5,011 results match your criteria determined transcriptome


Macrophage-Related SPP1 as a Potential Biomarker for Early Lymph Node Metastasis in Lung Adenocarcinoma.

Front Cell Dev Biol 2021 27;9:739358. Epub 2021 Sep 27.

Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.

Lymph node metastasis is a major factor that affects prognosis in patients with lung adenocarcinoma (LUAD). In some cases, lymph node metastasis has already occurred when the primary tumors are still small (i.e. Read More

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September 2021

Genetic predisposition of SNPs in miRNA-149 (rs2292832) and FOXE1 (rs3758249) in thyroid Cancer.

Mol Biol Rep 2021 Oct 13. Epub 2021 Oct 13.

Department of Zoology, PMAS-Arid Agriculture University, Rawalpindi, Pakistan.

Background: Many efforts have been made in recent years to investigate the alterations in protein-coding genes as well as non-coding RNAs that are playing an emerging role in the development and progression of cancers. These miRNAs are short non-coding functional RNAs that are involved in the regulation of transcriptome. In different studies, it was found that human miRNA-149 is an important microRNA that is functioning either as onco-miRNAs or acting as tumor suppressors, in different conditions. Read More

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October 2021

A systems-level analysis of bile acids effects on rat colon epithelial cells.

Am J Physiol Gastrointest Liver Physiol 2021 Oct 13. Epub 2021 Oct 13.

Department of Biomedicine, Aarhus University, Aarhus, Denmark.

Bile acid diarrhoea is a chronic condition caused by increased delivery of bile acids to the colon. The underlying mechanisms remain to be elucidated. To investigate genes involved in bile acid diarrhoea, systems-level analyses were employed on a rat bile acid diarrhoea model. Read More

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October 2021

Differential Marker Expression between Keratinocyte Stem Cells and Their Progeny Generated from a Single Colony.

Int J Mol Sci 2021 Oct 6;22(19). Epub 2021 Oct 6.

Cell Therapy Center, The University of Jordan, Amman 11942, Jordan.

The stemness in keratinocyte stem cells (KSCs) is determined by their gene expression patterns. KSCs are crucial in maintaining epidermal homeostasis and wound repair and are widely used candidates for therapeutic applications. Although several studies have reported their positive identifiers, unique biomarkers for KSCs remain elusive. Read More

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October 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail.

Genomics Inform 2021 Sep 30;19(3):e32. Epub 2021 Sep 30.

Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Read More

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September 2021

Photosynthetic contribution and characteristics of cucumber stems and petioles.

BMC Plant Biol 2021 Oct 6;21(1):454. Epub 2021 Oct 6.

Department of Vegetable Science, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops. College of Horticulture, China Agricultural University, Yuanmingyuan Xilu 2#, HaiDian District, Beijing, 100193, China.

Background: Photosynthesis in the green leafless blade tissues or organs of plants has been studied in some plants, but the photosynthetic characteristics of stems and petioles are poorly understood. Cucurbitaceous plants are climbing plants that have substantial stem and petiole biomass. Understanding the photosynthetic contribution of cucumber stems and petioles to their growth and the underlying molecular mechanisms are important for the regulating of growth in cucumber production. Read More

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October 2021

Transcriptome Analysis of Effects of Folic Acid Supplement on Gene Expression in Liver of Broiler Chickens.

Front Vet Sci 2021 16;8:686609. Epub 2021 Sep 16.

School of Life Sciences, Linyi University, Linyi, China.

Folic acid is a water-soluble B vitamin, and plays an important role in regulating gene expression and methylation. The liver is the major site of lipid biosynthesis in the chicken. Nevertheless, how gene expression and regulatory networks are affected by folic acid in liver of broilers are poorly understood. Read More

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September 2021

Tumor-Infiltrating PD-1CD8-T-Cell Signature as an Effective Biomarker for Immune Checkpoint Inhibitor Therapy Response Across Multiple Cancers.

Front Oncol 2021 15;11:695006. Epub 2021 Sep 15.

Institute of Thoracic Oncology and Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China.

Background: Stratification of patients who could benefit from immune checkpoint inhibitor (ICI) therapy is of much importance. PD-1CD8 T cells represent a newly identified and effective biomarker for ICI therapy response biomarker in lung cancer. Accurately quantifying these T cells using commonly available RNA sequencing (RNA-seq) data may extend their applications to more cancer types. Read More

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September 2021

Landscape of T Cells Transcriptional and Metabolic Modules During HIV Infection Based on Weighted Gene Co-expression Network Analysis.

Front Genet 2021 16;12:756471. Epub 2021 Sep 16.

Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, China.

Human immunodeficiency virus (HIV) causes acquired immunodeficiency syndrome (AIDS). HIV infection affects the functions and metabolism of T cells, which may determine the fate of patients; however, the specific pathways activated in different T-cell subtypes (CD4 and CD8 T cells) at different stages of infection remain unclear. We obtained transcriptome data of five individuals each with early HIV infection, chronic progressive HIV infection, and no HIV infection. Read More

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September 2021

DZNep protects against retinal ganglion cell death in an NMDA-induced mouse model of retinal degeneration.

Exp Eye Res 2021 Sep 30;212:108785. Epub 2021 Sep 30.

Research Laboratory of Ophthalmology, West China Hospital, Sichuan University, Chengdu, 610041, China. Electronic address:

Epigenetic gene enhancer of zeste homolog-2 (Ezh2) is reported to be associated with ocular neurodegenerative diseases; however, its underlying mechanism is poorly understood. The present study aimed to determine the role of 3-deazaneplanocin A (DZNep), which inhibits the transcription of Ezh2 by reducing the trimethylation of histone 3 lysine 27 (H3K27me3), in a retinal ganglion cell (RGC) degeneration model. Retinal damage was caused by intravitreal injection of N-methyl-D-aspartate (NMDA). Read More

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September 2021

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation.

Hortic Res 2021 Oct 1;8(1):218. Epub 2021 Oct 1.

Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, PR China.

Valencia orange (Citrus sinensis Osbeck) (VO) is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange (CO). Notably, the mastication trait of VO fruit is inferior to that of CO fruit. To date, how inferior pulp mastication trait forms in VO has not been determined. Read More

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October 2021

Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC.

Sci Rep 2021 Sep 29;11(1):19304. Epub 2021 Sep 29.

Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.

Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. Read More

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September 2021

Transcriptome analyses reveal tau isoform-driven changes in transposable element and gene expression.

PLoS One 2021 29;16(9):e0251611. Epub 2021 Sep 29.

Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States of America.

Alternative splicing of the gene MAPT produces several isoforms of tau protein. Overexpression of these isoforms is characteristic of tauopathies, which are currently untreatable neurodegenerative diseases. Though non-canonical functions of tau have drawn interest, the role of tau isoforms in these diseases has not been fully examined and may reveal new details of tau-driven pathology. Read More

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September 2021

Pulmonary implications of acetaminophen exposures independent of hepatic toxicity.

Am J Physiol Lung Cell Mol Physiol 2021 Sep 29. Epub 2021 Sep 29.

Section of Neonatology, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.

Both pre-clinical and clinical studies have demonstrated that exposures to acetaminophen (APAP) at levels that cause hepatic injury cause pulmonary injury as well. However, whether exposures that do not result in hepatic injury have acute pulmonary implications is unknown. Thus, we sought to determine the how APAP exposures at levels that do not result in significant hepatic injury impact the mature lung. Read More

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September 2021

Examining the Developmental Trajectory of an Model of Mouse Primordial Germ Cells following Exposure to Environmentally Relevant Bisphenol A Levels.

Environ Health Perspect 2021 Sep 29;129(9):97013. Epub 2021 Sep 29.

UCLA Institute for Society & Genetics, University of California, Los Angeles, Los Angeles, California, USA.

Background: Animal-based studies indicate that bisphenol A (BPA) exposure is detrimental to reproductive health, but its impact on the earliest stages of germ cell development remains poorly defined.

Objectives: Using a murine model of early germ cell specification and differentiation, we sought to assess whether exposure to low levels of BPA prior to formation of primordial germ cells (PGCs) alters their differentiation trajectory and unique molecular program.

Methods: We used an established method of differentiation of mouse embryonic stem cells (ESCs) into epiblast-like cells (EpiLCs) followed by PGC-like cells (PGCLCs), which together recapitulate defined stages of early germ cell development. Read More

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September 2021

Immune response of silver pomfret (Pampus argenteus) to Amyloodinium ocellatum infection.

J Fish Dis 2021 Sep 28. Epub 2021 Sep 28.

Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China.

Amyloodinium ocellatum (AO) infection in silver pomfret (Pampus argenteus) causes extensive mortality. Insufficient information exists on the molecular immune response of silver pomfret to AO infestation, so herein we simulated the process of silver pomfret being infected by AO. Translucent trophosomes were observed on the gills of AO-infected fish. Read More

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September 2021

Growth performance, antioxidant response, biodegradation and transcriptome analysis of Chlorella pyrenoidosa after nonylphenol exposure.

Sci Total Environ 2021 Sep 22;806(Pt 1):150507. Epub 2021 Sep 22.

College of Marine and Environmental Sciences, Tianjin University of Science and Technology, Tianjin 300457, China; Key Laboratory of Marine Resource Chemistry and Food Technology (TUST), Ministry of Education, Tianjin 300457, China; Tianjin Key Laboratory of Marine Resources and Chemistry, Tianjin 300457, China. Electronic address:

Chlorella pyrenoidosa was exposed to nonylphenol (NP) to investigate the tolerance, antioxidant response, removal efficiency, and biodegradation mechanism. We conducted studies on algal biomass, chlorophyll a content, and photosynthetic activity, and found that C. pyrenoidosa exhibited a high tolerance even at 8 mg L of NP. Read More

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September 2021

[Transcriptome analysis and validation of key genes involved in biosynthesis of iridoids in Gentiana lhassica].

Zhongguo Zhong Yao Za Zhi 2021 Sep;46(18):4704-4711

Tibetan Traditional Medical College Lhasa 850000, China Beijing University of Chinese Medicine Beijing 100029, China.

As the main chemical constituents, iridoids are widely distributed within Gentiana, Gentianaceae, with promising bioactivities. Based on the previous work, the transcriptome of G. lhassica, an original plant of Tibetan herb "Jieji Nabao", was sequenced and analyzed in this study, and the transcriptome databases of roots, stems, leaves, and flowers were constructed so as to explore unigenes that may encode the key enzymes in the biosynthetic pathway of iridoids. Read More

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September 2021

[Effects of density on growth and gene transcription characteristics of Rehmannia glutinosa].

Zhongguo Zhong Yao Za Zhi 2021 Sep;46(17):4367-4379

College of Agriculture, Fujian Agriculture and Forestry University Fuzhou 350002, China.

The present study analyzed the effects of planting density on the development, quality, and gene transcription characte-ristics of Rehmannia glutinosa using 85-5 and J9 as materials with three planting densities of 5 000, 25 000, and 50 000 plants/Mu(1 Mu≈667 m~2). The agronomic characteristics of leaves and tuberous roots, the content of catalpol and acteoside, and the changes of gene expression were determined. The results showed that the leaf size, the diameter of tuberous root, leaf biomass, tuberous root number, and tuberous root biomass per plant at low density were significantly higher than those of medium and high densities. Read More

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September 2021

Characterization of Circulating IL-7R Positive Cell Populations for Early Detection of Pancreatic Ductal Adenocarcinoma.

J Clin Med 2021 Sep 15;10(18). Epub 2021 Sep 15.

Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea.

(1) Background: Pancreatic cancer is a high devastating disease with the lowest survival rate among all common cancers due to difficulties in early diagnosis. The purpose of this study was to identify and characterize the distinct subset of blood cell population elevated in peripheral blood mononuclear cells (PBMC) of pancreatic cancer to evaluate the potential markers for diagnosis of pancreatic cancer; (2) Methods: We analyzed differential gene expression in PBMC from normal individuals and pancreatic cancer patients utilizing transcriptome analysis. Flow cytometry analysis was applied to identify the discrete subset of interleukin-7 receptor (IL-7R) expressing cells in these cells. Read More

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September 2021

A naturally occurring FXR agonist, alisol B 23-acetate, protects against renal ischemia-reperfusion injury.

Am J Physiol Renal Physiol 2021 09 27. Epub 2021 Sep 27.

Health Science Center, East China Normal University, Shanghai, China.

The ligand-activated nuclear receptor, farnesoid X receptor (FXR), plays a pivotal role in regulating renal function. Activation of FXR by its specific agonists exerts renoprotective action in animals with acute kidney injury (AKI). In the present study, we aimed to identify naturally occurring agonists of FXR with potential as therapeutic agents in renal ischemia-perfusion injury (IRI). Read More

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September 2021

Robust metabolic transcriptional components in 34,494 patient-derived cancer-related samples and cell lines.

Cancer Metab 2021 Sep 26;9(1):35. Epub 2021 Sep 26.

Department of Medical Oncology, Cancer Research Center Groningen, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.

Background: Patient-derived bulk expression profiles of cancers can provide insight into the transcriptional changes that underlie reprogrammed metabolism in cancer. These profiles represent the average expression pattern of all heterogeneous tumor and non-tumor cells present in biopsies of tumor lesions. Hence, subtle transcriptional footprints of metabolic processes can be concealed by other biological processes and experimental artifacts. Read More

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September 2021

Transcriptome-based analysis of blood samples reveals elevation of DNA damage response, neutrophil degranulation, cancer and neurodegenerative pathways in Plasmodium falciparum patients.

Malar J 2021 Sep 26;20(1):383. Epub 2021 Sep 26.

Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich-Heine University, 40225, Düsseldorf, Germany.

Background: Malaria caused by Plasmodium falciparum results in severe complications including cerebral malaria (CM) especially in children. While the majority of falciparum malaria survivors make a full recovery, there are reports of some patients ending up with neurological sequelae or cognitive deficit.

Methods: An analysis of pooled transcriptome data of whole blood samples derived from two studies involving various P. Read More

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September 2021

Comprehensive Transcriptome Analyses in Sea Louse Reveal Novel Delousing Drug Responses Through MicroRNA regulation.

Mar Biotechnol (NY) 2021 Sep 25. Epub 2021 Sep 25.

Interdisciplinary Center for Aquaculture Research, University of Concepción, O'Higgins 1695, Concepción, Chile.

The role of miRNAs in pharmacological responses through gene regulation related to drug metabolism and the detoxification system has recently been determined for terrestrial species. However, studies on marine ectoparasites have scarcely been conducted to investigate the molecular mechanisms of pesticide resistance. Herein, we explored the sea louse Caligus rogercresseyi miRNome responses exposed to delousing drugs and the interplaying with coding/non-coding RNAs. Read More

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September 2021

Monocyte transcriptomes from patients with axial spondyloarthritis reveal dysregulated monocytopoiesis and a distinct inflammatory imprint.

Arthritis Res Ther 2021 Sep 24;23(1):246. Epub 2021 Sep 24.

Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Hindenburgdamm 30, 12200, Berlin, Germany.

Background: In patients with axial spondyloarthritis (axSpA), monocytes show a pre-activated phenotype. Gut inflammation is a trigger of monocyte activation and may also affect their development in the bone marrow (BM). As gut inflammation is commonly observed in axSpA patients, we performed a detailed analysis of monocyte transcriptomes of axSpA patients in two cohorts and searched for signs of activation and developmental adaptations as putative imprints of gut inflammation. Read More

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September 2021

Expression and Tumor-Promoting Effect of Tyrosine Phosphatase Receptor Type N (PTPRN) in Human Glioma.

Front Oncol 2021 7;11:676287. Epub 2021 Sep 7.

Department of Neurosurgery, Tianjin Huanhu Hospital, Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Neurosurgical Institute, Tianjin, China.

Tyrosine phosphatase receptor type N (PTPRN) plays an important role in the regulation of the secretion pathways of various neuroendocrine cells. Moreover, PTPRN was demonstrated to play a crucial role in the initiation and progression of the signalling cascade regulating cell function. In this study, fifty-seven glioma patients were enrolled for clinical and prognostic analyses. Read More

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September 2021

Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae).

PLoS One 2021 23;16(9):e0255660. Epub 2021 Sep 23.

Department of Animal and Food Science, Oklahoma State University, Stillwater, Oklahoma, United States of America.

Nicrophorus is a genus of beetles that bury and transform small vertebrate carcasses into a brood ball coated with their oral and anal secretions to prevent decay and that will serve as a food source for their young. Nicrophorus pustulatus is an unusual species with the ability to overtake brood of other burying beetles and whose secretions, unlike other Nicrophorus species, has been reported not to exhibit antimicrobial properties. This work aims to better understand how the presence or absence of a food source influences the expression of genes involved in the feeding process of N. Read More

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September 2021

Integrated analysis of mRNA and long non-coding RNA expression profiles reveals the potential roles of lncRNA-mRNA network in carp macrophage immune regulation.

In Vitro Cell Dev Biol Anim 2021 Sep 23. Epub 2021 Sep 23.

School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.

Long non-coding RNAs (lncRNAs) have emerged as a hot topic in research as mounting evidence has indicated their transcriptional or post-transcriptional regulatory potential in multiple biological processes. Previous studies have revealed the involvement of lncRNAs in the immunoregulation of mammalian macrophages by changing mRNA expression; however, studies on the lncRNAs in fish macrophages and their potential roles in the immune system remain unknown. Primary macrophages were isolated from the head kidney (HK) of red common carp (Cyprinus carpio) and high-throughput lncRNA-mRNA sequencing was performed using the Illumina HiSeq platform. Read More

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September 2021

Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated.

BMC Genomics 2021 Sep 21;22(1):681. Epub 2021 Sep 21.

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.

Background: Freezing temperatures are an abiotic stress that has a serious impact on plant growth and development in temperate regions and even threatens plant survival. The wild apple tree (Malus sieversii) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in wild apple trees. Read More

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September 2021

Sex differences in skeletal muscle revealed through fiber type, capillarity, and transcriptomics profiling in mice.

Physiol Rep 2021 Sep;9(18):e15031

Department of Surgery, University of California Davis School of Medicine, Sacramento, California, USA.

Skeletal muscle anatomy and physiology are sexually dimorphic but molecular underpinnings and muscle-specificity are not well-established. Variances in metabolic health, fitness level, sedentary behavior, genetics, and age make it difficult to discern inherent sex effects in humans. Therefore, mice under well-controlled conditions were used to determine female and male (n = 19/sex) skeletal muscle fiber type/size and capillarity in superficial and deep gastrocnemius (GA-s, GA-d), soleus (SOL), extensor digitorum longus (EDL), and plantaris (PLT), and transcriptome patterns were also determined (GA, SOL). Read More

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September 2021