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Dian Jing et al.
Cell research, 28(8), 803-818 (2018-05-31)
Tissue clearing technique enables visualization of opaque organs and tissues in 3-dimensions (3-D) by turning tissue transparent. Current tissue clearing methods are restricted by limited types of tissues that can be cleared with each individual protocol, which inevitably led to
Ramón Cervantes-Rivera et al.
Bio-protocol, 10(18), e3757-e3757 (2021-03-05)
Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are
H H Lee et al.
Journal of food science and technology, 52(12), 7806-7816 (2015-11-26)
Whole grains consumption promotes health benefits, but demonstrates controversial impacts from phytic acid in meeting requirements of good health. Therefore, this study was aimed to determine the nutrient bioaccessibility and antioxidant properties of rice cultivars named "Adan" or "Bario" and
Karla Lucía F Alvarez et al.
Veterinary research, 51(1), 123-123 (2020-09-27)
Infectious coryza (IC), an upper respiratory tract disease affecting chickens, is caused by Avibacterium paragallinarum. The clinical manifestations of IC include nasal discharge, facial swelling, and lacrimation. This acute disease results in high morbidity and low mortality, while the course
Gabriel Mendoza-Rojas et al.
STAR protocols, 2(4), 100899-100899 (2021-11-13)
Here, we describe a detailed step-by-step protocol for the expression, purification, quantification, and activity determination of key enzymes for molecular detection of pathogens. Based on previous reports, we optimized the protocol for LbCas12a, Taq DNA polymerase, M-MLV reverse transcriptase, and
Eliseo A Eugenin et al.
Journal of neurochemistry, 151(5), 558-569 (2019-08-06)
Chemical and electrical synapses are the two major communication systems that permit cell-to-cell communication within the nervous system. Although most studies are focused on chemical synapses (glutamate, γ-aminobutyric acid, and other neurotransmitters), clearly both types of synapses interact and cooperate
Anne A M J Becker et al.
BMC microbiology, 14, 43-43 (2014-02-20)
Imbalanced feeding regimes may initiate gastrointestinal and metabolic diseases in endangered felids kept in captivity such as cheetahs. Given the crucial role of the host's intestinal microbiota in feed fermentation and health maintenance, a better understanding of the cheetah's intestinal
Yuzuru Taguchi et al.
Bio-protocol, 4(11) (2014-06-05)
Here we introduce a protocol for Triton X-114 extraction which we used in our recently-published paper (Taguchi et al., 2013). It is a versatile method to concentrate or partially purify hydrophobic proteins. The presented protocol is based on the protocol
Neha Tiwari et al.
Cell stem cell, 23(4), 557-571 (2018-10-06)
A broad molecular framework of how neural stem cells are specified toward astrocyte fate during brain development has proven elusive. Here we perform comprehensive and integrated transcriptomic and epigenomic analyses to delineate gene regulatory programs that drive the developmental trajectory
Christos D Georgiou et al.
Redox biology, 17, 236-245 (2018-05-05)
A new fluorometric assay is presented for the ultrasensitive quantification of total protein carbonyls, and is based on their specific reaction with rhodamine B hydrazide (RBH), and the production of a protein carbonyl-RBH hydrazone the fluorescence of which (at ex/em
Qasim Ali et al.
MethodsX, 6, 259-264 (2019-02-23)
Extraction of high-quality DNA from Gossypium (Cotton) species is notoriously difficult due to high contents of polysaccharides, quinones and polyphenols other secondary metabolites. Here, we describe a simple, rapid and modified procedure for high-quality DNA extraction from cotton, which is
Yuzuru Taguchi et al.
Bio-protocol, 4(11) (2014-06-05)
Here, we introduce the protocol for small-scale and simple subcellular fractionation used in our recent publication (Taguchi et al., 2013), which uses homogenization by passing through needles and sucrose step-gradient. Subcellular fractionation is a very useful technique but usually a
Nike Walther et al.
The Journal of cell biology, 217(7), 2309-2328 (2018-04-11)
The two Condensin complexes in human cells are essential for mitotic chromosome structure. We used homozygous genome editing to fluorescently tag Condensin I and II subunits and mapped their absolute abundance, spacing, and dynamic localization during mitosis by fluorescence correlation
Anne A M J Becker et al.
PloS one, 10(4), e0123933-e0123933 (2015-04-24)
Understanding the symbiotic relationship between gut microbes and their animal host requires characterization of the core microbiota across populations and in time. Especially in captive populations of endangered wildlife species such as the cheetah (Acinonyx jubatus), this knowledge is a
Saskia V Vijver et al.
Frontiers in immunology, 12, 733561-733561 (2021-10-26)
The tumor microenvironment (TME) is a complex structure comprised of tumor, immune and stromal cells, vasculature, and extracellular matrix (ECM). During tumor development, ECM homeostasis is dysregulated. Collagen remodeling by matrix metalloproteinases (MMPs) generates specific collagen fragments, that can be
Patryk Ludzia et al.
Structure (London, England : 1993), 29(9), 1014-1028 (2021-04-30)
The kinetochore is the macromolecular machinery that drives chromosome segregation by interacting with spindle microtubules. Kinetoplastids (such as Trypanosoma brucei), a group of evolutionarily divergent eukaryotes, have a unique set of kinetochore proteins that lack any significant homology to canonical
Xuping Xie et al.
Nature protocols, 16(3), 1761-1784 (2021-01-31)
Reverse genetic systems are a critical tool for studying viruses and identifying countermeasures. In response to the ongoing COVID-19 pandemic, we recently developed an infectious complementary DNA (cDNA) clone for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The reverse genetic
Katrine Pilely et al.
Atherosclerosis, 283, 35-42 (2019-02-18)
Cholesterol crystal (CC)-induced inflammation is a critical step in the development of atherosclerosis. CCs activate the complement system and induce an inflammatory response resulting in phagocytosis of the CCs, production of reactive oxygen species (ROS) and release of cytokines. The
Christos D Georgiou et al.
Redox biology, 17, 128-142 (2018-04-24)
A new 2,4-dinitrophenylhydrazine (DNPH)-based photometric assay is developed for the quantification of carbonyls in protein samples from any biological source by protein carbonyl-DNPH hydrazone formation at acidic pH in the presence of denaturing urea, and subsequent hydrazone solubilization in the
David S Goldstein et al.
The Journal of pharmacology and experimental therapeutics, 379(3), 253-259 (2021-09-11)
The endogenous catecholamines dopamine (DA), norepinephrine (NE), and epinephrine (EPI) play key roles in neurobehavioral, cardiovascular, and metabolic processes; various clinical disorders; and effects of numerous drugs. Steps in intracellular catecholamine synthesis and metabolism were delineated long ago, but there
Magdalena Pezzoni et al.
Bio-protocol, 8(11), e2869-e2869 (2018-06-05)
Bacteria in nature and as pathogens commonly face oxidative stress which causes damage to proteins, lipids and DNA. This damage is produced by the action of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), singlet oxygen, superoxide anion and
Grace C Lin et al.
Pharmaceutics, 13(2) (2021-03-07)
C-reactive protein (CRP) is a commonly used serum biomarker for detecting sepsis in neonates. After the onset of sepsis, serial measurements are necessary to monitor disease progression; therefore, a non-invasive detection method is beneficial for neonatal well-being. While some studies
Karla Lucía F Alvarez et al.
BMC veterinary research, 16(1), 230-230 (2020-07-08)
In the poultry industry, quantitative analysis of chicken T cell proliferation is important in many biological applications such as drug screening, vaccine production, and cytotoxicity assessment. Several assays have been established to evaluate this immunological response in chicken cells. However
Camilla Adler Sørensen et al.
Frontiers in immunology, 9, 1153-1153 (2018-06-14)
Enteroaggregative Escherichia coli (EAEC) causes acute and persistent diarrhea worldwide. Still, the involvement of host factors in EAEC infections is unresolved. Binding of recognition molecules from the lectin pathway of complement to EAEC strains have been observed, but the importance
Michael C Yoon et al.
ACS chemical biology, 16(9), 1628-1643 (2021-08-21)
Cathepsin B is a cysteine protease that normally functions within acidic lysosomes for protein degradation, but in numerous human diseases, cathepsin B translocates to the cytosol having neutral pH where the enzyme activates inflammation and cell death. Cathepsin B is
Roberto Alcántara et al.
STAR protocols, 2(4), 100878-100878 (2021-10-05)
Here, we describe a detailed step-by-step protocol to detect SARS-CoV-2 RNA using RT-PCR-mediated amplification and CRISPR/Cas-based visualization. The optimized assay uses basic molecular biology equipment such as conventional thermocyclers and transilluminators for qualitative detection. Alternatively, a fluorescence plate reader can
Irene Andrés-Blasco et al.
Nutrients, 12(10) (2020-10-18)
Macronutrients represent risk factors for hyperlipidemia or diabetes. Lipid alterations and type 2 diabetes mellitus are global health problems. Overexpression of sterol regulatory element-binding factor (Srebf2) in transgenic animals is linked to elevated cholesterol levels and diabetes development. We investigated
Katrine Pilely et al.
Journal of immunology (Baltimore, Md. : 1950), 196(12), 5064-5074 (2016-05-18)
Cholesterol crystals (CC) play an essential role in the formation of atherosclerotic plaques. CC activate the classical and the alternative complement pathways, but the role of the lectin pathway is unknown. We hypothesized that the pattern recognition molecules (PRMs) from
Jacob P van Vloten et al.
Molecular therapy. Methods & clinical development, 13, 154-166 (2019-02-23)
Immunotherapies are at the forefront of the fight against cancers, and researchers continue to develop and test novel immunotherapeutic modalities. Ideal cancer immunotherapies induce a patient's immune system to kill their own cancer and develop long-lasting immunity. Research has demonstrated
Peter Kip et al.
Nutrients, 13(11) (2021-11-28)
(1) Background: Vascular surgery operations are hampered by high failure rates and frequent occurrence of peri-operative cardiovascular complications. In pre-clinical studies, pre-operative restriction of proteins and/or calories (PCR) has been shown to limit ischemia-reperfusion damage, slow intimal hyperplasia, and improve
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