observational study was performed. Patients with Class II and III malocclusion (aged 18 to 35) were evaluated and monitored preoperatively, and postoperatively at 48 h, 2 weeks, 1 month, and 3 months postsurgery. A questionnaire was used to assess pain and anesthesia/hypoesthesia. The most common objective and subjective signs that were correlated with the healing process were edema, hematoma, trismus, pain, and anesthesia/hypoesthesia. Edema peaked at 48–72 h postoperatively (distance between eye’s external canthus and gonion, mean difference = 4.53, between tragus and cheilion, mean difference = 7, between tragus and gnathion, mean difference = 4.65, p < 0.001); mouth opening amplitude was significantly decreased during the first two weeks postsurgery (class II, mean difference = 32.42, p = 0.006, class III, mean difference = 44.57, p < 0.001), but it steadily and considerably improved over three months. The nose tended to widen postsurgery. The most severe pain experienced by patients was of medium intensity in the mandibular body, described as pressure, and usually did not spread. Patients were most severely and persistently impacted by anesthesia/hypoesthesia.
The Latent Class Analysis of Adverse Childhood Experiences among Chinese Children and Early Adolescents in Rural Areas and Their Association with Depression and Suicidal Ideation
Authors: Chen Chun , Sun Yu , Liu Boyuan , Zhang Xiao , Song Yingquan
Published: November 2022

Exposure to adverse childhood experiences (ACEs) is a global public health concern that is detrimental to the psychological outcomes of Chinese children in rural areas due to the lack of public awareness of ACEs and mental health resources. The objective of this study was to identify the patterns of ACEs and the impact of ACE patterns on depression and suicidal ideation among 4683 students (mean age = 10.08 years, SD = 0.99; 48.17% female students) from 63 elementary schools in rural areas in Guizhou Province, China. Latent class analysis was conducted to identify the best class pattern. A three-step approach was undertaken to explore the association between the class patterns and demographic covariates and depression and suicidal thoughts. An overall three-class pattern of ACEs was identified, which was: (1) high ACEs, (2) high verbal abuse and emotional neglect and low household dysfunction, and (3) low ACEs. The results also showed that children in the high ACEs class tended to show higher depression rates and more frequent suicidal ideation across the three groups. Being female and younger and having a lower socioeconomic status were risk factors. Our study identified a class pattern that was not found in previous research, which is high verbal abuse and emotional neglect and low household dysfunction.
The Influence of Overeducation on Chinese Workers’ Job Satisfaction from China Household Tracking Survey (2014–2018)
Authors: Ma Wenbo , Baek Jongnam , Qi Meng , Li Junjie , Liu Bangfan
Published: November 2022

Overeducation means that the rapid growth in the numbers of secondary and higher education graduates begins to exceed the actual demand of the labor market due to this excessive expansion of education. Consequently, educated workers are faced with knowledge unemployment, or are engaged in jobs that do not match their academic qualifications, resulting in a decline in income and a waste of educational resources. In order to explore the effect of overeducation on workers’ job satisfaction, we selected data from China Household Tracking Survey (CFPS) and conducted a fixed-effect ordered logit model regression analysis. It was found that overeducation has a negative impact on employees’ job satisfaction and an impact on wage penalty. Wage income has a mediating effect on the relationship between overeducation and job satisfaction. We present three policy suggestions: for the Government’s administration department, it is necessary to actively create an environment for matching education and occupation; to improve the possibility of matching education and occupation; and to reduce the negative effect of labor contracts on the improvement of human capital and the job satisfaction of overeducators by adjusting the flexibility and stability of the labor contract. For institutions of higher learning: it is necessary to make forward-looking adjustments to the educational structure, according to the actual needs of economic and social development to adapt to the social demand for talent and development trends; to train highly skilled and high-quality workers needed for social development; and to reduce the unreasonable distribution of resources caused by overeducation. For enterprises: employees should be guided to correctly understand the unpredictable relationship between education and work and reasonably reduce the job expectations of new employees, according to their own work experience and technical level.
Association between Physical Activity, Sedentary Behavior, Satisfaction with Sleep Fatigue Recovery and Smartphone Dependency among Korean Adolescents: An Age- and Gender-Matched Study
Authors: Hwang In-Whi , Choe Ju-Pil , Park Jeong-Hui , Lee Jung-Min
Published: November 2022

The purpose of this study was to identify the association between physical activity (PA), sedentary behavior (SB), satisfaction with sleep fatigue recovery (SSFR), and smartphone dependency in South Korean adults. We analyzed data from the National Health and Nutrition Examination Survey 2020 data. We selected participants who answered Internet addiction-related questions as “Very much” (n = 241) and answered Internet addiction-related questions as “Not at all” (n = 241) in the questionnaire. The participants were matched by age and gender, then divided into two groups. Between the two groups, there were considerable differences in the number of days participating in moderate to vigorous PA (5 days or more, p = 0.01), the number of strength training days (1 day, p = 0.02), the number of light PA days for more than 60 min (every day for the last 7 days, p = 0.01), and the SSFR over the past 7 days (p < 0.05). Additionally, the mean smartphone usage time and mean sedentary behavior time between the two groups showed significant differences. The study demonstrated that there were significant associations between PA, SB, SSFR, and smartphone dependency among Korean adolescents matched by age and gender. Additionally, this study highlights the importance of increasing overall PA and number of days participating in MVPA, decreasing SB time and smartphone usage time could reduce the incidence of smartphone overdependence.
Air Pollution: Possible Interaction between the Immune and Nervous System?
Authors: Serafini Melania Maria , Maddalon Ambra , Iulini Martina , Galbiati Valentina
Published: November 2022

Exposure to environmental pollutants is a serious and common public health concern associated with growing morbidity and mortality worldwide, as well as economic burden. In recent years, the toxic effects associated with air pollution have been intensively studied, with a particular focus on the lung and cardiovascular system, mainly associated with particulate matter exposure. However, epidemiological and mechanistic studies suggest that air pollution can also influence skin integrity and may have a significant adverse impact on the immune and nervous system. Air pollution exposure already starts in utero before birth, potentially causing delayed chronic diseases arising later in life. There are, indeed, time windows during the life of individuals who are more susceptible to air pollution exposure, which may result in more severe outcomes. In this review paper, we provide an overview of findings that have established the effects of air pollutants on the immune and nervous system, and speculate on the possible interaction between them, based on mechanistic data.
γδ T Lymphocytes as a Double-Edged Sword—State of the Art in Gynecological Diseases
Authors: Pawłowska Anna , Natochina Yelizaveta , Zardzewiały Witold , Skiba Wiktoria , Włodarczyk Karolina , Maciejczyk Aleksandra , Suszczyk Dorota , Wertel Iwona
Published: November 2022

Human gamma-delta (γδ) T cells are a heterogeneous cell population that bridges the gap between innate and acquired immunity. They are involved in a variety of immunological processes, including tumor escape mechanisms. However, by being prolific cytokine producers, these lymphocytes also participate in antitumor cytotoxicity. Which one of the two possibilities takes place depends on the tumor microenvironment (TME) and the subpopulation of γδ T lymphocytes. The aim of this paper is to summarize existing knowledge about the phenotype and dual role of γδ T cells in cancers, including ovarian cancer (OC). OC is the third most common gynecological cancer and the most lethal gynecological malignancy. Anticancer immunity in OC is modulated by the TME, including by immunosuppressive cells, cytokines, and soluble factors. Immune cells are exposed in the TME to many signals that determine their immunophenotype and can manipulate their functions. The significance of γδ T cells in the pathophysiology of OC is enigmatic and remains to be investigated.
Discovery of a Novel Bloom’s Syndrome Protein (BLM) Inhibitor Suppressing Growth and Metastasis of Prostate Cancer
Authors: Ma Xiao-Yan , Xu Hou-Qiang , Zhao Jia-Fu , Ruan Yong , Chen Bin
Published: November 2022

Prostate cancer (PCa) is a common cancer and a major cause of cancer-related death worldwide in men, necessitating novel targets for cancer therapy. High expression of Bloom’s syndrome protein (BLM) helicase is associated with the occurrence and development of PCa. Therefore, the identification and development of new BLM inhibitors may be a new direction for the treatment of PCa. Here, we identified a novel inhibitor by molecular docking and put it to systematic evaluation via various experiments, AO/854, which acted as a competitive inhibitor that blocked the BLM-DNA interaction. Cellular evaluation indicated that AO/854-suppressed tumor growth and metastasis in PC3 cells by enhancing DNA damage, phosphorylating Chk1/Chk2, and altering the p53 signaling pathway. Collectively, the study highlights the potential of BLM as a therapeutic target in PCa and reveals a distinct mechanism by which AO/854 competitively inhibits the function of BLM.
PSSNet—An Accurate Super-Secondary Structure for Protein Segmentation
Authors: Petrovsky Denis V. , Rudnev Vladimir R. , Nikolsky Kirill S. , Kulikova Liudmila I. , Malsagova Kristina M. , Kopylov Arthur T. , Kaysheva Anna L.
Published: November 2022

A super-secondary structure (SSS) is a spatially unique ensemble of secondary structural elements that determine the three-dimensional shape of a protein and its function, rendering SSSs attractive as folding cores. Understanding known types of SSSs is important for developing a deeper understanding of the mechanisms of protein folding. Here, we propose a universal PSSNet machine-learning method for SSS recognition and segmentation. For various types of SSS segmentation, this method uses key characteristics of SSS geometry, including the lengths of secondary structural elements and the distances between them, torsion angles, spatial positions of Cα atoms, and primary sequences. Using four types of SSSs (βαβ-unit, α-hairpin, β-hairpin, αα-corner), we showed that extensive SSS sets could be reliably selected from the Protein Data Bank and AlphaFold 2.0 database of protein structures.
Using Genomic Variation to Distinguish Ovarian High-Grade Serous Carcinoma from Benign Fallopian Tubes
Authors: Gonzalez-Bosquet Jesus , Cardillo Nicholas D. , Reyes Henry D. , Smith Brian J. , Leslie Kimberly K. , Bender David P. , Goodheart Michael J. , Devor Eric J.
Published: November 2022

The preoperative diagnosis of pelvic masses has been elusive to date. Methods for characterization such as CA-125 have had limited specificity. We hypothesize that genomic variation can be used to create prediction models which accurately distinguish high grade serous ovarian cancer (HGSC) from benign tissue. Methods: In this retrospective, pilot study, we extracted DNA and RNA from HGSC specimens and from benign fallopian tubes. Then, we performed whole exome sequencing and RNA sequencing, and identified single nucleotide variants (SNV), copy number variants (CNV) and structural variants (SV). We used these variants to create prediction models to distinguish cancer from benign tissue. The models were then validated in independent datasets and with a machine learning platform. Results: The prediction model with SNV had an AUC of 1.00 (95% CI 1.00–1.00). The models with CNV and SV had AUC of 0.87 and 0.73, respectively. Validated models also had excellent performances. Conclusions: Genomic variation of HGSC can be used to create prediction models which accurately discriminate cancer from benign tissue. Further refining of these models (early-stage samples, other tumor types) has the potential to lead to detection of ovarian cancer in blood with cell free DNA, even in early stage.
Detecting the Hydrogen Bond Cooperativity in a Protein β-Sheet by H/D Exchange
Authors: Li Jingwen , Chen Jingfei , Wang Yefei , Yao Lishan
Published: November 2022

The hydrogen bond (H-bond) cooperativity in the β-sheet of GB3 is investigated by a NMR hydrogen/deuterium (H/D) exchange method. It is shown that the weakening of one backbone N–H…O=C H-bond between two β-strands, β1 and β2, due to the exchange of NH to ND of the H-bond donor in β1, perturbs the chemical shift of 13Cα, 13Cβ, 1Hα, 1HN, and 15N of the H-bond acceptor and its following residue in β2. Quantum mechanical calculations suggest that the -H-bond chemical shift isotope effect is caused by the structural reorganization in response to the H-bond weakening. This structural reorganization perturbs four neighboring H-bonds, with three being weaker and one being stronger, indicating that three H-bonds are cooperative and one is anticooperative with the perturbed H-bond. The sign of the cooperativity depends on the relative position of the H-bonds. This H-bond cooperativity, which contributes to β-sheet stability overall, can be important for conformational coupling across the β-sheet.
Identification of a Cardiac Glycoside Exhibiting Favorable Brain Bioavailability and Potency for Reducing Levels of the Cellular Prion Protein
Authors: Eid Shehab , Zerbes Thomas , Williams Declan , Wang Xinzhu , Sackmann Chris , Meier Sammy , Dulin Nickolai O. , Nagorny Pavel , Schmitt-Ulms Gerold
Published: November 2022

Several strands of investigation have established that a reduction in the levels of the cellular prion protein (PrPC) is a promising avenue for the treatment of prion diseases. We recently described an indirect approach for reducing PrPC levels that targets Na,K-ATPases (NKAs) with cardiac glycosides (CGs), causing cells to respond with the degradation of these pumps and nearby molecules, including PrPC. Because the therapeutic window of widely used CGs is narrow and their brain bioavailability is low, we set out to identify a CG with improved pharmacological properties for this indication. Starting with the CG known as oleandrin, we combined in silico modeling of CG binding poses within human NKA folds, CG structure-activity relationship (SAR) data, and predicted blood–brain barrier (BBB) penetrance scores to identify CG derivatives with improved characteristics. Focusing on C4′-dehydro-oleandrin as a chemically accessible shortlisted CG derivative, we show that it reaches four times higher levels in the brain than in the heart one day after subcutaneous administration, exhibits promising pharmacological properties, and suppresses steady-state PrPC levels by 84% in immortalized human cells that have been differentiated to acquire neural or astrocytic characteristics. Finally, we validate that the mechanism of action of this approach for reducing cell surface PrPC levels requires C4′-dehydro-oleandrin to engage with its cognate binding pocket within the NKA α subunit. The improved brain bioavailability of C4′-dehydro-oleandrin, combined with its relatively low toxicity, make this compound an attractive lead for brain CG indications and recommends its further exploration for the treatment of prion diseases.
Transcriptome Profiling in the Hippocampi of Mice with Experimental Autoimmune Encephalomyelitis
Authors: Weerasinghe-Mudiyanselage Poornima D. E. , Kang Sohi , Kim Joong-Sun , Kim Jong-Choon , Kim Sung-Ho , Wang Hongbing , Shin Taekyun , Moon Changjong
Published: November 2022

Experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), approximates the key histopathological, clinical, and immunological features of MS. Hippocampal dysfunction in MS and EAE causes varying degrees of cognitive and emotional impairments and synaptic abnormalities. However, the molecular alterations underlying hippocampal dysfunctions in MS and EAE are still under investigation. The purpose of this study was to identify differentially expressed genes (DEGs) in the hippocampus of mice with EAE in order to ascertain potential genes associated with hippocampal dysfunction. Gene expression in the hippocampus was analyzed by RNA-sequencing and validated by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression analysis revealed 1202 DEGs; 1023 were upregulated and 179 were downregulated in the hippocampus of mice with EAE (p-value < 0.05 and fold change >1.5). Gene ontology (GO) analysis showed that the upregulated genes in the hippocampi of mice with EAE were associated with immune system processes, defense responses, immune responses, and regulation of immune responses, whereas the downregulated genes were related to learning or memory, behavior, and nervous system processes in the GO biological process. The expressions of hub genes from the search tool for the retrieval of interacting genes/proteins (STRING) analysis were validated by RT-qPCR. Additionally, gene set enrichment analysis showed that the upregulated genes in the hippocampus were associated with inflammatory responses: interferon-γ responses, allograft rejection, interferon-α responses, IL6_JAK_STAT3 signaling, inflammatory responses, complement, IL2_STAT5 signaling, TNF-α signaling via NF-κB, and apoptosis, whereas the downregulated genes were related to synaptic plasticity, dendritic development, and development of dendritic spine. This study characterized the transcriptome pattern in the hippocampi of mice with EAE and signaling pathways underpinning hippocampal dysfunction. However, further investigation is needed to determine the applicability of these findings from this rodent model to patients with MS. Collectively, these results indicate directions for further research to understand the mechanisms behind hippocampal dysfunction in EAE.
Ligand-Based Discovery of a Small Molecule as Inhibitor of α-Synuclein Amyloid Formation
Authors: De Luca Laura , Vittorio Serena , Peña-Díaz Samuel , Pitasi Giovanna , Fornt-Suñé Marc , Bucolo Federica , Ventura Salvador , Gitto Rosaria
Published: November 2022

α-Synuclein (α-Syn) aggregates are implicated in Parkinson’s disease (PD), so inhibitors of α-Syn aggregation have been intensively explored. It has been demonstrated that small molecules might be able to reduce α-Syn aggregation in fibrils, thus exerting neuroprotective effects in models of PD. To expand our knowledge about the structural requirements for blocking the recognition process into the oligomeric assembly of α-Syn aggregates, we performed a ligand-based virtual screening procedure using two well-known α-Syn aggregation inhibitors, SynuClean-D and ZPD-2, as query compounds. A collection of thirty-four compounds bearing distinct chemical functionalities and mutual chemical features were studied in a Th-T fluorescence test, thus identifying 5-(2,6-dinitro-4-(trifluoromethyl)benzyl)-1-methyl-1H-tetrazole (named MeSC-04) as a potent α-Syn amyloid formation inhibitor that demonstrated similar behavior when compared to SynuClean-D in the thioflavin-T-monitored kinetic assays, with both molecules reducing the number and size of amyloid fibrils, as evidenced by electron microscopy. Molecular modeling studies suggested the binding mode of MeSC-04 through the identification of putative druggable pockets on α-syn fibrils and a subsequent consensus docking methodology. Overall, this work could furnish new insights in the development of α-Syn amyloid inhibitors from synthetic sources.
Characterization and Genomic Analysis of Escherichia coli O157:H7 Phage UAE_MI-01 Isolated from Birds
Authors: Sultan-Alolama Mohamad Ismail , Amin Amr , El-Tarabily Khaled A. , Vijayan Ranjit
Published: November 2022

Verotoxin-producing Escherichia coli O157:H7 is responsible for the majority of foodborne outbreaks worldwide and may lead to death. Bacteriophages are natural killers of bacteria. All previously reported E. coli O157:H7 phages were isolated from ruminants or swine. Here, we report for the first time a phage isolated from bird feces in the United Arab Emirates (UAE), designated as UAE_MI-01, indicating birds as a good source of phages. Thus, phages could be a tool for predicting the presence of the host bacteria in an animal or the environment. UAE_MI-01 was found to be a lytic phage that was stable at wide ranges of pH, temperature, and chemical disinfectants, and with a burst size of almost 100 plaque-forming units per host cell after a latent period of 20 min and an adsorption rate constant (K) of 1.25 × 10−7 mL min−1. The phage genome was found to be 44,281 bp long with an average GC content of 54.7%. The presence of the phage indicates the presence of the host cell E. coli O157:H7 in wild birds. Therefore, other birds, mainly poultry, could be also investigated for the presence of this pathogenic bacterium. To the best of our knowledge, this is the first report of an E. coli O157:H7 bacteriophage isolated from a bird.
Complete and Prolonged Inhibition of Herpes Simplex Virus Type 1 Infection In Vitro by CRISPR/Cas9 and CRISPR/CasX Systems
Authors: Karpov Dmitry S. , Demidova Natalia A. , Kulagin Kirill A. , Shuvalova Anastasija I. , Kovalev Maxim A. , Simonov Ruslan A. , Karpov Vadim L. , Snezhkina Anastasiya V. , Kudryavtseva Anna V. , Klimova Regina R. , Kushch Alla A.
Published: November 2022

Almost all people become infected with herpes viruses, including herpes simplex virus type 1 (HSV-1), during their lifetime. Typically, these viruses persist in a latent form that is resistant to all available antiviral medications. Under certain conditions, such as immunosuppression, the latent forms reactivate and cause disease. Moreover, strains of herpesviruses that are drug-resistant have rapidly emerged. Therefore, it is important to develop alternative methods capable of eradicating herpesvirus infections. One promising direction is the development of CRISPR/Cas systems for the therapy of herpesvirus infections. We aimed to design a CRISPR/Cas system for relatively effective long-term and safe control of HSV-1 infection. Here, we show that plasmids encoding the CRISPR/Cas9 system from Streptococcus pyogenes with a single sgRNA targeting the UL30 gene can completely suppress HSV-1 infection of the Vero cell line within 6 days and provide substantial protection within 9 days. For the first time, we show that CRISPR/CasX from Deltaproteobacteria with a single guide RNA against UL30 almost completely suppresses HSV-1 infection of the Vero cell line for 3 days and provides substantial protection for 6 days. We also found that the Cas9 protein without sgRNAs attenuates HSV-1 infection. Our results show that the developed CRISPR/Cas systems are promising therapeutic approaches to control HSV-1 infections.
H2S Enhanced the Tolerance of Malus hupehensis to Alkaline Salt Stress through the Expression of Genes Related to Sulfur-Containing Compounds and the Cell Wall in Roots
Authors: Li Huan , Zhang Weiwei , Han Mengyuan , Song Jianfei , Ning Yuansheng , Yang Hongqiang
Published: November 2022

Malus is an economically important plant that is widely cultivated worldwide, but it often encounters saline–alkali stress. The composition of saline–alkali land is a variety of salt and alkali mixed with the formation of alkaline salt. Hydrogen sulfide (H2S) has been reported to have positive effects on plant responses to abiotic stresses. Our previous study showed that H2S pretreatment alleviated the damage caused by alkaline salt stress to Malus hupehensis Rehd. var. pingyiensis Jiang (Pingyi Tiancha, PYTC) roots by regulating Na+/K+ homeostasis and oxidative stress. In this study, transcriptome analysis was used to investigate the overall mechanism through which H2S alleviates alkaline salt stress in PYTC roots. Simultaneously, differentially expressed genes (DEGs) were explored. Transcriptional profiling of the Control-H2S, Control-AS, Control-H2S + AS, and AS-H2S + AS comparison groups identified 1618, 18,652, 16,575, and 4314 DEGs, respectively. Further analysis revealed that H2S could alleviate alkaline salt stress by increasing the energy maintenance capacity and cell wall integrity of M. hupehensis roots and by enhancing the capacity for reactive oxygen species (ROS) metabolism because more upregulated genes involved in ROS metabolism and sulfur-containing compounds were identified in M. hupehensis roots after H2S pretreatment. qRT-PCR analysis of H2S-induced and alkaline salt-response genes showed that these genes were consistent with the RNA-seq analysis results, which indicated that H2S alleviation of alkaline salt stress involves the genes of the cell wall and sulfur-containing compounds in PYTC roots.
Identification of a Novel Pleiotropic Transcriptional Regulator Involved in Sporulation and Secondary Metabolism Production in Chaetomium globosum
Authors: Zhao Shanshan , Zhang Kai , Lin Congyu , Cheng Ming , Song Jinzhu , Ru Xin , Wang Zhengran , Wang Wan , Yang Qian
Published: November 2022

Chaetoglobosin A (CheA), a well-known macrocyclic alkaloid with prominently highly antimycotic, antiparasitic, and antitumor properties, is mainly produced by Chaetomium globosum. However, a limited understanding of the transcriptional regulation of CheA biosynthesis has hampered its application and commercialization in agriculture and biomedicine. Here, a comprehensive study of the CgXpp1 gene, which encodes a basic helix-loop-helix family regulator with a putative role in the regulation of fungal growth and CheA biosynthesis, was performed by employing CgXpp1-disruption and CgXpp1-complementation strategies in the biocontrol species C. globosum. The results suggest that the CgXpp1 gene could be an indirect negative regulator in CheA production. Interestingly, knockout of CgXpp1 considerably increased the transcription levels of key genes and related regulatory factors associated with the CheA biosynthetic. Disruption of CgXpp1 led to a significant reduction in spore production and attenuation of cell development, which was consistent with metabolome analysis results. Taken together, an in-depth analysis of pleiotropic regulation influenced by transcription factors could provide insights into the unexplored metabolic mechanisms associated with primary and secondary metabolite production.
Transcriptome Analysis Reveals Potential Mechanism in Storage Protein Trafficking within Developing Grains of Common Wheat
Authors: Buttar Zeeshan Ali , Shalmani Abdullah , Niaz Mohsin , Wang Chaojie , Hussain Shahid , Wang Chengshe
Published: November 2022

Gluten proteins are the major storage protein fraction in the mature wheat grain. They are restricted to the starchy endosperm, which defines the viscoelastic properties of wheat dough. The synthesis of these storage proteins is controlled by the endoplasmic reticulum (ER) and is directed into the vacuole via the Golgi apparatus. In the present study, transcriptome analysis was used to explore the potential mechanism within critical stages of grain development of wheat cultivar “Shaannong 33” and its sister line used as the control (CK). Samples were collected at 10 DPA (days after anthesis), 14 DPA, 20 DPA, and 30 DPA for transcriptomic analysis. The comparative transcriptome analysis identified that a total of 18,875 genes were differentially expressed genes (DEGs) between grains of four groups “T10 vs. CK10, T14 vs. CK14, T20 vs. CK20, and T30 vs. CK30”, including 2824 up-regulated and 5423 down-regulated genes in T30 vs. CK30. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted the maximum number of genes regulating protein processing in the endoplasmic reticulum (ER) during grain enlargement stages (10–20 DPA). In addition, KEGG database analysis reported 1362 and 788 DEGs involved in translation, ribosomal structure, biogenesis, flavonoid biosynthesis pathway and intracellular trafficking, secretion, and vesicular transport through protein processing within ER pathway (ko04141). Notably, consistent with the higher expression of intercellular storage protein trafficking genes at the initial 10 DPA, there was relatively low expression at later stages. Expression levels of nine randomly selected genes were verified by qRT-PCR, which were consistent with the transcriptome data. These data suggested that the initial stages of “cell division” played a significant role in protein quality control within the ER, thus maintaining the protein quality characteristics at grain maturity. Furthermore, our data suggested that the protein synthesis, folding, and trafficking pathways directed by a different number of genes during the grain enlargement stage contributed to the observed high-quality characteristics of gluten protein in Shaannong 33 (Triticum aestivum L.).
Theoretical Analysis of Polynuclear Zinc Complexes Isolobally Related to Hydrocarbons
Authors: Ayala Regla , Galindo Agustín
Published: November 2022

Based on the isolobal analogy of ZnCp (Cp = η5-C5H5) and ZnR (R = alkyl or aryl group) fragments with hydrogen atom and fragment [Zn(CO)2] with a CH2 carbene, the following complexes [(ZnCp)2{µ-Zn(CO)2}], 1, [(ZnPh)2{µ-Zn(CO)2}], 2, [(ZnPh){µ-Zn(CO)2}(ZnCp)], 3, [(ZnCp)2{µ-Zn2(CO)4}], 4, [(ZnPh)2{µ-Zn2(CO)4}], 5, [(ZnPh){µ-Zn(CO)2}2(ZnCp)], 6, [Zn3(CO)6], 7 and [Zn5(CO)10], 8, were built. These polynuclear zinc compounds are isolobally related to simple hydrocarbons (methane, ethane, cyclopropane and cyclopentane). They have been studied by density functional theory (DFT) and quantum theory of atoms in molecules (QTAIM) to compare the nature and topology of the Zn–Zn bond with previous studies. There are bond critical points (BCPs) between each pair of adjacent Zn centers in complexes 1–8 with Zn–Zn distances within the range 2.37–2.50 Å. The nature of the Zn–Zn bond in these complexes can be described as polar rather than pure covalent bonds. Although in a subtle way, the presence of different ligands and zinc oxidation states introduces asymmetry and polarity in the Zn–Zn bond. In addition, the Zn–Zn bond is delocalized in nature in complex 7 whereas it can be described as a localized bond for the remaining zinc complexes here studied.
Structural Anomaly in Glasses: Molecular Dynamics Study of Organic Radical in Dibutylphthalate at Different Temperatures
Authors: Alimov Dmitry V. , Ivanov Mikhail Yu. , Pylaeva Svetlana , Fedin Matvey V.
Published: November 2022

Understanding the heterogeneous nano/microscopic structures of various organic glasses is fundamental and necessary for many applications. Recently, unusual structural phenomena have been observed experimentally in various organic glasses near their glass transition temperatures (Tg), including dibutyl phthalate (DBP). In particular, the librational motion of radical probe in the glass is progressively suppressed upon temperature increase. In this work, we report in-depth molecular dynamics studies of structural anomalies in DBP glass, that revealed insights into the general mechanism of these phenomena. In particular, we have evidenced that the two types of solvation within alkyl chains coexist, allowing only small-angle wobbling of the solute molecule (TEMPO radical), and another favouring large-angle rotations. The former solvation assumes constrained location of the solute near carboxyl groups of DBP, while the latter is coupled to the concerted movement of butyl chains. Remarkably, excellent qualitative and quantitative agreement with previous experimental results were obtained. As such, we are certain that the above-mentioned dynamic phenomena explain the intriguing structural anomalies observed in DBP and some other glasses in the vicinity of Tg.
SNA077, an Extract of Marine Streptomyces sp., Inhibits Melanogenesis by Downregulating Melanogenic Proteins via Inactivation of cAMP/PKA/CREB Signaling
Authors: Lim Su-Jin , Jung Da-Won , Hillman Prima F. , Nam Sang-Jip , Lee Chang-Seok
Published: November 2022

Excess melanin in skin is known to be the main cause of hyper-pigmentary skin diseases such as freckles and lentigo. This study aimed to evaluate the depigmenting efficacy of an extract from the marine microorganism strain, Streptomyces sp. SNA077. To determine the anti-melanogenic efficacy of SNA077, we assessed the melanin contents of SNA077-treated B16, Melan-a, and MNT-1 cells. We observed the expression of key enzymes in melanogenesis via qRT-PCR and Western blot analyses. We further estimated the skin-whitening effect of SNA077 using a skin-equivalent model. SNA077 dramatically decreased the melanin production of B16 cells, Melan-a, and MNT-1 cells. In B16 cells treated with SNA077, the activity of cellular tyrosinase was clearly inhibited. In addition, the mRNA and protein expression levels of melanogenic genes were suppressed by SNA077 treatment in B16 and MNT-1 cells. Upstream of tyrosinase, the expression levels of phospho-CREB, phospho-p38, PKA activity, cyclic AMP production, and MC1R gene expression were inhibited by SNA077. Finally, SNA077 clearly showed a skin-brightening effect with a reduced melanin content in the skin tissue model. Collectively, our results suggest for the first time that an extract of marine Streptomyces sp. SNA077 could be a novel anti-melanogenic material for skin whitening.
Upregulated FKBP1A Suppresses Glioblastoma Cell Growth via Apoptosis Pathway
Authors: Cai Shaoyi , Chen Zhiyou , Tang Heng , Meng Siyan , Tao Liang , Wang Qin
Published: November 2022

Glioblastoma (GBM), the most deadly primary brain tumor, presents a major medical difficulty. The need for better therapeutic targets in GBM is therefore urgent. A growing body of evidence suggests that the gene FKBP1A plays an important role in tumor progression and may be therapeutically useful. However, the role of FKBP1A in glioblastoma and the underlying biologic mechanism remain unclear. The purpose of this study was to identify the role of FKBP1A in GBM and its molecular mechanism. We demonstrated that FKBP1A was the hub gene in GBM via a weighted correlation network analysis (WGCNA) and differentially expressed genes (DEGs) analysis based on the bulk RNA-seq data from TCGA and GTEx. Afterwards, we proved that the upregulated FKBP1A protein could promote GBM cell death by CCK-8 assays in U87MG and t98g GBM cell lines. We further demonstrated two key pathways of FKBP1A in GBM by bioinformatics methods: ‘Apoptosis’ and ‘mTOR signaling pathway’. Subsequently, the key pathways were verified by flow cytometry and Western blot. We identified that upregulated FKBP1A could inhibit GBM growth via the apoptosis pathway. Together, these findings may contribute to future GBM treatment.
Overexpression of CpADC from Chinese Cherry (Cerasus pseudocerasus Lindl. ‘Manaohong’) Promotes the Ability of Response to Drought in Arabidopsis thaliana
Authors: Ran Jiaxin , Shang Chunqiong , Mei Lina , Li Shuang , Tian Tian , Qiao Guang
Published: November 2022

Polyamines (PA) play an important role in the growth, development and stress resistance of plants, and arginine decarboxylase (ADC) is one of the key enzymes in the biosynthetic pathway of polyamines. Previously, the transcriptional regulation of the ‘Manaohong’ cherry under the shelter covering was carried out, and the PA synthase-related genes, particularly the ADC gene, were differentially expressed as exposure to drought stress. However, the mechanisms of how ADC is involved in the response of cherry to abiotic stress (especially drought stress) are still unknown. In the present work, the full-length coding sequence of this gene was isolated and named CpADC. Bioinformatics analysis indicated that the coding sequence of CpADC was 2529 bp in length. Cluster analysis showed that CpADC had the highest homologies with those of sweet cherry (Prunus avium, XP_021806331) and peach (Prunus persica, XP_007200307). Subcellular localization detected that the CpADC was localized in the plant nucleus. The qPCR quantification showed that CpADC was differentially expressed in roots, stems, leaves, flower buds, flowers, and fruits at different periods. Drought stress treatments were applied to both wild-type (WT) and transgenic Arabidopsis lines, and relevant physiological indicators were measured, and the results showed that the putrescine content of transgenic Arabidopsis was higher than that of WT under high-temperature treatment. The results showed that the MDA content of WT was consistently higher than that of transgenic plants and that the degree of stress in WT was more severe than in transgenic Arabidopsis, indicating that transgenic CpADC was able to enhance the stress resistance of the plants. Both the transgenic and WT plants had significantly higher levels of proline in their leaves after the stress treatment than before, but the WT plant had lower levels of proline than that of transgenic Arabidopsis in both cases. This shows that the accumulation of proline in the transgenic plants was higher than that in the wild type under drought and high and low-temperature stress, suggesting that the transgenic plants are more stress tolerant than the WT. Taken together, our results reveal that, under drought stress, the increase in both expressions of CpADC gene and Put (putrescine) accumulation regulates the activity of ADC, the content of MDA and Pro to enhance the drought resistance of Arabidopsis thaliana.
CRISPR/Cas9-Mediated Targeted Mutagenesis of BnaCOL9 Advances the Flowering Time of Brassica napus L.
Authors: Guo Jian , Zeng Lei , Chen Hui , Ma Chaozhi , Tu Jinxing , Shen Jinxiong , Wen Jing , Fu Tingdong , Yi Bin
Published: November 2022

Rapeseed (Brassica napus L.) is one of the most important oil crops in the world. The planting area and output of rapeseed are affected by the flowering time, which is a critical agronomic feature. COL9 controls growth and development in many different plant species as a member of the zinc finger transcription factor family. However, BnaCOL9 in rapeseed has not been documented. The aim of this study was to apply CRISPR/Cas9 technology to create an early-flowering germplasm resource to provide useful material for improving the early-maturing breeding of rapeseed. We identified four COL9 homologs in rapeseed that were distributed on chromosomes A05, C05, A03, and C03. We successfully created quadruple BnaCOL9 mutations in rapeseed using the CRISPR/Cas9 platform. The quadruple mutants of BnaCOL9 flowered earlier than the wild-type. On the other hand, the flowering time of the BnaCOL9 overexpression lines was delayed. An analysis of the expression patterns revealed that these genes were substantially expressed in the leaves and flowers. A subcellular localization experiment demonstrated that BnaCOL9 was in the nucleus. Furthermore, we discovered that two key flowering-related genes, BnaCO and BnaFT, were highly elevated in the BnaCOL9 mutants, but dramatically downregulated in the BnaCOL9 overexpression lines. Our findings demonstrate that BnaCOL9 is a significant flowering inhibitor in rapeseed and may be employed as a crucial gene for early-maturing breeding.
Choosing the Probe for Single-Molecule Fluorescence Microscopy
Authors: Schirripa Spagnolo Chiara , Luin Stefano
Published: November 2022

Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
N-Linked Glycosylation in Chinese Hamster Ovary Cells Is Critical for Insulin-like Growth Factor 1 Signaling
Authors: Salvi Rupashree , Kumar Chandan , Brahmbhatt Krupanshi , Subedi Rambhadur , Idicula-Thomas Susan , Madan Taruna , Biswas Barnali
Published: November 2022

Cell surface proteins carrying N-glycans play important roles in inter- and intracellular processes including cell adhesion, development, and cellular recognition. Dysregulation of the glycosylation machinery has been implicated in various diseases, and investigation of global differential cell surface proteome effects due to the loss of N-glycosylation will provide comprehensive insights into their pathogenesis. Cell surface proteins isolated from Parent Pro–5 CHO cells (W5 cells), two CHO mutants with loss of N-glycosylation function derived from Pro–5 CHO (Lec1 and Lec4 cells), were subjected to proteome analysis via high-resolution LCMS. We identified 44 and 43 differentially expressed membrane proteins in Lec1 and Lec4 cells, respectively, as compared to W5 cells. The defective N-glycosylation mutants showed increased abundance of integrin subunits in Lec1 and Lec4 cells at the cell surface. We also found significantly reduced levels of IGF-1R (Insulin like growth factor-1 receptor); a receptor tyrosine kinase; and the GTPase activating protein IQGAP1 (IQ motif-containing GTPase activating protein), a highly conserved cytoplasmic scaffold protein) in Lec1 and Lec4 cells. In silico docking studies showed that the IQ domain of IQGAP1 interacts with the kinase domain of IGF-1R. The integrin signaling and insulin growth factor receptor signaling were also enriched according to GSEA analysis and pathway analysis of differentially expressed proteins. Significant reductions of phosphorylation of ERK1 and ERK2 in Lec1 and Lec4 cells were observed upon IGF-1R ligand (IGF-1 LR3) stimulation. IGF-1 LR3, known as Long arginine3-IGF-1, is a synthetic protein and lengthened analog of insulin-like growth factor 1. The work suggests a novel mechanism for the activation of IGF-1 dependent ERK signaling in CHO cells, wherein IQGAP1 plausibly functions as an IGF-1R-associated scaffold protein. Appropriate glycosylation by the enzymes MGAT1 and MGAT5 is thus essential for processing of cell surface receptor IGF-1R, a potential binding partner in IQGAP1 and ERK signaling, the integral components of the IGF pathway.