Whole proteome analysis of germinating and outgrowing Bacillus subtilis 168.

In this study, we present a high-resolution dataset and bioinformatic analysis of the proteome of Bacillus subtilis 168 trp+ (BSB1) during germination and spore outgrowth. Samples were collected at 14 different time points (ranging from 0 to 130 min) in three biological replicates after spore inoculation into germination medium. A total of 2191 proteins were identified and categorized based on their expression kinetics. We observed four distinct clusters that were analyzed for functional categories and KEGG pathways annotations. The examination of newly synthesized proteins between successive time points revealed significant changes, particularly within the first 50 min. The dataset provides an information base that can be used for modeling purposes and inspire the design of new experiments.

Latest Developments of the Julia-Kocienski Olefination Reaction: Mechanistic Considerations.

Since its discovery, the Julia-Kocienski olefination reaction has over past 30 years become one of the key C-C connective methods that is used in late-stage natural product synthesis. The reaction proceeds under mild reaction conditions, with a wide substrate scope and functional group tolerance range and with high (E) selectivity. In this focused review, we discuss the reaction from a mechanistic point of view and disclose key features that play an important role in reaction selectivity. Finally, the mechanistic aspects of the newly developed modification of the Julia-Kocienski reaction, which allows the formation of both (E) and (Z) olefins from the same reaction partners, are discussed.

Spatio-temporal control of asymmetric septum positioning during sporulation in Bacillus subtilis.

During sporulation, Bacillus subtilis forms an asymmetric septum, dividing the cell into two compartments, a mother cell and a forespore. The site of asymmetric septation is linked to the membrane where FtsZ and SpoIIE initiate the formation of the Z-ring and the E-ring, respectively. These rings then serve as a scaffold for the other cell division and peptidoglycan synthesizing proteins needed to build the septum. However, despite decades of research, not enough is known about how the asymmetric septation site is determined. Here, we identified and characterized the interaction between SpoIIE and RefZ. We show that these two proteins transiently colocalize during the early stages of asymmetric septum formation when RefZ localizes primarily from the mother cell side of the septum. We propose that these proteins and their interplay with the spatial organization of the chromosome play a role in controlling asymmetric septum positioning.

σE of Streptomyces coelicolor can function both as a direct activator or repressor of transcription.

σ factors are considered as positive regulators of gene expression. Here we reveal the opposite, inhibitory role of these proteins. We used a combination of molecular biology methods and computational modeling to analyze the regulatory activity of the extracytoplasmic σE factor from Streptomyces coelicolor. The direct activator/repressor function of σE was then explored by experimental analysis of selected promoter regions in vivo. Additionally, the σE interactome was defined. Taken together, the results characterize σE, its regulation, regulon, and suggest its direct inhibitory function (as a repressor) in gene expression, a phenomenon that may be common also to other σ factors and organisms.

Formation of Domains within a Lower-to-Higher Symmetry Structural Transition in CrI3.

CrI3 represents one of the most important van der Waals systems on the route to understanding 2D magnetic phenomena. Being arranged in a specific layered structure, it also provides a unique opportunity to investigate structural transformations in dimension-confined systems. CrI3 is dimorphic and possesses a higher symmetry low-temperature phase, which is quite uncommon. It contrasts with vanadium trihalides, which show a higher symmetry high-temperature phase. An explanation of this distinct behavior, together with a large cycle-dependent transition hysteresis, is still an open question. Our low-temperature X-ray diffraction study conducted on CrI3 single crystals complemented by magnetization and specific heat measurements was focused mainly on specific features of the structural transition during cooling. Our results manifest that the structural transition during cooling relates to the formation of structural domains despite the lower symmetry structure transforming to a higher symmetry one. We propose that these domains could control the size of thermal hysteresis.

Nd:YAG Single Crystals Grown by the Floating Zone Method in a Laser Furnace.

We report on single crystal growth of laser material Nd:YAG widely used in the applications by the innovative crucible-free floating zone method implemented in an advanced laser optical furnace. We have optimized the parameters for the production of high-quality single crystals of the size typical for laser rods. To reduce the strain and improve machinability, we have developed an afterheater to thermalize the grown part of a single crystal below the hot zone, which is a technique unavailable in common mirror furnaces. The high quality of the single crystals was verified by Laue diffraction, and the internal strain was documented by neutron diffraction. The absorption spectrum corresponds with the parameters of the commercially used material produced by the Czochralski method. The presented methodology for the single crystal growth by the floating zone method with laser heating is applicable for the preparation of other high-quality single crystals of oxide-based materials, particularly in an oxidizing environment unattainable in commonly used crucible methods.

Large Orbital Magnetic Moment in VI3.

The existence of the V3+-ion orbital moment is an open issue of the nature of magnetism in the van der Waals ferromagnet VI3. The huge magnetocrystalline anisotropy in conjunction with the significantly reduced ordered magnetic moment compared to the spin-only value provides strong but indirect evidence of a large V orbital moment. We used the unique capability of X-ray magnetic circular dichroism to determine the orbital component of the total magnetic moment and provide a direct proof of an exceptionally sizable orbital moment of the V3+ ion in VI3. Our ligand field multiplet simulations of the XMCD spectra in synergy with the results of DFT calculations agree with the existence of two V sites with different orbital occupations and OM magnitudes in the ground state.

Enantioselective ß-Selective Addition of Isoxazolidin-5-ones to Allenoates Catalyzed by Quaternary Ammonium Salts.

The enantioselective addition of isoxazolidin-5-ones to the ß-carbon of allenoates has been carried out by using a novel spirobiindane-based quaternary ammonium salt catalyst. This protocol, which proceeds under classical liquid-solid phase-transfer conditions, gives access to unprecedented highly functionalized ß2,2-amino acid derivatives with good enantioselectivities and in high yields, and further manipulations of these products have been carried out as well.

Terahertz Magnetic and Lattice Excitations in van der Waals Ferromagnet VI3.

We use the synergy of infrared, terahertz, and Raman spectroscopies with DFT calculations to shed light on the magnetic and lattice properties of VI3. The structural transition at TS1 = 79 K is accompanied by a large splitting of polar phonon modes. Below TS1, strong ferromagnetic fluctuations are observed. The variations of phonon frequencies at 55 K induced by magnetoelastic coupling enhanced by spin-orbit interaction indicate the proximity of long-range ferromagnetic order. Below TC = 50 K, two Raman modes simultaneously appear and show dramatic softening in the narrow interval around the temperature TS2 of the second structural transition associated with the order-order magnetic phase transition. Below TS2, a magnon in the THz range appears in Raman spectra. The THz magnon observed in VI3 indicates the application potential of 2D van der Waals ferromagnets in ultrafast THz spintronics, which has previously been considered the exclusive domain of antiferromagnets.

LEGO-Lipophosphonoxins: A Novel Approach in Designing Membrane Targeting Antimicrobials.

The alarming rise of bacterial antibiotic resistance requires the development of new compounds. Such compounds, lipophosphonoxins (LPPOs), were previously reported to be active against numerous bacterial species, but serum albumins abolished their activity. Here we describe the synthesis and evaluation of novel antibacterial compounds termed LEGO-LPPOs, loosely based on LPPOs, consisting of a central linker module with two attached connector modules on either side. The connector modules are then decorated with polar and hydrophobic modules. We performed an extensive structure-activity relationship study by varying the length of the linker and hydrophobic modules. The best compounds were active against both Gram-negative and Gram-positive species including multiresistant strains and persisters. LEGO-LPPOs act by first depleting the membrane potential and then creating pores in the cytoplasmic membrane. Importantly, their efficacy is not affected by the presence of serum albumins. Low cytotoxicity and low propensity for resistance development demonstrate their potential for therapeutic use.

Crystal structure evolution in the van der Waals vanadium trihalides.

Most transition-metal trihalides are dimorphic. The representative chromium-based triad, CrCl3, CrBr3, CrI3, is characterized by the low-temperature (LT) phase adopting the trigonal BiI3-type while the structure of the high-temperature (HT) phase is monoclinic of AlCl3type (C2/m). The structural transition between the two crystallographic phases is of the first-order type with large thermal hysteresis in CrCl3and CrI3. We studied crystal structures and structural phase transitions of vanadium-based counterparts VCl3, VBr3, and VI3by measuring specific heat, magnetization, and x-ray diffraction as functions of temperature and observed an inverse situation. In these cases, the HT phase has a higher symmetry while the LT structure reveals a lower symmetry. The structural phase transition between them shows no measurable hysteresis in contrast to CrX3. Possible relations of the evolution of the ratioc/aof the unit cell parameters, types of crystal structures, and nature of the structural transitions in V and Cr trihalides are discussed.

Sulfated phenolic acids in plants.

MAIN CONCLUSION: Sulfated phenolic acids are widely occurring metabolites in plants, including fruits, vegetables and crops. The untargeted UHPLC-QTOF-MS metabolomics of more than 50 samples from plant, fungi and algae lead to the discovery of a small group of sulfated metabolites derived from phenolic acids. These compounds were detected in land plants for the first time. In this study, zosteric acid, 4-(sulfooxy)benzoic acid, 4-(sulfoooxy)phenylacetic acid, ferulic acid 4-sulfate and/or vanillic acid 4-sulfate were detected in a number of edible species/products, including oat (Avena sativa L.), wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), tomato (Solanum lycopersicum L.), carrot (Daucus carota subsp. Sativus Hoffm.), broccoli (Brassica oleracea var. Italica Plenck), celery (Apium graveolens L.), cabbage (Brassica oleracea convar. sabauda L.), banana tree (Musa tropicana L.), pineapple fruit (Ananas comosus L.), radish bulb (Raphanus sativus L.) and olive oil (Olea europaea L.). The structural identification of sulfated compounds was performed by comparing retention times and mass spectral data to those of synthesized standards. In addition to above-mentioned compounds, isoferulic acid 3-sulfate and caffeic acid 4-sulfate were putatively identified in celery bulb (Apium graveolens L.) and broccoli floret (Brassica oleracea var. Italica Plenck), respectively. While sulfated phenolic acids were quantified in concentrations ranging from 0.34 to 22.18 µg·g-1 DW, the corresponding non-sulfated acids were mostly undetected or present at lower concentrations. The subsequent analysis of oat symplast and apoplast showed that they are predominantly accumulated in the symplast (> 70%) where they are supposed to be biosynthesized by sulfotransferases.

Heteroaryl sulfonamide synthesis: scope and limitations.

Heteroaryl sulfonamides are important structural motifs in the medicinal and agrochemical industries. However, their synthesis often relies on the use of heteroaryl sulfonyl chlorides, which are unstable and toxic reagents. Herein, we report a protocol that allows direct oxidative coupling of heteroaryl thiols and primary amines, readily available and inexpensive commodity chemicals. The transformation proceeds under mild reaction conditions and yields the desired N-alkylated sulfonamides in good yields. N-alkyl heteroaryl sulfonamides can be further transformed using a microwave-promoted Fukuyama-Mitsunobu reaction to N,N-dialkyl heteroaryl sulfonamides. The developed protocols thus enable the preparation of previously difficult to prepare sulfonamides (toxic reagents, harsh conditions, and low yields) under mild conditions.

Parameters Influencing the Emission of Ultrafine Particles during 3D Printing.

This paper presents a complex and extensive experimental evaluation of fine particle emissions released by an FDM 3D printer for four of the most common printing materials (ABS, PLA, PET-G, and TPU). These thermoplastic filaments were examined at three printing temperatures within their recommended range. In addition, these measurements were extended using various types of printing nozzles, which influenced the emissions considerably. This research is based on more than a hundred individual measurements for which a standardized printing method was developed. The study presents information about differences between particular printing conditions in terms of the amount of fine particles emitted as well as the particle size distributions during printing periods. This expands existing knowledge about the emission of ultrafine particles during 3D printing, and it can help reduce the emissions of these devices to achieve cleaner and safer 3D printer operations.

Unified Approach to Benzo[d]thiazol-2-yl-Sulfonamides.

In this paper, we report a unified approach to N-substituted and N,N-disubstituted benzothiazole (BT) sulfonamides. Our approach to BT-sulfonamides starts from simple commercially available building blocks (benzo[d]thiazole-2-thiol and primary and secondary amines) that are connected via (a) a S oxidation/S-N coupling approach, (b) a S-N coupling/S-oxidation sequence, or via (c) a S-oxidation/S-F bond formation/SuFEx approach. The labile N-H bond in N-monoalkylated BT-sulfonamides (pKa (BTSO2N(H)Bn) = 3.34 ± 0.05) further allowed us to develop a simple weak base-promoted N-alkylation method and a stereoselective microwave-promoted Fukuyama-Mitsunobu reaction. N-Alkyl-N-aryl BT-sulfonamides were accessed with the help of the Chan-Lam coupling reaction. Developed methods were further used in stereo and chemoselective transformations of podophyllotoxin and several amino alcohols.

Antileishmanial Activity of Lignans, Neolignans, and Other Plant Phenols.

Secondary metabolites (SM) from organisms have served medicinal chemists over the past two centuries as an almost inexhaustible pool of new drugs, drug-like skeletons, and chemical probes that have been used in the "hunt" for new biologically active molecules with a "beneficial effect on human mind and body." Several secondary metabolites, or their derivatives, have been found to be the answer in the quest to search for new approaches to treat or even eradicate many types of diseases that oppress humanity. A special place among SM is occupied by lignans and neolignans. These phenolic compounds are generated biosynthetically via radical coupling of two phenylpropanoid monomers, and are known for their multitarget activity and low toxicity. The disadvantage of the relatively low specificity of phenylpropanoid-based SM turns into an advantage when structural modifications of these skeletons are made. Indeed, phenylpropanoid-based SM previously have proven to offer great potential as a starting point in drug development. Compounds such as Warfarin® (a coumarin-based anticoagulant) as well as etoposide and teniposide (podophyllotoxin-based anticancer drugs) are just a few examples. At the beginning of the third decade of the twenty-first century, the call for the treatment of more than a dozen rare or previously "neglected" diseases remains for various reasons unanswered. Leishmaniasis, a neglected disease that desperately needs new ways of treatment, is just one of these. This disease is caused by more than 20 leishmanial parasites that are pathogenic to humans and are spread by as many as 800 sandfly species across subtropical areas of the world. With continuing climate changes, the presence of Leishmania parasites and therefore leishmaniasis, the disease caused by these parasites, is spreading from previous locations to new areas. Thus, leishmaniasis is affecting each year a larger proportion of the world's population. The choice of appropriate leishmaniasis treatment depends on the severity of the disease and its form of manifestation. The success of current drug therapy is often limited, due in most cases to requiring long hospitalization periods (weeks to months) and the toxicity (side effects) of administered drugs, in addition to the increasing resistance of the parasites to treatment. It is thus important to develop new drugs and treatments that are less toxic, can overcome drug resistance, and require shorter periods of treatment. These aspects are especially important for the populations of developing countries. It was reported that several phenylpropanoid-based secondary metabolites manifest interesting antileishmanial activities and are used by various indigenous people to treat leishmaniasis. In this chapter, the authors shed some light on the various biological activities of phenylpropanoid natural products, with the main focus being on their possible applications in the context of antileishmanial treatment.

Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.

RNA synthesis is central to life, and RNA polymerase (RNAP) depends on accessory factors for recovery from stalled states and adaptation to environmental changes. Here, we investigated the mechanism by which a helicase-like factor HelD recycles RNAP. We report a cryo-EM structure of a complex between the Mycobacterium smegmatis RNAP and HelD. The crescent-shaped HelD simultaneously penetrates deep into two RNAP channels that are responsible for nucleic acids binding and substrate delivery to the active site, thereby locking RNAP in an inactive state. We show that HelD prevents non-specific interactions between RNAP and DNA and dissociates stalled transcription elongation complexes. The liberated RNAP can either stay dormant, sequestered by HelD, or upon HelD release, restart transcription. Our results provide insights into the architecture and regulation of the highly medically-relevant mycobacterial transcription machinery and define HelD as a clearing factor that releases RNAP from nonfunctional complexes with nucleic acids.

Author Correction: Bacterial nanotubes as a manifestation of cell death.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.