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https://www.readbyqxmd.com/read/28319794/apoplastic-gamma-glutamyl-transferase-activity-encoded-by-ggt1-and-ggt2-is-important-for-vegetative-and-generative-development
#1
Sabrina Giaretta, Dinesh Prasad, Ilaria Forieri, Teofilo Vamerali, Anna Rita Trentin, Markus Wirtz, Rüdiger Hell, Antonio Masi
Gamma-glutamyl transferase (GGT; EC 2.3.2.2) is the only enzyme capable of degrading glutathione (GSH) in extra-cytosolic spaces. In plant cells, the GGT1 and GGT2 isoforms are located in the apoplast, bound respectively to the cell wall and the plasma membrane. GGT1 is expressed throughout plants, mainly in the leaves and vascular system, while GGT2 is more specifically expressed in seeds and trichomes, and weakly in roots. Their role in plant physiology remains to be clarified, however. Obtaining the ggt1/ggt2 double mutant can offer more clues than the corresponding single mutants, and to prevent any compensatory expression between the two isoforms...
March 10, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28319088/reference-component-analysis-of-single-cell-transcriptomes-elucidates-cellular-heterogeneity-in-human-colorectal-tumors
#2
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan, Mark Wong, Paul Jongjoon Choi, Lawrence J K Wee, Axel M Hillmer, Iain Beehuat Tan, Paul Robson, Shyam Prabhakar
Intratumoral heterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA-seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. Using RCA, we identified two distinct subtypes of cancer-associated fibroblasts (CAFs)...
March 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28319085/synergistic-drug-combinations-for-cancer-identified-in-a-crispr-screen-for-pairwise-genetic-interactions
#3
Kyuho Han, Edwin E Jeng, Gaelen T Hess, David W Morgens, Amy Li, Michael C Bassik
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs...
March 20, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28318141/zika-virus-induced-cellular-remodeling
#4
Evan D Rossignol, Kristen N Peters, John H Connor, Esther Bullitt
Zika virus (ZIKV) has been associated with morbidities such as Guillain-Barré, infant microcephaly, and ocular disease. The spread of this positive-sense, single-stranded RNA virus and its growing public health threat underscore gaps in our understanding of basic ZIKV virology. To advance knowledge of the virus replication cycle within mammalian cells, we use serial section three-dimensional electron tomography to demonstrate the widespread remodeling of intracellular membranes upon infection with ZIKV. We report extensive structural rearrangements of the endoplasmic reticulum and reveal stages of the ZIKV viral replication cycle...
March 20, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28317836/microscale-symmetrical-electroporator-array-as-a-versatile-molecular-delivery-system
#5
Mengxing Ouyang, Winfield Hill, Jung Hyun Lee, Soojung Claire Hur
Successful developments of new therapeutic strategies often rely on the ability to deliver exogenous molecules into cytosol. We have developed a versatile on-chip vortex-assisted electroporation system, engineered to conduct sequential intracellular delivery of multiple molecules into various cell types at low voltage in a dosage-controlled manner. Micro-patterned planar electrodes permit substantial reduction in operational voltages and seamless integration with an existing microfluidic technology. Equipped with real-time process visualization functionality, the system enables on-chip optimization of electroporation parameters for cells with varying properties...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28315749/integrated-structural-biology-to-unravel-molecular-mechanisms-of-protein-rna-recognition
#6
REVIEW
Andreas Schlundt, Jan-Niklas Tants, Michael Sattler
Recent advances in RNA sequencing technologies have greatly expanded our knowledge of the RNA landscape in cells, often with spatiotemporal resolution. These techniques identified many new (often non-coding) RNA molecules. Large-scale studies have also discovered novel RNA binding proteins (RBPs), which exhibit single or multiple RNA binding domains (RBDs) for recognition of specific sequence or structured motifs in RNA. Starting from these large-scale approaches it is crucial to unravel the molecular principles of protein-RNA recognition in ribonucleoprotein complexes (RNPs) to understand the underlying mechanisms of gene regulation...
March 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28315051/development-of-antibody-modified-chitosan-nanoparticles-for-the-targeted-delivery-of-sirna-across-the-blood-brain-barrier-as-a-strategy-for-inhibiting-hiv-replication-in-astrocytes
#7
Jijin Gu, Karam Al-Bayati, Emmanuel A Ho
RNA interference (RNAi)-mediated gene silencing offers a novel treatment and prevention strategy for human immunodeficiency virus (HIV) infection. HIV was found to infect and replicate in human brain cells and can cause neuroinfections and neurological deterioration. We designed dual-antibody-modified chitosan/small interfering RNA (siRNA) nanoparticles to deliver siRNA across the blood-brain barrier (BBB) targeting HIV-infected brain astrocytes as a strategy for inhibiting HIV replication. We hypothesized that transferrin antibody and bradykinin B2 antibody could specifically bind to the transferrin receptor (TfR) and bradykinin B2 receptor (B2R), respectively, and deliver siRNA across the BBB into astrocytes as potential targeting ligands...
March 17, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28306242/excision-repair-initiated-enzyme-assisted-bicyclic-cascade-signal-amplification-for-ultrasensitive-detection-of-uracil-dna-glycosylase
#8
Li-Juan Wang, Ming Ren, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification...
March 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28304078/moving-messages-in-the-developing-brain-emerging-roles-for-mrna-transport-and-local-translation-in-neural-stem-cells
#9
REVIEW
Louis-Jan Pilaz, Debra L Silver
The mammalian cerebral cortex is a complex brain structure integral to our higher cognition. During embryonic cortical development, radial glial progenitors (RGCs) produce neurons and serve as physical structures for migrating neurons. Recent discoveries highlight new roles for RNA localization and local translation in RGCs, both at the cell body and at distal structures called basal endfeet. By implementing technologies from the field of RNA research to brain development, investigators can manipulate RNA binding proteins as well as visualize single molecule RNAs, live movement of mRNAs and their binding proteins, and translation...
March 17, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28303895/total-extracellular-small-rna-profiles-from-plasma-saliva-and-urine-of-healthy-subjects
#10
Ashish Yeri, Amanda Courtright, Rebecca Reiman, Elizabeth Carlson, Taylor Beecroft, Alex Janss, Ashley Siniard, Ryan Richholt, Chris Balak, Joel Rozowsky, Robert Kitchen, Elizabeth Hutchins, Joseph Winarta, Roger McCoy, Matthew Anastasi, Seungchan Kim, Matthew Huentelman, Kendall Van Keuren-Jensen
Interest in circulating RNAs for monitoring and diagnosing human health has grown significantly. There are few datasets describing baseline expression levels for total cell-free circulating RNA from healthy control subjects. In this study, total extracellular RNA (exRNA) was isolated and sequenced from 183 plasma samples, 204 urine samples and 46 saliva samples from 55 male college athletes ages 18-25 years. Many participants provided more than one sample, allowing us to investigate variability in an individual's exRNA expression levels over time...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28303477/effect-of-co-overexpression-of-nisin-key-genes-on-nisin-production-improvement-in-lactococcus-lactis-ls01
#11
Zhi-Jian Ni, Xiao-Yuan Zhang, Fei Liu, Miao Wang, Rong-Hua Hao, Pei-Xue Ling, Xi-Qiang Zhu
Nisin is a small antimicrobial peptide produced by several subset strains of Lactococcus lactis. To improve nisin yield in the producer L. lactis LS01, we proposed a successive fusion of nisA with nisRK and nisFEG into a single shuttle expression vector pMG36e under the control of the native strong constitutive promoter p32. Subsequently, the recombinant vectors were transplanted into the producer cell through electroporation. Nisin productivity was determined through sodium dodecyl sulfate-polyacrylamide gel electrophoresis and bioactivity assays...
March 16, 2017: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/28303391/transcriptional-sequencing-and-analysis-of-major-genes-involved-in-the-adventitious-root-formation-of-mango-cotyledon-segments
#12
Yun-He Li, Hong-Na Zhang, Qing-Song Wu, Gloria K Muday
A total of 74,745 unigenes were generated and 1975 DEGs were identified. Candidate genes that may be involved in the adventitious root formation of mango cotyledon segment were revealed. Adventitious root formation is a crucial step in plant vegetative propagation, but the molecular mechanism of adventitious root formation remains unclear. Adventitious roots formed only at the proximal cut surface (PCS) of mango cotyledon segments, whereas no roots were formed on the opposite, distal cut surface (DCS). To identify the transcript abundance changes linked to adventitious root development, RNA was isolated from PCS and DCS at 0, 4 and 7 days after culture, respectively...
March 16, 2017: Planta
https://www.readbyqxmd.com/read/28301970/disclosing-the-parameters-leading-to-high-productivity-of-retroviral-producer-cells-lines-evaluating-random-vs-targeted-integration
#13
Vanessa Sofia Bandeira, Hélio A Tomás, Evren Alici, Manuel J C T Carrondo, Ana Sofia Coroadinha
Gammaretrovirus and lentivirus are the preferred viral vectors to genetically modify T- and NK- cells to be used in immune-cell therapies. The transduction efficiency of hematopoietic and T cells is more efficient using Gibbon ape leukemia virus (GaLV) pseudotyping. In this context gammaretroviral vector producer cells offer competitive higher titers than transient lentiviral vectors productions. The main aim of this work was to identify the key parameters governing GalV pseudotyped gammaretroviral vector productivity in stable producer cells using a retroviral vector expression cassette enabling positive (facilitating cell enrichment) and negative cell selection (allowing cell elimination)...
March 16, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#14
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301688/multiplex-single-cell-quantification-of-rare-rna-transcripts-from-protoplasts-in-a-model-plant-system
#15
Ulhas S Kadam, Burkhard Schulz, Joseph M K Irudayaraj
Here we demonstrate multiplex and simultaneous detection of four different rare RNA species from plant, Arabidopsis thaliana, using surface enhanced Raman spectroscopy and gold nanoprobes at single cell resolution. We show the applicability of nanoparticle-based Raman spectroscopic sensor to study intracellular RNA copies. First, we demonstrate that gold-nanoparticles decorate with Raman probes and carrying specific nucleic acid probe sequences can be uptaken by the protoplasts. We confirm the internalization of gold nanoprobes by TEM, ICP-MS, and fluorescence imaging...
March 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28301575/generation-of-murine-tumor-cell-lines-deficient-in-mhc-molecule-surface-expression-using-the-crispr-cas9-system
#16
Krishna Das, David Eisel, Clarissa Lenkl, Ashish Goyal, Sven Diederichs, Elke Dickes, Wolfram Osen, Stefan B Eichmüller
In this study, the CRISPR/Cas9 technology was used to establish murine tumor cell lines, devoid of MHC I or MHC II surface expression, respectively. The melanoma cell line B16F10 and the murine breast cancer cell line EO-771, the latter stably expressing the tumor antigen NY-BR-1 (EO-NY), were transfected with an expression plasmid encoding a β2m-specific single guide (sg)RNA and Cas9. The resulting MHC I negative cells were sorted by flow cytometry to obtain single cell clones, and loss of susceptibility of peptide pulsed MHC I negative clones to peptide-specific CTL recognition was determined by IFNγ ELISpot assay...
2017: PloS One
https://www.readbyqxmd.com/read/28299927/supramolecular-hydrogels-based-on-dna-self-assembly
#17
Yu Shao, Haoyang Jia, Tianyang Cao, Dongsheng Liu
Extracellular matrix (ECM) provides essential supports three dimensionally to the cells in living organs, including mechanical support and signal, nutrition, oxygen, and waste transportation. Thus, using hydrogels to mimic its function has attracted much attention in recent years, especially in tissue engineering, cell biology, and drug screening. However, a hydrogel system that can merit all parameters of the natural ECM is still a challenge. In the past decade, deoxyribonucleic acid (DNA) has arisen as an outstanding building material for the hydrogels, as it has unique properties compared to most synthetic or natural polymers, such as sequence designability, precise recognition, structural rigidity, and minimal toxicity...
March 16, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28299324/micrornas-and-cardiovascular-disease-in-diabetes-mellitus
#18
REVIEW
Yue Ding, Xue Sun, Peng-Fei Shan
Cardiovascular disease (CVD) is the major macrovascular complication of diabetes mellitus. Recently, although CVD morbidity and mortality have decreased as a result of comprehensive control of CVD risk factors, CVD remains the leading cause of death of patients with diabetes in many countries, indicating the potential underlying pathophysiological mechanisms. MicroRNAs are a class of noncoding, single-stranded RNA molecules that are involved in β-cell function, insulin secretion, insulin resistance, skeletal muscle, and adipose tissue and which play an important role in glucose homeostasis and the pathogenesis of diabetic complications...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28298915/transcriptomic-analysis-reveals-mechanisms-of-sterile-and-fertile-flower-differentiation-and-development-in-viburnum-macrocephalum-f-keteleeri
#19
Zhaogeng Lu, Jing Xu, Weixing Li, Li Zhang, Jiawen Cui, Qingsong He, Li Wang, Biao Jin
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28298438/single-cell-analysis-reveals-lineage-segregation-in-early-post-implantation-mouse-embryos
#20
Jing Wen, Yanwu Zeng, Zhuoqing Fang, Junjie Gu, Laixiang Ge, Fan Tang, Zepeng Qu, Jing Hu, Yaru Cui, Kunshan Zhang, Junbang Wang, Siguang Li, Yi Sun, Ying Jin
The mammalian post-implantation embryo has been extensively investigated at the tissue level. However, to unravel the molecular basis for the cell-fate plasticity and determination, it is essential to study the characteristics of individual cells. Especially, the individual definitive endoderm (DE) cells have not been characterized in vivo. Here, we report gene expression patterns in single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (Fgf) ligands and receptors...
March 15, 2017: Journal of Biological Chemistry
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