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Cell Reprogram 2021 Apr;23(2):139-148

Department of Biochemistry, Erciyes University School of Medicine, Kayseri, Turkey.

Although the molecular pathogenesis of hepatocellular carcinoma (HCC) is uncertain, it is known that the epithelial-mesenchymal transition (EMT) mechanism and epigenetic changes have an important role. This study was focused on evaluating the relationship of 3-Deazaneplanocin A (DZNep) with the EMT mechanism, which is a histone methyltransferase inhibitor on HCC and is also known as an enhancer of zeste homolog 2 (EZH2) inhibitor. Cell viability of HepG2 cells (HCC cell line) assessed for DZNep over 72 hours with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Read More

Am J Physiol Heart Circ Physiol 2021 Apr 16. Epub 2021 Apr 16.

Lillehei Heart Institute, University of Minnesota College of Medicine, Department of Medicine, Minneapolis, MN 55455, United States.

Background: The interaction of phospholamban (PLB) and the sarcoplasmic reticulum Ca-ATPase (Serca2a) is a key regulator of cardiac contractility and a therapeutic target in heart failure (HF). PLB mediated increases in Serca2a activity improve cardiac function and HF. Clinically this mechanism can only be exploited by a general activation of the proteinkinase A (PKA) which is associated with side effects and adverse clinical outcomes. Read More

Acc Chem Res 2021 Apr 16. Epub 2021 Apr 16.

Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada.

ConspectusThis Account highlights the structural features that render 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA) an ideal tool for mimicking DNA secondary structures and probing biomolecular interactions relevant to chemical biology.The high binding affinity of FANA to DNA and RNA has had implications in therapeutics. FANA can hybridize to complementary RNA, resulting in a predominant A-form helix stabilized by a network of 2'F-H8(purine) pseudohydrogen bonding interactions. Read More

PeerJ 2021 2;9:e11087. Epub 2021 Apr 2.

Medical College, China Three Gorges University, Yichang, China.

Background: Guizhi Fuling Wan (GZFLW) is a widely used classical Chinese herbal formulae prescribed for the treatment of endometriosis (EMs). This study aimed to predict the key targets and mechanisms of GZFLW in the treatment of EMs by network pharmacology and molecular docking.

Methods: Firstly, related compounds and targets of GZFLW were identified through the TCMSP, BATMAN-TCM and CASC database. Read More

Theranostics 2021 11;11(11):5232-5247. Epub 2021 Mar 11.

Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan.

NRF2, a redox sensitive transcription factor, is up-regulated in head and neck squamous cell carcinoma (HNSCC), however, the associated impact and regulatory mechanisms remain unclear. The protein expression of NRF2 in HNSCC specimens was examined by IHC. The regulatory effect of c-MYC on NRF2 was validated by ChIP-qPCR, RT-qPCR and western blot. Read More

Reprod Fertil Dev 2021 Apr 16. Epub 2021 Apr 16.

Vitellogenesis is essential for oocyte maturation. Vitellogenin (Vtg), a yolk precursor protein, plays an important role in oogenesis and vitellogenesis. Chinese hook snout carp Opsariichthys bidens is an economically important freshwater fish in China whose reproductive and developmental biology are not well understood. Read More

Photodiagnosis Photodyn Ther 2021 Apr 12:102292. Epub 2021 Apr 12.

Department of Dental Materials and Prosthodontics, School of Dentistry at Araraquara, Univ Estadual Paulista - UNESP, Rua Humaitá, 1680, 14801-903, Araraquara, SP, Brazil. Electronic address:

The study evaluated the effect of antimicrobial photodynamic therapy (aPDT) and nystatin (NYS) in the expression of genes (ACT1, ALS1, CAP1, CAT1, EFG1, HWP1, LIP3, PLB1, SAP1, and SOD1) involved in the virulence of Candida albicans strains recovered from patients with denture stomatitis (DS). These strains were isolated from the patients before (initial) and after treatment (final), and 45 days after the treatments (follow-up). For gene expression analyses, RNA was isolated from the clinical strains, followed by cDNA synthesis and qPCR using specific primers for each target gene. Read More

PLoS One 2021 15;16(4):e0249288. Epub 2021 Apr 15.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, Henan Province, P.R. China.

Circular RNAs (circRNAs) play important roles in adipogenesis. However, studies on circRNA expression profiles associated with the development of abdominal adipose tissue are lacking in chickens. In this study, 12 cDNA libraries were constructed from the abdominal adipose tissue of Chinese domestic Gushi chickens at 6, 14, 22, and 30 weeks. Read More

Front Mol Biosci 2021 29;8:654718. Epub 2021 Mar 29.

Department of Urology, Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Shenzhen, China.

LncRNAs are defined as non-coding RNAs that are longer than 200 nucleotides in length. The previous studys has shown that lncRNAs played important roles in the regulation of gene expression and were essential in mammalian development and disease processes. Inspired by the observation that lncRNAs are aberrantly expressed in tumors, we extracted RNA from Bladder urothelial carcinoma and matched histologically normal urothelium from each patient and bladder carcinoma cell lines. Read More

Physiol Mol Biol Plants 2021 Mar 14;27(3):577-586. Epub 2021 Mar 14.

Senckenberg Biodiversity and Climate Research Center, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany.

polyamine oxidase 5 gene () functions as a thermospermine (T-Spm) oxidase. Aerial growth of its knock-out mutant () was significantly repressed by low dose(s) of T-Spm but not by other polyamines. To figure out the underlying mechanism, massive analysis of 3'-cDNA ends was performed. Read More

Langmuir 2021 Apr 13. Epub 2021 Apr 13.

Toshiba Corporation, 1 Komukai-Toshiba-cho, Saiwai, Kawasaki 212-8582, Japan.

Graphene's remarkable attributes make it suitable for application to biosensors for biomolecular recognition. Specific and precise target detection is realized by designing robust methods for immobilization of probe molecules, such as oligonucleotides, antibodies, receptors, and sugar chains, to a device surface. In this research, we developed a chemical modification method with a plasma treatment of amino groups on natural defects of graphene, which is compatible with a wafer-scalable semiconductor process, to prevent deterioration of the carrier mobility. Read More

Fish Shellfish Immunol 2021 Apr 10. Epub 2021 Apr 10.

Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Fishery Drug Development, Ministry of Agriculture and Rural Affairs, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Provinces, Guangzhou, 510380, China.

In fish, interleukin-6 (IL-6) is a very important immune-regulatory cytokine that plays a polyfunctional role in inflammation, metabolism, regeneration, and neural processes. IL-6 signal transducer (IL-6ST) is a specific receptor for IL-6 and expressed mainly in immune cells and hepatocytes. In this study, the complete cDNA and genomic DNA sequences of mandarin fish (Siniperca chuatsi) IL-6 and IL-6ST genes were identified and analyzed. Read More

Nat Plants 2021 Apr 12. Epub 2021 Apr 12.

Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.

Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). Read More

Sci Rep 2021 Apr 12;11(1):7883. Epub 2021 Apr 12.

Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), 43600, Bangi, Selangor Darul Ehsan, Malaysia.

Ferrocene or ferrocenium has been widely studied in the field of organometallic complexes because of its stable thermodynamic, kinetic and redox properties. Novel hexaferrocenium tri[hexa(isothiocyanato)iron(III)]trihydroxonium (HexaFc) complex was the product from the reaction of ferrocene, maleic acid and ammonium thiocyanate and was confirmed by elemental analysis CHNS, FTIR and single crystal X-ray crystallography. In this study, HexaFc was used for the first time as an electroactive indicator for porcine DNA biosensor. Read More

Comp Biochem Physiol B Biochem Mol Biol 2021 Apr 9:110599. Epub 2021 Apr 9.

College of Life Sciences, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China. Electronic address:

The p38 mitogen-activated protein kinase (MAPK) is one important member of MAPK family and reported to serve a predominant function in regulating innate immunity after the occurrence of certain infection. In the present study, one novel p38 MAPK gene was acquired from Cyclina sinensis based on the RNA-seq analysis and designated as Csp38 MAPK. This novel gene contained a full length of 1781 bp, 1104 bp of which was deemed as open reading frames and gave rise to a peptide of 367 amino acids with a predicted molecular weight of 42. Read More

J Hepatol 2021 Apr 9. Epub 2021 Apr 9.

Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany; German Centre for Infection Research (DZIF), partner site Heidelberg, Heidelberg, Germany. Electronic address:

Background & Aims: Chronic hepatitis D virus (HDV) infections cause the most severe form of viral hepatitis. HDV requires hepatitis B virus (HBV) envelope proteins for hepatocyte entry, particle assembly and release. Eight HDV and eight HBV genotypes are presently distinguished. Read More

Environ Sci Technol 2021 Apr 12. Epub 2021 Apr 12.

College of Wildlife and Protected Area, Northeast Forestry University, Harbin, Heilongjiang 150040, PR China.

Cypermethrin (CMN) is a man-made insecticide, and its abuse has led to potential adverse effects, particularly in sensitive populations such as aquatic organisms. The present study was focused on the toxic phenotype and detoxification mechanism in grass carp () after treatment with waterborne CMN (0.651 μg/L) for 6 weeks in vivo or 6. Read More

Data Brief 2021 Apr 15;35:106951. Epub 2021 Mar 15.

Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France.

Pervasive transcription originating from the ubiquitous activity of RNA Polymerase II (RNAPII) generates a vast mass of non-coding RNAs (ncRNAs) that represent a potential harm to gene expression. In the compact genome of the yeast , the main genomewide safeguard against pervasive ncRNAs is the Nrd1-Nab3-Sen1 (NNS) complex, composed of two RNA-binding proteins (Nrd1 and Nab3) and the helicase Sen1. The NNS complex directs transcription termination of ncRNA genes and promotes the rapid degradation of pervasive transcripts from yeast nuclei through its physical and functional coupling to the nuclear RNA exosome. Read More

Front Chem 2021 24;9:653869. Epub 2021 Mar 24.

Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.

Aflatoxin M (AFM), one of the most toxic mycotoxins, is a feed and food contaminant of global concern. In this study, we developed a fast and simple method for detection of AFM based on a structure-switching signaling aptamer. This aptasensor is based on the change in fluorescence signal due to formation of an AFM/aptamer complex. Read More

Front Genet 2021 25;12:644803. Epub 2021 Mar 25.

Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.

Telomeres, repetitive nucleoprotein complexes that protect chromosomal termini and prevent them from activating inappropriate DNA damage responses (DDRs), shorten with cell division and thus with aging. Here, we characterized the human cellular response to targeted telomeric double-strand breaks (DSBs) in telomerase-positive and telomerase-independent alternative lengthening of telomere (ALT) cells, specifically in G1 phase. Telomeric DSBs in human G1 cells elicited early signatures of a DDR; however, localization of 53BP1, an important regulator of resection at broken ends, was not observed at telomeric break sites. Read More

Colloids Surf B Biointerfaces 2021 Apr 6;203:111747. Epub 2021 Apr 6.

Applied Biotechnology Group, Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Urbanización El Bosque, 28670 Villaviciosa De Odón, Madrid, Spain; Grupo de Investigación en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia.

Fenneropenaeus merguiensis (commonly named banana shrimp) is one of the most important farmed crustacean worldwide species for the fisheries and aquaculture industry. Besides its nutritional value, it is a good source of chitinase, an enzyme with excellent biological and catalytic properties for many industrial applications. In the present study, a putative chitinase-encoding cDNA was synthesized from mRNA from F. Read More

Photodiagnosis Photodyn Ther 2021 Apr 8:102290. Epub 2021 Apr 8.

Nanomedicine and Nanobiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Department of Medical Physics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran. Electronic address:

Trichomoniasis, an infectious disease caused by a parasite called Trichomonas vaginalis (T. Vaginalis), enhances the risk of HIV infection, cervical and prostate cancer, and infertility. Therefore, more efforts have to be made for accurate, specific, and rapid diagnoses and treatment of trichomoniasis. Read More

Cell Rep 2021 Apr 1:109014. Epub 2021 Apr 1.

Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Diseases Education and Research, Osaka University, Suita, Osaka 565-0871, Japan. Electronic address:

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the causative agent of coronavirus disease 2019 (COVID-19). Although multiple mutations have been observed in SARS-CoV-2, functional analysis of each mutation of SARS-CoV-2 has been limited by the lack of convenient mutagenesis methods. In this study, we establish a PCR-based, bacterium-free method to generate SARS-CoV-2 infectious clones. Read More

Biophys J 2021 Apr 7. Epub 2021 Apr 7.

Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104. Electronic address:

Many biologically important cell binding processes, such as the rolling of leukocytes in the vasculature, are multivalent, being mediated by large numbers of weak binding ligands. Quantitative agreement between experiments and models of rolling has been elusive, and often limited by the poor understanding of the binding and unbinding kinetics of the ligands involved. Here we present a cell-free experimental model for such rolling, consisting of polymer microspheres whose adhesion to a glass surface is mediated by ligands with well-understood force-dependent binding free energy-short complementary DNA strands. Read More

Luminescence 2021 Apr 10. Epub 2021 Apr 10.

Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, China.

A simple, rapid and highly sensitive method for the detection of double-stranded DNA (dsDNA) was developed using a novel fluorescence probe which was composed of RecA-GFP fusion protein and specific recognition of ssDNA complexes (RecA-GFP-DNA filament). The RecA-GFP fusion protein not only has strong fluorescence, but also can occur to homologous recombination. In the presence of the target dsDNA, the complementary ssDNA of RecA-GFP-DNA filaments invaded into one end of the dsDNA chain, meanwhile, the other end of ssDNA dissociated RecA-GFP filaments. Read More

BMC Plant Biol 2021 Apr 9;21(1):170. Epub 2021 Apr 9.

Department of Biochemistry, Max Planck Institute for Chemical Ecology (MPI-CE), Hans-Knöll-Str. 8, 07745, Jena, Germany.

Background: Protease inhibitors are defense proteins widely distributed in the plant kingdom. By reducing the activity of digestive enzymes in insect guts, they reduce the availability of nutrients and thus impair the growth and development of the attacking herbivore. One well-characterized class of protease inhibitors are Kunitz-type trypsin inhibitors (KTIs), which have been described in various plant species, including Populus spp. Read More

Cancer Genet 2021 Mar 24;256-257:21-25. Epub 2021 Mar 24.

Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States; Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, United States. Electronic address:

Background: Adrenocortical carcinoma (ACC) is a rare malignancy arising from the adrenal cortex. ACC carries a dismal prognosis and surgery offers the only chance for a cure. Germline pathogenic variants among certain oncogenes have been implicated in ACC. Read More

J Clin Virol 2021 Mar 31;139:104814. Epub 2021 Mar 31.

IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France. Electronic address:

Introduction: The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD. Read More

Toxicon 2021 Apr 6;196:63-73. Epub 2021 Apr 6.

Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Basic Medicine, Hubei University of Medicine, Shiyan, 442000, China; Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China. Electronic address:

Methicillin-resistant staphylococci have become growing threats to human health, and novel antimicrobials are urgently needed. Natural antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics. Here, two novel cationic α-helical antimicrobial peptides, Lausporin-1 and Lausporin-2, were identified from the venom gland of the scorpion L. Read More

Methods Mol Biol 2021 ;2284:569-578

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

The recent advent of Nanopore sequencing allows for the sequencing of full-length RNA or cDNA molecules. This new type of data introduces new challenges from the computational point of view, and requires new software as well as dedicated analysis pipelines. In this chapter, we guide the reader through the typical analysis steps required to process the raw data produced by the instrument into a table of counts suitable for downstream analyses. Read More