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https://www.readbyqxmd.com/read/29768001/crystal-structures-of-the-mango-ii-rna-aptamer-reveal-heterogeneous-fluorophore-binding-and-guide-engineering-of-variants-with-improved-selectivity-and-brightness
#1
Robert Trachman, Amir Abdolahzadeh, Alessio Andreoni, Razvan Cojocaru, Jay R Knutson, Michaël Ryckelynck, Peter John Unrau, Adrian Ferré-D'Amaré
Several RNA aptamers that bind small molecules and enhance their fluorescence have been successfully used to tag and track RNAs in vivo, but these genetically encodable tags have not yet achieved single-fluorophore resolution. Recently, Mango-II, an RNA that binds TO1-Biotin with ~1 nM affinity and enhances its fluorescence by >1,500-fold was isolated by fluorescence selection from the pool that yielded the original RNA Mango. We determined the crystal structures of Mango-II in complex with two fluorophores, TO1-Biotin and TO3-Biotin, and found that despite their high affinity, the ligands adopt multiple distinct conformations, indicative of a binding pocket with modest stereoselectivity...
May 16, 2018: Biochemistry
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#2
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29765362/tachyplesin-causes-membrane-instability-that-kills-multidrug-resistant-bacteria-by-inhibiting-the-3-ketoacyl-carrier-protein-reductase-fabg
#3
Cunbao Liu, Jialong Qi, Bin Shan, Yanbing Ma
Tachyplesin is a type of cationic β-hairpin antimicrobial peptide discovered in horseshoe crab approximately 30 years ago that is well known for both its potential antimicrobial activities against multidrug-resistant bacteria and its cytotoxicity to mammalian cells. Though its physical interactions with artificial membranes have been well studied, details of its physiological mechanism of action the physiological consequences of its action remain limited. By using the DNA-binding fluorescent dye propidium iodide to monitor membrane integrity, confocal microscopy to assess the intracellular location of FITC-tagged tachyplesin, and RNA sequencing of the differentially expressed genes in four Gram-negative bacteria ( Escherichia coli, Acinetobacter baumannii, Klebsiella pneumoniae , and Pseudomonas aeruginosa ) treated with lethal or sublethal concentrations of tachyplesin, we found that compared with levofloxacin-treated bacteria, tachyplesin-treated bacteria showed significant effects on the pathways underlying unsaturated fatty acid biosynthesis...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29750518/altered-microbiome-leads-to-significant-phenotypic-and-transcriptomic-differences-in-a-lipid-accumulating-chlorophyte
#4
Lubna Richter, Cresten B Mansfeldt, Michael M Kuan, Alexandra Cesare, Stephen T Menefee, Ruth E Richardson, Beth A Ahner
Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, e.g., triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp...
May 11, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29747012/comparative-transcriptome-analysis-reveals-the-gene-expression-profiling-in-bighead-carp-aristichthys-nobilis-in-response-to-acute-nitrite-toxicity
#5
Ling-Hong Miao, Yan Lin, Wen-Jing Pan, Xin Huang, Xian-Ping Ge, Qun-Lan Zhou, Bo Liu, Ming-Chun Ren, Wu-Xiao Zhang, Hua-Liang Liang, Han Yu, Ke Ji
OBJECTIVE: Nitrite exposure induces growth inhibition, metabolic disturbance, oxidative stress, organic damage, and infection-mediated mortality of aquatic organism. This study aimed to investigate the mechanism in responses to acute nitrite toxicity in bighead carp (Aristichthys nobilis, A. nobilis) by RNA-seq analysis. METHODS: Bighead carps were exposed to water with high nitrite content (48.63 mg/L) for 72 h, and fish livers and gills were separated for RNA-seq analysis...
May 7, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29743927/functional-characterization-of-the-hyles-euphorbiae-hawkmoth-transcriptome-reveals-strong-expression-of-phorbol-ester-detoxification-and-seasonal-cold-hardiness-genes
#6
M Benjamin Barth, Katja Buchwalder, Akito Y Kawahara, Xin Zhou, Shanlin Liu, Nicolas Krezdorn, Björn Rotter, Ralf Horres, Anna K Hundsdoerfer
Background: The European spurge hawkmoth, Hyles euphorbiae (Lepidoptera, Sphingidae), has been intensively studied as a model organism for insect chemical ecology, cold hardiness and evolution of species delineation. To understand species isolation mechanisms at a molecular level, this study aims at determining genetic factors underlying two adaptive ecological trait candidates, phorbol ester (TPA) detoxification and seasonal cold acclimation. Method: A draft transcriptome of H...
2018: Frontiers in Zoology
https://www.readbyqxmd.com/read/29743820/use-of-rna-immunoprecipitation-method-for-determining-sinorhizobium-meliloti-rna-hfq-protein-associations-in-vivo
#7
Mengsheng Gao, Anne Benge, Julia M Mesa, Regina Javier, Feng-Xia Liu
Background: Soil bacterium Sinorhizobium meliloti ( S. meliloti ) forms an endosymbiotic partnership with Medicago truncatula ( M. truncatula ) roots which results in root nodules. The bacteria live within root nodules where they function to fix atmospheric N2 and supply the host plant with reduced nitrogen. The bacterial RNA-binding protein Hfq (Hfq) is an important regulator for the effectiveness of the nitrogen fixation. RNA immunoprecipitation (RIP) method is a powerful method for detecting the association of Hfq protein with specific RNA in cultured bacteria, yet a RIP method for bacteria living in root nodules remains to be described...
2018: Biological Procedures Online
https://www.readbyqxmd.com/read/29717160/transcriptional-profiling-of-somatostatin-interneurons-in-the-spinal-dorsal-horn
#8
Alexander Chamessian, Michael Young, Yawar Qadri, Temugin Berta, Ru-Rong Ji, Thomas Van de Ven
The spinal dorsal horn (SDH) is comprised of distinct neuronal populations that process different somatosensory modalities. Somatostatin (SST)-expressing interneurons in the SDH have been implicated specifically in mediating mechanical pain. Identifying the transcriptomic profile of SST neurons could elucidate the unique genetic features of this population and enable selective analgesic targeting. To that end, we combined the Isolation of Nuclei Tagged in Specific Cell Types (INTACT) method and Fluorescence Activated Nuclei Sorting (FANS) to capture tagged SST nuclei in the SDH of adult male mice...
May 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29709588/potential-of-sirna-albumin-complex-against-cancer
#9
Na Liu, Yan-Hua Qi, Chuan-Tao Cheng, Wen Bin Yang, Anshoo Malhotra, Qi Zhou
RNA interference is a highly specific as well as efficient technology for gene therapy application in molecular oncology. The present study was planned to develop an efficient and stable tumor selective delivery mechanism for siRNA gene therapy for the purpose of both diagnosis as well as therapy. We have used 20 Male wistar rats for the formation of colon cancer model and utilized albumin as carrier molecule for the delivery of siRNA against vascular endothelial growth factor receptor 2 (VEGF R2). The study results confirmed efficient delivery of siRNA at tumor site as confirmed by tagging of siRNA-albumin complex with 99m TC...
April 27, 2018: Chemico-biological Interactions
https://www.readbyqxmd.com/read/29708631/comparative-proteomic-analysis-of-hypothalamus-tissue-from-huoyan-geese-between-pre-laying-period-and-laying-period-using-an-itraq-based-approach
#10
Zhongzan Cao, Ruiming Fan, Bo Meng, Zhe Xing, Mei Liu, Ming Gao, Xinhong Luan
The hypothalamus plays a central role in controlling poultry endocrine and reproductive activities. So far there is limited information focused on the proteome profiles of the hypothalamus from geese during different stages of the egg-laying cycle. In order to identify proteins regulating the egg-laying process of Huoyan geese, we investigated the proteome profiles of the hypothalamus from Huoyan geese during the laying period and pre-laying period by applying an isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic technology...
April 30, 2018: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/29708548/using-mouse-oocytes-to-assess-human-gene-function-during-meiosis-i
#11
Diego Marin, Alexandra L Nguyen, Richard T Scott, Karen Schindler
Embryonic aneuploidy is the major genetic cause of infertility in humans. Most of these events originate during female meiosis, and albeit positively correlated with maternal age, age alone is not always predictive of the risk of generating an aneuploid embryo. Therefore, gene variants might account for incorrect chromosome segregation during oogenesis. Given that access to human oocytes is limited for research purposes, a series of assays were developed to study human gene function during meiosis I using mouse oocytes...
April 10, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29703785/a-cloning-free-method-for-crispr-cas9-mediated-genome-editing-in-fission-yeast
#12
Xiao-Ran Zhang, Jia-Bei He, Yi-Zheng Wang, Li-Lin Du
The CRISPR/Cas9 system, which relies on RNA-guided DNA cleavage to induce site-specific DNA double-strand breaks, is a powerful tool for genome editing. This system has been successfully adapted for the fission yeast Schizosaccharomyces pombe by expressing Cas9 and the single-guide RNA (sgRNA) from a plasmid. In the procedures published to date, the cloning step that introduces a specific sgRNA target sequence into the plasmid is the most tedious and time-consuming. To increase the efficiency of applying the CRISPR/Cas9 system in fission yeast, we here developed a cloning-free procedure that uses gap repair in fission yeast cells to assemble two linear DNA fragments, a gapped Cas9-encoding plasmid and a PCR-amplified sgRNA insert, into a circular plasmid...
April 27, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29684792/global-effects-of-ddx3-inhibition-on-cell-cycle-regulation-identified-by-a-combined-phosphoproteomics-and-single-cell-tracking-approach
#13
Marise R Heerma van Voss, Kai Kammers, Farhad Vesuna, Justin Brilliant, Yehudit Bergman, Saritha Tantravedi, Xinyan Wu, Robert N Cole, Andrew Holland, Paul J van Diest, Venu Raman
DDX3 is an RNA helicase with oncogenic properties. The small molecule inhibitor RK-33 is designed to fit into the ATP binding cleft of DDX3 and hereby block its activity. RK-33 has shown potent activity in preclinical cancer models. However, the mechanism behind the antineoplastic activity of RK-33 remains largely unknown. In this study we used a dual phosphoproteomic and single cell tracking approach to evaluate the effect of RK-33 on cancer cells. MDA-MB-435 cells were treated for 24 hours with RK-33 or vehicle control...
April 20, 2018: Translational Oncology
https://www.readbyqxmd.com/read/29684399/a-cas9-transgenic-plasmodium-yoelii-parasite-for-efficient-gene-editing
#14
Pengge Qian, Xu Wang, Zhenke Yang, Zhenkui Li, Han Gao, Xin-Zhuan Su, Huiting Cui, Jing Yuan
The RNA-guided endonuclease Cas9 has applied as an efficient gene-editing method in malaria parasite Plasmodium. However, the size (4.2 kb) of the commonly used Cas9 from Streptococcus pyogenes (SpCas9) limits its utility for genome editing in the parasites only introduced with cas9 plasmid. To establish the endogenous and constitutive expression of Cas9 protein in the rodent malaria parasite P. yoelii, we replaced the coding region of an endogenous gene sera1 with the intact SpCas9 coding sequence using the CRISPR/Cas9-mediated genome editing method, generating the cas9-knockin parasite (PyCas9ki) of the rodent malaria parasite P...
April 20, 2018: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29684322/modified-beacon-probe-assisted-dual-signal-amplification-for-visual-detection-of-microrna
#15
Xiuwei Sun, Na Ying, Chuanjing Ju, Zhongyi Li, Na Xu, Guijuan Qu, Wensen Liu, Jiayu Wan
In a recent study, we reported a novel assay for the detection of microRNA-21 based on duplex-specific nuclease (DSN)-assisted isothermal cleavage and hybridization chain reaction (HCR) dual signal amplification. The Fam modified double-stranded DNA products were generated after the HCR, another biotin modified probe was digested by DSN and released from the magnetic beads after the addition of the target miRNA. The released sequence was then combined with HCR products to form a double-tagging dsDNA, which can be recognized by the lateral flow strips...
April 20, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29678725/cloning-and-characterization-of-a-second-lamprey-pituitary-glycoprotein-hormone-thyrostimulin-gpa2-gpb5
#16
Krist N Hausken, Belen Tizo, Michal Shpilman, Shannon Barton, Wayne Decatur, David Plachetzki, Scott Kavanaugh, Sabah Ul-Hasan, Berta Levavi-Sivan, Stacia A Sower
A novel heterodimeric glycoprotein hormone (GpH) comprised of alpha (GpA2) and beta (GpB5) subunits was discovered in 2002 and called thyrostimulin for its ability to activate the TSH receptor in mammals, but its central function in vertebrates has not been firmly established. We report here the cloning and expression of lamprey (l)GpB5, and its ability to heterodimerize with lGpA2 to form a functional l-thyrostimulin. The full-length cDNA of lGpB5 encodes 174 amino acids with ten conserved cysteine residues and one glycosylation site that is conserved with other vertebrate GpB5 sequences...
April 17, 2018: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29676930/high-value-bioproducts-from-microalgae-strategies-and-progress
#17
Ming-Hua Liang, Jianhua Zhu, Jian-Guo Jiang
Microalgae have been considered as alternative sustainable resources for high-value bioproducts such as lipids (especially triacylglycerides [TAGs]), polyunsaturated fatty acids (PUFAs), and carotenoids, due to their relatively high photosynthetic efficiency, no arable land requirement, and ease of scale-up. It is of great significance to exploit microalgae for the production of high-value bioproducts. How to improve the content or productivity of specific bioproducts has become one of the most urgent challenges...
April 20, 2018: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/29674963/a-bivalent-securinine-compound-sn3-l6-induces-neuronal-differentiation-via-translational-upregulation-of-neurogenic-transcription-factors
#18
Yumei Liao, Xiaoji Zhuang, Xiaojie Huang, Yinghui Peng, Xuanyue Ma, Zhi-Xing Huang, Feng Liu, Junyu Xu, Ying Wang, Wei-Min Chen, Wen-Cai Ye, Lei Shi
Developing therapeutic approaches that target neuronal differentiation will be greatly beneficial for the regeneration of neurons and synaptic networks in neurological diseases. Protein synthesis (mRNA translation) has recently been shown to regulate neurogenesis of neural stem/progenitor cells (NSPCs). However, it has remained unknown whether engineering translational machinery is a valid approach for manipulating neuronal differentiation. The present study identifies that a bivalent securinine compound SN3-L6, previously designed and synthesized by our group, induces potent neuronal differentiation through a novel translation-dependent mechanism...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29673865/tagging-snps-in-the-hotair-gene-are-associated-with-bladder-cancer-risk-in-a-chinese-population
#19
Xiang Wang, Wenying Wang, Qiang Zhang, Damin Gu, Ke Zhang, Yuqiu Ge, Haiyan Chu, Mulong Du, Bin Xu, Meilin Wang, Xu Lv, Zhengdong Zhang, Lin Yuan, Weida Gong
BACKGROUND: The HOX transcript antisense intergenic RNA (HOTAIR) is a well-known long noncoding RNA (lncRNA) that plays a critical role in biological processes in most cancers. However, the function of HOTAIR in bladder cancer remains largely unknown. In this study, we hypothesize that tag single nucleotide polymorphisms (tagSNPs) in HOTAIR are associated with bladder cancer (BCa) risk. METHODS: We performed a hospital-based case-control study of 1050 cases and 1407 controls to investigate the associations between tagSNPs and the risk of BCa in a Chinese population...
April 16, 2018: Gene
https://www.readbyqxmd.com/read/29661190/a-manually-annotated-actinidia-chinensis-var-chinensis-kiwifruit-genome-highlights-the-challenges-associated-with-draft-genomes-and-gene-prediction-in-plants
#20
Sarah M Pilkington, Ross Crowhurst, Elena Hilario, Simona Nardozza, Lena Fraser, Yongyan Peng, Kularajathevan Gunaseelan, Robert Simpson, Jibran Tahir, Simon C Deroles, Kerry Templeton, Zhiwei Luo, Marcus Davy, Canhong Cheng, Mark McNeilage, Davide Scaglione, Yifei Liu, Qiong Zhang, Paul Datson, Nihal De Silva, Susan E Gardiner, Heather Bassett, David Chagné, John McCallum, Helge Dzierzon, Cecilia Deng, Yen-Yi Wang, Lorna Barron, Kelvina Manako, Judith Bowen, Toshi M Foster, Zoe A Erridge, Heather Tiffin, Chethi N Waite, Kevin M Davies, Ella P Grierson, William A Laing, Rebecca Kirk, Xiuyin Chen, Marion Wood, Mirco Montefiori, David A Brummell, Kathy E Schwinn, Andrew Catanach, Christina Fullerton, Dawei Li, Sathiyamoorthy Meiyalaghan, Niels Nieuwenhuizen, Nicola Read, Roneel Prakash, Don Hunter, Huaibi Zhang, Marian McKenzie, Mareike Knäbel, Alastair Harris, Andrew C Allan, Andrew Gleave, Angela Chen, Bart J Janssen, Blue Plunkett, Charles Ampomah-Dwamena, Charlotte Voogd, Davin Leif, Declan Lafferty, Edwige J F Souleyre, Erika Varkonyi-Gasic, Francesco Gambi, Jenny Hanley, Jia-Long Yao, Joey Cheung, Karine M David, Ben Warren, Ken Marsh, Kimberley C Snowden, Kui Lin-Wang, Lara Brian, Marcela Martinez-Sanchez, Mindy Wang, Nadeesha Ileperuma, Nikolai Macnee, Robert Campin, Peter McAtee, Revel S M Drummond, Richard V Espley, Hilary S Ireland, Rongmei Wu, Ross G Atkinson, Sakuntala Karunairetnam, Sean Bulley, Shayhan Chunkath, Zac Hanley, Roy Storey, Amali H Thrimawithana, Susan Thomson, Charles David, Raffaele Testolin, Hongwen Huang, Roger P Hellens, Robert J Schaffer
BACKGROUND: Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. RESULTS: A second genome of an A...
April 16, 2018: BMC Genomics
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