18,340 results match your criteria long encoding


Sex differences in synaptic plasticity underlying learning.

J Neurosci Res 2021 Apr 12. Epub 2021 Apr 12.

Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA.

Although sex differences in learning behaviors are well documented, sexual dimorphism in the synaptic processes of encoding is only recently appreciated. Studies in male rodents have built upon the discovery of long-term potentiation (LTP), and acceptance of this activity-dependent increase in synaptic strength as a mechanism of encoding, to identify synaptic receptors and signaling activities that coordinate the activity-dependent remodeling of the subsynaptic actin cytoskeleton that is critical for enduring potentiation and memory. These molecular substrates together with other features of LTP, as characterized in males, have provided an explanation for a range of memory phenomena including multiple stages of consolidation, the efficacy of spaced training, and the location of engrams at the level of individual synapses. Read More

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Computational prediction of potential siRNA and human miRNA sequences to silence orf1ab associated genes for future therapeutics against SARS-CoV-2.

Inform Med Unlocked 2021 Apr 8:100569. Epub 2021 Apr 8.

Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh.

The coronavirus disease 2019 (COVID-19) is an ongoing pandemic caused by an RNA virus termed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). SARS-CoV-2 possesses an almost 30kbp long genome. The genome contains open-reading frame 1ab (ORF1ab) gene, the largest one of SARS-CoV-2, encoding polyprotein PP1ab and PP1a responsible for viral transcription and replication. Read More

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Characteristics of fosA-carrying plasmids in E. coli and Klebsiella spp. isolates originating from food and environmental samples.

J Antimicrob Chemother 2021 Apr 11. Epub 2021 Apr 11.

Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 272, 8057 Zurich, Switzerland.

Objectives: Fosfomycin is an important antibiotic for the treatment of MDR Enterobacteriaceae infections. High susceptibility rates are, however, threatened by the spread of plasmids encoding fosfomycin-modifying enzymes. In this study, we sought to characterize the genetic context of fosA in plasmids from Escherichia coli and Klebsiella spp. Read More

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Genetic Causes of Non-pathogenic pv. Isolates in Kiwifruit Orchards.

Front Microbiol 2021 25;12:650099. Epub 2021 Mar 25.

Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China.

Bacterial canker disease has become the largest threat to kiwifruit cultivation and production. A monomorphic subpopulation of pv. biovar 3 (Psa3) is responsible for the pandemic worldwide. Read More

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Axially- and torsionally-polarized radially converging shear wave MRE in an anisotropic phantom made via Embedded Direct Ink Writing.

J Mech Behav Biomed Mater 2021 Mar 31;119:104483. Epub 2021 Mar 31.

University of Illinois at Chicago, Richard and Loan Hill Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607, USA.

Magnetic Resonance Elastography (MRE) is a non-invasive imaging method to quantitatively map the shear viscoelastic properties of soft tissues. In this study, Embedded Direct Ink Writing is used to fabricate a muscle mimicking anisotropic phantom that may serve as a standard for imaging studies of anisotropic materials. The technique allowed us to obtain a long shelf life silicone-based phantom expressing transverse isotropic mechanical properties. Read More

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A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment.

Nat Commun 2021 04 9;12(1):2085. Epub 2021 Apr 9.

Department of Infection Microbiology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.

Long-term infection of the stomach with Helicobacter pylori can cause gastric cancer. However, the mechanisms by which the bacteria adapt to the stomach environment are poorly understood. Here, we show that a small non-coding RNA of H. Read More

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Improving protein domain classification for third-generation sequencing reads using deep learning.

BMC Genomics 2021 Apr 9;22(1):251. Epub 2021 Apr 9.

Electrical Engineering, City University of Hong Kong, Hong Kong, People's Republic of China.

Background: With the development of third-generation sequencing (TGS) technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow protein domain annotation without assembly, thus can produce important insights into the biological functions of the underlying data. However, the high error rate in TGS data raises a new challenge to established domain analysis pipelines. Read More

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Mapping of sequences in the 5' region and 3' UTR of tomato ringspot virus RNA2 that facilitate cap-independent translation of reporter transcripts in vitro.

PLoS One 2021 9;16(4):e0249928. Epub 2021 Apr 9.

Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada.

Tomato ringspot virus (ToRSV, genus Nepovirus, family Secoviridae, order Picornavirales) is a bipartite positive-strand RNA virus, with each RNA encoding one large polyprotein. ToRSV RNAs are linked to a 5'-viral genome-linked protein (VPg) and have a 3' polyA tail, suggesting a non-canonical cap-independent translation initiation mechanism. The 3' untranslated regions (UTRs) of RNA1 and RNA2 are unusually long (~1. Read More

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Comprehensive Preclinical Assessment of ADVM-022, an Intravitreal Anti-VEGF Gene Therapy for the Treatment of Neovascular AMD and Diabetic Macular Edema.

J Ocul Pharmacol Ther 2021 Apr;37(3):181-190

Adverum Biotechnologies, Inc., Redwood City, California, USA.

Inhibition of vascular endothelial growth factor is the mode of action for several approved therapies, including aflibercept, for the treatment of neovascular age-related macular degeneration (nAMD) and diabetic macular edema (DME). Lack of compliance due to the frequent intravitreal dosing requirements may result in inadequately treated disease, leading to irreversible vision impairment. To date, the majority of gene therapy clinical trials providing sustained anti-VEGF levels in the retina have been limited to subretinal injections requiring a vitrectomy. Read More

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Temporal context actively shapes EEG signatures of time perception.

J Neurosci 2021 Apr 7. Epub 2021 Apr 7.

Department of Psychology, University of Groningen, Grote Kruisstraat 2/1, 9712 TS, Groningen, the Netherlands.

Our subjective perception of time is optimized to temporal regularities in the environment. This is illustrated by the central tendency effect: when estimating a range of intervals, short intervals are overestimated whereas long intervals are underestimated to reduce the overall estimation error. Most models of interval timing ascribe this effect to the weighting of the current interval with previous memory traces the interval has been perceived. Read More

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The immediate early gene is not required for hippocampal long-term potentiation.

J Neurosci 2021 Apr 6. Epub 2021 Apr 6.

Department of Neurobiology, University of Utah.

Memory consolidation is thought to occur through protein synthesis-dependent synaptic plasticity mechanisms such as long-term potentiation (LTP). Dynamic changes in gene expression and epigenetic modifications underlie the maintenance of LTP. Similar mechanisms may mediate the storage of memory. Read More

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A Systems Biology Approach Identifies B Cell Maturation Antigen (BCMA) as a Biomarker Reflecting Oral Vaccine Induced IgA Antibody Responses in Humans.

Front Immunol 2021 22;12:647873. Epub 2021 Mar 22.

Gothenburg University Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

Vaccines against enteric diseases could improve global health. Despite this, only a few oral vaccines are currently available for human use. One way to facilitate such vaccine development could be to identify a practical and relatively low cost biomarker assay to assess oral vaccine induced primary and memory IgA immune responses in humans. Read More

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The autism-associated protein CHD8 is required for cerebellar development and motor function.

Cell Rep 2021 Apr;35(1):108932

Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan. Electronic address:

Mutations in the gene encoding the chromatin remodeler chromodomain helicase DNA-binding protein 8 (CHD8) are a highly penetrant risk factor for autism spectrum disorder (ASD). Although cerebellar abnormalities have long been thought to be related to ASD pathogenesis, it has remained largely unknown whether dysfunction of CHD8 in the cerebellum contributes to ASD phenotypes. We here show that cerebellar granule neuron progenitor (GNP)-specific deletion of Chd8 in mice impairs the proliferation and differentiation of these cells as well as gives rise to cerebellar hypoplasia and a motor coordination defect, but not to ASD-like behavioral abnormalities. Read More

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Neural correlates of episodic memory modulated by temporally delayed rewards.

PLoS One 2021 7;16(4):e0249290. Epub 2021 Apr 7.

Department of Psychology, Yonsei University, Seoul, Republic of Korea.

When a stimulus is associated with an external reward, its chance of being consolidated into long-term memory is boosted via dopaminergic facilitation of long-term potentiation in the hippocampus. Given that higher temporal distance (TD) has been found to discount the subjective value of a reward, we hypothesized that memory performance associated with a more immediate reward will result in better memory performance. We tested this hypothesis by measuring both behavioral memory performance and brain activation using functional magnetic resonance imaging (fMRI) during memory encoding and retrieval tasks. Read More

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Limiting the priming dose of a SARS CoV-2 vaccine improves virus-specific immunity.

bioRxiv 2021 Apr 1. Epub 2021 Apr 1.

Since late 2019, SARS-CoV-2 has caused a global pandemic that has infected 128 million people worldwide. Although several vaccine candidates have received emergency use authorization (EUA), there are still a limited number of vaccine doses available. To increase the number of vaccinated individuals, there are ongoing discussions about administering partial vaccine doses, but there is still a paucity of data on how vaccine fractionation affects vaccine-elicited immunity. Read More

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Feingold syndrome type 2 in a patient from China.

Am J Med Genet A 2021 Apr 5. Epub 2021 Apr 5.

Department of Clinical Laboratory, Shenzhen Nanshan Maternity and Child Healthcare Hospital, Shenzhen, China.

Feingold syndrome type 2 (FGLDS2, MIM614326) is a genetic congenital malformation syndrome, caused by germline heterozygous deletion of MIR17HG on chromosome 13q31, which is extremely rare worldwide. To date, less than 25 patients have been described in the literature. Here, we report on a 3-year-old girl presented with hip dysplasia, polysyndactyly of the left thumb, brachymesophalangy of the fifth digit, microcephaly, intellectual disability, and growth delay. Read More

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Maternal fish oil consumption has a negative impact on mammary gland tumorigenesis in C3(1) Tag mice offspring.

Eur J Nutr 2021 Apr 4. Epub 2021 Apr 4.

Joan C. Edwards School of Medicine, Department of Biomedical Sciences, Marshall University, Huntington, WV, USA.

Purpose: Omega-3 fatty acids have been shown to reduce the incidence and slow the growth of mammary gland cancer in rodent models. Since exposure to dietary components during the critical developmental times of gestation and lactation may alter risk for mammary gland cancer in females, we tested whether exposure to increased levels of long-chain omega-3 fatty acids from fish oils would be preventive or promotional to mammary gland cancer in the offspring.

Methods: Normal SV129 female mice were fed AIN 76 diets containing either 10% corn oil (control, 50% omega 6, n-6) or 5% of an omega-3 (n-3) fatty acid concentrate (fish oil 60% n-3) + 5% canola oil (10% n-3 + 20% n-6). Read More

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Comparison of machine learning and deep learning techniques in promoter prediction across diverse species.

PeerJ Comput Sci 2021 9;7:e365. Epub 2021 Feb 9.

Computer Science, Symbiosis Institute of Technology, Symbiosis International (Deemed University), Pune, MH, India.

Gene promoters are the key DNA regulatory elements positioned around the transcription start sites and are responsible for regulating gene transcription process. Various alignment-based, signal-based and content-based approaches are reported for the prediction of promoters. However, since all promoter sequences do not show explicit features, the prediction performance of these techniques is poor. Read More

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February 2021

Role of long polar fimbriae type 1 and 2 in pathogenesis of mammary pathogenic Escherichia coli.

J Dairy Sci 2021 Apr 1. Epub 2021 Apr 1.

Institute of Veterinary Immunology & Engineering, National Research Center of Engineering and Technology for Veterinary Biologicals, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; School of Pharmacy, Jiangsu University, Zhenjiang 212013, China. Electronic address:

Escherichia coli is a leading cause of bovine mastitis worldwide. The bacteria can rapidly grow in milk and elicit a strong lipopolysaccharide (LPS)/toll-like receptor-4 (TLR4)-dependent inflammatory response. Recently, the long polar fimbriae (LPF) were identified as a promising virulence factor candidate widely distributed in mammary pathogenic E. Read More

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MRI Guided Intervention: Evaluation of MR conditional Biopsy and Ablation Needle Tip Artifacts at 3T using a balanced fast field echo sequence.

J Vasc Interv Radiol 2021 Mar 31. Epub 2021 Mar 31.

Centre of Medical Imaging, University College London, London, UK; Interventional Oncology Service, University College London Hospital, London, UK. Electronic address:

Purpose: This study systematically investigates artifacts produced by biopsy and ablation needles imaged at various trajectories with respect to the static magnetic field (B0).

Materials And Methods: An acrylic phantom was scanned using a rapid balanced fast field echo sequence (FFE) with 3.0-T MRI. Read More

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Breast Cancer Patient Prognosis Is Determined by the Interplay between Mutation and Alternative Transcript Expression: Insights from Long Amplicon Digital PCR Assays.

Cancers (Basel) 2021 Mar 26;13(7). Epub 2021 Mar 26.

Department of Molecular Medicine and Pathology, School of Medical Sciences, University of Auckland, Auckland 1142, New Zealand.

The gene locus is capable of producing multiple RNA transcripts encoding the different p53 protein isoforms. We recently described multiplex long amplicon droplet digital PCR (ddPCR) assays to quantify seven of eight reference transcripts in human tumors. Here, we describe a new long amplicon ddPCR assay to quantify expression of the eighth reference transcript encoding ∆40p53α. Read More

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Metabolic Capacity of the Antarctic Cyanobacterium That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide.

Genes (Basel) 2021 Mar 16;12(3). Epub 2021 Mar 16.

Department of Earth and Planetary Sciences, University of California, Davis, CA 95616, USA.

Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between HO and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium creates a 1-2 mm thick layer of 50 µmol L O in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. Read More

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Genetic Polymorphisms of Receptors and Antipsychotic-Induced Metabolic Dysfunction in Patients with Schizophrenia.

J Pers Med 2021 Mar 5;11(3). Epub 2021 Mar 5.

Mental Health Research Institute, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634014 Tomsk, Russia.

Background: Antipsychotic-induced metabolic syndrome (MetS) is a multifactorial disease with a genetic predisposition. Serotonin and its receptors are involved in antipsychotic-drug-induced metabolic disorders. The present study investigated the association of nine polymorphisms in the four 5-hydroxytryptamine receptor () genes , , , and and the gene encoding for the serotonin transporter with MetS in patients with schizophrenia. Read More

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Expanding the Spectrum of Pancreatic Cancers Responsive to Vesicular Stomatitis Virus-Based Oncolytic Virotherapy: Challenges and Solutions.

Cancers (Basel) 2021 Mar 9;13(5). Epub 2021 Mar 9.

Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy with poor prognosis and a dismal survival rate, expected to become the second leading cause of cancer-related deaths in the United States. Oncolytic virus (OV) is an anticancer approach that utilizes replication-competent viruses to preferentially infect and kill tumor cells. Vesicular stomatitis virus (VSV), one such OV, is already in several phase I clinical trials against different malignancies. Read More

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A Novel Position-Specific Encoding Algorithm (SeqPose) of Nucleotide Sequences and Its Application for Detecting Enhancers.

Int J Mol Sci 2021 Mar 17;22(6). Epub 2021 Mar 17.

Health Informatics Lab, College of Computer Science and Technology, Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, Jilin University, Changchun 130012, China.

Enhancers are short genomic regions exerting tissue-specific regulatory roles, usually for remote coding regions. Enhancers are observed in both prokaryotic and eukaryotic genomes, and their detections facilitate a better understanding of the transcriptional regulation mechanism. The accurate detection and transcriptional regulation strength evaluation of the enhancers remain a major bioinformatics challenge. Read More

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Host Response against Virus Infection in an Insect: Bidensovirus Infection Effect on Silkworm ().

Antioxidants (Basel) 2021 Mar 27;10(4). Epub 2021 Mar 27.

Department of Research Promotion, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8634, Japan.

Silk cocoons obtained from silkworms are the primary source of commercial silk, making the silkworm an economically important insect. However, the silk industry suffers significant losses due to various virus infections. bidensovirus (BmBDV) is one of the pathogens that cause flacherie disease in silkworms. Read More

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The complete chloroplast genome of (Lamiaceae), a traditional Tibetan medicinal herb.

Mitochondrial DNA B Resour 2021 Mar 24;6(3):1186-1188. Epub 2021 Mar 24.

Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang, PR China.

The species is a medicinal herb mainly distributed in southwest China. The first complete plastid genome sequence of reported here was 151,747 bp long, with the large single copy (LSC) region of 83,181 bp, the small single copy (SSC) region of 17,372 bp and two inverted repeats (IRa and IRb) of 25,597 bp. The plastome contained 114 genes, including 80 protein-coding genes, four encoding rRNAs, and 30 encoding tRNAs. Read More

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Modulation of Gene Expression in Actinobacteria by Translational Modification of Transcriptional Factors and Secondary Metabolite Biosynthetic Enzymes.

Front Microbiol 2021 16;12:630694. Epub 2021 Mar 16.

Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, Mexico.

Different types of post-translational modifications are present in bacteria that play essential roles in bacterial metabolism modulation. Nevertheless, limited information is available on these types of modifications in actinobacteria, particularly on their effects on secondary metabolite biosynthesis. Recently, phosphorylation, acetylation, or phosphopantetheneylation of transcriptional factors and key enzymes involved in secondary metabolite biosynthesis have been reported. Read More

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New generation of DNA-based immunotherapy induces a potent immune response and increases the survival in different tumor models.

J Immunother Cancer 2021 Apr;9(4)

Louvain Drug Research Institute, Advanced Drug Delivery and Biomaterials, Université catholique de Louvain, Brussels, Belgium.

Background: Strategies to increase nucleic acid vaccine immunogenicity are needed to move towards clinical applications in oncology. In this study, we designed a new generation of DNA vaccines, encoding an engineered vesicular stomatitis virus glycoprotein as a carrier of foreign T cell tumor epitopes (plasmid to deliver T cell epitopes, pTOP). We hypothesized that pTOP could activate a more potent response compared with the traditional DNA-based immunotherapies, due to both the innate immune properties of the viral protein and the specific induction of CD4 and CD8 T cells targeting tumor antigens. Read More

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A gene regulatory network for antenna size control in carbon dioxide-deprived Chlamydomonas reinhardtii cells.

Plant Cell 2021 Jan 27. Epub 2021 Jan 27.

In green microalgae, prolonged exposure to inorganic carbon depletion requires long-term acclimation responses, involving modulated gene expression and the adjustment of photosynthetic activity to the prevailing supply of carbon dioxide. Here, we describe a microalgal regulatory cycle that adjusts the light-harvesting capacity at photosystem II (PSII) to the prevailing supply of carbon dioxide in Chlamydomonas (Chlamydomonas reinhardtii). It engages low carbon dioxide response factor (LCRF), a member of the squamosa promoter-binding protein (SBP) family of transcription factors, and the previously characterized cytosolic translation repressor nucleic acid-binding protein 1 (NAB1). Read More

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January 2021