scholarly journals A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhonghua Tu ◽  
Yufang Shen ◽  
Shaoying Wen ◽  
Huanhuan Liu ◽  
Lingmin Wei ◽  
...  
Keyword(s):  
Shoot Apex ◽  
Alternative Polyadenylation ◽  
Deciduous Tree ◽  
Specific Gene ◽  
Hub Genes ◽  
Tissue Specific ◽  
Liriodendron Chinense ◽  
The One ◽  
Tissue Characteristics

Liriodendron chinense is an economically and ecologically important deciduous tree species. Although the reference genome has been revealed, alternative polyadenylation (APA), transcription factors (TFs), long non-coding RNAs (lncRNAs), and co-expression networks of tissue-specific genes remain incompletely annotated. In this study, we used the bracts, petals, sepals, stamens, pistils, leaves, and shoot apex of L. chinense as materials for hybrid sequencing. On the one hand, we improved the annotation of the genome. We detected 13,139 novel genes, 7,527 lncRNAs, 1,791 TFs, and 6,721 genes with APA sites. On the other hand, we found that tissue-specific genes play a significant role in maintaining tissue characteristics. In total, 2,040 tissue-specific genes were identified, among which 9.2% of tissue-specific genes were affected by APA, and 1,809 tissue-specific genes were represented in seven specific co-expression modules. We also found that bract-specific hub genes were associated plant defense, leaf-specific hub genes were involved in energy metabolism. Moreover, we also found that a stamen-specific hub TF Lchi25777 may be involved in the determination of stamen identity, and a shoot-apex-specific hub TF Lchi05072 may participate in maintaining meristem characteristic. Our study provides a landscape of APA, lncRNAs, TFs, and tissue-specific gene co-expression networks in L. chinense that will improve genome annotation, strengthen our understanding of transcriptome complexity, and drive further research into the regulatory mechanisms of tissue-specific genes.

scholarly journals Gene co-expression analysis and tissue-specific gene identification in Liriodendron chinense via hybrid sequencing

2020 ◽  
Author(s):  
zhonghua tu ◽  
Yufang Shen ◽  
Shaoying Wen ◽  
Huanhuan Liu ◽  
Lingmin Wei ◽  
...  
Keyword(s):  
Shoot Apex ◽  
Expression Profiles ◽  
Plant Defence ◽  
Pathway Enrichment Analysis ◽  
Specific Gene ◽  
Mads Box ◽  
Mads Box Genes ◽  
Vegetative Organs ◽  
Tissue Specific ◽  
Liriodendron Chinense

Abstract Background Liriodendron chinense (Hemsl.) Sarg. is an economically and ecologically important deciduous tree species that has been studied for many years. Although the complete L. chinense genome has been sequenced, the gene co-expression modules and tissue-specific genes of L. chinense remain unknown. Results Here, we used the bracts, petals, sepals, stamens, pistils, leaves, and the shoot apex of L. chinense as materials and analysed their gene co-expression modules and tissue-specific genes via hybrid sequencing. We identified 3,032 DEGs between the floral and vegetative tissues and 2,126 tissue-specific genes. By using WGCNA analysis, we identified 13 gene co-expression modules, and KEGG pathway enrichment analysis revealed that tissue-specific genes and genes from different modules were enriched in different pathways. Genes associated with plant defence were highly expressed in the bracts, genes participating in plant hormone signal transduction were highly expressed in the shoot apex, and genes participating in photosynthesis were highly expressed in the leaves, petals and sepals. Moreover, we identified 10 MIKC-type MADS-box genes that were classified as member of the AP3/PI, SVP, SEP, AG/SHP/STK, AGL12, SOC1 and TM8 subfamily. Phylogenetic analysis showed that the expression profiles of these ten genes were consistent with those reported in Arabidopsis and Populus , indicating that these genes are highly conserved evolutionarily and related to floral and vegetative tissue development. The small number of MIKC-type MADS-box genes in L. chinense was probably owing to its incomplete genome annotation. Conclusions In this work, we provided a reference transcriptome for L. chinense research by using hybrid sequencing. We identified 2,126 tissue-specific genes and 3,032 DEGs that contributed greatly to the functional differences between vegetative organs and floral organs. By using WGCNA analysis, 13 gene co-expression modules and 52 hub genes from six co-expression modules of interest were identified. Moreover, we identified 10 MIKC-type MADS-box genes that might be related to the development and growth regulation of floral and vegetative organs. These findings will improve our understanding of gene co-expression, tissue specific genes and flower development model of L. chinense .

Determination of the unequal fate of cotyledons of a one-leaf plant, Monophyllaea

Development ◽  
1997 ◽  
Vol 124 (7) ◽  
pp. 1275-1280
Author(s):  
H. Tsukaya
Keyword(s):  
Shoot Apex ◽  
Apical Dominance ◽  
Plant Morphology ◽  
Common Mechanism ◽  
Leaf Phenotype ◽  
The Family ◽  
The Common ◽  
The One ◽  
First Time

One-leaf plants, belonging to the family Gesneriaceae, were described for the first time more than 150 years ago. One such unusual plant, Monophyllaea, has only one leaf at maturity. Only one of the two cotyledons grows continuously, without the formation of true leaves, and this feature, known as anisocotyledonous development, has been repeatedly mentioned in textbooks of plant morphology. However, the mechanism for the determination of the one-leaf phenotype remains to be ascertained. In this study, meristematic regions were identified, by monitoring DNA synthesis, at the base of both cotyledons just after germination, while no such regions were found in the shoot apex. Surgical experiments with seedlings and analysis of the anisocotyledonous development revealed that the fate of the cotyledons is determined during their growth. Anisocotyledonous development seems to be the result of competition between the two cotyledons. The mechanism that governs the development of the shoot in the genus Monophyllaea is discussed in relation to apical dominance, which is the common mechanism that regulates shoot development in many plants.

Two-Stage Procedure for the Quantitative Determination of Autoprothrombin III Concentration and Some Applications

1967 ◽  
Vol 18 (01/02) ◽  
pp. 198-210 ◽  
Author(s):  
Ronald S Reno ◽  
Walter H Seegers
Keyword(s):  
Prothrombin Time ◽  
Factor Vii ◽  
Two Stage ◽  
Pronounced Increase ◽  
One Stage ◽  
Assay Procedure ◽  
Bovine Plasma ◽  
The One ◽  
Autoprothrombin C

SummaryA two-stage assay procedure was developed for the determination of the autoprothrombin C titre which can be developed from prothrombin or autoprothrombin III containing solutions. The proenzyme is activated by Russell’s viper venom and the autoprothrombin C activity that appears is measured by its ability to shorten the partial thromboplastin time of bovine plasma.Using the assay, the autoprothrombin C titre was determined in the plasma of several species, as well as the percentage of it remaining in the serum from blood clotted in glass test tubes. Much autoprothrombin III remains in human serum. With sufficient thromboplastin it was completely utilized. Plasma from selected patients with coagulation disorders was assayed and only Stuart plasma was abnormal. In so-called factor VII, IX, and P.T.A. deficiency the autoprothrombin C titre and thrombin titre that could be developed was normal. In one case (prethrombin irregularity) practically no thrombin titre developed but the amount of autoprothrombin C which generated was in the normal range.Dogs were treated with Dicumarol and the autoprothrombin C titre that could be developed from their plasmas decreased until only traces could be detected. This coincided with a lowering of the thrombin titre that could be developed and a prolongation of the one-stage prothrombin time. While the Dicumarol was acting, the dogs were given an infusion of purified bovine prothrombin and the levels of autoprothrombin C, thrombin and one-stage prothrombin time were followed for several hours. The tests became normal immediately after the infusion and then went back to preinfusion levels over a period of 24 hrs.In other dogs the effect of Dicumarol was reversed by giving vitamin K1 intravenously. The effect of the vitamin was noticed as early as 20 min after administration.In response to vitamin K the most pronounced increase was with that portion of the prothrombin molecule which yields thrombin. The proportion of that protein with respect to the precursor of autoprothrombin C increased during the first hour and then started to go down and after 3 hrs was equal to the proportion normally found in plasma.

SIMPLIFIED DEXAMETHASONE SUPPRESSION TEST

1969 ◽  
Vol 61 (2) ◽  
pp. 219-231 ◽  
Author(s):  
V. H. Asfeldt
Keyword(s):  
Cushing’S Syndrome ◽  
Normal Subjects ◽  
Cushing's Syndrome ◽  
Dexamethasone Suppression Test ◽  
Clinical Value ◽  
Suppression Test ◽  
The One ◽  
Steroid Excretion ◽  
Dexamethasone Suppression

ABSTRACT This is an investigation of the practical clinical value of the one mg dexamethasone suppression test of Nugent et al. (1963). The results, evaluated from the decrease in fluorimetrically determined plasma corticosteroids in normal subjects, as well as in cases of exogenous obesity, hirsutism and in Cushing's syndrome, confirm the findings reported in previous studies. Plasma corticosteroid reduction after one mg of dexamethasone in cases of stable diabetes was not significantly different from that observed in control subjects, but in one third of the insulin-treated diabetics only a partial response was observed, indicating a slight hypercorticism in these patients. An insufficient decrease in plasma corticosteroids was observed in certain other conditions (anorexia nervosa, pituitary adenoma, patients receiving contraceptive or anticonvulsive treatment) with no hypercorticism. The physiological significance of these findings is discussed. It is concluded that the test, together with a determination of the basal urinary 17-ketogenic steroid excretion, is suitable as the first diagnostic test in patients in whom Cushing's syndrome is suspected. In cases of insufficient suppression of plasma corticosteroids, further studies, including the suppression test of Liddle (1960), must be carried out.

A Validated 2D-LC-UV Method for Simultaneous Determination of Imatinib and N-demethylimatinib in Plasma and Its Clinical Application for Therapeutic Drug Monitoring with GIST Patients

2020 ◽  
Vol 17 ◽  
Author(s):  
Houli Li ◽  
Di Zhang ◽  
Xiaoliang Cheng ◽  
Qiaowei Zheng ◽  
Kai Cheng ◽  
...  
Keyword(s):  
Therapeutic Drug Monitoring ◽  
One Dimension ◽  
Therapeutic Drug ◽  
Plasma Samples ◽  
Column Temperature ◽  
Injection Volume ◽  
Target Analytes ◽  
The One ◽  
Middle Column

Background: The trough concentration (Cmin) of Imatinib (IM) is closely related to the treatment outcomes and adverse reactions of patients with gastrointestinal stromal tumors (GIST). However, the drug plasma level has great interand intra-individual variability, and therapeutic drug monitoring (TDM) is highly recommended. Objective: To develop a novel, simple, and economical two-dimensional liquid chromatography method with ultraviolet detector (2D-LC-UV) for simultaneous determination of IM and its major active metabolite, N-demethyl imatinib (NDIM) in human plasma, and then apply the method for TDM of the drug. Method: Sample was processed by simple protein precipitation. Two target analytes were separated on the one-dimension column, captured on the middle column, and then transferred to the two-dimension column for further analysis. The detection was performed at 264 nm. The column temperature was maintained at 40˚C and the injection volume was 500 μL. Totally 32 plasma samples were obtained from patients with GIST who were receiving IM. Method: Sample was processed by simple protein precipitation. Two target analytes were separated on the one-dimension column, captured on the middle column, and then transferred to the two-dimension column for further analysis. The detection was performed at 264 nm. The column temperature was maintained at 40˚C and the injection volume was 500 μL. Totally 32 plasma samples were obtained from patients with GIST who were receiving IM. Conclusion: The novel 2D-LC-UV method is simple, stable, highly automated and independent of specialized technicians, which greatly increases the real-time capability of routine TDM for IM in hospital.

scholarly journals A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation

2021 ◽  
Author(s):  
Isabel Regadas ◽  
Olle Dahlberg ◽  
Roshan Vaid ◽  
Oanh Ho ◽  
Sergey Belikov ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Specific Gene ◽  
Chromatin Signature ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Histone 3
Sign in / Sign up

Export Citation Format

Share Document