CRISPR/Cas9-introduced single and multiple mutagenesis in strawberry

正CRISPR/Cas9-mediated genome editing is a powerful tool for life science research. Recently, strawberry (Fragaria × ananassa), an important horticultural crop, has emerged as a model organism for investigating the regulatory mechanisms of fruit development and ripening (Shulaev et al., 2011; Jia et al., 2013, 2017; Kang et al., 2013; Han et al., 2015). While most cultivated strawberries     

Efficient generation of pink-fruited tomatoes using CRISPR/Cas9 system

正Tomato(Solanum lycopersicum)is the leading vegetable crop worldwide and an essential component of a healthy diet(Lin et al.,2014;Du et al.,2017).Fruit color is regarded as one of the most important commercial traits in tomato(The Tomato Genome Consortium,2012).Consumers in different regions have different color preferences.For example,European and American     

Rapid breeding of pink-fruited tomato hybrids using the CRISPR/Cas9 system

<正>As one of the most important vegetables,tomato (Solanum lycopersicum) is extensively produced and consumed worldwide and substantially contributes to human nutrition and health (The Tomato Genome Consortium,2012).Although red tomatoes are the most common,pink tomatoes are more popular in Asia,particularly in China and Japan,because of their better taste (Ballester et al.,2010;Zhu et al.,2018).Compared with red tomatoes,pink tomatoes fail to accumulate the yellow-colored flavonoid pigment,naringenin chalcone (NarCh),in their peels,resulting in a colorless peel phenotype (Adato et al,2009;Ballester et al.,2010).Genetic     

Ultrasound Molecular Imaging with Targeted Microbubbles for Cancer Diagnostics: From Bench to Bedside

Background

Ultrasound plays an important role in cancer diagnosis. B-mode imaging and contrast-enhanced ultrasound are routinely used to detect cancerous lesions in breast and liver. The use of ultrasound contrast agents (UCAs) such as microbubbles (MBs), which can be functionalized with targeting ligands, has further enabled ultrasound molecular imaging (USMI) of specific molecular markers in pre-clinical and the first clinical studies. As targeted MBs have a diameter of 1–4 μm, they are limited to the blood vasculature upon intravenous injection, and can bind to markers of the vascular endothelium. USMI with targeted MBs was applied for imaging of markers of inflammation, angiogenesis, and the tumor endothelium.

Spatial Cytoskeleton Organization Supports Targeted Intracellular Transport

The efficiency of intracellular cargo transport from specific sources to target locations is strongly dependent upon molecular motor-assisted motion along the cytoskeleton. Radial transport along microtubules and lateral transport along the filaments of the actin cortex underneath the cell membrane are characteristic for cells with a centrosome. The interplay between the specific cytoskeleton organization and the motor performance results in a spatially inhomogeneous intermittent search strategy. To analyze the efficiency of such intracellular search strategies, we formulate a random velocity model with intermittent arrest states. We evaluate efficiency in terms of mean first passage times for three different, frequently encountered intracellular transport tasks: 1) the narrow escape problem, which emerges during cargo transport to a synapse or other specific region of the cell membrane; 2) the reaction problem, which considers the binding time of two particles within the cell; and 3) the reaction-escape problem, which arises when cargo must be released at a synapse only after pairing with another particle. Our results indicate that cells are able to realize efficient search strategies for various intracellular transport tasks economically through a spatial cytoskeleton organization that involves only a narrow actin cortex rather than a cell body filled with randomly oriented actin filaments.     

Understanding human diseases using Drosophila

One of the major goals of biomedical research is to elucidate the causal relationships of critical factors involved in the initiation and progression of human diseases at the molecular and cellular levels. This knowledge is required for developing effective treatments for major diseases including cancer, cardiovascular and metabolic diseases, as well as neurodegenerative diseases and neurological disorders. Because of their phylogenetic representations and relative ease of experimental manipulation, model organisms such as the budding yeast (Saccharomyces cerevisiae), the nematode worm (Caenorhabditis elegans), the fruit fly (Drosophila melanogaster'), the thale cress (Arabidopsis thaliana), the zebrafish (Danio rerio'), the frog (Xenopus laevis), and the mouse (Mus musculus}, have been extensively studied over the past century (Hedges, 2002;Muller and Grossniklaus, 2010;Dietrich et al., 2014).     

Disruptor of telomeric silencing 1-like (DOT1L) is involved in breast cancer metastasis via transcriptional regulation of MALAT1 and ZEB2

<正>Epigenetics refers to how chromatin-associated factors and reversible chromatin modifications maintain DNA-based programs by regulating the chromatin structure (Strahl and Allis,2000).In recent years,genome sequencing studies of cancer have shown that genes encoding epigenetic factors are commonly mutated in cancer(Garraway and Lander,2013).Dys regulated,or mutant,epigenetic factors influence tumorigenesis progression (Dawson and Kouzarides,     

The emerging impact of tRNA modifications in the brain and nervous system

A remarkable number of neurodevelopmental disorders have been linked to defects in tRNA modifications. These discoveries place tRNA modifications in the spotlight as critical modulators of gene expression pathways that are required for proper organismal growth and development. Here, we discuss the emerging molecular and cellular functions of the diverse tRNA modifications linked to cognitive and neurological disorders. In particular, we describe how the structure and location of a tRNA modification influences tRNA folding, stability, and function. We then highlight how modifications in tRNA can impact multiple aspects of protein translation that are instrumental for maintaining proper cellular proteostasis. Importantly, we describe how perturbations in tRNA modification lead to a spectrum of deleterious biological outcomes that can disturb neurodevelopment and neurological function. Finally, we summarize the biological themes shared by the different tRNA modifications linked to cognitive disorders and offer insight into the future questions that remain to decipher the role of tRNA modifications. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.     

Effect of insulin on alpha1-adrenergic actions in hepatocytes from euthyroid and hypothyroid rats. Possible involvement of two pathways in alpha1-adrenergic actions

The effect of insulin on the alpha1-adrenergic stimulation of glycogenolysis and ureogenesis, which is very small or undetectable in hepatocytes from control animals, is marked in hepatocytes from hypothyroid rats; the metabolic actions due to alpha1-adrenergic activation, but not those due to glucagon, were nearly blocked by insulin in cells from hypothyroid rats. The alpha1-adrenergic-mediated stimulation of phosphatidylinositol labelling was not affected by insulin in cells from either control or hypothyroid rats. The data suggest that the alpha1-adrenergic action proceeds through two pathways, one of which is very sensitive to insulin and predominates in cells from hypothyroid rats.     

Highly efficient genome editing using oocyte-specific zcas9 transgenic zebrafish

正Since its first application to induce mutations in mammalian cells (Cong et al., 2013; Mali et al., 2013), CRISPR/Cas9 has rapidly become a routine technique to perform genome editing in a variety of biological systems due to its facile, robust, and multiplexable features (Hwang et al., 2013; Wang et al., 2013; Guo et al., 2014; Liu,     

IRESfinder: Identifying RNA internal ribosome entry site in eukaryotic cell using framed k-mer features

正In eukaryotic cells,initiation of protein translation is to recruit the ribosome to a specific mRNA,which is generally dependent on the 5'cap structure.However,protein translation can also be initiated in a cap-independent manner by using a cis-regulatory element termed the internal ribosome entry site(IRES).The first experimentally validated IRES was reported in the poliovirus     

The synergy between RSC,Nap1 and adjacent nucleosome in nucleosome remodeling

Eukaryotes have evolved a specific strategy to package DNA. The nucleosome is a 147-base-pair DNA segment wrapped around histone core proteins that plays important roles regulating DNA-dependent biosynthesis and gene expression. Chromatin remodeling complexes (RSC, Remodel the Structure of Chromatin) hydrolyze ATP to perturb DNA-histone contacts, leading to nucleosome sliding and ejection. Here, we utilized tethered particle motion (TPM) experiments to investigate the mechanism of RSC-mediated nucleosome remodeling in detail. We observed ATP-dependent RSC-mediated DNA looping and nucleosome ejection along individual mononucleosomes and dinucleosomes. We found that nucleosome assembly protein 1 (Nap1) enhanced RSC-mediated nucleosome ejection in a two-step disassembly manner from dinucleosomes but not from mononucleosomes. Based on this work, we provide an entire reaction scheme for the RSC-mediated nucleosome remodeling process that includes DNA looping, nucleosome ejection, the influence of adjacent nucleosomes, and the coordinated action between Nap1 and RSC.     

Discovery of covalent enzyme inhibitors using virtual docking of covalent fragments

Here we present a virtual docking screen of 1648 commercially available covalent fragments, and identified covalent inhibitors of cysteine protease cathepsin L. These inhibitors did not inhibit closely related protease cathepsin B. Thus, we have established virtual docking of covalent fragments as an approach to discover covalent enzyme inhibitors.     

Dual Role for DsbA in Attacking and Targeted Bacterial Cells during Type VI Secretion System-Mediated Competition

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Thioether-stapled macrocyclic inhibitors of the EH domain of EHD1

Recycling of receptors from the endosomal recycling compartment to the plasma membrane is a critical cellular process, and recycling is particularly important for maintaining invasiveness in solid tumors. In this work, we continue our efforts to inhibit EHD1, a critical adaptor protein involved in receptor recycling. We applied a diversity-oriented macrocyclization approach to produce cyclic peptides with varied conformations, but that each contain a motif that binds to the EH domain of EHD1. Screening these uncovered several new inhibitors for EHD1’s EH domain, the most potent of which bound with a K_d of 3.1 μM. Several of the most potent inhibitors were tested in a cellular assay that measures extent of vesicle recycling. Inhibiting EHD1 could potentially slow cancer invasiveness and metastasis, and these cyclic peptides represent the most potent inhibitors of EHD1 to date.     

CycLS: Accurate,whole-library sequencing of cyclic peptides using tandem mass spectrometry

Cyclic peptides are of great interest as therapeutic compounds due to their potential for specificity and intracellular activity, but specific compounds can be difficult to identify from large libraries without resorting to molecular encoding techniques. Large libraries of cyclic peptides are often DNA-encoded or linearized before sequencing, but both of those deconvolution strategies constrain the chemistry, assays, and quantification methods which can be used. We developed an automated sequencing program, CycLS, to identify cyclic peptides contained within large synthetic libraries. CycLS facilitates quick and easy identification of all library-members via tandem mass spectrometry data without requiring any specific chemical moieties or modifications within the library. Validation of CycLS against a library of 400 cyclic hexapeptide peptoid hybrids (peptomers) of unique mass yielded a result of 95% accuracy when compared against a simulated library size of 234,256 compounds. CycLS was also evaluated by resynthesizing pure compounds from a separate 1800-member library of cyclic hexapeptides and hexapeptomers with high mass redundancy. Of 22 peptides resynthesized, 17 recapitulated the retention times and fragmentation patterns assigned to them from the whole-library bulk assay results. Implementing a database-matching approach, CycLS is fast and provides a robust method for sequencing cyclic peptides that is particularly applicable to the deconvolution of synthetic libraries.