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The capability of synthesized zeolite A (SZ) to immobilize Ag ions (Ag-SZ) and Ag nanoparticles (AgNp-SZ) were comparatively studied. A novel approach of in situ biosynthesized AgNP-incorporated synthesized zeolite A (AgNp-SZ) was synthesized at an optimum volume of 0.4 mL of the Orthosiphon aristatus (O. aristatus) leaves plant extract (5%) using an in situ approach. In comparison, Ag-SZ was produced by loading the synthesized zeolite with Ag ions. All synthesized materials were characterized for their morphologies and physicochemical properties. The characterization analyses validate that the biosynthesized AgNP (

A practical focusing on the synthesis, isolation, and hydrolysis of ammonia borane (AB), H3N·BH3, was developed for first-year undergraduate students. By requiring students to propose their own experimental setup to measure the amount of gas produced upon hydrolysis, experimental design skills were introduced and developed during the practical. As a result of the COVID-19 pandemic, remote and face-to-face versions of the practical were created to enable inclusivity in which experimental design skills were a key feature. Students identified and reported an appreciable increase in their experimental design skills. The multifaceted nature of the practical allows for flexibility in its implementation, dependent on students’ prior knowledge, local logistical considerations, and the learning objectives of an institution.

The Williston Basin has proven to be a global super basin. Initially, development across this basin was dominated by conventional production from the Madison Group and Ordovician oil systems; however, with the development of unconventional play opportunities, the biggest resource in the Williston Basin is now the Middle Member of the Bakken Formation. The Middle Member was not pursued as a reservoir because of its low porosity and permeability, the low thermal maturity of the juxtaposed Bakken shales, low resistivity, and perceived lack of oil saturation. This paper will review how geochemical data were used to challenge and explain those initial assumptions with particular focus on the discovery and development of the Parshall field. Unconventional and hybrid plays are complex systems, and although much of the geochemical focus details organofacies or maturity concerns, numerous other processes including sorption, alteration, mixing, and evaporative fractionation can and commonly will influence the interpretation of the results and therefore must be considered. The geochemical techniques discussed in this paper are used to calculate oil saturation and more appropriately, mobile oil saturation, from core data requiring accounting for oil evaporative losses to fully define the workings of the Bakken petroleum system and the Middle Member as the key reservoir.

Sulfenyl dipyrroles feature two pyrroles linked via a sulfenyl bridge. The synthesis of sulfenyl dipyrroles has typically involved SCl2 as the sulfur source. However, SCl2 is no longer readily available within North America and Europe. Herein we report a new synthesis of sulfenyl dipyrroles using SOCl2 as the sulfur source and reductant. Although five new sulfenyl dipyrroles were synthesized and isolated via this route, functional group tolerance proved limited. A potential mechanism for the reaction, involving reduction of a sulfinyl moiety by SOCl2, is briefly explored.

The present work involves the study of the removal of Cu2+, Fe3+, Pb2+and Zn2+from synthetic metal solutions using natural zeolite. Laboratory experiments were used to investigate the efficiency of adsorbents in the uptake of heavy metals from industrial wastewater. The kinetic study was used to identify the effect of parameters that affect the rate of adsorption and evaluated their impact on the efficiency of the zeolite in the removal of heavy metals from industrial wastewater. Natural zeolite (clinoptilolite) as adsorbent contacted with multi-component synthetic solutions containing Cu2+, Fe3+, Pb2+and Zn2+ions without any pre-modifications and every hour 15 ml of the samples were filtered and taken for metal ion concentration analysis using the ICP-OES. The pH values were monitored and adjusted regularly. The results showed that the capacity of the adsorbents for the removal of heavy metals increased with a greater mass of absorbent, increased initial solution pH, increased agitation speed and higher solution concentration.

F-BODIPYs substituted with BPin functionality have been coupled to aryl halides using a mild and efficient catalyst system involving Pd2(dba)3 and XPhos. The methodology enables the Suzuki–Miyaura cross-coupling of electron-rich, electron-poor, and sterically encumbered BPin-substituted F-BODIPYs to aryl halides bearing various functional groups, thus presenting an opportunity for the preparation of highly functionalised F-BODIPYs without need for the corresponding aryl moiety to be available in borylated form.

Introduction Hydrazines are highly toxic inorganic liquids that are used as propellants in military and aviation industries, such as the U.S. Air Force F-16 Emergency Power Unit and SpaceX SuperDraco Rockets. The most commonly used derivatives include hydrazine, monomethylhydrazine, and 1,1-dimethylhydrazine (unsymmetrical dimethylhydrazine). Industrial workers in close contact with hydrazines during routine maintenance tasks can be exposed to levels well above the National Institute for Occupational Safety and Health relative exposure limits. Materials and Methods A systematic review was performed using PubMed, Web of Science, Google Scholar, National Aeronautics and Space Administration Technical Server, and Defense Technical Information Center, and data related to hydrazine exposures were searched from inception to April 2020. Publications or reports addressing hydrazine toxicity, pathophysiology, and treatment of hydrazine fuel exposure were selected. Results Acute toxic exposures to hydrazine and its derivatives are rare. There are few case reports of acute toxic exposure in humans, and data are largely based on animal studies. The initial search identified 741 articles, manuscripts, and government reports. After screening for eligibility, 51 were included in this review. Eight articles reported acute exposures to hydrazine propellant in humans, and an additional 14 articles reported relevant animal data. Conclusions Exposure to small amounts of hydrazine and its derivatives can cause significant soft tissue injury, pulmonary injury, seizures, coma, and death. Neurologic presentations can vary based on exposure compound and dose. Decontamination is critical as treatment is mainly supportive. High-dose intravenous pyridoxine has been suggested as treatment for hydrazine-related neurologic toxicity, but this recommendation is based on limited human data. Despite recent research efforts to generate less toxic alternatives to hydrazine fuel, it will likely continue to have a role in military and aviation industries. Aerospace and military physicians should be aware of the toxicity associated with hydrazine exposure and be prepared to treat hydrazine toxicity in at-risk populations.

Background: Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry. However, FF samples are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results. Methods: Proteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF samples were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37°C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods. Results: Among 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value < 0.05; |log2 FC| > 1) between FF/HOM vs. OCT/LMD-T and FF/HOM vs. OCT/LMD-TS, respectively, with most proteins being more highly abundant in the FF/HOM samples. PCA and unsupervised hierarchical clustering analysis with these 216 and 171 proteins were able to distinguish FF/HOM from OCT/LMD-T and OCT/LMD-TS samples, respectively. Likewise, PCA analysis and unsupervised clustering analysis using the 402 and 60 significantly differentially enriched GO terms (adjusted p-value (BH) < 0.2) in the FF/HOM vs. OCT/LMD-T and FF/HOM vs OCT/LMD-TS comparisons, respectively, not only distinguished OCT/LMD from FF/HOM samples but also separated LA and LB1 breast cancer subtypes within each storage/preparation method from one another. Although FF/HOM appears to be more similar to OCT/LMD-TS than OCT/LMD-T based on the number of differentially enriched proteins (216 vs. 171; p=0.022) and GO terms (402 vs. 60; p < 2.2 x 10-16), FF/HOM shows no greater similarity to OCT/LMD-TS than OCT/LMD-T based on PCA analysis with either proteins or GO terms ( based on weighted distance for pairwise samples, p = 0.97 from paired t-test). No significantly differentially enriched proteins or GO terms were detected between the OCT/LMD-T and OCT/LMD-TS samples but trended differences were detected. Conclusions: The proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC-MS/MS proteomic studies, FF/HOM samples exhibit different protein profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared. Our study also provides preliminary data for designing new studies to explore why OCT/LMD-TS samples are more similar to OCT/LMD-T than to FF/HOM samples, and to separate LA from LB1 samples. Disclaimer: The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DOD or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Lori A. Sturtz, Guisong Wang, Punit Shah, Richard Searfoss, Praveen-Kumar Raj-Kumar, Jeffrey A. Hooke, J. Leigh Fantacone-Campbell, Brenda Deyarmin, Mary Lou Cutler, Rangaprasad Sarangarajan, Niven R. Narain, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-38.

Arginine methylation has been recognized as a post-translational modification with pleiotropic effects that span from regulation of transcription to metabolic processes that contribute to aberrant cell proliferation and tumorigenesis. This has brought significant attention to the development of therapeutic strategies aimed at blocking the activity of protein arginine methyltransferases (PRMTs), which catalyze the formation of various methylated arginine products on a wide variety of cellular substrates. GSK3368715 is a small molecule inhibitor of type I PRMTs currently in clinical development. Here, we evaluate the effect of type I PRMT inhibition on arginine methylation in normal human peripheral blood mononuclear cells and utilize a broad proteomic approach to identify type I PRMT substrates. This work identified heterogenous nuclear ribonucleoprotein A1 (hnRNP-A1) as a pharmacodynamic biomarker of type I PRMT inhibition. Utilizing targeted mass spectrometry (MS), methods were developed to detect and quantitate changes in methylation of specific arginine residues on hnRNP-A1. This resulted in the development and validation of novel MS and immune assays useful for the assessment of GSK3368715 induced pharmacodynamic effects in blood and tumors that can be applied to GSK3368715 clinical trials.

The mesic montane grasslands of the uKhahlamba-Drakensberg, which produce cured flammable fuel, have evolved under and are sustained by recurrent fires. The Brotherton burning trial (12 replicated treatments) was established at Cathedral Peak (1 890 m asl) in 1980 to understand how burn season and frequency control the composition and diversity of the montane catchment grassland. Multivariate methods were used to examine the long-term (almost 40 years). compositional stability under different burning regimes. The species composition deviated steadily and markedly from the initial state (Bray–Curtis dissimilarity) by 43.4 ± 9.32% with quinquennial burning (alternating autumn/spring) and by 64.6 ± 2.24% with attempted fire exclusion (three unplanned burns). Composition was rapidly transformed (by 53.1 ± 4.6%) by biennial summer burning (discontinued in 1991). Dominance shifted from Themeda triandra to other grasses (Stiburus alopecuroides, Tristachya leucothrix, Harpochloa falx) with biennial summer and infrequent burning. In contrast, regular dormant season burning annually or biennially (in autumn, winter, or spring) maintained a stable grassland close to the original composition (mean deviation 23.08%). Burning homogenised the composition, overriding the initial extant small-scale spatial variation. Results support the current practice to burn biennially in the dormant season to maintain stable grassland in the Drakensberg catchments.

The aim of this article is to study the sodalite synthesis from sepiolite through an alkali fusion method followed by hydrothermal process, and to investigate its application in heavy metal removal...

This study deals with the synthesis of zeolite from natural kaolinite using hydrothermal treatment and evaluation of its phase transformation behaviors. The synthesized zeolites were modified with silver ion by using the ion exchange method for the enhancement of antibacterial properties. The characterizations were performed by using X-ray diffraction spectroscopy, Fourier-transform infrared spectroscopy, field emission scanning electron microscopy, and energy-dispersive X-ray. Disk diffusion technique (DDT) was used for the evaluation of the antibacterial property of the modified zeolites. This study observed the transformation of kaolinite into amorphous metakaolin after calcination treatment at 900°C and the successful reconstruction of amorphous metakaolin into synthesized crystal zeolite in the presence of sodium hydroxide as an activating agent. It was also found that the zeolite type A was produced at 100°C, while sodalites were produced at 120 and 140°C. DDT analysis revealed that the modified zeolites showed significant antibacterial capability against Escherichia coli ATCC 11229 and Staphylococcus aureus ATCC 6538. In general, the present study has proven that the zeolites can be synthesized from natural material and can be modified with silver ion to enhance their antibacterial activity.

Protein aggregation and abnormal lipid homeostasis are both implicated in neurodegeneration through unknown mechanisms. Here we demonstrate that aggregate-membrane interaction is critical to induce a form of cell death called ferroptosis. Importantly, the aggregate-membrane interaction that drives ferroptosis depends both on the conformational structure of the aggregate, as well as the oxidation state of the lipid membrane. We generated human stem cell-derived models of synucleinopathy, characterized by the intracellular formation of α-synuclein aggregates that bind to membranes. In human iPSC-derived neurons with SNCA triplication, physiological concentrations of glutamate and dopamine induce abnormal calcium signaling owing to the incorporation of excess α-synuclein oligomers into membranes, leading to altered membrane conductance and abnormal calcium influx. α-synuclein oligomers further induce lipid peroxidation. Targeted inhibition of lipid peroxidation prevents the aggregate-membrane interaction, abolishes aberrant calcium fluxes, and restores physiological calcium signaling. Inhibition of lipid peroxidation, and reduction of iron-dependent accumulation of free radicals, further prevents oligomer-induced toxicity in human neurons. In summary, we report that peroxidation of polyunsaturated fatty acids underlies the incorporation of β-sheet-rich aggregates into the membranes, and that additionally induces neuronal death. This suggests a role for ferroptosis in Parkinson’s disease, and highlights a new mechanism by which lipid peroxidation causes cell death.

4-(2-Fluorophenyl)-7-methoxycoumarin (6) was synthesized by Pechmann reaction under mild conditions via a three-step reaction. The solution-state 1H NMR spectra of 6 showed a strong intramolecular interaction between F and H5 (JFH = 2.6 Hz) and 13C NMR suggested that this C–F···H–C coupling is a through-space interaction. The 2D 19F-{1H} HOESY and 1H-{19F} 1D experiments were done to confirm this F···H interaction. The single crystal X-ray structure and the DFT-optimized structure showed that the fluorinated phenyl ring favors the orientation with the fluorine atom closer to H5 than H3. The X-ray structure also showed the existence of the intermolecular C–F···H–C interaction.

4,4-Difluoro-4-bora-3a,4a-diaza-s-indacenes (F-BODIPYs) are deprotected through removal of the –BF2 moiety upon treatment with methylboronic acid. The tolerance of various substitution patterns about the dipyrrinato core is demonstrated via the deprotection of thirteen F-BODIPYs and an F-aza-BODIPY. Work-up with aq. HBr affords the desired dipyrin HBr salt in quantitative yield without need for purification.

Three imidazole-derived Schiff base compounds comprising an N-methyl imidazole group coupled to a phenol ring through an imine bond were synthesised. The structures differ by the substituent on the phenol ring at the 4-position: methyl (1), tert-butyl (2) and hydrogen (3). The compounds were synthesised using both a traditional reflux in solvent as well as an environmentally friendly solid-state reaction. Compounds (1)–(3) as well as the hemihydrate of (3) were all studied by single crystal X-ray diffraction. The asymmetric unit of compound (1) consists of two nominally planar molecules linked by hydrogen bonds to form a dimeric supramolecular structure. This dimeric structure was ubiquitous for the anhydrous forms of (1)–(3). The complementary hydrogen bonding motif between the imidazole N atoms and the phenol OH results in a stable 16-membered hydrogen-bonded ring. The asymmetric unit of (3) comprises two symmetry-independent molecules one of which has co-planar imidazole and phenol rings while the other shows a significantly oblique orientation. The hemihydrate of (3) similarly forms extensive hydrogen bonds, though in the form of a water-bridged dimeric structure. The hydrogen bond lengths (D⋯A) for compounds (1)–(3) are relatively short, ranging from 2.662(1) to 2.688(1) A. DFT was used to understand the relative stability of the monomeric and dimeric species. These showed the hydrogen-bonded supramolecular structures were ca. 101 kJ mol−1 lower in energy than the non-interacting monomers. Scan simulations were used to calculate the total energy of the molecule as a function of phenyl ring rotation and showed why the expected planar configuration for a conjugated π-system was not observed experimentally. The barrier to rotation was found to be relatively low, 7.97(6) kJ mol−1, with the lowest energy conformations subtending dihedral angles of 22.319, 24.265 and 25.319° for molecules (1), (2) and (3), respectively. The electrostatic potential maps are able to succinctly explain the stability of the hydrogen bonds through the partial charges of the interacting atoms. TD-DFT simulations and analysis of the simulated and experimental UV/visible spectra suggest that the dimeric supramolecular structure is a stable species in solution. This was confirmed through 1H NMR titrations and an equilibrium constant of 0.16(5) M−1 was estimated.

Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here, we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, NTP substrate levels, and RNA polymerase II (Pol II) activity to TSS selection by "promoter scanning" inSaccharomyces cerevisiae(Pol II MAssively Systematic Transcript End Readout, "Pol II MASTER"). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities ofS. cerevisiaeTSS -8, -1, and +1 positions quantitatively in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to GTP levels at the first five transcript positions and to CTP and UTP levels at the second position genome wide. These results suggest individual NTP levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.

Foundational hypotheses addressing plant–insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other’s state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.

Significance We report a rapid COVID-19 assay that gives a sample-to-signal time of under 10 min. The current gold-standard COVID-19 assay uses PCR, where strands of DNA are copied (amplified) many times to generate a read-out signal. However, as the virus genome is RNA, first conversion into DNA is required using reverse transcription (RT) before amplification. While just as sensitive, our assay is faster because 1) we have designed a method for generating DNA (the trigger strand) from RNA, bypassing the lengthy RT step, and 2) a quicker amplification process than PCR, called exponential amplification reaction (EXPAR), is used to amplify the trigger. This methodology could ultimately be applied to any RNA-based assay, including the detection of other infectious agents., A rapid isothermal method for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, is reported. The procedure uses an unprecedented reverse transcription–free (RTF) approach for converting genomic RNA into DNA. This involves the formation of an RNA/DNA heteroduplex whose selective cleavage generates a short DNA trigger strand, which is then rapidly amplified using the exponential amplification reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection, via a fluorescence read-out, of single figure copy numbers per microliter of SARS-CoV-2 RNA in under 10 min. In direct three-way comparison studies, the assay has been found to be faster than both RT-qPCR and reverse transcription loop-mediated isothermal amplification (RT-LAMP), while being just as sensitive. The assay protocol involves the use of standard laboratory equipment and is readily adaptable for the detection of other RNA-based pathogens.

The current study evaluates the effect of seawater physico-chemical characteristics on the relationship between the concentration of metals measured by Diffusive Gradients in Thin films (DGT) passive samplers (i.e., DGT-labile concentration) and the concentrations measured in discrete water samples. Accordingly, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was used to measure the total dissolved metal concentrations in the discrete water samples and the labile metal concentrations obtained by DGT samplers; additionally, lead and cadmium conditional labile fractions were determined by Anodic Stripping Voltammetry (ASV) and total dissolved nickel was measured by Cathodic Stripping Voltammetry (CSV). It can be concluded that, in general, the median ratios of DGT/ICP and DGT/ASV(CSV) were lower than 1, except for Ni (median ratio close to 1) and Zn (higher than 1). This indicates the importance of speciation and time-integrated concentrations measured using passive sampling techniques, which is in line with the WFD suggestions for improving the chemical assessment of waterbodies. It is the variability in metal content in waters rather than environmental conditions to which the variability of the ratios can be attributed. The ratios were not significantly affected by the temperature, salinity, pH, oxygen, DOC or SPM, giving a great confidence for all the techniques used. Within a regulatory context such as the EU Water Framework Directive this is a great advantage, since the simplicity of not needing to use corrections to minimize the effects of environmental variables could help in implementing DGTs within monitoring networks.

The versatile nucleotide excision repair (NER) pathway initiates as the XPC–RAD23B–CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4–Rad23-Rad33 (yeast homologue of XPC–RAD23B–CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9–9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification., The conserved eukaryotic nucleotide excision repair (NER) pathway protects the genome from a wide variety of environmentally induced DNA lesions. Here, the authors provide insights into how NER is initiated on lesions by determining the cryo-EM structure of the yeast TFIIH/Rad4–Rad23-Rad33 complex bound to a DNA containing a single carcinogen-DNA adduct.

Three experiments were conducted to determine the effect of three fermented amino acids (AA) with their respective biomass compared to crystalline AA on the growth performance of swine and poultry. In experiment 1, 315 barrows (DNA 200 × 400, initially 11.3 ± 0.69 kg) were allotted to 1 of 4 dietary treatments with 5 pigs per pen and 15 or 16 pens per treatment. Dietary treatments included a negative control (16% standardized ileal digestible [SID] Tryptophan:lysine [Trp:Lys] ratio), positive control (21% SID Trp:Lys ratio from crystalline Trp), or diets containing Trp with biomass to provide 21 or 23.5% SID Trp:Lys ratios, respectively. Pigs fed the positive control or low Trp with biomass diet had increased (P < 0.05) ADG compared to pigs fed the negative control diet, with pigs fed the high Trp with biomass diet intermediate. Pigs fed the low Trp with biomass diet had increased (P < 0.05) G:F compared to the negative control diet, with others intermediate. In experiment 2, 1,320 1-d-old male broilers (Cobb 500, initially 45.2 g) were allotted to one of four dietary treatments with 33 birds per pen and 10 pens per treatment. Dietary treatments included a negative control (58/58% Threonine:lysine [Thr:Lys] ratio), positive control (65/66% Thr:Lys ratio from crystalline Thr), or diets containing Thr with biomass to provide 65/66 or 69/70% Thr:Lys ratios in starter and grower diets, respectively. Broilers fed the positive control or Thr with biomass diets had increased (P < 0.05) ADG compared to broilers fed the negative control diet. Broilers fed the positive control or the low Thr with biomass diet had increased (P < 0.05) G:F compared to the negative control and high Thr with biomass treatments. In experiment 3, 2,100 one-day-old male broilers (Cobb 500, initially 39.4 g) were allotted to one of four dietary treatments with 35 birds per pen and 15 pens per treatment. Dietary treatments included a negative control (59/63% Valine:lysine [Val:Lys] ratio), positive control (75/76% Val:Lys ratio from crystalline Val), or diets containing Val with biomass to provide 75/76 or 84/83% Val:Lys ratios in starter and grower diets, respectively. Broilers fed the positive control or Val with biomass diets had increased (P < 0.05) ADG, ADFI, and G:F compared to those fed the negative control diet. In conclusion, Trp, Thr, or Val with their respective biomass appear to be equally bioavailable and a suitable alternative to crystalline AA in swine and poultry diets.

σV is an extracytoplasmic function (ECF) σ factor that is found exclusively in Firmicutes including Bacillus subtilis and the opportunistic pathogens Clostridioides difficile and Enterococcus faecalis. σV is activated by lysozyme and is required for lysozyme resistance. The activity of σV is normally inhibited by the anti-σ factor RsiV, a transmembrane protein. RsiV acts as a receptor for lysozyme. The binding of lysozyme to RsiV triggers a signal transduction cascade which results in degradation of RsiV and activation of σV . Like the anti-σ factors for several other ECF σ factors, RsiV is degraded by a multistep proteolytic cascade that is regulated at the step of site-1 cleavage. Unlike other anti-σ factors, site-1 cleavage of RsiV is not dependent upon a site-1 protease whose activity is regulated. Instead constitutively active signal peptidase cleaves RsiV at site-1 in a lysozyme-dependent manner. The activation of σV leads to the transcription of genes, which encode proteins required for lysozyme resistance.

The sequential vapor infiltration (SVI) method, based on atomic layer deposition chemistry, allows the creation of a polymer–inorganic hybrid material through the diffusion of metal–organic vapor reagents into a polymer substrate. This study investigates the reactivity of the ester, amide, and carboxylic acid functional groups of poly(methyl methacrylate) (PMMA), poly(vinylpyrrolidone) (PVP), and poly(acrylic acid) (PAA), respectively, in the presence of trimethylaluminum (TMA) vapor. This work explores the possible reaction mechanisms of these functional groups through in situ Fourier transform infrared spectroscopy and ab initio quantum chemical analysis. At temperatures of ≤100 °C, TMA physisorbs to the carbonyl groups of PMMA. As the temperature is increased, TMA forms a covalent bond with PMMA. TMA physisorbs to PVP and then partially desorbs in the presence of water for all studied temperatures of ≤150 °C. PAA readily reacts with TMA to form a covalent bond with the carbonyl group at 60 °C. This inc...

2-Functionalised pyrroles exhibit considerable synthetic utility. Herein, the synthesis and reactivity of 2-thionoester (-C(S)OR) pyrroles is reported. 2-Thionoester pyrroles were synthesised using a Knorr-type approach from aliphatic starting materials. 2-Thionoester pyrroles were reduced to the corresponding 2-formyl pyrroles, or the deuterated formyl variant, in one step using RANEY® nickel, thereby removing the need for the much-utilised hydrolysis/decarboxylation/formylation steps that are typically required to convert Knorr-type 2-carboxylate pyrroles into 2-formyl pyrroles. 2-Thionoester pyrroles proved tolerant of typical functional group interconversions for which the parent 2-carboxylate pyrroles have become known.

Replacement of the exocrine parenchyma by fibrous tissue is a main characteristic of chronic pancreatitis. Understanding the mechanisms of pancreatic fibrogenesis is critical for the development of preventive and therapeutic interventions. Cyclooxygenase-2 (COX-2), a rate-limiting enzyme for prostaglandin synthesis, is expressed in patients with chronic pancreatitis. However, it is unknown whether COX-2 can cause chronic pancreatitis. To investigate the roles of pancreatic acinar COX-2 in fibrogenesis and the development of chronic pancreatitis, COX-2 was ectopically expressed specifically in pancreatic acinar cells in transgenic mice. Histopathological changes and expression levels of several profibrogenic factors related to chronic pancreatitis were evaluated. COX-2 was expressed in the pancreas of the transgenic mice, as detected by Western blot analysis. Immunohistochemical staining showed COX-2 was specifically expressed in pancreatic acinar cells. COX-2 expression led to progressive changes in the pancreas, including pancreas megaly, persistent inflammation, collagen deposition, and acinar-to-ductal metaplasia. Quantitative RT-PCR and immunostaining showed that profibrogenic factors were upregulated and pancreatic stellate cells were activated in the COX-2 transgenic mice. Expression of COX-2 in pancreatic acinar cells is sufficient to induce chronic pancreatitis. Targeting this pathway may be valuable in the prevention of chronic pancreatitis. NEW & NOTEWORTHY COX-2 expression is observed in pancreatic tissues of human chronic pancreatitis. In this study, we showed that COX-2 expression caused the development of chronic pancreatitis in transgenic mice, supporting the idea that COX-2 inhibition may be an effective preventive and therapeutic strategy.

Purpose. Lutein, RR-zeaxanthin, and RS-zeaxanthin (L-Z) are antioxidants which can reduce endoplasmic reticulum stress (ERS) and oxidative stress (OS), and ameliorate neurodegenerative diseases. However, their treatment effect in the Pde6brd10 (rd10) mouse model of retinitis pigmentosa (RP) and the underlying cellular mechanisms have not been studied. ERS is an important factor which causes photoreceptor apoptosis. The aim of the current project is to test the treatment effect of L-Z in rd10 mice and to investigate the underlying molecular mechanisms of ERS. Methods. L-Z (Lutemax 2020, 10 mg/kg) diluted in sunflower oil (SFO, 1 mg/ml) or the same volume of SFO was administrated via gavage from postnatal day 6 (P6) to P20 daily in L-Z group (n=5) or SFO group (n=6) of rd10 mice. At P21, electroretinography (ERG) was performed to show the functional change of retinas. 78 kDa glucose-regulated protein (GRP78) and endoplasmic reticulum protein 29 (ERp29) were tested by western blot and immunostaining. Results. The ERG amplitudes were larger in the L-Z group than those of the SFO group in all flash luminances of dark-adapted and light-adapted ERG (all p < 0.01). Western blot revealed that GRP78 in the retinas of the L-Z group was significantly downregulated compared to that of the SFO group (p < 0.01). Meanwhile, the retinal ERp29 protein was significantly upregulated in the L-Z treatment group than that of the SFO group (p < 0.01). Conclusions. L-Z provide protection to the photoreceptors of rd10 mouse model of RP, which is probably associated with the reduction of ERS.

A new method of brominating aromatic and heteroaromatic ring systems is investigated. The combination of hydrobromic acid as the halogen source, hydrogen peroxide as the oxidant, and ethanol, water, or no solvent are evaluated as greener conditions than those that have been previously published. The new conditions give high yields and good regioselectivity for a variety of substrates when the ring is activated by electron-donating groups or heteroatoms. Phenols, anisole, thiophenes, and pyrrole give comparable or superior results when compared to a traditional bromination by N-bromosuccinimide in tetrahydrofuran. Other nitrogen-containing heterocycles do not react under the conditions because they are protonated and hence deactivated; similarly, substrates with electron-withdrawing groups are not brominated. The reaction is very tolerant of a variety of functional groups.

The critical role that bacterial methanotrophs have in regulating the environmental concentrations of the potent greenhouse gas, methane, under aerobic conditions is dependent on monooxygenase enzymes which oxidise the substrate as both a carbon and energy source. Despite the importance of these organisms, the evolutionary origins of aerobic methane oxidation capability and its relationship to proteobacterial evolution is not well understood. Here we investigated the phylogenetic relationship of proteobacterial methanotrophs with related, non-methanotrophic bacteria using 16S rRNA and the evolution of two forms of methane monooxygenase: membrane bound (pMMO and pXMO) and cytoplasmic (sMMO). Through analysis we have concluded that extant proteobacterial methanotrophs evolved from up to five ancestral species, and that all three methane monooxygenase systems, pMMO, pXMO and sMMO, were likely present in the ancestral species (although pXMO and sMMO are not present in most of the present day methanotrophs). Here we propose that the three monooxygenase systems entered the ancestral species by horizontal gene transfer, with these likely to have pre-existing physiological and metabolic attributes that supported conversion to methanotrophy. Further, we suggest that prior to these enzyme systems developing methane oxidation capabilities, the membrane-bound and cytoplasmic monooxygenases were already both functionally and phylogenetically associated. These results not only suggest that sMMO and pXMO have a far greater role in methanotrophic evolution than previously understood but also implies that the co-inheritance of membrane bound and cytoplasmic monooxygenases have roles additional to that of supporting methanotrophy.

In Saccharomyces cerevisiae, RNA Polymerase II (Pol II) selects transcription start sites (TSS) by a unidirectional scanning process. During scanning, a preinitiation complex (PIC) assembled at an upstream core promoter initiates at select positions within a window ∼40-120 basepairs downstream. Several lines of evidence indicate that Ssl2, the yeast homolog of XPB and an essential and conserved subunit of the general transcription factor (GTF) TFIIH, drives scanning through its DNA-dependent ATPase activity, therefore potentially controlling both scanning rate and scanning extent (processivity). To address questions of how Ssl2 functions in promoter scanning and interacts with other initiation activities, we leveraged distinct initiation-sensitive reporters to identify novel ssl2 alleles. These ssl2 alleles, many of which alter residues conserved from yeast to human, confer either upstream or downstream TSS shifts at the model promoter ADH1 and genome-wide. Specifically, tested ssl2 alleles alter TSS selection by increasing or narrowing the distribution of TSSs used at individual promoters. Genetic interactions of ssl2 alleles with other initiation factors are consistent with ssl2 allele classes functioning through increasing or decreasing scanning processivity but not necessarily scanning rate. These alleles underpin a residue interaction network that likely modulates Ssl2 activity and TFIIH function in promoter scanning. We propose that the outcome of promoter scanning is determined by two functional networks, the first being Pol II activity and factors that modulate it to determine initiation efficiency within a scanning window, and the second being Ssl2/TFIIH and factors that modulate scanning processivity to determine the width of the scanning widow.

Thiolutin is a well-known and long-used natural product transcription inhibitor with an unresolved mode of action. Recent studies have identified Zn2+-chelation activity for both thiolutin and the related dithiolopyrrolone holomycin, with direct inhibition of RNA polymerases ruled out as a mode of action. However, negative results for direct transcription inhibition of RNA polymerases in recent studies are contradicted by previously observed thiolutin inhibition of extract fractions containing yeast RNA Polymerases I, II, and III. Here, we present chemical genetic and biochemical approaches to investigate the mode of action of thiolutin. We identify diverse classes of mutant that alter sensitivity to thiolutin. We functionally dissect the multidrug resistance and thioredoxin pathways controlling thiolutin sensitivity. We provide genetic evidence that thiolutin causes oxidation of thioredoxinsin vivoand suggest that thiolutin both induces oxidative stress and alters Zn2+, Cu2+and Mn2+homeostasisin vivo, recapitulating previously observed thiolutin interactions with Zn2+. Finally, our results resolve contradictory biochemical results for thiolutin inhibition of transcription by direct demonstration of thiolutin inhibition of RNA polymerase II (Pol II)in vitro. Inhibitory activity requires both appropriate reduction of thiolutin and the presence of Mn2+. Thio/Mn2+inhibition is abrogated when template DNA is pre-bound to Pol II or when excess DTT is present, and renders Pol II pause prone in elongation if initiation is bypassed using a pre-formed Pol II elongation complex. Together, we propose that thiolutin directly inhibits Pol II transcription through a novel mechanism distinct from known transcription inhibitors.

β-Lactams are a class of antibiotics that target the synthesis of peptidoglycan, an essential component of the cell wall. β-Lactams inhibit the function of penicillin-binding proteins (PBPs), which form the cross-links between strands of peptidoglycan. Resistance to β-lactams complicates the treatment of bacterial infections. In recent years, the spread of β-lactam resistance has increased with growing intensity. Resistance is often conferred by β-lactamases, which inactivate β-lactams, or the expression of alternative β-lactam-resistant PBPs. σP is an extracytoplasmic function (ECF) σ factor that controls β-lactam resistance in the species Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis σP is normally held inactive by the anti-σ factor RsiP. σP is activated by β-lactams that trigger the proteolytic destruction of RsiP. Here, we identify the penicillin-binding protein PbpP and demonstrate its essential role in the activation of σP Our data show that PbpP is required for σP activation and RsiP degradation. Our data suggest that PbpP acts as a β-lactam sensor since the binding of a subset of β-lactams to PbpP is required for σP activation. We find that PbpP likely directly or indirectly controls site 1 cleavage of RsiP, which results in the degradation of RsiP and, thus, σP activation. σP activation results in increased expression of β-lactamases and, thus, increased β-lactam resistance. This work is the first report of a PBP acting as a sensor for β-lactams and controlling the activation of an ECF σ factor.IMPORTANCE The bacterial cell envelope is the target for numerous antibiotics. Many antibiotics target the synthesis of peptidoglycan, which is a central metabolic pathway essential for bacterial survival. One of the most important classes of antibiotics has been β-lactams, which inhibit the transpeptidase activity of penicillin-binding proteins to decrease the cross-linking of peptidoglycan and the strength of the cell wall. While β-lactam antibiotics have historically proven to be effective, resistance to β-lactams is a growing problem. The ECF σ factor σP is required for β-lactam resistance in B. thuringiensis and close relatives, including B. anthracis Here, we provide insight into the mechanism of activation of σP by β-lactams.

Branched-chain amino acids (BCAA) and their cognate α-ketoacids (BCKA) are elevated in an array of cardiometabolic diseases. Here we demonstrate that the major metabolic fate of uniformly-13C-labeled α-ketoisovalerate ([U-13C]KIV) in the heart is reamination to valine. Activation of cardiac branched-chain α-ketoacid dehydrogenase (BCKDH) by treatment with the BCKDH kinase inhibitor, BT2, does not impede the strong flux of [U-13C]KIV to valine. Sequestration of BCAA and BCKA away from mitochondrial oxidation is likely due to low levels of expression of the mitochondrial BCAA transporter SLC25A44 in the heart, as its overexpression significantly lowers accumulation of [13C]-labeled valine from [U-13C]KIV. Finally, exposure of perfused hearts to levels of BCKA found in obese rats increases phosphorylation of the translational repressor 4E-BP1 as well as multiple proteins in the MEK-ERK pathway, leading to a doubling of total protein synthesis. These data suggest that elevated BCKA levels found in obesity may contribute to pathologic cardiac hypertrophy via chronic activation of protein synthesis., Systemic modulation of branched-chain keto acid (BCKA) metabolism alters cardiac health. Here, the authors define the major fates of BCKA in the heart and demonstrate that acute exposure to BCKA levels found in obesity activates cardiac protein synthesis and markedly alters the heart phosphoproteome.

Detection of single molecules in biological systems has rapidly increased in resolution over the past decade. However, delivery of single molecules has remained a challenge. Currently there is no effective method that can both introduce a precise amount of molecules onto or into a single cell at a defined position, and then image the cellular response. Here we have combined light sheet microscopy with local delivery, using a nanopipette, to accurately deliver individual proteins to a defined position. We call this method local delivery selective plane illumination microscopy (ldSPIM). ldSPIM uses a nanopipette and the ionic feedback current at the nanopipette tip to control the position from which molecules are delivered. The number of proteins delivered can be controlled by varying the voltage applied. For single-molecule detection, we implemented single-objective SPIM using a reflective atomic force microscopy cantilever to create a 2µm thin sheet. Using this setup, we demonstrate that ldSPIM can deliver single fluorescently-labeled proteins onto the plasma membrane of HK293 cells or into the cytoplasm. Next, we deposited aggregates of amyloid-β, which causes proteotoxicity relevant to Alzheimer’s disease, onto a single macrophage stably expressing a MyDD88-eGFP fusion construct. Whole-cell imaging in 3D mode enables live detection of MyDD88 accumulation and formation of MyDDosome signaling complexes, as a result of aggregate-induced triggering of toll-like receptor 4. Overall, we demonstrate a novel multifunctional imaging system capable of precise delivery of single proteins to a specific location on the cell surface or inside the cytoplasm and high-speed 3D detection at single-molecule resolution within live cells.Statement of SignificanceThis paper describes and validates a new method to study biological processes based on the controlled local delivery of molecules onto or into the cell, combined with single molecule imaging using light sheet microscopy. we not only demonstrate the instrument’s capability of delivering controlled numbers of molecules to a defined position, down to the level of single molecules, but also its potential in study of the triggering of the innate immune response by protein aggregates, a key process in the development of neurodegenerative diseases such as Alzheimer’s disease. The same approach could be applied to a wide range of other important biological processes allowing them to be followed in live cells in real-time, hence it will be of great interest to the biophysical community.

The coat protein I (COPI) complex mediates retrograde trafficking from the Golgi to the endoplasmic reticulum (ER). Five siblings with persistent bacterial and viral infections and defective humoral and cellular immunity had a homozygous p.K652E mutation in the γ1 subunit of COPI (γ1-COP). The mutation disrupts COPI binding to the KDEL receptor and impairs the retrieval of KDEL-bearing chaperones from the Golgi to the ER. Homozygous Copg1(K652E) mice had increased ER stress in activated T and B cells, poor antibody responses, and normal numbers of T cells that proliferated normally, but underwent increased apoptosis upon activation. Exposure of the mutants to pet store mice caused weight loss, lymphopenia, and defective T cell proliferation that recapitulated the findings in the patients. The ER stress-relieving agent tauroursodeoxycholic acid corrected the immune defects of the mutants and reversed the phenotype they acquired following exposure to pet store mice. This study establishes the role of γ1-COP in the ER retrieval of KDEL-bearing chaperones and thereby the importance of ER homeostasis in adaptive immunity.

We report a rapid isothermal method for detecting SARS-CoV-2, the virus responsible for COVID-19. The procedure uses a novel reverse transcriptase-free (RTF) approach for converting RNA into DNA, which triggers a rapid amplification using the Exponential Amplification Reaction (EXPAR). Deploying the RNA-to-DNA conversion and amplification stages of the RTF-EXPAR assay in a single step results in the detection of a sample of patient SARS-CoV-2 RNA in under 5 minutes.