keyword
MENU ▼
Read by QxMD icon Read
search

Ribosome profiling

keyword
https://www.readbyqxmd.com/read/29330118/using-the-ribodeblur-pipeline-to-recover-a-sites-from-yeast-ribosome-profiling-data
#1
Hao Wang, Carl Kingsford, C Joel McManus
Ribosome profiling has emerged as a powerful technique to study mRNA translation. Ribosome profiling has the potential to determine the relative quantities and locations of ribosomes on mRNA genome wide. Taking full advantage of this approach requires accurate measurement of ribosome locations. However, experimental inconsistencies often obscure the positional information encoded in ribosome profiling data. Here, we describe the Ribodeblur pipeline, a computational analysis tool that uses a maximum likelihood framework to infer ribosome positions from heterogeneous datasets...
January 9, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29325778/nonstructural-proteins-nsp2tf-and-nsp2n-of-porcine-reproductive-and-respiratory-syndrome-virus-prrsv-play-important-roles-in-suppressing-host-innate-immune-responses
#2
Y Li, P Shang, D Shyu, C Carrillo, P Naraghi-Arani, Crystal J Jaing, G J Renukaradhya, A E Firth, E J Snijder, Y Fang
Recently, we identified a unique -2/-1 ribosomal frameshift mechanism in PRRSV, which yields two truncated forms of nonstructural protein (nsp) 2 variants, nsp2TF and nsp2N. Here, in vitro expression of individual PRRSV nsp2TF and nsp2N demonstrated their ability to suppress cellular innate immune responses in transfected cells. Two recombinant viruses were further analyzed, in which either nsp2TF was C-terminally truncated (vKO1) or expression of both nsp2TF and nsp2N was knocked out (vKO2). Host cellular mRNA profiling showed that a panel of cellular immune genes, in particular those involved in innate immunity, was upregulated in cells infected with vKO1 and vKO2...
January 8, 2018: Virology
https://www.readbyqxmd.com/read/29324785/phylogenetic-diversity-antimicrobial-susceptibility-and-virulence-gene-profiles-of-brachyspira-hyodysenteriae-isolates-from-pigs-in-germany
#3
Jessica Joerling, Stefanie A Barth, Karen Schlez, Hermann Willems, Werner Herbst, Christa Ewers
Swine dysentery (SD) is an economically important diarrheal disease in pigs caused by different strongly hemolytic Brachyspira (B.) species, such as B. hyodysenteriae, B. suanatina and B. hampsonii. Possible associations of epidemiologic data, such as multilocus sequence types (STs) to virulence gene profiles and antimicrobial susceptibility are rather scarce, particularly for B. hyodysenteriae isolates from Germany. In this study, B. hyodysenteriae (n = 116) isolated from diarrheic pigs between 1990 and 2016 in Germany were investigated for their STs, susceptibility to the major drugs used for treatment of SD (tiamulin and valnemulin) and genes that were previously linked with virulence and encode for hemolysins (tlyA, tlyB, tlyC, hlyA, BHWA1_RS02885, BHWA1_RS09085, BHWA1_RS04705, and BHWA1_RS02195), outer membrane proteins (OMPs) (bhlp16, bhlp17...
2018: PloS One
https://www.readbyqxmd.com/read/29322263/comparative-transcriptomic-analysis-of-skeletal-muscle-tissue-during-prenatal-stages-in-tongcheng-and-yorkshire-pig-using-rna-seq
#4
Huijing Liu, Yu Xi, Guorong Liu, Yuqiang Zhao, Ji Li, Minggang Lei
Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK...
January 10, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29321322/dengue-virus-selectively-annexes-endoplasmic-reticulum-associated-translation-machinery-as-a-strategy-for-co-opting-host-cell-protein-synthesis
#5
David W Reid, Rafael K Campos, Jessica R Child, Tianli Zheng, Kitti Wing Ki Chan, Shelton S Bradrick, Subhash G Vasudevan, Mariano A Garcia-Blanco, Christopher V Nicchitta
A primary question in Dengue virus (DENV) biology is the molecular strategy for recruitment of host cell protein synthesis machinery. Here we combined cell fractionation, ribosome profiling, and RNA-seq to investigate the subcellular organization of viral genome translation and replication as well as host cell translation and its response to DENV infection. We report that throughout the viral life cycle, DENV (+) and (-) strand RNAs were highly partitioned to the endoplasmic reticulum (ER), identifying the ER as the primary site of DENV translation...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29319912/transcriptomics-in-the-wild-hibernation-physiology-in-free-ranging-dwarf-lemurs
#6
Sheena L Faherty, José Luis Villanueva-Cañas, Marina B Blanco, Mar M Albà, Anne D Yoder
Hibernation is an adaptive strategy some mammals use to survive highly seasonal or unpredictable environments. We present the first investigation on the transcriptomics of hibernation in a natural population of primate hibernators: Crossley's dwarf lemurs (Cheirogaleus crossleyi). Using capture-mark-recapture techniques to track the same animals over a period of seven months in Madagascar, we used RNA-seq to compare gene expression profiles in white adipose tissue (WAT) during three distinct physiological states...
January 10, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29319171/the-key-genes-underlying-pathophysiology-association-between-the-type-2-diabetic-and-colorectal-cancer
#7
Wen-Fang Peng, Feng Bai, Kan Shao, Li-Sha Shen, Hui-Hua Li, Shan Huang
Althoughdiabetes mellitus (DM) is reported as an independent risk factor for colorectal cancer (CRC) in many researches, the underlying pathophysiology is still unclear. We investigated the differentiallyexpressedgenes (DEGs)for the diabetes and CRC to reveal the underlying pathophysiological association between the type 2-diabetic (T2D) and CRC. Gene expression profiles for T2D (GSE55650), CRC (GSE8671) and Metformin treated cell lines (GSE67342) were downloaded from GEO database. The DEGs between T2D samples and their control samples were identified with t-test and variance analysis...
January 10, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29318340/evaluating-protocols-for-porcine-faecal-microbiome-recollection-storage-and-dna-extraction-from-the-farm-to-the-lab
#8
Anixa Muiños-Bühl, Oscar González-Recio, María Muñoz, Cristina Óvilo, Juan García-Casco, Ana I Fernández
There is a growing interest in understanding the role of the gut microbiome on productive and meat quality-related traits in livestock species in order to develop new useful tools for improving pig production systems and industry. Faecal samples are analysed as a proxy of gut microbiota and here the selection of suitable protocols for faecal sampling and DNA isolation is a critical first step in order to obtain reliable results, even more to compare results obtained from different studies. The aim of the current study was to establish in a cost-effective way, using automated ribosomal intergenic spacer analysis technique, a protocol for porcine faecal sampling and storage at farm and slaughterhouse and to determine the most efficient microbiota DNA isolation kit among those most widely used...
January 9, 2018: Current Microbiology
https://www.readbyqxmd.com/read/29316319/protein-profile-in-aspergillus-nidulans-recombinant-strains-overproducing-heterologous-enzymes
#9
Mariane Paludetti Zubieta, Fabiano Jares Contesini, Marcelo Ventura Rubio, Any Elisa de Souza Schmidt Gonçalves, Jaqueline Aline Gerhardt, Rolf Alexander Prade, André Ricardo de Lima Damasio
Filamentous fungi are robust cell factories and have been used for the production of large quantities of industrially relevant enzymes. However, the production levels of heterologous proteins still need to be improved. Therefore, this article aimed to investigate the global proteome profiling of Aspergillus nidulans recombinant strains in order to understand the bottlenecks of heterologous enzymes production. About 250, 441 and 424 intracellular proteins were identified in the control strain Anid_pEXPYR and in the recombinant strains Anid_AbfA and Anid_Cbhl respectively...
January 8, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29313485/biological-and-molecular-characterization-of-trypanosoma-cruzi-strains-from-four-states-of-brazil
#10
Aline Rimoldi Ribeiro, Luciana Lima, Larissa Aguiar de Almeida, Joana Monteiro, Cláudia Jassica Gonçalves Moreno, Juliana Damieli Nascimento, Renato Freitas de Araújo, Fernanda Mello, Luciamáre Perinetti Alves Martins, Márcia Aparecida Silva Graminha, Marta Maria Geraldes Teixeira, Marcelo Sousa Silva, Mário Steindel, João Aristeu da Rosa
Chagas disease affects between six and seven million people. Its etiological agent, Trypanosoma cruzi, is classified into six discrete typing units (DTUs). The biological study of 11 T. cruzi strains presented here included four parameters: growth kinetics, parasitemia curves, rate of macrophage infection, and serology to evaluate IgM, total IgG, IgG1, IgG2a, and IgG3. Sequencing of small subunit of ribosomal RNA (SSU rRNA)was performed and the T. cruzi strains were classified into three DTUs. When their growth in liver infusion tryptose medium was represented in curves, differences among the strains could be noted...
January 8, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29299797/transcriptome-assembly-and-expression-profiling-of-the-molecular-responses-to-cadmium-toxicity-in-cerebral-ganglia-of-wolf-spider-pardosa-pseudoannulata-araneae-lycosidae
#11
Huilin Yang, Yuande Peng, Yixue Shi, Jianxiang Tian, Juan Wang, Xianjin Peng, Chunliang Xie, Xiang Xu, Qisheng Song, Zhi Wang, Zhiyue Lv
Cadmium (Cd) is a heavy metal that can cause irreversible toxicity to animals, and is an environmental pollutant in farmlands. Spiders are considered to be an excellent model for investigating the impacts of heavy metals on the environment. To date, the changes at the molecular level in the cerebral ganglia of spiders are poorly understood. Cd exposure leads to strong damage in the nervous system, such as apoptosis and necrosis of nerve cells, therefore we conducted a transcriptomic analysis of Pardosa pseudoannulata cerebral ganglia under Cd stress to profile differential gene expression (DGE)...
January 3, 2018: Ecotoxicology
https://www.readbyqxmd.com/read/29298822/plastid-ribosome-pausing-is-induced-by-multiple-features-and-is-linked-to-protein-complex-assembly
#12
Lars B Scharff, Piotr Gawroński, Poul Erik Jensen, Stanislaw Karpinski, Dario Leister
Many mRNAs contain pause sites that briefly interrupt the progress of translation. Specific features that induce ribosome pausing have been described; however, their individual contributions to pause-site formation, and the overall biological significance of ribosome pausing, remain largely unclear. We have taken advantage of the compact genome of chloroplasts to carry out a plastid genome-wide survey of pause sites, as a basis for studying the impact of pausing on post-translational processes. Based on ribosomal profiling of Arabidopsis thaliana chloroplast mRNAs, we demonstrate that a combination of factors - mRNA secondary structure, internal Shine-Dalgarno sequences, and positively charged amino acids in the nascent peptide chain - explains 95% of the major pause sites on plastid mRNAs, while codon usage has little impact...
January 3, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29295561/exploring-the-mechanisms-of-electroacupuncture-induced-analgesia-through-rna-sequencing-of-the-periaqueductal-gray
#13
Man-Li Hu, Hong-Mei Zhu, Qiu-Lin Zhang, Jing-Jing Liu, Yi Ding, Ju-Ming Zhong, Vitaly Vodyanoy, Ming-Xing Ding
Electroacupuncture (EA) can relieve various pains. However, its mechanism in terms of the transcriptome is still not well-known. To explore the full profile of EA-induced molecular modification in the central nerve system, three twins of goats were selected for a match-paired experiment: EA stimulation (60 Hz, 30 min) and none-EA (control). Goats in the EA group showed an increased (p < 0.05) nociceptive threshold compared with the control goats. Experimental goats were sacrificed at 4 h of the experiment, and the periaqueductal grays were harvested for RNA sequencing...
December 25, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29287594/comprehensive-molecular-biomarker-identification-in-breast-cancer-brain-metastases
#14
Hans-Juergen Schulten, Mohammed Bangash, Sajjad Karim, Ashraf Dallol, Deema Hussein, Adnan Merdad, Fatma K Al-Thoubaity, Jaudah Al-Maghrabi, Awatif Jamal, Fahad Al-Ghamdi, Hani Choudhry, Saleh S Baeesa, Adeel G Chaudhary, Mohammed H Al-Qahtani
BACKGROUND: Breast cancer brain metastases (BCBM) develop in about 20-30% of breast cancer (BC) patients. BCBM are associated with dismal prognosis not at least due to lack of valuable molecular therapeutic targets. The aim of the study was to identify new molecular biomarkers and targets in BCBM by using complementary state-of-the-art techniques. METHODS: We compared array expression profiles of three BCBM with 16 non-brain metastatic BC and 16 primary brain tumors (prBT) using a false discovery rate (FDR) p < 0...
December 29, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29286414/genome-wide-quantification-of-translation-in-budding-yeast-by-ribosome-profiling
#15
Carine Beaupere, Rosalyn B Chen, William Pelosi, Vyacheslav M Labunskyy
Translation of mRNA into proteins is a complex process involving several layers of regulation. It is often assumed that changes in mRNA transcription reflect changes in protein synthesis, but many exceptions have been observed. Recently, a technique called ribosome profiling (or Ribo-Seq) has emerged as a powerful method that allows identification, with high accuracy, which regions of mRNA are translated into proteins and quantification of translation at the genome-wide level. Here, we present a generalized protocol for genome-wide quantification of translation using Ribo-Seq in budding yeast...
December 21, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29282095/impact-of-fhit-loss-on-the-translation-of-cancer-associated-mrnas
#16
Daniel L Kiss, William Baez, Kay Huebner, Ralf Bundschuh, Daniel R Schoenberg
BACKGROUND: FHIT is a genome caretaker/tumor suppressor that is silenced in >50% of cancers. Although it was identified more than 20 years ago, questions remain as to how FHIT loss contributes to cancer, and conversely, how FHIT acts to maintain genome integrity and suppress malignancy. Fhit belongs to the histidine triad family of enzymes that catalyze the degradation of nucleoside 5',5'-triphosphates, including the m7GpppN 'caps' that are generated when mRNAs undergo 3'-5' decay...
December 28, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/29280134/a-retrospective-pilot-study-to-determine-whether-the-reproductive-tract-microbiota-differs-between-women-with-a-history-of-infertility-and-fertile-women
#17
Bryan A Wee, Mark Thomas, Emma Louise Sweeney, Francesca D Frentiu, Melanie Samios, Jacques Ravel, Pawel Gajer, Garry Myers, Peter Timms, John A Allan, Wilhelmina M Huston
BACKGROUND: We know very little about the microbiota inhabiting the upper female reproductive tract and how it impacts on fertility. AIMS: This pilot study aimed to examine the vaginal, cervical and endometrial microbiota for women with a history of infertility compared to women with a history of fertility. MATERIALS AND METHODS: Using a retrospective case-control study design, women were recruited for collection of vaginal, cervical and endometrial samples...
December 26, 2017: Australian & New Zealand Journal of Obstetrics & Gynaecology
https://www.readbyqxmd.com/read/29277868/comparative-metagenomics
#18
Andrew Maltez Thomas, Felipe Prata Lima, Livia Maria Silva Moura, Aline Maria da Silva, Emmanuel Dias-Neto, João C Setubal
Thanks in large part to newer, better, and cheaper DNA sequencing technologies, an enormous number of metagenomic sequence datasets have been and continue to be generated, covering a huge variety of environmental niches, including several different human body sites. Comparing these metagenomes and identifying their commonalities and differences is a challenging task, due not only to the large amounts of data, but also because there are several methodological considerations that need to be taken into account to ensure an appropriate and sound comparison between datasets...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29248718/proteomic-characterization-of-prostate-cancer-to-distinguish-nonmetastasizing-and-metastasizing-primary-tumors-and-lymph-node-metastases
#19
Ann-Kathrin Müller, Melanie Föll, Bianca Heckelmann, Selina Kiefer, Martin Werner, Oliver Schilling, Martin L Biniossek, Cordula Annette Jilg, Vanessa Drendel
Patients with metastatic prostate cancer (PCa) have a poorer prognosis than patients with organ-confined tumors. We strove to uncover the proteome signature of primary PCa and associated lymph node metastases (LNMs) in order to identify proteins that may indicate or potentially promote metastases formation. We performed a proteomic comparative profiling of PCa tissue from radical prostatectomy (RPE) of patients without nodal metastases or relapse at the time of surgical resection (n=5) to PCa tissue from RPE of patients who suffered from nodal relapse (n=5)...
December 14, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29244193/comparative-peptidomic-profile-between-human-hypertrophic-scar-tissue-and-matched-normal-skin-for-identification-of-endogenous-peptides-involved-in-scar-pathology
#20
Jingyun Li, Ling Chen, Qian Li, Jing Cao, Yanli Gao, Jun Li
Endogenous peptides recently attract increasing attention for their participation in various biological processes. Their roles in the pathogenesis of human hypertrophic scar remains poorly understood. In this study, we used liquid chromatography-tandem mass spectrometry to construct a comparative peptidomic profiling between human hypertrophic scar tissue and matched normal skin. A total of 179 peptides were significantly differentially expressed in human hypertrophic scar tissue, with 95 upregulated and 84 downregulated peptides between hypertrophic scar tissue and matched normal skin...
December 15, 2017: Journal of Cellular Physiology
keyword
keyword
116090
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"