1,659,641 results match your criteria sequence


Sequence dependence of Pd(II)-mediated base pairing by palladacyclic nucleobase surrogates.

J Inorg Biochem 2021 Jun 2;222:111506. Epub 2021 Jun 2.

Department of Chemistry, University of Turku, Vatselankatu 2, 20014 Turku, Finland. Electronic address:

A C-nucleoside derivative of phenylpyridine or the respective palladacycle was incorporated at either 3'- or 5'-terminus of a short oligodeoxynucleotide. Hybridization properties of these modified oligonucleotides were studied in a fluorescence-based competition assay in addition to conventional UV melting temperature analysis and compared with those of a previously prepared analogue featuring the modified nucleoside in the middle of the sequence. With the unpalladated phenylpyridine oligonucleotides, UV melting temperature qualitatively correlated with the ability to displace a strand from a double helix in the competition assay, decreasing in the order 5' > 3' > middle. Read More

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The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana.

Phytochemistry 2021 Jun 9;189:112822. Epub 2021 Jun 9.

Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria. Electronic address:

Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are utilized as coenzymes in many biochemical reduction-oxidation reactions owing to the ability of the tricyclic isoalloxazine ring system to employ the oxidized, radical and reduced state. We have analyzed the genome of Arabidopsis thaliana to establish an inventory of genes encoding flavin-dependent enzymes (flavoenzymes) as a basis to explore the range of flavin-dependent biochemical reactions that occur in this model plant. Expectedly, flavoenzymes catalyze many pivotal reactions in primary catabolism, which are connected to the degradation of basic metabolites, such as fatty and amino acids as well as carbohydrates and purines. Read More

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Affecting RNA biology genome-wide by binding small molecules and chemically induced proximity.

Curr Opin Chem Biol 2021 Jun 9;62:119-129. Epub 2021 Jun 9.

Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458 USA. Electronic address:

The ENCODE and genome-wide association projects have shown that much of the genome is transcribed into RNA and much less is translated into protein. These and other functional studies suggest that the druggable transcriptome is much larger than the druggable proteome. This review highlights approaches to define druggable RNA targets and structure-activity relationships across genomic RNA. Read More

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Deep sequence modelling for Alzheimer's disease detection using MRI.

Comput Biol Med 2021 Jun 1;134:104537. Epub 2021 Jun 1.

School of Electrical Engineering and Computing, The University of Newcastle, NSW 2308, Australia.

Background: Alzheimer's disease (AD) is one of the deadliest diseases in developed countries. Treatments following early AD detection can significantly delay institutionalisation and extend patients' independence. There has been a growing focus on early AD detection using artificial intelligence. Read More

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Atmospheric washout of S during single rain events - Implications for S sampling schemes.

J Environ Radioact 2021 Jun 9;237:106669. Epub 2021 Jun 9.

UFZ Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, 06120, Halle, Germany.

Cosmogenic radiosulfur (S; half-life: 87.4 days) is transferred with the rain to the groundwater (as SO) and can be used as residence time tracer for the detection of sub-yearly groundwater residence times. Due to the distinct but non-regular annual S pattern in precipitation, related data evaluation requires consideration of aS input function that is based on representative rain samples. Read More

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β3-Endonexin interacts with ninein in vascular endothelial cells to promote angiogenesis.

Biochem Biophys Res Commun 2021 Jun 9;566:75-79. Epub 2021 Jun 9.

School of Environmental and Chemical Engineering, Shanghai University, Shanghai, China; School of Life Sciences, Shanghai University, Shanghai, China; Versiti Blood Research Institute, Milwaukee, WI, USA; Department of Biochemistry, Medical College of Milwaukee, Wisconsin, USA. Electronic address:

Anti-angiogenesis serves as an effective tumor therapy approach. In a previous study, we found that β3-endonexin expressed in vascular endothelial cells was involved in promoting proliferation and angiogenesis partially by facilitating VEGF expression. However, it still remains unclear if β3-endonexin in vascular endothelial cells also employs other mechanisms in regulating angiogenesis. Read More

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Combining tunable proteolytic sequences and a VEGF-mimetic peptide for the spatiotemporal control of angiogenesis within Elastin-Like Recombinamer scaffolds.

Acta Biomater 2021 Jun 9. Epub 2021 Jun 9.

G.I.R. BIOFORGE (Group for Advanced Materials and Nanobiotechnology), CIBER-BBN, Edificio LUCIA, Universidad de Valladolid, Paseo Belén 19, 47011 Valladolid, Spain. Electronic address:

One of the main challenges in regenerative medicine is the spatiotemporal control of angiogenesis, which is key for the successful repair of many tissues, and determines the proper integration of the implant through the generation of a functional vascular network. To this end, we have designed a three-dimensional (3D) model consisting of a coaxial binary elastin-like recombinamer (ELR) tubular construct. It displays fast and slow proteolytic hydrogels on its inner and outer part, respectively, both sensitive to the urokinase plasminogen activator protease. Read More

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Genome sequence of the cardiopulmonary canid nematode Angiostrongylus vasorum reveals species-specific genes with potential involvement in coagulopathy.

Genomics 2021 Jun 9. Epub 2021 Jun 9.

Institute of Parasitology, Vetsuisse-Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland.

Angiostrongylus vasorum is an emerging parasitic nematode of canids and causes respiratory distress, bleeding, and other signs in dogs. Despite its clinical importance, the molecular toolbox allowing the study of the parasite is incomplete. To address this gap, we have sequenced its nuclear genome using Oxford nanopore sequencing, polished with Illumina reads. Read More

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mA modification of RNA and its role in cancer, with a special focus on lung cancer.

Genomics 2021 Jun 9. Epub 2021 Jun 9.

ICAR-Indian Veterinary Research Institute, Izatnagar, UP, India.

Epitranscriptomics involves functionally relevant biochemical modifications of RNA taking place at the transcriptome level without a change in the sequence of ribonucleotides. Several types of modifications that affect the processing and function of differentRNA types have been reported. Methylation at N of Adenosine called mA is one such modification, quite widespread in occurrence and reported in snRNAs, lncRNAs, circRNAs, rRNAs, miRNAs, and most abundantly, in mRNAs. Read More

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Interpretation of genomic sequence variants in genetic skin diseases: A primer for clinicians.

J Am Acad Dermatol 2021 Jun 9. Epub 2021 Jun 9.

Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, and Jefferson Institute of Molecular Medicine, Thomas Jefferson University Philadelphia, PA; Jefferson Center for Heritable Connective Tissue and Skin Diseases, Thomas Jefferson University Hospital, Philadelphia, PA.

Over 1,000 heritable disorders have cutaneous manifestations, some of them being syndromic in association with extracutaneous manifestations, while others being limited to the skin. The genetic basis of many of these conditions has been deciphered, and mutation analysis by next-generation sequencing approaches, including whole-exome sequencing, whole-genome sequencing, and whole-transcriptome analysis, are now increasingly part of the diagnostic process. Besides confirming the diagnosis, information on the specific mutations can be used for sub-classification with prognostication and identification of carriers leading to accurate genetic counseling, and it also forms the basis for prenatal testing and preimplantation genetic diagnosis. Read More

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Expression profiling, immune functions, and molecular characteristics of the tetraspanin molecule CD63 from Amphiprion clarkii.

Dev Comp Immunol 2021 Jun 9:104168. Epub 2021 Jun 9.

Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju 63333, Republic of Korea. Electronic address:

CD63, a member of the tetraspanin family, is involved in the activation of immune cells, antiviral immunity, and signal transduction. The economically important anemonefishes Amphiprion sp. often face disease outbreaks, and the present study aimed to characterize CD63 in Amphiprion clarkii (denoted AcCD63) to enable better disease management. Read More

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New Insight To The Rol Of Α-Enolase (Eno-1) As Immunological Marker In Rainbow Trout Fry.

Dev Comp Immunol 2021 Jun 9:104163. Epub 2021 Jun 9.

Grupo de Marcadores Inmunológicos, Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223, Valparaíso, Chile; Núcleo Biotecnológico de Curauma (NBC), Pontificia Universidad Católica de Valparaíso, Avenida Universidad #330, 2373223, Valparaíso, Chile. Electronic address:

α-Enolase is an enzyme of the glycolytic pathway that has also been involved in vertebrate inflammatory processes through its interaction with plasminogen. However, its participation in the immune response of lower vertebrates during early life development is unknown. Opportunistic pathogens in salmon farming are the principal cause of mortality in the fry stage. Read More

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Single-Dose Pharmacokinetics and Tolerability of the Oral Epidermal Growth Factor Receptor Inhibitor Mobocertinib (TAK-788) in Healthy Volunteers: Low-Fat Meal Effect and Relative Bioavailability of 2 Capsule Products.

Clin Pharmacol Drug Dev 2021 Jun 12. Epub 2021 Jun 12.

Millennium Pharmaceuticals, Inc., Cambridge, Massachusetts, USA, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited.

Mobocertinib (TAK-788) is a tyrosine kinase inhibitor under investigation for treatment of non-small cell lung cancer with activating EGFR exon 20 insertions. This study examined the safety; tolerability; pharmacokinetics (PK), including food effects; and bioavailability of mobocertinib in healthy volunteers. In part 1, fasted volunteers were randomized to placebo or mobocertinib in single-ascending-dose cohorts (20-160 mg). Read More

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From Kuru to Alzheimer: a personal outlook.

Authors:
Maurizio Brunori

Protein Sci 2021 Jun 12. Epub 2021 Jun 12.

Accademia Nazionale dei Lincei and Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, Rome, Italy.

Seventy years ago we learned from Chris Anfinsen that the stereochemical code necessary to fold a protein is embedded into its amino acid sequence. In water, protein morphogenesis is a spontaneous reversible process leading from an ensemble of disordered structures to the ordered functionally competent protein; conforming to Aristotle's definition of substance, the synolon of matter and form. The overall process of folding is generally consistent with a two state transition between the native and the denatured protein: not only the denatured state is an ensemble of several structures, but also the native protein populates distinct functionally relevant conformational (sub)states. Read More

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Computer-Aided Prediction of Protein Mitochondrial Localization.

Methods Mol Biol 2021 ;2275:433-452

Biocomputing Group, University of Bologna, Bologna, Italy.

Protein sequences, directly translated from genomic data, need functional and structural annotation. Together with molecular function and biological process, subcellular localization is an important feature necessary for understanding the protein role and the compartment where the mature protein is active. In the case of mitochondrial proteins, their precursor sequences translated by the ribosome machinery include specific patterns from which it is possible not only to recognize their final destination within the organelle but also which of the mitochondrial subcompartments the protein is intended for. Read More

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January 2021

Sequence-Specific Control of Mitochondrial Gene Transcription Using Programmable Synthetic Gene Switches Called MITO-PIPs.

Methods Mol Biol 2021 ;2275:217-225

Institute of Integrated Cell Material Sciences (WPI-iCeMS), Kyoto University Institute for Advanced Study, Kyoto, Japan.

Mitochondria possess multiple copies of mitochondrial DNA (mtDNA) that encode 37 genes and their transcription and replication get controlled by unique molecular codes different from that in the nuclear DNA. The mtDNA has been gaining increased attention as one of the critical therapeutic targets as mutations in them impair the function of mitochondria and cause mitochondrial diseases like MELAS. In this chapter, we describe artificial control of mitochondrial transcription based on mtDNA sequence information with a new type of compounds termed MITO-PIPs, which encompasses two domains: pyrrole-imidazole polyamide as DNA recognition domain and mitochondrial penetrating peptide as the mitochondria-targeting domain. Read More

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January 2021

Description of the Metacercaria of Cardiocephaloides sp. (Digenea, Diplostomoidea), Newly Recorded from the Brain of Gangetic Leaffish (Nandus nandus) and Its Genetic Characterization in India.

Acta Parasitol 2021 Jun 12. Epub 2021 Jun 12.

Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut, 250004, UP, India.

Purpose: Cardiocephaloides comprises strigeid trematodes that represent a small genus. In this study, metacercaria identified as Cardiocephaloides sp. was collected from the Gangetic leaffish Nandus nandus from the Ganga River at Bairaj, Bijnor (29º01'N, 77º45'E) in the state of Uttar Pradesh (U. Read More

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Improving sequence-based modeling of protein families using secondary structure quality assessment.

Bioinformatics 2021 Jun 12. Epub 2021 Jun 12.

Laboratory of Physics of the Ecole Normale Superieure, PSL Research, CNRS UMR 8023, Sorbonne Université, Université de Paris, Paris, France.

Motivation: Modeling of protein family sequence distribution from homologous sequence data recently received considerable attention, in particular for structure and function predictions, as well as for protein design. In particular, Direct Coupling Analysis, a method to infer effective pairwise interactions between residues, was shown to capture important structural constraints and to successfully generate functional protein sequences. Building on this and other graphical models, we introduce a new framework to assess the quality of the secondary structures of the generated sequences with respect to reference structures for the family. Read More

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Puffaligner : A Fast, Efficient, and Accurate Aligner Based on the Pufferfish Index.

Bioinformatics 2021 Jun 12. Epub 2021 Jun 12.

Computer Science Department, University of Maryland, College Park, USA.

Motivation: Sequence alignment is one of the first steps in many modern genomic analyses, such as variant detection, transcript abundance estimation and metagenomic profiling. Unfortunately, it is often a computationally expensive procedure. As the quantity of data and wealth of different assays and applications continue to grow, the need for accurate and fast alignment tools that scale to large collections of reference sequences persists. Read More

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Quantitative Susceptibility Mapping for Staging Acute Cerebral Hemorrhages: Comparing the Conventional and Multiecho Complex Total Field Inversion magnetic resonance imaging MR Methods.

J Magn Reson Imaging 2021 Jun 11. Epub 2021 Jun 11.

Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.

Background: The perceived acuity of intracerebral hemorrhage (ICH) impacts the management of patients, both within emergent and outpatient/urgent settings. Morphology enabled dipole inversion (MEDI) quantitative susceptibility imaging (QSM) has improved characterization of ICH acuity, despite outstanding limitations in distinguishing blood products.

Purpose/hypothesis: Using improved susceptibility quantification, novel postprocessing QSM method from multiecho complex total field inversion (mcTFI) may better discriminate between acute and subacute ICH, compared to MEDI. Read More

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Predictors of Respiratory Dysfunction at Diagnosis of Robin Sequence.

Laryngoscope 2021 Jun 12. Epub 2021 Jun 12.

Department of Plastic and Craniofacial Surgery, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.

Objectives/hypothesis: Robin sequence (RS) consists of associated micrognathia, glossoptosis, and respiratory dysfunction, with or without cleft palate. Studies on how different patient characteristics impact the severity of respiratory dysfunction are scarce and contradictory; this study investigates how different features affect respiratory obstruction severity at diagnosis of RS in controlled analysis.

Study Design: Retrospective cohort study that enrolled 71 RS patients under 90 days old who received care in our institution from 2009 to 2020. Read More

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The Dryas iulia genome supports multiple gains of a W chromosome from a B chromosome in butterflies.

Genome Biol Evol 2021 Jun 12. Epub 2021 Jun 12.

School of Biological Sciences, University of Bristol, Bristol, UK.

In butterflies and moths, which exhibit highly variable sex determination mechanisms, the homogametic Z chromosome is deeply conserved and is featured in many genome assemblies. The evolution and origin of the female W sex chromosome, however, remains mostly unknown. Previous studies have proposed that a ZZ/Z0 sex determination system is ancestral to Lepidoptera, and that W chromosomes may originate from sex-linked B chromosomes. Read More

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High resolution crystal structure of the Borreliella burgdorferi PlzA protein in complex with c-di-GMP: new insights into the interaction of c-di-GMP with the novel xPilZ domain.

Pathog Dis 2021 Jun 12. Epub 2021 Jun 12.

Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, 1112 East Clay Street, Room 101 McGuire Hall, Richmond, VA 23298-0678 USA.

In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Read More

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A new method to accurately identify single nucleotide variants using small FFPE breast samples.

Brief Bioinform 2021 Jun 11. Epub 2021 Jun 11.

Arizona Cancer Evolution Center, Arizona State University, 1001 S. McAllister Ave., Tempe, AZ, 85287, USA.

Most tissue collections of neoplasms are composed of formalin-fixed and paraffin-embedded (FFPE) excised tumor samples used for routine diagnostics. DNA sequencing is becoming increasingly important in cancer research and clinical management; however it is difficult to accurately sequence DNA from FFPE samples. We developed and validated a new bioinformatic pipeline to use existing variant-calling strategies to robustly identify somatic single nucleotide variants (SNVs) from whole exome sequencing using small amounts of DNA extracted from archival FFPE samples of breast cancers. Read More

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Quantifying Bone Marrow Fat Fraction and Iron by MRI for Distinguishing Aplastic Anemia from Myelodysplastic Syndromes.

J Magn Reson Imaging 2021 Jun 11. Epub 2021 Jun 11.

Radiology Department, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China.

Background: Bone marrow of patients with aplastic anemia (AA) is different from that of patients with myelodysplastic syndrome (MDS) and is difficult to identify by blood examination. IDEAL-IQ (iterative decomposition of water and fat with echo asymmetry and least-squares estimation) imaging might be able to quantify fat fraction (FF) and iron content in bone tissues.

Purpose: To determine if IDEAL-IQ measurements of bone marrow FF and iron content can distinguish between patients with AA and MDS. Read More

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Pseudoxanthomonas beigongshangi sp. nov., a novel bacteria with predicted nitrite and nitrate reduce ability isolated from pit mud of Baijiu.

Antonie Van Leeuwenhoek 2021 Jun 11. Epub 2021 Jun 11.

Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing, 100048, China.

A Gram-negative and rod-shape bacterium designated REN9, was isolated from pit mud of Baijiu in Sichuan, China. The 16S rRNA sequence of strain REN9 had a high similarity to Pseudoxanthomonas indica P15 (99.21%), P. Read More

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Maximum slope using ultrafast breast DCE-MRI at 1.5 Tesla: a potential tool for predicting breast lesion aggressiveness.

Eur Radiol 2021 Jun 11. Epub 2021 Jun 11.

Department of Radiology, Institut de Cancérologie de Lorraine, 6 avenue de Bourgogne, 54 519, Vandoeuvre-les-Nancy, France.

Objectives: We evaluated the relationship between the maximum slope (MS) based on ultrafast breast DCE-MRI sequences, and the clinical parameters and routine prognostic factors of breast cancer.

Methods: 210 lesions were retrospectively evaluated: 150 malignant (30 each of luminal A invasive carcinoma, luminal B invasive carcinoma, HER2 overexpression (HER2), triple negative (TN), invasive lobular carcinoma (ILC)), and 60 benign. For each lesion, the MS was obtained with an ultrafast sequence and semi-quantitative curves were classified into three types with a conventional DCE sequence. Read More

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Emamectin benzoate induced enzymatic and transcriptional alternation in detoxification mechanism of predatory beetle Paederus fuscipes (Coleoptera: Staphylinidae) at the sublethal concentration.

Ecotoxicology 2021 Jun 11. Epub 2021 Jun 11.

Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China.

In this study, the detoxification enzyme activity and the transcriptional profile changes in the second instar through RNA-sequencing technology due to emamectin benzoate (EB) were assessed. The cytochrome P450 monooxygenases (P450) enzyme activity was not altered by EB due to the change in concentration and exposure time in all treatments. The glutathione S-transferase (GST) enzyme was not considerably varying in all treatments, while exposure time significantly changed the enzyme activity. Read More

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Characterization of taro reovirus and its status in taro (Colocasia esculenta) germplasm from the Pacific.

Arch Virol 2021 Jun 11. Epub 2021 Jun 11.

Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA.

Taro reovirus (TaRV) has been reported infecting taro (Colocasia esculenta) in the South Pacific, but information on the virus is limited. Here, we report the genome sequence of a reovirus infecting taro in Papua New Guinea that had 10 genomic segments ranging from 1.1 to 3. Read More

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Complete genome analysis of the newly isolated Shigella sonnei phage vB_SsoM_Z31.

Arch Virol 2021 Jun 11. Epub 2021 Jun 11.

Dalian SEM Bio-Engineering Technology Co. Ltd, Dalian, 116620, China.

This work describes the characterization and genome annotation of the newly isolated lytic phage vB_SsoM_Z31 (referred to as Z31), isolated from wastewater samples collected in Dalian, China. Transmission electron microscopy revealed that phage Z31 belongs to the family Myoviridae, order Caudovirales. This phage specifically infects Shigella sonnei, Shigella dysenteriae, and Escherichia coli. Read More

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