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Chang, T.-H.

Publications and source records attributed to Chang, T.-H..

At least 19 recordsLinked to original sources

HSC70 prevents TDP-43 nuclear puncta formation and toxicity in a novel nuclear puncta cell model for ALS

Amyotrophic lateral sclerosis (ALS) is categorized by TDP-43 proteinopathy, however, the nuclear pathological events remain poorly defined. While cytoplasmic TDP-43 inclusions dominate the late disease stages, accumulating evidence indicates that nuclear TDP-43 assemblies arise earlier and impair RNA splicing. Here, we characterized a single RRM-proximal TDP-43 variant, G148V, designed to disrupt nucleic-acid engagement without altering canonical RNA-binding residues. Structural and biophysical analyses revealed conformational changes and loss of DNA/RNA binding. In mammalian cells, TDP-43 G148V robustly formed nuclear puncta with high penetrance, exhibiting solid-like properties, pathological phosphorylation, splicing dysfunction, and toxicity. Furthermore, we identified molecular chaperone HSC70 as an important regulator of the nuclear puncta assembly. HSC70 redistributed into G148V nuclear puncta to modulate their material state, whereas HSC70 depletion significantly promoted puncta solidification, increased insoluble TDP-43 accumulation, and enhanced cytotoxicity. Disease-associated K181E and K263E mutants also formed nuclear puncta and induced HSC70 nuclear redistribution. These findings establish G148V as a model of early nuclear TDP-43 pathology and highlight HSC70-mediated regulation as a key factor of TDP-43 nuclear assembly. HighlightsO_LIA single TDP-43 mutation, G148V, in RRM1 domain robustly induces nuclear puncta without exogenous stress. C_LIO_LIG148V disrupts nucleic-acid binding, driving solid-like nuclear assemblies with hyperphosphorylation. C_LIO_LINuclear G148V puncta impair splicing regulation and reduce cell viability, recapitulating early ALS pathology. C_LIO_LIThe molecular chaperone HSC70 modulates puncta material states and mitigates G148V-associated cytotoxicity. C_LI Graphical abstrac O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/739729v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@d019c8org.highwire.dtl.DTLVardef@4ca632org.highwire.dtl.DTLVardef@331fd9org.highwire.dtl.DTLVardef@6fe8e4_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC blurbA structure-guided TDP-43 G148V mutation reveals how loss of nucleic-acid engagement promotes early nuclear condensation, splicing dysfunction, and toxicity, while uncovering a protective role for HSC70 in regulating condensate properties during ALS pathogenesis.

cell biology↗

Chitin oligomers induce atypical NLRP3 inflammasome activation and innate immune training

Chitin is a highly abundant poly- N-acetyl-glucosamine (GlcNAc) and linked to immune recognition of fungal infections and asthma in humans. Ubiquitous in fungi and insects, in mammals and plants chitin represents a microbe-associated molecular pattern (MAMP) and whereas highly polymeric chitin is insoluble and immunologically inert, soluble chitin oligomers of 6 to 15 GlcNAc activate immediate pro-inflammatory cytokine release via TLR2 in human immune cells. However, TLR2 ligands do not the most typical activators of the NLRP3 inflammasome pathway or innate immune training, a phenomenon of long-term immunological remodeling. Here we show that especially 16-20 GlcNAc long chitin oligomers activate NLRP3-dependent IL-1{beta} and IL-18 release in human myeloid immune cells in an atypical, phagocytosis-dependent manner. Moreover, phagocytosis and methyl transferase activity were essential for innate immune training, by which the same chito-oligomer-training enhanced TNF release in primary murine and human immune cells. Collectively, this suggests that oligomer length impacts on the immune features of chitin which can be customized using glycan assembly.

immunology↗

A Streamlined Protocol for Small-scale Protoplast Generation and CRISPR/Cpf1-mediated Genome Editing in Fusarium oxysporum

Fusarium oxysporum is a significant threat to agriculture and One Health, requiring advanced molecular tools for functional genomics analyses and biological control agent development. Existing gene-editing methods are hampered by costly protoplast preparation protocols and by CRISPR/Cas9 limitations, such as restricted PAM sequences and complex guide RNA requirements. We engineered an efficient CRISPR/Cpf1 system that overcomes these issues through three main innovations: small-scale protoplast generation using novel filter columns that greatly reduces enzyme consumption while simplifying workflows, a CRISPR/Cpf1 system with flexible PAM recognition and staggered DNA cleavage to promote homologous recombination, and minimal homology arm strategies that significantly decrease cloning complexity. Extensive validation confirms successful gene targeting with molecular verification and functional analysis via standardized pathogenicity assays. This integrated platform offers affordable, accessible tools for systematic F. oxysporum research, enhancing fundamental understanding of plant-pathogen interactions and supporting high-throughput screening vital for agricultural biotechnology and biological agent development. MOTIVATIONFusarium oxysporum plays crucial roles as both a damaging plant pathogen and a model for studying host-pathogen interactions. It is well established that systematic functional genomics approaches are vital for advancing agricultural biotechnology and developing biological agents. Creating efficient gene-editing systems can help elucidate virulence mechanisms and enable rapid production of modified strains for practical use. However, current transformation methods face major challenges, such as high enzyme costs, and CRISPR/Cas9 systems are limited by PAM sequence availability and by blunt-end DNA cleavage, which hampers homologous recombination. Furthermore, complex guide RNA scaffolds complicate large-scale functional studies with traditional methods. To address these challenges, we have developed a streamlined CRISPR/Cpf1 (Cas12a) platform that combines small-scale protoplast preparation with significantly reduced enzyme use, exploiting Cpf1s unique features, such as flexible PAM recognition, staggered DNA cuts that promote recombination, improved target specificity, and simpler guide RNA design. This platform can also accelerate the development of biological agents and support high-throughput screening applications essential to the progress of agricultural biotechnology. HIGH LIGHTSO_LIReduced enzyme costs by 95% through small-scale protoplast preparation C_LIO_LICRISPR/Cpf1 system established for efficient gene editing in Fusarium oxysporum C_LIO_LIStreamlined workflow enables routine gene targeting and rapid mutant screening C_LIO_LIComplete workflow validated with EGFP-marked pathogenicity C_LI

microbiology↗

S-nitrosylation of the CLIP-protease, Persephone, Regulates Drosophila innate immunity

Nitric oxide (NO) modulates innate immunity, but its molecular targets in Drosophila melanogaster are largely undefined. A key mechanism of NO signalling is S-nitrosylation, the modification of cysteine thiols. The homeostasis of S-nitrosylation is maintained by S-nitrosoglutathione reductase (Gsnor), encoded by the fdh gene in D. melanogaster. As reduced Gsnor activity enhances pathogen sensitivity in plants, we investigated its role in D. melanogaster. Here, we show that flies lacking fdh exhibit increased susceptibility to the fungus Beauveria bassiana and the bacterium Staphylococcus aureus, pathogens combatted by the Toll pathway. This immune deficiency correlates with impaired Toll-dependent antimicrobial peptide expression. We demonstrate that the Toll pathway protease Persephone (Psh) is S-nitrosylated in vivo and that loss of Gsnor prevents its proteolytic activation following infection. We propose a model where Gsnor-mediated regulation of NO is essential for Toll activation, preventing excessive S-nitrosylation of Psh and ensuring a robust immune response.

molecular biology↗

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

Newly transcribed introns are immediately identified by early splicing factors that recognize the intron 5 splice site (5SS) and branch site (BS). In the budding yeast, these critical splice-site sequences are generally constrained, whereas degeneracy is the rule in higher eukaryotes. Yet, [~]40% of the yeast introns do diverge, to a certain degree, from the canonical sequences. Exactly how these non-canonical introns are recognized and spliced remains unknown. Here we show that the conserved Prp40 WW domains promote non-canonical intron splicing by enhancing stable U1 snRNP and BBP recruitments. AlphaFold predicts a topologically conserved unstructured region between Prp40 WW and FF domains. Alignment of the AlphaFold Prp40 structure with published U1 snRNP structure positions WW domains adjacent to 5SS and Luc7, which is known to be critical for 5SS recognition. Indeed, deletion of this unstructured region negatively impacts on splicing of the non-canonical 5SS introns. Taken together, our results suggest that the conserved WW domains may have evolved to deal with the highly degenerate 5SS and BS sequences in higher eukaryotes, so as to accommodate increased splicing complexity. HighlightsO_LIThe evolutionarily conserved Prp40 WW domains promote splicing of introns harboring non-canonical 5 splice site or branch site. C_LIO_LIPrp40 WW domains enhance stable U1 snRNP and BBP recruitments to nascent transcripts containing non-canonical splice sites. C_LIO_LIA topologically conserved unstructured region between WW and FF domains helps to position Prp40 WW domains close to the 5 splice site. C_LIO_LIThe N-terminal WW domain sterically hinders conformational rearrangements required for efficient release of a BBP variant during spliceosome assembly. C_LIO_LIA reporter assay identified 13 non-canonical introns whose splicing, under various environmental conditions, depend on Prp40 WW domains. C_LI

biochemistry↗

Genome-wide screen uncovers novel host factors for L-A virus maintenance and a mutualistic-symbiosis relationship in yeast

Viruses are often regarded as obligate intracellular parasites that exploit host resources for their own propagation. However, emerging evidence suggests that virus-host interactions can be more complex than simple antagonism. Here, we performed a genome-wide screen in Saccharomyces cerevisiae to identify host factors required for the maintenance of the L-A double-stranded RNA virus, a persistent and non-lytic resident of most laboratory yeast strains. Using two complementary mutant collections encompassing [~]6,000 yeast genes ([~]93% genome coverage), we identified 96 host genes essential for L-A maintenance, spanning diverse biological functions. Transcriptome profiling revealed that the presence of L-A virus alters the host stress-response gene expression program. Strikingly, competitive fitness assays under environmental stress conditions showed that L-A enhances host stress tolerance, revealing a previously unrecognized mutualistic relationship. Together, our findings redefine the L-A-yeast interaction as a form of stable mutualism and highlight the utility of functional genomics and systems-level approaches in uncovering hidden dimensions of virus-host coevolution. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/655038v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@4bfa69org.highwire.dtl.DTLVardef@25205forg.highwire.dtl.DTLVardef@1703f19org.highwire.dtl.DTLVardef@3e9375_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

Spatial Expression of Long Non-Coding RNAs in Human Brains of Alzheimer's Disease

BackgroundLong non-coding RNAs (lncRNAs) are critical regulators of physiological and pathological processes, with their dysregulation increasingly implicated in aging and Alzheimers disease (AD). To investigate the spatial and cellular distribution of lncRNAs in the aging brain, we leveraged published spatial transcriptomics (ST), single-nucleus RNA sequencing (snRNA-seq), and bulk RNA-seq datasets from the dorsolateral prefrontal cortex (DLPFC) of ROSMAP participants with and without pathological AD. ResultsLncRNAs exhibited greater subregion-specific expression than mRNAs, with enrichment in antisense and lincRNA biotypes. Subregion-enriched lncRNAs were generally not cell-type specific, and vice versa. Differential expression analysis of ST data identified AD-associated lncRNAs with distinct spatial patterns and moderate overlap with differentially expressed (DE) lncRNAs from bulk RNA-seq. Gene set enrichment revealed their involvement in chromatin remodeling, epigenetic regulation, and RNA metabolism. We also identified AD DE lncRNAs across major brain cell types using snRNA-seq but overlap with ST DE lncRNAs was limited. Among previously reported lncRNAs, OIP5-AS1 was consistently upregulated in AD in all cortical subregions. Antisense oligonucleotide (ASO) knockdown of OIP5-AS1 in iPSC-derived microglia led to upregulation of pro-inflammatory genes and downregulation of DNA replication and repair pathways. Immunoassays confirmed increased secretion of pro-inflammatory cytokines. The knockdown expression pattern was enriched for microglia-specific AD DE genes and microglia states. ConclusionsThis study provides a spatial and cellular map of lncRNAs in the aging human cortex and identifies subregion-and cell-type-enriched DE lncRNAs in AD. Our findings implicate OIP5-AS1 in microglial activation, suggesting its potential contribution to AD pathogenesis.

neuroscience↗

Structural basis of Norrin recognition by Lgr4/5/6

Lgr4/5/6 have been identified as stem cell markers and canonical Wnt signalling enhancers via complexing with R-spondin and Rnf43/Znrf3. Lgr4/5/6 have been reported to interact with Norrin, a cystine-knot growth factor that activates Wnt signalling via binding to Frizzled4 cysteine-rich domain (Fz4CRD). Norrin-Fz4 signalling axis regulates central nervous system vascularization. However, the molecular basis of Norrin and Lgr4/5/6 recognition remains lacking. Here, we present the structure of Norrin in complex with an ectodomain variant of Lgr4 (Norrin-Lgr4ECD), revealing a 2:2 stoichiometry. Our analyses show that residues of Lgr4/5/6ECD for Norrin binding are highly conserved. Structural comparisons of Norrin-Lgr4ECD with Rspo1- Lgr4ECD and Norrin-Fz4CRD complexes reveal that Norrin binding site on Lgr4 overlaps with Rspo1 binding site on Lgr4 and Fz4 binding site on Norrin overlaps with Lgr4 binding site on Norrin. The present work opens new avenues to elucidate the function of Norrin-Lgr4/5/6 signalling axis.

biochemistry↗

Structural insights into Frizzled assembly by acylated Wnt and Frizzled Connector domain

Frizzled (Fz1-10) serve as the principal cell surface receptors for Wnt signalling. Aberrant expression of Fz is associated with cancer and neurodegeneration. The N-terminal extracellular domains of Fz include Cysteine-Rich Domain (CRD), Connector, and Linker. How the palmitoleate moiety (PAM) modified Wnt bound to Fz transduces the extracellular signal across the membrane remains incomplete. Here, we report the structures of Fz4 CRD and Connector (Fz4CRD-Connector), in complex with PAM modified Wnt7a peptide (PAM peptide). Fz4CRD-Connector structures reveal an open-form of dimer - a flat-shaped hydrophobic groove to accommodate one PAM peptide at the dimer interface. Interestingly, the structure of Fz7CRD bound to PAM peptide shows a dimeric closed-form - a curved-shaped hydrophobic groove at the dimer interface for one PAM peptide bound. We also reveal that Fz4Connector has extensive interactions with Fz4CRD and contributes to the Fz4 function. The studies shed insight on the development of novel strategies to modulate Fz function.

biochemistry↗

Chitin oligomers directly promote lymphoid innate and adaptive immune cell activation

BackgroundChitin is a highly abundant N-acetyl-glucosamine (GlcNAc) polysaccharide which has been linked to immune responses in the context of fungal infections and allergic asthma, especially T helper 2 (Th2) immune responses. Unfortunately, due to the frequent use of crude chitin preparations of unknown purity and degree of polymerization there is still great uncertainty how chitin activates different parts of the human immune system. ObjectiveWe recently identified chitin oligomers of six GlcNAc units as the smallest immunologically active chitin motif and the innate immune receptor TLR2 as primary chitin sensor on human and murine myeloid cells, but the response of lymphoid cells to oligomeric chitin has not been investigated and was addressed here. MethodsFlow cytometric analysis of primary human immune cells upon stimulation with oligomeric chitin. For detailed Methods, please see the Methods section in this articles Online Repository at www.jacionline.org. ResultHere we report that chitin oligomers also activate immune responses by both primary lymphoid innate and adaptive immune cells: Notably, chitin oligomers activated Natural Killer (NK) cells and B lymphocytes. Moreover, the maturation of dendritic cells enabled CD8 T cell recall responses. ConclusionsOur results suggest that chitin oligomers not only trigger immediate innate responses in limited range of myeloid cells but exert critical activities across the entire human immune system. Key messagesChitin oligomers are microbe-associated molecular patterns involved in TLR2-dependent fungal recognition by myeloid immune cells. Here we show that lymphoid cells, most notably Natural Killer (NK) cells and B cells, are activated by oligomeric chitin. Oligomeric chitin also promotes antigen-presenting cell (APC) maturation and CD8 T cell recall responses. Capsule summaryOligomeric chitin is a novel microbe-associated molecular patterns involved in TLR2-dependent fungal recognition by myeloid innate immune cells. Here we show that lymphoid innate and adaptive immune responses are also promoted by oligomeric chitin.

immunology↗

Transkingdom mechanism of MAMP generation by chitotriosidase (CHIT1) feeds oligomeric chitin from fungal pathogens and allergens into TLR2-mediated innate immune sensing

Chitin is a highly abundant polysaccharide in nature and linked to immune recognition of fungal infections and asthma in humans. Ubiquitous in fungi and insects, chitin is absent in mammals and plants and, thus, represents a microbe-associated molecular pattern (MAMP). However, the highly polymeric chitin is insoluble, which potentially hampers recognition by host immune sensors. In plants, secreted chitinases degrade polymeric chitin into diffusible oligomers, which are fed to innate immune receptors and co-receptors. In human and murine immune cells, a similar enzymatic activity was shown for human chitotriosidase (CHIT1) and oligomeric chitin is sensed via an innate immune receptor, Toll-like receptor (TLR) 2. However, a complete system of generating MAMPs from chitin and feeding them into a specific receptor/co-receptor-aided sensing mechanism has remained unknown in mammals. Here, we show that the secreted chitinolytic host enzyme, CHIT1, converts inert polymeric chitin into diffusible oligomers that can be sensed by TLR1-TLR2 co-receptor/receptor heterodimers, a process promoted by the lipopolysaccharide binding protein (LBP) and CD14. Furthermore, we observed that Chit1 is induced via the {beta}-glucan receptor Dectin-1 upon direct contact of immortalized human macrophages to the fungal pathogen Candida albicans, whereas the defined fungal secreted aspartyl proteases, Sap2 and Sap6, from C. albicans were able to degrade CHIT1 in vitro. Our study shows the existence of an inducible system of MAMP generation in the human host that enables contact-independent immune activation by diffusible MAMP ligands with striking similarity to the plant kingdom. Moreover, this study highlights CHIT1 as a potential therapeutic target for TLR2-mediated inflammatory processes that are fueled by oligomeric chitin.

immunology↗

Structure of the Shaker Kv channel and mechanism of slow C-type inactivation

Voltage-activated potassium (Kv) channels open upon membrane depolarization and proceed to spontaneously inactivate. Inactivation controls neuronal firing rates and serves as a form of short-term memory, and is implicated in various human neurological disorders. Here, we use high-resolution cryo-electron microscopy and computer simulations to determine one of the molecular mechanisms underlying this physiologically crucial process. Structures of the activated Shaker Kv channel and of its W434F mutant in lipid bilayers demonstrate that C-type inactivation entails the dilation of the ion selectivity filter, and the repositioning of neighboring residues known to be functionally critical. Microsecond-scale molecular dynamics trajectories confirm these changes inhibit rapid ion permeation through the channel. This long-sought breakthrough establishes how eukaryotic K+ channels self-regulate their functional state through the plasticity of their selectivity filters. One-Sentence SummaryStructures of the Shaker Kv channel reveal the mechanism of slow C-type inactivation involves dilation of the selectivity filter.

biophysics↗

Antibody Display of cell surface receptor Tetraspanin12 and SARS-CoV-2 spike protein

In previous work, Hsieh and Higgins presented a novel structure of antibodies identified from malaria-exposed individuals, in which the extracellular immunoglobulin (Ig)-like domain of leukocyte-associated immunoglobulin-like receptor 1 (LAIR1) is presented on the third complementarity determining regions (CDR3) of the Ig heavy chain. Here we develop an Antibody Display technology based on this LAIR1-containing antibody, by grafting proteins of interest (POI) onto the heavy chain CDR3 while retaining the biological properties of the POI. As a proof of principle, we displayed the second extracellular domain of Tetraspanin12 (Tspan12EC2) and the receptor-binding domain (RBD) of SARS-CoV-2 spike protein on the heavy chain CDR3. Our data revealed that Antibody Display Tspan12EC2 bound to Norrie Disease Protein (Norrin) and Antibody Display SARS-CoV-2 RBD bound to angiotensin-converting enzyme 2 (ACE2) and neutralizing nanobodies. Collectively, Antibody Display technology offers the general strategy of designing novel antibodies by grafting POI onto the CDR3.

bioengineering↗

An all-solid-state heterojunction oxide transistor for the rapid detection of biomolecules and SARS-CoV-2 spike S1 protein

Solid-state transistor sensors that can detect biomolecules in real time are highly attractive for emerging bioanalytical applications. However, combining cost-effective manufacturing with high sensitivity, specificity and fast sensing response, remains challenging. Here we develop low-temperature solution-processed In2O3/ZnO heterojunction transistors featuring a geometrically engineered tri-channel architecture for rapid real-time detection of different biomolecules. The sensor combines a high electron mobility channel, attributed to the quasi-two-dimensional electron gas (q2DEG) at the buried In2O3/ZnO heterointerface, in close proximity to a sensing surface featuring tethered analyte receptors. The unusual tri-channel design enables strong coupling between the buried q2DEG and the minute electronic perturbations occurring during receptor-analyte interactions allowing for robust, real-time detection of biomolecules down to attomolar (aM) concentrations. By functionalizing the tri-channel surface with SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) antibody receptors, we demonstrate real-time detection of the SARS-CoV-2 spike S1 protein down to attomolar concentrations in under two minutes.

bioengineering↗

Degenerated virulence and irregular development of Fusarium oxysporum f. sp. niveum induced by successive subculture

Successive cultivation of fungus has been reported to cause the sectorization, which leads to degeneration of developmental phenotype, and virulence. Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon Fusarium wilt, demonstrated that successive cultivation formed the degenerated sectors. In the present research, we demonstrated that subculture with aged mycelium increased the incidence of degenerations. To further investigate the differences between the Fon wild type (sporodochial type, ST) and variants (MT: mycelium type and PT: pionnotal type), developmental phenotypes and pathogenicity to watermelon were examined. Results have shown that degeneration variants (PT2, PT3, PT11 and MT6) were different from ST with mycelium growth, conidia production and chlamydospore formation. Virulence of degenerated variants on susceptible watermelon Grand Baby (GB) cultivar was determined after inoculated with Fon variants and Fon ST. In root dipping methods, all Fon variants showed slightly increased disease severity than ST. Conversely, all Fon variants showed a significant decrease in disease progression compared with ST through infested soil inoculation. The contrary results of two inoculation methods suggest that the changes of successive cultural degeneration may lead to the loss of pathogen virulence-related factors of the early stage of Fon infection process. Therefore, Cell wall-degrading enzymes (CWDEs; cellulase, pectinase, and xylanase) activities of different variants were analysed. All Fon degenerated variants demonstrated significantly decreased of CWDEs activities compared with ST. Additionally, transcripts level of 9 virulence-related genes (fmk1, fgb1, pacC, xlnR, pl1, rho1, gas1, wc1 and fow1) were assessed in normal state. The degenerated variants demonstrated a significantly low level of tested virulence-related genes transcripts except for fmk1, xlnR and fow1. In summary, the degeneration of Fon is triggered with successive subculture through aged mycelium. The degeneration showed significant impacts on virulence to watermelon, which caused by the reduction of CWDEs activities and declining expression of a set of virulence-related genes.

microbiology↗

Rapidly predicting vancomycin resistance of Enterococcus faecium through MALDI-TOF MS spectra obtained in real-world clinical microbiology laboratory

Enterococcus faecium is one of the leading pathogens in the world. In this study, we proposed a strategy to rapidly and accurately distinguish vancomycin-resistant Enterococcus faecium (VREfm) and vancomycin-susceptible E. faecium (VSEfm) to help doctors correctly determine the use of vancomycin by a machine learning (ML)-based algorithm. A predictive model was developed and validated to distinguish VREfm and VSEfm by analyzing MALDI-TOF MS spectra of unique E. faecium isolates from different specimen types. Firstly, 5717 mass spectra, including 2795 VREfm and 2922 VSEfm, were used to develop the algorithm. And 2280 mass spectra of isolates, namely 1222 VREfm and 1058 VSEfm, were used to externally validate the algorithm. The random forest-based algorithm demonstrated good classification performances for overall specimens, whose mean AUROC in 5-fold cross validation, time-wise validation, and external validation was all greater than 0.84. For the detection of VREfm in blood, sterile body fluid, urinary tract, and wound, the AUROC in external validation was also greater than 0.84. The predictions with algorithms were significantly more accurate than empirical antibiotic use. The accuracy of antibiotics administration could be improved by 30%. And the algorithm could provide rapid antibiotic susceptibility results at least 24 hours ahead of routine laboratory tests. The turn-around-time of antibiotic susceptibility could be reduced by 50%. In conclusion, a ML algorithm using MALDI-TOF MS spectra obtained in routine workflow accurately differentiated VREfm from VSEfm, especially in blood and sterile body fluid, which can be applied to facilitate the clinical testing process due to its accuracy, generalizability, and rapidness.

microbiology↗

The Avocado Genome Informs Deep Angiosperm Phylogeny, Highlights Introgressive Hybridization, and Reveals Pathogen Influenced Gene Space Adaptation

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently-diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that [~]39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced two lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent \"tuning knobs\" in the genome adaptive landscapes of given species.\n\nSIGNIFICANCE STATEMENTAvocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings, the admixed nature of Hass, and provide a look at how pathogen interactions have shaped avocados more recent genomic evolutionary history.

genomics↗

Bloodstream Infection with Extended-spectrum Beta-lactamase-producing Escherichia coli: the role of virulence genes

BackgroundVarious bacterial putative virulence factors are involved in the pathogenesis of bacterial infection. However, the effect of comorbidities or infection syndrome in the association of virulence factors and mortality remains inconclusive.\n\nMethodThis study addressed whether specific sequence type (ST) and virulence factors of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) are associated with different outcomes in patients with bloodstream infection.121 adults from southern Taiwan with ESBL-producing E. coli bloodstream infections were enrolled during a 6-year period. Demographic data, including infection syndromes, underlying disease and outcomes, were collected. The virulence factors in isolates were analyzed by PCR and multilocus sequence typing.\n\nResultPositivity for the virulence genes iha, hlyD, sat, iut, fyu, malX, ompT, usp and traT was associated with ST131 positivity (P<0.05). Some ESBL-EC virulence genes associated with urinary tract infection (UTI) were revealed. Positivity for ST405 and the virulence genes iroN and iss was significantly associated with increased 30-day mortality (death within 30 days) on univariate analysis (P<0.05). Independent risk factors of 30-day mortality in bacteremic patients with UTI included underlying chronic liver disease and malignancy. ST131 was borderline associated with 30-day mortality. Independent risk factors associated with 30-day mortality among bacteremic patients without UTI included comorbidities and iroN positivity.\n\nConclusionIn bacteremic patients with UTI, and the ST131 clone was borderline associated with mortality. Positivity for the virulence gene iroN may be linked to mortality in bacteremic patients without UTI.

microbiology↗