Genome‑wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN‑in Physcomitrella patens and stress responses

Xiaolong Huang,Huiqing Yan,Yanjing Liu,Yin Yi 한국유전학회 2020 Genes & Genomics Vol.42 No.6

Background LBDs, as the plant-specific gene family, play essential roles in lateral organ development, plant regeneration, as well as abiotic stress and pathogen response. However, the number and characteristic of LBD genes in Pyscomitrella patens were still obscure. Objective This study was performed to identify the LBD family gene in moss and to determine the expression profiles of LBDs under the abiotic and pathogen stress. Methods Complete genome sequences and transcriptomes of P. patens were downloaded from the Ensembl plant database. The hidden Markov model-based profile of the conserved LOB domain was submitted as a query to identify all potential LOB domain sequences with HMMER software. Expression profiles of PpLBDs were obtained based on the GEO public database and qRT-PCR analysis. Results In this study, a total of 31 LBDs were identified in the P. patens genome, divided into two classes based on the presence of the leucine zipper-like coiled-coil motif. A phylogenetic relationship was obtained between 31 proteins from P. patens and 43 proteins from the Arabidopsis thaliana genome, providing insights into their conserved and potential functions. Furthermore, the exon–intron organization of each PpLBD were analyzed. All PpLBD contain the conserved DNA binding motif (CX2CX6CX3C zinc finger-like motif), and were predicted to be located in cell nuclear. The 31 PpLBD genes were unevenly assigned to 18 out of 27 chromosomes based on the physical positions. Among these genes, PpLBD27 was not only remarkably highest expressed in desiccation, but also a susceptible gene to pathogens through jasmonic acid-mediated signaling pathway. Most of PpLBDs were up-regulated with the treatment of mannitol. These results showed they were differentially induced and their potential functions in the environmental stimulus of the early terrestrial colonizers. Conclusion Despite significant differences in the life cycle in P. patens and flowering plants, their functions involved in abiotic and biotic stress-regulated by LBDs have been identified and appear to be conserved in the two lineages. These results provided a comprehensive analysis of PpLBDs and paved insights into studies aimed at a better understanding of PpLBDs.

Iron metabolism protein transferrin receptor 1 involves in cervical cancer progression by affecting gene expression and alternative splicing in HeLa cells

Huang Nan,Wei Yaxun,Cheng Yi,Wang Xiaolong,Wang Qi,Chen Dong,Li Wenjing 한국유전학회 2022 Genes & Genomics Vol.44 No.6

Background: Transferrin receptor 1 (TfR1), encoded by TFRC, is a key regulator of iron homeostasis and plays important roles in many diseases, including cancers. Objective: To decipher the underlying molecular functions of TfR1 based on its influence on transcriptome profile in cancer cells. Methods: In this study, we first identified the expression pattern and prognostic influence of TFRC in cervical cancer patients from TCGA database. To explore the regulatory outcomes of TfR1 from the view of whole transcriptome profile, we generated TFRC knockdown (TFRC-KD) HeLa cells and negative control (NC) cells using short hairpin RNA (shRNA) method. Unbiased transcriptome sequencing (RNA-seq) experiment was used to analyze the global expression level and alternative splicing (AS) changes between TFRC-KD and NC cells. Results: We found TFRC was consistently elevated in cervical cancer samples and tightly associated with prognosis of patients. Differential expression analysis revealed that 629 differentially expressed genes (DEGs) were identified between TFRC-KD and NC. Functional enrichment analysis of these DEGs revealed that TFRC-KD extensively disturbed cell physiology related pathways, including immunity, cell metabolism and gene expression. Moreover, dysregulated AS profile also indicated that TfR1 has important roles in the AS regulation. Hundreds of TfR1-regulated AS genes were involved in DNA repair, cell death, transcription and viral reproduction pathways, which were tightly associated with cancer cell progression. Conclusions: In summary, we for the first time explored the molecular functions of TfR1 at transcriptional and post-transcriptional levels. These results demonstrate TfR1 participates in the progression of cervical cancer by affecting the expression and AS levels of genes in cancer associated pathways, which greatly extends our understanding of TfR1 functions besides iron homeostasis and provide novel options in cancer treatment by targeting TfR1.

Genome wide association study on feed conversion ratio using imputed sequence data in chickens

Jiaying Wang,Xiaolong Yuan,Shaopan Ye,Shuwen Huang,Yingting He,Hao Zhang,Jiaqi Li,Xiquan Zhang,Zhe Zhang 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.4

Objective: Feed consumption contributes a large percentage for total production costs in the poultry industry. Detecting genes associated with feeding traits will be of benefit to improve our understanding of the molecular determinants for feed efficiency. The objective of this study was to identify candidate genes associated with feed conversion ratio (FCR) via genome-wide association study (GWAS) using sequence data imputed from single nucleotide polymorphism (SNP) panel in a Chinese indigenous chicken population. Methods: A total of 435 Chinese indigenous chickens were phenotyped for FCR and were genotyped using a 600K SNP genotyping array. Twenty-four birds were selected for sequencing, and the 600K SNP panel data were imputed to whole sequence data with the 24 birds as the reference. The GWAS were performed with GEMMA software. Results: After quality control, 8,626,020 SNPs were used for sequence based GWAS, in which ten significant genomic regions were detected to be associated with FCR. Ten candidate genes, ubiquitin specific peptidase 44, leukotriene A4 hydrolase, ETS transcription factor, R-spondin 2, inhibitor of apoptosis protein 3, sosondowah ankyrin repeat domain family member D, calmodulin regulated spectrin associated protein family member 2, zinc finger and BTB domain containing 41, potassium sodium-activated channel subfamily T member 2, and member of RAS oncogene family were annotated. Several of them were within or near the reported FCR quantitative trait loci, and others were newly reported. Conclusion: Results from this study provide valuable prior information on chicken genomic breeding programs, and potentially improve our understanding of the molecular mechanism for feeding traits.

The study of blood transcriptome profiles in Holstein cows with miscarriage during peri-implantation

Guoli Zhao,Yanyan Li,Xiaolong Kang,Liang Huang,Peng Li,Jinghang Zhou,Yuangang Shi 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.1

Objective: In this study, the transcriptome profile of cow experiencing miscarriage during peri-implantation was investigated. Methods: Total transcriptomes were checked by RNA sequencing, and the analyzed by bioinformatics methods, the differentially expressed genes (DEGs) were analysed with hierarchical clustering and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Results: The results suggested that serum progesterone levels were significantly decreased in cows that miscarried as compared to the pregnant cows at 18, 21, 33, 39, and 51 days after artificial insemination. The RNA sequencing results suggested that 32, 176, 5, 10, and 2 DEGs were identified in the pregnant cows and miscarried cows at 18, 21, 33, 39, and 51 d after artificial insemination. And 15, 101, 1, 2, and 2 DEGs were upregulated, and 17, 74, 4, and 8 DEGs were downregulated in the cows in the pregnant and miscarriage groups, respectively at 18, 21, 33, and 39, but no gene was downregulated at 51 d after artificial insemination. These DEGs were distributed to 13, 20, 3, 6, and 20 pathways, and some pathway essential for pregnancy, such as cell adhesion molecules, tumor necrosis factor signaling pathway and PI3K-Akt signaling pathway. Conclusion: This analysis has identified several genes and related pathways crucial for pregnancy and miscarriage in cows, as well as these genes supply molecular markers to predict the miscarriage in cows.

Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata

Guo Mengpei,Ma Xiaolong,Zhou Yan,Bian Yinbing,Liu Gaolei,Cai Yingli,Huang Tianji,Dong Hongxia,Cai Dingjun,Wan Xueji,Wang Zhihong,Xiao Yang,Kang Heng 한국미생물학회 2023 The journal of microbiology Vol.61 No.1

The basidiomycetous edible mushroom Stropharia rugosoannulata has excellent nutrition, medicine, bioremediation, and biocontrol properties. S. rugosoannulata has been widely and easily cultivated using agricultural by-products showing strong lignocellulose degradation capacity. However, the unavailable high-quality genome information has hindered the research on gene function and molecular breeding of S. rugosoannulata. This study provided a high-quality genome assembly and annotation from S. rugosoannulata monokaryotic strain QGU27 based on combined Illumina-Nanopore data. The genome size was about 47.97 Mb and consisted of 20 scaffolds, with an N50 of 3.73 Mb and a GC content of 47.9%. The repetitive sequences accounted for 17.41% of the genome, mostly long terminal repeats (LTRs). A total of 15,726 coding gene sequences were putatively identified with the BUSCO score of 98.7%. There are 142 genes encoding plant cell wall degrading enzymes (PCWDEs) in the genome, and 52, 39, 30, 11, 8, and 2 genes related to lignin, cellulose, hemicellulose, pectin, chitin, and cutin degradation, respectively. Comparative genomic analysis revealed that S. rugosoannulata is superior in utilizing aldehyde-containing lignins and is possible to utilize algae during the cultivation.

Increased Wall Enhancement Extent Representing Higher Rupture Risk of Unruptured Intracranial Aneurysms

Jiang, Yeqing,Xu, Feng,Huang, Lei,Lu, Gang,Ge, Liang,Wan, Hailin,Geng, Daoying,Zhang, Xiaolong The Korean Neurosurgical Society 2021 Journal of Korean neurosurgical society Vol.64 No.2

Objective : This study aims to investigate the relationship between aneurysm wall enhancement and clinical rupture risks based on the magnetic resonance vessel wall imaging (MR-VWI) quantitative methods. Methods : One hundred and eight patients with 127 unruptured aneurysms were prospectively enrolled from Feburary 2016 to October 2017. Aneurysms were divided into high risk (≥10) and intermediate-low risk group (<10) according to the PHASES (Population, Hypertension, Age, Size of aneurysm, Earlier SAH history from another aneurysm, Site of aneurysm) scores. Clinical risk factors, aneurysm morphology, and wall enhancement index (WEI) calculated using 3D MR-VWI were analyzed and compared. Results : In comparison of high-risk and intermediated-low risk groups, univariate analysis showed that neck width (4.5±3.3 mm vs. 3.4±1.7 mm, p=0.002), the presence of wall enhancement (100.0% vs. 62.9%, p<0.001), and WEI (1.6±0.6 vs. 0.8±0.8, p<0.001) were significantly associated with high rupture risk. Multivariate regression analysis revealed that WEI was the most important factor in predicting high rupture risk (odds ratio, 2.6; 95% confidence interval, 1.4-4.9; p=0.002). The receiver operating characteristic (ROC) curve analysis can efficiently differentiate higher risk aneurysms (area under the curve, 0.780; p<0.001) which have a reliable WEI cutoff value (1.04; sensitivity, 0.833; specificity, 0.67) predictive of high rupture risk. Conclusion : Aneurysms with higher rupture risk based on PHASES score demonstrate increased neck width, wall enhancement, and the enhancement intensity. Higher WEI in unruptured aneurysms has a predictive value for increased rupture risk.

Nanofibrous Membranes with High Air Permeability and Fluffy Structure based on Low Temperature Electrospinning Technology

Siying Lin,Xiang Huang,Zhenxiang Bu,Zhihong Lin,Peiqin Xie,Xiaolong Lin,Lingyun Wang,Wenlong Lv 한국섬유공학회 2020 Fibers and polymers Vol.21 No.7

Due to its small diameter and high density, electrospun nanofiber membranes have high resistance which obstaclestheir application. In this paper, we proposed a new electrospinning method based on low-temperature, which can affect thedeposition process of electrospinning by utilizing the freezing process of steam in the receiving plate. The filling andsupporting of ice could enlarge the pores of membranes and intervals among fibers, which caused the high porosity (92 %),rough surface, fluffy structure and low pressure drop (123 Pa) of polyvinylidene fluoride (PVDF) nanofibrous membranes. The results suggested that the electrospinning method is a promising way to prepare nanofibrous membranes with high airpermeability and fluffy structure for air filtration.

Systemic Reactions to Dust Mite Subcutaneous Immunotherapy: A 3-Year Follow-up Study

Xiang Dong,Nan Huang,Wenjing Li,Lintao Hu,Xiaolong Wang,Yin Wang,Ning Xiang,Guanghui Liu,Rongfei Zhu 대한천식알레르기학회 2016 Allergy, Asthma & Immunology Research Vol.8 No.5

Purpose: The incidence of allergen specific immunotherapy-related systemic reactions (SRs) varies among different studies, and many factors are likely to contribute to SRs. This study aims to investigate the incidence, characteristics, and risk factors of SRs to standardize dust mite-specific subcutaneous immunotherapy (SCIT) in Central China. Methods: All patients receiving standardized dust mites (100-100,000 SQ-U/mL; Alutard SQ, Hørsholn, Denmark) immunotherapy were followed up. Recorded data included demographics, diagnosis, patient status, pulmonary function testing results before and after each injection, allergen dosage, and details of SRs. Results: From June 2011 to August 2014, a total of 208 patients received 4,369 injections; 27 (13.0%) patients experienced 48 (1.1%) systemic reactions. Most of the SRs were grade 2 reactions (n=30, 62.5%), followed by grade 1 (n=11, 22.9%), grade 3 (n=7, 14.6%), and no fatal reactions occurred. Forty-six SRs (95.8%) occurred within 30 minutes. Higher SR rates were associated with high concentration extracts (100,000 SQ-U/mL), injections with concomitant local reactions (LRs), children, asthma and high sensitivity (skin prick test 3+/4+ and/or sIgE≥17.5 kUA/L) (P<0.05). The estimated odds of SRs increased in children (OR=6.57; 95% CI: 1.88-22.97, P=0.003), asthmatic patients (OR=4.10; 95% CI: 1.72-9.80, P=0.002), and injections with LRs (OR=2.41; 95% CI: 1.33-4.36, P=0.004).Conclusions: The incidence of SRs to dust mite SCIT was low, and multiple factors were associated with the increased incidence of SRs. Children, asthmatics and patients with concomitant LR may be prone to develop SRs.

Long-Term Outcomes of Stenting on Non-Acute Phase Extracranial Supra-Aortic Dissections

Jiang, Yeqing,Di, Ruoyu,Lu, Gang,Huang, Lei,Wan, Hailin,Ge, Liang,Zhang, Xiaolong The Korean Neurosurgical Society 2022 Journal of Korean neurosurgical society Vol.65 No.3

Objective : Extracranial supra-aortic dissections (ESADs) with severe stenosis, occlusion and/or pseudoaneurysm presents potential risk of stroke. Endovascular stenting to reconstruct non acute phase ESADs (NAP-ESADs) is an alternative to anticoagulant or antiplatelet therapy. However, its feasibility, safety and efficacy of stenting in NAP-ESADs is unclear. This study aims to investigate the long-term outcomes of the feasibility, safety and efficacy of stenting in NAP-ESADs. Methods : Seventy-four patients with 91 NAP-ESAD vessels with severe stenosis, occlusion and/or pseudoaneurysm presents potential risk of stroke who underwent stent remodeling were enrolled into this respective study from December 2008 to March 2020. Technical success rate, complications, clinical and angiographic results were harvested and analyzed. Results : Success rate of stent deployment was 99% (90/91) with no procedural mortality or morbidity. Transient ischemic attack occurred in three patients during operation (4.1%, 3/74). Asymptomatic embolisms of distal intracranial vessels were found in two patients (2.7%, 2/74). One hundred and forty-two stents deployed at 85 carotid (135 stents) and six vertebral (seven stents) vessels. Six stent types (Wingspan, 28/135, 20.7%; Solitaire, 10/135, 7.4%; Neuroform, 8/135, 5.9%; LVIS, 2/135, 1.5%; Precise, 75/135, 55.6%; Acculink, 12/135, 8.9%) were deployed at carotid arterial dissection while two types (Wingspan, 5/7, 71.4%; Solitaire 2/7, 28.6%) at vertebral arterial dissection. Digital subtracted angiography (56%, 51/91), computational tomography angiography (41.8%, 38/91) and high resolution magnetic resonance imaging (2.2%, 2/91) were adopted for follow up, with a mean time of 17.2±15.4 months (5-77). All patient modified Rankin Scale scores showed no increase at discharge or follow-up. Angiographically, dissections in 86 vessels in 69 patients (94.5%, 86/91) were completely reconstructed with only minor remnant dissections in four vessels in four patients (4.4%, 4/91). Severe re-stenosis in the stented segment required re-stenting in one patient (1.1%, 1/91). Conclusion : Stent remodeling technique provides feasible, safe and efficacious treatment of ESADs patients with severe stenosis, occlusion and/or pseudoaneurysm.

Consistency of Existing Decay Data Bases

V. Chechev,S. Badikov,T. Golashvili,Huang Xiaolong,Ge Zhigang,Wu Zhendong 한국물리학회 2011 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.59 No.23

Consistency of the widely used decay data bases (ENSDF, NUBASE, NWC (Nuclear Wallet Cards), DDEP (Decay Data Evaluation Project) ) were analyzed within the framework of joint Chinese-Russian research project. Two decay characteristics (the half-life and the average energies of radiation) - were considered.The evaluated half-life data for nuclides important for applications is consistent within declared uncertainties. The only deficiency is an absence of generally accepted procedure for evaluation of the half-life values and their uncertainties on the basis of the discrepant experimental data. As a result some agreements (like the 0.1% rule) are used for correction of calculated uncertainties of the half-life evaluations. To justify and check the half-life evaluated data a new statistical procedure taking unrecognized experimental errors into account was developed. The procedure was applied for processing discrepant experimental data. The results of the calculations are compared to the ENSDF and DDEP evaluations. Applying new procedure results in more realistic uncertainties of the half-life evaluations. There are essential inconsistencies between the ENSDF, NUBASE and NWC evaluations for short-lived nuclides. A list of nuclides with the largest discrepancies was compiled and presented. For resolving the inconsistencies new measurements must be carried out.The average energies of radiation for nuclides important for applications were calculated. There exists a good agreement between the calculated values and the ENDF/B-VII (converted from the ENSDF) and JEFF-3.1 evaluations. In both the libraries the discrete gamma-ray spectra are presented as a set of the gamma-ray energies and absolute intensities. It was emphasized that the calculation of the average gamma-ray energy on the basis of this information results in systematical underestimating the uncertainty of the energy compared to a value calculated with using relative intensities. This effect is similar to so called Peelle's Pertinent Puzzle.