33,300 results match your criteria transcriptomes sequence

miR-351-3p promotes rat amniotic fluid-derived mesenchymal stromal cell proliferation via targeting the coding sequence of Abca4.

Stem Cells 2021 May 10. Epub 2021 May 10.

Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shenyang, Liaoning, People's Republic of China.

Amniotic fluid-derived mesenchymal stromal cells (AFMSCs) present different features, depending on the isolation timing and culture conditions. The lack of uniform experimental standards hinders the comparison of results from different studies on AFMSCs. Moreover, understanding the molecular mechanisms that underlie the features of AFMSCs isolated at different embryonic developmental stages might allow the obtention of more viable and highly proliferative AFMSCs through genetic modification. Read More

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Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity.

Clin Chem 2021 May 10. Epub 2021 May 10.

Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA.

Background: Among the approximately 8000 Mendelian disorders, >1000 have cutaneous manifestations. In many of these conditions, the underlying mutated genes have been identified by DNA-based techniques which, however, can overlook certain types of mutations, such as exonic-synonymous and deep-intronic sequence variants. Whole-transcriptome sequencing by RNA sequencing (RNA-seq) can identify such mutations and provide information about their consequences . Read More

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Combined Analysis of RNA Sequence and Microarray Data Reveals a Competing Endogenous RNA Network as Novel Prognostic Markers in Malignant Pleural Mesothelioma.

Front Oncol 2021 23;11:615234. Epub 2021 Apr 23.

Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.

Malignant pleural mesothelioma (MPM) is a highly aggressive cancer with short survival time. Unbalanced competing endogenous RNAs (ceRNAs) have been shown to participate in the tumor pathogenesis and served as biomarkers for the clinical prognosis. However, the comprehensive analyses of the ceRNA network in the prognosis of MPM are still rarely reported. Read More

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Transcriptome analysis of mild hypothermia protection against radiationinduced rat lung injury based on RNAseq.

Zhong Nan Da Xue Xue Bao Yi Xue Ban 2021 Apr;46(4):345-350

Drug Safety Evaluation Center of China Institute for Radiation Protection; Shanxi Key Laboratory of Drug Toxicology and Drug for Radiation Injury; Key Laboratory on Radiotoxicology and Radiopharmaceutical Preclinical Evaluation, China National Nuclear Corporation, Taiyuan 030006, China.

Objectives: To analyze the differentially expressed genes (DEGs) with radiation-induced rat lung injury, and to reveal the protective mechanism for mild hypothermia in the radiation-induced lung injury in rats at the transcriptome level.

Methods: A total of 10 male SD rats aged 6-8 weeks were randomly divided into 2 groups to establish a rat model of radiation-induced lung injury, and one group was treated with mild hypothermia. RNA was extracted from left lung tissue of each group, and sequenced by BGISEQ-500 platform. Read More

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Molecular characterization of cathelicidin in tiger frog (Hoplobatrachus rugulosus): Antimicrobial activity and immunomodulatory activity.

Comp Biochem Physiol C Toxicol Pharmacol 2021 May 6:109072. Epub 2021 May 6.

College of Ecology, Lishui University, Lishui 323000, China. Electronic address:

Cathelicidins are an important antimicrobial peptide family and are expressed in many different vertebrates. They play an important role in the innate immune system of the host. However, amphibian cathelicidins are poorly understood. Read More

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Effect of gamma rays and colchicine on silymarin production in cell suspension cultures of Silybum marianum: a transcriptomic study of key genes involved in the biosynthetic pathway.

Gene 2021 May 5:145700. Epub 2021 May 5.

Department of Biology, Health, and Environment, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.

The aim of this study was to investigate secondary metabolite production in Silybum marianum L. cell suspension cultures obtained from seeds treated with gamma rays (200 and 600Gy) and 0.05% colchicine. Read More

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GmMs1 encodes a kinesin-like protein essential for male fertility in soybean (Glycine max L.).

J Integr Plant Biol 2021 May 7. Epub 2021 May 7.

The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

The application of heterosis is a promising approach for greatly increasing yield in soybean (Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Read More

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Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection.

Cell Rep 2021 Apr 23:109108. Epub 2021 Apr 23.

Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia; Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3000, Australia; Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK; Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia. Electronic address:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses subgenomic RNA (sgRNA) to produce viral proteins for replication and immune evasion. We apply long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA upregulates earlier in infection than TRS-independent sgRNA. Read More

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Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.

Am J Hum Genet 2021 May;108(5):857-873

GeneDx, Gaithersburg, MD 20877, USA.

The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Read More

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Comparison and Functional Analysis of Chemosensory Protein Genes From Motschulsky and Harold.

Front Physiol 2021 20;12:661310. Epub 2021 Apr 20.

Beijing Key Laboratory for Forest Pests Control, College of Forestry, Beijing Forestry University, Beijing, China.

The tree-of-heaven root weevil () and the tree-of-heaven trunk weevil () are closely related species that monophagously feed on the same host plant, the (Mill) Swingle, at different locations. However, the mechanisms of how they select different parts of the host tree are unclear. As chemosensory systems play important roles in host location and oviposition, we screened candidate chemosensory protein genes from the transcriptomes of the two weevils at different developmental stages. Read More

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Molecular evidence of the avocado defense response to infection: a deep transcriptome analysis using RNA-Seq.

PeerJ 2021 14;9:e11215. Epub 2021 Apr 14.

Catedrático CONACyT en la Red de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Xalapa, Veracruz, México.

is a novel member of the Ambrosia Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and during the infection process and disease establishment remain unknown. Read More

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Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome.

mSystems 2021 May 4;6(3). Epub 2021 May 4.

Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea

Identification of transcriptional regulatory elements in the GC-rich genome is essential for the production of novel biochemicals from secondary metabolite biosynthetic gene clusters (smBGCs). Despite many efforts to understand the regulation of transcription initiation in smBGCs, information on the regulation of transcription termination and posttranscriptional processing remains scarce. In this study, we identified the transcriptional regulatory elements in β-lactam antibiotic-producing ATCC 27064 by determining a total of 1,427 transcript 3'-end positions (TEPs) using the term-seq method. Read More

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Identification of Novel Toxin Genes from the Stinging Nettle Caterpillar (Cramer, 1799): Insights into the Evolution of Lepidoptera Toxins.

Insects 2021 Apr 29;12(5). Epub 2021 Apr 29.

Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand.

Many animal species can produce venom for defense, predation, and competition. The venom usually contains diverse peptide and protein toxins, including neurotoxins, proteolytic enzymes, protease inhibitors, and allergens. Some drugs for cancer, neurological disorders, and analgesics were developed based on animal toxin structures and functions. Read More

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RNAi-Mediated Silencing of the Chitinase 5 Gene for Fall Webworm () Can Inhibit Larval Molting Depending on the Timing of dsRNA Injection.

Insects 2021 Apr 30;12(5). Epub 2021 Apr 30.

Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.

Chitinases, which are crucial enzymes required for chitin degradation and reconstruction, are often selectively considered to be effective molecular targets for pest control due to their critical roles in insect development. Although the chitinase gene has been reported previously, its sequence characteristics, gene function, and feasibility as a potential target for pest management were absent. In the present study, we characterized the chitinase gene and designated it . Read More

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In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid.

Nucleic Acids Res 2021 May 3. Epub 2021 May 3.

Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.

FinO-domain proteins represent an emerging family of RNA-binding proteins (RBPs) with diverse roles in bacterial post-transcriptional control and physiology. They exhibit an intriguing targeting spectrum, ranging from an assumed single RNA pair (FinP/traJ) for the plasmid-encoded FinO protein, to transcriptome-wide activity as documented for chromosomally encoded ProQ proteins. Thus, the shared FinO domain might bear an unusual plasticity enabling it to act either selectively or promiscuously on the same cellular RNA pool. Read More

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Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis.

Phytochemistry 2021 Apr 28;187:112749. Epub 2021 Apr 28.

Pharmacognosy, Department of Pharmaceutical Biosciences, Uppsala University, 751 23, Uppsala, Sweden. Electronic address:

Cyclotides are an extremely stable class of peptides, ubiquitously distributed in Violaceae. The aim of the present study was to investigate the presence of cyclotides in Sri Lankan Violaceae plants, using combined tools of transcriptomics and mass spectrometry. New cyclotides were discovered for the first time in the wild flora of Sri Lanka, within Viola betonicifolia, a plant used in traditional medicine as an antimicrobial. Read More

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Genome and transcriptome sequencing of a newly isolated 2,4-dinitrophenol-degrading strain Rhodococcus imtechensis XM24D.

Genes Genomics 2021 May 1. Epub 2021 May 1.

College of Medicine, Xi'an International University, Xi'an, 710077, Shanxi, China.

Background: 2,4-Dinitrophenol (2,4-DNP) is an important organic environmental pollutant that is highly toxic to all forms of living organisms. A gram-positive strain (designated XM24D) was isolated from 2,4-DNP-contaminated soil by an enrichment technique.

Objective: The study was designed to analyze the ability of XM24D to degrade 2,4-DNP and its analogs and to reveal the degradation pathways of these aromatic compounds. Read More

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A histone-like nucleoid structuring protein regulates several virulence traits in .

Appl Environ Microbiol 2021 Apr 30. Epub 2021 Apr 30.

Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Av. Rovisco Pais, 1049-001 Lisboa, Portugal

complex bacteria comprises opportunistic pathogens causing chronic respiratory infections in cystic fibrosis (CF) patients. These microorganisms produce an exopolysaccharide named cepacian, which is considered a virulence determinant. To find genes implicated in the regulation of cepacian biosynthesis, we characterized an evolved nonmucoid variant (17616nmv) derived from the ancestor, ATCC 17616, after prolonged stationary phase. Read More

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Impact of male trait exaggeration on sex-biased gene expression and genome architecture in a water strider.

BMC Biol 2021 Apr 30;19(1):89. Epub 2021 Apr 30.

Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Université Claude Bernard Lyon1, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, 46, allée d'Italie, 69364, Lyon Cedex 07, France.

Background: Exaggerated secondary sexual traits are widespread in nature and often evolve under strong directional sexual selection. Although heavily studied from both theoretical and empirical viewpoints, we have little understanding of how sexual selection influences sex-biased gene regulation during the development of exaggerated secondary sexual phenotypes, and how these changes are reflected in genomic architecture. This is primarily due to the limited availability of representative genomes and associated tissue and sex transcriptomes to study the development of these traits. Read More

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Comparative transcriptomic analysis reveals the regulatory mechanism of the gibberellic acid pathway of Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) dwarf mutants.

BMC Plant Biol 2021 Apr 30;21(1):206. Epub 2021 Apr 30.

College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.

Background: Tartary buckwheat is an important minor crop species with high nutritional and medicinal value and is widely planted worldwide. Cultivated Tartary buckwheat plants are tall and have hollow stems that lodge easily, which severely affects their yield and hinders the development of the Tartary buckwheat industry.

Methods: Heifeng No. Read More

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Dynamic landscape of immune cell-specific gene regulation in immune-mediated diseases.

Cell 2021 Apr 21. Epub 2021 Apr 21.

Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa 247-8530, Japan.

Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Read More

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Induction and Resuscitation of Viable but Nonculturable .

Microorganisms 2021 Apr 26;9(5). Epub 2021 Apr 26.

Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo 208-0011, Japan.

Many pathogenic bacteria, including and , can become viable but nonculturable (VBNC) following exposure to specific stress conditions. , a known human pathogen causing diphtheria, has not previously been shown to enter the VBNC state. Here, we report that can become VBNC when exposed to low temperatures. Read More

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The Mitochondrial Genome of the Sea Anemone Reveals Catalytic Introns, Insertion-Like Element, and Unexpected Phylogeny.

Life (Basel) 2021 Apr 28;11(5). Epub 2021 Apr 28.

Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.

A hallmark of sea anemone mitochondrial genomes (mitogenomes) is the presence of complex catalytic group I introns. Here, we report the complete mitogenome and corresponding transcriptome of the carpet sea anemone (family Stichodactylidae). The mitogenome is vertebrate-like in size, organization, and gene content. Read More

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Transcriptome Sequence Reveals Candidate Genes Involving in the Post-Harvest Hardening of Trifoliate Yam .

Plants (Basel) 2021 Apr 16;10(4). Epub 2021 Apr 16.

Institute for Biology and Environmental Sciences, Carl-von-Ossietzky University Oldenburg, Carl-von-Ossietzky Str. 9-11, 26111 Oldenburg, Germany.

Storage ability of trifoliate yam () is restricted by a severe post-harvest hardening (PHH) phenomenon, which starts within the first 24 h after harvest and renders tubers inedible. Previous work has only focused on the biochemical changes affecting PHH in . To the best of our knowledge, the candidate genes responsible for the hardening of have not been identified. Read More

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An Integrated-Omics/Chemistry Approach Unravels Enzymatic and Spontaneous Steps to Form Flavoalkaloidal Nudicaulin Pigments in Flowers of L.

Int J Mol Sci 2021 Apr 16;22(8). Epub 2021 Apr 16.

Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany.

Flower colour is an important trait for plants to attract pollinators and ensure their reproductive success. Among yellow flower pigments, the nudicaulins in L. (Iceland poppy) are unique due to their rarity and unparalleled flavoalkaloid structure. Read More

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Increased expression of ANAC017primes for accelerated senescence.

Plant Physiol 2021 Apr 29. Epub 2021 Apr 29.

ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Crawley.

Recent studies in Arabidopsis (Arabidopsis thaliana) have reported conflicting roles for NAC DOMAIN CONTAINING PROTEIN 17 (ANAC017), a transcription factor regulating mitochondria-to-nuclear signalling, and its closest paralog NAC DOMAIN CONTAINING PROTEIN 16 (ANAC016), in leaf senescence. By synchronising senescence in individually darkened leaves of knock-out and overexpressing mutants from these contrasting studies, we demonstrate that elevated ANAC017 expression consistently causes accelerated senescence and cell death. A time-resolved transcriptome analysis revealed that senescence-associated pathways such as autophagy are not constitutively activated in ANAC017 overexpression lines, but require a senescence-stimulus to trigger accelerated induction. Read More

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Differential expressions of anthocyanin synthesis genes underlie flower color divergence in a sympatric Rhododendron sanguineum complex.

BMC Plant Biol 2021 Apr 28;21(1):204. Epub 2021 Apr 28.

CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.

Background: The Rhododendron sanguineum complex is endemic to alpine mountains of northwest Yunnan and southeast Tibet of China. Varieties in this complex exhibit distinct flower colors even at the bud stage. However, the underlying molecular regulations for the flower color variation have not been well characterized. Read More

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Kallmann syndrome in a patient with Weiss-Kruszka syndrome and a de novo deletion in 9q31.2.

Eur J Endocrinol 2021 Apr 1. Epub 2021 Apr 1.

T Raivio, Institute of Biomedicine/Physiology, University of Helsinki, Helsinki, Finland.

Patients with deletions in chromosome 9q31.2 may exhibit delayed puberty, craniofacial phenotype including cleft lip/palate, and olfactory bulb hypoplasia. We report a patient with congenital HH with anosmia (Kallmann syndrome, KS) and a de novo 2. Read More

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Deciphering the principles of the RNA editing code via large-scale systematic probing.

Mol Cell 2021 Apr 20. Epub 2021 Apr 20.

Department of Molecular Genetics, Weizmann Institute of Science, 7610001 Rehovot, Israel. Electronic address:

Adenosine-to-inosine editing is catalyzed by ADAR1 at thousands of sites transcriptome-wide. Despite intense interest in ADAR1 from physiological, bioengineering, and therapeutic perspectives, the rules of ADAR1 substrate selection are poorly understood. Here, we used large-scale systematic probing of ∼2,000 synthetic constructs to explore the structure and sequence context determining editability. Read More

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Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67.

BMC Genomics 2021 Apr 26;22(1):303. Epub 2021 Apr 26.

Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892-8132, USA.

Background: Rodent malaria parasites are important models for studying host-malaria parasite interactions such as host immune response, mechanisms of parasite evasion of host killing, and vaccine development. One of the rodent malaria parasites is Plasmodium yoelii, and multiple P. yoelii strains or subspecies that cause different disease phenotypes have been widely employed in various studies. Read More

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