Mov Disord. 2023 Apr;38(4):714-715. doi: 10.1002/mds.29353.

NO ABSTRACT

PMID:37061880 | DOI:10.1002/mds.29353

Plant Physiol. 2023 Apr 15:kiad225. doi: 10.1093/plphys/kiad225. Online ahead of print.

NO ABSTRACT

PMID:37061831 | DOI:10.1093/plphys/kiad225

Antimicrob Resist Infect Control. 2023 Apr 15;12(1):33. doi: 10.1186/s13756-023-01236-w.

ABSTRACT

BACKGROUND: Hospitals with their high antimicrobial selection pressure represent the presumably most important reservoir of multidrug-resistant human pathogens. Antibiotics administered in the course of treatment are excreted and discharged into the wastewater system. Not only in patients, but also in the sewers, antimicrobial substances exert selection pressure on existing bacteria and promote the emergence and dissemination of multidrug-resistant clones. In previous studies, two main clusters were identified in all sections of the hospital wastewater network that was investigated, one K. pneumoniae ST147 cluster encoding NDM- and OXA-48 carbapenemases and one VIM-encoding P. aeruginosa ST823 cluster. In the current study, we investigated if NDM- and OXA-48-encoding K. pneumoniae and VIM-encoding P. aeruginosa isolates recovered between 2014 and 2021 from oncological patients belonged to those same clusters.

METHODS: The 32 isolates were re-cultured, whole-genome sequenced, phenotypically tested for their antimicrobial susceptibility, and analyzed for clonality and resistance genes in silico.

RESULTS: Among these strains, 25 belonged to the two clusters that had been predominant in the wastewater, while two others belonged to a sequence-type less prominently detected in the drains of the patient rooms.

CONCLUSION: Patients constantly exposed to antibiotics can, in interaction with their persistently antibiotic-exposed sanitary facilities, form a niche that might be supportive for the emergence, the development, the dissemination, and the maintenance of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure. Technical and infection control solutions might help preventing transmission of microorganisms from the wastewater system to the patient and vice versa, particularly concerning the shower and toilet drainage. However, a major driving force might also be antibiotic induced selection pressure and parallel antimicrobial stewardship efforts could be essential.

PMID:37061726 | DOI:10.1186/s13756-023-01236-w

Nat Commun. 2023 Apr 15;14(1):2162. doi: 10.1038/s41467-023-37876-0.

ABSTRACT

Generating reference maps of interactome networks illuminates genetic studies by providing a protein-centric approach to finding new components of existing pathways, complexes, and processes. We apply state-of-the-art methods to identify binary protein-protein interactions (PPIs) for Drosophila melanogaster. Four all-by-all yeast two-hybrid (Y2H) screens of > 10,000 Drosophila proteins result in the 'FlyBi' dataset of 8723 PPIs among 2939 proteins. Testing subsets of data from FlyBi and previous PPI studies using an orthogonal assay allows for normalization of data quality; subsequent integration of FlyBi and previous data results in an expanded binary Drosophila reference interaction network, DroRI, comprising 17,232 interactions among 6511 proteins. We use FlyBi data to generate an autophagy network, then validate in vivo using autophagy-related assays. The deformed wings (dwg) gene encodes a protein that is both a regulator and a target of autophagy. Altogether, these resources provide a foundation for building new hypotheses regarding protein networks and function.

PMID:37061542 | DOI:10.1038/s41467-023-37876-0

Toxicol Lett. 2023 Apr 13:S0378-4274(23)00163-7. doi: 10.1016/j.toxlet.2023.04.005. Online ahead of print.

ABSTRACT

In silico methods are essential to the safety evaluation of chemicals. Computational risk assessment offers several approaches, with data science and knowledge-based methods becoming an increasingly important sub-group. One of the substantial attributes of data science is that it allows using existing data to find correlations, build strong hypotheses, and create new, valuable knowledge that may help to reduce the number of resource intensive experiments. In choosing a suitable method for toxicity prediction, the available data and desired toxicity endpoint are two essential factors to consider. The complexity of the endpoint can impact the success rate of the in silico models. For highly complex endpoints such as hepatotoxicity, it can be beneficial to decipher the toxic event from a more systemic point of view. We propose a data science-based modelling pipeline that uses compounds` connections to tissue-specific biological targets, interactome, and biological pathways as descriptors of compounds. Models trained on different combinations of the collected, compound-target, compound-interactor, and compound-pathway profiles, were used to predict the hepatotoxicity of drug-like compounds. Several tree-based models were trained, utilizing separate and combined target, interactome and pathway level variables. The model using combined descriptors of all levels and the random forest algorithm was further optimized. Descriptor importance for model performance was addressed and examined for a biological explanation to define which targets or pathways can have a crucial role in toxicity. Descriptors connected to cytochromes P450 enzymes, heme degradation and biological oxidation received high weights. Furthermore, the involvement of other, less discussed processes in connection with toxicity, such as the involvement of RHO GTPase effectors in hepatotoxicity, were marked as fundamental. The optimized combined model using only the selected descriptors yielded the best performance with an accuracy of 0.766. The same dataset using classical Morgan fingerprints for compound representation yielded models with similar performance measures, as well as the combination of systems biology-based descriptors and Morgan fingerprints. Consequently, adding the structural information of compounds did not enhance the predictive value of the models. The developed systems biology-based pipeline comprises a valuable tool in predicting toxicity, while providing novel insights about the possible mechanisms of the unwanted events.

PMID:37061207 | DOI:10.1016/j.toxlet.2023.04.005

Ultrason Sonochem. 2023 Apr 11;95:106400. doi: 10.1016/j.ultsonch.2023.106400. Online ahead of print.

ABSTRACT

The COVID -19 pandemic reminded us that we need better contingency plans to prevent the spread of infectious agents and the occurrence of epidemics or pandemics. Although the transmissibility of SARS-CoV-2 in water has not been confirmed, there are studies that have reported on the presence of infectious coronaviruses in water and wastewater samples. Since standard water treatments are not designed to eliminate viruses, it is of utmost importance to explore advanced treatment processes that can improve water treatment and help inactivate viruses when needed. This is the first study to investigate the effects of hydrodynamic cavitation on the inactivation of bacteriophage phi6, an enveloped virus used as a SARS-CoV-2 surrogate in many studies. In two series of experiments with increasing and constant sample temperature, virus reduction of up to 6.3 logs was achieved. Inactivation of phi6 at temperatures of 10 and 20 °C occurs predominantly by the mechanical effect of cavitation and results in a reduction of up to 4.5 logs. At 30 °C, the reduction increases to up to 6 logs, where the temperature-induced increased susceptibility of the viral lipid envelope makes the virus more prone to inactivation. Furthermore, the control experiments without cavitation showed that the increased temperature alone is not sufficient to cause inactivation, but that additional mechanical stress is still required. The RNA degradation results confirmed that virus inactivation was due to the disrupted lipid bilayer and not to RNA damage. Hydrodynamic cavitation, therefore, has the potential to inactivate current and potentially emerging enveloped pathogenic viruses in water at lower, environmentally relevant temperatures.

PMID:37060711 | DOI:10.1016/j.ultsonch.2023.106400

J Am Soc Nephrol. 2023 Apr 15. doi: 10.1681/ASN.0000000000000146. Online ahead of print.

ABSTRACT

The phenotypic diversity of tuberous sclerosis complex (TSC) kidney pathology is enigmatic. Despite a well-established monogenic etiology, an incomplete understanding of lesion pathogenesis persists. In this review, we explore the question: how do TSC kidney lesions arise? We appraise literature findings in the context of mutational timing and cell-of-origin. Through a developmental lens, we integrate critical results from clinical studies, human specimens, and genetic animal models. We also review novel insights gleaned from emerging organoid and single cell sequencing technologies. We present a new model of pathogenesis which posits a phenotypic continuum, whereby lesions arise by mutagenesis during development from variably timed second-hit events. This model can serve as a conceptual framework for testing hypotheses of TSC lesion pathogenesis, both in the kidney and other affected tissues.

PMID:37060140 | DOI:10.1681/ASN.0000000000000146

Sci China Life Sci. 2023 Apr 14. doi: 10.1007/s11427-023-2316-2. Online ahead of print.

ABSTRACT

Protein-biomolecule interactions play pivotal roles in almost all biological processes. For a biomolecule of interest, the identification of the interacting protein(s) is essential. For this need, although many assays are available, highly robust and reliable methods are always desired. By combining a substrate-based proximity labeling activity from the pupylation pathway of Mycobacterium tuberculosis and the streptavidin (SA)-biotin system, we developed the Specific Pupylation as IDEntity Reporter (SPIDER) method for identifying protein-biomolecule interactions. Using SPIDER, we validated the interactions between the known binding proteins of protein, DNA, RNA, and small molecule. We successfully applied SPIDER to construct the global protein interactome for m6A and mRNA, identified a variety of uncharacterized m6A binding proteins, and validated SRSF7 as a potential m6A reader. We globally identified the binding proteins for lenalidomide and CobB. Moreover, we identified SARS-CoV-2-specific receptors on the cell membrane. Overall, SPIDER is powerful and highly accessible for the study of protein-biomolecule interactions.

PMID:37059927 | DOI:10.1007/s11427-023-2316-2

Nat Struct Mol Biol. 2023 Apr 14. doi: 10.1038/s41594-023-00994-w. Online ahead of print.

NO ABSTRACT

PMID:37059902 | DOI:10.1038/s41594-023-00994-w

Eur J Pharmacol. 2023 Apr 12:175722. doi: 10.1016/j.ejphar.2023.175722. Online ahead of print.

ABSTRACT

Circular RNAs (circRNAs) have been demonstrated to exert pivotal functions in cancer progression but are poorly understood in colorectal cancer (CRC). This work intends to investigate the effect and mechanism of a novel cirRNA (circCOL1A2) in CRC. Exosomes were identified via transmission electron microscope (TEM) and nanoparticle tracking analysis (NTA). Quantitative real-time polymerase chain reaction (qRT-PCR) and western blot were used to analyze the levels of genes and proteins. Proliferation, migration, and invasion were detected via cell counting kit-8 (CCK8), 5-Ethynyl-2'-deoxyuridine (EDU), and transwell experiments. RNA pull-down, luciferase reporter, and RNA immunoprecipitation (RIP) assays were performed to assess the binding between genes. Animal studies were carried out to evaluate the function of circCOL1A2 in vivo. We found that circCOL1A2 was highly expressed in CRC cells. And circCOL1A2 was packaged from cancerous cells into exosomes. The proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) properties were inhibited after the reduction of exosomal circCOL1A2. Mechanism studies proved the binding of miR-665 with circCOL1A2 or LASP1 Rescue experiments validated the reverse effects of miR-665 knockdown on circCOL1A2 silencing and LASP1 overexpression on miR-665. Animal studies further confirmed the oncogenic function of exosomal circCOL1A2 in CRC tumorigenesis. In conclusion, exosomal circCOL1A2 sponges miR-665 to enhance LASP1 expression and modulated CRC phenotypes. Thus, circCOL1A2 might be a valuable therapeutic target for CRC, offering novel insight into CRC treatment.

PMID:37059374 | DOI:10.1016/j.ejphar.2023.175722

Transl Res. 2023 Apr 12:S1931-5244(23)00057-9. doi: 10.1016/j.trsl.2023.04.001. Online ahead of print.

ABSTRACT

Focal segmental glomerulosclerosis (FSGS) is a glomerular lesion often associated with nephrotic syndrome. It is also associated with a high risk of progression to end-stage kidney disease. Current treatment of FSGS is limited to systemic corticosteroids or calcineurin inhibition, along with inhibitors of the renin-angiotensin-aldosterone system. FSGS is heterogeneous in etiology, and novel therapies targeting specific, dysregulated molecular pathways represent a major unmet medical need. We have generated a network-based molecular model of FSGS pathophysiology using previously established systems biology workflows to allow computational evaluation of compounds for their predicted interference with molecular processes contributing to FSGS. We identified the anti-platelet drug clopidogrel as a therapeutic option to counterbalance dysregulated FSGS pathways. This prediction of our computational screen was validated by testing clopidogrel in the adriamycin FSGS mouse model. Clopidogrel improved key FSGS outcome parameters and significantly reduced urinary albumin to creatinine ratio (p<0.01) and weight loss (p<0.01), and ameliorated histopathological damage (p<0.05). Clopidogrel is used to treat several cardiovascular diseases linked to chronic kidney disease. Clopidogrel's favorable safety profile and its efficacy in the adriamycin mouse FSGS model thus recommend it as an attractive drug repositioning candidate for clinical trial in FSGS.

PMID:37059330 | DOI:10.1016/j.trsl.2023.04.001

Cancer Cell. 2023 Apr 8:S1535-6108(23)00088-0. doi: 10.1016/j.ccell.2023.03.015. Online ahead of print.

ABSTRACT

Lymphocytes are key for immune surveillance of tumors, but our understanding of the spatial organization and physical interactions that facilitate lymphocyte anti-cancer functions is limited. We used multiplexed imaging, quantitative spatial analysis, and machine learning to create high-definition maps of lung tumors from a Kras/Trp53-mutant mouse model and human resections. Networks of interacting lymphocytes ("lymphonets") emerged as a distinctive feature of the anti-cancer immune response. Lymphonets nucleated from small T cell clusters and incorporated B cells with increasing size. CXCR3-mediated trafficking modulated lymphonet size and number, but T cell antigen expression directed intratumoral localization. Lymphonets preferentially harbored TCF1+ PD-1+ progenitor CD8+ T cells involved in responses to immune checkpoint blockade (ICB) therapy. Upon treatment of mice with ICB or an antigen-targeted vaccine, lymphonets retained progenitor and gained cytotoxic CD8+ T cell populations, likely via progenitor differentiation. These data show that lymphonets create a spatial environment supportive of CD8+ T cell anti-tumor responses.

PMID:37059105 | DOI:10.1016/j.ccell.2023.03.015

CBE Life Sci Educ. 2023 Jun;22(2):ar25. doi: 10.1187/cbe.22-01-0001.

ABSTRACT

In-person undergraduate research experiences (UREs) promote students' integration into careers in life science research. In 2020, the COVID-19 pandemic prompted institutions hosting summer URE programs to offer them remotely, raising questions about whether undergraduates who participate in remote research can experience scientific integration and whether they might perceive doing research less favorably (i.e., not beneficial or too costly). To address these questions, we examined indicators of scientific integration and perceptions of the benefits and costs of doing research among students who participated in remote life science URE programs in Summer 2020. We found that students experienced gains in scientific self-efficacy pre- to post-URE, similar to results reported for in-person UREs. We also found that students experienced gains in scientific identity, graduate and career intentions, and perceptions of the benefits of doing research only if they started their remote UREs at lower levels on these variables. Collectively, students did not change in their perceptions of the costs of doing research despite the challenges of working remotely. Yet students who started with low cost perceptions increased in these perceptions. These findings indicate that remote UREs can support students' self-efficacy development, but may otherwise be limited in their potential to promote scientific integration.

PMID:37058442 | DOI:10.1187/cbe.22-01-0001

J Agric Food Chem. 2023 Apr 14. doi: 10.1021/acs.jafc.3c00535. Online ahead of print.

ABSTRACT

Hemp seed-derived inhibitors of dipeptidyl peptidase IV (DPP-IV) demonstrate potential as novel therapeutics for diabetes; however, their proteome and genome remain uncharacterized. We used multi-omics technology to mine peptides capable of inhibiting DPP-IV. First, 1261 and 1184 proteins were identified in fresh and dry hemp seeds, respectively. Simulated protease cleavage of dry seed proteins yielded 185,446 peptides for virtual screening to select the potential DPP-IV-inhibiting peptides. Sixteen novel peptides were selected according to their DPP-IV-binding affinity determined via molecular docking. In vitro DPP-IV inhibition assays identified the peptides LPQNIPPL, YPYY, YPW, LPYPY, WWW, YPY, YPF, and WS with half-maximal inhibitory concentration (IC50) values lower than 0.5 mM, which were 0.08 ± 0.01, 0.18 ± 0.03, 0.18 ± 0.01, 0.20 ± 0.03, 0.22 ± 0.03, 0.29 ± 0.02, 0.42 ± 0.03, and 0.44 ± 0.09 mM, respectively. The dissociation constants (KD) of the 16 peptides ranged from 1.50 × 10-4 to 1.82 × 10-7 M. Furthermore, Caco2 and INS-1 cell assays showed that all 16 peptides could efficiently inhibit DPP-IV activity and increase insulin and glucagon-like peptide-1 concentrations. These results demonstrate a well-established and efficient method to isolate food-derived therapeutic DPP-IV-inhibiting peptides.

PMID:37058363 | DOI:10.1021/acs.jafc.3c00535

J Proteome Res. 2023 Apr 14. doi: 10.1021/acs.jproteome.3c00125. Online ahead of print.

ABSTRACT

Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition, or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information. Methods based on cofractionation paired with mass spectrometry have demonstrated the capability for deep biological insight, but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. There has been little uptake of this strategy into the broader life science community despite its rich biological information content. We present a rapid integrated experimental and computational workflow to assess the reorganization of protein complexes across multiple cellular states. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in a complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and subsequent stimulation of macrophage cells with lipopolysaccharide. We observed substantial proteome reorganization on differentiation and less pronounced changes in macrophage stimulation. We establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization.

PMID:37058003 | DOI:10.1021/acs.jproteome.3c00125

J Am Chem Soc. 2023 Apr 14. doi: 10.1021/jacs.2c11027. Online ahead of print.

ABSTRACT

Modular polyketide synthases (PKSs) are polymerases that employ α-carboxyacyl-CoAs as extender substrates. This enzyme family contains several catalytic modules, where each module is responsible for a single round of polyketide chain extension. Although PKS modules typically use malonyl-CoA or methylmalonyl-CoA for chain elongation, many other malonyl-CoA analogues are used to diversify polyketide structures in nature. Previously, we developed a method to alter an extension substrate of a given module by exchanging an acyltransferase (AT) domain while maintaining protein folding. Here, we report in vitro polyketide biosynthesis by 13 PKSs (the wild-type PKS and 12 AT-exchanged PKSs with unusual ATs) and 14 extender substrates. Our ∼200 in vitro reactions resulted in 13 structurally different polyketides, including several polyketides that have not been reported. In some cases, AT-exchanged PKSs produced target polyketides by >100-fold compared to the wild-type PKS. These data also indicate that most unusual AT domains do not incorporate malonyl-CoA and methylmalonyl-CoA but incorporate various rare extender substrates that are equal to in size or slightly larger than natural substrates. We developed a computational workflow to predict the approximate AT substrate range based on active site volumes to support the selection of ATs. These results greatly enhance our understanding of rare AT domains and demonstrate the benefit of using the proposed PKS engineering strategy to produce novel chemicals in vitro.

PMID:37057992 | DOI:10.1021/jacs.2c11027

Cell Rep Methods. 2023 Feb 20;3(3):100421. doi: 10.1016/j.crmeth.2023.100421. eCollection 2023 Mar 27.

ABSTRACT

Serological assays are important diagnostic tools for surveying exposure to the pathogen, monitoring immune response post vaccination, and managing spread of the infectious agent among the population. Current serological laboratory assays are often limited because they require the use of specialized laboratory technology and/or work with a limited number of sample types. Here, we evaluate an alternative by developing time-resolved Förster resonance energy transfer (TR-FRET) homogeneous assays that exhibited exceptional versatility, scalability, and sensitivity and outperformed or matched currently used strategies in terms of sensitivity, specificity, and precision. We validated the performance of the assays measuring total immunoglobulin G (IgG) levels; antibodies against severe acute respiratory syndrome coronavirus (SARS-CoV) or Middle Eastern respiratory syndrome (MERS)-CoV spike (S) protein; and SARS-CoV-2 S and nucleocapsid (N) proteins and applied it to several large sample sets and real-world applications. We further established a TR-FRET-based ACE2-S competition assay to assess the neutralization propensity of the antibodies. Overall, these TR-FRET-based serological assays can be rapidly extended to other antigens and are compatible with commonly used plate readers.

PMID:37056371 | PMC:PMC10088089 | DOI:10.1016/j.crmeth.2023.100421

BMC Genomics. 2023 Apr 13;24(1):201. doi: 10.1186/s12864-023-09287-4.

ABSTRACT

BACKGROUND: Nucleosome remodeling factors regulate the occupancy and positioning of nucleosomes genome-wide through ATP-driven DNA translocation. While many nucleosomes are consistently well-positioned, some nucleosomes and alternative nucleosome structures are more sensitive to nuclease digestion or are transitory. Fragile nucleosomes are nucleosome structures that are sensitive to nuclease digestion and may be composed of either six or eight histone proteins, making these either hexasomes or octasomes. Overlapping dinucleosomes are composed of two merged nucleosomes, lacking one H2A:H2B dimer, creating a 14-mer wrapped by ~ 250 bp of DNA. In vitro studies of nucleosome remodeling suggest that the collision of adjacent nucleosomes by sliding stimulates formation of overlapping dinucleosomes.

RESULTS: To better understand how nucleosome remodeling factors regulate alternative nucleosome structures, we depleted murine embryonic stem cells of the transcripts encoding remodeler ATPases BRG1 or SNF2H, then performed MNase-seq. We used high- and low-MNase digestion to assess the effects of nucleosome remodeling factors on nuclease-sensitive or "fragile" nucleosome occupancy. In parallel we gel-extracted MNase-digested fragments to enrich for overlapping dinucleosomes. We recapitulate prior identification of fragile nucleosomes and overlapping dinucleosomes near transcription start sites, and identify enrichment of these features around gene-distal DNaseI hypersensitive sites, CTCF binding sites, and pluripotency factor binding sites. We find that BRG1 stimulates occupancy of fragile nucleosomes but restricts occupancy of overlapping dinucleosomes.

CONCLUSIONS: Overlapping dinucleosomes and fragile nucleosomes are prevalent within the ES cell genome, occurring at hotspots of gene regulation beyond their characterized existence at promoters. Although neither structure is fully dependent on either nucleosome remodeling factor, both fragile nucleosomes and overlapping dinucleosomes are affected by knockdown of BRG1, suggesting a role for the complex in creating or removing these structures.

PMID:37055726 | DOI:10.1186/s12864-023-09287-4

Nat Microbiol. 2023 Apr 13. doi: 10.1038/s41564-023-01360-8. Online ahead of print.

ABSTRACT

Babesiosis is a malaria-like disease in humans and animals that is caused by Babesia species, which are tick-transmitted apicomplexan pathogens. Babesia duncani causes severe to lethal infection in humans, but despite the risk that this parasite poses as an emerging pathogen, little is known about its biology, metabolic requirements or pathogenesis. Unlike other apicomplexan parasites that infect red blood cells, B. duncani can be continuously cultured in vitro in human erythrocytes and can infect mice resulting in fulminant babesiosis and death. We report comprehensive, detailed molecular, genomic, transcriptomic and epigenetic analyses to gain insights into the biology of B. duncani. We completed the assembly, 3D structure and annotation of its nuclear genome, and analysed its transcriptomic and epigenetics profiles during its asexual life cycle stages in human erythrocytes. We used RNA-seq data to produce an atlas of parasite metabolism during its intraerythrocytic life cycle. Characterization of the B. duncani genome, epigenome and transcriptome identified classes of candidate virulence factors, antigens for diagnosis of active infection and several attractive drug targets. Furthermore, metabolic reconstitutions from genome annotation and in vitro efficacy studies identified antifolates, pyrimethamine and WR-99210 as potent inhibitors of B. duncani to establish a pipeline of small molecules that could be developed as effective therapies for the treatment of human babesiosis.

PMID:37055610 | DOI:10.1038/s41564-023-01360-8

Br J Cancer. 2023 Apr 13. doi: 10.1038/s41416-023-02261-7. Online ahead of print.

NO ABSTRACT

PMID:37055522 | DOI:10.1038/s41416-023-02261-7