MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor.

MOTIVATION: Imaging-based spatial transcriptomics (ST) technologies have achieved subcellular resolution, enabling detection of individual molecules in their native tissue context. Data associated with these technologies promise unprecedented opportunity toward understanding cellular and subcellular biology. However, in R/Bioconductor, there is a scarcity of existing computational infrastructure to represent such data, and particularly to summarize and transform it for existing widely adopted computational tools in single-cell transcriptomics analysis, including SingleCellExperiment and SpatialExperiment (SPE) classes. With the emergence of several commercial offerings of imaging-based ST, there is a pressing need to develop consistent data structure standards for these technologies at the individual molecule-level. RESULTS: To this end, we have developed MoleculeExperiment, an R/Bioconductor package, which (i) stores molecule and cell segmentation boundary information at the molecule-level, (ii) standardizes this molecule-level information across different imaging-based ST technologies, including 10× Genomics' Xenium, and (iii) streamlines transition from a MoleculeExperiment object to a SpatialExperiment object. Overall, MoleculeExperiment is generally applicable as a data infrastructure class for consistent analysis of molecule-resolved spatial omics data. AVAILABILITY AND IMPLEMENTATION: The MoleculeExperiment package is publicly available on Bioconductor at https://bioconductor.org/packages/release/bioc/html/MoleculeExperiment.html. Source code is available on Github at: https://github.com/SydneyBioX/MoleculeExperiment. The vignette for MoleculeExperiment can be found at https://bioconductor.org/packages/release/bioc/html/MoleculeExperiment.html.

Repurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast.

Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1ABA/HAB1 and PYR1*MANDI/HAB1*) for high dynamic-range gene activation and repression controlled by either abscisic acid (ABA) or mandipropamid (mandi). To redirect metabolic flux towards ethyl acetate biosynthesis, we simultaneously repress pyruvate dehydrogenase (PDA1) and activate pyruvate decarboxylase (PDC1) to enhance ethyl acetate titers. Thus, we have developed new tools for chemically tuning gene expression in K. marxianus and S. cerevisiae that should be deployable across many non-conventional eukaryotic hosts.

Optimized genome-wide CRISPR screening enables rapid engineering of growth-based phenotypes in Yarrowia lipolytica.

CRISPR-Cas9 functional genomic screens uncover gene targets linked to various phenotypes for metabolic engineering with remarkable efficiency. However, these genome-wide screens face a number of design challenges, including variable guide RNA activity, ensuring sufficient genome coverage, and maintaining high transformation efficiencies to ensure full library representation. These challenges are prevalent in non-conventional yeast, many of which exhibit traits that are well suited to metabolic engineering and bioprocessing. To address these hurdles in the oleaginous yeast Yarrowia lipolytica, we designed a compact, high-activity genome-wide sgRNA library. The library was designed using DeepGuide, a sgRNA activity prediction algorithm and a large dataset of ∼50,000 sgRNAs with known activity. Three guides per gene enables redundant targeting of 98.8% of genes in the genome in a library of 23,900 sgRNAs. We deployed the optimized library to uncover genes essential to the tolerance of acetate, a promising alternative carbon source, and various hydrocarbons present in many waste streams. Our screens yielded several gene knockouts that improve acetate tolerance on their own and as double knockouts in media containing acetate as the sole carbon source. Analysis of the hydrocarbon screens revealed genes related to fatty acid and alkane metabolism in Y. lipolytica. The optimized CRISPR gRNA library and its successful use in Y. lipolytica led to the discovery of alternative carbon source-related genes and provides a workflow for creating high-activity, compact genome-wide libraries for strain engineering.

Quantification of Free Radicals from Vaping Electronic Cigarettes Containing Nicotine Salt Solutions with Different Organic Acid Types and Concentrations.

Electronic (e-) cigarette formulations containing nicotine salts from a range of organic acid conjugates and pH values have dominated the commercial market. The acids in the nicotine salt formulations may alter the redox environment in e-cigarettes, impacting free radical formation in e-cigarette aerosol. Here, the generation of aerosol mass and free radicals from a fourth-generation e-cigarette device was evaluated at 2 wt % nicotine salts (pH 7, 30:70 mixture propylene glycol to vegetable glycerin) across eight organic acids used in e-liquids: benzoic acid (BA), salicylic acid (SLA), lactic acid (LA), levulinic acid (LVA), succinic acid (SA), malic acid (MA), tartaric acid (TA), and citric acid (CA). Furthermore, 2 wt % BA nicotine salts were studied at the following nicotine to acid ratios: 1:2 (pH 4), 1:1 (pH 7), and 2:1 (pH 8), in comparison with freebase nicotine (pH 10). Radical yields were quantified by spin-trapping and electron paramagnetic resonance (EPR) spectroscopy. The EPR spectra of free radicals in the nicotine salt aerosol matched those generated from the Fenton reaction, which are primarily hydroxyl (OH) radicals and other reactive oxygen species (ROS). Although the aerosol mass formation was not significantly different for most of the tested nicotine salts and acid concentrations, notable ROS yields were observed only from BA, CA, and TA under the study conditions. The e-liquids with SLA, LA, LVA, SA, and MA produced less ROS than the 2 wt % freebase nicotine e-liquid, suggesting that organic acids may play dual roles in the production and scavenging of ROS. For BA nicotine salts, it was found that the ROS yield increased with a higher acid concentration (or a lower nicotine to acid ratio). The observation that BA nicotine salts produce the highest ROS yield in aerosol generated from a fourth-generation vape device, which increases with acid concentration, has important implications for ROS-mediated health outcomes that may be relevant to consumers, manufacturers, and regulatory agencies.

Intraoperative Comparison of Measured Resection and Gap Balancing Using a Force Sensor: A Prospective, Randomized Controlled Trial.

BACKGROUND: For establishing femoral component position, gap-balancing (GB) and measured resection (MR) techniques were compared using a force sensor. METHODS: Ninety-one patients were randomized to undergo primary total knee arthroplasty using either MR (n = 43) or GB (n = 48) technique using a single total knee arthroplasty design. GB was performed with an instrumented tensioner. Force sensor data were obtained before the final implantation. RESULTS: GB resulted in greater range of femoral component rotation vs MR (1.5° ± 2.9° vs 3.1° ± 0.5°, P < .05) and posterior condylar cut thickness medially (10.2 ± 2.0 mm vs 9.0 ± 1.3 mm) and laterally (8.5 ± 1.9 mm vs 6.4 ± 1.0 mm). Force sensor data showed a decreased intercompartmental force difference at full flexion in GB (.8 ± 2.3 vs 2.0 ± 3.3u, 1u ≈ 15 N, P < .05). CONCLUSION: GB resulted in a greater range of femoral component rotation and thicker posterior condylar cuts resulting in an increased flexion space relative to MR. Intercompartmental force difference trended toward a more uniform distribution between full extension and full flexion in the GB vs MR group.

Lack of Ikaros cripples expression of Foxo1 and its targets in naive T cells.

Ikaros is a transcription factor that regulates lymphocyte development from the level of the haematopoietic stem cell. Lack of Ikaros reduces the ability of progenitor cells to commit to the T-cell lineage, resulting in reduced numbers of early thymic T-cell progenitors and mature T cells. Mature CD4 T cells that lack Ikaros have defects in proliferation, T helper cell differentiation, cytokine expression and the ability to become anergic. A role for Ikaros in the naive T cell has not yet been identified. The receptors interleukin-7 receptor α (IL-7Rα) and l-selectin are important for ensuring survival and proper homing of naive T cells, respectively. Here we show that lack of Ikaros leads to reduced expression of these receptors in naive T cells, which impacts their ability to home and survive in response to IL-7. We define the mechanism underlying this phenotype as a requirement for Ikaros in maintenance of expression of Foxo1, a transcriptional regulator that is required for their expression. We also demonstrate that CD4 T cells lacking Ikaros are significantly crippled in their ability to become induced regulatory T cells, a phenotype also linked to reduced Foxo1 expression. Finally, we show that restoring Ikaros function to Ikaros-deficient CD4 T cells increases levels of Foxo1 message. Together, these studies define, for the first time, a role for Ikaros in naive T cells and establish it as the first transcriptional regulator required for maintaining levels of Foxo1 gene expression in these cells.

Highly selective pressure-dependent (transfer) hydrogenative depolymerization of polybutylene succinate.

Ru-MACHO®-BH is an effective catalyst for controlled depolymerization of polybutylene succinate. Under low pressure hydrogen the catalyst produces gamma-butyrolactone via a novel transfer hydrogenation wherein dehydrogenation and hydrogenation deconstruct the polymer chain. Simply increasing the hydrogen pressure selectively generates 1,4-butanediol.

GMMA Can Stabilize Proteins Across Different Functional Constraints.

Stabilizing proteins without otherwise hampering their function is a central task in protein engineering and design. PYR1 is a plant hormone receptor that has been engineered to bind diverse small molecule ligands. We sought a set of generalized mutations that would provide stability without affecting functionality for PYR1 variants with diverse ligand-binding capabilities. To do this we used a global multi-mutant analysis (GMMA) approach, which can identify substitutions that have stabilizing effects and do not lower function. GMMA has the added benefit of finding substitutions that are stabilizing in different sequence contexts and we hypothesized that applying GMMA to PYR1 with different functionalities would identify this set of generalized mutations. Indeed, conducting FACS and deep sequencing of libraries for PYR1 variants with two different functionalities and applying a GMMA analysis identified 5 substitutions that, when inserted into four PYR1 variants that each bind a unique ligand, provided an increase of 2-6 °C in thermal inactivation temperature and no decrease in functionality.

Decoding the hallmarks of allograft dysfunction with a comprehensive pan-organ transcriptomic atlas.

The pathogenesis of allograft (dys)function has been increasingly studied using 'omics'-based technologies, but the focus on individual organs has created knowledge gaps that neither unify nor distinguish pathological mechanisms across allografts. Here we present a comprehensive study of human pan-organ allograft dysfunction, analyzing 150 datasets with more than 12,000 samples across four commonly transplanted solid organs (heart, lung, liver and kidney, n = 1,160, 1,241, 1,216 and 8,853 samples, respectively) that we leveraged to explore transcriptomic differences among allograft dysfunction (delayed graft function, acute rejection and fibrosis), tolerance and stable graft function. We identified genes that correlated robustly with allograft dysfunction across heart, lung, liver and kidney transplantation. Furthermore, we developed a transfer learning omics prediction framework that, by borrowing information across organs, demonstrated superior classifications compared to models trained on single organs. These findings were validated using a single-center prospective kidney transplant cohort study (a collective 329 samples across two timepoints), providing insights supporting the potential clinical utility of our approach. Our study establishes the capacity for machine learning models to learn across organs and presents a transcriptomic transplant resource that can be employed to develop pan-organ biomarkers of allograft dysfunction.

Synthesis of high molecular weight polyesters via in vacuo dehydrogenation polymerization of diols.

The Milstein catalyst has proven to be highly effective for the conversion of alcohols to esters, as well as alcohols and amines to amides and polyamides. We have recently found that the catalyst's range can be extended to very efficient in vacuo dehydrogenation polymerization of α,ω-diols to generate polyesters. The gaseous hydrogen byproduct that is produced is easily removed to drive the equilibrium toward product, which leads to the formation of high molecular weight polymer (M(n) up to 145,000 g mol(-1)). This optimized methodology works well to polymerize diols with a spacer of six carbons or more. Diols with fewer carbons are cyclized to lactone; the dividing point is the dehydrogenation of 1,5-pentanediol, which leads to a mixture of polyester and lactone. Reported herein is the synthesis and characterization of five aliphatic polyesters prepared via this novel dehydrogenation polymerization approach.

Rapid biosensor development using plant hormone receptors as reprogrammable scaffolds.

A general method to generate biosensors for user-defined molecules could provide detection tools for a wide range of biological applications. Here, we describe an approach for the rapid engineering of biosensors using PYR1 (Pyrabactin Resistance 1), a plant abscisic acid (ABA) receptor with a malleable ligand-binding pocket and a requirement for ligand-induced heterodimerization, which facilitates the construction of sense-response functions. We applied this platform to evolve 21 sensors with nanomolar to micromolar sensitivities for a range of small molecules, including structurally diverse natural and synthetic cannabinoids and several organophosphates. X-ray crystallography analysis revealed the mechanistic basis for new ligand recognition by an evolved cannabinoid receptor. We demonstrate that PYR1-derived receptors are readily ported to various ligand-responsive outputs, including enzyme-linked immunosorbent assay (ELISA)-like assays, luminescence by protein-fragment complementation and transcriptional circuits, all with picomolar to nanomolar sensitivity. PYR1 provides a scaffold for rapidly evolving new biosensors for diverse sense-response applications.

Tunable high performance cross-linked alkaline anion exchange membranes for fuel cell applications.

Fuel cells are energy conversion devices that show great potential in numerous applications ranging from automobiles to portable electronics. However, further development of fuel cell components is necessary for them to become commercially viable. One component critical to their performance is the polymer electrolyte membrane, which is an ion conductive medium separating the two electrodes. While proton conducting membranes are well established (e.g., Nafion), hydroxide conducting membranes (alkaline anion exchange membranes, AAEMs) have been relatively unexplored by comparison. Operating under alkaline conditions offers significant efficiency benefits, especially for the oxygen reduction reaction; therefore, effective AAEMs could significantly advance fuel cell technologies. Here we demonstrate the use of ring-opening metathesis polymerization to generate new cross-linked membrane materials exhibiting high hydroxide ion conductivity and good mechanical properties. Cross-linking allows for increased ion incorporation, which, in turn supports high conductivities. This facile synthetic approach enables the preparation of cross-linked materials with the potential to meet the demands of hydrogen-powered fuel cells as well as direct methanol fuel cells.

A ring-opening metathesis polymerization route to alkaline anion exchange membranes: development of hydroxide-conducting thin films from an ammonium-functionalized monomer.

We report the development of a facile ring-opening olefin metathesis route to alkaline anion exchange membranes via the copolymerization of a tetraalkylammonium-functionalized norbornene with dicyclopentadiene. The thin films generated are mechanically strong and exhibit high hydroxide conductivities and exceptional methanol tolerance.

Association of surgical approach with complication rate, progression-free survival time, and disease-specific survival time in cats with mammary adenocarcinoma: 107 cases (1991-2014).

OBJECTIVE To evaluate potential associations between surgical approach and complication rate, progression-free survival time, and disease-specific survival time in cats with mammary adenocarcinoma. DESIGN Retrospective case series. ANIMALS 107 client-owned cats. PROCEDURES Medical records of cats that underwent surgical excision of mammary adenocarcinoma by means of a unilateral or bilateral (staged or single-session) mastectomy at 9 hospitals between 1991 and 2014 were reviewed. Relevant clinicopathologic data and details of surgical and adjuvant treatments were recorded. Outcome data were obtained, including postoperative complications, progression-free survival time, and disease-specific survival time. RESULTS Complications occurred in 12 of 61 (19.7%) cats treated with unilateral mastectomy, 5 of 14 (35.7%) cats treated with staged bilateral mastectomy, and 13 of 32 (40.6%) cats treated with single-session bilateral mastectomy. Complications were significantly more likely to occur in cats undergoing bilateral versus unilateral mastectomy. Median progression-free survival time was longer for cats treated with bilateral mastectomy (542 days) than for cats treated with unilateral mastectomy (289 days). Significant risk factors for disease progression included unilateral mastectomy, tumor ulceration, lymph node metastasis, and tumors arising in the fourth mammary gland. Significant risk factors for disease-specific death included lymph node metastasis and development of regional or distant metastasis. Among cats that did not develop metastasis, unilateral mastectomy was a significant risk factor for disease-specific death. Treatment with chemotherapy was associated with a significantly decreased risk of disease-specific death. CONCLUSIONS AND CLINICAL RELEVANCE Results supported bilateral mastectomy for the treatment of mammary adenocarcinoma in cats to improve progression-free and disease-specific survival time. Performing bilateral mastectomy in a staged fashion may help to decrease the complication rate.

Controlled hydrogenative depolymerization of polyesters and polycarbonates catalyzed by ruthenium(II) PNN pincer complexes.

Ruthenium(II) PNN complexes depolymerize many polyesters into diols and polycarbonates into glycols plus methanol via hydrogenation. Notably, polyesters with two methylene units between ester linkages depolymerize to carboxylic acids rather than diols. This methodology represents a new approach for producing useful chemicals from waste plastics.

Childhood metatarsal shaft fractures: treatment outcomes and relative indications for surgical intervention.

PURPOSE: Although the epidemiology of childhood metatarsal fractures is known, the appropriate treatment has not been elucidated. This study was undertaken to ascertain the outcomes of both non-operative and surgical treatment of these common childhood injuries and to discern any indications for treatment. METHODS: A retrospective review was performed of all children identified from 2006 to 2007 with a metatarsal fracture by the ICD-9 code, 825.25. After dividing the cohort into groups by age in years (0-5, 6-10, 11-15, 16 and older), we collected demographics, mechanism of injury, and associated injuries, as well as clinical information concerning metatarsal involvement, treatment, complications, return to activities/sports, and residual pain. Radiographic information was also collected, including fracture location, displacement, comminution, and union. RESULTS: We identified 337 children that met the criteria. The mean age was 10.5 years (range 1.8-20.6). Only ten children had surgery. Only age, multiplicity of metatarsal fracture, and fracture translation was statistically different between the non-surgical and surgical cohorts. None of the patients under the age of 12 years underwent surgical intervention (p = 0.005). Evidence of multiple metatarsal fractures was seen in only 28 % of the non-surgical group compared to 70 % of the surgical group (p = 0.009). The amount of fragment translation significantly correlated with a decision for surgery (p = 0.001), but not angulation. Logistic regression demonstrated that, for every year of age, the likelihood for surgery increased by 32 % and that children were 6.6 times more likely to have surgery if they had multiple metatarsal fractures. Complete union was achieved in 84.6 %, with no difference in treatment groups regarding the time of release to full activities, and of the 50 delayed unions, only two required subsequent operative interventions. Return to sports took longer in the operative group, with a mean of 4.0 compared to 2.1 months (p < 0.001). Only 14 children complained of residual post-treatment pain and all of those cases had been treated without surgery. The presence of post-treatment pain did not correlate with the mechanism of injury or the amount of displacement. CONCLUSION: Each metatarsal injury pattern is unique and surgeons should utilize their clinical judgment to determine appropriate treatment; however, there appears to be some relative indications for surgical treatment. Whereas open and articular fractures may be absolute indications for surgery, the relative indications for surgical intervention in metatarsal shaft fractures appear to be adolescent age and multiple fractures. Successful non-surgical management may consist of a short-leg walking cast for a mean of 4 weeks and activity restrictions for an additional month. However, children should be followed to radiographic union, since 15.4 % may have a delayed union and 4.3 % have short-term residual problems related to the injury.

Probing the adhesive footprints of Mytilus californianus byssus.

California mussels Mytilus californianus owe their tenacity to a holdfast known as the byssus, a fibrous extracellular structure that ends distally in flattened adhesive plaques. The "footprints" of freshly secreted plaques deposited onto glass coverslips were shown by matrix-assisted laser desorption ionization time of flight mass spectrometry to consist chiefly of proteins ranging in mass from 5200 to 6700 Da. These proteins, variants of a family known as mcfp3 (M. californianus foot protein 3), were purified from acetic acid/urea extracts of plaques and foot tissue. Mcfp3 appears to sort into fast and slow electrophoretic variants. Both are rich in Gly and Asn and exhibit post-translational hydroxylation of Tyr and Arg to Dopa and 4-hydroxyarginine, respectively, with the fast variant containing more than twice as much Lys + Arg. Both the slow and fast variants were partially sequenced from the N terminus, and the complete sequences of 12 variants were deduced from cDNA using degenerate oligonucleotides, PCR, and rapid amplification of cDNA ends. Mcfp3s are highly polar molecules and contain up to 28 mol % Dopa, which remains intact and may be crucial for adhesion to metal and mineral surfaces.

Two-dimensional double metal cyanide complexes: highly active catalysts for the homopolymerization of propylene oxide and copolymerization of propylene oxide and carbon dioxide.

The synthesis of two-dimensional double metal cyanide complexes of the formula Co(H2O)2[M(CN)4].4H2O (M=Ni, Pd or Pt) and the X-ray crystal structure of Co(H2O)2[Pd(CN)4].4H2O are presented. The anhydrous forms of these complexes were found to be effective catalyst precursors for the homopolymerization of propylene oxide as well as the random copolymerization of propylene oxide and carbon dioxide to produce poly(propylene oxide-co-propylene carbonate) with no propylene carbonate byproduct. A detailed copolymer microstructure is proposed.

Chromium(II) and chromium(III) complexes supported by tris(2-pyridylmethyl)amine: synthesis, structures, and reactivity.

This report describes the synthesis, structural characterization, and polymerization behavior of a series of chromium(II) and chromium(III) complexes ligated by tris(2-pyridylmethyl)amine (TPA), including chromium(III) organometallic derivatives. For instance, the combination of TPA with CrCl(2) yields monomeric (TPA)CrCl(2) (1). A similar reaction of CrCl(2) with TPA, followed by chloride abstraction with NaBPh(4) or NaBAr(F)(4) (Ar(F) = 3,5-(CF(3))(2)C(6)H(3)), provides the weakly associated cationic dimers [(TPA)CrCl](2)[BPh(4)](2) (2A) and [(TPA)CrCl](2)[BAr(F)(4)](2) (2B), respectively. X-ray crystallographic analysis reveals that each chromium(II) center in 1, 2A, and 2B is a tetragonally elongated octahedron; such Jahn-Teller distortions are consistent with the observed high spin (S = 2) electronic configurations for these chromium(II) complexes. Likewise, reaction of CrCl(3)(THF)(3) with TPA, followed by anion metathesis with NaBPh(4) or NaBAr(F)(4), yields the monomeric, cationic chromium(III) complexes [(TPA)CrCl(2)][BPh(4)] (4A) and [(TPA)CrCl(2)][BAr(F)(4)] (4B), respectively. Treatment of 4A with methyl and phenyl Grignard reagents produces the cationic chromium(III) organometallic derivatives [(TPA)Cr(CH(3))(2)][BPh(4)] (5) and [(TPA)CrPh(2)][BPh(4)] (6), respectively. Similar reactions of 4A with organolithium reagents leads to intractable solids, presumably due to overreduction of the chromium(III) center. X-ray crystallographic analysis of 4A, 5, and 6 confirms that each possesses a largely undistorted octahedral chromium center, consistent with the observed S = (3)/(2) electronic ground states. Compounds 1, 2A, 2B, 4A, 4B, 5, and 6 are all active polymerization catalysts in the presence of methylalumoxane, producing low to moderate molecular weight high-density polyethylene.