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Large-Scale Multiplexing Permits Full-Length Transcriptome Annotation of 32 Bovine Tissues From a Single Nanopore Flow Cell.

Front Genet 2021 20;12:664260. Epub 2021 May 20.

Department of Animal Science, University of California, Davis, Davis, CA, United States.

A comprehensive annotation of transcript isoforms in domesticated species is lacking. Especially considering that transcriptome complexity and splicing patterns are not well-conserved between species, this presents a substantial obstacle to genomic selection programs that seek to improve production, disease resistance, and reproduction. Recent advances in long-read sequencing technology have made it possible to directly extrapolate the structure of full-length transcripts without the need for transcript reconstruction. Read More

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PTENP1-AS contributes to BRAF inhibitor resistance and is associated with adverse clinical outcome in stage III melanoma.

Sci Rep 2021 May 26;11(1):11023. Epub 2021 May 26.

Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden.

BRAF inhibitors (BRAFi) selectively target oncogenic BRAF and are effective in 80% of advanced cutaneous malignant melanoma cases carrying the V600 mutation. However, the development of drug resistance limits their clinical efficacy. Better characterization of the underlying molecular processes is needed to further improve treatments. Read More

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Carbon Dioxide Concentration Mechanisms in Natural Populations of Marine Diatoms: Insights From Oceans.

Front Plant Sci 2021 30;12:657821. Epub 2021 Apr 30.

CSIR National Institute of Oceanography, Biological Oceanography Division, Dona Paula, India.

Marine diatoms, the most successful photoautotrophs in the ocean, efficiently sequester a significant part of atmospheric CO to the ocean interior through their participation in the biological carbon pump. However, it is poorly understood how marine diatoms fix such a considerable amount of CO, which is vital information toward modeling their response to future CO levels. The Oceans expeditions generated molecular data coupled with biogeochemical measurements across the main ocean regions, and thus provides a framework to compare diatom genetic and transcriptional flexibility under natural CO variability. Read More

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Membrane-Enriched Proteomics Link Ribosome Accumulation and Proteome Reprogramming With Cold Acclimation in Barley Root Meristems.

Front Plant Sci 2021 30;12:656683. Epub 2021 Apr 30.

School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.

Due to their sessile nature, plants rely on root systems to mediate many biotic and abiotic cues. To overcome these challenges, the root proteome is shaped to specific responses. Proteome-wide reprogramming events are magnified in meristems due to their active protein production. Read More

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SREBP2 gene therapy targeting striatal astrocytes ameliorates Huntington's disease phenotypes.

Brain 2021 May 11. Epub 2021 May 11.

Department of Biosciences, University of Milan, 20133, Milan, Italy.

Brain cholesterol is produced mainly by astrocytes and is important for neuronal function. Its biosynthesis is severely reduced in mouse models of Huntington's disease. One possible mechanism is a diminished nuclear translocation of the transcription factor sterol regulatory element binding protein 2 (SREBP2) and, consequently, reduced activation of SREBP-controlled genes in the cholesterol biosynthesis pathway. Read More

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Phytohormone-dependent plant defense signaling orchestrated by oral bacteria of the herbivore Spodoptera litura.

New Phytol 2021 May 1. Epub 2021 May 1.

Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, Tokyo, 125-8585, Japan.

A vast array of herbivorous arthropods live with symbiotic microorganisms. However, little is known about the nature and functional mechanism of bacterial effects on plant defense responses towards herbivores. We explored the role of microbes present in extracts of oral secretion (OS) isolated from larvae of Spodoptera litura, a generalist herbivore, in phytohormone signaling-dependent defense responses in Arabidopsis thaliana (arabidopsis). Read More

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Riboswitch control of bacterial RNA stability.

Mol Microbiol 2021 Apr 2. Epub 2021 Apr 2.

Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.

Although riboswitches have long been known to regulate translation initiation and transcription termination, a growing body of evidence indicates that they can also control bacterial RNA lifetimes by acting directly to hasten or impede RNA degradation. Ligand binding to the aptamer domain of a riboswitch can accelerate RNA decay by triggering a conformational change that exposes sites to endonucleolytic cleavage or by catalyzing the self-cleavage of a prefolded ribozyme. Alternatively, the conformational change induced by ligand binding can protect RNA from degradation by blocking access to an RNA terminus or internal region that would otherwise be susceptible to attack by an exonuclease or endonuclease. Read More

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miR-744/eNOS/NO axis: A novel target to halt triple negative breast cancer progression.

Breast Dis 2021 Mar 19. Epub 2021 Mar 19.

Department of Biochemistry, German University in Cairo, New Cairo City, Main Entrance Al Tagamoa Al Khames, Cairo, Egypt.

Background: Nitric oxide (NO) may have a dual role in cancer. At low concentrations, endogenous NO promotes tumor growth and proliferation. However, at very high concentrations, it mediates cancer cell apoptosis and inhibits cancer growth. Read More

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A PAS Protein Directs Metabolic Reprogramming during Cryptococcal Adaptation to Hypoxia.

mBio 2021 03 16;12(2). Epub 2021 Mar 16.

Department of Microbiology, University of Georgia, Athens, Georgia, USA

To aerobic organisms, low oxygen tension (hypoxia) presents a physiological challenge. To cope with such a challenge, metabolic pathways such as those used in energy production have to be adjusted. Many of such metabolic changes are orchestrated by the conserved hypoxia-inducible factors (HIFs) in higher eukaryotes. Read More

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(+)-Usnic acid modulates the Nrf2-ARE pathway in FaDu hypopharyngeal carcinoma cells.

Mol Cell Biochem 2021 Jun 26;476(6):2539-2549. Epub 2021 Feb 26.

Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznan, Poland.

Naturally occurring phytochemicals of different origin and structure, arctigenin, bergenin, usnic acid and xanthohumol, were shown to affect Nrf2 pathway in the context of various diseases, but their effect on this pathway in cancer cells was not extensively investigated. This study aimed to evaluate the effect of these compounds on Nrf2 expression and activation in hypopharyngeal FaDu squamous cell carcinoma cells. FaDu cells were treated with 2 or 10 μM arctigenin, bergenin, (+)-usnic acid or xanthohumol for 24 h. Read More

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Expression profiles of interferon-related genes in cells infected with influenza A viruses or transiently transfected with plasmids encoding viral RNA polymerase.

Turk J Biol 2021 9;45(1):88-103. Epub 2021 Feb 9.

Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Marmara University, İstanbul Turkey.

Influenza A viruses frequently change their genetic characteristics, which leads to the emergence of new viruses. Consequently, elucidation of the relationship between influenza A virus and host cells has a great importance to cope with viral infections. In this study, it was aimed to determine expression profiles of interferon response genes in human embryonic kidney 293 (HEK293) cells infected with human (A/WSN-H1N1) and avian influenza A viruses (duck/Pennsylvania/10218/84/H5N2) or transfected with plasmids encoding viral RdRP subunits and, to obtain clues about the genes that may be important for the viral pathogenesis. Read More

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February 2021

Downregulated microRNA-129-5p by Long Non-coding RNA NEAT1 Upregulates PEG3 Expression to Aggravate Non-alcoholic Steatohepatitis.

Front Genet 2020 26;11:563265. Epub 2021 Jan 26.

Department of Hepatobiliary Surgery II, Zhujiang Hospital, Southern Medical University, Guangzhou, China.

Long non-coding RNAs (lncRNAs) have recently emerged as inflammation-associated biological molecules with a specific role in the progression of liver fibrosis conditions including non-alcoholic steatohepatitis (NASH). The aim of this study was to elucidate the effects of lncRNA nuclear enriched abundant transcript 1 (NEAT1), microRNA-129-5p (miR-129-5p), and paternally expressed gene 3 (PEG3) on the biological activities of hepatic stellate cells (HSCs) subjected to NASH. First, microarray-based analysis revealed upregulated PEG3 in NASH. Read More

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January 2021

Integrative Transcriptomic Network Analysis of Butyrate Treated Colorectal Cancer Cells.

Cancers (Basel) 2021 Feb 5;13(4). Epub 2021 Feb 5.

Flinders Health and Medical Research Institute-Cancer Program, Flinders University, Bedford Park, SA 5042, Australia.

Diet-derived histone deacetylase inhibitor (HDACi), butyrate, alters global acetylation and consequently global gene expression in colorectal cancer (CRC) cells to exert its anticancer effects. Aberrant microRNA (miRNA) expression contributes to CRC development and progression. Butyrate-mediated modulation of microRNA (miRNA) expression remains under-investigated. Read More

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February 2021

, a Ribonucleoprotein Gene, Regulates Chloroplast mRNA Stability That Confers Drought and Cold Tolerance.

Int J Mol Sci 2021 Feb 7;22(4). Epub 2021 Feb 7.

Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea.

Chloroplast ribonucleoproteins (cpRNPs) are nuclear-encoded and highly abundant proteins that are proposed to function in chloroplast RNA metabolism. However, the molecular mechanisms underlying the regulation of chloroplast RNAs involved in stress tolerance are poorly understood. Here, we demonstrate that (), a rice () cpRNP gene, is essential for stabilization of RNAs from the NAD(P)H dehydrogenase (NDH) complex, which in turn enhances drought and cold stress tolerance. Read More

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February 2021

BSGatlas: a unified genome and transcriptome annotation atlas with enhanced information access.

Microb Genom 2021 02;7(2)

Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871 Frederiksberg, Denmark.

A large part of our current understanding of gene regulation in Gram-positive bacteria is based on , as it is one of the most well studied bacterial model systems. The rapid growth in data concerning its molecular and genomic biology is distributed across multiple annotation resources. Consequently, the interpretation of data from further experiments becomes increasingly challenging in both low- and large-scale analyses. Read More

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February 2021

Transcript-Activated Coatings on Titanium Mediate Cellular Osteogenesis for Enhanced Osteointegration.

Mol Pharm 2021 03 25;18(3):1121-1137. Epub 2021 Jan 25.

IBE, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, 6200 MD Maastricht, The Netherlands.

Osteointegration is one of the most important factors for implant success. Several biomolecules have been used as part of drug delivery systems to improve implant integration into the surrounding bone tissue. Chemically modified mRNA (cmRNA) is a new form of therapeutic that has been used to induce bone healing. Read More

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Alt-RPL36 downregulates the PI3K-AKT-mTOR signaling pathway by interacting with TMEM24.

Nat Commun 2021 01 21;12(1):508. Epub 2021 Jan 21.

Department of Chemistry, Yale University, New Haven, CT, 06520, USA.

Thousands of human small and alternative open reading frames (smORFs and alt-ORFs, respectively) have recently been annotated. Many alt-ORFs are co-encoded with canonical proteins in multicistronic configurations, but few of their functions are known. Here, we report the detection of alt-RPL36, a protein co-encoded with human RPL36. Read More

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January 2021

Xyloglucan endotransglycosylase/hydrolase increases tightly-bound xyloglucan and chain number but decreases chain length contributing to the defense response that Glycine max has to Heterodera glycines.

PLoS One 2021 14;16(1):e0244305. Epub 2021 Jan 14.

Department of Biological Sciences, Mississippi State University, Starkville, Mississippi State, United States of America.

The Glycine max xyloglucan endotransglycosylase/hydrolase (EC 2.4.1. Read More

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Tobacco smoking and its impact on the expression level of sperm nuclear protein genes: H2BFWT, TNP1, TNP2, PRM1 and PRM2.

Andrologia 2021 Apr 13;53(3):e13964. Epub 2021 Jan 13.

Department of Obstetrics, Gynecology and Reproductive Medicine, Saarland University Clinic, Homburg, Germany.

The aim of this current study was to investigate the influence of tobacco smoke on sperm quality determined by standard parameters, on sperm DNA maturity tested by chromomycin A3 (CMA3) staining, on sperm DNA fragmentation tested by TUNEL assay and on the transcript level of sperm nuclear proteins H2BFWT, PRM1, PRM2, TNP1 and TNP2 genes quantified by RT-PCR. One hundred forty-one (141) sperm samples (43 nonsmokers (G.1) and 98 heavy smokers (G. Read More

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Human Adipose-Derived Stem Cells' Paracrine Factors in Conditioned Medium Can Enhance Porcine Oocyte Maturation and Subsequent Embryo Development.

Seok Hee Lee

Int J Mol Sci 2021 Jan 8;22(2). Epub 2021 Jan 8.

Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Seoul National University, Seoul 08826, Korea.

An essential requirement for the success of in vitro maturation (IVM) of the oocyte is to provide an optimal microenvironment similar to in vivo conditions. Recently, somatic cell-based coculture or supplementation of a conditioned medium during IVM has been performed to obtain better quality of oocytes, because they mimic the in vivo reproductive tract by secreting paracrine factors. In this study, human adipose-derived stem cells (ASC) and their conditioned medium (ASC-CM) were applied to IVM of porcine oocytes to evaluate the effectiveness of ASC on oocyte development and subsequent embryo development. Read More

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January 2021

Mutation of Aggravates Chilling-Induced Oxidative Stress by Impairing Glutathione Biosynthesis and Suppressing Ascorbate-Glutathione Recycling in Tomato Plants.

Front Plant Sci 2020 22;11:565701. Epub 2020 Dec 22.

College of Forestry, Northwest A&F University, Yangling, China.

Sedoheptulose-1,7-bisphosphatase (SBPase) is a crucial enzyme for photosynthetic carbon assimilation in the Calvin-Benson cycle. Previous studies have shown that overexpression of SBPase is advantageous to chilling tolerance in plants; however, the mechanisms of SBPase acting in the improvement of chilling tolerance remain largely unknown. In the present study, we aimed to uncover the essential role of SBPase in the response of tomato plants to oxidative stress induced by low temperature. Read More

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December 2020

Long-Term Consumption of Anthocyanin-Rich Fruit Juice: Impact on Gut Microbiota and Antioxidant Markers in Lymphocytes of Healthy Males.

Antioxidants (Basel) 2020 Dec 29;10(1). Epub 2020 Dec 29.

Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Waehringerstrasse 38, 1090 Vienna, Austria.

Polyphenols are considered protective against diseases associated with oxidative stress. Short-term intake of an anthocyanin-rich fruit juice resulted in significantly reduced deoxyribonucleic acid (DNA) strand-breaks in peripheral blood lymphocytes (PBLs) and affected antioxidant markers in healthy volunteers. Consequently, effects of long-term consumption of fruit juice are of particular interest. Read More

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December 2020

Nuclear-Encoded Maturase Protein 3 Is Required for the Splicing of Various Group II Introns in Mitochondria during Maize (Zea mays L.) Seed Development.

Plant Cell Physiol 2021 May;62(2):293-305

Center of Seed Science and Technology, Beijing Innovation Center for Seed Technology (MOA), Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.

Splicing of plant organellar group II introns from precursor-RNA transcripts requires the assistance of nuclear-encoded splicing factors. Maturase (nMAT) is one such factor, as its three homologs (nMAT1, 2 and 4) have been identified as being required for the splicing of various mitochondrial introns in Arabidopsis. However, the function of nMAT in maize (Zea mays L. Read More

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Metabolic Reprogramming by Malat1 Depletion in Prostate Cancer.

Cancers (Basel) 2020 Dec 22;13(1). Epub 2020 Dec 22.

National Research Council (CNR)-IASI, Department of Engineering, ICT and Technologies for Energy and Transportation, 00185 Rome, Italy.

The lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) promotes growth and progression in prostate cancer (PCa); however, little is known about its possible impact in PCa metabolism. The aim of this work has been the assessment of the metabolic reprogramming associated with MALAT1 silencing in human PCa cells and in an ex vivo model of organotypic slice cultures (OSCs). Cultured cells and OSCs derived from primary tumors were transfected with MALAT1 specific gapmers. Read More

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December 2020

Relative DNA Methylation and Demethylation Efficiencies during Postnatal Liver Development Regulate Hepatitis B Virus Biosynthesis.

J Virol 2021 02 24;95(6). Epub 2021 Feb 24.

Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA

Hepatitis B virus (HBV) transcription and replication increase progressively throughout postnatal liver development with maximal viral biosynthesis occurring at around 4 weeks of age in the HBV transgenic mouse model of chronic infection. Increasing viral biosynthesis is associated with a corresponding progressive loss of DNA methylation. The loss of DNA methylation is associated with increasing levels of 5-hydroxymethylcytosine (5hmC) residues which correlate with increased liver-enriched pioneer transcription factor Forkhead box protein A (FoxA) RNA levels, a rapid decline in postnatal liver DNA methyltransferase (Dnmt) transcripts, and a very modest reduction in ten-eleven translocation (Tet) methylcytosine dioxygenase expression. Read More

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February 2021

targets lncRNA ENO1-IT1 to promote glycolysis and oncogenesis in colorectal cancer.

Gut 2020 Dec 14. Epub 2020 Dec 14.

State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology; Shanghai Cancer Institute; Shanghai Institute of Digestive Disease, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China

Objective: Microbiota disorder promotes chronic inflammation and carcinogenesis. High glycolysis is associated with poor prognosis in patients with colorectal cancer (CRC). However, the potential correlation between the gut microbiota and glucose metabolism is unknown in CRC. Read More

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December 2020

Fermented Maillard reaction products attenuate stress-induced testicular dysfunction in mice.

J Dairy Sci 2021 Feb 30;104(2):1384-1393. Epub 2020 Nov 30.

Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea. Electronic address:

Chronic stress can cause psychological diseases and affect male fertility and the reproductive system. Maillard reaction of milk proteins improves their functional and nutritional properties through modification of proteins. Previously, we determined that Maillard reaction product (MRP) from milk casein and MRP fermented (FMRP) with Lactobacillus rhamnosus 4B15 (4B15) had anti-anxiolytic effects in mice under chronic stress. Read More

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February 2021

The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation.

RNA 2020 Dec 2. Epub 2020 Dec 2.

Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France);

SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. Read More

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December 2020

The AMPK-mTOR axis requires increased MALAT1 expression for promoting granulosa cell proliferation in endometriosis.

Exp Ther Med 2021 Jan 6;21(1):21. Epub 2020 Nov 6.

Department of Reproductive Medicine, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261000, P.R. China.

Endometriosis is a common reproductive disorder in women, with a global prevalence of 10-15%. Long noncoding RNAs (lncRNAs) are critical to gene transcription, cell cycle modulation and immune response. The lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) reportedly mediates autophagy of endometrial stromal cells in endometriosis. Read More

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January 2021

Morpholino Oligomer-Induced Dystrophin Isoforms to Map the Functional Domains in the Dystrophin Protein.

Mol Ther Nucleic Acids 2020 Dec 21;22:263-272. Epub 2020 Aug 21.

Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia.

Dystrophin plays a crucial role in maintaining sarcolemma stability during muscle contractions, and mutations that prevent the expression of a functional protein cause Duchenne muscular dystrophy (DMD). Antisense oligonucleotide-mediated manipulation of pre-messenger RNA splicing to bypass Duchenne-causing mutations and restore functional dystrophin expression has entered the clinic for the most common mutations. The rationale of "exon skipping" is based upon genotype-phenotype correlations observed in Becker muscular dystrophy, a milder allelic disorder generally characterized by in-frame deletions and internally truncated but semi-functional dystrophin isoforms. Read More

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December 2020