A novel L1 retrotransposon marker for HeLa cell line identification

PCR-based analytics of gene therapies using adeno-associated virus vectors: Considerations for cGMP method development

The field of gene therapy has evolved and improved so that today the treatment of thousands of genetic diseases is now possible. An integral aspect of the drug development process is generating analytical methods to be used throughout clinical and commercial manufacturing. Enumeration and identification assays using genetic testing are critical to ensure the safety, efficacy, and stability of many active pharmaceutical ingredients. While nucleic acid-based methods are already reliable and rapid, there are unique biological, technological, and regulatory aspects in gene therapies that must be considered. This review surveys aspects of method development and validation using nucleic acid-based testing of gene therapies by focusing on adeno-associated virus (AAV) vectors and their co-transfection factors. Key differences between quantitative PCR and droplet digital technologies are discussed to show how improvements can be made while still adhering to regulatory guidance. Example validation parameters for AAV genome titers are described to demonstrate the scope of analytical development. Finally, several areas for improving analytical testing are presented to inspire future innovation, including next-generation sequencing and artificial intelligence. Reviewing the broad characteristics of gene therapy assessment serves as an introduction for new researchers, while clarifying processes for professionals already involved in pharmaceutical manufacturing.

Conditional Cell Reprogramming and Air-Liquid Interface Modeling Life Cycle of Oncogenic Viruses (HPV and EBV) in Epithelial Cells and Virus-Associated Human Carcinomas

Several oncogenic viruses are associated with approximately 20% of human cancers. Experimental models are crucial for studying the pathogenicity and biological aspects of oncogenic viruses and their potential mechanisms in tumorigenesis. Current cell models have considerable limitations such as: their low yield, genetic and epigenetic modification, and reduction in tumor heterogeneity during long propagation. Cancer cell lines are limited and not appropriate for studying the viral life cycle, for example, natural viral life cycles of HPV and EBV, and their persistence and latency in epithelial cells are poorly understood, since these processes are highly related to epithelial differentiation. Therefore, there is an urgent need of reliable human physiological cell models to study viral life cycle and cancer initiation. Conditional cell reprogramming (CCR) is a rapid and robust cell culture system, where the cells can be established from minimally invasive or noninvasive specimens and their lineage functions preserved during the long-term culture. These CR cells retain their ability to differentiate at air-liquid interface (ALI). Here, we recapitulated the applications of CR and ALI approaches in modeling host-virus interactions and viral-mediated tumorigenesis.

ProInfer: An interpretable protein inference tool leveraging on biological networks

In mass spectrometry (MS)-based proteomics, protein inference from identified peptides (protein fragments) is a critical step. We present ProInfer (Protein Inference), a novel protein assembly method that takes advantage of information in biological networks. ProInfer assists recovery of proteins supported only by ambiguous peptides (a peptide which maps to more than one candidate protein) and enhances the statistical confidence for proteins supported by both unique and ambiguous peptides. Consequently, ProInfer rescues weakly supported proteins thereby improving proteome coverage. Evaluated across THP1 cell line, lung cancer and RAW267.4 datasets, ProInfer always infers the most numbers of true positives, in comparison to mainstream protein inference tools Fido, EPIFANY and PIA. ProInfer is also adept at retrieving differentially expressed proteins, signifying its usefulness for functional analysis and phenotype profiling. Source codes of ProInfer are available at https://github.com/PennHui2016/ProInfer.

Impact of Training Data, Ground Truth and Shape Variability in the Deep Learning-Based Semantic Segmentation of HeLa Cells Observed with Electron Microscopy

This paper investigates the impact of the amount of training data and the shape variability on the segmentation provided by the deep learning architecture U-Net. Further, the correctness of ground truth (GT) was also evaluated. The input data consisted of a three-dimensional set of images of HeLa cells observed with an electron microscope with dimensions 8192×8192×517. From there, a smaller region of interest (ROI) of 2000×2000×300 was cropped and manually delineated to obtain the ground truth necessary for a quantitative evaluation. A qualitative evaluation was performed on the 8192×8192 slices due to the lack of ground truth. Pairs of patches of data and labels for the classes nucleus, nuclear envelope, cell and background were generated to train U-Net architectures from scratch. Several training strategies were followed, and the results were compared against a traditional image processing algorithm. The correctness of GT, that is, the inclusion of one or more nuclei within the region of interest was also evaluated. The impact of the extent of training data was evaluated by comparing results from 36,000 pairs of data and label patches extracted from the odd slices in the central region, to 135,000 patches obtained from every other slice in the set. Then, 135,000 patches from several cells from the 8192×8192 slices were generated automatically using the image processing algorithm. Finally, the two sets of 135,000 pairs were combined to train once more with 270,000 pairs. As would be expected, the accuracy and Jaccard similarity index improved as the number of pairs increased for the ROI. This was also observed qualitatively for the 8192×8192 slices. When the 8192×8192 slices were segmented with U-Nets trained with 135,000 pairs, the architecture trained with automatically generated pairs provided better results than the architecture trained with the pairs from the manually segmented ground truths. This suggests that the pairs that were extracted automatically from many cells provided a better representation of the four classes of the various cells in the 8192×8192 slice than those pairs that were manually segmented from a single cell. Finally, the two sets of 135,000 pairs were combined, and the U-Net trained with these provided the best results.

Nizatidine interacts with ct-DNA causing genotoxicity and cytotoxicity: an assessment by in vitro, in vivo, and in silico studies

H2 receptor antagonists are the medication given for treating stomach ulcers, but lately, reports have shown their role in healing several malignant ulcers. The present work entails the interaction of H2 blocker nizatidine with calf thymus (ct)-DNA for determining the binding mode and energetics of the interaction. Multi-spectroscopic, calorimetric, viscometric and bioinformatic analysis revealed that nizatidine interacted with ct-DNA via groove-binding mode and is characterised by exothermic reaction. Moreover, assessment of genotoxic potential of nizatidine in vitro was carried out in peripheral human lymphocytes by alkaline comet assay. DNA damage occurred at high concentrations of nizatidine. Genotoxicity of nizatidine was also evaluated in vivo by assessing cytogenetic biomarkers viz. micronuclei formation and chromosomal aberration test. Nizatidine was able to induce micronuclei formation and chromosomal damage at high dose. Additionally, cytotoxic activity of nizatidine was determined in cancer cell lines, namely HeLa and HCT-116 and compared with the normal human cell line HEK-293 employing MTT assay. It was observed that nizatidine was more toxic towards HeLa and HCT-116 than HEK-293. Cell morphology analysis by compound inverted microscopy further strengthens the finding obtained through MTT assay.

In Vitro and In Vivo Biological Assays of Dextran Coated Iron Oxide Aqueous Magnetic Fluids

The iron oxide nanoparticles coated with different surface coatings were studied and characterized by multiple physicochemical and biological methods. The present paper aims at estimating the toxicity in vitro and in vivo of dextran coated iron oxide aqueous magnetic fluids. The in vitro studies were conducted by quantifying the viability of HeLa cells after their incubation with the samples (concentrations of 62.5−125−250−500 μg/mL at different time intervals). The estimation of the toxicity in vivo of administering dextran coated iron oxide aqueous magnetic fluids (DIO-AMF) with hydrodynamic diameter of 25.73 ± 4 nm to Male Brown Norway rats has been made. Different concentrations (62.5−125−250−500 μg/mL) of dextran coated iron oxide aqueous magnetic fluids were administered for 7 consecutive days. Hematology and biochemistry of the Male Brown Norway rats assessment was performed at various time intervals (24−72 h and 21−28 days) after intra-peritoneal injection. The results showed that high concentrations of DIO-AMF (250 and 500 μg/mL) significantly increased white blood cells, red blood cells, hemoglobin and hematocrit compared to the values obtained for the control group (p < 0.05). Moreover, following the administration of DIO-AMF, the levels of alkaline phosphatase and aspartate aminotransferase increased compared to the control group (p < 0.05). After DIO-AMF administration, no significant difference was observed in the levels of alanine aminotransferase, gamma-glutamyl transpeptidase, urea and creatinine compared to the control group (p < 0.05). The results of the present study showed that dextran coated iron oxide aqueous magnetic fluids in concentrations lower than 250 μg/mL are reliable for medical and pharmaceutical applications.

Preparation and Evaluation of 64Cu-Radiolabled Dual-Ligand Multifunctional Gold Nanoparticles for Tumor Theragnosis

Gold nanoparticles (AuNPs) are cutting-edge platforms for combined diagnostic and therapeutic approaches due to their exquisite physicochemical and optical properties. Using the AuNPs physically produced by femtosecond pulsed laser ablation of bulk Au in deionized water, with a capping agent-free surface, the conjugation of functional ligands onto the AuNPs can be tunable between 0% and 100% coverage. By taking advantage of this property, AuNPs functionalized by two different types of active targeting ligands with predetermined ratios were fabricated. The quantitatively controllable conjugation to construct a mixed monolayer of multiple biological molecules at a certain ratio onto the surface of AuNPs was achieved and a chelator-free ⁶⁴Cu-labeling method was developed. We report here the manufacture, radiosynthesis and bioevaluation of three different types of dual-ligand AuNPs functionalized with two distinct ligands selected from glucose, arginine-glycine-aspartate (RGD) peptide, and methotrexate (MTX) for tumor theragnosis. The preclinical evaluation demonstrated that tumor uptakes and retention of two components AuNP conjugates were higher than that of single-component AuNP conjugates. Notably, the glucose/MT- modified dual-ligand AuNP conjugates showed significant improvement in tumor uptake and retention. The novel nanoconjugates prepared in this study make it possible to integrate several modalities with a single AuNP for multimodality imaging and therapy, combining the power of chemo-, thermal- and radiation therapies together.

Content Size-Dependent Alginate Microcapsule Formation Using Centrifugation to Eliminate Empty Microcapsules for On-Chip Imaging Cell Sorter Application

Alginate microcapsules are one of the attractive non-invasive platforms for handling individual cells and clusters, maintaining their isolation for further applications such as imaging cell sorter and single capsule qPCR. However, the conventional cell encapsulation techniques provide huge numbers of unnecessary empty homogeneous alginate microcapsules, which spend an excessive majority of the machine time on observations and analysis. Here, we developed a simple alginate cell encapsulation method to form content size-dependent alginate microcapsules to eliminate empty microcapsules using microcapillary centrifugation and filtration. Using this method, the formed calcium alginate microcapsules containing the HeLa cells were larger than 20m, and the other empty microcapsules were less than 3m under 4000 rpm centrifugation condition. We collected cell-containing alginate microcapsules by eliminating empty microcapsules from the microcapsule mixture with simple one-step filtration of a 20 m cell strainer. The electrical surface charge density and optical permeability of those cell-encapsulated alginate microcapsules were also evaluated. We found that the surface charge density of cell-encapsulated alginate microbeads is more than double that of cells, indicating that less voltage is required for electrical cell handling with thin alginate gel encapsulation of samples. The permeability of the alginate microcapsule was not improved by changing the reflective index of the medium buffer, such as adding alginate ester. However, the minimized thickness of the alginate gel envelope surrounding cells in the microcapsules did not degrade the detailed shapes of encapsulated cells. Those results confirmed the advantage of alginate encapsulation of cells with the centrifugation method as one of the desirable tools for imaging cell sorting applications.

Role of Patient-Derived Models of Cancer in Translational Oncology

Cancer is a heterogeneous disease. Each individual tumor is unique and characterized by structural, cellular, genetic and molecular features. Therefore, patient-derived cancer models are indispensable tools in cancer research and have been actively introduced into the healthcare system. For instance, patient-derived models provide a good reproducibility of susceptibility and resistance of cancer cells against drugs, allowing personalized therapy for patients. In this article, we review the advantages and disadvantages of the following patient-derived models of cancer: (1) PDC-patient-derived cell culture, (2) PDS-patient-derived spheroids and PDO-patient-derived organoids, (3) PDTSC-patient-derived tissue slice cultures, (4) PDX-patient-derived xenografts, humanized PDX, as well as PDXC-PDX-derived cell cultures and PDXO-PDX-derived organoids. We also provide an overview of current clinical investigations and new developments in the area of patient-derived cancer models. Moreover, attention is paid to databases of patient-derived cancer models, which are collected in specialized repositories. We believe that the widespread use of patient-derived cancer models will improve our knowledge in cancer cell biology and contribute to the development of more effective personalized cancer treatment strategies.

Label-free, non-invasive, and repeatable cell viability bioassay using dynamic full-field optical coherence microscopy and supervised machine learning

We present a novel method that can assay cellular viability in real-time using supervised machine learning and intracellular dynamic activity data that is acquired in a label-free, non-invasive, and non-destructive manner. Cell viability can be an indicator for cytology, treatment, and diagnosis of diseases. We applied four supervised machine learning models on the observed data and compared the results with a trypan blue assay. The cell death assay performance by the four supervised models had a balanced accuracy of 93.92 ± 0.86%. Unlike staining techniques, where criteria for determining viability of cells is unclear, cell viability assessment using machine learning could be clearly quantified.

Cervical anticancer activities of Annona squamosa Linn. leaf isolate

Background and Aim:

Cancer is one of the leading causes of death, the need for new anticancer herbal drugs is becoming more urgent considering the side effects of synthetic drugs. This study aimed to determine the anticancer activity of isolates derived from the methanol extract of Annona squamosa Linn. leaves and to identify the compounds that have an active effect against HeLa cells.

Materials and Methods:

The leaf metabolites of A. squamosa L. were extracted using methanol at room temperature (28°C) and were partitioned into n-hexane, chloroform, and n-butanol. The toxicity test of these extracts was conducted using a brine shrimp lethality assay. Furthermore, the most toxic extracts were separated and purified using silica gel column chromatography to yield four isolate fractions: FA, FB, FC, and FD. The most toxic isolates were tested for anticancer against HeLa cells, and their compounds were identified using liquid chromatography-mass spectrometry.

Results:

The results showed that the most toxic isolate with an LC₅₀ value of 100.00 ppm had a potency similar to that of an anticancer agent with an IC₅₀ value of 70.9021 ppm. Furthermore, the five compounds identified in this isolate include (6S, 7aR)-6-hydroxy-4,4,7a-trimethyl-6,7-dihydro-5H-1-benzofuran-2-one or loliolide, cocamidopropyl betaine, N-[3-(dimethylamino)propyl]dodecanamide or lauramidopropyl dimethylamine, linolenic acid, and 1-dodecyl-2-azepanone or laurocapram.

Conclusion:

It can be concluded that the leaf isolates of A. squamosa Linn. had shown anticancer activities against cervical cancer.

Phthalocyanine and Its Formulations: A Promising Photosensitizer for Cervical Cancer Phototherapy

Cervical cancer is one of the most common causes of cancer-related deaths in women worldwide. Despite advances in current therapies, women with advanced or recurrent disease present poor prognosis. Photodynamic therapy (PDT) has emerged as an effective therapeutic alternative to treat oncological diseases such as cervical cancer. Phthalocyanines (Pcs) are considered good photosensitizers (PS) for PDT, although most of them present high levels of aggregation and are lipophilic. Despite many investigations and encouraging results, Pcs have not been approved as PS for PDT of invasive cervical cancer yet. This review presents an overview on the pathophysiology of cervical cancer and summarizes the most recent developments on the physicochemical properties of Pcs and biological results obtained both in vitro in tumor-bearing mice and in clinical tests reported in the last five years. Current evidence indicates that Pcs have potential as pharmaceutical agents for anti-cervical cancer therapy. The authors firmly believe that Pc-based formulations could emerge as a privileged scaffold for the establishment of lead compounds for PDT against different types of cervical cancer.

Naproxen release aspect from boron-doped carbon nanodots as a bifunctional agent in cancer therapy

In this present study, boron-carbon nanodots were synthesized by the hydrothermal method. Boron-carbon nanodots were prepared by varying the concentration ratios of boronic acid and citric acid: 1 : 25, 2 : 1, and 25 : 1, respectively. The precursors were then poured into a Teflon autoclave and heated at 240° for 4 h. This research aims to synthesise and evaluate the potential of boron-carbon nanodots as a bioimaging agent and naproxen delivery carrier. An X-ray diffractogram showed that the boron-carbon nanodots were amorphous. To analyse the functional groups, FTIR and XPS analysis was carried out. Spectrofluorometric analysis (λ ex 320 nm) showed that the formulation of boron-carbon nanodots 2 : 1 (BCD 2 : 1) has the most ideal fluorescent properties at λ em 453 nm, whereas UV-vis analysis showed λ max at 223 nm, with a quantum yield of 52.29%. A confocal laser scanning micrograph and toxicity test (MTT assays) showed that boron-carbon nanodots delivered naproxen efficiently with loading amount and loading efficiency of naproxen 28% and 65%, respectively. Furthermore, it induced an anticancer effect in HeLa cells. This result indicated that boron-carbon nanodots can be used as a bioimaging agent and naproxen delivery carrier.

Preparation and Characterization of Dextran Coated Iron Oxide Nanoparticles Thin Layers

In the present study, we report the synthesis of a dextran coated iron oxide nanoparticles (DIO-NPs) thin layer on glass substrate by an adapted method. The surface morphology of the obtained samples was analyzed by Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM), optical, and metallographic microscopies. In addition, the distribution of the chemical elements into the DIO-NPs thin layer was analyzed by Glow Discharge Optical Emission Spectrometry (GDOES). Furthermore, the chemical bonds formed between the dextran and iron oxide nanoparticles was investigated by Fourier Transform Infrared Spectroscopy (FTIR). Additionally, the HepG2 viability incubated with the DIO-NPs layers was evaluated at different time intervals using MTT (3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. The goal of this study was to obtain a DIO-NPs thin layer which could be used as a coating for medical devices such as microfluidic channel, microchips, and catheter. The results of the surface morphology investigations conducted on DIO-NPs thin layer suggests the presence of a continuous and homogeneous layer. In addition, the GDOES results indicate the presence of C, H, Fe, and O signal intensities characteristic to the DIO-NPs layers. The presence in the IR spectra of the Fe-CO metal carbonyl vibration bonds prove that the linkage between iron oxide nanoparticles and dextran take place through carbon–oxygen bonds. The cytotoxicity assays highlighted that HepG2 cells morphology did not show any noticeable modifications after being incubated with DIO-NPs layers. In addition, the MTT assay suggested that the DIO-NPs layers did not present any toxic effects towards HEpG2 cells.

Development of an Acid-Labile Ketal Linked Amphiphilic Block Copolymer Nanoparticles for pH-Triggered Release of Paclitaxel

Here, we report on the construction of biodegradable poly(ethylene oxide monomethyl ether) (MPEO)-b-poly(ε-caprolactone) (PCL) nanoparticles (NPs) having acid-labile (acyclic ketal group) linkage at the block junction. In the presence of acidic pH, the nanoassemblies were destabilized as a consequence of cleaving this linkage. The amphiphilic MPEO-b-PCL diblock copolymer self-assembled in PBS solution into regular spherical NPs. The structure of self-assemble and disassemble NPs were characterized in detail by dynamic (DLS), static (SLS) light scattering, small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM). The key of the obtained NPs is using them in a paclitaxel (PTX) delivery system and study their in vitro cytostatic activity in a cancer cell model. The acid-labile ketal linker enabled the disassembly of the NPs in a buffer simulating an acidic environment in endosomal (pH ~5.0 to ~6.0) and lysosomal (pH ~4.0 to ~5.0) cell compartments resulting in the release of paclitaxel (PTX) and formation of neutral degradation products. The in vitro cytotoxicity studies showed that the activity of the drug-loaded NPs was increased compared to the free PTX. The ability of the NPs to release the drug at the endosomal pH with concomitant high cytotoxicity makes them suitable candidates as a drug delivery system for cancer therapy.

Non-metal sensory electrode design and protocol of DNA-nucleobases in living cells exposed to oxidative stresses

Sensory protocols for evaluation of DNA distortion due to exposure to various harmful chemicals and environments in living cells are needed for research and clinical investigations. Here, a design of non-metal sensory (NMS) electrode was built by using boron-doped carbon spherules for detection of DNA nucleobases, namely, guanine (Gu), adenine (Ad), and thymine (Th) in living cells. The key-electrode based nanoscale NMS structures lead to voids with a facile diffusion, and strong binding events of the DNA nucleobases. Furthermore, the NMS geometric structures would significantly create electrode surfaces with numerous centrally active sites, curvature topographies, and anisotropic spherules. The NMS shows potential as sensitive protocol for DNA-nucleobases in living cells exposed to oxidative stresses. In one-step signaling assay, NMS shows high signaling transduction of Gu-, Ad-, and Th-DNA nucleobases targets with ultra-sensitive and low detection limits of 3.0, 0.36, and 0.34 nM, respectively, and a wide linear range of up to 1 μM. The NMS design and protocol show evidence of the role of surface construction features and B-atoms incorporated into the graphitic carbon network for creating abundant active sites with facile electron diffusion and heavily target loads along with within-/out-plane circular spheres. Indeed NMS, with spherule-rich interstitial surfaces can be used for sensitive and selective evaluation of damaged-DNA to various dysfunctional metabolism in the human body.

Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching

A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. A mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth is used. To this end, this strategy leverages TMTpro16-based sample multiplexing, high-field asymmetric ion mobility spectrometry, and real-time database searching. The data show that the differences in the relative protein abundance profiles reflect cell line diversity. The authors also determine several hundred proteins to be highly enriched for a given cell line, and perform gene ontology and pathway analysis on these cell line-enriched proteins. An R Shiny application is designed to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection for addressing a given scientific inquiry or for improving an experimental design.

Melatonin sensitises shikonin-induced cancer cell death mediated by oxidative stress via inhibition of the SIRT3/SOD2-AKT pathway

Recent research suggests that melatonin (Mel), an endogenous hormone and natural supplement, possesses anti-proliferative effects and can sensitise cells to anti-cancer therapies. Although shikonin (SHK) also possesses potential anti-cancer properties, the poor solubility and severe systemic toxicity of this compound hinders its clinical usage. In this study, we combined Mel and SHK, a potentially promising chemotherapeutic drug combination, with the aim of reducing the toxicity of SHK and enhancing the overall anti-cancer effects. We demonstrate for the first time that Mel potentiates the cytotoxic effects of SHK on cancer cells by inducing oxidative stress via inhibition of the SIRT3/SOD2-AKT pathway. Particularly, Mel-SHK treatment induced oxidative stress, increased mitochondrial calcium accumulation and reduced the mitochondrial membrane potential in various cancer cells, leading to apoptosis. This drug combination also promoted endoplasmic reticulum (ER) stress, leading to AKT dephosphorylation. In HeLa cells, Mel-SHK treatment reduced SIRT3/SOD2 expression and SOD2 activity, while SIRT3 overexpression dramatically reduced Mel-SHK-induced oxidative stress, ER stress, mitochondrial dysfunction and apoptosis. Hence, we propose the combination of Mel and SHK as a novel candidate chemotherapeutic regimen that targets the SIRT3/SOD2-AKT pathway in cancer.

The Significance of Biobanking in the Sustainability of Biomedical Research: A Review

Biobank, defined as a functional unit for facilitating and improving research by storing biospecimen and their accompanying data, is a key resource for advancement in life science. The history of biobanking goes back to the time of archiving pathology samples. Nowadays, biobanks have considerably improved and are classified into two categories: diseased-oriented and population-based biobanks. UK biobank as a population-based biobank with about half a million samples, Biobank Graz as one of the largest biobanks in terms of sample size, and The International Agency for Research on Cancer biobank as a specialized the World Health Organization cancer agency are few examples of successful biobanks worldwide. The present review provides a history of biobanking, and after presenting different biobanks, we discuss in detail the challenges in the field of biobanking and its future, as well. In the end, ICR biobank, as the first cancer biobank in Iran established in 1998, is thoroughly described.

Cellular Toxicity Study of Silicon Nanowires

The objective of this study was to achieve the practical bioapplications of silicon nanowires (SiNWs). In this study, the tumor and normal cell lines were used as models to systematically investigate the cytotoxicity of SiNWs synthesized by HF-assisted etching methods. Morphology observation, Cell Counting Kit 8, real-time polymerase chain reaction, and flow cytometry analysis were used to elucidate the cytotoxicity of SiNWs. The results showed that the cytotoxicity of SiNWs is greatly dependent on cell lines, SiNWs concentration, and incubation time. Particularly, SiNWs show better biocompatibility with tumor cell lines (eg, human epithelial cervical cancer [Hela] cells and human hepatocellular liver carcinoma [HepG2] cells) than normal cell lines (eg, human normal liver [HL-7702] cells and human embryonic kidney [HEK293T] cells). The reasons may be that SiNWs could tightly attach to the cell membrane in the cell medium, which obviously affects cell adhesion and inhibits their cell viability, especially for normal cell lines. From systematical analysis and comparison, we obtain the concentration limits of SiNWs, which may advance SiNWs applications and its toxicological study in vitro.

Impact of pH and cell medium on the interaction of doxorubicin with lipoic acid cyclodextrin conjugate as the drug carrier

Lipoic acid derivative of cyclodextrin, βCDLip, was used as the drug carrier for doxorubicin (DOX) and the stability constants of the DOX–βCDLip were determined in the environment of the cell medium. The experiments were performed in neutral (pH 7.6) and acidified (pH 6.3) cell media containing more than forty interferences including: amino acids, vitamins, lipids and proteins. We proved that the pH of the medium has a noticeable impact on the affinity of the drug towards the carrier. At neutral pH, the formation constants of the complex are higher than at pH 6.3, what is characteristic for the cancer cells microenvironment. Furthermore, the values obtained in both cell media are twice smaller than the values obtained previously for the same complex but in the absence of common cell media components indicating that there is a competition between DOX and some hydrophobic medium components for the complex formation with βCDLip. On the other hand at pH 7.6, the amount of free DOX is highly limited due to the fact that most of DOX is still in the complexed form, while at pH 6.3 the cell media ingredients become strong interferences in the formation of the complex between DOX and the drug carrier. The observed behaviour is due to partial protonation of DOX and to competition between the drug and the lipoic side arm of cyclodextrin for the cyclodextrin cavity. The stability constants of the DOX–βCDLip complex in acidic pH are similar to the values for DOX with native β-cyclodextrin, demonstrating that the strengthening effect of DOX–CD complex resulting from the presence of cyclodextrin’s aromatic substituent (Lip) occurs only in the case of neutral pH. The high value of the stability constant of the DOX–βCDLip complex in cell medium at pH 7.6 indicates high selectivity of βCDLip ligand which would be of importance both for the effective drug delivery and for its application in DOX sensing devices.

Biomedical perfluorohexane-loaded nanocapsules prepared by low-energy emulsification and selective solvent diffusion

Perfluorohexane-loaded nanocapsules are interesting materials for many biomedical applications such as oxygen delivery systems or contrast agents. However, their formulation into stable colloidal systems is challenging because of their hydro- and lipophobicity, high density and high vapour pressure. In this study, perfluorohexane-loaded polymeric nanocapsules are prepared for the first time by low-energy emulsification and selective solvent diffusion. The colloidal stability of the perfluorohexane nano-emulsion templates has been improved by the incorporation of an apolar low-density oil (isopropyl myristate) in the dispersed phase, thus addressing droplet coarsening and migration phenomena. The perfluorohexane-loaded nanocapsules prepared from the nano-emulsions show sizes smaller than the corresponding emulsion templates (below 150 nm by dynamic light scattering) and exhibit good stability under storage conditions. Hyperspectral enhanced dark field microscopy revealed a layered core/shell structure and allowed also to confirm the encapsulation of perfluorohexane which was quantified by elemental microanalysis. Although isopropyl myristate has an unfavourable biocompatibility profile, cell viability is enhanced when perfluorohexane is present in the nanocapsules, which is attributed to its high oxygen transport capacity.

Biocompatible Layers Obtained from Functionalized Iron Oxide Nanoparticles in Suspension

Iron oxide nanoparticles have been extensively studied for challenges in applicable areas such as medicine, pharmacy, and the environment. The functionalization of iron oxide nanoparticles with dextran opens new prospects for application. Suspension characterization methods such as dynamic light scattering (DLS) and zeta potential (ZP) have allowed us to obtain information regarding the stability and hydrodynamic diameter of these suspended particles. For rigorous characterization of the suspension of dextran-coated iron oxide nanoparticles (D-MNPs), studies have been performed using ultrasound measurements. The results obtained from DLS and ZP studies were compared with those obtained from ultrasound measurements. The obtained results show a good stability of D-MNPs. A comparison between the D-MNP dimension obtained from transmission electron microscopy (TEM), X-ray diffraction (XRD), and DLS studies was also performed. A scanning electron spectroscopy (SEM) image of a surface D-MNP layer obtained from the stable suspension shows that the particles are spherical in shape. The topographies of the elemental maps of the D-MNP layer showed a uniform distribution of the constituent elements. The homogeneity of the layer was also observed. The morphology of the HeLa cells incubated for 24 and 48 h with the D-MNP suspension and D-MNP layers did not change relative to the morphology presented by the control cells. The cytotoxicity studies conducted at different time intervals have shown that a slight decrease in the HeLa cell viability after 48 h of incubation for both samples was observed.

Rational synthesis of three-dimensional core-double shell upconversion nanodendrites with ultrabright luminescence for bioimaging application

Herein, we rationally fabricated three-dimensional upconversion core–double shell nanodendrites as efficient and safe luminescent probes for in vitro and in vivo bioimaging.

Engineering the morphology of rare-earth doped NaYF₄-based upconversion nanoparticles (UCNPs) can effectively tune their upconversion luminescence emission (UCLE) properties. Herein, we rationally synthesized a new class of three-dimensional upconversion core–double-shell nanodendrites (UCNDs) including an active core (NaYF₄:Yb,Er,Ca) capped by a transition layer (NaYF₄:Yb,Ca) and an active outer shell (NaNdF₄:Yb,Ca). The high concentration of the Nd³⁺ sensitizer in the outer dendritic shell enhances the luminescence intensity, while the transition layer enriched with Yb³⁺ acts as an efficient energy migration network between the outer shell and inner core along with preventing the undesired quenching effects resulting from Nd³⁺. These unique structural and compositional merits enhanced the UCLE of UCNDs by 5 and 15 times relative to NaYF₄:Yb,Er,Ca@NaYF₄:Yb,Ca truncated core–shell UCNPs and NaYF₄:Yb,Er,Ca spherical core UCNPs, respectively, under excitation at 980 nm. The SiO₂–COOH layer coated UCNDs (UCND@SiO₂–COOH) were successfully used as efficient long-term luminescent probes for in vitro and in vivo bioimaging without any significant toxicity. The uptake and retention of UCND@SiO₂–COOH were mostly found in the liver and spleen. This study may open the way towards the preparation of three-dimensional UCND nanostructures for biomedical applications.

methyl-ATAC-seq measures DNA methylation at accessible chromatin

Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA. For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying data sets. Here, we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, including subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin and reveals, unambiguously, the DNA methylation state of the underlying DNA. Such combinatorial methods eliminate the need to perform assays independently and infer where features are coincident.

Evaluation of a single amino acid substitution at position 79 of human IFN-α2b in interferon-receptor assembly and activity

Type I interferons (IFNs) are homologous cytokines that bind to a cell surface receptor and establish signaling pathways that motivate immune responses. The purpose of the current study is to assess the activity of a novel-engineered IFN-α2b. The crystallographic structure of IFN-α2b and its receptors was acquired from Protein Data Bank. Various amino acid substitutions were designed based on structural properties and other biological characteristics of residues to find the most effective amino acid on IFN affinity to advanced activities. The IFN-α2b mutants and receptors have been modeled and the interactions between two proteins have been studied as in silico by protein-protein docking for both mutants and native forms. The proper nucleic acid sequence IFN-α2 (T79Q) has been prepared based on the selected mutant. The modified IFN gene was cloned in pcDNA 3.1(-) and introduced to Chinese Hamster Ovary (CHO) cell line. Antiviral and antiproliferative assays of native and IFN-α2 (T79Q) proteins were performed in vitro. The results showed two-fold increasing in IFN-α2 (T79Q) activity (antiviral and antiproliferative activity) in comparison to native IFN-α2b. This engineered IFN-α2b may have significant novel therapeutic applications and in silico studies can be an influential method for practical research function and structure of these molecules.

Mammalian cell viability on hydrophobic and superhydrophobic fabrics

Surface properties like hydrophobicity and morphology of the substrate are essential for cell proliferation affecting its growth, survival and also for its communication with other cells on fabrics. The combination of low surface energy and a specific surface morphology (micro/nano-roughness) leads to significantly less wettable surfaces, known as superhydrophobic characterized by high contact angle above 150° and a very small hysteresis. Such high water repellent coatings feature small area available to be exploited in many applications where interactions with aqueous environment are strongly to be avoided. In this work, the authors have investigated the influence of coating polyester fabric at different degree of hydrophobicity by mixed organic-inorganic coating with moderated to highly water repellence. Depending on the coating composition and structure, the hydrophobicity of the fabric can be finely modulated by an easy-to-prepare method applicable to commercial, low cost fabric substrates providing advanced performance. In vitro experiments have been performed in order to establish the influence of surface modification on adhesion of representative model mammalian cell lines such as 3T3 fibroblasts, HaCaT keratinocytes and HeLa epithelial carcinoma cells. The obtained results suggested that, in addition to the chemistry and morphology of the coating, the characteristics of the substrate are important parameters on the final cell viabilities.

Current Research Method in Transporter Study

Transporters play an important role in the absorption, distribution, metabolism, and excretion (ADME) of drugs. In recent years, various in vitro, in situ/ex vivo, and in vivo methods have been established for studying transporter function and drug-transporter interaction. In this chapter, the major types of in vitro models for drug transport studies comprise membrane-based assays, cell-based assays (such as primary cell cultures, immortalized cell lines), and transporter-transfected cell lines with single transporters or multiple transporters. In situ/ex vivo models comprise isolated and perfused organs or tissues. In vivo models comprise transporter gene knockout models, natural mutant animal models, and humanized animal models. This chapter would be focused on the methods for the study of drug transporters in vitro, in situ/ex vivo, and in vivo. The applications, advantages, or limitations of each model and emerging technologies are also mentioned in this chapter.

The Wnt modulator ICG‑001 mediates the inhibition of nasopharyngeal carcinoma cell migration in vitro via the miR‑150/CD44 axis

The Wnt signaling pathway is known to serve an important role in the control of cell migration. The present study analyzed the mechanisms underlying the in vitro modulation of the migration of nasopharyngeal carcinoma (NPC) cells by the CREB‑binding protein/catenin antagonist and Wnt modulator ICG‑001. The results revealed that ICG‑001‑mediated inhibition of tumor cell migration involved downregulated mRNA and protein expression of the Wnt target gene cluster of differentiation (CD)44. It was also demonstrated that ICG‑001 downregulated the expression of CD44, and this effect was accompanied by restored expression of microRNA (miRNA)‑150 in various NPC cell lines. Using a CD44 3'‑untranslated region luciferase reporter assay, miR‑150 was confirmed to be a novel CD44‑targeting miRNA, which could directly target CD44 and subsequently regulate the migration of NPC cells. The present study provides further insight into the inhibition of tumor cell migration through the modulation of miRNA expression by the Wnt modulator ICG‑001.

Microsphere-based interferometric optical probe

Fluorescent optical probes have rapidly transformed our understanding of complex biological systems by providing specific information on biological targets in the natural living state. However, their utility is often limited by insufficient brightness, photostability, and multiplexing capacity. Here, we report a conceptually new optical probe, termed ‘reflectophore’, which is based on the spectral interference from a dielectric microsphere. Reflectophores are orders-of-magnitudes brighter than conventional fluorophores and are free from photobleaching, enabling practically unlimited readout at high fidelity. They also offer high-degree multiplexing, encoded in their optical size, which can be readily decoded through interferometric detection with nanoscale accuracy, even in turbid biological media. Furthermore, we showcase their biological applications in cellular barcoding and microenvironmental sensing of a target protein and local electric field.

Tagging and tracking cells with multiplexed labels can help study complex cellular behaviors in living systems. Here, Jo et al. propose and demonstrate the use of Fabry-Perot-like resonances in dielectric microspheres as such a label and call these reflectophores.

Bioactive Heterometallic CuII-ZnII Complexes with Potential Biomedical Applications

A series of multinuclear heterometallic Cu-Zn complexes of molecular formula [(CuL)₂Zn(dca)₂] (1), [(CuL)₂Zn(NO₃)₂] (2), [(CuL)₂Zn₂(Cl)₄] (3), and [(CuL)₂Zn₂(NO₂)₄] (4) have been synthesized by reacting [CuL] as a "metalloligand (ML)" (where HL = N,N'-bis(5-chloro-2-hydroxybenzylidene)-2,2-dimethylpropane-1,3-diamine) and by varying the anions or coligands using the same molar ratios of the reactants. All of the four products including the ML have been characterized by infrared and UV-vis spectroscopies and elemental and single-crystal X-ray diffraction analyses. By varying the anions, different structures and topologies are obtained which we have tried to rationalize by means of thorough density functional theory calculations. All of the complexes (1-4) have now been applied for several biological investigations to verify their therapeutic worth. First, their cytotoxicity properties were assessed against HeLa human cervical carcinoma along with the determination of IC₅₀ values. The study was extended with extensive DNA and protein binding experiments followed by detailed fluorescence quenching study with suitable reagents to comprehend the mechanistic pathway. From all of these biological studies, it has been found that all of these heterometallic complexes show more than a few fold improvement of their therapeutic values as compared to the similar homometallic ones probably because of the simultaneous synergic effect of copper and zinc. Among all of the four heterometallic complexes, complex 3 exhibits highest binding constants and IC₅₀ values suggest for their better interaction toward the biological targets and hence have better clinical importance.

Combinational light emitting diode-high frequency focused ultrasound treatment for HeLa cell

PURPOSE

Light sources such as laser and light emitting diode or ultrasound devices have been widely used for cancer therapy and regenerative medicines, since they are more cost-effective and less harmful than radiation therapy, chemotherapy or magnetic treatment. Compared to laser and low intensity ultrasound techniques, light emitting diode and high frequency focused ultrasound shows enhanced therapeutic effects, especially for small tumors.

MATERIALS AND METHODS

We propose combinational light emitting diode-high frequency focused ultrasound treatment for human cervical cancer HeLa cells. Individual red, green, and blue light emitting diode light only, high frequency focused ultrasound only, or light emitting diode light combined with high frequency focused ultrasound treatments were applied in order to characterize the responses of HeLa cells.

RESULTS

Cell density exposed by blue light emitting diode light combined with high frequency focused ultrasound (2.19 ± 0.58%) was much lower than that of cells exposed by red and green light emitting diode lights (81.71 ± 9.92% and 61.81 ± 4.09%), blue light emitting diode light (11.19 ± 2.51%) or high frequency focused ultrasound only (9.72 ± 1.04%).

CONCLUSIONS

We believe that the proposed combinational blue light emitting diode-high frequency focused ultrasound treatment could have therapeutic benefits to alleviate cancer cell proliferation.

Design, semisynthesis and cytotoxic activity of novel ester derivatives of betulinic acid-1,2,4 oxadiazoles

Taking into consideration of the biological activity of betulinic acid derivatives containing a oxadiazole ring, the semisynthetic betulinic acid-1,2,4-oxadiazole esters (14-25) were synthesized starting from betulinic acid (1) and 5-(bromomethyl)-3-aryl-1,2,4-oxadiazoles (2-13) and final compounds were tested for cytotoxic activity on three human cancer cell lines in vitro. All tested compounds showed good cytotoxic activity. The structures of synthesized compounds are established based on infrared (IR), nuclear magnetic resonance (NMR), and mass spectrometry.