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1.
Biomark Res ; 12(1): 48, 2024 May 11.
Article in English | MEDLINE | ID: mdl-38730450

ABSTRACT

BACKGROUND: Tumors exhibit metabolic heterogeneity, influencing cancer progression. However, understanding metabolic diversity in retinoblastoma (RB), the primary intraocular malignancy in children, remains limited. METHODS: The metabolic landscape of RB was constructed based on single-cell transcriptomic sequencing from 11 RB and 5 retina samples. Various analyses were conducted, including assessing overall metabolic activity, metabolic heterogeneity, and the correlation between hypoxia and metabolic pathways. Additionally, the expression pattern of the monocarboxylate transporter (MCT) family in different cell clusters was examined. Validation assays of MCT1 expression and function in RB cell lines were performed. The therapeutic potential of targeting MCT1 was evaluated using an orthotopic xenograft model. A cohort of 47 RB patients was analyzed to evaluate the relationship between MCT1 expression and tumor invasion. RESULTS: Distinct metabolic patterns in RB cells, notably increased glycolysis, were identified. This metabolic heterogeneity correlated closely with hypoxia. MCT1 emerged as the primary monocarboxylate transporter in RB cells. Disrupting MCT1 altered cell viability and energy metabolism. In vivo studies using the MCT1 inhibitor AZD3965 effectively suppressed RB tumor growth. Additionally, a correlation between MCT1 expression and optic nerve invasion in RB samples suggested prognostic implications. CONCLUSIONS: This study enhances our understanding of RB metabolic characteristics at the single-cell level, highlighting the significance of MCT1 in RB pathogenesis. Targeting MCT1 holds promise as a therapeutic strategy for combating RB, with potential prognostic implications.

2.
BMC Genomics ; 25(1): 117, 2024 Jan 26.
Article in English | MEDLINE | ID: mdl-38279081

ABSTRACT

BACKGROUND: In cellular activities, essential proteins play a vital role and are instrumental in comprehending fundamental biological necessities and identifying pathogenic genes. Current deep learning approaches for predicting essential proteins underutilize the potential of gene expression data and are inadequate for the exploration of dynamic networks with limited evaluation across diverse species. RESULTS: We introduce ECDEP, an essential protein identification model based on evolutionary community discovery. ECDEP integrates temporal gene expression data with a protein-protein interaction (PPI) network and employs the 3-Sigma rule to eliminate outliers at each time point, constructing a dynamic network. Next, we utilize edge birth and death information to establish an interaction streaming source to feed into the evolutionary community discovery algorithm and then identify overlapping communities during the evolution of the dynamic network. SVM recursive feature elimination (RFE) is applied to extract the most informative communities, which are combined with subcellular localization data for classification predictions. We assess the performance of ECDEP by comparing it against ten centrality methods, four shallow machine learning methods with RFE, and two deep learning methods that incorporate multiple biological data sources on Saccharomyces. Cerevisiae (S. cerevisiae), Homo sapiens (H. sapiens), Mus musculus, and Caenorhabditis elegans. ECDEP achieves an AP value of 0.86 on the H. sapiens dataset and the contribution ratio of community features in classification reaches 0.54 on the S. cerevisiae (Krogan) dataset. CONCLUSIONS: Our proposed method adeptly integrates network dynamics and yields outstanding results across various datasets. Furthermore, the incorporation of evolutionary community discovery algorithms amplifies the capacity of gene expression data in classification.


Subject(s)
Protein Interaction Maps , Saccharomyces cerevisiae , Animals , Mice , Humans , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Algorithms , Proteins/metabolism , Caenorhabditis elegans/genetics , Caenorhabditis elegans/metabolism
3.
Invest Ophthalmol Vis Sci ; 65(1): 31, 2024 Jan 02.
Article in English | MEDLINE | ID: mdl-38231525

ABSTRACT

Purpose: To explore the expression patterns and clinical significance of minichromosome maintenance (MCM) complex members in retinoblastoma (RB). Methods: Single-cell RNA sequencing datasets from five normal retina, six intraocular, and five extraocular RB samples were integrated to characterize the expression patterns of MCM complex members at the single-cell level. Western blot and quantitative PCR were used to detect the expression of MCM complex members in RB cell lines. Immunohistochemistry was conducted to validate the expression of MCM complex members in RB patient samples and a RB mouse model. Results: The expression of MCM2-7 is increased in RB tissue, with MCM2/3/7 showing particularly higher levels in extraocular RB. MCM3/7 are abundantly detected in cell types associated with oncogenesis. Both mRNA and protein levels of MCM3/4/6/7 are increased in RB cell lines. Immunohistochemistry further confirmed the elevated expression of MCM3 in extraocular RB, with MCM6 being the most abundantly expressed MCM in RB. Conclusions: The distinct MCM expression patterns across various RB cell types suggest diverse functional roles, offering valuable insights for targeted therapeutic strategies. The upregulation of MCM3, MCM4, MCM6, and MCM7 in RB, with a specific emphasis on MCM6 as a notable marker, highlights their potential significance.


Subject(s)
Retinal Neoplasms , Retinoblastoma , Animals , Mice , Humans , Clinical Relevance , Retinoblastoma/genetics , Cell Nucleus , Blotting, Western , Retinal Neoplasms/genetics
4.
Medicine (Baltimore) ; 103(2): e36889, 2024 Jan 12.
Article in English | MEDLINE | ID: mdl-38215100

ABSTRACT

RATIONALE: Diffuse multivessel coronary artery spasm (DMV-CAS) was defined as a severe and reversible diffuse spasm occurring in more than 2 major coronary arteries, which is rare in clinical practice. Due to a wide lesion scope, DMV-CAS often occurs in the form of complications. It is not easy to be clinically diagnosed because it is too brief to be caught. Here, we report a rare case of spontaneous subtotal occlusion of 3 major coronary arteries induced by Vasalva action, which was confirmed in real-time by CAG. PATIENT CONCERNS: A 68-year-old man had sudden chest pain after forced defecation during hospitalization. The electrocardiogram showed transient ST segment elevation of the inferior wall lead, inversion of the anterior wall, and lateral wall leads T waves. Emergency CAG revealed elongated vessel beds in 3 coronary arteries and multiple diffuse stenosis, but none of the coronary arteries were completely occlusive. DIAGNOSES: Diagnoses of DMV-CAS were made based on CAG findings and postmedication response. INTERVENTIONS: Nitroglycerin was administered in the coronary arteries. The anti-vasospasm, antiplatelet aggregation and lipid-regulating drugs were administered orally. OUTCOMES: The patient was discharged on the 7th day with complete resolution of symptoms and normalization of the electrocardiography findings. No ischemic events occurred during a follow-up for 5 months. LESSONS: This case highlights the identification of multivessel diffuse coronary spasm and acute myocardial infarction, and the prevention of CAS triggers, which requires the attention of clinicians.


Subject(s)
Coronary Vasospasm , Myocardial Infarction , Male , Humans , Aged , Coronary Vessels/diagnostic imaging , Coronary Angiography/adverse effects , Coronary Vasospasm/complications , Coronary Vasospasm/diagnosis , Myocardial Infarction/complications , Nitroglycerin/therapeutic use , Electrocardiography , Arrhythmias, Cardiac/drug therapy
5.
J Genet Genomics ; 51(4): 433-442, 2024 Apr.
Article in English | MEDLINE | ID: mdl-37751845

ABSTRACT

T-box transcription factor T (TBXT; T) is required for mesodermal formation and axial skeletal development. Although it has been extensively studied in various model organisms, human congenital vertebral malformations (CVMs) involving T are not well established. Here, we report a family with 15 CVM patients distributed across 4 generations. All affected individuals carry a heterozygous mutation, T c.596A>G (p.Q199R), which is not found in unaffected family members, indicating co-segregation of the genotype and phenotype. In vitro assays show that T p.Q199R increases the nucleocytoplasmic ratio and enhances its DNA-binding affinity, but reduces its transcriptional activity compared to the wild-type. To determine the pathogenicity of this mutation in vivo, we generated a Q199R knock-in mouse model that recapitulates the human CVM phenotype. Most heterozygous Q199R mice show subtle kinked or shortened tails, while homozygous mice exhibit tail filaments and severe vertebral deformities. Overall, we show that the Q199R mutation in T causes CVM in humans and mice, providing previously unreported evidence supporting the function of T in the genetic etiology of human CVM.

6.
Clin Nutr ; 42(11): 2207-2213, 2023 11.
Article in English | MEDLINE | ID: mdl-37804577

ABSTRACT

AIM: To investigate nutritional risk across children in their first 2 years at child health care clinics in Jiangsu, China, and to highlight the importance of nutritional risk screening in outpatient clinics. METHODS: A multi-centre, cross-sectional, observational study was conducted among outpatients in child health care clinics. Nutritional risk screening using the STRONGkids tool and anthropometric assessments were performed on children under 2 years old at outpatient initial visits in ten hospitals from March 2021 to March 2022. RESULTS: There were 11,454 children enrolled. The percentages of children with high, moderate and low nutritional risk were 2.0% (228), 28.2% (3229) and 69.8% (7997), respectively. The occurrence rate of high nutritional risk was higher in female children than in male children (p < 0.05). The incidence of moderate nutritional risk in infants was significantly higher than in children aged ≥12 months (p < 0.01). Children with moderate or high nutritional risk more frequently answered 'yes' to the STRONGkids item 'high risk disease or major surgery planned'. The top three diagnoses related to nutritional risk were prematurity (50.5%), food allergy (14.3%) and recurrent respiratory disease (10.7%). In addition, the incidence of chronic undernutrition in children with moderate (14.0%) or high nutritional risk (36.4%) was significantly higher than acute undernutrition (p < 0.01). CONCLUSION: Among children up to 2 years of age seen in child health clinics, nutritional risk associated with prematurity and potential disease requires special attention. Nutritional risk screening should be part of child health care, and STRONGkids is a useful screening tool.


Subject(s)
Malnutrition , Nutritional Status , Child , Infant , Humans , Male , Female , Nutrition Assessment , Outpatients , Child Health , Cross-Sectional Studies , Malnutrition/diagnosis , Malnutrition/epidemiology
7.
Hortic Res ; 10(8): uhad127, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37560017

ABSTRACT

A high-quality genome is the basis for studies on functional, evolutionary, and comparative genomics. The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences, along with the emergence of a new 'telomere-to-telomere (T2T) assembly' era. However, the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited. Here, we developed a user-friendly web toolkit, quarTeT, which currently includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. First, AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome. Then, GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences. Finally, TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome. These four modules can be used alone or in combination with each other for T2T genome assembly and characterization. As a case study, by adopting the entire modular functions of quarTeT, we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0, which was assembled with the addition of manual handling. Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods. Collectively, quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration.

8.
Int J Mol Sci ; 24(14)2023 Jul 23.
Article in English | MEDLINE | ID: mdl-37511578

ABSTRACT

Garlic (Allium sativum L.) is a popular condiment used as both medicine and food. Garlic production in China is severely affected by continuous cropping and is especially affected by leaf blight disease. Garlic is sterile, so it is very important to develop specialized genotypes, such as those for disease resistance, nutritional quality, and plant architecture, through genetic modification and innovation. In this experiment, we applied the induction method using EMS to mutate garlic cloves of cultivar G024. From the mutations, 5000 M0 mutants were generated and planted in the field. Then, 199 M1 mutant lines were screened according to growth potential and resistance to leaf blight. From M2 to M3, 169 generational lines were selected that grew well and were resistant to leaf blight in the field. Thereafter, their resistance to leaf blight was further analyzed in the lab; 21 lines resistant to leaf blight that had good growth potential were identified, among which 3 mutants were significantly different, and these were further screened. Also, transcriptome analysis of two mutants infected with Pleospora herbarum, A150 and G024, was performed, and the results revealed 2026 and 4678 differentially expressed genes (DEGs), respectively. These DEGs were highly enriched in hormone signaling pathway, plant-pathogen interaction, and MAPK signaling pathway. Therefore, the results provide a theoretical and technical basis for the creation of garlic germplasm resistant to leaf blight.


Subject(s)
Ascomycota , Garlic , Garlic/genetics , Ethyl Methanesulfonate/metabolism , Plants , Methane/metabolism
9.
Plant Dis ; 107(12): 3851-3857, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37272044

ABSTRACT

Plant grafting can provide resistance to nematodes. There is a distinct need to determine the role of Meloidogyne incognita-resistant rootstocks on the growth and quality of grafted cucumber plants. Cucumber (Cucumis sativus L.) cultivar Jinchun No. 4 (J) was hole grafted onto the pumpkin (Cucurbita moschata) cultivars Xiuli (X), Banzhen No. 3 (B), and its root to generate JX, JB, and JJ plants. The histopathology and M. incognita development associated with JX, JB, and JJ were analyzed under incubator and high plastic tunnel conditions. Under incubator conditions, M. incognita root galls and egg mass indices associated with the JX and JB resistant rootstocks were significantly (P < 0.05) lower than those associated with JJ susceptible rootstocks. In addition, the number of eggs were 73.3 ± 8.8% and 85.3 ± 7.7% less, respectively. The number of second-stage juveniles (J2s) in JX roots decreased by 57.1 ± 9.2% compared with that in JJ, and the giant cell and J2 development were poor in JX and JB roots. In pot experiments under a high plastic tunnel, plant height, stem diameter, leaf area, and yield of M. incognita-infected JX plants were not significantly different from those of noninoculated control. There was no significant difference in fruit weight, length, firmness, soluble solids, and color among the three grafted plants. The yield per JB plant was increased compared with that of JJ, irrespective of nematode presence. In the M. incognita-infested soil experiment in a high plastic tunnel, the yield per JX and JB plant were significantly higher than JJ (P < 0.05). Thus, the pumpkin rootstock Xiuli and Banzhen No. 3 are promising rootstocks for managing M. incognita without affecting cucumber fruit quality. Grafting provides a good basis for studying the defense mechanism of rootstocks against M. incognita.


Subject(s)
Cucumis sativus , Cucurbita , Tylenchoidea , Animals , Fruit , Plant Roots
10.
Ophthalmic Res ; 66(1): 1014-1019, 2023.
Article in English | MEDLINE | ID: mdl-37311441

ABSTRACT

INTRODUCTION: The enhancer of zeste homolog 2 (EZH2) is a member of the polycomb repressive complex 2 (PRC2) and is important in cell-cycle regulation. Increased expression of EZH2 has been reported in retinoblastoma (RB). The aim of the study was to determine EZH2 expression, compare this with clinicopathological parameters in RB, and assess its relationship with tumor cell proliferation. METHODS: Ninety-nine retrospective cases of enucleated RB were included in the present study. Expression of EZH2 and the marker of cell proliferation, Ki67, were investigated by immunohistochemistry. RESULTS: Among the 99 cases of RB in this study, EZH2 was found highly expressed (positive expression rate ≥70%) in 92 cases. EZH2 was expressed in tumor cells but absent in normal retinal tissues. The expression of EZH2 was positively linked to Ki67 expression (r = 0.65, p < 0.001). CONCLUSION: Elevated EZH2 expression was found in most RB cases, indicating that EZH2 could be a potential therapeutic target for RB.


Subject(s)
Retinal Neoplasms , Retinoblastoma , Humans , Enhancer of Zeste Homolog 2 Protein , Ki-67 Antigen , Retrospective Studies , Cell Proliferation
11.
Opt Express ; 31(6): 9515-9525, 2023 Mar 13.
Article in English | MEDLINE | ID: mdl-37157520

ABSTRACT

Topological insulator bismuth has attracted considerable attention for the fabrication of room-temperature, wide bandwidth, and high-performance photodetectors due to the gapless edge state and insulating bulk state properties. However, both the photoelectric conversion and carrier transportation of the bismuth films are extremely affected by the surface morphology and grain boundaries to limit optoelectronic properties further. Here, we demonstrate a strategy of femtosecond laser treatment for upgrading the quality of bismuth films. After the treatment with proper laser parameters, the measurement of average surface roughness can be reduced from Ra = 44 nm to 6.9 nm, especially with accompany of the evident grain boundary elimination. Consequently, the photoresponsivity of the bismuth films increases approximately 2 times within an ultra-broad spectrum range from the visible to mid-infrared. This investigation suggests that the femtosecond laser treatment can help to benefit the performance of topological insulator ultra-broadband photodetectors.

12.
SAGE Open Med Case Rep ; 11: 2050313X231172873, 2023.
Article in English | MEDLINE | ID: mdl-37187494

ABSTRACT

In patients with symptomatic atrial fibrillation refractory to optimal medical therapy, atrioventricular node ablation followed by permanent pacemaker implantation is an effective treatment option. A 66-year-old woman with symptomatic persistent atrial fibrillation refractory to multiple ablation procedures was referred to our institution. After optimal drug therapy, the patient still had obvious symptoms. Sequential His-Purkinje conduction system pacing and atrioventricular node ablation were performed. Left bundle branch pacing was used as a backup pacing method if thresholds of His bundle pacing were too high or loss of His bundle capture occurred in the follow-up. At the 6-month follow-up, the European Heart Rhythm Association classification for AF was improved, the score of the Atrial Fibrillation Effect on Quality of Life was enhanced, and the 6-Minute Walk Test was ameliorated. The present case was subjected to His-Purkinje conduction system pacing in combination with atrioventricular node ablation as treatment for a symptomatic persistent atrial fibrillation refractory to multiple ablation procedures, and this procedure alleviated symptoms and improved the quality of life in a short-term follow-up.

13.
Eur J Med Chem ; 254: 115346, 2023 Jun 05.
Article in English | MEDLINE | ID: mdl-37043994

ABSTRACT

A series of quinazolin-4(3H)-one derivatives was designed through scaffold-hopping strategy and synthesized as novel multifunctional anti-AD agents demonstrating both cholinesterase inhibition and anti-inflammatory activities. Their inhibitory activities against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) were evaluated, and the enzyme kinetics study as well as detailed binding mode via molecular docking were performed for selected compounds. MR2938 (B12) displayed promising AChE inhibitory activity with an IC50 value of 5.04 µM and suppressed NO production obviously (IC50 = 3.29 µM). Besides, it was able to decrease the mRNA levels of pro-inflammatory cytokines IL-1ß, TNF-α, IL-6 and CCL2 at 1.25 µM. Further mechanism study suggested that MR2938 suppressed the neuroinflammation through blocking MAPK/JNK and NF-κB signaling pathways. All these results indicate that MR2938 is a good starting point to develop multifunctional anti-AD lead compounds.


Subject(s)
Alzheimer Disease , Cholinesterase Inhibitors , Humans , Cholinesterase Inhibitors/chemistry , Butyrylcholinesterase/metabolism , Acetylcholinesterase/metabolism , Molecular Docking Simulation , Structure-Activity Relationship
14.
Biotechnol Genet Eng Rev ; : 1-11, 2023 Mar 30.
Article in English | MEDLINE | ID: mdl-36994831

ABSTRACT

To explore the value of ultrasound elastography combined with serological indicators in the diagnosis of liver fibrosis in chronic hepatitis B. A total of 156 patients with chronic hepatitis B from April 2020 to February 2022 were enrolled in this study as subjects. They were assigned to the liver fibrosis group (n=115) and the non-liver fibrosis group (n=41) according to whether the patients had liver fibrosis. They were divided into S1 stage (n=48), S2 stage (n=38), and S3 stage (n=29) according to histopathological staging criteria. Shear wave elastography (SWE) values, serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), procollagen type III (PCIII), and laminin (LN) were compared among patients in each stage. Spearman's method was utilized to analyze the correlation of liver serum biochemical indicators and SWE value with liver fibrosis. The predictive performance of SWE value and serological indicators was analyzed using receiver operating characteristic curves. According to Spearman's method, the liver fibrosis stage was positively correlated with SWE value. Serological indicators combined with ultrasound elastography can accurately assess the degree of liver fibrosis in patients with chronic hepatitis B and provide a basis for clinical judgment.

15.
Hepatol Commun ; 7(2): e0021, 2023 02 01.
Article in English | MEDLINE | ID: mdl-36724124

ABSTRACT

Endothelial cell (EC) function declines with age and contributes to the development of many vascular-related disease processes. Currently, the effects of aging on the molecular regulatory mechanisms of liver ECs have not been fully elucidated. Here, we employed single-cell RNA sequencing to map the transcriptome of ECs and analyzed their relationship with aging. We identified 8 different EC subtypes, interestingly, 2 of which were specially expressed in aged mice ECs namely aged capillary ECs (Aged ECs) and pro-inflammation capillary ECs (Proinfla.ECs). Double immunostaining for an EC marker (Cd31) and a marker of these specialized EC phenotypes confirmed the single-cell RNA sequencing data. Gene ontology analysis revealed that Aged ECs and Proinfla.ECs were associated with inflammatory response. Then we found that liver proliferating capillary ECs (Prolife.ECs) were most affected by senescence. Single-cell transcript analysis suggests that Prolife.ECs and angiogenic capillary ECs may form a poor microenvironment that promotes angiogenesis and tumorigenesis. Pseudo-temporal trajectories revealed that Prolife.ECs have different differentiation pathways in young and aged mice. In aged mice, Prolife.ECs could specifically differentiate into an unstable state, which was mainly composed of angiogenic capillary ECs. Intercellular communication revealed inflammatory activation in old group. Overall, this work compared the single-cell RNA profiles of liver ECs in young and aged mice. These findings provide a new insight into liver aging and its molecular mechanisms, and further exploration of Aged ECs and Proinfla.ECs may help to elucidate the molecular mechanisms associated with senescence.


Subject(s)
Endothelial Cells , Liver , Animals , Mice , Cell Differentiation , Sequence Analysis, RNA
16.
Hortic Res ; 9: uhac212, 2022.
Article in English | MEDLINE | ID: mdl-36479584

ABSTRACT

Mutants are crucial to extending our understanding of genes and their functions in higher plants. In this study a spontaneous cucumber mutant, yf, showed yellow color leaves, had significant decreases in related physiological indexes of photosynthesis characteristics, and had more abnormal chloroplasts and thylakoids. Inheritance analysis indicated that the yellow color of the leaf was controlled by a recessive nuclear locus, yf. A candidate gene, CsSRP43, encoding a chloroplast signal recognition particle 43 protein, was identified through map-based cloning and whole-genome sequence analysis. Alignment of the CsSRP43 gene homologs between both parental lines revealed a 7-kb deletion mutation including the promoter region and the coding sequence in the yf mutant. In order to determine if the CsSRP43 gene was involved in the formation of leaf color, the CRISPR/Cas9-mediate system was used to modify CsSRP43 in the 9930 background; two independent transgenic lines, srp43-1 and srp43-2, were generated, and they showed yellow leaves with abnormal chloroplasts and thylakoids. Transcriptomic analysis revealed that differentially expressed genes associated with the photosynthesis-related pathway were highly enriched between srp43-1 and wild type, most of which were significantly downregulated in line srp43-1. Furthermore, yeast two-hybrid and biomolecular fluorescence complementation assays were used to confirm that CsSRP43 directly interacted with LHCP and cpSRP54 proteins. A model was established to explain the molecular mechanisms by which CsSRP43 participates in the leaf color and photosynthesis pathway, and it provides a valuable basis for understanding the molecular and genetic mechanisms of leaf color in cucumber.

17.
Int J Mol Sci ; 23(22)2022 Nov 14.
Article in English | MEDLINE | ID: mdl-36430508

ABSTRACT

Fruit shape and size are complex traits influenced by numerous factors, especially genetics and environment factors. To explore the mechanism of fruit shape and size development in cucumber, a pair of near-isogenic lines (NIL) Ln35 and Ln37 were used. The fruit length and diameter, cell length and diameter, and related gene expression were measured. Both the fruit length, diameter, and cell length and diameter showed sigmate curves in the two lines. The cell length and diameter were significantly positively correlated with fruit length and diameter both in two lines. The expression of CsACS2 and CsLNG showed significant positive correlations with fruit length and diameter increment in Ln35, and there was no correlation in Ln37. Furthermore, there were significant positive correlations between fruit size and thermal effectiveness (TE), as well as between fruit size and photosynthetic active radiation (PAR), both in two lines. Two models using logistic regression were formulated to assess the relationships among fruit length and diameter in Ln35 and Ln37, respectively, based on thermal effectiveness and photosynthetic active radiation (TEP). The coefficient R2 values of the models were 0.977 and 0.976 in Ln35, and 0.987 and 0.981 in Ln37, respectively. The root mean square error (RMSE) was 12.012 mm and 4.338 mm in Ln35, and 5.17 mm and 7.082 mm in Ln37, respectively, which illustrated the accurate and efficient of these models. These biologically interpreted parameters will provide precision management for monitoring fruit growth and forecasting the time of harvesting under different temperatures and light conditions.


Subject(s)
Cucumis sativus , Cucumis sativus/genetics , Fruit/genetics , Chromosome Mapping , Quantitative Trait Loci , Phenotype
18.
Hortic Res ; 9: uhac151, 2022.
Article in English | MEDLINE | ID: mdl-36196068

ABSTRACT

The fresh and unique flavor of cucumber fruits, mainly composed of aldehydes and alcohols, is one of its most important fruit qualities. However, little is known about the genetic basis of aroma compounds in cucumber fruit and the related quantitative trait loci (QTLs). In this study, genomic screening of QTLs underlying aroma compounds was performed based on the genetic linkage map constructed using 1301 single-nucleotide polymorphism (SNP) markers from genotyping-by-sequencing of a recombinant inbred line (RIL) population developed from Q16 × Q24. Significant genetic variations of aroma compounds in the RIL population were observed, and a total of 28 QTLs were screened. A major QTL (qol8-2.1) related to (E,Z)-2,6-nonadien-1-ol was detected with a markedly high LOD score (10.97 in 2020 and 3.56 in 2019) between mk190 and mk204 on chromosome 2. Genome scans identified a cluster of nine lipoxygenase genes in this region. A significant positive correlation was detected between CsaV3_2G005360 (CsLOX08) and (E,Z)-2,6-nonadien-1-ol, and five amino acid variations were detected between the CsLOX08 protein sequences of the two parental lines. Based on the genome variation of CsLOX08, we developed an InDel marker. Genotyping of InDel markers was consistent with the content of (E,Z)-2,6-nonadien-1-ol in RILs, which were also verified in nine cucumber inbred lines. The results will give breeders guidance for obtaining better flavor in cucumber.

19.
Invest Ophthalmol Vis Sci ; 63(11): 28, 2022 Oct 03.
Article in English | MEDLINE | ID: mdl-36315123

ABSTRACT

Purpose: Retinoblastoma (RB) is the most common type of aggressive intraocular malignancy in children. The alteration of immunity during RB progression and invasion has not yet been well defined. This study investigated significantly altered immune-associated genes and cells related to RB invasion. Methods: The differentially expressed immune-related genes (IRGs) in noninvasive RB and invasive RB were identified by analysis of two microarray datasets (GSE97508 and GSE110811). Hub IRGs were further identified by real time PCR. The single-sample gene set enrichment analysis algorithm and Pearson correlation analysis were used to define immune cell infiltration and the relationships between hub IRGs and immune cells. Cell viability and migration were evaluated by CCK-8 and Transwell assays. A xenograft mouse model was used to verify the relationship between Src homology 3 (SH3) domain GRB2-like 2 (SH3GL2) expression and myeloid-derived suppressor cells (MDSCs). Results: Eight upregulated genes and six downregulated IRGs were identified in invasive RB. Seven IRGs were confirmed by real-time PCR. Moreover, the proportions of MDSCs were higher in invasive RB tissues than in noninvasive RB tissues. Furthermore, correlation analysis of altered immune genes and cells suggested that SH3GL2, Langerhans cell protein 1 (LCP1) and transmembrane immune signaling adaptor TYROBP have strong connections with MDSCs. Specifically, decreased SH3GL2 expression promoted the migration of RB cells in vitro, increased the tumor size and weight, and increased the numbers of MDSCs in the tumor and spleen in vivo. Conclusions: This study indicated that SH3GL2 and MDSCs play a critical role in RB progression and invasion and provide candidate targets for the treatment of RB.


Subject(s)
Retinal Neoplasms , Retinoblastoma , Animals , Humans , Mice , Cell Line, Tumor , Cell Proliferation/genetics , Computational Biology , Gene Expression Regulation, Neoplastic , Retinal Neoplasms/pathology , Retinoblastoma/pathology , Tumor Cells, Cultured
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