The Roles of CircRNAs in Mitochondria.

Mitochondria participate in varieties of cellular events. It is widely accepted that human mitochondrial genome encodes 13 proteins, 2 rRNAs, and 22 tRNAs. Gene variation derived from human nuclear genome cannot completely explain mitochondrial diseases. The advent of high-throughput sequencing coupled with novel bioinformatic analyses decode the complexity of mitochondria-derived transcripts. Recently, circular RNAs (circRNAs) from both human mitochondrial genome and nuclear genome have been found to be located at mitochondria. Studies about the roles and molecular mechanisms underlying trafficking of the nucleus encoded circRNAs to mitochondria and mitochondria encoded circRNAs to the nucleus or cytoplasm in mammals are only beginning to emerge. These circRNAs have been associated with a variety of diseases, especially cancers. Here, we discuss the emerging field of mitochondria-located circRNAs by reviewing their identification, expression patterns, regulatory roles, and functional mechanisms. Mitochondria-located circRNAs have regulatory roles in cellular physiology and pathology. We also highlight future perspectives and challenges in studying mitochondria-located circRNAs, as well as their potential biomedical applications.

Cancer cell-specific protein delivery by optoporation with laser-irradiated gold nanorods.

The delivery of macromolecules into living cells is challenging since in most cases molecules are endocytosed and remain in the endo-lysosomal pathway where they are degraded before reaching their target. Here, a method is presented to selectively improve cell membrane permeability by nanosecond laser irradiation of gold nanorods (GNRs) with visible or near-infrared irradiation in order to deliver proteins across the plasma membrane, avoiding the endo lysosomal pathway. GNRs were labeled with the anti-EGFR (epidermal growth factor receptor) antibody Erbitux to target human ovarian carcinoma cells OVCAR-3. Irradiation with nanosecond laser pulses at wavelengths of 532 nm or 730 nm is used for transient permeabilization of the cell membranes. As a result of the irradiation, the uptake of an anti-Ki-67 antibody was observed in about 50 % of the cells. The results of fluorescence lifetime imaging show that the GNR detached from the membrane after irradiation.

Classification and Segmentation of Hyperspectral Data of Hepatocellular Carcinoma Samples Using 1-D Convolutional Neural Network.

Pathological diagnosis plays an important role in the diagnosis and treatment of hepatocellular carcinoma (HCC). The traditional method of pathological diagnosis of most cancers requires freezing, slicing, hematoxylin and eosin staining, and manual analysis, limiting the speed of the diagnosis process. In this study, we designed a one-dimensional convolutional neural network to classify the hyperspectral data of HCC sample slices acquired by our hyperspectral imaging system. A weighted loss function was employed to promote the performance of the model. The proposed method allows us to accelerate the diagnosis process of identifying tumor tissues. Our deep learning model achieved good performance on our data set with sensitivity, specificity, and area under receiver operating characteristic curve of 0.871, 0.888, and 0.950, respectively. Meanwhile, our deep learning model outperformed the other machine learning methods assessed on our data set. The proposed method is a potential tool for the label-free and real-time pathologic diagnosis. © 2019 International Society for Advancement of Cytometry.

Impact of immunization technology and assay application on antibody performance--a systematic comparative evaluation.

Antibodies are quintessential affinity reagents for the investigation and determination of a protein's expression patterns, localization, quantitation, modifications, purification, and functional understanding. Antibodies are typically used in techniques such as Western blot, immunohistochemistry (IHC), and enzyme-linked immunosorbent assays (ELISA), among others. The methods employed to generate antibodies can have a profound impact on their success in any of these applications. We raised antibodies against 10 serum proteins using 3 immunization methods: peptide antigens (3 per protein), DNA prime/protein fragment-boost ("DNA immunization"; 3 per protein), and full length protein. Antibodies thus generated were systematically evaluated using several different assay technologies (ELISA, IHC, and Western blot). Antibodies raised against peptides worked predominantly in applications where the target protein was denatured (57% success in Western blot, 66% success in immunohistochemistry), although 37% of the antibodies thus generated did not work in any of these applications. In contrast, antibodies produced by DNA immunization performed well against both denatured and native targets with a high level of success: 93% success in Western blots, 100% success in immunohistochemistry, and 79% success in ELISA. Importantly, success in one assay method was not predictive of success in another. Immunization with full length protein consistently yielded the best results; however, this method is not typically available for new targets, due to the difficulty of generating full length protein. We conclude that DNA immunization strategies which are not encumbered by the limitations of efficacy (peptides) or requirements for full length proteins can be quite successful, particularly when multiple constructs for each protein are used.