scholarly journals Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11586
Author(s):  
Jiaqi Gao ◽  
Tong Chen ◽  
Chao Jiang ◽  
Tielin Wang ◽  
Ou Huang ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Dna Barcode ◽  
Gene Expression Profiles ◽  
Color Variation ◽  
Aquilaria Sinensis ◽  
Pr Genes ◽  
Leaf Sample ◽  
Chlorophyll Metabolism ◽  
Sequencing Studies ◽  
The Difference

Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.

PSIV-6 Differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 301-301
Author(s):  
Chaoyang Li ◽  
Qianglin Liu ◽  
Matt Welborn ◽  
Leshan Wang ◽  
Yuxia Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Meat Quality ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cattle Breed ◽  
Intramuscular Fat ◽  
Brahman Cattle ◽  
Differential Gene ◽  
The Difference

Abstract The amount of intramuscular fat directly influences the meat quality. However, significant differences in the ability to accumulate intramuscular fat are present among different beef cattle breeds. While Wagyu, a cattle breed that originated from Japan, is renowned for abundant intramuscular fat, Brahman cattle generally have very little intramuscular fat accumulation and produce tougher meat. We identified that bovine intramuscular fat is derived from a group of bipotent progenitor cells named fibro/adipogenic progenitors (FAPs) which also give rise to fibroblasts. Thus, the variation in intramuscular fat development between Wagyu and Brahman is likely attributed to the difference in FAPs between these two breeds. In order to understand the gene expression difference between FAPs of the two breeds, single-cell RNA-seq was performed using total single-nucleated cells isolated from the longissimus muscle of young purebred Wagyu, purebred Brahman, and Wagyu-Brahman cross cattle. FAPs constitute the largest single-nucleated cell population in both Wagyu and Brahman skeletal muscle. Multiple subpopulations of FAPs with different gene expression profiles were identified, suggesting that FAP is a heterogeneous population. A unique FAP cluster expressing lower levels of fibrillar collagen and extracellular remodeling enzyme genes but higher levels of select proadipogenic genes was identified exclusively in Wagyu skeletal muscle, which likely contributes to the robust intramuscular adipogenic efficiency of Wagyu FAPs. In conclusion, the difference in the cellular composition and gene expression of FAPs between Wagyu and Brahman cattle likely contribute to their distinct meat quality.

Kruppel-Like Factor, Klf9, Promotes Proliferation of Notch-Independent Precursor T-Cell Lymphoblastic Lymphomas

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3496-3496
Author(s):  
Peggy P. C. Wong ◽  
Daniele Merico ◽  
Irina Matei ◽  
Vicki Ling ◽  
Shaheena Bashir ◽  
...  
Keyword(s):  
T Cell ◽  
Conformational Changes ◽  
Conflicts Of Interest ◽  
Expression Profiles ◽  
Functional Dependence ◽  
Lymphoblastic Leukemia ◽  
Gene Expression Profiles ◽  
Notch1 Signaling ◽  
The Difference ◽  
Notch1 Mutations

Abstract Abstract 3496 Notch1 signaling is required at multiple stages of normal T-lymphocyte development. Notch1 is a transmembrane receptor that is physiologically activated when Notch ligands induce conformational changes that allow Notch1 cleavage by the intramembranous γ-secretase complex, releasing active intracellular Notch1 (ICN1) fragment from the plasma membrane. Activating NOTCH1 mutations are very frequent in human and mouse T-cell lymphoblastic leukemia/lymphoma (T-LL). Typically, these mutations promote ligand-independent Notch1 cleavage by γ-secretase or increase ICN1 stability by truncating the C-terminal PEST domain. Understandably, much effort has focused on elucidating mechanisms of normal and oncogenic Notch1 signaling. However, some studies suggest that the absence of NOTCH1 mutations portends a worse prognosis for human T-LL. Therefore, we set out to define signals that promote proliferation and survival of T-LL cells lacking activated Notch1. We used Western blotting to detect γ-secretase cleaved ICN1 protein in a cohort of 35 primary T-LLs that developed spontaneously in mice lacking the Ataxia telangiectasia mutated (Atm) tumor suppressor. We identified 3 ICN1 subgroups: 63% expressed PEST-truncated ICN1 (T-ICN1); 17% expressed non-truncated ICN1 (NT-ICN1); and 20% had undetectable ICN1 (UD-ICN1), most lacked Notch1 mRNA. We confirmed the difference in Notch transcriptional activity and functional dependence between the UD-ICN1 and T-ICN1 subgroups and then compared their gene expression profiles to define pathways unique to the UD-ICN1 group. Gene set enrichment analyses revealed that UD-ICN1 T-LLs expressed higher levels of Klf9 and other transcription factors associated with a highly proliferative stage of normal T-cell development. siRNA knock-down studies demonstrated that Klf9 promoted proliferation of UD-ICN1 but not T-ICN1 T-LL cells. Collectively, these data demonstrate that Klf9 can regulate proliferation of Notch-independent T-LLs and suggest that Klf9 may provide a novel therapeutic target for human T-LLs lacking activating NOTCH1 mutations. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Metabolomic, Biochemical, and Gene Expression Analyses Reveal the Underlying Responses of Resistant and Susceptible Banana Species during Early Infection with Fusarium oxysporum f. sp. cubense

Plant Disease ◽  
2017 ◽  
Vol 101 (4) ◽  
pp. 534-543 ◽  
Author(s):  
Wenbin Li ◽  
Chunqiang Li ◽  
Jianbo Sun ◽  
Ming Peng
Keyword(s):  
Gene Expression ◽  
Fusarium Oxysporum ◽  
Early Stage ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Early Infection ◽  
Total Phenolic ◽  
Pr Genes ◽  
Banana Production ◽  
Infection Period

Banana (Musa spp.) is an important staple and economic fruit crop, especially in Africa, Southeast Asia, and Latin America. The wilt disease caused by Fusarium oxysporum f. sp. cubense, especially F. oxysporum f. sp. cubense strain TR4, is disastrous for banana production. Banana plants infected by F. oxysporum f. sp. cubense TR4 gradually die from leaf blight or vascular rot. There is no efficient method to control this disease, and the underlying response of banana plants to F. oxysporum f. sp. cubense remains unknown. In this study, the responses of an economically important banana cultivar, the F. oxysporum f. sp. cubense-susceptible ‘BX’, and a wild banana relative, the F. oxysporum f. sp. cubense-resistant Musa yunnanensis (‘YN’), to F. oxysporum f. sp. cubense infection were investigated using metabolomic, biochemical, and molecular biological methods. Numerous metabolomic compounds, including defense-responsive signaling molecules, phytohormones, phenolics, and antioxidants, were identified through metabolomic analysis. Changes in salicylic acid (SA), methyl-jasmonic acid, abscisic acid (ABA), cytokinin, 3-indoleacetic acid, gibberellic acid, and total phenolic levels were detected using liquid chromatography-mass spectrometry and the Folin-Ciocalteu method. The expression levels of genes involved in the biosynthesis of some defense-responsive compounds were studied through quantitative real-time polymerase chain reaction. The results revealed that the resistant YN had a larger change in SA content and a lower ABA level throughout the early infection period, compared with the levels in BX. The susceptible BX had a lower phenolic content. The resistant YN also expressed pathogenesis-related (PR) genes, especially PR1, PR4, PR5-1, and PDF2.2, at higher levels than the susceptible BX. These dynamic metabolic and gene-expression profiles from susceptible and resistant banana during the early stage of F. oxysporum f. sp. cubense infection increase our understanding of the complex interaction response between this crop and its pathogen.

scholarly journals Elucidation of the molecular responses during the primary infection of wild blueberry phenotypes with Monilinia vaccinii-corymbosi under field conditions

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Sherin Jose ◽  
Joel Abbey ◽  
Laura Jaakola ◽  
David Percival
Keyword(s):  
Primary Infection ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Defense Responses ◽  
Flavonoid Pathway ◽  
Temporal Expression ◽  
Pr Genes ◽  
Starting Point ◽  
Intermediate Response ◽  
Wild Blueberry

Abstract Background Monilinia blight caused by Monilinia vaccinii-corymbosi (Reade) Honey (M.vc) is a major disease of wild blueberry that can result in severe crop losses in the absence of an integrated disease management programme. The fungus causes blight in the emerging floral and vegetative buds, but the degree of susceptibility varies among the different wild blueberry phenotypes, ranging from the highly susceptible V. a. f. nigrum to the moderately susceptible V. angustifolium and the least susceptible V. myrtilloides. Results The present study evaluated the defense responses of these major phenotypes during their primary infection (floral buds) with M.vc. The temporal expression profiles of PR genes (PR3 and PR4) and the flavonoid pathway structural genes (CHS, ANS, ANR, DFR and FLS) were analysed. The PR3 and PR4 gene expression profiles revealed that V. myrtilloides responded to M.vc infection by activating the expression of both PR genes. V. a. f. nigrum, on the other hand, failed to activate these genes, while V. angustifolium, exhibited an intermediate response. Our study with the flavonoid pathway genes indicated variability in activation of the genes during post-infection time points with ANS and ANR in V. myrtilloides, FLS in V. angustifolium and no response observed in V. a. f. nigrum. Conclusions Altogether, this study highlights that the degree of phenotype susceptibility is associated with the timely activation of host defense responsive genes. Data obtained in this study provided a starting point for a better understanding of the wild blueberry- M. vaccinii-corymbosi pathosystem.

scholarly journals A COMPARATIVE ANALAYSIS OF INTER-SITE GENE EXPRESSION HETEROGENICITY OF NORMAL HUMAN BUCCAL MUCOSA WITH NORMAL GINGIVAL MUCOSA

2021 ◽  
Author(s):  
Rooban Thavarajah ◽  
Kannan Ranganathan
Keyword(s):  
Gene Expression ◽  
Buccal Mucosa ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Gene Expression Omnibus ◽  
Genotypic Difference ◽  
Mesenchymal Transition ◽  
Normal Human ◽  
The Difference

BACKGROUND: Description of heterogeneity of gene expression of various human intraoral sites are not adequate. The aim of this study was to explore the difference of gene expression profiles of whole tissue obtained from apparently normal human gingiva and buccal mucosa (HGM, HBM). MATERIALS AND METHODS: Gene sets fulfilling inclusion and exclusion criteria of HGM and HBM in gene Expression Omnibus(GEO) database were identified, segregated, filtered and analysed using the ExAtlas online web tool using pre-determined cut-off. The differentially expressed genes were studied for epithelial keratinization related, housekeeping(HKG), extracellular matrix related(ECMRG) and epithelial-mesenchymal transition related genes(EMTRGs). RESULTS: In all 40 HBM and 64 HGM formed the study group. In all there were 18012 significantly expressed genes. Of this, 1814 were over-expressed and 1862 under-expressed HBM genes as compared to HGM. One in five of all studied genes significantly differed between HBM and HGM. For the keratinization genes, 1 in 6 differed. One of every 5 HKG-proteomics genes differed between HBM and HGM, while this ratio was 1-in 4 for all ECMRGs and EMTRGs. DISCUSSION: This difference in the gene expression between the HBM and HGM could possibly influence a multitude of biological pathways. This result could explain partly the difference in clinicopathological features of oral lesions occurring in HBM and HGM. The innate genotypic difference between the two intra-oral niches could serve as confounding factor in genotypic studies. Hence studies that compare the HBM and HGM should factor-in these findings while evaluating their results.

scholarly journals Comparative transcriptomic analysis of surf clams (Paphia undulate) infected with two strains of Vibrio spp. reveals the identity of key immune genes involved in host defense

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjia Yu ◽  
Lin Zheng ◽  
Xiaobo Wang ◽  
Minfu Wu ◽  
Ming Qi ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Host Defense ◽  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cytokine Signaling ◽  
Immune Genes ◽  
The Difference ◽  
Vibrio Spp

Abstract Background Vibrio spp. is the major infection-producing marine bacteria in commercially important bivalve Paphia undulata. The host resistance is the major determining factor for the development of pathogenesis. To explore defense mechanisms, researchers have focused primarily on the study of differential expression of individual or specific groups of host immune genes during pathogen-challenge. Results We compared the expression profile in the surf clams infected with avirulent V. alginolyticus and virulent V. parahaemolyticus to mark the possible molecular mechanisms of pathogenesis. Comparison of the differentially expressed genes between the two groups of Vibrio-infected clams revealed that the number of down-regulate genes in V. parahaemolyticus injected clams (1433) were significantly higher than the other group (169). Based on Gene Ontology classification, a large proportion of these down-regulate genes were found to be associated with cellular and molecular mechanisms for pathogen recognition, and immunity development thereby explaining the low survival rate for the V. parahaemolyticus-treated clams and suggesting a higher virulence of this bacterium towards the surf clams. Quantitative real-time PCR of 24 candidate genes related to immunity involving the JAK-STAT signaling pathway, complementary cascade, cytokine signaling pathway, oxidative stress, phagocytosis and apoptosis down regulated under V. parahaemolyticus infection, indicating compromised host defense. Furthermore, we could demonstrate a central role of JAK-STAT pathway in bacterial clearance. dsRNA mediated depletion of a clam STAT homolog gene results in dramatic increase in the infection by V. alginolyticus, a mildly pathogenic strain under control conditions. Conclusions The difference in gene expression profiles in surf clams treated with two Vibrio species with a differential pathogenicity to P. undulate and downstream molecular analysis could enlighten on the probable molecular mechanisms of the Vibrio pathogenesis and the virulence of V. parahaemolyticus in surf clams, which also benefits to develop new strategies for disease control in surf calm aquaculture.

Comparing migraine with and without aura to healthy controls using RNA sequencing

Cephalalgia ◽  
2019 ◽  
Vol 39 (11) ◽  
pp. 1435-1444 ◽  
Author(s):  
Lisette JA Kogelman ◽  
Katrine Falkenberg ◽  
Gisli H Halldorsson ◽  
Lau U Poulsen ◽  
Jacob Worm ◽  
...  
Keyword(s):  
Gene Expression ◽  
Migraine With Aura ◽  
Migraine Without Aura ◽  
Expression Profiles ◽  
Venous Blood ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
The Difference ◽  
Or Gene

Background Migraine mechanisms are *These authors contributed equally to this work. only partly known. Some studies have previously described genes differentially expressed between blood from migraineurs and controls. The objective of this study was to describe gene expression in subtypes of migraine outside of attack and in healthy controls. Methods We extensively phenotyped 17 migraine without aura and nine migraine with aura female patients, and 20 age-matched female controls. Cubital venous blood was RNA sequenced. Genes differentially expressed between migraineurs (migraine without aura and migraine with aura) and controls, and between migraine without aura and migraine with aura were identified using a case-control design. A co-expression network was constructed to investigate the difference between migraineurs and healthy controls at the network level. Results We found two differentially expressed genes: NMNAT2 and RETN. Both were differentially expressed between migraine with aura and controls, but they could not be replicated in an independent cohort. Co-expression network analysis resulted in one cluster of highly interconnected genes that was nominally significantly associated with migraine; however, no pathways or gene ontology terms were detected. Conclusions We showed no clear distinct difference in gene expression profiles of peripheral blood of migraineurs and controls and were not able to replicate findings from previous studies. A larger sample size may be needed to detect minor differences.

scholarly journals Gene expression-based immune infiltration analyses of renal cancer and their associations with survival outcome

2020 ◽  
Author(s):  
Lei Chen ◽  
Liang Yin ◽  
Zilong Qi ◽  
Jinmin Li ◽  
Xinning Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
Renal Cancer ◽  
Wilms Tumor ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Survival Outcome ◽  
Distinct Cluster ◽  
Clinical Surveillance ◽  
The Difference

Abstract Renal cancer is a common malignant tumor with an increasing incidence rate. In this study, based on the gene expression profiles, we analyzed the compositions of tumor infiltrating immune cells (TIICs) in renal cancer and paracancerous samples by using CIBERSORT. The proportions of 22 TIICs subsets in 122 paired renal cancer and paracancerous samples, and 224 Wilms tumor (WT) samples varied between intragroup and intergroup. After analyzed the difference in TIICs composition between renal cancer and paired paracancerous samples, we found that compared with paracancerous samples, M0 macrophages and CD8 T cells were significantly elevated, while naive B cells were significantly decreased in renal cancer samples. Survival analysis showed that high overall TIICs proportion, low proportion of resting mast cells and high proportion of activated memory CD4 T cells were associated with poor prognosis of renal cancer patients. In addition, 3 clusters were identified by hierarchical clustering analysis and they presented distinct prognosis. Cluster 1 had superior survival outcome, while cluster 2 had inferior survival outcome. In summary, our study indicated that overall TIICs proportion, certain TIICs subset proportion, and distinct cluster patterns were associated with the prognosis of renal cancer, which was significant for the clinical surveillance and treatment of renal cancer.

scholarly journals Identification of the difference of neutrophils in different locations in RA patients

2021 ◽  
Author(s):  
Hanming Gu
Keyword(s):  
Cellular Structure ◽  
Homo Sapiens ◽  
Expression Profiles ◽  
Systemic Disease ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Illumina Hiseq ◽  
Biochemical Pathways ◽  
Numerous Cell ◽  
The Difference

Abstract Rheumatoid Arthritis (RA) is a complex systemic disease in which numerous cell types are involved. Neutrophils play an important role in the onset and development of RA. In our study, we aim to identify different functions of neutrophils in different conditions (blood and synovium) of RA patients by using a bioinformatics method to clarify their potential pathogenesis. The gene expression profiles of the GSE154474 dataset were originally produced by using the high-throughput Illumina HiSeq 2000 (Homo sapiens). The biological categories and biochemical pathways were identified and analyzed by the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG), Gene Ontology (GO), and Reactom enrichment. KEGG and GO results showed the biological pathways related to the immune and cellular structure were mainly different. Moreover, we identified several genes including GNB4, RHOA, and TECB2 were involved in the regulation of inflammation. Therefore, this study provides different insights into the pathogenesis of RA.

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