Filamentous fungi are historically known to be a rich reservoir of bioactive compounds that are applied in a myriad of fields ranging from crop protection to medicine. The surge of genomic data ...available shows that fungi remain an excellent source for new pharmaceuticals. However, most of the responsible biosynthetic gene clusters are transcriptionally silent under laboratory growth conditions. Therefore, generic strategies for activation of these clusters are required. Here, we present a genome-editing-free, transcriptional regulation tool for filamentous fungi, based on the CRISPR activation (CRISPRa) methodology. Herein, a nuclease-defective mutant of Cas9 (dCas9) was fused to a highly active tripartite activator VP64-p65-Rta (VPR) to allow for sgRNA directed targeted gene regulation. dCas9-VPR was introduced, together with an easy to use sgRNA "plug-and-play" module, into a non-integrative AMA1-vector, which is compatible with several filamentous fungal species. To demonstrate its potential, this vector was used to transcriptionally activate a fluorescent reporter gene under the control of the penDE core promoter in Penicillium rubens. Subsequently, we activated the transcriptionally silent, native P. rubens macrophorin biosynthetic gene cluster by targeting dCas9-VPR to the promoter region of the transcription factor macR. This resulted in the production of antimicrobial macrophorins. This CRISPRa technology can be used for the rapid and convenient activation of silent fungal biosynthetic gene clusters, and thereby aid in the identification of novel compounds such as antimicrobials.
Ir‐catalyzed asymmetric alkene hydrogenation is presented as the strategy par excellence to prepare saturated isoprenoids and mycoketides. This highly stereoselective synthesis approach is combined ...with an established 13C‐NMR method to determine the enantioselectivity of each methyl‐branched stereocenter. It is shown that this analysis is fit for purpose and the combination allows the synthesis of the title compounds with a significant increase in efficiency.
Cyclo‐archaeol, iso‐caldarchaeol, caldarchaeol, and mycoketide are prepared by employing asymmetric hydrogenation to generate the multiple stereocenters.
Antimicrobial resistance is one of the leading concerns in medical care. Here we study the mechanism of action of an antimicrobial cationic tripeptide, AMC-109, by combining high speed-atomic force ...microscopy, molecular dynamics, fluorescence assays, and lipidomic analysis. We show that AMC-109 activity on negatively charged membranes derived from Staphylococcus aureus consists of two crucial steps. First, AMC-109 self-assembles into stable aggregates consisting of a hydrophobic core and a cationic surface, with specificity for negatively charged membranes. Second, upon incorporation into the membrane, individual peptides insert into the outer monolayer, affecting lateral membrane organization and dissolving membrane nanodomains, without forming pores. We propose that membrane domain dissolution triggered by AMC-109 may affect crucial functions such as protein sorting and cell wall synthesis. Our results indicate that the AMC-109 mode of action resembles that of the disinfectant benzalkonium chloride (BAK), but with enhanced selectivity for bacterial membranes.
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or ...exploited for synthetic applications. This review aims to provide a general overview of the most important Fd‐dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non‐heme iron‐dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure–function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd‐dependent enzyme classes for synthetic applications.
In the spotlight! Ferredoxin‐dependent enzymes often rely on a complicated electron‐transfer chain to enable the catalysis of challenging chemical reactions. In this review, we showcase several Fd‐dependent enzymes and their potential biocatalytic applications, while particularly focusing on Rieske oxygenases as a class of enzymes with huge application potential in synthetic organic chemistry that are nonetheless still not very well understood.
In theranostics, radiolabeled compounds are used to determine a treatment strategy by combining therapeutics and diagnostics in the same agent. Monoclonal antibodies (mAbs) and antibody-related ...therapeutics represent a rapidly expanding group of cancer medicines. Theranostic approaches using these drugs in oncology are particularly interesting because antibodies are designed against specific targets on the tumor cell membrane and immune cells as well as targets in the tumor microenvironment. In addition, these drugs are relatively easy to radiolabel. Noninvasive molecular imaging techniques, such as SPECT and PET, provide information on the whole-body distribution of radiolabeled mAbs and antibody-related therapeutics. Molecular antibody imaging can potentially elucidate drug target expression, tracer uptake in the tumor, tumor saturation, and heterogeneity for these parameters within the tumor. These data can support drug development and may aid in patient stratification and monitoring of the treatment response. Selecting a radionuclide for theranostic purposes generally starts by matching the serum half-life of the mAb or antibody-related therapeutic and the physical half-life of the radionuclide. Furthermore, PET imaging allows better quantification than the SPECT technique. This information has increased interest in theranostics using PET radionuclides with a relatively long physical half-life, such as
Zr. In this review, we provide an overview of ongoing research on mAbs and antibody-related theranostics in preclinical and clinical oncologic settings. We identified 24 antibodies or antibody-related therapeutics labeled with PET radionuclides for theranostic purposes in patients. For this approach to become integrated in standard care, further standardization with respect to the procedures involved is required.
Validation experiments were conducted of a simple, fast, and inexpensive method for the determination of 229 pesticides fortified at 10-100 ng/g in lettuce and orange matrixes. The method is known as ...the quick, easy, cheap, effective, rugged, and safe (QuEChERS) method for pesticide residues in foods. The procedure involved the extraction of a 15 g sample with 15 mL acetonitrile, followed by a liquid-liquid partitioning step performed by adding 6 g anhydrous MgSO4 plus 1.5 g NaCl. After centrifugation, the extract was decanted into a tube containing 300 mg primary secondary amine (PSA) sorbent plus 1.8 g anhydrous MgSO4, which constituted a cleanup procedure called dispersive solid-phase extraction (dispersive SPE). After a second shaking and centrifugation step, the acetonitrile extract was transferred to autosampler vials for concurrent analysis by gas chromatography/mass spectrometry with an ion trap instrument and liquid chromatography/tandem mass spectrometry with a triple quadrupole instrument using electrospray ionization. Each analytical method was designed to analyze 144 pesticides, with 59 targeted by both instruments. Recoveries for all but 11 of the analytes in at least one of the matrixes were between 70-120% (90-110% for 206 pesticides), and repeatabilities typically <10% were achieved for a wide range of fortified pesticides, including methamidophos, spinosad, imidacloprid, and imazalil. Dispersive SPE with PSA retained carboxylic acids (e.g., daminozide), and <50% recoveries were obtained for asulam, pyridate, dicofol, thiram, and chlorothalonil. Many actual samples and proficiency test samples were analyzed by the method, and the results compared favorably with those from traditional methods.
Cellular membranes are essential for compartmentalization, maintenance of permeability, and fluidity in all three domains of life. Archaea belong to the third domain of life and have a distinct ...phospholipid composition. Membrane lipids of archaea are ether-linked molecules, specifically bilayer-forming dialkyl glycerol diethers (DGDs) and monolayer-forming glycerol dialkyl glycerol tetraethers (GDGTs). The antifungal allylamine terbinafine has been proposed as an inhibitor of GDGT biosynthesis in archaea based on radiolabel incorporation studies. The exact target(s) and mechanism of action of terbinafine in archaea remain elusive.
is a strictly aerobic crenarchaeon thriving in a thermoacidophilic environment, and its membrane is dominated by GDGTs. Here, we comprehensively analyzed the lipidome and transcriptome of
in the presence of terbinafine. Depletion of GDGTs and the accompanying accumulation of DGDs upon treatment with terbinafine were growth phase-dependent. Additionally, a major shift in the saturation of caldariellaquinones was observed, which resulted in the accumulation of unsaturated molecules. Transcriptomic data indicated that terbinafine has a multitude of effects, including significant differential expression of genes in the respiratory complex, motility, cell envelope, fatty acid metabolism, and GDGT cyclization. Combined, these findings suggest that the response of
to terbinafine inhibition involves respiratory stress and the differential expression of genes involved in isoprenoid biosynthesis and saturation.
Due to the growing concern over environmental issues, regardless of whether companies are going to voluntarily incorporate green policies in practice, or will be forced to do so in the context of new ...legislation, change is foreseen in the future of transportation management. Assigning and scheduling vehicles to service a pre‐determined set of clients is a common distribution problem. Accounting for time‐dependent travel times between customers, we present a model that considers travel time, fuel, and CO2 emissions costs. Specifically, we propose a framework for modeling CO2 emissions in a time‐dependent vehicle routing context. The model is solved via a tabu search procedure. As the amount of CO2 emissions is correlated with vehicle speed, our model considers limiting vehicle speed as part of the optimization. The emissions per kilometer as a function of speed are minimized at a unique speed. However, we show that in a time‐dependent environment this speed is sub‐optimal in terms of total emissions. This occurs if vehicles are able to avoid running into congestion periods where they incur high emissions. Clearly, considering this trade‐off in the vehicle routing problem has great practical potential. In the same line, we construct bounds on the total amount of emissions to be saved by making use of the standard VRP solutions. As fuel consumption is correlated with CO2 emissions, we show that reducing emissions leads to reducing costs. For a number of experimental settings, we show that limiting vehicle speeds is desired from a total cost perspective. This namely stems from the trade‐off between fuel and travel time costs.
Rheumatoid arthritis-associated autoantibodies (RA-AAB) can be present in serum years before clinical onset of rheumatoid arthritis (RA). It has been hypothesized that initiation of RA-AAB generation ...occurs at inflamed mucosal surfaces, such as in the oral cavity or lungs. The aim of this study was to assess systemic presence of RA-AAB in patients without RA who had oral or lung mucosal inflammation.
The presence of RA-AAB (immunoglobulin A IgA and IgG anti-cyclic citrullinated peptide 2 antibodies (anti-CCP2), IgM and IgA rheumatoid factor (RF), IgG anti-carbamylated protein antibodies and IgG and IgA anti-citrullinated peptide antibodies against fibrinogen, vimentin and enolase) were determined in sera of non-RA patients with periodontitis (PD, n = 114), bronchiectasis (BR, n = 80) or cystic fibrosis (CF, n = 41). Serum RA-AAB levels were compared with those of periodontally healthy controls (n = 36). Patients with established RA (n = 86) served as a reference group. Association of the diseases with RA-AAB seropositivity was assessed with a logistic regression model, adjusted for age, sex and smoking.
Logistic regression analysis revealed that IgG anti-CCP seropositivity was associated with BR and RA, whereas the association with PD was borderline significant. IgA anti-CCP seropositivity was associated with CF and RA. IgM RF seropositivity was associated with RA, whereas the association with BR was borderline significant. IgA RF seropositivity was associated with CF and RA. Apart from an influence of smoking on IgA RF in patients with RA, there was no influence of age, sex or smoking on the association of RA-AAB seropositivity with the diseases. Anti-CarP levels were increased only in patients with RA. The same held for IgG reactivity against all investigated citrullinated peptides.
Although overall levels were low, RA-AAB seropositivity was associated with lung mucosal inflammation (BR and CF) and may be associated with oral mucosal inflammation (PD). To further determine whether mucosal inflammation functions as a site for induction of RA-AAB and precedes RA, longitudinal studies are necessary in which RA-AAB of specifically the IgA isotype should be assessed in inflamed mucosal tissues and/or in their inflammatory exudates.
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