219,531 results match your criteria Assembly Automation[Journal]


Whole genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines.

Plant Biotechnol J 2022 May 22. Epub 2022 May 22.

Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK.

Wheat is a globally vital crop, but its limited genetic variation creates a challenge for breeders aiming to maintain or accelerate agricultural improvements over time. Introducing novel genes and alleles from wheat's wild relatives into the wheat breeding pool via introgression lines is an important component of overcoming this low variation but is constrained by poor genomic resolution and limited understanding of the genomic impact of introgression breeding programmes. By sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines and the parent lines, we have precisely pinpointed the borders of introgressed segments, most of which occur within genes. Read More

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A Rationally Designed Building Block of the Putative Magnetoreceptor MagR.

Bioelectromagnetics 2022 May 21. Epub 2022 May 21.

State Key Laboratory of Membrane Biology, Laboratory of Molecular Biophysics, School of Life Sciences, Peking University, Beijing, China.

The ability of animals to perceive guidance cues from Earth's magnetic field for orientation and navigation has been supported by a wealth of behavioral experiments, yet the nature of this sensory modality remains fascinatingly unresolved and wide open for discovery. MagR has been proposed as a putative magnetoreceptor based on its intrinsic magnetism and its complexation with a previously suggested key protein in magnetosensing, cryptochrome, to form a rod-like polymer structure. Here, we report a rationally designed single-chain tetramer of MagR (SctMagR), serving as the building block of the hierarchical assembly of MagR polymer. Read More

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Inability to phosphorylate Y88 of p27 enforces reduced p27 protein levels and accelerates leukemia progression.

Leukemia 2022 May 21. Epub 2022 May 21.

Institute of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.

The cyclin-dependent kinase (CDK) inhibitor p27 regulates cell proliferation. Phosphorylation of tyrosine residue 88 (Y88) converts the inhibitor into an assembly factor and activator of CDKs, since Y88-phosphorylation restores activity to cyclin E,A/CDK2 and enables assembly of active cyclin D/CDK4,6. To investigate the physiological significance of p27 tyrosine phosphorylation, we have generated a knock-in mouse model where Y88 was replaced by phenylalanine (p27-Y88F). Read More

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Knee Arthrodesis Using a Compression Clamp and a Single-Plane External Fixator to Treat Infection.

Orthop Traumatol Surg Res 2022 May 18:103330. Epub 2022 May 18.

Service de chirurgie orthopédique, hôpital Trousseau, CHRU de Tours, avenue de la République, Chambray-lès-Tours, 37044 Tours cedex 9, France; Faculté de Médecine, Université de Tours, France.

Background: In patients with knee infection, arthrodesis by external fixation is a limb-salvage procedure appropriate in highly selected patients. No hardware that might lead to infection is left in situ. However, the fusion rate is limited. Read More

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Role of the TATA-box binding protein (TBP) and associated family members in transcription regulation.

Gene 2022 May 18:146581. Epub 2022 May 18.

Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco, C.P. 07360 Mexico City, Mexico. Electronic address:

The assembly of transcription complexes on eukaryotic promoters involves a series of steps, including chromatin remodeling, recruitment of TATA-binding protein (TBP)-containing complexes, the RNA polymerase II holoenzyme, and additional basal transcription factors. This review describes the transcriptional regulation by TBP and its corresponding homologs that constitute the TBP family and their interactions with promoter DNA. The C-terminal core domain of TBP is highly conserved and contains two structural repeats that fold into a saddle-like structure, essential for the interaction with the TATA-box on DNA. Read More

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Type C mutation of nucleophosmin 1 acute myeloid leukemia: Consequences of intrinsic disorder.

Biochim Biophys Acta Gen Subj 2022 May 18:130173. Epub 2022 May 18.

Department of Pharmacy, University of Naples "Federico II", 80131 Naples, Italy. Electronic address:

Background: Nucleophosmin 1 (NPM1) protein is a multifunctional nucleolar chaperone and its gene is the most frequently mutated in Acute Myeloid Leukemia (AML). AML mutations cause the unfolding of the C-terminal domain (CTD) and the protein delocalizing in the cytosol (NPM1c+). Marked aggregation endowed with an amyloid character was assessed as consequences of mutations. Read More

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Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters.

Water Res 2022 May 11;219:118590. Epub 2022 May 11.

Environmental Microbiome Engineering and Biotechnology Laboratory, Center for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China. Electronic address:

A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Read More

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The ethanolic extract of Artemisia anomala exerts anti-inflammatory effects via inhibition of NLRP3 inflammasome.

Phytomedicine 2022 May 10;102:154163. Epub 2022 May 10.

Laboratory of Natural Product Drugs, State Key Laboratory of Biotherapy and Cancer Center, West China Medical School, West China Hospital, Sichuan University, Chengdu 610041, PR China.

Background: Artemisia anomala S. Moore (Compositae), known as "Nan-Liu-Ji-Nu" in traditional Chinese medicine (TCM), has been used to treat many inflammatory diseases, including enteritis, acute icteric hepatitis, rheumatism, toothache, tonsillitis, and chronic bronchitis, for centuries. Our preliminary studies have demonstrated that the ethanolic extract of A. Read More

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Carbon vacancy-mediated exciton dissociation in TiCT/g-CN Schottky junctions for efficient photoreduction of CO.

J Colloid Interface Sci 2022 May 15;623:487-499. Epub 2022 May 15.

School of Chemistry and Chemical Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China. Electronic address:

Earth-abundant g-CN is a promising photocatalyst for CO reduction, but its practical application is severely limited by the excitonic effect of g-CN derived from strong binding energy and lack of electron-enriched active sites. Herein, we design a novel 2D/2D Schottky junction photocatalysts comprising of TiCT-modified defective g-CN nanosheets with carbon vacancy (denoted as TiCT/V-CN) by a self-assembly method. The carbon vacancies in g-CN promote exciton dissociation into free charge, while the formed Schottky junctions between TiCT and V-CN further enables a directional charge transfer, thus providing an electron-rich catalytic surface for the CO reduction. Read More

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Bifunctional 2D/2D g-CN/BiO nanosheets heterojunction for bacterial disinfection mechanisms under visible and near-infrared light irradiation.

J Hazard Mater 2022 May 11;436:129123. Epub 2022 May 11.

Key Laboratory of Jiangsu Province for Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China. Electronic address:

The efficient deployment of visible and near-infrared (NIR) light for photocatalytic disinfection is of great concern a matter. Herein, we report a specific bifunctional 2D/2D g-CN/BiO nanosheets heterojunction, prepared through a self-assembly approach. Delightfully, the obtained 2D/2D heterojunctions exhibited satisfactory photocatalytic disinfection performance towards Escherichia coli K-12 (E. Read More

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Combinatorial Self-Assembly of Coordination Cages with Systematically Fine-Tuned Cavities for Efficient Co-Encapsulation and Catalysis.

Angew Chem Int Ed Engl 2022 May 21. Epub 2022 May 21.

Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, State Key Laboratory of Structural Chemistry, 155 Yangqiao Road West, 350002, Fuzhou, CHINA.

Controllable arrangement of different ligands in a single assembly will not only bring increased complexity but also offers a new route to fine-tune the function of the designed architecture. We report here a combinatorial self-assembly with enPd(NO 3 ) 2 and three different ligands ( L 1-3 ), which gave rise to a family of six palladium-organic cages ( C1-6 ) with systematically varied shapes and cavities, including three new heteroleptic ( Pd 5 L 1 2 L 2 , Pd 5 L 1 2 L 3 , Pd 4 L 2 L 3 ), one new homoleptic ( Pd 4 L 3 2 ) cage, and two known homoleptic ( Pd 6 L 1 4 , Pd 4 L 2 2 ) cages . Emergent functions due to the fusion of two half cavities on the heteroleptic cages from their parent homoleptic cages have been observed: the heteroleptic cages can form ternary complexes by co-encapsulation of both aromatic and aliphatic guests, while their homoleptic counterparts can only form binary complexes. Read More

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Specific sequence of arrival promotes coexistence via spatial niche pre-emption by the weak competitor.

Ecol Lett 2022 May 21. Epub 2022 May 21.

Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences University of Lisbon, Lisbon, Portugal.

Historical contingency, such as the order of species arrival, can modify competitive outcomes via niche modification or pre-emption. However, how these mechanisms ultimately modify stabilising niche and average fitness differences remains largely unknown. By experimentally assembling two congeneric spider mite species feeding on tomato plants during two generations, we show that order of arrival affects species' competitive ability and changes the outcome of competition. Read More

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Micro-Gel Ensembles for Accelerated Healing of Chronic Wound via pH Regulation.

Adv Sci (Weinh) 2022 May 21:e2201254. Epub 2022 May 21.

Department of General Surgery, Jinling Hospital, Nanjing Medical University, Nanjing, 210002, China.

The pH value in the wound milieu plays a key role in cellular processes and cell cycle processes involved in the process of wound healing. Here, a microfluidic assembly technique is employed to fabricate micro-gel ensembles that can precisely tune the pH value of wound surface and accelerate wound healing. The micro-gel ensembles consist of poly (hydroxypropyl acrylate-co-acrylic acid)-magnesium ions (poly-(HPA-co-AA)-Mg ) gel and carboxymethyl chitosan (CMCS) gel, which can release and absorb hydrogen ion (H ) separately at different stages of healing in response to the evolution of wound microenvironment. Read More

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Construction and characterization of a de novo draft genome of garden cress (Lepidium sativum L.).

Funct Integr Genomics 2022 May 20. Epub 2022 May 20.

Department of Biotechnology, Necmettin Erbakan University, Meram, Konya, 42090, Turkey.

Garden cress (Lepidium sativum L.) is a Brassicaceae crop recognized as a healthy vegetable and a medicinal plant. Lepidium is one of the largest genera in Brassicaceae, yet, the genus has not been a focus of extensive genomic research. Read More

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Engineered CRISPR/Cas9 System for Transcriptional Gene Silencing in Arthrobacter Species Indicates Bacterioruberin is Indispensable for Growth at Low Temperatures.

Curr Microbiol 2022 May 20;79(7):199. Epub 2022 May 20.

Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115, Bonn, Germany.

Pink-pigmented Arthrobacter species produce the rare C carotenoid bacterioruberin, which is suspected to be part of the cold adaptation mechanism. In silico analysis of the repertoire of genes encoded by the Arthrobacter agilis and Arthrobacter bussei genome revealed the biosynthetic pathway of bacterioruberin. Although genetic analysis is an essential tool for studying the physiology of Arthrobacter species, genetic manipulation of Arthrobacter is always time and labor intensive due to the lack of genetic engineering tools. Read More

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A print-and-fuse Strategy for Sacrificial Filaments Enables Biomimetically Structured Perfusable Microvascular Networks with Functional Endothelium Inside 3D Hydrogels.

Adv Mater 2022 May 20:e2200653. Epub 2022 May 20.

Chair for Functional Materials for Medicine and Dentistry at the Institute for Functional Materials and Biofabrication (IFB) and Bavarian Polymer Institute (BPI), University of Würzburg, Pleicherwall 2, 97070, Würzburg, Germany.

Current methods of microvessel fabrication mostly rely on self-assembly in tiny volumes, prefabricated designs of microchannels, or demand complicated multi-step procedures based on sacrificial templating to achieve specific geometrical features. Such application-oriented geometries subsequently require a design-specific and functional perfusion system that must be developed in parallel. In this study, we present a facile and flexible approach for the integration of biomimetically branched microvasculature within bulk hydrogels. Read More

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Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly.

FEMS Microbiol Ecol 2022 May 20. Epub 2022 May 20.

Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.

Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L. Read More

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Spindle Assembly and Mitosis in Plants.

Annu Rev Plant Biol 2022 May;73:227-254

Department of Plant Biology, University of California, Davis, California, USA; email:

In contrast to well-studied fungal and animal cells, plant cells assemble bipolar spindles that exhibit a great deal of plasticity in the absence of structurally defined microtubule-organizing centers like the centrosome. While plants employ some evolutionarily conserved proteins to regulate spindle morphogenesis and remodeling, many essential spindle assembly factors found in vertebrates are either missing or not required for producing the plant bipolar microtubule array. Plants also produce proteins distantly related to their fungal and animal counterparts to regulate critical events such as the spindle assembly checkpoint. Read More

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A chromosome-level genome assembly of the pollinating fig wasp Valisia javana.

DNA Res 2022 May 20. Epub 2022 May 20.

Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou, 510650, China.

Fig wasp has always been thought the species-specific pollinator for their host fig (Moraceae, Ficus) and constitute a model system with its host to study co-evolution and co-speciation. The availability of a high-quality genome will help to further reveal the mechanisms underlying these characteristics. Here we present a high-quality chromosome-level genome for V. Read More

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Deciphering the Molecular Mechanisms of Insecticide Resistance From the Transcriptome Data of Field Evolved Spinosad Resistant and Susceptible Populations of Plutella xylostella (Lepidoptera: Plutellidae).

J Econ Entomol 2022 May 20. Epub 2022 May 20.

ICAR-National Bureau of Agricultural Insect Resources, P.B. No. 2491, H.A. Farm Post, Hebbal, Bangalore 560024, India.

Diamondback moth, Plutella xylostella is a serious pest of cruciferous vegetables and causes substantial economic loss all over the world. This study was undertaken to decipher the molecular mechanisms involved in the field evolved insecticide resistance in P. xylostella upon exposure to spinosad. Read More

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Spn1 and its dynamic interactions with Spt6, histones and nucleosomes.

J Mol Biol 2022 May 17:167630. Epub 2022 May 17.

Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA.

Histone chaperones facilitate the assembly and disassembly of nucleosomes and regulate DNA accessibility for critical cellular processes. Spn1 is an essential, highly conserved histone chaperone that functions in transcription initiation and elongation in a chromatin context. Here we demonstrate that Spn1 binds H3-H4 with low nanomolar affinity, residues 85-99 within the acidic N-terminal region of Spn1 are required for H3-H4 binding, and Spn1 binding to H3-H4 dimers does not impede (H3-H4) tetramer formation. Read More

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The interaction of spongistatin 1 with tubulin.

Arch Biochem Biophys 2022 May 17:109296. Epub 2022 May 17.

Molecular Pharmacology Branch (RB, EH), Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA. Electronic address:

A tritiated derivative of the sponge-derived natural product spongistatin 1 was prepared, and its interactions with tubulin were examined. [H]Spongistatin 1 was found to bind rapidly to tubulin at a single site (the low specific activity of the [H]spongistatin 1, 0.75 Ci/mmol, prevented our defining an association rate), and the inability of spongistatin 1 to cause an aberrant assembly reaction was confirmed. Read More

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Review of 2022 WHO guidelines on the control and elimination of schistosomiasis.

Lancet Infect Dis 2022 May 17. Epub 2022 May 17.

Department of Control of Neglected Tropical Diseases, WHO, Geneva, Switzerland.

Schistosomiasis is a helminthiasis infecting approximately 250 million people worldwide. In 2001, the World Health Assembly (WHA) 54.19 resolution defined a new global strategy for control of schistosomiasis through preventive chemotherapy programmes. Read More

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Human NLRP1 is a sensor of pathogenic coronavirus 3CL proteases in lung epithelial cells.

Mol Cell 2022 May 16. Epub 2022 May 16.

Critical Care Unit, University Hospital of Purpan, Toulouse, France.

Inflammation observed in SARS-CoV-2-infected patients suggests that inflammasomes, proinflammatory intracellular complexes, regulate various steps of infection. Lung epithelial cells express inflammasome-forming sensors and constitute the primary entry door of SARS-CoV-2. Here, we describe that the NLRP1 inflammasome detects SARS-CoV-2 infection in human lung epithelial cells. Read More

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Local adaptation and the evolution of genome architecture in threespine stickleback.

Genome Biol Evol 2022 May 20. Epub 2022 May 20.

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada, T2N 1N4.

Theory predicts that local adaptation should favour the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine vs. freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harbouring multiple quantitative trait loci (QTL) for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. Read More

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A Target-Feedback Rolling-Cleavage signal amplifier for ultrasensitive electrochemical detection of miRNA with Self-Assembled [email protected] hybrid nanoflowers.

Bioelectrochemistry 2022 May 4;146:108152. Epub 2022 May 4.

Key Laboratory of Medical Diagnostics of Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China. Electronic address:

Currently, developing an effective and easy-to-operate signal amplification assay to detect the trace-amount miRNAs in serum remains a significant challenge. Herein, an ultrasensitive [email protected] hybrid nanoflower ([email protected] HNF)-labeled electrochemical biosensor was developed for sensing miRNA, based on a target-feedback rolling-cleavage (TFRC) signal amplifier. [email protected] HNFs possessing a unique three-dimensional layered structure were synthesized without any complex reaction conditions, such as heating and vacuum. Read More

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Collagen and elastic fiber remodeling in the pregnant mouse myometrium.

Biol Reprod 2022 May 19. Epub 2022 May 19.

Department of Obstetrics, Gynecology, and Reproductive Sciences, Larner College of Medicine University of Vermont, Burlington, VT.

The myometrium undergoes progressive tissue remodeling from early to late pregnancy to support fetal growth and transitions to contractile phase to deliver a baby at term. Much of our effort has been focused on understanding the functional role of myometrial smooth muscle cells, but the role of extracellular matrix is not clear. This study was aimed to demonstrate the expression profile of sub-sets of genes involved in the synthesis, processing, and assembly of collagen and elastic fibers, their structural remodeling during pregnancy, and hormonal regulation. Read More

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Self-Assembled Liposomes Enhance Electron Transfer for Efficient Photocatalytic CO Reduction.

J Am Chem Soc 2022 May 20. Epub 2022 May 20.

Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.

Light-driven conversion of CO to chemicals provides a sustainable alternative to fossil fuels, but homogeneous systems are typically limited by cross reactivity between different redox half reactions and inefficient charge separation. Herein, we present the bioinspired development of amphiphilic photosensitizer and catalyst pairs that self-assemble in lipid membranes to overcome some of these limitations and enable photocatalytic CO reduction in liposomes using precious metal-free catalysts. Using sodium ascorbate as a sacrificial electron source, a membrane-anchored alkylated cobalt porphyrin demonstrates higher catalytic CO production (1456 vs 312 turnovers) and selectivity (77 vs 11%) compared to its water-soluble nonalkylated counterpart. Read More

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Planar 2D wireframe DNA origami.

Sci Adv 2022 May 20;8(20):eabn0039. Epub 2022 May 20.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Two-dimensional (2D) DNA origami is widely used for applications ranging from excitonics to single-molecule biophysics. Conventional, single-layer 2D DNA origami exhibits flexibility and curvature in solution; however, that may limit its suitability as a 2D structural template. In contrast, 2D wireframe DNA origami rendered with six-helix bundle edges offers local control over duplex orientations with enhanced in-plane rigidity. Read More

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MAECI: A pipeline for generating consensus sequence with nanopore sequencing long-read assembly and error correction.

Authors:
Jidong Lang

PLoS One 2022 20;17(5):e0267066. Epub 2022 May 20.

Department of Bioinformatics, Qitan Technology (Beijing) Co., Ltd, Beijing, China.

Nanopore sequencing produces long reads and offers unique advantages over next-generation sequencing, especially for the assembly of draft bacterial genomes with improved completeness. However, assembly errors can occur due to data characteristics and assembly algorithms. To address these issues, we developed MAECI, a pipeline for generating consensus sequences from multiple assemblies of the same nanopore sequencing data and error correction. Read More

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