Volume: 9 Issue: 15 —BIO-PROTOCOL

Cancer Biology

Photodynamic Therapy in a 3D Model of Ovarian Cancer Authors: Shubhankar Nath and Kaitlin Moore, date: 08/05/2019, view: 2764, Q&A: 0

Photodynamic therapy (PDT), is a clinically-approved light-based anti-cancer treatment modality in which a photoactivatable photosensitizer is irradiated with an appropriate wavelength of light to generate cytotoxic molecules to kill cancer cells. In this article, we describe an in vitro PDT protocol using a 3-dimensional (3D) model of ...

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Cell Biology

QUEEN-based Spatiotemporal ATP Imaging in Budding and Fission Yeast Author: Masak Takaine, date: 08/05/2019, view: 3524, Q&A: 0

Yeasts have provided an exceptional model for studying metabolism and bioenergetics in eukaryotic cells. Among numerous metabolites, adenosine triphosphate (ATP) is a major metabolite that is essential for all living organisms. Therefore, a clearer understanding of ATP dynamics in living yeast cells is important for deciphering cellular energy ...

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Immunology

Precision Technique for Splenectomy Limits Mouse Stress Responses for Accurate and Realistic Measurements for Investigating Inflammation and Immunity Authors: Shengwen Calvin Li, Anthony D. Rangel and Mustafa H. Kabeer, date: 08/05/2019, view: 2879, Q&A: 0

Splenectomy in an animal model requires a standardized technique utilizing best practice to avoid variability which can result in adverse impact to the animal resulting in flawed physiologic responses simply due to technique rather than to the studied variables. In the case of the spleen, often investigators are analyzing the animal immune or ...

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Visualizing Hypoxia in a Murine Model of Candida albicans Infection Using in vivo Biofluorencence Authors: José Pedro Lopes and Constantin F. Urban, date: 08/05/2019, view: 2394, Q&A: 0

Candida albicans is a leading human fungal pathogen that uses several metabolic adaptations to escape immune cells and causes systemic disease. Here, we describe a protocol for measuring one of these adaptations, the ability to thrive in hypoxic niches. Hypoxia was generated after successful subdermal infection with C. albicans ...

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Microbiology

Optimized Protocol for the Incorporation of FDAA (HADA Labeling) for in situ Labeling of Peptidoglycan Authors: Katharina Peters, Manuel Pazos, Michael S. VanNieuwenhze and Waldemar Vollmer, date: 08/05/2019, view: 4598, Q&A: 0

The essential peptidoglycan (PG) layer surrounds the cytoplasmic membrane in nearly all bacteria. It is needed to maintain the shape of the cell and protect it from lysis due to high turgor. Growth of the PG layer is a complex process that involves the activities of PG synthases and hydrolases during elongation and cell division. PG growth sites ...

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Image-based Quantification of Direct Cell-to-cell Transmission of Bovine Viral Diarrhea Virus Authors: Fernando Merwaiss and Diego E. Alvarez, date: 08/05/2019, view: 2691, Q&A: 0

Different viruses rely on direct cell-to-cell transmission to propagate infection within the infected host. Measuring this mode of transmission in cultured cells is often complicated by the contribution of cell free viruses to spread, and the difficulty to distinguish between primary infected cells that produce the virus and neighboring cells that ...

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Endocytosis Detection in Magnaporthe oryzae Authors: Muxing Liu and Zhengguang Zhang, date: 08/05/2019, view: 2190, Q&A: 0

Endocytosis is an intracellular trafficking pathway that occurs in nutrient uptake, signal transduction and reconstruction of cell polarity and is conserved in eukaryotic cells. In fungi, endocytosis plays crucial roles in the physiology of hyphal growth and pathogenicity. vidence for endocytosis in filamentous fungi is detected by the ...

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Solid Phase PCR on 3D Microstructure ArrayChip for Pathogen Detection Application Authors: Krishna Kant and Tien Anh Ngo, date: 08/05/2019, view: 3089, Q&A: 0

Advanced free angle photolithography (FAPL) is presented for making 3D supercritical angle fluorescence (SAF) microstructures and transfer them on to polymeric chips using injection molding technique for low-cost microfluidic devices embedded with optical sensing structures. A solid phase polymerase chain reaction (SP-PCR) is used as model ...

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Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes Authors: Takahiro Masuda, Nobuaki Kono, Masaru Tomita and Kazuharu Arakawa, date: 08/05/2019, view: 3725, Q&A: 0

Most bacterial genomes have biased nucleotide composition, and the asymmetry is considered to be caused by a single-stranded DNA (ssDNA) deamination arising from the bacterial replication machinery. In order to evaluate the relationship experimentally, the position and frequency of ssDNA formed during replication must be verified clearly. Although ...

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Molecular Biology

Ex vivo Analysis of DNA Repair Capacity of Human Peripheral Blood Mononuclear Cells by a Modified Host Cell Reactivation Assay Authors: Katja Matt and Jörg Bergemann, date: 08/05/2019, view: 2316, Q&A: 0

The ability of humans to repair DNA damages decreases with increasing age. In order to be able to repair daily occurring DNA damages, it becomes more and more important to preserve repair capability of cells with aging. The preservation of DNA repair processes contributes to preventing DNA mutations and subsequently the onset of age-related ...

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Cell Type-specific mRNA Purification in Caenorhabditis elegans via Translating Ribosome Affinity Purification Authors: Ian G. McLachlan and Steven W. Flavell, date: 08/05/2019, view: 2818, Q&A: 0

Cell type-specific molecular profiling is widely used to gain new insights into the diverse cell types that make up complex biological tissues. Translating ribosome affinity purification (TRAP) is a method in which the cell type-specific expression of epitope-tagged ribosomal subunits allows one to purify actively translating mRNAs without the ...

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Neuroscience

Looking through Brains with Fast Passive CLARITY: Zebrafish, Rodents, Non-human Primates and Humans Authors: Farzad Mortazavi, Alexander J. Stankiewicz and Irina V. Zhdanova, date: 08/05/2019, view: 5159, Q&A: 0

Recently developed CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ-hybridization-compatible Tis-sue-hYdrogel) technique renders the tissue transparent by removing lipids in the tissue, while preserving and stabilizing the cellular and subcellular structures. This provides effective penetration of diverse ...

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Quantification of Prostaglandin E₂ Concentration in Interstitial Fluid from the Hypothalamic Region of Free-moving Mice Authors: Yoshinobu Nakamura, Takatoshi Sakaguchi, Ikumi Tamai and Takeo Nakanishi, date: 08/05/2019, view: 2939, Q&A: 0

Prostaglandin E₂ (PGE₂) is a well-established chemical mediator for the generation of the fever at the hypothalamus of the brain. PGE₂ mediates fever generation via PGE receptor 3 (i.e., EP3) on neurons in the preoptic area. The role of PGE₂ has been analyzed by measuring PGE₂ ...

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Plant Science

Measuring Protein Half-life in Arabidopsis thaliana Authors: Hongqing Guo and Yanhai Yin, date: 08/05/2019, view: 2802, Q&A: 0

Post-translational modifications play important roles in controlling protein function and can lead to altered protein stability. Protein stability can be determined after treatment with the protein synthesis inhibitor Cycloheximide. Cycloheximide is a translational inhibitor that inhibits protein synthesis via cytoplasmic ribosomes. Here we ...

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Tensile Testing Assay for the Measurement of Tissue Stiffness in Arabidopsis Inflorescence Stem Authors: Kouki Yoshida, Shingo Sakamoto and Nobutaka Mitsuda, date: 08/05/2019, view: 6567, Q&A: 1

Lignocellulosic biomass is a versatile renewable resource for fuels, buildings, crafts, and biomaterials. Strategies of molecularly designing lignocellulose for industrial application has been developed by the discoveries of novel genes after the screenings of various mutants and transformed lines of Arabidopsis whose cell walls could be ...

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Past Issues in 2019

Volume: 9 Issue: 15

Cancer Biology

Cell Biology

Immunology

Microbiology

Molecular Biology

Neuroscience

Plant Science