As a new trend in plasma surface engineering, plasma conditions that allow more-defined chemical reactions at the surface are being increasingly investigated. This is achieved by avoiding high energy deposition via ion bombardment during direct plasma exposure (DPE) causing destruction, densification, and a broad variety of chemical reactions. In this work, a novel approach is introduced by placing a polymer mesh with large open area close to the plasma-sheath boundary above the plasma-treated sample, thus enabling near-plasma chemistry (NPC). The mesh size effectively extracts ions, while reactive neutrals, electrons, and photons still reach the sample surface. The beneficial impact of this on the plasma activation of poly (tetrafluoroethylene) (PTFE) to enhance wettability and on the plasma polymerization of siloxanes, combined with the etching of residual hydrocarbons to obtain highly porous SiOx coatings at low temperatures, is discussed. Characterization of the treated samples indicates a predominant chemical modification yielding enhanced film structures and durability.

Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in the presence of GVL, we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast.

Protein-based therapeutics have led to new paradigms in disease treatment. Projected to be half of the top ten selling drugs in 2023, proteins have emerged as rivaling and, in some cases, superior alternatives to historically used small molecule-based medicines. This review chronicles both well-established and emerging design strategies that have enabled this paradigm shift by transforming protein-based structures that are often prone to denaturation, degradation, and aggregation in vitro and in vivo into highly effective therapeutics. In particular, we discuss strategies for creating structures with increased affinity and targetability, enhanced in vivo stability and pharmacokinetics, improved cell permeability, and reduced amounts of undesired immunogenicity.

Trimethoprim and sulfamethoxazole are used commonly together as cotrimoxazole for the treatment of urinary tract and other infections. The evolution of resistance to these and other antibacterials threatens therapeutic options for clinicians. We generated and analysed a chemical-biology-whole-genome data set to predict new targets for antibacterial combinations with trimethoprim and sulfamethoxazole. For this we used a large transposon mutant library in Escherichia coli BW25113 where an outward-transcribing inducible promoter was engineered into one end of the transposon. This approach allows regulated expression of adjacent genes in addition to gene inactivation at transposon insertion sites, a methodology that has been called TraDIS-Xpress. These chemical genomic data sets identified mechanisms for both reduced and increased susceptibility to trimethoprim and sulfamethoxazole. The data identified that over-expression of FolA reduced trimethoprim susceptibility, a known mechanism for reduced susceptibility. In addition, transposon insertions into the genes tdk, deoR, ybbC, hha, ldcA, wbbK and waaS increased susceptibility to trimethoprim and likewise for rsmH, fadR, ddlB, nlpI and prc with sulfamethoxazole, while insertions in ispD, uspC, minC, minD, yebK, truD and umpG increased susceptibility to both these antibiotics. Two of these genes' products, Tdk and IspD, are inhibited by AZT and fosmidomycin respectively, antibiotics that are known to synergise with trimethoprim. Thus, the data identified two known targets and several new target candidates for the development of co-drugs that synergise with trimethoprim, sulfamethoxazole or cotrimoxazole. We demonstrate that the TraDIS-Xpress technology can be used to generate information-rich chemical-genomic data sets that can be used for antibacterial development.

Tessellation of self-assembling molecular building blocks is a promising strategy to design metal-organic materials exhibiting geometrical frustration and ensuing frustrated physical properties. Appearing in two-dimensional quasiperiodic phases, tilings consisting of five-vertex nodes are regarded as approximants for quasicrystals. Unfortunately, these structural motifs are exceedingly rare due to the complications of acquiring five-fold coordination confined to the plane. Lanthanide ions display the sufficient coordinative plasticity, and large ionic radii, to allow their incorporation into irregular molecule-based arrays. We herein present the use of ytterbium(II) as a five-vertex node in a two-dimensional coordination solid, YbI2(4,4'-bipyridine)2.5. The semi-regular Archimedean tessellation structure verges on quasicrystallinity and paves the way for lanthanide-based metal-organic materials with interesting photonic and magnetic properties.

Target identification for biologically active small molecules remains a major barrier for drug discovery. Cancer cells exhibiting defective DNA mismatch repair (dMMR) have been used as a forward genetics system to uncover compound targets. However, this approach has been limited by the dearth of cancer cell lines that harbor naturally arising dMMR. Here, we establish a platform for forward genetic screening using CRISPR/Cas9 to engineer dMMR into mammalian cells. We demonstrate the utility of this approach to identify mechanisms of drug action in mouse and human cancer cell lines using in vitro selections against three cellular toxins. In each screen, compound-resistant alleles emerged in drug-resistant clones, supporting the notion that engineered dMMR enables forward genetic screening in mammalian cells.

Cell-based transcriptional reporters are invaluable in high-throughput compound and CRISPR screens for identifying compounds or genes that can impact a pathway of interest. However, many transcriptional reporters have weak activities and transient responses. This can result in overlooking therapeutic targets and compounds that are difficult to detect, necessitating the resource-consuming process of running multiple screens at various timepoints. Here, we present RADAR, a digitizer circuit for amplifying reporter activity and retaining memory of pathway activation. Reporting on the AP-1 pathway, our circuit identifies compounds with known activity against PKC-related pathways and shows an enhanced dynamic range with improved sensitivity compared to a classical reporter in compound screens. In the first genome-wide pooled CRISPR screen for the AP-1 pathway, RADAR identifies canonical genes from the MAPK and PKC pathways, as well as non-canonical regulators. Thus, our scalable system highlights the benefit and versatility of using genetic circuits in large-scale cell-based screening.

Information about the interactions between chemical compounds and proteins is indispensable for understanding the regulation of biological processes and the development of therapeutic drugs. Manually extracting such information from biomedical literature is very time and resource consuming. In this study, we propose a computational method to automatically extract chemical-protein interactions (CPIs) from a given text. Our method extracts CPI pairs and CPI triplets from sentences, where a CPI pair consists of a chemical compound and a protein name, and a CPI triplet consists of a CPI pair along with an interaction word describing their relationship. We extracted a diverse set of features from sentences that were used to build multiple machine learning models. Our models contain both simple features, which can be directly computed from sentences, and more sophisticated features derived using sentence structure analysis techniques. For example, one set of features was extracted based on the shortest paths between the CPI pairs or among the CPI triplets in the dependency graphs obtained from sentence parsing. We designed a three-stage approach to predict the multiple categories of CPIs. Our method performed the best among systems that use non-deep learning methods and outperformed several deep-learning-based systems in the track 5 of the BioCreative VI challenge. The features we designed in this study are informative and can be applied to other machine learning methods including deep learning.

Introduction of selectively chemical reactive groups at the cell surface enables site-specific cell surface labeling and modification opportunity, thus facilitating the capability to study the cell surface molecular structure and function and the molecular mechanism it underlies. Further, it offers the opportunity to change or improve a cell's functionality for interest of choice. In this study, two chemical reactive anchor lipids, phosphatidylethanolamine-poly(ethylene glycol)-dibenzocyclooctyne (DSPE-PEG2000-DBCO) and cholesterol-PEG-dibenzocyclooctyne (CHOL-PEG2000-DBCO) were synthesized and their potential application for cell surface re-engineering via lipid fusion were assessed with RAW 264.7 cells as a model cell. Briefly, RAW 264.7 cells were incubated with anchor lipids under various concentrations and at different incubation times. The successful incorporation of the chemical reactive anchor lipids was confirmed by biotinylation via copper-free click chemistry, followed by streptavidin-fluorescein isothiocyanate binding. In comparison, the cholesterol-based anchor lipid afforded a higher cell membrane incorporation efficiency with less internalization than the phospholipid-based anchor lipid. Low cytotoxicity of both anchor lipids upon incorporation into the RAW 264.7 cells was observed. Further, the cell membrane residence time of the cholesterol-based anchor lipid was evaluated with confocal microscopy. This study suggests the potential cell surface re-engineering applications of the chemical reactive anchor lipids.

The stabilizing and function-preserving effects of ectoines have attracted considerable biotechnological interest up to industrial scale processes for their production. These rely on the release of ectoines from high-salinity-cultivated microbial producer cells upon an osmotic down-shock in rather complex processor configurations. There is growing interest in uncoupling the production of ectoines from the typical conditions required for their synthesis, and instead design strains that naturally release ectoines into the medium without the need for osmotic changes, since the use of high-salinity media in the fermentation process imposes notable constraints on the costs, design, and durability of fermenter systems.

The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.

Small interfering RNAs are a new class of drugs, exhibiting sequence-driven, potent, and sustained silencing of gene expression in vivo. We recently demonstrated that siRNA chemical architectures can be optimized to provide efficient delivery to the CNS, enabling development of CNS-targeted therapeutics. Many genetically-defined neurodegenerative disorders are dominant, favoring selective silencing of the mutant allele. In some cases, successfully targeting the mutant allele requires targeting single nucleotide polymorphism (SNP) heterozygosities. Here, we use Huntington's disease (HD) as a model. The optimized compound exhibits selective silencing of mutant huntingtin protein in patient-derived cells and throughout the HD mouse brain, demonstrating SNP-based allele-specific RNAi silencing of gene expression in vivo in the CNS. Targeting a disease-causing allele using RNAi-based therapies could be helpful in a range of dominant CNS disorders where maintaining wild-type expression is essential.

Gas fermentation is one of the promising bioprocesses to convert CO2 or syngas to important chemicals. Thermophilic gas fermentation of volatile chemicals has the potential for the development of consolidated bioprocesses that can simultaneously separate products during fermentation. This study reports the production of acetone from CO2 and H2, CO, or syngas by introducing the acetone production pathway using acetyl-coenzyme A (Ac-CoA) and acetate produced via the Wood-Ljungdahl pathway in Moorella thermoacetica. Reducing the carbon flux from Ac-CoA to acetate through genetic engineering successfully enhanced acetone productivity, which varied on the basis of the gas composition. The highest acetone productivity was obtained with CO-H2, while autotrophic growth collapsed with CO2-H2. By adding H2 to CO, the acetone productivity from the same amount of carbon source increased compared to CO gas only, and the maximum specific acetone production rate also increased from 0.04 to 0.09 g-acetone/g-dry cell/h. Our development of the engineered thermophilic acetogen M. thermoacetica, which grows at a temperature higher than the boiling point of acetone (58 °C), would pave the way for developing a consolidated process with simplified and cost-effective recovery via condensation following gas fermentation.

The current study aimed to describe the fabrication of a composite patch by incorporating marine algae powders (MAPs) into poly-lactic acid (PLA) for bone tissue engineering. The prepared composite patch was functionalized with the co-polymer, poly (2-hydroxyethyl methacrylate-co-ethylene glycol dimethacrylate) (p(HEMA-co-EGDMA)) via initiated chemical vapor deposition (iCVD) to improve its wettability and overall biocompatibility. The iCVD functionalized MAP-PLA composite patch showed superior cell interaction of human osteoblasts. Following the surface functionalization by p(HEMA-co-EGDMA) via the iCVD technique, a highly hydrophilic patch was achieved without tailoring any morphological and structural properties. Moreover, the iCVD modified composite patch exhibited ideal cell adhesion for human osteoblasts, thus making the proposed patch suitable for potential biomedical applications including bone tissue engineering, especially in the fields of dentistry and orthopedy.

We report on a quick, simple, and cost-effective solution-phase approach to prepare centimeter-sized morphology-graded vertically aligned Si nanowire arrays. Gradients in the nanowire diameter and shape are encoded through the macroscale substrate via a "dip-etching" approach, where the substrate is removed from a KOH etching solution at a constant rate, while morphological control at the nanowire level is achieved via sequential metal-assisted chemical etching and KOH etching steps. This combined approach provides control over light absorption and reflection within the nanowire arrays at both the macroscale and nanoscale, as shown by UV-vis spectroscopy and numerical three-dimensional finite-difference time-domain simulations. Macroscale morphology gradients yield arrays with gradually changing optical properties. Nanoscale morphology control is demonstrated by synthesizing arrays of bisegmented nanowires, where the nanowires are composed of two distinct segments with independently controlled lengths and diameters. Such nanowires are important to tailor light-matter interactions in functional devices, especially by maximizing light absorption at specific wavelengths and locations within the nanowires.

An appropriate and reliable sterilization technique is crucial for tissue engineering scaffolds. Skeletal muscle scaffolds are often fabricated using microfilaments of a wide variety of polymers. One method for sterilization is 25 kGy of gamma irradiation. In addition, sterilization through irradiation should administer a dose within a specific range. Radiation directly affects the chemical and mechanical properties of scaffolds. The accuracy and effects of irradiation are often not considered during sterilization procedures; however, these are important since they provide insight on whether the sterilization procedure is reliable and reproducible. This study focused on the chemical and mechanical characterization of 25 kGy gamma-irradiated scaffold. The accuracy and uncertainty of the irradiation procedure were also obtained. X-ray diffraction (XRD) and differential scanning calorimetry (DSC) analyses were performed to determine whether the crystallinity of the polymer changed after irradiation and whether gamma rays influenced its thermal properties. The tensile parameters of the microfilaments were analyzed by comparing irradiated and nonirradiated scaffolds to determine whether gamma radiation changed their elastic behavior. Dose distribution and uncertainty were recorded with several dosimeters. The results showed that the irradiation process slightly affected the mechanical parameters of the scaffold; however, it did not modify its crystallinity or thermal properties. The irradiation was uniform, since the measured uncertainty was low. The scaffold was pathogen-free after 7 days; this meant sterilization was achieved. These results indicated that gamma-sterilized scaffolds were a promising material for use as a skeletal muscle analog material for tissue-engineering applications because they can be sterilized with gamma rays without changing their chemical structure and mechanical properties. This study provided the dose distribution measurement and uncertainty calculations for the sterilization procedure.

Liver transplantation is the ultimate treatment for severe hepatic failure to date. However, the limited supply of donor organs has severely hampered this treatment. So far, great potentials of using mesenchymal stem cells (MSCs) to replenish the hepatic cell population have been shown; nevertheless, there still is a lack of an optimal three-dimensional scaffold for generation of well-transplantable hepatic tissues. In this study, we utilized a cryo-chemical decellularization method which combines physical and chemical approach to generate acellular liver scaffolds (ALS) from the whole liver. The produced ALS provides a biomimetic three-dimensional environment to support hepatic differentiation of MSCs, evidenced by expression of hepatic-associated genes and marker protein, glycogen storage, albumin secretion, and urea production. It is also found that hepatic differentiation of MSCs within the ALS is much more efficient than two-dimensional culture in vitro. Importantly, the hepatic-like tissues (HLT) generated by repopulating ALS with MSCs are able to act as functional grafts and rescue lethal hepatic failure after transplantation in vivo. In summary, the cryo-chemical method used in this study is suitable for decellularization of liver and create acellular scaffolds that can support hepatic differentiation of MSCs and be used to fabricate functional tissue-engineered liver constructs.

A novel bioanalogue hydroxyapatite (HAp)/chitosan phosphate (CSP) nanocomposite has been synthesized by a solution-based chemical methodology with varying HAp contents from 10 to 60% (w/w). The interfacial bonding interaction between HAp and CSP has been investigated through Fourier transform infrared absorption spectra (FTIR) and x-ray diffraction (XRD). The surface morphology of the composite and the homogeneous dispersion of nanoparticles in the polymer matrix have been investigated through scanning electron microscopy (SEM) and transmission electron microscopy (TEM), respectively. The mechanical properties of the composite are found to be improved significantly with increase in nanoparticle contents. Cytotoxicity test using murine L929 fibroblast confirms that the nanocomposite is cytocompatible. Primary murine osteoblast cell culture study proves that the nanocomposite is osteocompatible and highly in vitro osteogenic. The use of CSP promotes the homogeneous distribution of particles in the polymer matrix through its pendant phosphate groups along with particle-polymer interfacial interactions. The prepared HAp/CSP nanocomposite with uniform microstructure may be used in bone tissue engineering applications.

Engineering remains the least gender diverse of the science, technology, engineering and mathematics fields. Chemical engineering (ChE) and electrical engineering (EE) are exemplars of relatively high and low gender diversity, respectively. Here, we investigate departmental, institutional, and regional factors associated with gender diversity among BS graduates within the US, 2010-2016. For both fields, gender diversity was significantly higher at private institutions (p < 1x10-6) and at historically black institutions (p < 1x10-5). No significant association was observed with gender diversity among tenure-track faculty, PhD-granting status, and variations in departmental name beyond the standard "chemical engineering" or "electrical engineering". Gender diversity among EE graduates was significantly decreased (p = 8x10-5) when a distinct degree in computer engineering was available; no such association was observed between ChE gender diversity and the presence of biology-associated degrees. States with a highly gender diverse ChE workforce had a significantly higher degree of gender diversity among BS graduates (p = 3x10-5), but a significant association was not observed for EE. State variation in funding of support services for K-12 pupils significantly impacted gender diversity of graduates in both fields (p < 1x10-3), particularly in regards to instructional staff support (p < 5x10-4). Nationwide, gender diversity could not be concluded to be either significantly increasing or significantly decreasing for either field.