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Abstract Fluorescence-guided surgery has emerged as an innovative technique with promising applications in the treatment of various tumors, including colon cancer. Tumor-initiating probe yellow (TiY) has been discovered for identifying tumorigenic cells by unbiased phenotypic screening with thousands of diversity-oriented fluorescence library (DOFL) compounds in a patient-derived lung cancer cell model. This study demonstrated the clinical feasibility of TiY for tumor-specific fluorescence imaging in the tissues of patients with colorectal cancer (CRC). To evaluate the efficacy of TiY in tumor imaging, surgical specimens were obtained, consisting of 36 tissues from 18 patients with CRC, for ex vivo molecular fluorescence imaging, histology, and immunohistochemistry. Orthotopic and chemically induced CRC mice models were administered TiY topically, and distinct tumor lesions were observed in 10 min by real-time fluorescence colonoscopy and ex vivo imaging. In a hepatic metastasis mouse model using splenic injection, TiY accumulation was detected in metastatic liver lesions through fluorescence imaging. Correlation analysis between TiY intensity and protein expression, assessed via immunohistochemistry and Western blotting, revealed a positive correlation between TiY and vimentin and Zeb1, which are known as epithelial–mesenchymal transition (EMT) markers of cancers. A comparative analysis of TiY with other FDA-approved fluorescence probes such as ICG revealed greater quantitative differences in TiY fluorescence intensity between tumor and normal tissues than those observed with ICG. Altogether, these results demonstrated that TiY has a strong potential for visualizing CRC by fluorescence imaging in various preclinical models, which can be further translated for clinical use such as fluorescence-guided surgery. Furthermore, our data indicate that TiY is preferentially uptaken by cells with EMT induction and progression, and overexpressing vimentin and Zeb1 in patients with CRC.

Abstract Background Uncoupling protein 1 (UCP1) is a proton uncoupler located across the mitochondrial membrane generally involved in thermogenesis of brown adipose tissues. Although UCP1 is known to be strongly expressed in brown adipocytes, recent evidence suggest that white adipocytes can also express UCP1 under certain circumstances such as cold- or β-adrenergic receptor-stimulation, allowing them to acquire brown adipocyte-like features thereby becoming 'beige’ adipocytes. Results In this study, we report that UCP1 can be expressed in adipose-tissue macrophages (ATM) lacking functional hypoxia-inducible factor-1 (HIF-1) and this does not require cold- nor β-adrenergic receptor activation. By using myeloid-specific Hif-1α knockout (KO) mice, we observed that these mice were protected from diet-induced obesity and exhibited an improved thermogenic tolerance upon cold challenge. ATM isolated from white adipose tissues (WAT) of these mice fed with high fat diet exhibited significantly higher M2-polarization, decreased glycolysis, increased mitochondrial functions and acetyl-CoA levels, along with increased expression of Ucp1, peroxisome proliferator activated receptor-gamma co-activator-1a, and others involved in histone acetylation. Consistent with the increased Ucp1 gene expression, these ATM produced a significant amount of heat mediating lipolysis of co-cultured adipocytes liberating free fatty acid. Treating ATM with acetate, a substrate for acetyl-CoA synthesis was able to boost the heat production in wild-type or Hif-1α-deficient but not UCP1-deficient macrophages, indicating that UCP1 was necessary for the heat production in macrophages. Lastly, we observed a significant inverse correlation between the number of UCP1-expressing ATM in WAT and the body mass index of human individuals. Conclusions UCP1-expressing ATM produce the heat to mediate lipolysis of adipocytes, indicating that this can be a novel strategy to treat and prevent diet-induced obesity.

Cellular senescence, which is triggered by various stressors, manifests as irreversible cell cycle arrest, resulting in the disruption of multiple nuclear condensates. One of the affected structures is the nucleolus, whose tripartite layout, separated into distinct liquid phases, allows for the stepwise progression of ribosome biogenesis. The dynamic properties of dense fibrillar components, a sub-nucleolar phase, are crucial for mediating pre-rRNA processing. However, the mechanistic link between the material properties of dense fibrillar components and cellular senescence remains unclear. We established a significant association between cellular senescence and alterations in nucleolar materiality and characteristics, including the number, size, and sphericity of individual subphases of the nucleolus. Senescent cells exhibit reduced fibrillarin dynamics, aberrant accumulation of high-order protein assemblies, such as oligomers and fibrils, and increased dense fibrillar component density. Intriguingly, the addition of RNA-interacting entities mirrored the diminished diffusion of fibrillarin in the nucleolus during cellular senescence. Thus, our findings contribute to a broader understanding of the intricate changes in the materiality of the nucleolus associated with cellular senescence and shed light on nucleolar dynamics in the context of aging and cellular stress.

Although titanium-based metal implants have become a game changer in dental and orthopedic therapies, they still have several problems such as late osseointegration and immune response. In this study, we present a novel strategy to develop Ti6Al4V-based implants embedded with biogenic hydroxyapatite derived from equine bone to overcome these problems. A selective laser melting technique was employed for facile fabrication with flexible fusing feedstock and regular uniform distribution of equine bone. The physicochemical characteristics, cell attachment and proliferation, osteogenic differentiation, osseointegration, inflammatory response, and metabolomics of the developed Ti6Al4V/equine bone composite were then investigated. The Ti6Al4V-based composite integrated with equine bone at a certain concentration has improved the crystalline structure (β-Ti) suitable for implantation and exhibited higher hydrophilicity and protein adsorption. They significantly promoted cell attachment, osteogenic differentiation, and anti-inflammatory effects in vitro. In vivo study confirmed the osseointegration and alleviated inflammatory responses. Furthermore, the Ti6Al4V-based implants integrated with equine bone significantly reduced metabolites associated with inflammatory responses both in vitro and in vivo. The observed reduction in inflammatory responses suggests a subsequent promotion of osteogenesis. These promising results position the Ti6Al4V-based implant integrated with equine bone as a potential candidate for replacing conventional dental and orthopedic implants.

Loss of elastin due to aging, disease, or injury can lead to impaired tissue function. In this study, de novo tropoelastin (TE) synthesis is investigated in vitro and in vivo using different TE-encoding synthetic mRNA variants after codon optimization and nucleotide modification. Codon optimization shows a strong effect on protein synthesis without affecting cell viability in vitro, whereas nucleotide modifications strongly modulate translation and reduce cell toxicity. Selected TE mRNA variants (3, 10, and 30 μg) are then analyzed in vivo in porcine skin after intradermal application. Administration of 30 μg of native TE mRNA with a me1 Ψ modification or 10 and 30 μg of unmodified codon-optimized TE mRNA is required to increase TE protein expression in vivo. In contrast, just 3 μg of a codon-optimized TE mRNA variant with the me1 Ψ modification is able to increase protein expression. Furthermore, skin toxicity is investigated in vitro by injecting 30 μg of mRNA of selected TE mRNA variants into a human full-thickness skin model, and no toxic effects are observed. Thereby, for the first time, an increased dermal TE synthesis by exogenous administration of synthetic mRNA is demonstrated in vivo. Codon optimization of a synthetic mRNA can significantly increase protein expression and therapeutic outcome.

The development of efficient biomarkers and probes for monitoring and treating cancer, specifically metastatic cancer, is a critical research area that can have a significant impact on both patient outcomes and drug discovery. In this context, TiNIR has been developed to detect tumor-initiating cells (TICs), with heme oxygenase 2 (HO2) as a promising therapeutic biomarker for tumor-initiating cells. In this study, TiNIR has demonstrated its effectiveness as an in vivo metastatic lung cancer tracker, highlighting its potential as a valuable tool in cancer research and therapy. The development of innovative approaches that selectively target metastatic cancers represents a promising avenue for improving survival rates and enhancing the quality of life of cancer patients.

Based on studies with a fluorescent reporter dye, Mito Thermo Yellow (MTY), and the genetically encoded gTEMP ratiometric fluorescent temperature indicator targeted to mitochondria, the temperature of active mitochondria in four mammalian and one insect cell line was estimated to be up to 15°C above that of the external environment to which the cells were exposed. High mitochondrial temperature was maintained in the face of a variety of metabolic stresses, including substrate starvation or modification, decreased ATP demand due to inhibition of cytosolic protein synthesis, inhibition of the mitochondrial adenine nucleotide transporter and, if an auxiliary pathway for electron transfer was available via the alternative oxidase, even respiratory poisons acting downstream of oxidative phosphorylation (OXPHOS) complex I. We propose that the high temperature of active mitochondria is an inescapable consequence of the biochemistry of OXPHOS and is homeostatically maintained as a primary feature of mitochondrial metabolism.

Fluorescent bioprobes are invaluable tools for visualizing live cells and deciphering complex biological processes by targeting intracellular biomarkers without disrupting cellular functions. In addition to protein-binding concepts, fluorescent probes utilize various mechanisms, including membrane, metabolism, and gating-oriented strategies. This study introduces a novel fluorescent mechanism distinct from existing ways. Here, we developed a B cell selective probe, CDrB, with unique transport mechanisms. Through SLC-CRISPRa screening, we identified two transporters, SLCO1B3 and SLC25A41, by sorting out populations exhibiting higher and lower fluorescence intensities, respectively, demonstrating contrasting activities. We confirmed that SLCO1B3, with comparable expression levels in T and B cells, facilitates the transport of CDrB into cells, while SLC25A41, overexpressed in T lymphocytes, actively exports CDrB. This observation suggests that SLC25A41 plays a crucial role in discriminating between T and B lymphocytes. Furthermore, it reveals the potential for the reversible localization of SLC25A41 to demonstrate its distinct activity. This study is the first report to unveil a novel strategy of SLC by exporting the probe. We anticipate that this research will open up new avenues for developing fluorescent probes.

Studying the specific roles of macrophage subsets has been hampered by a lack of subset-specific probes. Here the authors report an M1 selective fluorescent probe named CDr17, and demonstrate the suitability of this probe for tracking M1 macrophages in vivo.

Abstract Background Trimethyltin (TMT) is a potent neurotoxicant that leads to hippocampal neurodegeneration. Regulatory T cells (Tregs) play an important role in maintaining the immune balance in the central nervous system (CNS), but their activities are impaired in neurodegenerative diseases. In this study, we aimed to determine whether adoptive transfer of Tregs, as a living drug, ameliorates hippocampal neurodegeneration in TMT-intoxicated mice. Methods CD4+CD25+ Tregs were expanded in vitro and adoptively transferred to TMT-treated mice. First, we explored the effects of Tregs on behavioral deficits using the Morris water maze and elevated plus maze tests. Biomarkers related to memory formation, such as cAMP response element-binding protein (CREB), protein kinase C (PKC), neuronal nuclear protein (NeuN), nerve growth factor (NGF), and ionized calcium binding adaptor molecule 1 (Iba1) in the hippocampus were examined by immunohistochemistry after killing the mouse. To investigate the neuroinflammatory responses, the polarization status of microglia was examined in vivo and in vitro using real-time reverse transcription polymerase chain reaction (rtPCR) and Enzyme-linked immunosorbent assay (ELISA). Additionally, the inhibitory effects of Tregs on TMT-induced microglial activation were examined using time-lapse live imaging in vitro with an activation-specific fluorescence probe, CDr20. Results Adoptive transfer of Tregs improved spatial learning and memory functions and reduced anxiety in TMT-intoxicated mice. Additionally, adoptive transfer of Tregs reduced neuronal loss and recovered the expression of neurogenesis enhancing molecules in the hippocampi of TMT-intoxicated mice. In particular, Tregs inhibited microglial activation and pro-inflammatory cytokine release in the hippocampi of TMT-intoxicated mice. The inhibitory effects of TMT were also confirmed via in vitro live time-lapse imaging in a Treg/microglia co-culture system. Conclusions These data suggest that adoptive transfer of Tregs ameliorates disease progression in TMT-induced neurodegeneration by promoting neurogenesis and modulating microglial activation and polarization.

Intracellular micro-temperature is closely related to cellular processes. Such local temperature inside cells can be measured by fluorescent thermometers, which are a series of fluorescent materials that convert the temperature information to detectable fluorescence signals. To investigate the intracellular temperature fluctuation in various organelles, it is essential to develop site-specific organelle thermometers. In this study, we develop a new series of fluorescent thermometers, Thermo Greens (TGs), to visualize the temperature change in almost all typical organelles. Through fluorescence lifetime-based cell imaging, it was proven that TGs allow the organelle-specific monitoring of temperature gradients created by external heating. The fluorescence lifetime-based thermometry shows that each organelle experiences a distinct temperature increment which depends on the distance away from the heat source. TGs are further demonstrated in the quantitative imaging of heat production at different organelles such as mitochondria and endoplasmic reticulum in brown adipocytes. To date, TGs are the first palette batch of small molecular fluorescent thermometers that can cover almost all typical organelles. These findings can inspire the development of new fluorescent thermometers and enhance the understanding of thermal biology in the future.

Fluorescence thermometry is a microscopy technique in which a fluorescent temperature sensor records temperature changes as alterations of fluorescence signals. Fluorescence lifetime imaging (FLIM) is a promising method for quantitative analysis of intracellular temperature. Recently, we developed small-molecule thermometers, termed Organelle Thermo Greens, that target various organelles and achieved quantitative temperature mapping using FLIM. Despite its highly quantitative nature, FLIM-based thermometry cannot be used widely due to expensive instrumentation. Here, we investigated the applicability and limitations of fluorescence intensity (FI)-based analysis, which is more commonly used than FLIM-based thermometry. Temperature gradients generated by artificial heat sources and physiological heat produced by brown adipocytes were visualized using FI- and FLIM-based thermometry. By comparing the two thermometry techniques, we examined how the shapes of organelles and cells affect the accuracy of the temperature measurements. Based on the results, we concluded that FI-based thermometry could be used for “qualitative”, rather than quantitative, thermometry under the limited condition that the shape change and the dye leakage from the target organelle were not critical.

In vivo blood vessels imaging is crucial to study blood vessels related diseases in real-time. For this purpose, fluorescent based imaging is one of the utmost techniques for imaging a living system. The discovery of a new near-infrared probe (CyA-B2) by screening chemical probe library in our previous report which showed the most specific binding on the blood capillaries of the 3D-tissue models give us interest to study more about the binding site of this probe to the surface of endothelial cells main component cell of blood capillaries. By studying the competition assays of CyA-B2 using several potential surface markers of endothelial cells found through the chemical database (ChEMBL) and manually selected, CD133 gave the lowest IC50 (half maximal inhibitory concentration) value. Hence, CD133 protein which is expressed on the endothelial cell membrane was postulated to be the binding site due to the suppression of CyA-B2 on the blood capillaries by the competition assays. Since, CD133 is also expressed on many types of cancer cells, it would be useful to use CyA-B2 as a bioprobe to monitor or diagnostic tumor growth.

The development of organelle-specific fluorescent probes has been impeded by the absence of a comprehensive understanding of the relationship between the physicochemical properties of fluorescent probes and their selectivity towards specific organelles. Although a few machine learning models have suggested several physicochemical parameters that control the target organelle of the probes and have attempted to predict the target organelles, they have been challenged by low accuracy and a limited range of applicable organelles. Herein, we report a multi-organelle prediction QSAR model that is capable of predicting the destination of probes among nine categories, including cytosol, endoplasmic reticulum, Golgi body, lipid droplet, lysosome, mitochondria, nucleus, plasma membrane, and no entry. The model is trained using the Random Forest algorithm with a dataset of 350 organelle-specific fluorescent probes and 786 descriptors, and it is able to predict the target organelles of fluorescent probes with an accuracy of 75%. The MDI analysis of the model identifies 38 key parameters that have a significant impact on the organelle selectivity of the probes, including LogD, pKa, hydrophilic-lipophilic balance (HLB), and topological polar surface area (TPSA). This prediction model may be useful in developing new organelle-specific fluorescent probes by providing crucial variables that determine the destination of the probes.

(1) Background: a small-molecule fluorescent chemosensor, CDr20, tracks the resident macrophages based on the UGT1A7C activity in the brain, raising the possibility that additional immune cells expressing the UGT1A7C can be labeled with CDr20. (2) Methods: we applied CDr20 to various types of blood cells derived from hematopoietic organs (spleen and bone marrow) as well as peripheral blood to test the degree and selectivity of labeling of CDr20 in these cell types; (3) Results: CDr20 fluorescently labels monocytes/macrophages and neutrophils as a result of glucuronidation reaction (CDr20-Gluc), which is mediated with UGT1A7C. The selectivity of CDr20 labeling highly correlates with the Ugt1a7c expression level in immune cells. Moreover, CDr20-Gluc is exported from cells by a mechanism of how glucuronides within cells are excreted into extracellular space. Interestingly, the exportation of CDr20-Gluc is mainly observed in monocytes, potentially due to the monocyte-specific expression of ABCC transporters and this resulted in large differences in the degree of fluorescence retention in neutrophils (CDr20bright), compared to monocytes (CDr20dim) upon one hour of CDr20 incubation; (4) Conclusions: CDr20 can differentially label monocytes and neutrophils due to the variance in two different cellular enzymatic activities of UGT1A7C and ABCC. By using this property, CDr20 can be used to distinguish specific cell types within blood.

Abstract Background Despite recent rapid progress in method development and biological understanding of induced pluripotent stem (iPS) cells, there has been a relative shortage of tools that monitor the early reprogramming process into human iPS cells. Methods We screened the in-house built fluorescent library compounds that specifically bind human iPS cells. After tertiary screening, the selected probe was analyzed for its ability to detect reprogramming cells in the time-dependent manner using high-content imaging analysis. The probe was compared with conventional dyes in different reprogramming methods, cell types, and cell culture conditions. Cell sorting was performed with the fluorescent probe to analyze the early reprogramming cells for their pluripotent characteristics and genome-wide gene expression signatures by RNA-seq. Finally, the candidate reprogramming factor identified was investigated for its ability to modulate reprogramming efficiency. Results We identified a novel BODIPY-derived fluorescent probe, BDL-E5, which detects live human iPS cells at the early reprogramming stage. BDL-E5 can recognize authentic reprogramming cells around 7 days before iPS colonies are formed and stained positive with conventional pluripotent markers. Cell sorting of reprogrammed cells with BDL-E5 allowed generation of an increased number and higher quality of iPS cells. RNA sequencing analysis of BDL-E5-positive versus negative cells revealed early reprogramming patterns of gene expression, which notably included CREB1. Reprogramming efficiency was significantly increased by overexpression of CREB1 and decreased by knockdown of CREB1. Conclusion Collectively, BDL-E5 offers a valuable tool for delineating the early reprogramming pathway and clinically applicable commercial production of human iPS cells.

Abstract Background Staphylococcus aureus is a human pathogen that is a common cause of nosocomial infections and infections on indwelling medical devices, mainly due to its ability to shift between the planktonic and the biofilm/sessile lifestyle. Biofilm infections present a serious problem in human medicine as they often lead to bacterial persistence and thus to chronic infections. The immune responses elicited by biofilms have been described as specific and ineffective. In the few experiments performed in vivo, the importance of neutrophils and macrophages as a first line of defence against biofilm infections was clearly established. However, the bilateral interactions between biofilms and myeloid cells remain poorly studied and analysis of the dynamic processes at the cellular level in tissues inoculated with biofilm bacteria is still an unexplored field. It is urgent, therefore, to develop biologically sound experimental approaches in vivo designed to extract specific immune signatures from the planktonic and biofilm forms of bacteria. Results We propose an in vivo transgenic mouse model, used in conjunction with intravital confocal microscopy to study the dynamics of host inflammatory responses to bacteria. Culture conditions were created to prepare calibrated inocula of fluorescent planktonic and biofilm forms of bacteria. A confocal imaging acquisition and analysis protocol was then drawn up to study the recruitment of innate immune cells in the skin of LysM-EGFP transgenic mice. Using the mouse ear pinna model, we showed that inflammatory responses to S. aureus can be quantified over time and that the dynamics of innate immune cells after injection of either the planktonic or biofilm form can be characterized. First results showed that the ability of phagocytic cells to infiltrate the injection site and their motility is not the same in planktonic and biofilm forms of bacteria despite the cells being considerably recruited in both cases. Conclusion We developed a mouse model of infection to compare the dynamics of the inflammatory responses to planktonic and biofilm bacteria at the tissue and cellular levels. The mouse ear pinna model is a powerful imaging system to analyse the mechanisms of biofilm tolerance to immune attacks.

The identification of T and B lymphocytes has relied on using antibodies against different biomarkers as the gold standard. Emerging small molecule-based fluorescent probes have the potential to replace antibodies. Herein, we report the first human-T-cell-selective fluorescent probe, Mito thermo yellow (MTY), achieving the live T cells’ distinction from B cells, which was previously impossible without the help of antibodies. The unexpected cell selectivity of MTY is attributed to the higher mitochondria mass and membrane potential of T cells over B cells. This study enriches the toolbox for live cell distinction from complex cell communities.

Attempts to image activated macrophages in vivo have been hampered by selectivity and delivery problems. Here the authors develop a small molecule fluorescent probe specific to activated M1 and M2 macrophages, identify the orphan receptor Slc18b1/SLC18B1 as the mechanism of uptake, and use it to image atherosclerosis in mice.

This study examines the optimal emission control at two competing public ports. We first develop a two-stage duopoly model in which governments determine the emission standard that restrains shipping operators’ fuel quality and ports are involved in price competition, taking the emission standards as given. Then, non-cooperative and cooperative emission control cases are analyzed. The main result of this study is surprising. The results suggest that shipping operators bear fuel cost, congestion externality cost, and port price. The port price comprises markups from market power, congestion externality, and emission externality cost. Regardless of cooperation and governments’ knowledge of port pricing, the emission standard is optimal if and only if shipping operators’ fuel cost equals the emission externality cost.

Abstract The identification of brown adipose deposits in adults has led to significant interest in targeting this metabolically active tissue for treatment of obesity and diabetes. Improved methods for the direct measurement of heat production as the signature function of brown adipocytes (BAs), particularly at the single cell level, would be of substantial benefit to these ongoing efforts. Here, we report the first application of a small molecule-type thermosensitive fluorescent dye, ERthermAC, to monitor thermogenesis in BAs derived from murine brown fat precursors and in human brown fat cells differentiated from human neck brown preadipocytes. ERthermAC accumulated in the endoplasmic reticulum of BAs and displayed a marked change in fluorescence intensity in response to adrenergic stimulation of cells, which corresponded to temperature change. ERthermAC fluorescence intensity profiles were congruent with mitochondrial depolarisation events visualised by the JC-1 probe. Moreover, the averaged fluorescence intensity changes across a population of cells correlated well with dynamic changes such as thermal power, oxygen consumption, and extracellular acidification rates. These findings suggest ERthermAC as a promising new tool for studying thermogenic function in brown adipocytes of both murine and human origins.

Ports create harmful effects on their adjacent population because ships discharge noxious gases like SOX, NOX, and particulate matter (PM). To tackle this problem, some ports started to control emission through regulations such as Emission Control Areas (ECA) and Reduced Speed Zone (RSZ). This paper estimates the social cost of ship emission and eco-efficiency at the Port of Incheon (POI). We further examine how the ECA and RSZ designation can reduce the social cost. The estimation is based on the activity-based approach, where ship type, engine, and movement are used to measure fuel consumption and then emission. Results suggest that the social cost of ship emission at the POI amounts to $90,805,478. The eco-efficiency of the POI, compared to the one at the Port of Las Palmas in another study, is substantially better. Under RSZ, the corresponding emission abatement values are $4,485,308, $2,642,009 and $21,932,435 from SO2, NOX and PM reduction, respectively. If 1.0% and 0.1% sulfur fuel are used complying with rules of the ECA, the social cost savings amount to $8,174,947 and $12,868,842 from SO2 reduction.

This study determines the top fifty authors in China and their university affiliations in the maritime transportation field, compared to their world ranking. We refer to China in the broad sense of the Chinese economies, including not only mainland China and Hong Kong, but also Chinese Taipei (Taiwan) and Singapore. This study analyzes sixty-five SSCI and SCI journals in the field of maritime and transportation between the years 2000 and 2015. In terms of ranking, three indicators are employed: total number of articles, weighted score (indication of author contribution), and the impact score. With the exception of Shanghai Jiao Tong University, no other universities selected in the first phase of Project 985, which received billions of dollars in government support/aid, were listed in the world ranking. Star authors are deemed to have contributed greatly to the rankings of their affiliated universities. The future of China’s rankings is bright in view of the increasing number of papers being published by Chinese authors and universities and their strong grounding in quantitative methodologies.

Mitochondria are the source of internal heat which influences all cellular processes. Hence, monitoring mitochondrial temperature provides a unique insight into cell physiology. Using a thermosensitive fluorescent probe MitoThermo Yellow (MTY), we have shown recently that mitochondria within human cells are maintained at close to 50 °C when active, increasing their temperature locally by about 10 °C. Initially reported in the HEK293 cell line, we confirmed this finding in the HeLa cell line. Delving deeper, using MTY and MTX (MitoThermo X), a modified version of MTY, we unraveled some caveats related to the nature of these charged fluorophores. While enabling the assessment of mitochondrial temperature in HEK and HeLa cell lines, the reactivity of MTY to membrane potential variations in human primary skin fibroblasts precluded local temperature monitoring in these cells. Chemical modification of MTY into MTX did not result in a temperature probe unresponsive to membrane potential variations that could be universally used in any cell type to determine mitochondrial temperature. Thus, the cell-type dependence of MTY in measuring mitochondrial temperature, which is likely due to the variable binding of this dye to specific internal mitochondrial components, should imply cautiousness while using these nanothermometers for mitochondrial temperature analysis.

The success of a fluorescent dye as a molecular probe to monitor the intracellular activity of biomolecules depends on its physicochemical characteristics. Here, the authors use a predictive model to identify key features that allow them to design cell permeable, background-free fluorescent probes.

Incomplete knowledge of the mechanisms at work continues to hamper efforts to maximize reprogramming efficiency. Here, we present a systematic genome-wide RNAi screen to determine the global regulators during the early stages of human reprogramming. Our screen identifies functional repressors and effectors that act to impede or promote the reprogramming process. Repressors and effectors form close interacting networks in pathways, including RNA processing, G protein signaling, protein ubiquitination, and chromatin modification. Combinatorial knockdown of five repressors (SMAD3, ZMYM2, SFRS11, SAE1, and ESET) synergistically resulted in ∼85% TRA-1-60-positive cells. Removal of the novel splicing factor SFRS11 during reprogramming is accompanied by rapid acquisition of pluripotency-specific spliced forms. Mechanistically, SFRS11 regulates exon skipping and mutually exclusive splicing of transcripts in genes involved in cell differentiation, mRNA splicing, and chromatin modification. Our study provides insights into the reprogramming process, which comprises comprehensive and multi-layered transcriptional, splicing, and epigenetic machineries.

Conventional microarray analysis usually deals with the monolayer or two-dimensional (2D) assays for the high-throughput screening applications. Even though these cell-based assays are effective for preliminary screening at least to have information on cytotoxicity, they do not adequately re-create the in vivo complexity of three-dimensional (3D) tissues. In this study, 3D-blood capillary models were constructed by using physiological collagen microfibers (CMF), which provide the extracellular matrix in the complex tissue. Micro-droplets of fibrin gels containing CMF, endothelial cells, and fibroblasts were cultured for five days in 48-wells plate to provide a medium-throughput system for screening applications. Blood capillaries networks were formed by optimizing the concentration of CMF used and the number of cells. Finally, this screening method was a powerful assay for the application on the selection of not only a specific chemical probe for blood capillary live-imaging, but also a drug, aptamer, and peptide with potential blood vessel targeting property.

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 °C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria.

A small-molecule fluorescent probe specific for human pluripotent stem cells would serve as a useful tool for basic cell biology research and stem cell therapy. Screening of fluorescent chemical libraries with human induced pluripotent stem cells (iPSCs) and subsequent evaluation of hit molecules identified a fluorescent compound (Kyoto probe 1 [KP-1]) that selectively labels human pluripotent stem cells. Our analyses indicated that the selectivity results primarily from a distinct expression pattern of ABC transporters in human pluripotent stem cells and from the transporter selectivity of KP-1. Expression of ABCB1 (MDR1) and ABCG2 (BCRP), both of which cause the efflux of KP-1, is repressed in human pluripotent stem cells. Although KP-1, like other pluripotent markers, is not absolutely specific for pluripotent stem cells, the identified chemical probe may be used in conjunction with other reagents.

Novel structures of an near-infrared (NIR) tetraarylazadipyrromethene (aza-BODIPY) series have been prepared. We designed the core structure containing two amido groups at the para-position of the aromatic rings. The amido group was incorporated to secure insensitivity to pH and to ensure a bathochromic shift to the NIR region. Forty members of aza-BODIPY compounds were synthesized by substitution of the acetyl group with commercial amines on the alpha bromide. The physicochemical properties and photostability were investigated and the fluorescence emission maxima (745~755 nm) were found to be in the near infrared (NIR) range of fluorescence.

This study explores the main factors considered when shippers and container shipping lines select their import/export and transshipment ports. In the present study, 38 container port selection indices were chosen from the previous research and field interviews. The scores of the 38 items were collected via survey to the three major maritime/port market players: shippers, shipping lines, and container terminal operators. In order to analyze the different priorities imposed on the port selection factors by the three market players, the ANOVA method has been employed. The empirical test shows the different perceptions about port selection attributes among service suppliers and demanders. In addition, the 38 items have been categorized into seven key factors through an exploratory factor analysis. The ANOVA technique was employed again to analyze the perspective differences for the port selection factors among the market players. The results show that there are significant differences among the players assessing the importance of the three port choice factors: liners and terminal operators give more weight to ‘hinterland and terminal basic conditions’ than shippers; terminal operators do not take ‘line operation’ as seriously as carriers and shippers; the factor of ‘terminal operation’ is more significantly considered by liners and terminal operators than by shippers.

Port competition attracted much scholarly attention in Northwest Europe during the 1980s. Following the rise of powerful economies in East Asia, particularly during the 1980s and 1990s, port competition has become an important phenomenon with the top five container ports in the world being located in the region. This paper aims to overview major port competition issues and outlines and analyzes the main alternative methodologies that researchers have employed to address them, referring to 70 items, mostly papers but including a few books and reports

We describe the use of the fluorescent reporter compound CDr10b to label mid-intestinal structures in zebrafish larvae after simple immersion. CDr10b is deposited into the gut where it initially fills the lumen and is excreted. Using laser-mediated injury of the intestine, we show that CDr10b provides a useful readout of the integrity and repair of the epithelial cell barrier. In addition, CDr10b specifically labels the absorptive mid-intestine segment that is analogous to the mammalian small intestine. By perturbing retinoic acid signaling, which regulates the size of the mid-intestine segment, we show that CDr10b is a valuable tool to rapidly assess developmental malformations of the intestine in live animals.

Macrophages are an essential component of the immune system and have protective and pathogenic functions in various diseases. Imaging of macrophages in vivo could furnish new tools to advance evaluation of disease and therapies. Critical limb ischemia is a disease in which macrophages have considerable pathogenic roles, and are potential targets for cell-based immunotherapy. We sought to develop a new near-infrared fluorescence (NIRF) imaging probe to target macrophages specifically in vivo in various pathological states, including hind-limb ischemia. We rapidly screened the photostable cyanine-based NIRF library against different blood cell lines. The identified monocyte/macrophage-selective hit was tested in vitro in live-cell labeling assay. Non-invasive NIRF imaging was performed with murine models of paw inflammation by lipopolysaccharide challenge and hind-limb ischemia with femoral artery ligation. in vivo macrophage targeting was further evaluated using intravital microscopy with Csf1r-EGFP transgenic mice and immunofluorescent staining with macrophage-specific markers. We discovered MF800, a Macrophage-specific near-infrared Fluorophore, which showed selective live-cell imaging performance in a panel of cell lines and primary human blood samples. MF800 outperforms the clinically-available NIRF contrast agent ICG for in vivo specificity in paw inflammation and hind-limb ischemia models. We observed a marked overlap of MF800-labeled cells and EGFP-expressing macrophages in intravital imaging of Csf1r-EGFP transgenic mice. In the histologic analysis, MF800-positive cells also expressed the macrophage markers CD68 and CD169. NIRF imaging showcased the potential of using MF800 to understand macrophage behavior in vivo, characterize macrophage-associated diseases, and may help in assessing therapeutic responses in the clinic.

Intracellular viscosity is a fundamental physical parameter that indicates the functioning of cells. In this work, we developed a simple boron-dipyrromethene (BODIPY)-based probe, BTV, for cellular mitochondria viscosity imaging by coupling a simple BODIPY rotor with a mitochondria-targeting unit. The BTV exhibited a significant fluorescence intensity enhancement of more than 100-fold as the solvent viscosity increased. Also, the probe showed a direct linear relationship between the fluorescence lifetime and the media viscosity, which makes it possible to trace the change of the medium viscosity. Furthermore, it was demonstrated that BTV could achieve practical applicability in the monitoring of mitochondrial viscosity changes in live cells through fluorescence lifetime imaging microscopy (FLIM).

INTRODUCTION: Compounds exhibiting low non-specific intracellular binding or non-stickiness are concomitant with rapid clearing and in high demand for live-cell imaging assays because they allow for intracellular receptor localization with a high signal/noise ratio. The non-stickiness property is particularly important for imaging intracellular receptors due to the equilibria involved. METHOD: Three mammalian cell lines with diverse genetic backgrounds were used to screen a combinatorial fluorescence library via high throughput live cell microscopy for potential ligands with high in- and out-flux properties. The binding properties of ligands identified from the first screen were subsequently validated on plant root hair. A correlative analysis was then performed between each ligand and its corresponding physiochemical and structural properties. RESULTS: The non-stickiness property of each ligand was quantified as a function of the temporal uptake and retention on a cell-by-cell basis. Our data shows that (i) mammalian systems can serve as a pre-screening tool for complex plant species that are not amenable to high-throughput imaging; (ii) retention and spatial localization of chemical compounds vary within and between each cell line; and (iii) the structural similarities of compounds can infer their non-specific binding properties. CONCLUSION: We have validated a protocol for identifying chemical compounds with non-specific binding properties that is testable across diverse species. Further analysis reveals an overlap between the non-stickiness property and the structural similarity of compounds. The net result is a more robust screening assay for identifying desirable ligands that can be used to monitor intracellular localization. Several new applications of the screening protocol and results are also presented.

Universal phenotyping techniques that can discriminate among various states of biological systems have great potential. We applied 557 fluorescent library compounds to NCI's 60 human cancer cell-lines (NCI-60) to generate a systematic fluorescence phenotypic profiling data. By the kinetic fluorescence intensity analysis, we successfully discriminated the organ origin of all the 60 cell-lines.

Prion diseases currently have no effective therapy. These illnesses affect both animal and human populations, and are characterized by the conformational change of a normal self protein PrP(C) (C for cellular) to a pathological and infectious conformer, PrP(Sc) (Sc for scrapie). We used a well characterized tissue culture model of prion infection, where mouse neuroblastoma cells (N2a) were infected with 22L PrP(Sc), to screen compounds for anti-prion activity. In a prior study we designed a library of styryl based, potential imaging compounds which were selected for high affinity binding to Alzheimer's disease β-amyloid plaques and good blood-brain barrier permeability. In the current study we screened this library for activity in the N2a/22L tissue culture system. We also tested the anti-prion activity of two clinically used drugs, trimipramine and fluphenazine, in the N2a/22L system. These were selected based on their structural similarity to quinacrine, which was previously reported to have anti-prion activity. All the compounds were also screened for toxicity in tissue culture and their ability to disaggregate amyloid fibrils composed of PrP and β-amyloid synthetic peptides in vitro. Two of the imaging agents, 23I and 59, were found to be both effective at inhibiting prion infection in N2a/22L tissue culture and to be non-toxic. These two compounds, as well as trimipramine and fluphenazine were evaluated in vivo using wild-type CD-1 mice infected peripherally with 139A PrP(Sc). All four agents significantly prolonged the asymptomatic incubation period of prion infection (p

CD1d-restricted natural killer T cells with invariant T cell receptor α chains (iNKT cells) are a unique lymphocyte subset that responds to recognition of specific lipid and glycolipid antigens. They are conserved between mice and humans and exert various immunoregulatory functions through their rapid secretion of a variety of cytokines and secondary activation of dendritic cells, B cells and NK cells. In the current study, we analyzed the range of functional activation states of human iNKT cells using a library of novel analogs of α-galactosylceramide (αGalCer), the prototypical iNKT cell antigen. Measurement of cytokines secreted by human iNKT cell clones over a wide range of glycolipid concentrations revealed that iNKT cell ligands could be classified into functional groups, correlating with weak versus strong agonistic activity. The findings established a hierarchy for induction of different cytokines, with thresholds for secretion being consistently lowest for IL-13, higher for interferon-γ (IFNγ), and even higher for IL-4. These findings suggested that human iNKT cells can be intrinsically polarized to selective production of IL-13 by maintaining a low level of activation using weak agonists, whereas selective polarization to IL-4 production cannot be achieved through modulating the strength of the activating ligand. In addition, using a newly designed in vitro system to assess the ability of human iNKT cells to transactivate NK cells, we found that robust secondary induction of interferon-γ secretion by NK cells was associated with strong but not weak agonist ligands of iNKT cells. These results indicate that polarization of human iNKT cell responses to Th2-like or anti-inflammatory effects may best be achieved through selective induction of IL-13 and suggest potential discrepancies with findings from mouse models that may be important in designing iNKT cell-based therapies in humans.

Chemical genetics is defined as a genetics study using chemical tools, which has grown into a major wing of chemical biology and a standard tool of many researchers. A survey of contemporary research in chemical genetics is provided with a special emphasis on the techniques and methods in use.

Peptide fragmentation and activity mapping of human lysozyme was carried out in order to define the structural and sequence requirements for anti-HIV activity. The findings suggest that the effects of HL9 on signaling pathways involved in survival, stress, TGF(beta), p53, NF(kappa)B, protein kinase C and hedgehog signaling may reflect changes in host cells that affect susceptibility to infection.

Research has been conducted on the optically active regioisomers. The complete synthesis of all possible IP (sub)3 and IP (sub)4 optically active regioisomers has been carried out via the use of CRL-catalyzed enzymatic resolution and benzoyl migration strategy and the details are discussed.

A tagged triazine library having a built-in linker that provides a straight-forward transition from phenotypic screening to target identification is discussed. The successful target identification has helped to make a breakthrough in showing the mechanism for the observed phenotype.

Summary: Inorganic polyphosphates (polyPs) are linear polymers of orthophosphate units linked by phosphoanhydride bonds. Polyphosphates represent important stores of phosphate and energy, and are abundant in many pro‐ and eukaryotic organisms. In plants, the existence of polyPs has been established using microscopy and biochemical extraction methods that are now known to produce artifacts. Here we use a polyP‐specific dye and a polyP‐binding domain to detect polyPs in plant and algal cells. To develop the staining protocol, we induced polyP granules in Nicotiana benthamiana and Arabidopsis cells by heterologous expression of Escherichia coli polyphosphate kinase 1 (PPK1). Over‐expression of PPK1 but not of a catalytically impaired version of the enzyme leads to severe growth phenotypes, suggesting that ATP‐dependent synthesis and accumulation of polyPs in the plant cytosol is toxic. We next crossed stable PPK1‐expressing Arabidopsis lines with plants expressing the polyP‐binding domain of E. coli exopolyphosphatase (PPX1c), which co‐localized with PPK1‐generated polyP granules. These granules were stained by the polyP‐specific dye JC‐D7 and appeared as electron‐dense structures in transmission electron microscopy sections. Using the polyP staining protocol derived from these experiments, we screened for polyP stores in different organs and tissues of both mono‐ and dicotyledonous plants. While we could not detect polyP granules in higher plants, we could visualize the polyP‐rich acidocalcisomes in the green alga Chlamydomonas reinhardtii. Significance Statement: A chemical dye and an inorganic polyphosphate‐binding domain are shown to specifically label inorganic polyphosphate granules in transgenic Arabidopsis lines and Chlamydomonas acidocalcisomes. Using these tools we show that, in contrast to many prokaryotic and eukaryotic organisms, higher plants do not seem to contain large stores of inorganic polyphosphate. [ABSTRACT FROM AUTHOR]