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. Cellpose is a deep learning network that is generalizable across diverse cell microscopy images and automatically segments single cells to improve throughput and reduce inter-human biases. This study aims to validate Cellpose for autofluorescence imaging, specifically from multiphoton intensity images of NAD(P)H. Manually segmented nuclear masks of NAD(P)H images were used to train new Cellpose models. These models were applied to PANC-1 cells treated with metabolic inhibitors and patient-derived cancer organoids (across 9 patients) treated with chemotherapies. These datasets include co-registered fluorescence lifetime imaging microscopy (FLIM) of NAD(P)H and FAD, so fluorescence decay parameters and the optical redox ratio (ORR) were compared between masks generated by the new Cellpose model and manual segmentation. The Dice score between repeated manually segmented masks was significantly lower than that of repeated Cellpose masks (p<0.0001) indicating greater reproducibility between Cellpose masks. There was also a high correlation (R2>0.9) between Cellpose and manually segmented masks for the ORR, mean NAD(P)H lifetime, and mean FAD lifetime across 2D and 3D cell culture treatment conditions. Masks generated from Cellpose and manual segmentation also maintain similar means, variances, and effect sizes between treatments for the ORR and FLIM parameters. Overall, Cellpose provides a fast, reliable, reproducible, and accurate method to segment single cells in autofluorescence microscopy images such that functional changes in cells are accurately captured in both 2D and 3D culture.

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. To identify targets for genomic improvement we screened 3,373 mutants from the whole genome knockout collection of the known REE-biosorbing microorganism Shewanella oneidensis MR-1. We found 130 genes that increased biosorption of the middle REE europium, and 112 that reduced it. We verified biosorption changes from the screen for a mixed solution of three REE (La, Eu, Yb) using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) in solution conditions with a range of ionic strengths and REE concentrations. We identified 18 gene ontologies and 13 gene operons that make up key systems that affect biosorption. We found, among other things, that disruptions of a key regulatory component of the arc system (hptA), which regulates cellular response to anoxic environments and polysaccharide biosynthesis related genes (wbpQ, wbnJ, SO_3183) consistently increase biosorption across all our solution conditions. Our largest total biosorption change comes from our SO_4685, a capsular polysaccharide (CPS) synthesis gene, disruption of which results in an up to 79% increase in biosorption; and nusA, a transcriptional termination/anti-termination protein, disruption of which results in an up to 35% decrease in biosorption. Knockouts of glnA, pyrD, and SO_3183 produce small but significant increases (≈ 1%) in relative biosorption affinity for ytterbium over lanthanum in multiple solution conditions tested, while many other genes we explored have more complex binding affinity changes. Modeling suggests that while these changes to lanthanide biosorption selectivity are small, they could already reduce the length of repeated enrichment process by up to 27%. This broad exploratory study begins to elucidate how genetics affect REE-biosorption by S. oneidensis, suggests new areas of investigation for better mechanistic understanding of the membrane chemistry involved in REE binding, and offer potential targets for improving biosorption and separation of REE by genetic engineering.

The Complexity of Comparative Adsorption of C6 Hydrocarbons (Benzene, Cyclohexane, n-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-NH2, UiO-66(F)4, UiO-67, DUT-67, NH2-MIL-125, MIL-125, MIL-101(Cr), ZIF-8, ZIF-11 and ZIF-7 were studied for their C6 sorption properties. An understanding of the uptake of the larger C6 molecules cannot simply be achieved with surface area and pore volume (from N2 sorption) but involves the complex micropore structure of the MOF. The maximum adsorption capacity at p p0-1 = 0.9 was shown by DUT-4 for benzene, MIL-101(Cr) for cyclohexane and DUT-5 for n-hexane. In the low-pressure range from p p0-1 = 0.1 down to 0.05 the highest benzene uptake is given by DUT-5, DUT-67/UiO-67 and MIL-101(Cr), for cyclohexane and n-hexane by DUT-5, UiO-67 and MIL-101(Cr). The highest uptake capacity at p p0-1 = 0.02 was seen with MIL-53 for benzene, MIL-125 for cyclohexane and DUT-5 for n-hexane. DUT-5 and MIL-101(Cr) are the MOFs with the widest pore window openings/cross sections but the low-pressure uptake seems to be controlled by a complex combination of ligand and pore-size effect. IAST selectivities between the three binary mixtures show a finely tuned and difficult to predict interplay of pore window size with (critical) adsorptive size and possibly a role of electrostatics through functional groups such as NH2.

Practical and thermodynamic constraints on electromicrobially accelerated CO2 mineralization.

By the end of the century, tens of gigatonnes of CO2 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 CO2 into ultra-stable carbonates. Although this will draw down all excess CO2, it will take thousands of years. CO2 mineralization could be accelerated by weathering ultramafic rocks with biodegradable lixiviants. We show that if these lixiviants come from cellulosic biomass, this demand could monopolize the world's biomass supply. We demonstrate that electromicrobial production technologies (EMP) that combine renewable electricity and microbial metabolism could produce lixiviants for as little as $200 to $400 per tonne at solar electricity prices achievable within the decade. We demonstrate that EMP could make enough lixiviants to sequester a tonne of CO2 for less than $100. This work highlights the potential of this approach and the need for extensive R&D.

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. We find 304 genes whose disruption alters the production of acidic biolixiviant. Disruption of genes underlying synthesis of the cofactor pyrroloquinoline quinone (PQQ) and the PQQ-dependent membrane-bound glucose dehydrogenase nearly eliminates bioleaching. Disruption of phosphate-specific transport system genes enhances bioleaching by up to 18%. Our results provide a comprehensive roadmap for engineering the genome of G. oxydans to further increase its bioleaching efficiency.

Tetrahydrothiophene-Based Ionic Liquids: Synthesis and Thermodynamic Characterizations.

S-alkyltetrahydrothiophenium, [Cn THT]+ bis(trifluorosulfonyl)imide, [NTf2 ]- room temperature ionic liquids (ILs) and tetraphenylborate, [BPh4 ]- salts with alkyl chain lengths from C4 to C10 have been prepared. The ILs and salts were characterized and their purity verified by 1 H- and 13 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. The experimental solubility of the [Cn THT][NTf2 ]-ILs in water (75 to 2.2 mg/L for C4 to C10 ) was modelled with very good agreement by Perturbed Chain Statistical Associating Fluid Theory (PC-SAFT), based on the extremely low vapor pressures for the [Cn THT][NTf2 ]-ILs measured in this work (4.15 to 0.037 ⋅ 10-7 ×psat for C4 to C10 ). PC-SAFT is able to predict and correlate different thermodynamic properties by estimating the Helmholtz residual energy.

Increase of network hydrophilicity from sql to lvt supramolecular isomers of Cu-MOFs with the bifunctional 4-(3,5-dimethyl-1H-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. After activation all three materials showed good CO2 adsorption capacity, demonstrated here for lvt-MeOH for the first time, with a saturation uptake of 113 cm3 g-1 (lvt-MeOH-act.), 111 cm3 g-1 (sql-DMF-act.) and 90 cm3 g-1 (sql-ACN-act.) at 195 K. The flexibility of the lvt-MeOH-act. network is evidenced by a gate-opening effect seen in the CO2 measurement at 195 K and under gravimetric high-pressure CO2 adsorption. According to the water and ethanol sorption measurements the new sql frameworks can be categorized as hydrophobic materials in contrast to the hydrophilic lvt framework. In the lvt-MeOH structure the crystal solvent can be replaced with water to yield the structurally authenticated water-only network lvt-H2O containing 3D arrays of S4-symmetric (H2O)20 clusters.

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. At the same time, the CAU-23 phase is accompanied by the polymorphic MIL-53-TDC phase with trans-only OH-bridges. The measurement of water vapor sorption isotherms was the method of choice to confirm the formation of mixed MOFs instead of mixed-linker phases. Thereby, the water sorption isotherms indicate the simultaneous formation of both MOF phases, albeit they do not exclude mixed-linker MOFs which may have formed at low levels of substitution. The differentiation via powder X-ray diffractometry (PXRD), IR-spectroscopy and nitrogen sorption was either not conclusive enough or impossible, due to similarities of the neat MOF phases. The synthesized MOF mixtures within the TDC : FDC ratios of 38 : 62 up to 82 : 18 exhibit two or three uptake steps in the water sorption isotherm, with the first two corresponding to an overlay from the individual water sorption isotherm of CAU-23 and MIL-160 and a third one from the additional MIL-53-TDC.

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. The bottom-up approaches resulted in crystalline FeAl NPs on an amorphous background. The top-down approach revealed small NPs and could be identified as Fe4Al13 NPs which in the IL [OPy][NTf2] yield two absorption bands in the green-blue to green spectral region at 475 and 520 nm which give rise to a complementary red color, akin to appropriate Au NPs.

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-1) in the alcohol dehydrogenase (ADH)-catalyzed synthesis of methylated 1-phenylethanol (Me-PE). We discovered an "odd-even" effect of the IL-cation chain length: Me-PE displayed beneficial interactions with THT ILs having odd-numbered chain lengths and deleterious interactions with those having even-numbered chain lengths. An intermolecular thermodynamic simulation of the bulk phase and critical micelle concentration investigations of the local surroundings of the THT-ILs proved the occurrence of these interactions, and these two methods confirmed the odd-even effect from different perspectives. Additionally, storing the ADH enzyme in pure THT IL at room temperature allowed for a boosted long-term stability of the enzyme (500 times greater than that in aqueous buffer) without the need for freezing.

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 (H3Isa-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. Consequently, rtl-[Cu(HIsa-az-dmpz)] shows S-shaped Type F-IV adsorption profiles or a gate-opening effect at cryogenic temperatures with high saturation uptakes of 360 cm3 g-1 for N2 at 77 K and 310 cm3 g-1 for CO2 at 195 K. These profiles together with the reversibility could be reproduced upon repeated measurements on the same materials. The gravimetric high-pressure CO2 adsorption shows a gate-opening at ∼10 bar with an uptake of 332 mg g-1. rtl-[Zn(HIsa-az-dmpz)] undergoes an irreversible transformation into a non-porous phase 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 Ru3(CO)12 and Ir4(CO)12 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(±0.1) to 3.9(±0.3) nm for Ru-NPs and to an average diameter of 1.4(±0.1) to 2.4(±0.1) nm for Ir-NPs. The TAAILs used contain the same bis(trifluoromethylsulfonyl)imide anion but differ in the substituents on the 1-aryl ring, e.g. 2-methyl-, 4-methoxy- and 2,4-dimethyl groups and in the 3-alkyl chain lengths (C4H9, C5H11, C8H17, C9H19, C11H23). All used TAAILs are suitable for the stabilization of Ru- and Ir-NPs over months in the IL dispersion. Different from all other investigations on M-NP/IL systems which we are aware of the particle separation properties of the TAAILs vary strongly as a function of the aryl substituent. Good NP separation can be achieved with the 4-methoxyphenyl- and 2,4-dimethylphenyl-substituted ILs, irrespective of the 3-alkyl chain lengths. Significant aggregation can be observed for 2-methylphenyl-substituted ILs. The good NP separation can be correlated with a negative electrostatic potential at the 4-methoxyphenyl or 4-methylphenyl substituent that is in the para-position of the aryl ring, whereas the 2-(ortho-)methylphenyl group assumes no negative potential. ε-ePC-SAFT calculations were used to validate that the interactions between ILs and the washing agents (required for TEM analyses) do not cause the observed aggregation/separation behaviour of the M-NPs. Ru-NPs were investigated as catalysts for the solvent-free hydrogenation of benzene to cyclohexane under mild conditions (70 °C, 10 bar) with activities up to 760 (mol cyclohexane) (mol Ru)-1 h-1 and over 95% conversion in ten consecutive runs for Ru-NPs. No significant loss of catalytic activity could be observed.

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

Metal-fluoride nanoparticles, (MF x -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)]2} n ) or [M(AMD) n ] with M = Fe(II), Co(II), Pr(III), and tris(2,2,6,6-tetramethyl-3,5-heptanedionato)europium, Eu(dpm)3, in the presence of TRGO in the ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIm][BF4]). The crystalline phases of the metal fluorides synthesized in [BMIm][BF4] were identified by powder X-ray diffraction (PXRD) to be MF2 for M = Fe, Co and MF3 for M = Eu, Pr. The diameters and size distributions of MF x @TRGO were from (6 ± 2) to (102 ± 41) nm. Energy-dispersive X-ray spectroscopy (EDX) and X-ray photoelectron spectroscopy (XPS) were used for further characterization of the MF x -NPs. Electrochemical investigations of the FeF2-NPs@TRGO as cathode material for lithium-ion batteries were evaluated by galvanostatic charge/discharge profiles. The results indicate that the FeF2-NPs@TRGO as cathode material can present a specific capacity of 500 mAh/g at a current density of 50 mA/g, including a significant interfacial charge storage contribution. The obtained nanomaterials show a good rate capacity as well (220 mAh/g and 130 mAh/g) at a current density of 200 and 500 mA/g, respectively.

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. Much has been discovered in the last decade concerning the signaling events during initiation of the AM symbiosis, including the identification of signaling molecules generated by both partners. This signaling occurs through symbiosis-specific gene products in the host plant, which are indispensable for normal AM development. At the same time, plants have adapted complex mechanisms for avoiding infection by pathogenic fungi, including an innate immune response to general microbial molecules, such as chitin present in fungal cell walls. How it is that AM fungal colonization is maintained without eliciting a defensive response from the host is still uncertain. In this review, we present a summary of the molecular signals and their elicited responses during initiation of the AM symbiosis, including plant immune responses and their suppression.

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. There are several methods, both for the generation of the RNAi constructs and the root transformation. Here we provide details of an RNAi and root transformation protocol that has been used successfully in M. truncatula and which can be scaled up to enable the analysis of several hundred constructs.

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. Here, using the newly described protein interaction platform assay, we demonstrate that type 3 secretion system class IB chaperones from one bacterium directly bind their own effectors as well as those from other species. In addition, we observe that expression of class IB homologs from seven species, including pathogens and endosymbionts, mediate the translocation of effectors from Shigella directly into host cells, demonstrating that class IB chaperones are often functionally interchangeable. Notably, class IB chaperones bind numerous effectors. However, as previously proposed, they are not promiscuous; rather they recognize a defined sequence that we designate the conserved chaperone-binding domain (CCBD) sequence [(LMIF)(1)XXX(IV)(5)XX(IV)(8)X(N)(10)]. This sequence is the first defined amino acid sequence to be identified for any interspecies bacterial secretion system, i.e., a system that delivers proteins directly into eukaryotic cells. This sequence provides a new means to identify substrates of type III secretion systems. Indeed, using a pattern search algorithm for the CCBD sequence, we have identified the first two probable effectors from an endosymbiont, Sodalis glossinidius. IMPORTANCE: Many Gram-negative pathogens utilize type 3 secretion systems to deliver tens of effectors into host cells. In order to understand the diverse ways that these organisms cause disease, it is necessary to identify their effectors, many of which require chaperones to be secreted. Here we establish that class IB chaperones are not promiscuous, as previously proposed, but rather recognize a conserved effector sequence. We demonstrate that pattern search algorithms based on this defined sequence can be used to identify previously unknown effectors. Furthermore, we observe that class IB chaperones from at least seven bacterial species are functionally interchangeable. Not only do they bind and mediate the delivery of their own set of effectors into host cells but they also bind to type 3 substrates from other bacteria, suggesting that inhibitors that block chaperone-effector interactions could provide a novel means to effectively treat infections due to Gram-negative pathogens, including organisms resistant to currently available antibiotics.

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.