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Cyclic, Hydrophobic Hexapeptide Fusahexin Is the Product of a Nonribosomal Peptide Synthetase in .

J Nat Prod 2021 Jul 22. Epub 2021 Jul 22.

Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK-9220 Aalborg, Denmark.

The plant pathogenic fungus is known to produce a wide array of secondary metabolites during plant infection. This includes several nonribosomal peptides. Recently, the fusaoctaxin (/9) and gramilin () gene clusters were shown to be induced by host interactions. Read More

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Study of Fe-S Cluster Proteins in Methanococcus maripaludis , a Model Archaeal Organism.

Methods Mol Biol 2021 ;2353:37-50

Corporate Strategic Research, ExxonMobil Research & Engineering Company, Annandale, NJ, USA.

Iron-sulfur (Fe-S) clusters are among the oldest and most versatile cofactors present in all domains of life. Many bacterial and eukaryotic Fe-S proteins have been well-characterized, whereas the archaeal ones are less studied. Fe-S proteins are particularly abundant and play essential roles in methanogenic archaea. Read More

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January 2021

Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice.

Sci Rep 2021 Jul 21;11(1):14887. Epub 2021 Jul 21.

School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.

WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. Read More

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A New Contact Killing Toxin Permeabilizes Cells and Belongs to a Broadly Distributed Protein Family.

mSphere 2021 Jul 21:e0031821. Epub 2021 Jul 21.

School of Biological Sciences, Georgia Institute of Technologygrid.213917.f, Atlanta, Georgia, USA.

Vibrio cholerae is an aquatic Gram-negative bacterium that causes severe diarrheal cholera disease when ingested by humans. To eliminate competitor cells in both the external environment and inside hosts, V. cholerae uses the type VI secretion system (T6SS). Read More

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Genetic Dissection of Seedling Root System Architectural Traits in a Diverse Panel of Hexaploid Wheat through Multi-Locus Genome-Wide Association Mapping for Improving Drought Tolerance.

Int J Mol Sci 2021 Jul 2;22(13). Epub 2021 Jul 2.

Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA.

Cultivars with efficient root systems play a major role in enhancing resource use efficiency, particularly water absorption, and thus in drought tolerance. In this study, a diverse wheat association panel of 136 wheat accessions including mini core subset was genotyped using Axiom 35k Breeders' Array to identify genomic regions associated with seedling stage root architecture and shoot traits using multi-locus genome-wide association studies (ML-GWAS). The association panel revealed a wide variation of 1. Read More

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Clusters-based silver nanorings: An active substrate for surface-enhanced Raman scattering.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Jul 6;263:120141. Epub 2021 Jul 6.

Interdisciplinary Research Center for Hydrogen and Energy Storage (IRC-HES), Research Institute, King Fahd University of Petroleum & Minerals (KFUPM), Dhahran 31261, Saudi Arabia.

Plasmonic nanostructures, particularly irregular surfaces of ring-like silver (Ag) nanostructures are promising candidates in surface-enhanced Raman scattering (SERS) spectroscopy. In this work, clusters-based Ag nanorings have been fabricated and characterized as SERS-active substrates. The rim of the as-fabricated Ag nanorings was found neither discontinuous nor linear aggregation of nanoparticles. Read More

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Interactive Visualization of Hyperspectral Images based on Neural Networks.

IEEE Comput Graph Appl 2021 Jul 19;PP. Epub 2021 Jul 19.

It is challenging to interpret hyperspectral images in an intuitive and meaningful way, as they usually contain hundreds of dimensions. We develop a visualization tool for hyperspectral images based on neural networks, which allows a user to specify the regions of interest, select bands of interest, and obtain hyperspectral clustering results in a scatterplot generated from hyperspectral features. A cascade neural network is trained to generate an scatterplot that matches the clustering centers labeled by the user. Read More

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Sorting of cadherin-catenin-associated proteins into individual clusters.

Proc Natl Acad Sci U S A 2021 Jul;118(29)

Department of Dermatology, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611;

The cytoplasmic tails of classical cadherins form a multiprotein cadherin-catenin complex (CCC) that constitutes the major structural unit of adherens junctions (AJs). The CCC in AJs forms junctional clusters, "E clusters," driven by and interactions in the cadherin ectodomain and stabilized by α-catenin-actin interactions. Additional proteins are known to bind to the cytoplasmic region of the CCC. Read More

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Multimorbidity networks of mental disorder symptom domains across psychopathology severity levels in community youth.

J Psychiatr Res 2021 Jul 7;141:267-275. Epub 2021 Jul 7.

Division of Clinical Psychology and Epidemiology, Department of Psychology, University of Basel, Missionsstrasse 62a, CH-4055, Basel, Switzerland; Department of Clinical Psychology and Cognitive Behavioral Therapy, International Psychoanalytic University, Stromstrasse 1, DE-10555, Berlin, Germany; Department of Psychosomatic Medicine, University Hospital Basel and University of Basel, Hebelstrasse 2, CH-4031, Basel, Switzerland. Electronic address:

Our aim was to scrutinize multimorbidity in a community sample of youths (Philadelphia Neurodevelopmental Cohort) in form of co-occurrences of DSM-IV disorder symptom domains, elucidating if and when specific symptom domain interrelations emerge as mental disorder severity levels increase. We estimated four multimorbidity networks based on four severity cut-offs ('at least symptomatic', 'at least subthreshold', 'at least threshold', and 'impaired') and compared them pairwise on two measures: global network strength and network structure. We further computed community clusters for each network to detect symptom domain interrelations. Read More

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An uncommon [K+(Mg2+)2] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.

RNA 2021 Jul 13. Epub 2021 Jul 13.

National Heart, Lung, and Blood Institute.

The widespread ykkC-I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the Burkholderia sp. TJI49 ykkC-I subtype-1 (Guanidine-I) riboswitch aptamer domain. Read More

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Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency.

Genome Biol 2021 Jul 12;22(1):206. Epub 2021 Jul 12.

State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.

Background: Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. Read More

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Vesicle capture by membrane-bound Munc13-1 requires self-assembly into discrete clusters.

FEBS Lett 2021 Jul 6. Epub 2021 Jul 6.

Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.

Munc13-1 is a large banana-shaped soluble protein that is involved in the regulation of synaptic vesicle docking and fusion. Recent studies suggest that multiple copies of Munc13-1 form nano-assemblies in active zones of neurons. However, it is not known if such clustering of Munc13-1 is correlated with multivalent binding to synaptic vesicles or specific plasma membrane domains at docking sites in the active zone. Read More

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A Bird's-Eye View of Exercise Intervention in Treating Depression Among Teenagers in the Last 20 Years: A Bibliometric Study and Visualization Analysis.

Front Psychiatry 2021 18;12:661108. Epub 2021 Jun 18.

Division of Sport Science and Physical Education, Tsinghua University, Beijing, China.

Exercise is medicine. Multiple studies on the effects and mechanisms of exercise in treating depression among teenagers and adolescents have been widely reported. However, literature involving scientometric analysis of this topic is sparse. Read More

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Fluorescence intensity fluctuation analysis of receptor oligomerization in membrane domains.

Biophys J 2021 Jun 30. Epub 2021 Jun 30.

Physics Department, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin; Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin. Electronic address:

Fluorescence micrographs of the plasma membrane of cells expressing fluorescently labeled G protein-coupled receptors (GPCRs) often exhibit small clusters of pixels (or puncta) with intensities that are higher than those of the surrounding pixels. Although studies of GPCR interactions in uniform membrane areas abound, understanding the details of the GPCR interactions within such puncta as well as the nature of the membrane formations underlying the puncta is hampered by the lack of adequate experimental techniques. Here, we introduce an enhancement of a recently developed method termed fluorescence intensity fluctuation spectrometry, which permits analysis of protein-protein interactions within the puncta in live cell membranes. Read More

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Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress.

Protoplasma 2021 Jul 1. Epub 2021 Jul 1.

Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences/Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan, 571339, People's Republic of China.

The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Read More

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Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Strains Causing Corynespora Leaf Fall (CLF) Disease.

J Fungi (Basel) 2021 Jun 16;7(6). Epub 2021 Jun 16.

Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, 4 Xueyuan Road, Haikou 571101, China.

Rubber tree leaf fall (CLF) disease, caused by the fungus , is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between species, and some virulent strains do not contain the cassiicolin gene. Read More

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PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution.

Viruses 2021 Jun 26;13(7). Epub 2021 Jun 26.

Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, 9000 Gent, Belgium.

Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-considered selections of phage lytic proteins in early research stages. Read More

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EGFR in Cancer: Signaling Mechanisms, Drugs, and Acquired Resistance.

Cancers (Basel) 2021 Jun 1;13(11). Epub 2021 Jun 1.

Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel.

The epidermal growth factor receptor (EGFR) has served as the founding member of the large family of growth factor receptors harboring intrinsic tyrosine kinase function. High abundance of EGFR and large internal deletions are frequently observed in brain tumors, whereas point mutations and small insertions within the kinase domain are common in lung cancer. For these reasons EGFR and its preferred heterodimer partner, HER2/ERBB2, became popular targets of anti-cancer therapies. Read More

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Alterations in Mucin-Associated Gene Expression on the Ocular Surface in Active and Stable Stages of Atopic and Vernal Keratoconjunctivitis.

J Ophthalmol 2021 31;2021:9914786. Epub 2021 May 31.

Division of Ophthalmology, Department of Visual Sciences, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-ku, Tokyo 173-8610, Japan.

Purpose: To evaluate the presence of ocular surface mucin in patients with atopic and vernal keratoconjunctivitis (AKC/VKC), we investigated the mRNA expression levels of SAM-pointed domain-containing ETS-like factor () and mucin-related genes on the ocular surface.

Methods: Nineteen patients with AKC or VKC were divided into two groups based on the severity of the disease as determined by their clinical scores for AKC/VKC: the stable group and the active group. Impression cytology was performed in all patients using filter paper, and the expression levels of , , , , , and eotaxin-2 mRNA were determined by real-time reverse-transcription polymerase chain reaction. Read More

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Cryptic association of B7-2 molecules and its implication for clustering.

Protein Sci 2021 Jun 30. Epub 2021 Jun 30.

Biological Sciences Division, Poornaprajna Institute of Scientific Research (PPISR), Bengaluru, India.

T-cell co-stimulation through CD28/CTLA4:B7-1/B7-2 axis is one of the extensively studied pathways that resulted in the discovery of several FDA-approved drugs for autoimmunity and cancer. However, many aspects of the signaling mechanism remain elusive, including oligomeric association and clustering of B7-2 on the cell surface. Here, we describe the structure of the IgV domain of B7-2 and its cryptic association into 1D arrays that appear to represent the pre-signaling state of B7-2 on the cell membrane. Read More

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Impact of atomistic or crystallographic descriptors for classification of gold nanoparticles.

Nanoscale 2021 Jul;13(27):11887-11898

School of Computing, Australian National University, Acton 2601, Australia.

Machine learning models are known to be sensitive to the features used to train them, but there is currently no way to predict the impact of using different features prior to feature extraction. This is particularly important to fields such as nanotechnology that are highly multi-disciplinary, and samples can be characterised many different ways depending on the preferences of individual researchers. Does it matter if nanomaterials are described using the interatomic coordinations or more complex order parameters? In this study we compare results of supervised and unsupervised learning on a single set of gold nanoparticles that has been characterised by two different descriptors, each with a unique feature space. Read More

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Temporal evolution, most influential studies and sleeping beauties of the coronavirus literature.

Scientometrics 2021 Jun 23:1-46. Epub 2021 Jun 23.

Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.

Following the outbreak of SARS-CoV-2 disease, within less than 8 months, the 50 years-old scholarly literature of coronaviruses grew to nearly three times larger than its size prior to 2020. Here, temporal evolution of the coronavirus literature over the last 30 years ( = 43,769) is analysed along with its subdomain of SARS-CoV-2 articles ( = 27,460) and the subdomain of reviews and meta-analytic studies ( = 1027). The analyses are conducted through the lenses of co-citation and bibliographic coupling of documents. Read More

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Antibody responses to collagen peptides and streptococcal collagen-like 1 proteins in acute rheumatic fever patients.

Pathog Dis 2021 Jul;79(6)

School of Medical Sciences, The University of Auckland, Auckland, New Zealand.

Acute rheumatic fever (ARF) is a serious post-infectious immune sequelae of Group A streptococcus (GAS). Pathogenesis remains poorly understood, including the events associated with collagen autoantibody generation. GAS express streptococcal collagen-like proteins (Scl) that contain a collagenous domain resembling human collagen. Read More

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Eukaryotic TYW1 Is a Radical SAM Flavoenzyme.

Biochemistry 2021 Jul 29;60(27):2179-2185. Epub 2021 Jun 29.

Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.

TYW1 is a radical -adenosyl-l-methionine (SAM) enzyme that catalyzes the condensation of pyruvate and -methylguanosine-containing tRNA, forming 4-demethylwyosine-containing tRNA. Homologues of TYW1 are found in both archaea and eukarya; archaeal homologues consist of a single domain, while eukaryal homologues contain a flavin binding domain in addition to the radical SAM domain shared with archaeal homologues. In this study, TYW1 from (TYW1) was heterologously expressed in and purified to homogeneity. Read More

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A data-driven spike sorting feature map for resolving spike overlap in the feature space.

J Neural Eng 2021 Jul 19;18(4). Epub 2021 Jul 19.

KU Leuven, Department of Electrical Engineering (ESAT), STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics and Leuven., Leuven, Belgium.

Spike sorting is the process of extracting neuronal action potentials, or spikes, from an extracellular brain recording, and assigning each spike to its putative source neuron. Spike sorting is usually treated as a clustering problem. However, this clustering process is known to be affected by overlapping spikes. Read More

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Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.

Front Microbiol 2021 10;12:675815. Epub 2021 Jun 10.

Institute for Information Transmission Problems of Russian Academy of Sciences (The Kharkevich Institute), Moscow, Russia.

The IclR-family is a large group of transcription factors (TFs) regulating various biological processes in diverse bacteria. Using comparative genomics techniques, we have identified binding motifs of IclR-family TFs, reconstructed regulons and analyzed their content, finding co-occurrences between the regulated COGs (clusters of orthologous genes), useful for future functional characterizations of TFs and their regulated genes. We describe two main types of IclR-family motifs, similar in sequence but different in the arrangement of the half-sites (boxes), with GKTYCRYWRYGRAMC and TGRAACANTGTTYCA consensuses, and also predict that TFs in 32 orthologous groups have binding sites comprised of three boxes with alternating direction, which implies two possible alternative modes of dimerization of TFs. Read More

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Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.).

Int J Biol Macromol 2021 Jun 24;184:1035-1061. Epub 2021 Jun 24.

Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Science, Anyang 455000, Henan, China. Electronic address:

Calmodulin (CaM) is considered as the most significant Ca signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. Read More

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Genome-Wide Comparative Analysis of Heat Shock Transcription Factors Provides Novel Insights for Evolutionary History and Expression Characterization in Cotton Diploid and Tetraploid Genomes.

Front Genet 2021 8;12:658847. Epub 2021 Jun 8.

Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China.

Heat shock transcription factors (HSFs) are involved in environmental stress response and plant development, such as heat stress and flowering development. According to the structural characteristics of the HSF gene family, HSF genes were classified into three major types (HSFA, HSFB, and HSFC) in plants. Using conserved domains of HSF genes, we identified 621 HSF genes among 13 cotton genomes, consisting of eight diploid and five tetraploid genomes. Read More

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Discovery and biosynthesis of guanipiperazine from a NRPS-like pathway.

Chem Sci 2021 Jan 5;12(8):2925-2930. Epub 2021 Jan 5.

State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University Nanjing 210023 China

Nonribosomal peptide synthetases (NRPSs) are modular enzymes that use a thiotemplate mechanism to assemble the peptide backbones of structurally diverse and biologically active natural products in bacteria and fungi. Unlike these canonical multi-modular NRPSs, single-module NRPS-like enzymes, which lack the key condensation (C) domain, are rare in bacteria, and have been largely unexplored to date. Here, we report the discovery of a gene cluster () encoding a NRPS-like megasynthetase through genome mining. Read More

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January 2021

Allelic variation in sugary1 gene affecting kernel sweetness among diverse-mutant and -wild-type maize inbreds.

Mol Genet Genomics 2021 Jun 23. Epub 2021 Jun 23.

ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.

Sweet corn is popular worldwide as vegetable. Though large numbers of sugary1 (su1)-based sweet corn germplasm are available, allelic diversity in su1 gene encoding SU1 isoamylase among diverse maize inbreds has not been analyzed. Here, we characterized the su1 gene in maize and compared with allied species. Read More

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