275 research outputs found

    The SET and ankyrin domains of the secreted Legionella pneumophila histone methyltransferase work together to modify host chromatin

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    ABSTRACT Legionella pneumophila is a bacterial pathogen ubiquitous in natural and man-made aquatic environments, where it replicates in protozoa. Its intracellular life cycle depends on the establishment of a Legionella-containing vacuole (LCV) where the bacteria replicate. To form the LCV, L. pneumophila depends on a type-4 secretion system that secretes more than 300 proteins in the host cell. Among these is RomA that encodes an N-terminal catalytic methyltransferase domain with a SET fold and a C-terminal domain containing six ankyrin repeats. We have reported that the SET domain has histone methyltransferase activity and specifically methylates lysine 14 of histone H3 during infection; however, the role of the ankyrin repeats is unknown. Here, we report the structure of RomA co-crystallized with a 15-mer peptide corresponding to the N-terminal tail of histone H3 at 2.2 Å. This structure revealed that the N-terminal arm of the peptide from Thr3-Ala7 binds to the ankyrin repeat domain and the C-terminal arm from Gly13-Arg17 and interacts with the SET domain, inserting Lys14 into the active site for methylation. Importantly, the interactions of the five N-terminal residues of the H3-peptide with the ankyrin domains account for ~50% of the peptide-RomA contacts, predicting that the ankyrin domains of RomA are essential for histone H3 binding and subsequent lysine methylation. In vitro enzymatic activity and binding assays confirmed these predictions. Thus, the six ankyrin domains are essential for chromatin binding, thereby allowing the SET domain to fulfill its histone transferase activity and to modify the host chromatin to the advantage of the pathogen. IMPORTANCE Legionella pneumophila is an intracellular bacterium responsible of Legionnaires’ disease, a severe pneumonia that is often fatal when not treated promptly. The pathogen’s ability to efficiently colonize the host resides in its ability to replicate intracellularly. Essential for intracellular replication is translocation of many different protein effectors via a specialized secretion system. One of them, called RomA, binds and directly modifies the host chromatin at a unique site (tri-methylation of lysine 14 of histone H3 [H3K14me]). However, the molecular mechanisms of binding are not known. Here, we resolve this question through structural characterization of RomA together with the H3 peptide. We specifically reveal an active role of the ankyrin repeats located in its C-terminal in the interaction with the histone H3 tail. Indeed, without the ankyrin domains, RomA loses its ability to act as histone methyltransferase. These results discover the molecular mechanisms by which a bacterial histone methyltransferase that is conserved in L. pneumophila strains acts to modify chromatin

    Genetic authentication of crocodile meat available in Hong Kong

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    The crocodilians include true crocodiles, alligators, caimans, and gharial, and the trade of crocodilian products is regulated in accordance with the Convention of Wild Fauna and Flora (CITES). Hong Kong does not have her own wild crocodilians; thus, all crocodilians meat available is presumably imported with proper license. Here, we sequenced the cytochrome oxidase I (COI) gene markers to reveal species identity of crocodilian meat available in the contemporary market. The COI sequences of 114 samples including frozen and dried crocodilian meat products were subjected to phylogenetic analysis, and four crocodile species including Crocodylus siamensis, C. porosus, C. niloticus and Alligator mississippiensis, and two samples belonging to snake Malayopython reticulatus, were detected.</p

    Whole‑Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

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    Unlike environmental P. koreensis isolated from soil, which has been studied extensively for its role in promoting plant growth, pathogenic P. koreensis isolated from fish has been rarely reported. Therefore, we investigated and isolated the possible pathogen that is responsible for the diseased state of Tor tambroides. Herein, we reported the morphological and biochemical characteristics, as well as whole-genome sequences of a newly identified P. koreensis strain. We assembled a high-quality draft genome of P. koreensis CM-01 with a contig N50 value of 233,601 bp and 99.5% BUSCO completeness. The genome assembly of P. koreensis CM-01 is consists of 6,171,880 bp with a G+C content of 60.5%. Annotation of the genome identified 5538 protein-coding genes, 3 rRNA genes, 54 tRNAs, and no plasmids were found. Besides these, 39 interspersed repeat and 141 tandem repeat sequences, 6 prophages, 51 genomic islands, 94 insertion sequences, 4 clustered regularly interspaced short palindromic repeats, 5 antibiotic-resistant genes, and 150 virulence genes were also predicted in the P. koreensis CM-01 genome. Culture-based approach showed that CM-01 strain exhibited resistance against ampicillin, aztreonam, clindamycin, and cefoxitin with a calculated multiple antibiotic resistance (MAR) index value of 0.4. In addition, the assembled CM-01 genome was successfully annotated against the Cluster of Orthologous Groups of proteins database, Gene Ontology database, and Kyoto Encyclopedia of Genes and Genome pathway database. A comparative analysis of CM-01 with three representative strains of P. koreensis revealed that 92% of orthologous clusters were conserved among these four genomes, and only the CM-01 strain possesses unique elements related to pathogenicity and virulence. This study provides fundamental phenotypic and genomic information for the newly identified P. koreensis strain

    Complete chloroplast genome data of Shorea macrophylla (Engkabang): Structural features, comparative and phylogenetic analysis

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    Shorea macrophylla belongs to the Shorea genus under the Dipterocarpaceae family. It is a woody tree that grows in the rainforest in Southeast Asia. The complete chloroplast (cp) genome sequence of S. macrophylla is reported here. The genomic size of S. macrophylla is 150,778 bp and it possesses a circular structure with conserved constitute regions of large single copy (LSC, 83,681 bp) and small single copy (SSC, 19,813 bp) regions, as well as a pair of inverted repeats with a length of 23,642 bp. It has 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The genome exhibits a similar GC content, gene order, structure, and codon usage when compared to previously reported chloroplast genomes from other plant species. The chloroplast genome of S. macrophylla contained 262 SSRs, the most prevalent of which was A/T, followed by AAT/ATT. Furthermore, the sequences contain 43 long repeat sequences, practically most of them are forward or palindrome type long repeats. The genome structure of S. macrophylla was compared to the genomic structures of closely related species from the same family, and eight mutational hotspots were discovered. The phylogenetic analysis demonstrated a close relationship between Shorea and Parashorea species, indicating that Shorea is not monophyletic. The complete chloroplast genome sequence analysis of S. macrophylla reported in this paper will contribute to further studies in molecular identification, genetic diversity, and phylogenetic research

    Cholesterol-linoleic acid liposomes induced extracellular vesicles secretion from immortalized adipose-derived mesenchymal stem cells for in vitro cell migration

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    AbstractExtracellular vesicles (EVs) are small vesicles that are naturally released by cells and play a crucial role in cell-to-cell communication, tissue repair and regeneration. As naturally secreted EVs are limited, liposomes with different physicochemical properties, such as 1,2-dioleoyl-3-trimethylammonium propane (DOTAP) and linoleic acid (LA) with modifications have been formulated to improve EVs secretion for in vitro wound healing. Various analyses, including dynamic light scattering (DLS) and transmission electron microscopy (TEM) were performed to monitor the successful preparation of different types of liposomes. The results showed that cholesterol–LA liposomes significantly improved the secretion of EVs from immortalized adipose-derived mesenchymal stem cells (AD-MSCs) by 1.5-fold. Based on the cell migration effects obtained from scratch assay, both LA liposomal-induced EVs and cholesterol–LA liposomal-induced EVs significantly enhanced the migration of human keratinocytes (HaCaT) cell line. These findings suggested that LA and cholesterol–LA liposomes that enhance EVs secretion are potentially useful and can be extended for various tissue regeneration applications

    The United States COVID-19 Forecast Hub dataset

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    Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

    Reprogramming of Fatty Acid Metabolism in Gynaecological Cancers: Is There a Role for Oestradiol?

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    Gynaecological cancers are among the leading causes of cancer-related death among women worldwide. Cancer cells undergo metabolic reprogramming to sustain the production of energy and macromolecules required for cell growth, division and survival. Emerging evidence has provided significant insights into the integral role of fatty acids on tumourigenesis, but the metabolic role of high endogenous oestrogen levels and increased gynaecological cancer risks, notably in obesity, is less understood. This is becoming a renewed research interest, given the recently established association between obesity and incidence of many gynaecological cancers, including breast, ovarian, cervical and endometrial cancers. This review article, hence, comprehensively discusses how FA metabolism is altered in these gynaecological cancers, highlighting the emerging role of oestradiol on the actions of key regulatory enzymes of lipid metabolism, either directly through its classical ER pathways, or indirectly via the IGIFR pathway. Given the dramatic rise in obesity and parallel increase in the prevalence of gynaecological cancers among premenopausal women, further clarifications of the complex mechanisms underpinning gynaecological cancers are needed to inform future prevention efforts. Hence, in our review, we also highlight opportunities where metabolic dependencies can be exploited as viable therapeutic targets for these hormone-responsive cancers

    ALMA/ACA CO Survey of the IC 1459 and NGC 4636 Groups: Environmental Effects on the Molecular Gas of Group Galaxies

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    International audienceWe present new results of a 12CO(J = 1-0) imaging survey using the Atacama Compact Array (ACA) for 31 H I detected galaxies in the IC 1459 and NGC 4636 groups. This is the first CO imaging survey for loose galaxy groups. We obtained well-resolved CO data (~0.7-1.5 kpc) for a total of 16 galaxies in two environments. By comparing our ACA CO data with the H I and UV data, we probe the impacts of the group environment on the cold gas components (CO and H I gas) and star formation activity. We find that CO and/or H I morphologies are disturbed in our group members, some of which show highly asymmetric CO distributions (e.g., IC 5264, NGC 7421, and NGC 7418). In comparison with isolated galaxies in the xCOLD GASS sample, our group galaxies tend to have low star formation rates and low H2 gas fractions. Our findings suggest that the group environment can change the distribution of cold gas components, including the molecular gas and star formation properties of galaxies. This is supporting evidence that preprocessing in the group-like environment can play an important role in galaxy evolution

    Remote Crop Disease Detection using Deep Learning with IoT

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    Agriculture is such a vital part of our society, and according to the United Nations’ Food and Agricultural Organization (FAO), plant diseases are considered one of the two main causes of decreasing food availability. This paper explores not only the methods and findings of building a CNN-based disease detection model, but that of building a deployable remote crop disease detection system incorporating IoT technology. By using transfer learning with AlexNet, we were able to predict with 89.8% accuracy tomato plant images into one of the ten pre-defined disease classes. Our proposed system tracks plant health throughout the day by using a microprocessor and a camera to automatically capture images, diagnose the plant, and report results. The system is a proof of concept of a technology that can significantly help increase crop yield, reduce food waste, and automate the tasks of detecting and caring for diseased crops

    Acceptability for COVID-19 vaccination: perspectives from Muslims

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    This study aims to assess COVID-19 vaccine acceptance among Muslims in Malaysia. A cross-sectional internet-based survey was to determine acceptance of COVID-19 vaccine. Other influential factors, namely socio-demographics, COVID-19 experience, self-perceived level of religiosity, support in immunization, COVID-19 immunization attitudes, and health fatalistic beliefs (measured using the Helpless Inevitability Subscale of the Religious Health Fatalism Questionnaire, RHFQ-HI) were investigated. The majority reported a definite intent to receive the COVID-19 vaccine (57.3%; 95% CI 55.0–59.6) followed by a probable intent (42.7%; 95% CI 40.4–45.0%). COVID-19 immunization attitudes measured by attitudinal barriers to vaccination scores were found to be the strongest influence of COVID-19 vaccination intent, whereby participants who have lower attitudinal barrier scores reported higher COVID-19 vaccination intent (OR = 6.75 ; 95% 5.20–8.75). Although religious health fatalism was not significantly associated with vaccination intent, a significantly higher proportion of participants with score 4–9 (61.9%) in the RHFQ-HI reported intent to receive COVID-19 vaccine than those with a score of 10–20 (53.5%), p < .001. Intervention for people with skeptical attitudes toward COVID-19 vaccination is warranted
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