53,558 results match your criteria assembly gene

PICALM regulates cathepsin D processing and lysosomal function.

Biochem Biophys Res Commun 2021 Jul 23;570:103-109. Epub 2021 Jul 23.

Lysosomal Health in Ageing, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia. Electronic address:

Degradation and clearance of cellular waste in the autophagic and endo-lysosomal systems is important for normal physiology and prevention of common late-onset diseases such as Alzheimer's disease (AD). Phosphatidylinostol-binding clathrin assembly protein (PICALM) is a robust AD risk factor gene and encodes an endosomal protein clathrin-binding cytosolic protein, reduction of which is known to exacerbate tauopathy. Although PICALM is known to regulate initiation of autophagy, its role in maturation of lysosomal enzymes required for proteolysis has not been studied. Read More

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Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus.

Plant J 2021 Jul 26. Epub 2021 Jul 26.

Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.

Northern Wild Rice (NWR; Zizania palustris L.) is an aquatic grass native to North America that is notable for its nutritious grain. This is an important species with ecological, cultural, and agricultural significance, specifically in the Great Lakes region of the United States. Read More

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DDIT4 S-Nitrosylation Aids p38-MAPK Signaling Complex Assembly to Promote Hepatic Reactive Oxygen Species Production.

Adv Sci (Weinh) 2021 Jul 26:e2101957. Epub 2021 Jul 26.

Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Translational Medicine, Nanjing Medical University, Nanjing, 211166, China.

Mitogen-activated protein kinase (MAPK) signaling plays a significant role in reactive oxygen species (ROS) production. The authors have previously shown that Brahma-related gene 1 (BRG1), a chromatin remodeling protein, contributes to hepatic ROS accumulation in multiple animal and cellular models of liver injury. Here it is reported that DNA damage-induced transcript 4 (DDIT4) is identified as a direct transcriptional target for BRG1. Read More

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New high-quality peach (Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits.

Plant J 2021 Jul 26. Epub 2021 Jul 26.

The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit Tree Breeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China.

Peach (Prunus persica L. Batsch) is an economically important fruit crop worldwide. Although a high-quality peach genome has previously been published, Sanger sequencing was used for its assembly, which generated short contigs. Read More

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Multiple G-quadruplex binding ligand induced transcriptomic map of cancer cell lines.

J Cell Commun Signal 2021 Jul 26. Epub 2021 Jul 26.

Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.

The G-quadruplexes (G4s) are a class of DNA secondary structures with guanine rich DNA sequences that can fold into four stranded non-canonical structures. At the genomic level, their pivotal role is well established in DNA replication, telomerase functions, constitution of topologically associating domains, and the regulation of gene expression. Genome instability mediated by altered G4 formation and assembly has been associated with multiple disorders including cancers and neurodegenerative disorders. Read More

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Transcriptome and proteome dynamics of cervical remodeling in the mouse during pregnancy.

Biol Reprod 2021 Jul 26. Epub 2021 Jul 26.

Department of Ob/Gyn and Cecil H. and Ida Green Center for Reproductive Biological Science, The University of Texas Southwestern Medical Center, Dallas, TX.

During gestation, the female reproductive tract must maintain pregnancy while concurrently preparing for parturition. Here, we explore the transitions in gene expression and protein turnover (fractional synthesis rates [FSR]) by which the cervix implements a transition from rigid to compliant. Shifts in gene transcription to achieve immune tolerance and alter epithelial cell programs begin in early pregnancy. Read More

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Modulation of the enzymatic activity of the flagellar lytic transglycosylase SltF by rod components, and the scaffolding protein FlgJ in .

J Bacteriol 2021 Jul 26:JB0037221. Epub 2021 Jul 26.

Instituto de Fisiología Celular and Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México.

Macromolecular cell-envelope-spanning structures such as the bacterial flagellum must traverse the cell wall. Lytic transglycosylases enzymes are capable of enlarging gaps in the peptidoglycan meshwork to allow the efficient assembly of supramolecular complexes. In the periplasmic space, the assembly of the flagellar rod requires the scaffold protein FlgJ, which includes a muramidase domain in the canonical models and . Read More

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Self-Assembling Peptidic Bolaamphiphiles for Biomimetic Applications.

ACS Biomater Sci Eng 2021 Jul 26. Epub 2021 Jul 26.

Department of Chemical and Biomolecular Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.

Bolaamphiphile, which is a class of amphiphilic molecules, has a unique structure of two hydrophilic head groups at the ends of the hydrophobic center. Peptidic bolaamphiphiles that employ peptides or amino acids as their hydrophilic groups exhibit unique biochemical activities when they self-organize into supramolecular structures, which are not observed in a single molecule. The self-assembled peptidic bolaamphiphiles hold considerable promise for imitating proteins with biochemical activities, such as specific affinity toward heterogeneous substances, a catalytic activity similar to a metalloenzyme, physicochemical activity from harmonized amino acid segments, and the capability to encapsulate genes like a viral vector. Read More

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Cdc4 phospho-degrons allow differential regulation of Ame1 protein stability across the cell cycle.

Elife 2021 Jul 26;10. Epub 2021 Jul 26.

Molecular Genetics I, University of Duisburg-Essen, Essen, Germany.

Kinetochores are multi-subunit protein assemblies that link chromosomes to microtubules of the mitotic and meiotic spindle. It is still poorly understood how efficient, centromere-dependent kinetochore assembly is accomplished from hundreds of individual protein building blocks in a cell cycle dependent manner. Here, by combining comprehensive phosphorylation analysis of native Ctf19 subunits with biochemical and functional assays in the model system budding yeast, we demonstrate that Cdk1 phosphorylation activates phospho-degrons on the essential subunit Ame1 which are recognized by the E3 ubiquitin ligase complex SCF-Cdc4. Read More

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Empirical evaluation of methods for genome assembly.

PeerJ Comput Sci 2021 9;7:e636. Epub 2021 Jul 9.

Department of Multimedia Engineering, Dongguk University, Seoul, South Korea.

Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms. A drastic reduction in the costs of generating short reads on the genomes of new organisms is attributable to recent advances in NGS technologies such as Ion Torrent, Illumina, and PacBio. Genome research has led to the creation of high-quality reference genomes for several organisms, and assembly is a key initiative that has facilitated gene discovery and other studies. Read More

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Engineering the Architecture of Elastin-Like Polypeptides: From Unimers to Hierarchical Self-Assembly.

Adv Ther (Weinh) 2020 Mar 3;3(3). Epub 2020 Feb 3.

Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.

Well-defined tunable nanostructures formed through the hierarchical self-assembly of peptide building blocks have drawn significant attention due to their potential applications in biomedical science. Artificial protein polymers derived from elastin-like polypeptides (ELPs), which are based on the repeating sequence of tropoelastin (the water-soluble precursor to elastin), provide a promising platform for creating nanostructures due to their biocompatibility, ease of synthesis, and customizable architecture. By designing the sequence and composition of ELPs at the gene level, their physicochemical properties can be controlled to a degree that is unmatched by synthetic polymers. Read More

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Melatonin Protects Against Mdivi-1-Induced Abnormal Spindle Assembly and Mitochondrial Superoxide Production During Porcine Oocyte Maturation.

Front Cell Dev Biol 2021 8;9:693969. Epub 2021 Jul 8.

Department of Biotechnology, College of Engineering, Daegu University, Gyeongsan, South Korea.

Mitochondrial division inhibitor 1 (Mdivi-1) reportedly provides a close connection between oocyte maturation and mitochondrial function in pigs. -acetyl-5-methoxy-tryptamine (melatonin) is known to be a representative antioxidant with the ability to rehabilitate meiotic maturation of porcine oocytes. However, the ability of melatonin to recover Mdivi-1-mediated disruption of spindle formation during meiotic maturation of porcine oocytes during maturation (IVM) has not been studied. Read More

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Increased SPC24 in prostatic diseases and diagnostic value of SPC24 and its interacting partners in prostate cancer.

Exp Ther Med 2021 Sep 30;22(3):923. Epub 2021 Jun 30.

Scientific Research Center, Guilin Medical University, Guilin, Guangxi 541100, P.R. China.

SPC24 is a crucial component of the mitotic checkpoint machinery in tumorigenesis. High levels of SPC24 have been found in various cancers, including breast cancer, lung cancer, liver cancer, osteosarcoma and thyroid cancer. However, to the best of our knowledge, the impact of SPC24 on prostate cancer (PCa) and other prostate diseases remains unclear. Read More

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September 2021

Draft Genome of the Mirrorwing Flyingfish ().

Front Genet 2021 7;12:695700. Epub 2021 Jul 7.

College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.

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Inhibitory Role of an TIR Domain Effector in Antibacterial Immunity by Targeting TLR Signaling Complexes in Zebrafish.

Front Microbiol 2021 8;12:694081. Epub 2021 Jul 8.

College of Life Sciences, Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, China.

The Toll/interleukin-1 receptor (TIR) domain is a structural unit responsible for the assembly of signal protein complexes in Toll-like receptor (TLR) and interleukin-1 receptor signaling pathways. TIR domain homologs are found in a considerable number of bacteria and enhance bacterial infection and survival in host organisms. However, whether TIR domain homologs exist in , a ubiquitous waterborne bacterium in aquatic environments, remains poorly understood. Read More

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Bioinformatics study on genes related to a high-risk postoperative recurrence of lung adenocarcinoma.

Sci Prog 2021 Jul-Sep;104(3):368504211018053

Department of Geriatric Medicine, Fujian Provincial Hospital, Fujian Provincial Center for Geriatrics, Fujian Medical University, Fuzhou, Fujian Province, China.

In this study, we aimed to screen out genes associated with a high risk of postoperative recurrence of lung adenocarcinoma and investigate the possible mechanisms of the involvement of these genes in the recurrence of lung adenocarcinoma. We identify Hub genes and verify the expression levels and prognostic roles of these genes. Datasets of GSE40791, GSE31210, and GSE30219 were obtained from the Gene Expression Omnibus database. Read More

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Phase separation in transcription factor dynamics and chromatin organization.

Curr Opin Struct Biol 2021 Jul 22;71:148-155. Epub 2021 Jul 22.

Department of Physics, University of Maryland, College Park, MD, 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD, 20742, USA. Electronic address:

Studies over the past decade have highlighted the key role of liquid-liquid phase separation in cellular organization and function. Dynamic compartmentalization of transcription factors and coactivators by such phase-separated condensates regulates the assembly of transcriptional machinery at genomic loci. Although rapid advances in microscopy have demonstrated the ubiquity of such condensates, a rigorous characterization of the physics of phase separation in transcription remains to be carried out. Read More

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Comparative transcriptome analysis of Chinese grass shrimp (Palaemonetes sinensis) hepatopancreas under ectoparasitic isopod (Tachaea chinensis) infection.

Fish Shellfish Immunol 2021 Jul 22. Epub 2021 Jul 22.

Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 110866, Shenyang, China. Electronic address:

Tachaea chinensis, a parasitic isopod, negatively affects the production of several commercially important shrimp species. To better understand the interaction between shrimp immunity and isopod infection, we performed a transcriptome analysis of the hepatopancreas of Palaemonetes sinensis challenged with T. chinensis. Read More

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A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans.

Genomics 2021 Jul 22. Epub 2021 Jul 22.

Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing 210017, China; Jiangsu Key laboratory for Conservation and Utilization of freshwater Fisheries Germplasm Resources, Nanjing 210017, China. Electronic address:

Red swamp crayfish Procambarus clarkii is an ecologically and economically important crustacean species. Here, based on a de novo assembly strategy combining PacBio with Hi-C sequencing, we presented a high quality chromosome-level P. clarkii genome. Read More

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A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.).

BMC Plant Biol 2021 Jul 24;21(1):350. Epub 2021 Jul 24.

Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences/National Wolfberry Engineering Research Center, Yinchuan, 750002, China.

Background: Lycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers. Read More

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Comparative transcriptome analysis reveals changes in gene expression in sea cucumber (Holothuria leucospilota) in response to acute temperature stress.

Comp Biochem Physiol Part D Genomics Proteomics 2021 Jul 16;40:100883. Epub 2021 Jul 16.

South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong, China; National Fishery Resources and Environment Dapeng Observation and Experimental Station, Shenzhen, China.

Ambient temperature is an important abiotic factor that influences growth performance and physiological functions in sea cucumbers. To understand the molecular responses of the sea cucumber Holothuria leucospilota to acute temperature stress, we performed a de novo transcriptome analysis of body wall tissue from H. leucospilota exposed to 2 hoursh of acute heat (35 ± 1 °C) and cold stress (15 ± 1 °C). Read More

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Adenosine-to-inosine Alu RNA editing controls the stability of the pro-inflammatory long noncoding RNA NEAT1 in atherosclerotic cardiovascular disease.

J Mol Cell Cardiol 2021 Jul 21. Epub 2021 Jul 21.

Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; Department of Cardiology, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK; Vascular Inflammation and RNA Metabolism Laboratory, Institute for Vascular Signalling, JW Goethe University Frankfurt, Frankfurt am Main, Germany. Electronic address:

Long non-coding RNAs (lncRNAs) have emerged as critical regulators in human disease including atherosclerosis. However, the mechanisms involved in the post-transcriptional regulation of the expression of disease-associated lncRNAs are not fully understood. Gene expression studies revealed that Nuclear Paraspeckle Assembly Transcript 1 (NEAT1) lncRNA expression was increased by >2-fold in peripheral blood mononuclear cells (PBMCs) derived from patients with coronary artery disease (CAD) or in carotid artery atherosclerotic plaques. Read More

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Assembly of the complete mitochondrial genome of an endemic plant, Scutellaria tsinyunensis, revealed the existence of two conformations generated by a repeat-mediated recombination.

Planta 2021 Jul 24;254(2):36. Epub 2021 Jul 24.

Key Laboratory of Horticulture Science for Southern Mountainous Regions from Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, No. 2 Tiansheng Road, Beibei District, Chongqing, 400716, China.

Main Conclusion: We assembled the complete mitochondrial genome of Scutellaria tsinyunensis in this study. Repeat-mediated recombination resulted in the formation of two conformations of the mitochondrial genome in S. tsinyunensis. Read More

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Extensive bidirectional genetic overlap between bipolar disorder and cardiovascular disease phenotypes.

Transl Psychiatry 2021 Jul 23;11(1):407. Epub 2021 Jul 23.

NORMENT, Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital, and Institute of Clinical Medicine, University of Oslo, Oslo, Norway.

Patients with bipolar disorder (BIP) have a high risk of cardiovascular disease (CVD), despite considerable individual variation. The mechanisms underlying comorbid CVD in BIP remain largely unknown. We investigated polygenic overlap between BIP and CVD phenotypes, including CVD risk factors and coronary artery disease (CAD). Read More

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Structures and implications of TBP-nucleosome complexes.

Proc Natl Acad Sci U S A 2021 Jul;118(30)

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany

The TATA box-binding protein (TBP) is highly conserved throughout eukaryotes and plays a central role in the assembly of the transcription preinitiation complex (PIC) at gene promoters. TBP binds and bends DNA, and directs adjacent binding of the transcription factors TFIIA and TFIIB for PIC assembly. Here, we show that yeast TBP can bind to a nucleosome containing the Widom-601 sequence and that TBP-nucleosome binding is stabilized by TFIIA. Read More

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Genomic architecture constrained placental mammal X Chromosome evolution.

Genome Res 2021 Jul 22. Epub 2021 Jul 22.

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843, USA.

Susumu Ohno proposed that the gene content of the mammalian X Chromosome should remain highly conserved due to dosage compensation. X Chromosome linkage (gene order) conservation is widespread in placental mammals but does not fall within the scope of Ohno's prediction and may be an indirect result of selection on gene content or selection against rearrangements that might disrupt X-Chromosome inactivation (XCI). Previous comparisons between the human and mouse X Chromosome sequences have suggested that although single-copy X Chromosome genes are conserved between species, most ampliconic genes were independently acquired. Read More

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The histone chaperone Nrp1 is required for chromatin stability and nuclear division in Tetrahymena thermophila.

Epigenetics Chromatin 2021 Jul 23;14(1):34. Epub 2021 Jul 23.

Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, 92 Wucheng Rd., Taiyuan, 030006, China.

Histone chaperones facilitate DNA replication and repair by promoting chromatin assembly, disassembly and histone exchange. Following histones synthesis and nucleosome assembly, the histones undergo posttranslational modification by different enzymes and are deposited onto chromatins by various histone chaperones. In Tetrahymena thermophila, histones from macronucleus (MAC) and micronucleus (MIC) have been comprehensively investigated, but the function of histone chaperones remains unclear. Read More

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AUY922 induces retinal toxicity through attenuating TRPM1.

J Biomed Sci 2021 Jul 23;28(1):55. Epub 2021 Jul 23.

National Institute of Cancer Research, National Health Research Institutes, No. 367, Sheng-Li Rd., North District, Tainan, 70456, Taiwan.

Background: Ocular adverse events are common dose-limiting toxicities in cancer patients treated with HSP90 inhibitors, such as AUY922; however, the pathology and molecular mechanisms that mediate AUY922-induced retinal toxicity remain undescribed.

Methods: The impact of AUY922 on mouse retinas and cell lines was comprehensively investigated using isobaric tags for relative and absolute quantitation (iTRAQ)‑based proteomic profiling and pathway enrichment analysis, immunohistochemistry and immunofluorescence staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, MTT assay, colony formation assay, and western blot analysis. The effect of AUY922 on the Transient Receptor Potential cation channel subfamily M member 1 (TRPM1)-HSP90 chaperone complex was characterized by coimmunoprecipitation. Read More

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Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae.

Microb Cell Fact 2021 Jul 23;20(1):142. Epub 2021 Jul 23.

State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China.

Background: Vanillin is one of the important phenolic inhibitors in Saccharomyces cerevisiae for bioconversion of lignocellulosic materials and has been reported to inhibit the translation process in cells. In our previous studies, it was confirmed that the deletion of the transcription factor gene YRR1 enhanced vanillin resistance by promoting some translation-related processes at the transcription level. In this work, we investigated the effects of proteomic changes upon induction of vanillin stress and deletion of YRR1 to provide unique perspectives from a transcriptome analysis for comprehending the mechanisms of YRR1 deletion in the protective response of yeast to vanillin. Read More

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Updating Insights into the Catalytic Domain Properties of Plant () and () Proteins.

Molecules 2021 Jul 17;26(14). Epub 2021 Jul 17.

Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece.

The wall is the last frontier of a plant cell involved in modulating growth, development and defense against biotic stresses. Cellulose and additional polysaccharides of plant cell walls are the most abundant biopolymers on earth, having increased in economic value and thereby attracted significant interest in biotechnology. Cellulose biosynthesis constitutes a highly complicated process relying on the formation of cellulose synthase complexes. Read More

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