Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion

Secondary amines, due to their reactivity, can transform protein templates into catalytically active entities, accelerating the development of artificial enzymes. However, existing methods, predominantly reliant on modified ligands or N-terminal prolines, impose significant limitations on template selection. In this study, genetic code expansion was used to break this boundary, enabling secondary amines to be incorporated into alternative proteins and positions of choice. Pyrrolysine analogues carrying different secondary amines could be incorporated into superfolder green fluorescent protein (sfGFP), multidrug-binding LmrR and nucleotide-binding dihydrofolate reductase (DHFR). Notably, the analogue containing a D-proline moiety demonstrated both proteolytic stability and catalytic activity, conferring LmrR and DHFR with the desired transfer hydrogenation activity. While the LmrR variants were confined to the biomimetic 1-benzyl-1,4-dihydronicotinamide (BNAH) as the hydride source, the optimal DHFR variant favorably used the pro-R hydride from NADPH for stereoselective reactions (e.r. up to 92 : 8), highlighting that a switch of protein template could broaden the nucleophile option for catalysis. Owing to the cofactor compatibility, the DHFR-based secondary amine catalysis could be integrated into an enzymatic recycling scheme. This established method shows substantial potential in enzyme design, applicable from studies on enzyme evolution to the development of new biocatalysts.

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling

Locomotor activity is an innate behavior that can be triggered by gut-motivated conditions, such as appetite and metabolic condition. Various nutrient-sensing receptors distributed in the vagal terminal in the gut are crucial for signal transduction from the gut to the brain. The levels of gut hormones are closely associated with the colonization status of the gut microbiota, suggesting a complicated interaction among gut bacteria, gut hormones, and the brain. However, the detailed mechanism underlying gut microbiota-mediated endocrine signaling in the modulation of locomotion is still unclear. Herein, we show that broad-spectrum antibiotic cocktail (ABX)-treated mice displayed hypolocomotion and elevated levels of the gut hormone glucagon-like peptide-1 (GLP-1). Blockade of the GLP-1 receptor and subdiaphragmatic vagal transmission rescued the deficient locomotor phenotype in ABX-treated mice. Activation of the GLP-1 receptor and vagal projecting brain regions led to hypolocomotion. Finally, selective antibiotic treatment dramatically increased serum GLP-1 levels and decreased locomotion. Colonizing Lactobacillus reuteri and Bacteroides thetaiotaomicron in microbiota-deficient mice suppressed GLP-1 levels and restored the hypolocomotor phenotype. Our findings identify a mechanism by which specific gut microbes mediate host motor behavior via the enteroendocrine and vagal-dependent neural pathways.

Butterflies in the gut: the interplay between intestinal microbiota and stress

Psychological stress is a global issue that affects at least one-third of the population worldwide and increases the risk of numerous psychiatric disorders. Accumulating evidence suggests that the gut and its inhabiting microbes may regulate stress and stress-associated behavioral abnormalities. Hence, the objective of this review is to explore the causal relationships between the gut microbiota, stress, and behavior. Dysbiosis of the microbiome after stress exposure indicated microbial adaption to stressors. Strikingly, the hyperactivated stress signaling found in microbiota-deficient rodents can be normalized by microbiota-based treatments, suggesting that gut microbiota can actively modify the stress response. Microbiota can regulate stress response via intestinal glucocorticoids or autonomic nervous system. Several studies suggest that gut bacteria are involved in the direct modulation of steroid synthesis and metabolism. This review provides recent discoveries on the pathways by which gut microbes affect stress signaling and brain circuits and ultimately impact the host's complex behavior.

Microbial metabolites regulate social novelty via CaMKII neurons in the BNST

Social novelty is a cognitive process that is essential for animals to interact strategically with conspecifics based on their prior experiences. The commensal microbiome in the gut modulates social behavior through various routes, including microbe-derived metabolite signaling. Short-chain fatty acids (SCFAs), metabolites derived from bacterial fermentation in the gastrointestinal tract, have been previously shown to impact host behavior. Herein, we demonstrate that the delivery of SCFAs directly into the brain disrupts social novelty through distinct neuronal populations. We are the first to observe that infusion of SCFAs into the lateral ventricle disrupted social novelty in microbiome-depleted mice without affecting brain inflammatory responses. The deficit in social novelty can be recapitulated by activating calcium/calmodulin-dependent protein kinase II (CaMKII)-labeled neurons in the bed nucleus of the stria terminalis (BNST). Conversely, chemogenetic silencing of the CaMKII-labeled neurons and pharmacological inhibition of fatty acid oxidation in the BNST reversed the SCFAs-induced deficit in social novelty. Our findings suggest that microbial metabolites impact social novelty through a distinct neuron population in the BNST.

Joint predictability of physical frailty/pre-frailty and subjective memory complaints on mortality risk among cognitively unimpaired older adults

The aim of the present study was to investigate how frailty/pre-frailty in combination with subjective memory complaints predicts all-cause mortality in community dwelling cognitively unimpaired older adults. There were 1904 community-dwelling cognitively unimpaired persons aged 65 years or older who participated in the 2013 Taiwan National Health Interview Survey with a 5-year follow-up. Frailty was determined based on the fatigue, resistance, ambulation, illness, and loss of weight (FRAIL) scale. Two questions ("Do you have difficulties with your memory or attention?" and "Do you have difficulties with your memory only or attention only or both?") were used to screen for subjective memory complaints (SMC). In this study, 11.9% of participants had both frailty/pre-frailty and SMC. A total of 239 deaths were recorded after 9009.5 person-years of follow-up. After adjustment for other factors, compared with participants who were physically robust with no SMC, participants who reported either SMC alone (HR = 0.88, 95% CI = 0.60-1.27) or were frail/pre-frail alone (HR = 1.32, 95% CI = 0.90-1.92) had no significantly increased mortality risk. However, coexisting frailty/pre-frailty and SMC was associated with a significantly increased hazard ratio for mortality of 1.48 (95% CI = [1.02-2.16]). Our results highlight the high prevalence of co-occurring frailty/pre-frailty and SMC and that this co-occurrence is associated with an increased risk of mortality among cognitively unimpaired older adults.

The deficiency of poly-β-1,6-N-acetyl-glucosamine deacetylase trigger A. baumannii to convert to biofilm-independent colistin-tolerant cells

Acinetobacter baumannii is a nosocomial pathogen that can be resistant to antibiotics by rapidly modulating its anti-drug mechanisms. The multidrug-resistant A. baumannii has been considered one of the most threatening pathogens to our society. Biofilm formation and persistent cells within the biofilm matrix are recognized as intractable problems, especially in hospital-acquired infections. Poly-β-1,6-N-acetyl-glucosamine (PNAG) is one of the important building blocks in A. baumannii's biofilm. Here, we discover a protein phosphoryl-regulation on PNAG deacetylase, AbPgaB1, in which residue Ser411 was phosphorylated. The phosphoryl-regulation on AbPgaB1 modulates the product turnover rate in which deacetylated PNAG is produced and reflected in biofilm production. We further uncovered the PgaB deficient A. baumannii strain shows the lowest level of biofilm production but has a high minimal inhibition concentration to antibiotic colistin and tetracycline. Based on bactericidal post-antibiotic effects and time-dependent killing assays with antibacterial drugs, we claim that the PgaB-deficient A. baumannii converts to colistin-tolerant cells. This study utilizes a biofilm-independent colistin-tolerant model of A. baumannii to further investigate its characteristics and mechanisms to better understand clinical outcomes.

Towards the use of an amino acid cleavable linker for solid-phase chemical synthesis of peptides and proteins

The synthesis of proteins by solid-phase chemical ligation (SPCL) suffers from the paucity of linkers that can be cleaved under mild conditions. Here, we deployed a spontaneous nickel-assisted cleavage (SNAC) tag, known to undergo spontaneous cleavage in the presence of nickel(II), as a linker for C-to-N SPCL.

Selective Inhibition of Kinase Activity in Mammalian Cells by Bioorthogonal Ligand Tethering

Enzymes are critical for cellular functions, and malfunction of enzymes is closely related to many human diseases. Inhibition studies can help in deciphering the physiological roles of enzymes and guide conventional drug development programs. In particular, chemogenetic approaches enabling rapid and selective inhibition of enzymes in mammalian cells have unique advantages. Here, we describe the procedure for rapid and selective inhibition of a kinase in mammalian cells by bioorthogonal ligand tethering (iBOLT). Briefly, a non-canonical amino acid bearing a bioorthogonal group is genetically incorporated into the target kinase by genetic code expansion. The sensitized kinase can react with a conjugate containing a complementary biorthogonal group linked with a known inhibitory ligand. As a result, tethering of the conjugate to the target kinase allows selective inhibition of protein function. Here, we demonstrate this method by using cAMP-dependent protein kinase catalytic subunit alpha (PKA-Cα) as the model enzyme. The method should be applicable to other kinases, enabling their rapid and selective inhibition.

Genetically Encoded 1,2-Aminothiol for Site-Specific Modification of a Cellular Membrane Protein via TAMM Condensation

Site-specific modification of proteins has wide applications in probing and perturbing biological systems. A popular means to achieve such a modification on a target protein is through a reaction between bioorthogonal functionalities. Indeed, various bioorthogonal reactions have been developed, including a recently reported reaction between 1,2-aminothiol and ((alkylthio)(aryl)methylene)malononitrile (TAMM). Here, we describe the procedure that combines genetic code expansion and TAMM condensation for site-specific modification of cellular membrane proteins. The 1,2-aminothiol functionality is introduced through a genetically incorporated noncanonical amino acid to a model membrane protein on mammalian cells. Treatment of the cells with a fluorophore-TAMM conjugate leads to fluorescent labeling of the target protein. This method can be applied to modify different membrane proteins on live mammalian cells.

Development and verification of the coaxial heterogeneous hyperspectral imaging system

A hyperspectral imaging system (HIS) is a helpful tool that acquires spatial and spectral information from a target. This study developed a coaxial heterogeneous HIS (CHHIS) to collect spectral images with wavelengths ranging from 400 to 1700 nm. In this system, a visible (VIS) spectrometer and a short-wave infrared (SWIR) spectrometer are combined with a coaxial optical path to share the same field of view. This structure reduces the complexity of spatial registration and maintains the scanning duration of two spectrometers as that of a single spectrometer. The spectrometers are also replaceable for extending the detecting spectral range of the system. The calibration methodologies, including spatial correction, spectral calibration, and reflectance calibration, were developed for this system. The signal-to-noise ratio of VIS and SWIR spectrometers in the CHHIS was up to 40 and 60 dB when the exposure time of the VIS and SWIR imaging sensors was 1000 and 10 ms, respectively. When the target distance was at 600 mm, the spatial error of VIS and SWIR images in the scanning direction was less than 1 pixel; these results proved that the system was stable.

Selective Inhibition of Cysteine-Dependent Enzymes by Bioorthogonal Tethering

A general approach for the rapid and selective inhibition of enzymes in cells using a common tool compound would be of great value for research and therapeutic development. We previously reported a chemogenetic strategy that addresses this challenge for kinases, relying on bioorthogonal tethering of a pan inhibitor to a target kinase through a genetically encoded non-canonical amino acid. However, pan inhibitors are not available for many enzyme classes. Here, we expand the scope of the chemogenetic strategy to cysteine-dependent enzymes by bioorthogonal tethering of electrophilic warheads. For proof of concept, selective inhibition of two E2 ubiquitin-conjugating enzymes, UBE2L3 and UBE2D1, was demonstrated in biochemical assays. Further development and optimization of this approach should enable its use in cells as well as with other cysteine-dependent enzymes, facilitating the investigation of their cellular function and validation as therapeutic targets.

Spatio-temporal control of cell death by selective delivery of photo-activatable proteins

Protein therapeutics offer exquisite selectivity in targeting cellular processes and behaviors, but are rarely used against non‐cell surface targets due to their poor cellular uptake. While cell‐penetrating peptides can be used to deliver recombinant proteins to the cytosol, it is generally difficult to selectively deliver active proteins to target cells. Here, we report a recombinantly produced, intracellular protein delivery and targeting platform that uses a photocaged intein to regulate the spatio‐temporal activation of protein activity in selected cells upon irradiation with light. The platform was successfully demonstrated for two cytotoxic proteins to selectively kill cancer cells after photoactivation of intein splicing. This platform can generically be applied to any protein whose activity can be disrupted by a fused intein, allowing it to underpin a wide variety of future protein therapeutics.

Acetylation at Lysine 86 of Escherichia coli HUβ Modulates the DNA-Binding Capability of the Protein

DNA-binding protein HU is highly conserved in bacteria and has been implicated in a range of cellular processes and phenotypes. Like eukaryotic histones, HU is subjected to post-translational modifications. Specifically, acetylation of several lysine residues have been reported in both homologs of Escherichia coli HU. Here, we investigated the effect of acetylation at Lys67 and Lys86, located in the DNA binding-loop and interface of E. coli HUβ, respectively. Using the technique of genetic code expansion, homogeneous HUβ(K67ac) and HUβ(K86ac) protein units were obtained. Acetylation at Lys86 seemed to have negligible effects on protein secondary structure and thermal stability. Nevertheless, we found that this site-specific acetylation can regulate DNA binding by the HU homodimer but not the heterodimer. Intriguingly, while Lys86 acetylation reduced the interaction of the HU homodimer with short double-stranded DNA containing a 2-nucleotide gap or nick, it enhanced the interaction with longer DNA fragments and had minimal effect on a short, fully complementary DNA fragment. These results demonstrate the complexity of post-translational modifications in functional regulation, as well as indicating the role of lysine acetylation in tuning bacterial gene transcription and epigenetic regulation.

Development of mammalian cell logic gates controlled by unnatural amino acids

Mammalian cell logic gates hold great potential for wide-ranging applications. However, most of those currently available are controlled by drug(-like) molecules with inherent biological activities. To construct truly orthogonal circuits and artificial regulatory pathways, biologically inert molecules are ideal molecular switches. Here, we applied genetic code expansion and engineered logic gates controlled by two biologically inert unnatural amino acids. Genetic code expansion relies on orthogonal aminoacyl-tRNA synthetase/tRNA pairs for co-translational and site-specific unnatural amino acid incorporation conventionally in response to an amber (UAG) codon. By screening 11 quadruplet-decoding pyrrolysyl tRNA variants from the literature, we found that all variants decoding CUAG or AGGA tested here are functional in mammalian cells. Using a quadruplet-decoding orthogonal pair together with an amber-decoding pair, we constructed logic gates that can be successfully controlled by two different unnatural amino acids, expanding the scope of genetic code expansion and mammalian cell logic circuits.

IL-33/ST2 Axis Plays a Protective Effect in Streptococcus pyogenes Infection through Strengthening of the Innate Immunity

Group A Streptococcus (GAS) causes invasive human diseases with the cytokine storm. Interleukin-33 (IL-33)/suppression of tumorigenicity 2 (ST2) axis is known to drive TH2 response, while its effect on GAS infection is unclear. We used an air pouch model to examine the effect of the IL-33/ST2 axis on GAS-induced necrotizing fasciitis. GAS infection induced IL-33 expression in wild-type (WT) C57BL/6 mice, whereas the IL-33- and ST2-knockout mice had higher mortality rates, more severe skin lesions and higher bacterial loads in the air pouches than those of WT mice after infection. Surveys of infiltrating cells in the air pouch of GAS-infected mice at the early stage found that the number and cell viability of infiltrating cells in both gene knockout mice were lower than those of WT mice. The predominant effector cells in GAS-infected air pouches were neutrophils. Absence of the IL-33/ST2 axis enhanced the expression of inflammatory cytokines, but not TH1 or TH2 cytokines, in the air pouch after infection. Using in vitro assays, we found that the IL-33/ST2 axis not only enhanced neutrophil migration but also strengthened the bactericidal activity of both sera and neutrophils. These results suggest that the IL-33/ST2 axis provided the protective effect on GAS infection through enhancing the innate immunity.

Tethering-based chemogenetic approaches for the modulation of protein function in live cells

Proteins are the workhorse molecules performing various tasks to sustain life. To investigate the roles of a protein under physiological conditions, the rapid modulation of the protein with high specificity in a living system would be ideal, but achieving this is often challenging. To address this challenge, researchers have developed chemogenetic strategies for the rapid and selective modulation of protein function in live cells. Here, the target protein is modified genetically to become sensitive to a designer molecule that otherwise has no effect on other cellular biomolecules. One powerful chemogenetic strategy is to introduce a tethering point into the target protein, allowing covalent or non-covalent attachment of the designer molecule. In this tutorial review, we focus on tethering-based chemogenetic approaches for modulating protein function in live cells. We first describe genetic, optogenetic and chemical means to study protein function. These means lay the basis for the chemogenetic concept, which is explained in detail. The next section gives an overview, including advantages and limitations, of tethering tactics that have been employed for modulating cellular protein function. The third section provides examples of the modulation of cell-surface proteins using tethering-based chemogenetics through non-covalent tethering and covalent tethering for irreversible modulation or functional switching. The fourth section presents intracellular examples. The last section summarizes key considerations in implementing tethering-based chemogenetics and shows perspectives highlighting future directions and other applications of this burgeoning research field.

Approaches for peptide and protein cyclisation

The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.

Large shift of resonance wavelengths of silver nanoslit arrays using electrowetting-on-dielectric cells

A simple design for shifting the resonance wavelength of silver nanoslits using an electrowetting-on-dielectric (EWOD) cell is proposed. The EWOD cell comprises a polycarbonate (PC) substrate with Teflon-coated silver nanoslits and a glass substrate with Teflon-coated electrodes. A glycerol droplet is placed between the two substrates, and out of the path of a probe beam at zero electric field. Application of an electric field smaller than 0.3 V/µm on the electrodes moves the glycerol droplet into the path of the probe beam, shifting the resonance wavelength of the silver nanoslits by 135 nm. A change (0.33) in the refractive index of the effective medium that is adjacent to the silver nanoslits causes a large shift in the resonance wavelength. The spectral shift of the silver nanoslits is repeatable by the electric field. This simple design is a great achievement for high-performance electro-optical devices with large wavelength shift ranges such as optical switches, variable optical attenuators, and sensor applications.

Dual GRIN lens two-photon endoscopy for high-speed volumetric and deep brain imaging

Studying neural connections and activities in vivo is fundamental to understanding brain functions. Given the cm-size brain and three-dimensional neural circuit dynamics, deep-tissue, high-speed volumetric imaging is highly desirable for brain study. With sub-micrometer spatial resolution, intrinsic optical sectioning, and deep-tissue penetration capability, two-photon microscopy (2PM) has found a niche in neuroscience. However, the current 2PM typically relies on a slow axial scan for volumetric imaging, and the maximal penetration depth is only about 1 mm. Here, we demonstrate that by integrating a gradient-index (GRIN) lens and a tunable acoustic GRIN (TAG) lens into 2PM, both penetration depth and volume-imaging rate can be significantly improved. Specifically, an ∼ 1-cm long GRIN lens allows imaging relay from any target region of a mouse brain, while a TAG lens provides a sub-second volume rate via a 100 kHz ∼ 1 MHz axial scan. This technique enables the study of calcium dynamics in cm-deep brain regions with sub-cellular and sub-second spatiotemporal resolution, paving the way for interrogating deep-brain functional connectome.

Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Genetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

Effect of membrane fusion protein AdeT1 on the antimicrobial resistance of Escherichia coli

Acinetobacter baumannii is a prevalent pathogen that can rapidly acquire resistance to antibiotics. Indeed, multidrug-resistant A. baumannii is a major cause of hospital-acquired infections and has been recognised by the World Health Organization as one of the most threatening bacteria to our society. Resistance-nodulation-division (RND) type multidrug efflux pumps have been demonstrated to convey antibiotic resistance to a wide range of pathogens and are the primary resistance mechanism employed by A. baumannii. A component of an RND pump in A. baumannii, AdeT1, was previously demonstrated to enhance the antimicrobial resistance of Escherichia coli. Here, we report the results of experiments which demonstrate that wild-type AdeT1 does not confer antimicrobial resistance in E. coli, highlighting the importance of verifying protein production when determining minimum inhibitory concentrations (MICs) especially by broth dilution. Nevertheless, using an agar-based MIC assay, we found that propionylation of Lys280 on AdeT1 renders E. coli cells more resistant to erythromycin.

Use of an asparaginyl endopeptidase for chemo-enzymatic peptide and protein labeling

Asparaginyl endopeptidases (AEPs) are ideal for peptide and protein labeling. However, because of the reaction reversibility, a large excess of labels or backbone modified substrates are needed. In turn, simple and cheap reagents can be used to label N-terminal cysteine, but its availability inherently limits the potential applications. Aiming to address these issues, we have created a chemo-enzymatic labeling system that exploits the substrate promiscuity of AEP with the facile chemical reaction between N-terminal cysteine and 2-formyl phenylboronic acid (FPBA). In this approach, AEP is used to ligate polypeptides with a Asn-Cys-Leu recognition sequence with counterparts possessing an N-terminal Gly-Leu. Instead of being a labeling reagent, the commercially available FPBA serves as a scavenger converting the byproduct Cys-Leu into an inert thiazolidine derivative. This consequently drives the AEP labeling reaction forward to product formation with a lower ratio of label to protein substrate. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP-ligation/FPBA-coupling system was further demonstrated by site-specifically labeling the N- or C-termini of various proteins.

Enabling protein-hosted organocatalytic transformations

In this review, the development of organocatalytic artificial enzymes will be discussed. This area of protein engineering research has underlying importance, as it enhances the biocompatibility of organocatalysis for applications in chemical and synthetic biology research whilst expanding the catalytic repertoire of enzymes. The approaches towards the preparation of organocatalytic artificial enzymes, techniques used to improve their performance (selectivity and reactivity) as well as examples of their applications are presented. Challenges and opportunities are also discussed.

Cyanine dye mediated mitochondrial targeting enhances the anti-cancer activity of small-molecule cargoes

Organelle-specific delivery systems are of significant clinical interest. We demonstrate the use of common cyanine dyes Cy3 and Cy5 as vectors for targeting and delivering cargoes to mitochondria in cancer cells. Specifically, conjugation to the dyes can increase cytotoxicity by up to 1000-fold.

Applying switchable Cas9 variants to in vivo gene editing for therapeutic applications

Progress in targeted gene editing by programmable endonucleases has paved the way for their use in gene therapy. Particularly, Cas9 is an endonuclease with high activity and flexibility, rendering it an attractive option for therapeutic applications in clinical settings. Many disease-causing mutations could potentially be corrected by this versatile new technology. In addition, recently developed switchable Cas9 variants, whose activity can be controlled by an external stimulus, provide an extra level of spatiotemporal control on gene editing and are particularly desirable for certain applications. Here, we discuss the considerations and difficulties for implementing Cas9 to in vivo gene therapy. We put particular emphasis on how switchable Cas9 variants may resolve some of these barriers and advance gene therapy in the clinical setting.

Using genetically incorporated unnatural amino acids to control protein functions in mammalian cells

Genetic code expansion allows unnatural (non-canonical) amino acid incorporation into proteins of interest by repurposing the cellular translation machinery. The development of this technique has enabled site-specific incorporation of many structurally and chemically diverse amino acids, facilitating a plethora of applications, including protein imaging, engineering, mechanistic and structural investigations, and functional regulation. Particularly, genetic code expansion provides great tools to study mammalian proteins, of which dysregulations often have important implications in health. In recent years, a series of methods has been developed to modulate protein function through genetically incorporated unnatural amino acids. In this review, we will first discuss the basic concept of genetic code expansion and give an up-to-date list of amino acids that can be incorporated into proteins in mammalian cells. We then focus on the use of unnatural amino acids to activate, inhibit, or reversibly modulate protein function by translational, optical or chemical control. The features of each approach will also be highlighted.

Cell-penetrating peptide sequence and modification dependent uptake and subcellular distribution of green florescent protein in different cell lines

Protein therapy holds great promise for treating a variety of diseases. To act on intracellular targets, therapeutic proteins must cross the plasma membrane. This has previously been achieved by covalent attachment to a variety of cell-penetrating peptides (CPPs). However, there is limited information on the relative performance of CPPs in delivering proteins to cells, specifically the cytosol and other intracellular locations. Here we use green fluorescent protein (GFP) as a model cargo to compare delivery capacity of five CPP sequences (Penetratin, R8, TAT, Transportan, Xentry) and cyclic derivatives in different human cell lines (HeLa, HEK, 10T1/2, HepG2) representing different tissues. Confocal microscopy analysis indicates that most fusion proteins when incubated with cells at 10 µM localise to endosomes. Quantification of cellular uptake by flow cytometry reveals that uptake depends on both cell type (10T1/2 > HepG2 > HeLa > HEK), and CPP sequence (Transportan > R8 > Penetratin≈TAT > Xentry). CPP sequence cyclisation or addition of a HA-sequence increased cellular uptake, but fluorescence was still contained in vesicles with no evidence of endosomal escape. Our results provide a guide to select CPP for endosomal/lysosomal delivery and a basis for developing more efficient CPPs in the future.

Control of pore structure in a porous gold nanoparticle for effective cancer cell damage

For tumor treatment, compared with gold nanoparticles (NPs) of other geometries, a porous gold NP (PGNP) has the advantages of stronger localized surface plasmon resonance (LSPR) due to the pore nanostructures and a larger surface area to link with more drug or photosensitizer (PS) molecules for more effective delivery into cancer cells. Different from the chemical synthesis methods, in this paper we demonstrate the fabrication procedures of PGNP based on shaped Au/Ag deposition on a Si substrate and elucidate the advantageous features. PGNPs fabricated under different conditions, including different deposited Au/Ag content ratios and different alloying annealing temperatures, are compared for optimizing the fabrication condition in terms of LSPR wavelength, PS linkage capability, and cancer cell damage efficiency. It is found that within the feasible fabrication parameter ranges, the Au/Ag content ratio of 3:7 and alloying annealing temperature at 600 °C are the optimized conditions. In comparing with widely used gold NPs of other geometries, PGNP fabricated under the optimized conditions can be used for achieving a significantly higher linked PS molecule number per unit gold weight.

Enhancements of Cancer Cell Damage Efficiencies in Photothermal and Photodynamic Processes through Cell Perforation and Preheating with Surface Plasmon Resonance of Gold Nanoring

The methods of cell perforation and preheating are used for increasing cell uptake efficiencies of gold nanorings (NRIs), which have the localized surface plasmon resonance wavelength around 1064 nm, and photosensitizer, AlPcS, and hence enhancing the cell damage efficiency through the photothermal (PT) and photodynamic (PD) effects. The perforation and preheating effects are generated by illuminating a defocused 1064-nm femtosecond (fs) laser and a defocused 1064-nm continuous (cw) laser, respectively. Cell damage is produced by illuminating cell samples with a focused 1064-nm cw laser through the PT effect, a focused 1064-nm fs laser through both PT and PD effects, and a focused 660-nm cw laser through the PD effect. Under various conditions with and without cell wash before laser illumination, through either perforation or preheating process, cell uptake and hence cell damage efficiencies can be enhanced. Under our experimental conditions, perforation can be more effective at enhancing cell uptake and damage when compared with preheating.

Nanoscale Removal of Picosecond Laser Ablation for Polymer

This paper analytically investigates the picosecond laser ablation of polymer. Laser-pulsed ablation is a well-established tool for polymer. However the ablation mechanism of laser processing for polymer has not been thoroughly understood yet. This study utilized a thermal transport model to analyze the relationship between the ablation rate and laser fluences. This model considered the energy balance at the decomposition interface as the ablation mechanisms and is applied to predict the laser-ablated depth of Acrylonitrile Butadiene Styrene/PolyVinyl Chloride (ABS/PVC). The calculated variation of the ablation rate with the logarithm of the laser fluence agrees with the measured data. The effects of material properties and processing parameters on the ablation depth per pulse are discussed for picosecond laser processing of ABS/PVC.

Carbapenems as water soluble organocatalysts

Background: Identification of organocatalysts functioning in aqueous environments will provide methods for more sustainable chemical transformations and allow tandem reactions with biocatalysts, like enzymes. Here we examine three water-soluble carbapenem antibiotics (meropenem, doripenem, and ertapenem) as secondary amine organocatalysts in aqueous environments. Methods: The Michael addition of nitromethane to cinnamaldehyde was used as the model reaction. The reactions were monitored by 1H NMR, and the enantioselectivity was determined by chiral HPLC.   Results: The effects of buffer components, pH, organic co-solvents and anchoring into a protein scaffold were investigated. Moderate yields of the Michael addition were obtained in buffer alone. The use of methanol as a co-solvent in a ratio of 1:1 increases the yield by 50%. Anchoring of the catalysts into a protein backbone reverses the enatioselectivity of the reaction. Conclusions: Despite only moderate yields and enantioselectivities being obtained, this study lays the foundations for future development of efficient organocatalysis in aqueous environments.

Switchable genome editing via genetic code expansion

Multiple applications of genome editing by CRISPR-Cas9 necessitate stringent regulation and Cas9 variants have accordingly been generated whose activity responds to small ligands, temperature or light. However, these approaches are often impracticable, for example in clinical therapeutic genome editing in situ or gene drives in which environmentally-compatible control is paramount. With this in mind, we have developed heritable Cas9-mediated mammalian genome editing that is acutely controlled by the cheap lysine derivative, Lys(Boc) (BOC). Genetic code expansion permitted non-physiological BOC incorporation such that Cas9 (Cas9BOC) was expressed in a full-length, active form in cultured somatic cells only after BOC exposure. Stringently BOC-dependent, heritable editing of transgenic and native genomic loci occurred when Cas9BOC was expressed at the onset of mouse embryonic development from cRNA or Cas9BOC transgenic females. The tightly controlled Cas9 editing system reported here promises to have broad applications and is a first step towards purposed, spatiotemporal gene drive regulation over large geographical ranges.

Exocytosis of gold nanoparticle and photosensitizer from cancer cells and their effects on photodynamic and photothermal processes

We first illustrate the faster decrease of the photothermal (PT) effect with the delay time of laser treatment, in which the illumination of a 1064 nm laser effectively excites the localized surface plasmon (LSP) resonance of cell-up-taken gold nanoring (NRI) linked with a photosensitizer (PS), when compared with the photodynamic (PD) effect produced by the illumination of a 660 nm laser for effective PS excitation. The measurement results of the metal contents of Au NRI and PS based on inductively coupled plasma mass spectroscopy and the PS fluorescence intensity based on flow cytometry show that the linkage of NRI and PS is rapidly broken for releasing PS through the effect of glutathione in lysosome after cell uptake. Meanwhile, NRI escapes from a cell with a high rate such that the PT effect decays fast while the released PS can stay inside a cell longer for producing a prolonged PD effect. The effective delivery of PS through the linkage with Au NRI for cell uptake and the advantageous effect of LSP resonance at a PS absorption wavelength on the PD process are also demonstrated.

Reaction Mechanism of Organocatalytic Michael Addition of Nitromethane to Cinnamaldehyde: A Case Study on Catalyst Regeneration and Solvent Effects

The Michael addition of nitromethane to cinnamaldehyde has been computationally studied in the absence of a catalyst and the presence of a biotinylated secondary amine by a combined computational and experimental approach. The calculations were performed at the density functional theory (DFT) level with the M06-2X hybrid functional, and a polarizable continuum model has been employed to mimic the effect of two different solvents: dichloromethane (DCM) and water. Contrary to common assumption, the product-derived iminium intermediate was absent in both of the solvents tested. Instead, hydrating the C1–C2 double bond in the enamine intermediate directly yields the tetrahedral intermediate, which is key for forming the product and regenerating the catalyst. Enamine hydration is concerted and found to be rate-limiting in DCM but segregated into two non-rate-limiting steps when the solvent is replaced with water. However, further analysis revealed that the use of water as solvent also raises the energy barriers for other chemical steps, particularly the critical step of C–C bond formation between the iminium intermediate and nucleophile; this consequently lowers both the reaction yield and enantioselectivity of this LUMO-lowering reaction, as experimentally detected. These findings provide a logical explanation to why water often enhances organocatalysis when used as an additive but hampers the reaction progress when employed as a solvent.

HDAC2 and HDAC5 Up-Regulations Modulate Survivin and miR-125a-5p Expressions and Promote Hormone Therapy Resistance in Estrogen Receptor Positive Breast Cancer Cells

Intrinsic or acquired resistance to hormone therapy is frequently reported in estrogen receptor positive (ER⁺) breast cancer patients. Even though dysregulations of histone deacetylases (HDACs) are known to promote cancer cells survival, the role of different HDACs in the induction of hormone therapy resistance in ER⁺ breast cancer remains unclear. Survivin is a well-known pro-tumor survival molecule and miR-125a-5p is a recently discovered tumor suppressor. In this study, we found that ER⁺, hormone-independent, tamoxifen-resistant MCF7-TamC3 cells exhibit increased expression of HDAC2, HDAC5, and survivin, but show decreased expression of miR-125a-5p, as compared to the parental tamoxifen-sensitive MCF7 breast cancer cells. Molecular down-regulations of HDAC2, HDAC5, and survivin, and ectopic over-expression of miR-125a-5p, increased the sensitivity of MCF7-TamC3 cells to estrogen deprivation and restored the sensitivity to tamoxifen. The same treatments also further increased the sensitivity to estrogen-deprivation in the ER⁺ hormone-dependent ZR-75-1 breast cancer cells in vitro. Kaplan-Meier analysis and receiver operating characteristic curve analysis of expression cohorts of breast tumor showed that high HDAC2 and survivin, and low miR-125a-5p, expression levels correlate with poor relapse-free survival in endocrine therapy and tamoxifen-treated ER⁺ breast cancer patients. Further molecular analysis revealed that HDAC2 and HDAC5 positively modulates the expression of survivin, and negatively regulates the expression miR-125a-5p, in ER⁺ MCF7, MCF7-TamC3, and ZR-75-1 breast cancer cells. These findings indicate that dysregulations of HDAC2 and HDAC5 promote the development of hormone independency and tamoxifen resistance in ERC breast cancer cells in part through expression regulation of survivin and miR-125a-5p.

Acetylome of Acinetobacter baumannii SK17 Reveals a Highly-Conserved Modification of Histone-Like Protein HU

Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. This work indicates that acetyllysine plays an important role in bacterial epigenetics.

Skeletal muscle fiber analysis by atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometric imaging at high mass and high spatial resolution

Skeletal muscles are composed of heterogeneous muscle fibers with various fiber types. These fibers can be classified into different classes based on their different characteristics. MALDI mass spectrometric imaging (MSI) has been applied to study and visualize different metabolomics profiles of different fiber types. Here, skeletal muscles were analyzed by atmospheric pressure scanning microprobe MALDI-MSI at high spatial and high mass resolution.

Cancer cell death pathways caused by photothermal and photodynamic effects through gold nanoring induced surface plasmon resonance

The different death pathways of cancer cells under the conditions of the photothermal (PT), effect, photodynamic (PD) effect, and their combination are evaluated. By incubating cells with Au nanoring (NRI) either linked with the photosensitizer, AlPcS, or not, the illumination of a visible continuous laser for exciting the photosensitizer or an infrared femtosecond laser for exciting the localized surface plasmon resonance of Au NRI, leads to various PT and PD conditions for study. Three different staining dyes are used for identifying the cell areas of different damage conditions at different temporal points of observation. The cell death pathways and apoptotic evolution speeds under different cell treatment conditions are evaluated based on the calibration of the threshold laser fluences for causing early-apoptosis (EA) and necrosis (NE) or late-apoptosis (LA). It is found that with the PT effect only, strong cell NE is generated and the transition from EA into LA is faster than that caused by the PD effect when the EA stage is reached within 0.5 h after laser illumination. By combining the PT and PD effects, in the first few hours, the transition speed becomes lower, compared to the case of the PT effect only, when both Au NRIs internalized into cells and adsorbed on cell membrane exist. When the Au NRIs on cell membrane is removed, in the first few hours, the transition speed becomes higher, compared to the case of the PD effect only.

The influence of dehydration on the prognosis of acute ischemic stroke for patients treated with tissue plasminogen activator

Background

Many studies have determined that dehydration is an independent predictor of outcome after ischemic stroke (IS); however, none have determined if the use of thrombolytic therapy modifies the negative impact of poor hydration. To inform the stroke registry established at our institution, we conducted a retrospective study to determine if dehydration remains a negative prognostic factor after IS patients treated with tissue plasminogen activator (tPA).

Methods

Between 2007 and 2012, we recruited 382 subjects; 346 had data available and were divided into 2 groups on the basis of their blood urea nitrogen/creatinine (BUN/Cr) ratio. Dehydrated subjects had a BUN/Cr ratio ≥ 15; hydrated subjects had a BUN/Cr < 15. The primary outcome was impairment at discharge as graded by the Barthel Index (BI) and the modified Rankin Scale (mRS).

Results

The dehydration group had a greater mean age; more women; lower mean levels of hemoglobin, triglycerides, and sodium; and higher mean potassium and glucose levels. A favorable outcome as assessed by the mRS (≤2) was significantly less frequent among dehydrated subjects, but a favorable outcome by the BI (≥60) was not. Logistic regression and multivariate models confirmed that dehydration is an independent predictor of poor outcome by both the mRS and the BI; however, it was not predictive when patients were stratified by Trial of Org 10,172 in Acute Stroke Treatment subtype.

Conclusions

Our findings indicate that use of thrombolytic therapy does not eliminate the need to closely monitor hydration status in patients with IS.

SPECTRAL CORRECTION FACTORS FOR CONVENTIONAL NEUTRON DOSE METERS USED IN HIGH-ENERGY NEUTRON ENVIRONMENTS-IMPROVED AND EXTENDED RESULTS BASED ON A COMPLETE SURVEY OF ALL NEUTRON SPECTRA IN IAEA-TRS-403

This paper presents improved and extended results of our previous study on corrections for conventional neutron dose meters used in environments with high-energy neutrons (En > 10 MeV). Conventional moderated-type neutron dose meters tend to underestimate the dose contribution of high-energy neutrons because of the opposite trends of dose conversion coefficients and detection efficiencies as the neutron energy increases. A practical correction scheme was proposed based on analysis of hundreds of neutron spectra in the IAEA-TRS-403 report. By comparing 252Cf-calibrated dose responses with reference values derived from fluence-to-dose conversion coefficients, this study provides recommendations for neutron field characterization and the corresponding dose correction factors. Further sensitivity studies confirm the appropriateness of the proposed scheme and indicate that (1) the spectral correction factors are nearly independent of the selection of three commonly used calibration sources: 252Cf, 241Am-Be and 239Pu-Be; (2) the derived correction factors for Bonner spheres of various sizes (6"-9") are similar in trend and (3) practical high-energy neutron indexes based on measurements can be established to facilitate the application of these correction factors in workplaces.

Work hours and turnover intention among hospital physicians in Taiwan: does income matter?

Background

Physician shortage has become an urgent and critical challenge to many countries. According to the workforce dynamic model, long work hours may be one major pressure point to the attrition of physicians. Financial incentive is a common tool to human power retention. Therefore, this large-scale physician study investigated how pay satisfaction may influence the relationship between work hours and hospital physician’s turnover intention.

Methods

Data were obtained from a nationwide survey of full-time hospital staff members working at 100 hospitals in Taiwan. The analysis sample comprised 2423 full-time physicians. Dependent variable was degree of the physicians’ turnover intention to leave the current hospital. The pay satisfaction was assessed by physicians themselves. We employed ordinal logistic regression models to analyze the association between the number of work hours and turnover intention. To consider the cluster effect of hospitals, we used the “gllamm” command in the statistical software package Stata Version 12.1.

Results

The results show that 351 (14.5%) of surveyed physicians reported strong intention to leave current hospital. The average work hours per week among hospital physicians was 59.8 h. As expected, work hours exhibited an independent relationship with turnover intention. More importantly, pay satisfaction could not effectively moderate the positive relationship between work hours and intentions to leave current hospital.

Conclusions

The findings show that overtime work is prevalent among hospital physicians in Taiwan. Both the Taiwanese government and hospitals must take action to address the emerging problem of physician high turnover rate. Furthermore, hospitals should not consider relying solely on financial incentives to solve the problem. This study encouraged tackling work hour problem, which would lead to the possibility of solving high turnover intention among hospital physicians in Taiwan.

Electronic supplementary material

The online version of this article (doi:10.1186/s12913-016-1916-2) contains supplementary material, which is available to authorized users.

Estimating spatio-temporal dynamics of stream total phosphate concentration by soft computing techniques

This study attempts to model the spatio-temporal dynamics of total phosphate (TP) concentrations along a river for effective hydro-environmental management. We propose a systematical modeling scheme (SMS), which is an ingenious modeling process equipped with a dynamic neural network and three refined statistical methods, for reliably predicting the TP concentrations along a river simultaneously. Two different types of artificial neural network (BPNN-static neural network; NARX network-dynamic neural network) are constructed in modeling the dynamic system. The Dahan River in Taiwan is used as a study case, where ten-year seasonal water quality data collected at seven monitoring stations along the river are used for model training and validation. Results demonstrate that the NARX network can suitably capture the important dynamic features and remarkably outperforms the BPNN model, and the SMS can effectively identify key input factors, suitably overcome data scarcity, significantly increase model reliability, satisfactorily estimate site-specific TP concentration at seven monitoring stations simultaneously, and adequately reconstruct seasonal TP data into a monthly scale. The proposed SMS can reliably model the dynamic spatio-temporal water pollution variation in a river system for missing, hazardous or costly data of interest.

Development of a wafer warpage measurement technique using Moiré-based method

This paper reports on a novel technique for measuring wafer warpage, using the design concepts of moiré shift, digital moiré, autocollimator, and the scanning profiling method. The measurement system is divided into two parts: an optical moiré system and a phase analysis system. The optical arrangement can be adjusted to control the projection of a linear grating image onto the surface of a wafer to be reflected back into a CCD camera. The grating image acquired by the CCD camera is used for measurement whereas a reference grating image is obtained using the digital moiré method. By overlapping the two images of the measurement and the reference gratings, the corresponding moiré fringes are formed. The phase of the moiré fringes will change proportionally to the degree of warpage in the wafer, which can be measured by detecting variations in the phase shift of the moiré fringes in the scanning profile across the surface of the entire wafer. Measurement resolution can be controlled by adjusting the pitch size of the grating or the focal length of the focusing lens, or by adjusting the angle between the images of the measurement and reference gratings. Experiment results demonstrate that the proposed method is able to achieve an angular resolution of 0.2 μrad. As compared to the current warpage measurement techniques, the proposed method has the ability of high measurement resolution, high stability, and high flexibility.

Isotopic Ratio Outlier Analysis of the S. cerevisiae Metabolome Using Accurate Mass Gas Chromatography/Time-of-Flight Mass Spectrometry: A New Method for Discovery

Isotopic ratio outlier analysis (IROA) is a (13)C metabolomics profiling method that eliminates sample to sample variance, discriminates against noise and artifacts, and improves identification of compounds, previously done with accurate mass liquid chromatography/mass spectrometry (LC/MS). This is the first report using IROA technology in combination with accurate mass gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS), here used to examine the S. cerevisiae metabolome. S. cerevisiae was grown in YNB media, containing randomized 95% (13)C, or 5%(13)C glucose as the single carbon source, in order that the isotopomer pattern of all metabolites would mirror the labeled glucose. When these IROA experiments are combined, the abundance of the heavy isotopologues in the 5%(13)C extracts, or light isotopologues in the 95%(13)C extracts, follows the binomial distribution, showing mirrored peak pairs for the molecular ion. The mass difference between the (12)C monoisotopic and the (13)C monoisotopic equals the number of carbons in the molecules. The IROA-GC/MS protocol developed, using both chemical and electron ionization, extends the information acquired from the isotopic peak patterns for formulas generation. The process that can be formulated as an algorithm, in which the number of carbons, as well as the number of methoximations and silylations are used as search constraints. In electron impact (EI/IROA) spectra, the artifactual peaks are identified and easily removed, which has the potential to generate "clean" EI libraries. The combination of chemical ionization (CI) IROA and EI/IROA affords a metabolite identification procedure that enables the identification of coeluting metabolites, and allowed us to characterize 126 metabolites in the current study.

Immobilization of silver nanoparticles on exfoliated mica nanosheets to form highly conductive nanohybrid films

Highly electrically conductive films were prepared by coating organic/inorganic nanohybrid solutions with a polymeric dispersant and exfoliated mica nanosheets (Mica) on which silver nanoparticles (AgNPs) had been dispersed in various components. Transmission electronic microscopy showed that the synthesized AgNPs had a narrow size distribution and a diameter of approximately 20 nm. Furthermore, a 60 μm thick film with a sheet resistance as low as 4.5 × 10(-2) Ω/sq could be prepared by controlling the heating temperature and by using AgNPs/POE-imide/Mica in a weight ratio of 20:20:1. During the heating process, the surface color of the hybrid film changed from dark golden to white, suggesting the accumulation of the AgNPs through surface migration and their melting to form an interconnected network. These nanohybrid films have potential for use in various electrically conductive devices.

Analysis for Heat Transfer in a High Current-Passing Carbon Nanosphere Using Nontraditional Thermal Transport Model

This paper investigates the thermal transport in hollow microscale and nanoscale spheres subject to electrical heat source using nontraditional thermal transport model. Working as supercapacitor electrodes, carbon hollow micrometer- and nanometer-sized spheres needs excellent heat transfer characteristics to maintain high specific capacitance, long cycle life, and high power density. In the nanoscale regime, the prediction of heat transfer from the traditional heat conduction equation based on Fourier's law deviates from the measured data. Consequently, the electrical heat source-induced heat transfer characteristics in hollow micrometer- and nanometer-sized spheres are studied using nontraditional thermal transport model. The effects of parameters on heat transfer in the hollow micrometer- and nanometer-sized spheres are discussed in this study. The results reveal that the heat transferred into the spherical interior, temperature and heat flux in the hollow sphere decrease with the increasing Knudsen number when the radius of sphere is comparable to the mean free path of heat carriers.