Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images.

Autofluorescence microscopy uses intrinsic sources of molecular contrast to provide cellular-level information without extrinsic labels. However, traditional cell segmentation tools are often optimized for high signal-to-noise ratio (SNR) images, such as fluorescently labeled cells, and unsurprisingly perform poorly on low SNR autofluorescence images. Therefore, new cell segmentation tools are needed for autofluorescence microscopy.

Genomic characterization of rare earth binding by Shewanella oneidensis.

Rare earth elements (REE) are essential ingredients of sustainable energy technologies, but separation of individual REE is one of the hardest problems in chemistry today. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for separation of rare earth elements (REE). The REE-biosorption capability of some microorganisms allows for REE separations that, under specialized conditions, are already competitive with solvent extractions, suggesting that genetic engineering could allow it to leapfrog existing technologies.

The Complexity of Comparative Adsorption of C Hydrocarbons (Benzene, Cyclohexane, -Hexane) at Metal-Organic Frameworks.

The relatively stable MOFs Alfum, MIL-160, DUT-4, DUT-5, MIL-53-TDC, MIL-53, UiO-66, UiO-66-NH, UiO-66(F), UiO-67, DUT-67, NH-MIL-125, MIL-125, MIL-101(Cr), ZIF-8, ZIF-11 and ZIF-7 were studied for their C sorption properties. An understanding of the uptake of the larger C molecules cannot simply be achieved with surface area and pore volume (from N sorption) but involves the complex micropore structure of the MOF. The maximum adsorption capacity at p p = 0.

Practical and thermodynamic constraints on electromicrobially accelerated CO mineralization.

By the end of the century, tens of gigatonnes of CO will need to be removed from the atmosphere every year to maintain global temperatures. Natural weathering of ultramafic rocks and subsequent mineralization reactions can convert CO into ultra-stable carbonates. Although this will draw down all excess CO, it will take thousands of years.

Generation of a Gluconobacter oxydans knockout collection for improved extraction of rare earth elements.

Bioleaching of rare earth elements (REEs), using microorganisms such as Gluconobacter oxydans, offers a sustainable alternative to environmentally harmful thermochemical extraction, but is currently not very efficient. Here, we generate a whole-genome knockout collection of single-gene transposon disruption mutants for G. oxydans B58, to identify genes affecting the efficacy of REE bioleaching.

Tetrahydrothiophene-Based Ionic Liquids: Synthesis and Thermodynamic Characterizations.

S-alkyltetrahydrothiophenium, [C THT] bis(trifluorosulfonyl)imide, [NTf ] room temperature ionic liquids (ILs) and tetraphenylborate, [BPh ] salts with alkyl chain lengths from C to C have been prepared. The ILs and salts were characterized and their purity verified by H- and C-nuclear magnetic resonance, elemental analysis, ion chromatography, Karl-Fischer titration, single crystal X-ray diffraction as well as thermogravimetric analysis. The experimentally determined density and viscosity decrease with increasing temperature.

Increase of network hydrophilicity from sql to lvt supramolecular isomers of Cu-MOFs with the bifunctional 4-(3,5-dimethyl-1-pyrazol-4-yl)benzoate linker.

The bifunctional linker 4-(3,5-dimethyl-1H-pyrazol-4-yl)benzoic acid (H2mpba) was used for the synthesis of new (square lattice) sql 2D metal-organic frameworks (MOFs) [Cu(Hmpba)2]·L (L = DMF or ACN) in a solvent-mixture of dimethylformamide/water and acetonitrile/water. These sql 2D MOFs are supramolecular isomers of the lvt 3D network [Cu(Hmpba)2]·4MeOH·1H2O (lvt-MeOH) that was synthesized previously by Richardson and co-workers. All these frameworks are potentially porous structures with solvent molecules included in the channels of the as synthesized materials.

Odd-even effect for efficient bioreactions of chiral alcohols and boosted stability of the enzyme.

We describe a holistic approach for achieving a nearly quantitative conversion for an enzymatic reaction while simultaneously increasing the long-term stability of the enzyme. The approach provided chemical control of bioreactions by utilizing newly synthesized tetrahydrothiophene-based ionic liquids (THT ILs). We showcased its power by using THT-ILs as additives at a low concentration (only 10 mmol L) in the alcohol dehydrogenase (ADH)-catalyzed synthesis of methylated 1-phenylethanol (Me-PE).

Probing the limits of linker substitution in aluminum MOFs through water vapor sorption studies: mixed-MOFs instead of mixed-linker CAU-23 and MIL-160 materials.

We report a systematic study on the possibility of forming mixed-linker metal-organic frameworks (MOFs) spanning between the aluminum MOFs CAU-23 and MIL-160 with their 2,5-thiophenedicarboxylate (TDC) and 2,5-furandicarboxylate (FDC) linkers, respectively. The planned synthesis of a mixed-linker MOF, combining TDC and FDC in the framework turned out to yield a rather largely intricate mixture of CAU-23 and MIL-160. This is due to the different opening angles of 150° for TDC versus 120° for FDC and the concomitant cis-trans versus cis-only OH-bridges in the infinite secondary building unit {Al(μ-OH)(O2C-)} chains.

Synthesis of plasmonic Fe/Al nanoparticles in ionic liquids.

Bottom-up and top-down approaches are described for the challenging synthesis of Fe/Al nanoparticles (NPs) in ionic liquids (ILs) under mild conditions. The crystalline phase and morphology of the metal nanoparticles synthesized in three different ionic liquids were identified by powder X-ray diffractometry (PXRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM), selected-area electron diffraction (SAED) and fast Fourier transform (FFT) of high-resolution TEM images. Characterization was completed by scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) for the analysis of the element composition of the whole sample consisting of the NPs and the amorphous background.

rtl-M-MOFs (M = Cu, Zn) with a T-shaped bifunctional pyrazole-isophthalate ligand showing flexibility and S-shaped Type F-IV sorption isotherms with high saturation uptakes for M = Cu.

Two new rtl-MOFs rtl-[Cu(HIsa-az-dmpz)] and rtl-[Zn(HIsa-az-dmpz)] have been synthesized by using the new bifunctional ligand 5-(4-(3,5-dimethyl-1H-pyrazolyl)azo)isophthalic acid (HIsa-az-dmpz). Both frameworks are potentially porous structures with DMF molecules included in the channels of the as synthesized materials. The flexible MOF rtl-[Cu(HIsa-az-dmpz)] undergoes a reversible phase change into a closed form upon activation.

Aggregation control of Ru and Ir nanoparticles by tunable aryl alkyl imidazolium ionic liquids.

Metal-nanoparticles (M-NPs) were synthesized in a wet-chemical synthesis route in tunable aryl alkyl ionic liquids (TAAILs) based on the 1-aryl-3-alkyl-substituted imidazolium motif from Ru(CO) and Ir(CO) by microwave-heating induced thermal decomposition. The size and size dispersion of the NPs were determined by transmission electron microscopy (TEM) to an average diameter of 2.2(±0.

Synthesis of metal-fluoride nanoparticles supported on thermally reduced graphite oxide.

Metal-fluoride nanoparticles, (MF -NPs) with M = Fe, Co, Pr, Eu, supported on different types of thermally reduced graphite oxide (TRGO) were obtained by microwave-assisted thermal decomposition of transition-metal amidinates, (M{MeC[N(iPr)]} ) or [M(AMD) ] with M = Fe(II), Co(II), Pr(III), and tris(2,2,6,6-tetramethyl-3,5-heptanedionato)europium, Eu(dpm), in the presence of TRGO in the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF]). The crystalline phases of the metal fluorides synthesized in [BMIm][BF] were identified by powder X-ray diffraction (PXRD) to be MF for M = Fe, Co and MF for M = Eu, Pr. The diameters and size distributions of MF @TRGO were from (6 ± 2) to (102 ± 41) nm.

Signaling events during initiation of arbuscular mycorrhizal symbiosis.

Under nutrient-limiting conditions, plants will enter into symbiosis with arbuscular mycorrhizal (AM) fungi for the enhancement of mineral nutrient acquisition from the surrounding soil. AM fungi live in close, intracellular association with plant roots where they transfer phosphate and nitrogen to the plant in exchange for carbon. They are obligate fungi, relying on their host as their only carbon source.

Gene silencing in Medicago truncatula roots using RNAi.

Medicago truncatula is used widely as a model system for studies of root symbioses, interactions with parasitic nematodes and fungal pathogens, as well as studies of development and secondary metabolism. In Medicago truncatula as well as other legumes, RNA interference (RNAi) coupled with Agrobacterium rhizogenes-mediated root transformation, has been used very successfully for analyses of gene function in roots. One of the major advantages of this approach is the ease and relative speed with which transgenic roots can be generated.

A new means to identify type 3 secreted effectors: functionally interchangeable class IB chaperones recognize a conserved sequence.

Unlabelled: Many Gram-negative bacteria utilize specialized secretion systems to inject proteins (effectors) directly into host cells. Little is known regarding how bacteria ensure that only small subsets of the thousands of proteins they encode are recognized as substrates of the secretion systems, limiting their identification through bioinformatic analyses. Many of these proteins require chaperones to direct their secretion.

Protein interaction platforms: visualization of interacting proteins in yeast.

Here we describe the protein interaction platform assay, a method for identifying interacting proteins in Saccharomyces cerevisiae. This assay relies on the reovirus scaffolding protein microNS, which forms large focal inclusions in living cells. When a query protein is fused to microNS and potential interaction partners are fused to a fluorescent reporter, interactors can be identified by screening for yeast that display fluorescent foci.