Tumor hypoxia represses γδ T cell-mediated antitumor immunity against brain tumors.

The anatomic location and immunologic characteristics of brain tumors result in strong lymphocyte suppression. Consequently, conventional immunotherapies targeting CD8 T cells are ineffective against brain tumors. Tumor cells escape immunosurveillance by various mechanisms and tumor cell metabolism can affect the metabolic states and functions of tumor-infiltrating lymphocytes. Here, we discovered that brain tumor cells had a particularly high demand for oxygen, which affected γδ T cell-mediated antitumor immune responses but not those of conventional T cells. Specifically, tumor hypoxia activated the γδ T cell protein kinase A pathway at a transcriptional level, resulting in repression of the activatory receptor NKG2D. Alleviating tumor hypoxia reinvigorated NKG2D expression and the antitumor function of γδ T cells. These results reveal a hypoxia-mediated mechanism through which brain tumors and γδ T cells interact and emphasize the importance of γδ T cells for antitumor immunity against brain tumors.

Cellular and Biophysical Applications of Genetic Code Expansion.

Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

Single-cell transcriptomics suggest distinct upstream drivers of IL-17A/F in hidradenitis versus psoriasis.

BACKGROUND: On the basis of the mounting evidence that type 17 T (T17) cells and increased IL-17 play a key role in driving hidradenitis suppurativa (HS) lesion development, biologic agents used previously in psoriasis that block signaling of IL-17A and/or IL-17F isoforms have been repurposed to treat HS. OBJECTIVE: Our research aimed to characterize the transcriptome of HS T17 cells compared to the transcriptome of psoriasis T17 cells, along with their ligand-receptor interactions with neighborhood immune cell subsets. METHODS: Single-cell data of 12,300 cutaneous immune cells from 8 deroofing surgical HS skin samples including dermal tunnels were compared to single-cell data of psoriasis skin (19,525 cells from 11 samples) and control skin (11,920 cells from 10 samples). All single-cell data were generated by the same protocol. RESULTS: HS T17 cells expressed lower levels of IL23R and higher levels of IL1R1 and IL17F compared to psoriasis T17 cells (P < .05). HS Treg cells expressed higher levels of IL1R1 and IL17F compared to psoriasis Treg cells (P < .05). Semimature dendritic cells were the major immune cell subsets expressing IL1B in HS, and IL-1ß ligand-receptor interactions between semimature dendritic cells and T17 cells were increased in HS compared to psoriasis (P < .05). HS dermal tunnel keratinocytes expressed inflammatory cytokines (IL17C, IL1A, IL1B, and IL6) that differed from the HS epidermis keratinocytes (IL36G) (P < .05). IL6, which synergizes with IL1B to maintain cytokine expression in T17 cells, was mainly expressed by fibroblasts in HS, which also expressed IL11+ inflammatory fibroblast genes (IL11, IL24, IL6, and POSTN) involved in the paracrine IL-1/IL-6 loop. CONCLUSION: The IL-1ß-T17 cell cytokine axis is likely a dominant pathway in HS with HS T17 cells activated by IL-1ß signaling, unlike psoriasis T17 cells, which are activated by IL-23 signaling.

Spatially and velocity-selective magnetization preparation for noncontrast-enhanced peripheral MR angiography.

The purpose of the current study was to develop spatially and velocity-selective (SVS) magnetization preparation pulses for noncontrast-enhanced peripheral MR angiography (MRA) to provide comparisons with velocity-selective (VS) MRA with comparison to velocity-selective (VS). VS preparation pulses were designed by concatenating multiple excitation steps, each of which was a combination of a hard RF pulse, VS unipolar gradient pulses, and refocusing RF pulses. SVS preparation pulses were designed by replacing the hard RF pulse with a sinc-shaped RF pulse combined with a symmetric tripolar gradient pulse (which does not perturb the velocity encoding by the VS unipolar gradient pulses). Numerical simulations were performed to verify the intended hybrid excitation selectivity of SVS pulses taking account of tissue relaxation, magnetic field errors, and eddy currents. In vivo experiments were performed in healthy subjects to verify the hybrid excitation selectivity, as well as to demonstrate the visualization of the entire peripheral arteries using six-station protocols. As demonstrated by numerical simulations, SVS preparation yielded a notch-shaped longitudinal magnetization (Mz )-velocity response within the spatial stopband (the same as VS preparation) and preserved the Mz of spins outside the stopband, regardless of its velocity. We confirmed these observations also through in vivo tests with good agreement in normalized arterial and muscle signal intensities. In six-station peripheral MRA experiments, the proposed SVS-MRA yielded significantly higher arterial signal-to-noise ratio (SNR) (51.6 ± 14.3 vs. 38.9 ± 10.9; p < 0.001) and contrast-to-noise ratio (CNR) (41.2 ± 13.0 vs. 31.3 ± 10.5; p < 0.001) compared with VS-MRA. The proposed SVS-MRA improves arterial SNR and CNR compared with VS-MRA by mitigating undesired presaturation of arterial blood upstream the imaging field of view.

MR-self Noise2Noise: self-supervised deep learning-based image quality improvement of submillimeter resolution 3D MR images.

OBJECTIVES: The study aimed to develop a deep neural network (DNN)-based noise reduction and image quality improvement by only using routine clinical scans and evaluate its performance in 3D high-resolution MRI. METHODS: This retrospective study included T1-weighted magnetization-prepared rapid gradient-echo (MP-RAGE) images from 185 clinical scans: 135 for DNN training, 11 for DNN validation, 20 for qualitative evaluation, and 19 for quantitative evaluation. Additionally, 18 vessel wall imaging (VWI) data were included to evaluate generalization. In each scan of the DNN training set, two noise-independent images were generated from the k-space data, resulting in an input-label pair. 2.5D U-net architecture was utilized for the DNN model. Qualitative evaluation between conventional MP-RAGE and DNN-based MP-RAGE was performed by two radiologists in image quality, fine structure delineation, and lesion conspicuity. Quantitative evaluation was performed with full sampled data as a reference by measuring quantitative error metrics and volumetry at 7 different simulated noise levels. DNN application on VWI was evaluated by two radiologists in image quality. RESULTS: Our DNN-based MP-RAGE outperformed conventional MP-RAGE in all image quality parameters (average scores = 3.7 vs. 4.9, p < 0.001). In the quantitative evaluation, DNN showed better error metrics (p < 0.001) and comparable (p > 0.09) or better (p < 0.02) volumetry results than conventional MP-RAGE. DNN application to VWI also revealed improved image quality (3.5 vs. 4.6, p < 0.001). CONCLUSION: The proposed DNN model successfully denoises 3D MR image and improves its image quality by using routine clinical scans only. KEY POINTS: • Our deep learning framework successfully improved conventional 3D high-resolution MRI in all image quality parameters, fine structure delineation, and lesion conspicuity. • Compared to conventional MRI, the proposed deep neural network-based MRI revealed better quantitative error metrics and comparable or better volumetry results. • Deep neural network application to 3D MRI whose pulse sequences and parameters were different from the training data showed improvement in image quality, revealing the potential to generalize on various clinical MRI.

Synthesis and biological evaluation of atropisomeric tetrahydroisoquinolines overcoming docetaxel resistance in triple-negative human breast cancer cells.

Herein, atropisomeric 8-aryltetrahydroisoquinolines have been synthesized and biologically evaluated. Based on our structure-activity relationship study, a highly bioactive racemic compound has been produced, and it exhibited high antiproliferative activities against various cancer cell lines, including docetaxel-resistant breast cancer cell lines. Each enantiomer can be synthesized in an enantioselective manner by employing the chiral phosphoric acid-catalyzed atroposelective Pictet-Spengler cyclization. An axially (R)-configured enantiomer showed a higher biological activity compared with the axially (S)-configured enantiomer. Further biological studies suggested that the (R)-enantiomer overcomes docetaxel resistance via the downregulation of signal transducer and activator of transcription 3 activation and consequently induces cellular apoptosis in docetaxel-resistant triple-negative breast cancer cell lines.

What are the risk factors for recurrent UTI with repeated ESBL-producing Enterobacteriaceae? A retrospective cohort study.

INTRODUCTION: A previous study has shown that two-thirds of patients with urinary tract infections (UTIs) caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae experience recurrence with the same bacteria on subsequent UTI episodes. However, little is known about which patients suffer from UTI due to ESBL-producing Enterobacteriaceae repeatedly. This study aimed to investigate the risk factors for recurrent UTI due to repeated ESBL-producing organism infections. METHODS: This retrospective, single-center, observational cohort study screened all patients with UTI caused by ESBL-producing strains between January 2012 and April 2019. Among the patients who were followed up, patients who experienced UTI recurrence were enrolled and divided into two groups: ESBL recurrence group and non-ESBL recurrence group. Multivariable Cox proportional hazards regression analyses were performed to evaluate the association between patient characteristics and the development of recurrent UTI caused by ESBL-producing Enterobacteriaceae. RESULTS: A total of 330 patients were followed up after the diagnosis of UTI caused by ESBL-producing organisms. Among the patients, 115 (34.8%) experienced UTI recurrence, and 71 (61.7%) of them experienced subsequent recurrent UTI due to ESBL-producing organisms. Patient's age (hazard ratio [HR], 1.02; 95% confidence interval [CI], 1.00-1.04; P = 0.046) and recurrent UTI history (HR, 1.69; 95% CI, 1.05-2.72; P = 0.031) were significantly associated with an increased risk of recurrence with ESBL-producing Enterobacteriaceae. CONCLUSION: These findings showed that a history of previous frequent UTI recurrence is the risk factor for recurrence of UTI due to repeated ESBL producing Enterobacteriaceae infections.

Bone Morphogenetic Protein 4 (BMP4) Enhances the Differentiation of Human Induced Pluripotent Stem Cells into Limbal Progenitor Cells.

Corneal epithelium maintains visual acuity and is regenerated by the proliferation and differentiation of limbal progenitor cells. Transplantation of human limbal progenitor cells could restore the integrity and functionality of the corneal surface in patients with limbal stem cell deficiency. However, multiple protocols are employed to differentiate human induced pluripotent stem (iPS) cells into corneal epithelium or limbal progenitor cells. The aim of this study was to optimize a protocol that uses bone morphogenetic protein 4 (BMP4) and limbal cell-specific medium. Human dermal fibroblast-derived iPS cells were differentiated into limbal progenitor cells using limbal cell-specific (PI) medium and varying doses (1, 10, and 50 ng/mL) and durations (1, 3, and 10 days) of BMP4 treatment. Differentiated human iPS cells were analyzed by real-time polymerase chain reaction (RT-PCR), Western blotting, and immunocytochemical studies at 2 or 4 weeks after BMP4 treatment. Culturing human dermal fibroblast-derived iPS cells in limbal cell-specific medium and BMP4 gave rise to limbal progenitor and corneal epithelial-like cells. The optimal protocol of 10 ng/mL and three days of BMP4 treatment elicited significantly higher limbal progenitor marker (ABCG2, ∆Np63α) expression and less corneal epithelial cell marker (CK3, CK12) expression than the other combinations of BMP4 dose and duration. In conclusion, this study identified a successful reprogramming strategy to induce limbal progenitor cells from human iPS cells using limbal cell-specific medium and BMP4. Additionally, our experiments indicate that the optimal BMP4 dose and duration favor limbal progenitor cell differentiation over corneal epithelial cells and maintain the phenotype of limbal stem cells. These findings contribute to the development of therapies for limbal stem cell deficiency disorders.

Single-shot pseudo-centric EPI for magnetization-prepared imaging.

PURPOSE: To implement a single-shot centric-reordered EPI (1sh-CenEPI), which reduces TE significantly, thus enabling to improve SNR for magnetization-prepared imaging. METHODS: We proposed a 1sh-CenEPI in which grouped oscillating readout gradients, phase-encoding blips within each group, and big phase-encoding jumps between two consecutive groups are incorporated to encode whole k-space from the center to the edges in a single shot. The concept was tested on phantoms and human brains at 3 T. In addition, the proposed reordering scheme was applied to pseudo-continuous arterial spin labeling for evaluating the efficiency of the centric reordering in magnetization-prepared imaging. RESULTS: The proposed 1sh-CenEPI reduced TE from 50 ms to 1.4 ms for gradient-echo EPI, and from 100 ms to 7 ms for spin-echo EPI, while the elongation of readout duration was below 10% of the whole readout duration in most cases. The 1sh-CenEPI images exhibited no distinct geometric distortion both in phantom and human brain, comparable to the conventional two-shot center-out EPI. In pseudo-continuous arterial spin labeling results, 3-fold temporal SNR increase and 2-fold spatial SNR increase in the perfusion-weighted images were achieved with 1sh-CenEPI compared with the conventional linear ordering, whereas the cerebral blood flow values were consistent with previous studies. CONCLUSION: The proposed 1sh-CenEPI significantly reduced TE while maintaining similar readout window and providing images comparable to the conventional linear and multishot center-out EPI images. It can be a qualified candidate as a new readout for various magnetization-prepared imaging techniques.

Traffic-related particulate matter aggravates ocular allergic inflammation by mediating dendritic cell maturation.

The aim of this study was to determine the effects of traffic-related particulate matter (PM) on allergic inflammation of ocular surfaces. BALB/c mice were sensitized with ovalbumin (OVA) and aluminum hydroxide via intraperitoneal injection. Two weeks later, mice were challenged with eye drops containing OVA concomitant with either traffic-related PM2.5 or vehicle eye drops. Topical OVA challenges were administered following unilateral subconjunctival injection of magnetic-bead-sorted CD11c+ dendritic cells (DC). The following were assessed: (1) clinical signs, (2) infiltration of inflammatory cells into conjunctiva, (3) serum levels of OVA-specific IgE production, and (4) T-cell cytokine secretion with topical application of PM2.5, compared to saline vehicle. PM2.5 was found to increase production of OVA-specific IgE in serum and Th2 immune response-related cytokines including interleukin (IL)-4, IL-17A, and IL-13 compared to vehicle control. It is of interest that PM2.5 treatment also elevated the population of mature DCs in draining lymph nodes (LNs). Exposure with PM2.5 was associated with a significant rise in conjunctival expression of IL-1ß, IL-6, IL-17, and TNF. After subconjunctival injection of CD11c+DCs from PM2.5-treated allergic conjunctivitis (AC) mice into naïve mice, T cell responses and OVA-specific IgE were also enhanced. Data suggest that traffic-related PM2.5 exacerbated allergic conjunctivitis as evidenced by increased infiltration of inflammatory cells into the conjunctiva and Th2 responses in the draining LNs associated with enhanced maturation of DCs. Our findings provide new insight into the hazardous potential of traffic-related PM2.5 on allergic diseases, such as asthma or atopic dermatitis.

TGF-ß/IL-7 Chimeric Switch Receptor-Expressing CAR-T Cells Inhibit Recurrence of CD19-Positive B Cell Lymphoma.

Chimeric antigen receptor (CAR)-T cells are effective in the treatment of hematologic malignancies but have shown limited efficacy against solid tumors. Here, we demonstrated an approach to inhibit recurrence of B cell lymphoma by co-expressing both a human anti-CD19-specific single-chain variable fragment (scFv) CAR (CD19 CAR) and a TGF-ß/IL-7 chimeric switch receptor (tTRII-I7R) in T cells (CD19 CAR-tTRII-I7R-T cells). The tTRII-I7R was designed to convert immunosuppressive TGF-ß signaling into immune-activating IL-7 signaling. The effect of TGF-ß on CD19 CAR-tTRII-I7R-T cells was assessed by western blotting. Target-specific killing by CD19 CAR-tTRII-I7R-T cells was evaluated by Eu-TDA assay. Daudi tumor-bearing NSG (NOD/SCID/IL2Rγ-/-) mice were treated with CD19 CAR-tTRII-I7R-T cells to analyze the in vivo anti-tumor effect. In vitro, CD19 CAR-tTRII-I7R-T cells had a lower level of phosphorylated SMAD2 and a higher level of target-specific cytotoxicity than controls in the presence of rhTGF-ß1. In the animal model, the overall survival and recurrence-free survival of mice that received CD19 CAR-tTRII-I7R-T cells were significantly longer than in control mice. These findings strongly suggest that CD19 CAR-tTRII-I7R-T cell therapy provides a new strategy for long-lasting, TGF-ß-resistant anti-tumor effects against B cell lymphoma, which may lead ultimately to increased clinical efficacy.

Conversion of Racemic Unnatural Amino Acids to Optically Pure Forms by a Coupled Enzymatic Reaction.

Genetic code expansion (GCE) technology is a useful tool for the site-specific modification of proteins. An unnatural amino acid (UAA) is one of the essential components of this technique, typically required at high concentration (1 mM or higher) in growth medium. The supply of UAAs is an important limitation to the application of GCE technology, as many UAAs are either expansive or commercially unavailable. In this study, two UAAs in a racemic mixture were converted into optically pure forms using two enzymes, the d-amino acid oxidase (RgDAAO) from Rhodotorula gracilis and the aminotransferase (TtAT) from Thermus thermophilus. In the coupled enzyme system, RgDAAO oxidizes the d-form of UAAs in a stereospecific manner and produces the corresponding α-keto acids, which are then converted into the l-form of UAAs by TtAT, resulting in the quantitative and stereospecific conversion of racemic UAAs to optically pure forms. The genetic incorporation of the optically pure UAAs into a target protein produced a better protein yield than the same experiments using the racemic mixtures of the UAAs. This method could not only be used for the preparation of optically pure UAAs from racemic mixtures, but also the broad substrate specificity of both enzymes would allow for its expansion to structurally diverse UAAs.

Evaluation of the Interaction between Bax and Hsp70 in Cells by Using a FRET System Consisting of a Fluorescent Amino Acid and YFP as a FRET Pair.

To gain insight into factors that lead to dissociation of Bax from a complex with Hsp70 during apoptosis, we recently constructed a fluorescence resonance energy transfer (FRET) system composed of the Hsp70-YFP (YFP=yellow fluorescent protein) fusion protein and fluorescent amino acid (ANAP=6-acetyl(naphthalen-2-ylamino)-2-aminopropanoic acid)-containing Bax (Bax-ANAP), which was produced by using the genetic code expansion technique. In the current study, the FRET system was employed to elucidate how brefeldin A (an endoplasmic reticulum stress inducer), chlorpromazine and apoptozole (lysosomal membrane destabilizers), bafilomycin A1 (an inhibitor of lysosomal acidification) as well as raptinal and Az-TPP-O3 (mitochondria-targeted apoptosis inducers) affect the interaction between Bax and Hsp70. Analyses of single live cell images together with results of co-immunoprecipitation assays reveal that brefeldin A, chlorpromazine, and apoptozole promote dissociation of the Bax/Hsp70 complex through activation of the activator BH3-only protein. However, the results show that bafilomycin A1, raptinal, and Az-TPP-O3 have no influence on the interaction of Bax with Hsp70. The combined observations made in the current and previous studies demonstrate that the FRET system consisting of Bax-ANAP and Hsp70-YFP is highly useful to understand apoptotic processes associated with the Bax-Hsp70 interaction.

Pdlim4 is essential for CCR7-JNK-mediated dendritic cell migration and F-actin-related dendrite formation.

Dendritic cells (DCs) are the most potent professional antigen (Ag)-presenting cells and inducers of T cell-mediated immunity. A previous microarray analysis identified PDZ and LIM domain protein 4 (Pdlim4) as a candidate marker for DC maturation. The aim of this study was to investigate whether Pdlim4 influences DC migration and maturation. Mouse bone marrow-derived DCs were transduced lentivirally with Pdlim4 short hairpin RNA and examined by confocal microscopy, flow cytometry, ELISA, and Western blotting. Pdlim4 was highly induced in LPS-stimulated mature DCs (mDCs). Pdlim4-knockdown mDCs showed reduced expression of molecules associated with Ag presentation and T-cell costimulation, reduced cytokine production, and functional defects in their ability to activate T cells. Moreover, Pdlim4 was necessary for mDC migration via C-C chemokine receptor type 7 (CCR7)-JNK in in vitro Transwell assays. The importance of Pdlim4 in DC migration was confirmed with an in vivo migration model in which C57BL/6 mice were injected with fluorescently labeled DCs in the footpad and migration to the popliteal lymph nodes was assessed by flow cytometry. Moreover, dendrite formation in mDCs was remarkably attenuated under Pdlim4 knockdown. Taken together, these results demonstrate that Pdlim4 is necessary for DC migration via CCR7-JNK, dendrite formation, and subsequent development of functional T-cell responses.-Yoo, J.-Y., Jung, N.-C., Lee, J.-H., Choi, S.-Y., Choi, H.-J., Park, S.-Y., Jang, J.-S., Byun, S.-H., Hwang, S.-U., Noh, K.-E., Park, Y., Lee, J., Song, J.-Y., Seo, H. G., Lee, H. S., Lim, D.-S. Pdlim4 is essential for CCR7-JNK-mediated dendritic cell migration and F-actin-related dendrite formation.

Metal-Mediated Protein Assembly Using a Genetically Incorporated Metal-Chelating Amino Acid.

Many natural proteins function in oligomeric forms, which are critical for their sophisticated functions. The construction of protein assemblies has great potential for biosensors, enzyme catalysis, and biomedical applications. In designing protein assemblies, a critical process is to create protein-protein interaction (PPI) networks at defined sites of a target protein. Although a few methods are available for this purpose, most of them are dependent on existing PPIs of natural proteins to some extent. In this report, a metal-chelating amino acid, 2,2'-bipyridylalanine (BPA), was genetically introduced into defined sites of a monomeric protein and used to form protein oligomers. Depending on the number of BPAs introduced into the protein and the species of metal ions (Ni2+ and Cu2+), dimers or oligomers with different oligomerization patterns were formed by complexation with a metal ion. Oligomer sizes could also be controlled by incorporating two BPAs at different locations with varied angles to the center of the protein. When three BPAs were introduced, the monomeric protein formed a large complex with Ni2+. In addition, when Cu2+ was used for complex formation with the protein containing two BPAs, a linear complex was formed. The method proposed in this report is technically simple and generally applicable to various proteins with interesting functions. Therefore, this method would be useful for the design and construction of functional protein assemblies.

Analysis of Protein-Protein Interaction in a Single Live Cell by Using a FRET System Based on Genetic Code Expansion Technology.

Hsp70 is known to directly bind to Bax for suppression of apoptosis. However, mechanisms on how Bax is dissociated from its complex with Hsp70 during apoptosis remain largely unknown. In the current study, we developed the efficient fluorescence resonance energy transfer (FRET) system which consisted of Hsp70-YFP and fluorescent amino acid (ANAP)-incorporated Bax, which was generated by using genetic code expansion technology, and applied the FRET system to elucidate mechanisms on how apoptosis-inducing substances dissociate Bax from Hsp70. Time-dependent analysis of single live cell images showed that Bax activators binding to Bax trigger sites inhibited the Bax-Hsp70 interaction but a Bax activator, which blocks phosphorylation of S184 via binding to the C-terminal S184 site, did not affect this interaction. Additionally, an inhibitor for Hsp70-Hsp40 interaction blocked the Bax-Hsp70 interaction. Furthermore, p53 activators promoted the dissociation of Bax from Hsp70 by reactivating p53 which disrupted the Bax-Hsp70 interaction. We also found that death ligands and a Bcl-2 inhibitor enhanced the dissociation of Bax from Hsp70 by activating activator BH3-only proteins. Results from this effort suggest that FRET systems consisting of the ANAP-incorporated protein and the YFP fusion protein will be valuable tools to gain an understanding of other types of protein-protein interactions.

Comparative immunological study of penetrating and anterior lamellar keratoplasty in a murine model.

In lamellar keratoplasty, the diseased part of a cornea is replaced while the healthy tissue remains lamellar keratoplasty has the advantage of better graft survival compared to penetrating keratoplasty (PK). We compared the immunological responses to PK and anterior lamellar keratoplasty (ALK) in a murine model. PK or ALK was performed using C57BL/6 donor grafts and BALB/c recipients, and graft opacity was assessed to evaluate graft rejection up to 8 weeks. We evaluated the immunological responses in both groups, which were not clinically considered as graft failure on postoperative day 21. PK mice showed reduced clinical graft survival compared to ALK mice. The mRNA expression of inflammatory mediators, such as IL-1ß, IFN-γ, and granzyme B, in grafted corneas of PK mice, was significantly increased compared to the levels in ALK mice at postoperative day 21. PK led to a higher delayed-type hypersensitivity response and IFN-γ secretion in an in vitro T cell assay from draining lymph nodes (LNs), as compared to ALK. Furthermore, PK showed increased angiogenesis and lymphangiogenesis in grafted corneas compared to ALK and led to greater infiltration of CD3+ T cells into grafted corneas and increased frequencies of mature antigen presenting cells (APC; MHC-IIhighCD11c + cells) and IL-12 + dendritic cells (DCs) in the draining LNs of transplanted mice. In conclusion, PK results in increased graft rejection compared to ALK through relatively increased neovascularization and lymphangiogenesis, which can induce infiltration of pathologic T cells and mature APC migration into grafted corneas and draining LNs.

DNA binding fluorescent proteins for the direct visualization of large DNA molecules.

Fluorescent proteins that also bind DNA molecules are useful reagents for a broad range of biological applications because they can be optically localized and tracked within cells, or provide versatile labels for in vitro experiments. We report a novel design for a fluorescent, DNA-binding protein (FP-DBP) that completely 'paints' entire DNA molecules, whereby sequence-independent DNA binding is accomplished by linking a fluorescent protein to two small peptides (KWKWKKA) using lysine for binding to the DNA phosphates, and tryptophan for intercalating between DNA bases. Importantly, this ubiquitous binding motif enables fluorescent proteins (Kd = 14.7 µM) to confluently stain DNA molecules and such binding is reversible via pH shifts. These proteins offer useful robust advantages for single DNA molecule studies: lack of fluorophore mediated photocleavage and staining that does not perturb polymer contour lengths. Accordingly, we demonstrate confluent staining of naked DNA molecules presented within microfluidic devices, or localized within live bacterial cells.

Single and double acquisition strategies for compensation of artifacts from eddy current and transient oscillation in balanced steady-state free precession.

PURPOSE: To develop single and double acquisition methods to compensate for artifacts from eddy currents and transient oscillations in balanced steady-state free precession (bSSFP) with centric phase-encoding (PE) order for magnetization-prepared bSSFP imaging. THEORY AND METHODS: A single and four different double acquisition methods were developed and evaluated with Bloch equation simulations, phantom/in vivo experiments, and quantitative analyses. For the single acquisition method, multiple PE groups, each of which was composed of N linearly changing PE lines, were ordered in a pseudocentric manner for optimal contrast and minimal signal fluctuations. Double acquisition methods used complex averaging of two images that had opposite artifact patterns from different acquisition orders or from different numbers of dummy scans. RESULTS: Simulation results showed high sensitivity of eddy-current and transient-oscillation artifacts to off-resonance frequency and PE schemes. The artifacts were reduced with the PE-grouping with N values from 3 to 8, similar to or better than the conventional pairing scheme of N = 2. The proposed double acquisition methods removed the remaining artifacts significantly. The proposed methods conserved detailed structures in magnetization transfer imaging well, compared with the conventional methods. CONCLUSION: The proposed single and double acquisition methods can be useful for artifact-free magnetization-prepared bSSFP imaging with desired contrast and minimized dummy scans. Magn Reson Med 78:254-263, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Engineering a periplasmic binding protein for amino acid sensors with improved binding properties.

Periplasmic binding proteins (PBPs) are members of a widely distributed protein superfamily found in bacteria and archaea, and are involved in the cellular uptake of solutes. In this report, a leucine-binding PBP was engineered to detect l-Leu based on a fluorescence resonance energy transfer (FRET) change upon ligand binding. A fluorescent unnatural amino acid, l-(7-hydroxycoumarin-4-yl)ethylglycine (CouA), was genetically incorporated into the protein as a FRET donor, and a yellow fluorescent protein (YFP) was fused with its N-terminus as a FRET acceptor. When CouA was incorporated into position 178, the sensor protein showed a 2.5-fold increase in the FRET ratio. Protein engineering significantly improved its substrate specificity, showing minimal changes in the FRET ratio with the other 19 natural amino acids and d-Leu. Further modification increased the sensitivity of the sensor protein (14-fold) towards l-Leu, and it recognized l-Met as well with moderate binding affinity. Selected mutant sensors were used to measure concentrations of l-Leu in a biological sample (fetal bovine serum) and to determine the optical purity of Leu and Met. This FRET-based sensor design strategy allowed us to easily manipulate the natural receptor to improve its binding affinity and specificity and to recognize other natural molecules, which are not recognized by the wild-type receptor. The design strategy can be applied to other natural receptors, enabling engineering receptors that sense biochemically interesting molecules.