Machine learning to support citizen science in urban environmental management

Machine learning (ML) and citizen science (CS) are increasingly prevalent and rapidly evolving approaches to studying and managing environmental challenges. Municipal and other governance actors can benefit from technology advances in ML and public engagement benefits of CS but must also address validity and other quality assurance concerns in their application to particular management contexts. In this article, we take up the pervasive challenge of urban litter to demonstrate how ML can support CS by providing quality assurance in the regulatory context of California's stormwater program. We gave quantitative CS-collected data to five ML models to compare their predictions of a qualitative, site-specific, multiclass "Litter Index" score, an important regulatory metric typically only assessed by trained experts. XGBoost had the best outcome, with scores of 0.98 for accuracy, precision, recall and F-1. These strong results show that ML can provide a reliable complement to CS assessments and increase quality assurance in a regulatory context. To date, ML and CS have each contributed to litter management in novel ways and we find that their integration can provide important synergies with additional applications in other environmental management domains.

Enrichment of aging yeast cells and budding polarity assay in Saccharomyces cerevisiae

Replicative lifespan, a measure of the number of times that a yeast cell can divide before senescence, is one model for aging. Here, we provide a protocol for enrichment of yeast as a function of replicative age using a miniature chemostat aging device (mCAD). This protocol allows for isolation of quantities of cells that are sufficient for biochemical or genomic analysis. We also describe an approach to assess bud site selection, a marker for cell polarity, during the aging process.

For complete details on the use and execution of this protocol, please refer to Yang et al. (2022).

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Step-by-step protocol to assemble a mini-chemostat aging device (mCAD)

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Protocol to use the mCAD to isolate yeast as a function of replicative age

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Characterization of basic aging phenotypes of cells isolated using the mCAD

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Protocol to analyze budding polarity in young and old yeast cells

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Touch and Go: Membrane Contact Sites Between Lipid Droplets and Other Organelles

Lipid droplets (LDs) have emerged not just as storage sites for lipids but as central regulators of metabolism and organelle quality control. These critical functions are achieved, in part, at membrane contact sites (MCS) between LDs and other organelles. MCS are sites of transfer of cellular constituents to or from LDs for energy mobilization in response to nutrient limitations, as well as LD biogenesis, expansion and autophagy. Here, we describe recent findings on the mechanisms underlying the formation and function of MCS between LDs and mitochondria, ER and lysosomes/vacuoles and the role of the cytoskeleton in promoting LD MCS through its function in LD movement and distribution in response to environmental cues.

Imaging the Actin Cytoskeleton in Live Budding Yeast Cells

Although budding yeast, Saccharomyces cerevisiae, is widely used as a model organism in biological research, studying cell biology in yeast was hindered due to its small size, rounded morphology, and cell wall. However, with improved techniques, researchers can acquire high-resolution images and carry out rapid multidimensional analysis of a yeast cell. As a result, imaging in yeast has emerged as an important tool to study cytoskeletal organization, function, and dynamics. This chapter describes techniques and approaches for visualizing the actin cytoskeleton in live yeast cells.

Live-Cell Imaging of Mitochondrial Redox State in Yeast Cells

The redox state of mitochondria is one indicator of the functional state of the organelles. Mitochondria are also the primary endogenous source of reactive oxygen species (ROS). Therefore, the redox state of the organelles also reflects their function in ROS production. Here, we provide step-by-step protocols for live-cell imaging and quantification of mitochondrial redox state using the genetically encoded fluorescent biosensor, mitochondria-targeted redox sensing GFP (mito-roGFP), and mitochondrial ROS using the membrane-permeant small molecule dihydroethidium (DHE) in budding yeast cells.

For complete details on the use and execution of this protocol, please refer to Liao et al. (2020c).

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Protocols for analysis of mitochondrial redox state and ROS in S. cerevisiae

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Analysis is performed in living cells at the resolution of individual organelles

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Methods for analysis using commercial and open-source software are provided

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These protocols can be adapted for use in other cell types

NCP activates chloroplast transcription by controlling phytochrome-dependent dual nuclear and plastidial switches

Phytochromes initiate chloroplast biogenesis by activating genes encoding the photosynthetic apparatus, including photosynthesis-associated plastid-encoded genes (PhAPGs). PhAPGs are transcribed by a bacterial-type RNA polymerase (PEP), but how phytochromes in the nucleus activate chloroplast gene expression remains enigmatic. We report here a forward genetic screen in Arabidopsis that identified NUCLEAR CONTROL OF PEP ACTIVITY (NCP) as a necessary component of phytochrome signaling for PhAPG activation. NCP is dual-targeted to plastids and the nucleus. While nuclear NCP mediates the degradation of two repressors of chloroplast biogenesis, PIF1 and PIF3, NCP in plastids promotes the assembly of the PEP complex for PhAPG transcription. NCP and its paralog RCB are non-catalytic thioredoxin-like proteins that diverged in seed plants to adopt nonredundant functions in phytochrome signaling. These results support a model in which phytochromes control PhAPG expression through light-dependent double nuclear and plastidial switches that are linked by evolutionarily conserved and dual-localized regulatory proteins.

Phytochrome signaling in the nucleus can activate expression of photosynthesis-associated genes in plastids. Here Yang et al. show that NCP is a dual-targeted protein that promotes phytochrome B localization to photobodies in the nucleus while facilitating PEP polymerase assembly in the plastids.

Recalcitrant anal and genital pruritus treated with dupilumab

Chronic anogenital pruritus can significantly impair affected patients’ quality of life by disrupting their sleep, mood, sexual function, and personal relationships. Although a significant portion of these patients can be managed with hygiene measures, topical therapy, oral anti-pruritics, and allergen avoidance after patch testing, guidelines to treat patients who do not respond to standard therapy have yet to be established. We describe the therapeutic response of a case of anogenital pruritus recalcitrant to multiple topical and systemic therapies. Treatment of this patient with dupilumab, an interleukin-4 receptor alpha blocker, resulted in clinical remission at 1 year from the initiation of the therapy, without significant adverse effects.

Purification and characterization of antifungal δ-dodecalactone from Lactobacillus plantarum AF1 isolated from kimchi

The aim of this study was to purify and identify an antifungal compound from Lactobacillus plantarum AF1, which was isolated from kimchi. The antifungal compound was purified by solid-phase extraction and recycling preparative high-performance liquid chromatography, and its structure was elucidated by using gas chromatography-mass spectrometry (GC-MS). The active compound from L. plantarum AF1 was confirmed to be δ-dodecalactone (molecular weight, 198.3) by comparison of its gas chromatographic retention time with the mass spectrum of standard δ-dodecalactone. The MICs of δ-dodecalactone against various fungi and bacteria ranged from 350 to 6,250 m g/ml. δ-Dodecalactone showed strong antifungal activity against molds Aspergillus flavus, A. fumigatus, A. petrakii, A. ochraceus, A. nidulans, and Penicillium roqueforti. The three tested yeast strains of Candida albicans were more resistant than the molds. Antibacterial activity was evident but less potent than the antifungal activity. δ-Dodecalactone produced pleasurable (fruity) organoleptic characteristics. The results indicate the potential of the δ-dodecalactone produced by L. plantarum AF1 as a biopreservative and flavoring compound, as well as a biosafe remedy for candidiasis.

Purification of a new antifungal compound produced by Lactobacillus plantarum AF1 isolated from kimchi

The aim of this study was to purify and to identify an antifungal compound of Lactobacillus plantarum AF1, which was isolated from kimchi, and to determine if Lb. plantarum AF1 can prevent fungal growth in a particular food model system. The antifungal compound was purified using SPE and recycling prep-HPLC and its structure was elucidated using NMR and ESI-MS. The active compound from Lb. plantarum AF1 is C(12)H(22)N(2)O(2), 3,6-bis(2-methylpropyl)-2,5-piperazinedion has a molecular mass of 226. This is a new antifungal compound produced by lactic acid bacteria (LAB). To investigate the potential application of the antifungal compound to eliminate fungal spoilage in food and feed, soybean was used as a model. White mycelia and dark green spores of Aspergillus flavus ATCC 22546 were observed in the control soybeans after 1 to 2days incubation. However, fungal growth was not observed in the soybeans treated with a 4-fold concentrated supernatant of Lb. plantarum AF1 culture, even after 2days. The end products produced from kimchi LAB, like 3,6-bis(2-methylpropyl)-2,5-piperazinedion identified in this study, may be a promising alternative to chemical preservatives as a potential biopreservative which prevent fungal spoilage and mycotoxin formation in food and feed.

Protein kinase Dyrk1 activates cAMP response element-binding protein during neuronal differentiation in hippocampal progenitor cells

Dyrk is a dual specific protein kinase thought to be involved in normal embryo neurogenesis and brain development. Defects/imperfections in this kinase have been suggested to play an important role in the mental retardation of patients with Down's syndrome. The transcriptional factor cAMP response element-binding protein (CREB) has been implicated in the formation of many types of synaptic plasticity, such as learning and memory. In the present study we show that Dyrk1 activity is markedly induced during the differentiation of immortalized hippocampal progenitor (H19-7) cells. The addition of a neurogenic factor, basic fibroblast growth factor, to the H19-7 cells results in an increased specific binding of Dyrk1 to active CREB. In addition, Dyrk1 directly phosphorylates CREB, leading to the stimulation of subsequent CRE-mediated gene transcription during the neuronal differentiation in H19-7 cells. Blockade of Dyrk1 activation significantly inhibits the neurite outgrowth as well as CREB phosphorylation induced by basic fibroblast growth factor. These findings suggest that Dyrk1 activation and subsequent CREB phosphorylation is important in the neuronal differentiation of central nervous system hippocampal cells.

Expression and detection of ScFvB9 and its mutant in recombinant phage antibody system

Recombinant single-chain antibody (ScFvB9) and its mutant (ScFvB9-6) were generated by using a polymerase chain reaction (PCR) from the Fab fragment of the murine monoclonal antibody (MAb) B9, MabB9 (gamma2b,kappa), which is specific for human plasma apolipoprotein (apo) B-100 of low density lipopreotein (LDL). In the recombinant phage antibody system (RPAS), the constructed ScFvB9 and ScFvB9-6 antibody genes were cloned into the pCANTAB5E phagemid vector and expressed in E. coli. The active forms of single-chain antibodies (ScFvB9 and ScFvB9-6) were produced as phage-displayed recombinant antibodies or soluble antibody forms in E. coli. The activities of ScFvB9 and ScFvB9-6 were confirmed by enzyme-linked immunosorbent assay (ELISA) and Western blotting analysis; the generated mutant ScFvB9-6 showed slightly higher antigen binding activity than native ScFvB9 as a soluble antibody in this RPAS.

Suppressive effects of Adenophora triphylla extracts on in vitro tumor cell growth and in vivo gastric epithelial proliferation

Adenophora triphylla (AT), an oriental medicinal plant, was extracted using water and several organic solvents and each fraction was assayed for its tumoricidal effects on human Jurkat T cells with 3-(4,5-dimethylthiazolyl)-2,5-diphenyltetrazolium bromide (MTT). The influence on induction of apoptosis and G1 arrest was also examined. The ethyl acetate fraction showed the most pronounced inhibitory effects on proliferation of Jurkat T cells. Apoptosis was induced in line with up-regulation of FasL, tyrosine phosphorylation and c-fos mRNA levels. Arrest in G1 of the cell cycle was observed in A2780 cells with a wild type p53 gene but not HT-29 cells with a mutant p53 gene. Modifying effects of AT on cell turnover and glutathione(GSH) levels in vivo were also investigated in the stomach of rats given 150 mg/kg of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) by gavage and then fed a diet supplemented with 5% or 1% pulverized AT and 0.5% or 0.2% ethylacetate-extracted AT for 42 hours. The 5% AT and both of the ethylacetate fractions caused significant reduction in proliferating cell nuclear antigen (PCNA)-labeling in the glandular stomach epithelium as compared with the value for the MNNG alone group. In addition, the treatments significantly increased the gastric GSH levels. These results suggest that AT could be a chemopreventive agent against gastric cancer.

Alpha1-adrenoceptors involvement in painful diabetic neuropathy: a role in allodynia

To investigate whether alpha1-adrenoceptors are involved in pain behaviors in streptozotocin (STZ)-induced diabetic rats, we measured the effects of phenylephrine or prazosin on allodynia in the diabetic rats. Phenylephrine aggravated allodynia, while prazosin alleviated allodynia in the diabetic rats. We also measured alpha1-adrenoceptors gene expression or density of [3H]-prazosin binding sites in the dorsal root ganglia (DRG) and spinal cord in painful diabetic rats. Alpha1-adrenoceptors mRNA and density of [3H]prazosin binding sites were increased in the DRG of the diabetic rats, however there were no significant differences in alpha1-adrenoceptors expression in the spinal cord between the control and diabetic rats. These results suggest increased alpha1-adrenoceptors in the DRG may play a role in the pathogenesis of painful diabetic neuropathy.