Biology subjects

Huang, W.

Publications and source records attributed to Huang, W..

At least 343 records · Page 19Linked to original sources

bioRxiv2020

AtCIPK16 Mediates Salt Stress Potentially Through Phytohormones and Transcription Factors

Soil salinity causes large productivity losses for agriculture worldwide. "Next-generation crops" that can tolerate salt stress are required for the sustainability of global food production. Previous research in Arabidopsis thaliana aimed at uncovering novel factors underpinning improved plant salinity tolerance identified the protein kinase AtCIPK16. Overexpression of AtCIPK16 enhanced shoot Na+ exclusion and increased biomass in both Arabidopsis and barley. Here, a comparative transcriptomic study on Arabidopsis lines expressing AtCIPK16 was conducted in the presence and absence of salt stress, using an RNA-Seq approach, complemented by AtCIPK16 interaction and localisation studies. We are now able to provide evidence for AtCIPK16 activity in the nucleus. Moreover, the results manifest the involvement of a transcription factor, AtTZF1, phytohormones and the ability to quickly reach homeostasis as components important for improving salinity tolerance in transgenics overexpressing AtCIPK16. Furthermore, we suggest the possibility of both biotic and abiotic tolerance through AtCIPK16, and propose a model for the salt tolerance pathway elicited through AtCIPK16.

plant biology↗

bioRxiv2020

Widespread targeting of development-related host transcription factors by phytoplasma effectors

Phytoplasmas are pathogenic bacteria that reprogram plant host development for their own benefit. Previous studies have characterized a few different phytoplasma effector proteins that destabilize specific plant transcription factors. However, these are only a small fraction of the potential effectors used by phytoplasmas; therefore, the molecular mechanisms through which phytoplasmas modulate their hosts require further investigation. To obtain further insights into the phytoplasma infection mechanisms, we generated a protein-protein interaction network between a broad set of phytoplasma effectors and a large, unbiased collection of Arabidopsis thaliana transcription factors and transcriptional regulators. We found widespread, but specific, interactions between phytoplasma effectors and host transcription factors, especially those related to host developmental processes. In particular, many unrelated effectors target specific sets of TCP transcription factors, which regulate plant development and immunity. Comparison with other host-pathogen protein interaction networks shows that phytoplasma effectors have unusual targets, indicating that phytoplasmas have evolved a unique and unusual infection strategy. This study contributes a rich and solid data source that guides further investigations of the functions of individual effectors, as demonstrated for some herein. Moreover, the dataset provides insights into the underlying molecular mechanisms of phytoplasma infection.

plant biology↗

bioRxiv2020

Association between ocular biometrical parameters and diabetic retinopathy in Chinese adults with type 2 diabetes mellitus

PurposeTo investigate the association between ocular biometrical parameters and diabetic retinopathy (DR) in ocular treatment naive patients with diabetes. MethodsThis cross-sectional study recruited type 2 diabetes mellitus patients with no history of ocular treatment in Guangzhou, China. The ocular biometrical parameters were obtained by Lenstar, including corneal diameter, central corneal thickness (CCT), corneal curvature (CC), anterior chamber depth (ACD), lens thickness (LT), and axial length (AL). The lens power and axial length-to-cornea radius ratio (AL/CR ratio) were calculated. Spherical equivalent (SE) was determined by auto-refraction after pupil dilation. Multivariate logistic regression analyses were performed to explore the associations of ocular biometry with any DR and vision threatening DR (VTDR). ResultsA total of 1838 patients were included in the final analysis, involving 145 5(79.2%) patients without DR and 383(20.8%) patients with DR. After adjusting confounding factors, any DR was independently associated with AL (OR = 0.84 per 1 mm increase, 95%CI: 0.74, 0.94), lens power (OR = 0.9951 per 1 D increase, 95%CI: 0.9904, 0.9998), and AL/CR ratio (OR = 0.26 per 1 increase, 95%CI: 0.10-0.70). Similarly, the presence of VTDR was independently related to AL (OR = 0.67 per 1 mm increase, 95%CI: 0.54-0.85), lens power (OR = 0.99 per 1 D increase, 95%CI: 0.98, 0.997), and AL/CR ratio (OR = 0.04 per 1 increase, 95%CI: 0.01, 0.25). The CC, corneal diameter, and refractive status were not significantly correlated with presence of DR or VTDR. ConclusionLonger AL, deeper ACD, higher lens power, and higher AL/CR ratio may be protective factors against DR. Considering the high prevalence of myopia in the Chinese juvenile population, it is worth paying attention to how the incidence of DR in this generation may change over time.

pathology↗

bioRxiv2020

The influence of insulin therapy on measurements of optical coherence tomography parameters in diabetic patients without retinopathy

PurposeTo determine whether there was a change in the fundus of the eye in diabetic patients without retinopathy after insulin therapy. MethodsThe diabetic patients without retinopathy were included in this study. A swept-source optical coherence tomography/angiography (SS-OCT/A) was used to obtain the measurements of macular retinal nerve fibre layer (mRNFL) thickness, ganglion cell-inner plexiform layer (GC-IPL) thickness, retinal thickness (RT), macular choroidal thickness (MCT), peripapillary retinal nerve fibre layer (pRNFL) thickness, peripapillary choroidal thickness (PCT), and perfused vascular density (PVD). Univariable and multivariable regression analyses were performed to explore the influence of insulin use on measurements of OCT/A. ResultsA total of 1140 patients used insulin (using group), and 126 patients did not use insulin (without group). The average MCT of the using group was 171.3{+/-}67.8 m, which was thinner than that in the without group (190.2{+/-}74.7 m) (P=0.012). The average PVD of the using group (48.0{+/-}2.1 m) was less than that in the without group (48.7{+/-}2.1 m) (P<0.001). After adjusting for age, gender, axial length, duration, HbA1c, systolic blood pressure, diastolic blood pressure, cholesterol, serum creatinine, insulin use was significantly associated with thinner MCT (beta=-16.12m; 95%CI:-29.42, -2.81m; P= 0.018) and lower PVD (beta=-0.79; 95%CI: -1.22, -0.36; P<0.001). ConclusionThe use of insulin by diabetic patients without retinopathy might decrease the MCT and PVD compared to patients who did not use insulin, which helps to better understanding the role of insulin use on higher risk for diabetic retinopathy.

physiology↗

bioRxiv2020

Species boundaries and molecular markers for classification among 16SrI phytoplasmas informed by genome analysis

Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus Candidatus Phytoplasma and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share <94% ANI and <75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.

genomics↗

bioRxiv2020

Neutralizing PD-L1 and PD-L2 Enhances the Efficacy of Immune Checkpoint Inhibitors in Ovarian Cancer.

Immune checkpoint inhibitors targeting the PD-1/PD-L1 pathway have improved for a number of solid tumors. Unfortunately, ovarian cancer represents a major clinical hurdle for immune checkpoint blockade (ICB) with reported low patient response rates. Using IHC staining, we find that PD-L2 is highly expressed in ovarian cancers and other malignancies with sub-optimal response to ICB, and is expressed at low levels in cancers responsive to ICB. Based on this observation, we hypothesized that the elevated expression of PD-L2 produced by both tumor and surrounding stromal cells contributes to immune-suppression. Since PD-L2 has been reported to have a 6- to10-fold higher native binding affinity to PD-1 compared with PD-L1, we hypothesized that high levels of PD-L2 can lead to insufficient blockade of the PD-1 signaling pathway. To overcome the immune repressive activity of PD-L2, we engineered a soluble PD-1 decoy molecule (sPD-1 mutant) that binds and neutralizes both PD-L1 and PD-L2 with a 10,000- and 200- fold improvement in binding affinity, respectively, when compared to wild-type binding to these same molecules. Such enhancement in binding affinity is facilitated by amino acid mutations both within and outside of the binding interface. Furthermore, this high affinity sPD-1 mutant molecule demonstrates superior in vivo efficacy in multiple cancer models including ovarian cancer where PD-L2 is highly expressed on the cell surface. One Sentence SummaryDual Inhibition of PD-L1 and PD-L2 using an affinity enhanced sPD-1 decoy molecule delivers superior antitumor activity when compared with PD-1 and PD-L1 antibodies in ovarian cancer.

cancer biology↗

bioRxiv2019

An antibody drug conjugate targeting a GSTA glycosite-signature epitope of mucin1 expressed by non-small cell lung cancer

BackgroundAntibodies targeting abnormally glycosylated proteins have been ineffective in treating cancer. Antibody-drug conjugates are emerging as an efficient option, which allow specific delivery of drugs into tumors. We and others have dissected the abnormally glycosylated tandem repeat region of MUC1 glycoprotein as three site-specific glycosylated neoantigen peptide motifs (PDTR, GSTA, GVTS) for monoclonal antibody binding. MethodsInternalization of monoclonal antibodies was studied by immunofluorescence staining and colocalization with lysosomal markers in live cells. Antibody positivity in tumor and peritumoral tissue samples were studied by immunohistochemistry. The efficacy of anti-MUC1 ADCs were evaluated with various cancer cell lines and mouse tumor xenograft model. ResultsWe describe an anti-MUC1 ADC by conjugating GSTA neoantigen-specific 16A with monomethyl auristatin E (MMAE). 16A-MMAE showed potent antitumoral efficacy with IC50 ranging from 0.2 to 49.4 nM toward multiple types of cancer cells. In vivo, 16A-MMAE showed dose-dependent inhibition of tumor growth in mouse xenograft of NCI-H838 NSCLC cell line, with minimum effective dose at 1 mg/kg. At the dose of 3 mg/kg, 16A-MMAE did not cause significant toxicity in a transgenic mouse expressing human MUC1. ConclusionsThe high antitumoral efficacy of 16A-MMAE suggest that aberrant glycosylated MUC1 neoantigen is a target with high positivity in multiple cancer types for ADC development. Personalized therapy may be achieved by development of glycosite-specific antibody-drug conjugates.

pharmacology and toxicology↗

bioRxiv2019

Prostatic osteopontin expression is associated with symptomatic benign prostatic hyperplasia

BackgroundMale lower urinary tract symptoms (LUTS) occur in more than half of men above 50 years of age. LUTS were traditionally attributed to benign prostatic hyperplasia (BPH) and therefore the clinical terminology often use LUTS and BPH interchangeably. More recently, LUTS were also linked to fibrogenic and inflammatory processes. We tested whether osteopontin (OPN), a pro-inflammatory and pro-fibrotic molecule, is increased in symptomatic BPH. We also tested whether prostate epithelial and stromal cells secrete OPN in response to pro-inflammatory stimuli and identified downstream targets of OPN in prostate stromal cells. MethodsImmunohistochemistry was performed on prostate sections obtained from the transition zone (TZ) of patients who underwent surgery (Holmium laser enucleation of the prostate) to relieve LUTS i.e. surgical BPH (S-BPH) or patients who underwent radical prostatectomy to remove low-grade prostate cancer (incidental BPH, I-BPH). Images of stained tissue sections were captured with a Nuance Multispectral Imaging system and histoscore, as a measure of OPN staining intensity, was determined with inForm software. OPN protein abundance was determined by Western blot. The ability of prostate cells to secrete osteopontin in response to IL-1{beta} and TGF-{beta}1 was determined in stromal (BHPrS-1) and epithelial (NHPrE-1 and BHPrE-1) cells by ELISA. qPCR was used to measure gene expression changes in these cells in response to OPN. ResultsOPN immunostaining (p=0.0107) and protein levels were more abundant in S-BPH than I-BPH. Staining was distributed across all cell types with highest levels in epithelial cells. Multiple OPN protein variants were identified in immortalized prostate stromal and epithelial cells. TGF-{beta}1 stimulated OPN secretion by NHPrE-1 cells and both IL-1{beta} and TGF-{beta}1 stimulated OPN secretion by BHPrS-1 cells. Interestingly, recombinant OPN increased the mRNA expression of CXCL1, CXCL2, CXCL8, PTGS2 and IL6 in BHPrS-1, but not in epithelial cell lines. ConclusionsOPN is more abundant in prostates of men with S-BPH compared to men with I-BPH. OPN secretion is stimulated by pro-inflammatory cytokines, and OPN acts directly on stromal cells to drive the synthesis of pro-inflammatory mRNAs. Pharmacological manipulation of prostatic OPN may have the potential to reduce LUTS by inhibiting both inflammatory and fibrotic pathways.

pathology↗

bioRxiv2019

Stochastic dynamics of extra-chromosomal DNA

Nuclear extra-chromosomal DNA (ecDNA) is highly prevalent in human tumours. ecDNA amplifications can promote accessible chromatin, oncogen over-expression and imply a worse clinical prognosis. Yet, little is known about the evolutionary process of ecDNA in human cancers. Here, we develop the theoretical foundation of the ecDNA somatic evolutionary process combining mathematical, computational and experimental approaches. We show that random ecDNA segregation leads to unintuitive dynamics even if ecDNA is under very strong positive selection. Patterns of inter- and intra-tumour ecDNA and chromosomal heterogeneity differ markedly and standard approaches are not directly applicable to quantify ecDNA evolution. We show that evolutionary informed modelling leads to testable predictions on how to distinguish positively selected from neutral ecDNA dynamics. Our predictions describe the dynamics of circular amplicons in GBM39 cell line experiments, suggesting a 300% fitness increase due to circular extra-chromosomal EGFRvIII amplifications. Our work lies the basis for further studies to quantitate ecDNA somatic evolutionary processes.

cancer biology↗

bioRxiv2019

Leveraging multiple layers of data to predict Drosophila complex traits

An important challenge in genetics is to be able to predict complex traits accurately. Despite recent advances, prediction accuracy for most complex traits remains low. Here, we used the Drosophila Genetic Reference Panel (DGRP), a collection of 200 lines with whole-genome sequences and deep RNA sequencing data, to evaluate the usefulness of using high-quality gene expression levels compared to relying on genotypes for predicting three complex traits. We found that expression levels provided higher accuracy than genotypes for starvation resistance, similar accuracy for chill coma recovery, and lower accuracy for startle response. Models including both genotype and expressions levels did not outperform the best single component model. However, accuracy increased considerably for all the three traits when we included another layer of information, i.e., gene ontology (GO). We found that a limited number of GO terms, some of which had a clear biological interpretation, were strongly predictive of the traits. In summary, this study shows that integrating different sources of information can improve prediction accuracy, especially when large samples are not available.

genetics↗

bioRxiv2019

Gene Expression Networks in the Drosophila Genetic Reference Panel

A major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences, and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, and genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.

genomics↗

bioRxiv2019

Genetic encoding of targeted MRI contrast agents for in vivo tumor imaging

Tumor-selective contrast agents have the potential to aid in the diagnosis and treatment of cancer using noninvasive imaging modalities such as magnetic resonance imaging (MRI). Such contrast agents can consist of magnetic nanoparticles incorporating functionalities that respond to cues specific to tumor environments. Genetically engineering magnetotactic bacteria to display peptides has been investigated as a means to produce contrast agents that combine the robust image contrast effects of magnetosomes with transgenic targeting peptides displayed on their surface. This work reports the first use of magnetic nanoparticles that display genetically-encoded pH low insertion peptide (pHLIP), a long peptide intended to enhance MRI contrast by targeting the extracellular acidity associated with the tumors. To demonstrate the modularity of this versatile platform to incorporate diverse targeting ligands by genetic engineering, we also incorporated the cyclic v integrin-binding peptide iRGD into separate magnetosomes. Specifically, we investigate their potential for enhanced binding and tumor imaging both in vitro and in vivo. Our experiments indicate that these tailored magnetosomes retain their magnetic properties, making them well-suited as T2 contrast agents, while exhibiting increased binding compared to wild-type magnetosomes.

synthetic biology↗

bioRxiv2019

Myeloid-secreted BDNF maintains innervation of inguinal adipose in male mice

BackgroundInnervation of adipose tissue is essential for the proper function of this critical metabolic organ. Numerous surgical and chemical denervation studies have demonstrated how maintenance of brain-adipose communication through both sympathetic efferent and sensory afferent nerves helps regulate adipocyte size, cell number, lipolysis, and browning of white adipose tissue. Neurotrophic factors are growth factors that promote neuron survival, regeneration and plasticity, including neurite outgrowth and synapse formation. Peripheral blood immune cells have been shown to be a source of neurotrophic factors in humans and mice. Although a number of immune cells reside in the adipose stromal vascular fraction (SVF), it has remained unclear what roles they play in adipose innervation. We previously demonstrated that adipose immune cells secrete brain derived neurotrophic factor (BDNF). MethodsWe now show that deletion of this neurotrophic factor from the myeloid lineage led to a genetic denervation of inguinal subcutaneous white adipose tissue (scWAT), thereby causing decreased energy expenditure, increased adipose mass, and a blunted UCP1 response to cold stimulation. ResultsWe and others have previously shown that noradrenergic stimulation via cold exposure increases adipose innervation in the inguinal depot. Here we have identified a subset of myeloid cells that home to scWAT upon cold exposure and are Ly6C + CCR2 + Cx3CR1 + monocytes/macrophages that express noradrenergic receptors and BDNF. ConclusionsWe propose that these cold induced neuroimmune cells (CINCs) are key players in maintaining adipose innervation as well as promoting adipose nerve remodeling under noradrenergic stimulation, such as cold exposure.

neuroscience↗

bioRxiv2019

Free fatty acid receptor 4 is a nutrient sensor that resolves inflammation to maintain cardiac homeostasis

BackgroundNon-{-}resolving activation of immune responses is central to the pathogenesis of heart failure (HF). Free fatty acid receptor 4 (Ffar4) is a G-protein coupled receptor (GPR) for medium-and long-chain fatty acids (FA) that regulates metabolism and attenuates inflammation in diabetes and obesity. Here, we tested the hypothesis that Ffar4 functions as a cardioprotective nutrient sensor that resolves inflammation to maintain cardiac homeostasis.\n\nMethodsMice with systemic deletion of Ffar4 (Ffar4KO) were subjected to pressure overload by transverse aortic constriction (TAC). Transcriptome analysis of cardiac myocytes was performed three days post-TAC. Additionally, Ffar4-mediated effects on inflammatory oxylipin production in cardiac myocytes and oxylipin composition in plasma lipoproteins were evaluated.\n\nResultsIn Ffar4KO mice, TAC induced more severe remodeling, identifying an entirely novel cardioprotective role for Ffar4 in the heart. Transcriptome analysis 3-days post-TAC indicated a failure to induce cell death and inflammatory genes in Ffar4KO cardiac myocytes, as well as a specific failure to induce cytoplasmic phospholipase A2 (cPLA2) signaling genes. In cardiac myocytes, Ffar4 signaling through cPLA2-cytochrome p450 {omega}/{omega}-1 hydroxylase induced production of the EPA-derived anti-inflammatory oxylipin 18-hydroxyeicosapentaenoic acid (18-HEPE). Systemically, loss of Ffar4 altered oxylipin content in circulating plasma lipoproteins consistent with a loss of anti-inflammatory oxylipins at baseline, and inability to produce both pro-inflammatory and pro-resolving oxylipins following TAC. Finally, we confirmed that Ffar4 is expressed in human heart and down-regulated in HF.\n\nConclusionsOur results identify a novel function for Ffar4 in the heart as a FA nutrient sensor that resolves inflammation to maintain cardiac homeostasis.

physiology↗

bioRxiv2019

Lyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii

Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance, but is usually with low-grade virulence. Although a mouse model revealed different virulence grades of clinical carbapenem-resistant A. baumannii (CRAB) strains, the genetic basis remains unknown. We collected 61 CRAB isolates from intensive care unit of Shenzhen Peoples Hospital (Shenzhen, China), and analyzed them used whole genome sequencing (WGS), multilocus sequence typing (MLST) and core genome MLST (cgMLST), transmission chain reconstruction and Comparative genomic tools. A mouse pneumonia model was used to confirm the hypervirulent phenotype. Eleven complex types (CT) were identified based on core genome multilocus sequence typing scheme. CT512 showed higher transmissibility and bloodstream infection rates than other CTs. A genomic region Lyb-2-4 was shared by CT512 and CT2092 but not CT2085. The mortality rates of patient infected with CRAB harboring Lyb-2-4 was significantly higher than those infected with CRAB isolates without Lyb-2-4 (77.8% vs 24.5%, p < 0.01). In the mouse model, the survival rates of strains containing the Lyb-2-4 region (LAC-4, 5122 and 2092) were significantly lower than for strains without Lyb-2-4 (7152, 71517, 20859 and ATCC17978). One open reading frame (ORF) was a marker for the presence of Lyb-2-4, and PCR of a segment of this ORF, designated as hvcT, served as a tag for hypervirulent CRAB. Our study should be very useful in advising the clinician to implement medical intervention earlier, and also making the worldwide surveillance of these hypervirulent CRAB strains easier.\n\nIMPORTANCEHypervirulent CRAB strains are expected to pose a threat to human health because infection of these strains is associated with high mortality and multidrug resistance. The rapid hypervirulent CRAB identification assay will facilitate prompt medical intervention. Our findings should provoke surveillance for hypervirulent CRAB strains harboring Lyb-2-4 in other countries. Further research should focus on the mechanism of hypervirulence, the acquisition of this genomic region and the development of control measures to prevent further dissemination.

microbiology↗

bioRxiv2019

ASlive: a database for alternative splicing atlas in livestock animals

We present in this study the development and implementation of a database for alternative splicing atlas in livestock animals (ASlive.org). Alternative splicing is an important biological process whose precision must be tightly regulated during growth and development. Using publicly available RNASeq data sets across many tissues, cell types, and biological conditions totaling 28.6 tera bases, we built a database of alternative splicing events in five major livestock animal species (cattle, sheep, pigs, horses, and chickens). The database contains many types of information on alternative splicing events, including basic information such as genomic locations, genes, and event types, quantitative measurements of alternative splicing in the form of percent spliced in (PSI), overlap with known DNA variants, as well as orthologous events across different lineage groups. This database, the first of its kind in livestock animals, will provide a useful exploratory tool to assist functional annotation of animal genomes.

genomics↗

bioRxiv2019

Sessile growth reveals novel paradigms of Pseudomonas aeruginosa iron-regulated antimicrobial activity against Staphylococcus aureus

Pseudomonas aeruginosa is an opportunistic pathogen that is frequently associated with both acute and chronic infections, the latter of which are often polymicrobial. P. aeruginosa possesses a complex regulatory network that modulates nutrient acquisition and virulence, but our knowledge of these networks is largely based on studies with shaking cultures, which are not likely representative of conditions during infection. Here, we provide proteomic, metabolic, and genetic evidence that regulation by iron, a critical metallo-nutrient, is altered in static P. aeruginosa cultures. We identified type VI secretion as a target of iron regulation in P. aeruginosa in static but not shaking conditions, and we present evidence that this regulation occurs via PrrF sRNA-dependent production of 2-alkyl-4(1H)-quinolone metabolites. We further discovered that iron-regulated interactions between P. aeruginosa and a Gram-positive opportunistic pathogen, Staphylococcus aureus, are mediated by distinct factors in shaking versus static bacterial cultures. These results yield new bacterial iron regulation paradigms and highlight the need to re-define iron homeostasis in static microbial communities.

microbiology↗

bioRxiv2019

Directed robust generation of functional retinal ganglion cells from Muller glia

Glaucoma and optic neuropathies cause progressive and irreversible degeneration of retinal ganglion cells (RGCs) and the optic nerve and are currently without any effective treatment. Previous research into cell replacement therapy of these neurodegenerative diseases has been stalled due to the limited capability for grafted RGCs to integrate into the retina and project properly along the long visual pathway to reach their brain targets. In vivo RGC regeneration would be a promising alternative approach but mammalian retinas lack regenerative capacity even though cold-blood vertebrates such as zebrafish have the full capacity to regenerate a damaged retina using Muller glia (MG) as retinal stem cells. Nevertheless, mammalian MG undergo limited neurogenesis when stimulated by retinal injury. Therefore, a fundamental question that remains to be answered is whether MG can be induced to efficiently regenerate functional RGCs for vision restoration in mammals. Here we show that without stimulating proliferation, the transcription factor (TF) Math5 together with a Brn3 TF family member are able to reprogram mature mouse MG into RGCs with exceedingly high efficiency while either alone has no or limited capacity. The reprogrammed RGCs extend long axons that make appropriate intra-retinal and extra-retinal projections through the entire visual pathway including the optic nerve, optic chiasm and optic tract to innervate both image-forming and non-image-forming brain targets. They exhibit typical neuronal electrophysiological properties and improve visual responses in two glaucoma mouse models: Brn3b null mutant mice and mice with the optic nerve crushed (ONC). Together, our data provide evidence that mammalian MG can be reprogrammed by defined TFs to achieve robust in vivo regeneration of functional RGCs as well as a promising new therapeutic approach to restore vision to patients with glaucoma and other optic neuropathies.

neuroscience↗