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Ribosome profiling

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https://www.readbyqxmd.com/read/28441930/ribosomal-subunit-protein-typing-using-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-for-the-identification-and-discrimination-of-aspergillus-species
#1
Sayaka Nakamura, Hiroaki Sato, Reiko Tanaka, Yoko Kusuya, Hiroki Takahashi, Takashi Yaguchi
BACKGROUND: Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species...
April 26, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28437732/weaving-through-a-cryptic-species-comparing-the-neotropical-ants-camponotus-senex-and-camponotus-textor-hymenoptera-formicidae
#2
Eduardo Gonçalves Paterson Fox, Daniel Russ Solis, Cristiano Lazoski, William Mackay
Camponotus senex (Fr. Smith 1858) and Camponotus textor Forel, 1899 are commonly confused species in the New World tropics. We provide morphological characteristics based on the larvae and adults, behavioural differences, together with evidence from molecular markers (cuticular hydrocarbon profiles, venom differences, nuclear ribosomal ITS-1, and mtDNA COI sequence comparisons) to separate the two species, demonstrating they are not immediately closely related. In conclusion we suggest new reliable morphological characters which can benefit from deeper phenetic analysis, and support the contextual usefulness of non-morphological tools in resolving sibling ant species...
April 3, 2017: Micron: the International Research and Review Journal for Microscopy
https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#3
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28427860/differential-mtor-pathway-profiles-in-bladder-cancer-cell-line-subtypes-to-predict-sensitivity-to-mtor-inhibition
#4
Andrew M Hau, Manando Nakasaki, Kazufumi Nakashima, Goutam Krish, Donna E Hansel
BACKGROUND: Molecular classification of bladder cancer has been increasingly proposed as a potential tool to predict clinical outcomes and responses to chemotherapy. Here we focused on mechanistic target of rapamycin (mTOR) inhibition as a chemotherapeutic strategy and characterized the expression profile of mTOR signaling targets in representative bladder cancer cell lines from basal, luminal, and either basal/luminal ("non-type") molecular subtypes. MATERIALS AND METHODS: Protein and mRNA expression of mTOR signaling components from representative luminal (RT4 and RT112), basal (SCaBER and 5637), and nontype (T24 and J82) bladder cancer cell line subtypes were determined by Western blot and database mining analysis of the Cancer Cell Line Encyclopedia...
April 18, 2017: Urologic Oncology
https://www.readbyqxmd.com/read/28423326/rapid-molecular-profiling-of-defined-cell-types-using-viral-trap
#5
Alexander R Nectow, Maria V Moya, Mats I Ekstrand, Awni Mousa, Kelly L McGuire, Caroline E Sferrazza, Bianca C Field, Gabrielle S Rabinowitz, Kirsty Sawicka, Yupu Liang, Jeffrey M Friedman, Nathaniel Heintz, Eric F Schmidt
Translational profiling methodologies enable the systematic characterization of cell types in complex tissues, such as the mammalian brain, where neuronal isolation is exceptionally difficult. Here, we report a versatile strategy for profiling CNS cell types in a spatiotemporally restricted fashion by engineering a Cre-dependent adeno-associated virus expressing an EGFP-tagged ribosomal protein (AAV-FLEX-EGFPL10a) to access translating mRNAs by translating ribosome affinity purification (TRAP). We demonstrate the utility of this AAV to target a variety of genetically and anatomically defined neural populations expressing Cre recombinase and illustrate the ability of this viral TRAP (vTRAP) approach to recapitulate the molecular profiles obtained by bacTRAP in corticothalamic neurons across multiple serotypes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#6
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#7
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28418253/species-level-discrimination-of-psychrotrophic-pathogenic-and-spoilage-gram-negative-raw-milk-isolates-using-a-combined-maldi-tof-ms-proteomics-bioinformatics-based-approach
#8
Nuwan R Vithanage, Thomas Richard Yeager, Jeevana Bhongir, Snehal R Jadhav, Chaminda Senaka Ranadheera, Enzo A Palombo, Nivedita Datta
Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as post-processing contaminants in pasteurised milk. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however may require optimisation for identification of pathogenic and spoilage bacteria in milk and dairy products...
April 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28412308/genistein-prevention-of-hyperglycemia-and-improvement-of-glucose-tolerance-in-adult-non-obese-diabetic-mice-are-associated-with-alterations-of-gut-microbiome-and-immune-homeostasis
#9
Guannan Huang, Joella Xu, Daniel E Lefever, Travis C Glenn, Tamas Nagy, Tai L Guo
Although studies have linked soy phytoestrogen 4,7,4-trihydroxyisoflavone genistein (GEN) to reduced type 1 diabetes (T1D) risk, the mechanism of dietary GEN on T1D remains unknown. In our studies, adult non-obese diabetic (NOD) mouse model was employed to investigate the effects of GEN exposure on blood glucose level (BGL), glucose tolerance, gut microbiome, and immune responses. Adult male and female NOD mice were fed with either soy-based or casein-based diet, and received GEN at 20mg/kg body weight by gavage daily...
April 12, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28410879/determination-of-reference-genes-that-are-independent-of-feeding-rhythms-for-circadian-studies-of-mouse-metabolic-tissues
#10
Reiko Nakao, Hiroki Okauchi, Chiaki Hashimoto, Naoyuki Wada, Katsutaka Oishi
Real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis is a popular method for the measurement of mRNA expression level and is a critical tool for basic research. The identification of suitable reference genes that are stable and not affected by experimental conditions is a critical step in the accurate normalization of RT-PCR. On the other hand, the levels of numerous transcripts exhibit circadian oscillation in various peripheral tissues and it is thought to be regulated by feeding rhythms in addition to the molecular circadian clock...
April 5, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28409998/suitability-of-various-dna-extraction-methods-for-a-traditional-chinese-paocai-system
#11
Nan Zhao, Jialiang Cai, Chuchu Zhang, Zhuang Guo, Wenwei Lu, Bo Yang, Feng-Wei Tian, Xiao-Ming Liu, Hao Zhang, Wei Chen
Traditional paocai brine (PB), which is continuously propagated by back-slopping and contains various species of lactic acid bacteria (LAB), is critical for the flavor of paocai. Culture-independent approaches are commonly used to investigate the microbial communities of fermented food. To evaluate the influence of different DNA (DNA) extraction methods on estimates of bacterial community profiles from 4 PBs, the lysis efficiency, DNA yield, purity and denaturing gradient gel electrophoresis (DGGE) profiles of V3 region of a 16S ribosomal ribonucleic acid gene were acquired...
April 14, 2017: Bioengineered
https://www.readbyqxmd.com/read/28406973/tre5-a-retrotransposition-profiling-reveals-putative-rna-polymerase-iii-transcription-complex-binding-sites-on-the-dictyostelium-extrachromosomal-rdna-element
#12
Thomas Spaller, Marco Groth, Gernot Glöckner, Thomas Winckler
The amoeba Dictyostelium discoideum has a haploid genome in which two thirds of the DNA encodes proteins. Consequently, the space available for selfish mobile elements to expand without excess damage to the host genome is limited. The non-long terminal repeat retrotransposon TRE5-A maintains an active population in the D. discoideum genome and apparently adapted to this gene-dense environment by targeting positions ~47 bp upstream of tRNA genes that are devoid of protein-coding regions. Because only ~24% of tRNA genes are associated with a TRE5-A element in the reference genome, we evaluated whether TRE5-A retrotransposition is limited to this subset of tRNA genes...
2017: PloS One
https://www.readbyqxmd.com/read/28402863/biotagging-of-specific-cell-populations-in-zebrafish-reveals-gene-regulatory-logic-encoded-in-the-nuclear-transcriptome
#13
Le A Trinh, Vanessa Chong-Morrison, Daria Gavriouchkina, Tatiana Hochgreb-Hägele, Upeka Senanayake, Scott E Fraser, Tatjana Sauka-Spengler
Interrogation of gene regulatory circuits in complex organisms requires precise tools for the selection of individual cell types and robust methods for biochemical profiling of target proteins. We have developed a versatile, tissue-specific binary in vivo biotinylation system in zebrafish termed biotagging that uses genetically encoded components to biotinylate target proteins, enabling in-depth genome-wide analyses of their molecular interactions. Using tissue-specific drivers and cell-compartment-specific effector lines, we demonstrate the specificity of the biotagging toolkit at the biochemical, cellular, and transcriptional levels...
April 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28400776/translation-and-co-translational-membrane-engagement-of-plastid-encoded-chlorophyll-binding-proteins-are-not-influenced-by-chlorophyll-availability-in-maize
#14
Reimo Zoschke, Prakitchai Chotewutmontri, Alice Barkan
Chlorophyll is an indispensable constituent of the photosynthetic machinery in green organisms. Bound by apoproteins of photosystems I and II, chlorophyll performs light-harvesting and charge separation. Due to the phototoxic nature of free chlorophyll and its precursors, chlorophyll synthesis is regulated to comply with the availability of nascent chlorophyll-binding apoproteins. Conversely, the synthesis and co-translational insertion of such proteins into the thylakoid membrane have been suggested to be influenced by chlorophyll availability...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28395173/particular-phosphorylation-of-pi3k-akt-on-thr308-via-pdk-1-and-pten-mediates-melatonin-s-neuroprotective-activity-after-focal-cerebral-ischemia-in-mice
#15
Ulkan Kilic, Ahmet Burak Caglayan, Mustafa Caglar Beker, Mehmet Yalcin Gunal, Berrak Caglayan, Esra Yalcin, Taha Kelestemur, Reyhan Zeynep Gundogdu, Burak Yulug, Bayram Yılmaz, Bilal Ersen Kerman, Ertugrul Kilic
Apart from its potent antioxidant property, recent studies have revealed that melatonin promotes PI3K/Akt phosphorylation following focal cerebral ischemia (FCI) in mice. However, it is not clear (i) whether increased PI3K/Akt phosphorylation is a concomitant event or it directly contributes to melatonin's neuroprotective effect, and (ii) how melatonin regulates PI3K/Akt signaling pathway after FCI. In this study, we showed that Akt was intensively phosphorylated at the Thr308 activation loop as compared with Ser473 by melatonin after FCI...
April 5, 2017: Redox Biology
https://www.readbyqxmd.com/read/28392784/structure-and-function-of-the-fecal-microbiota-in-diarrheic-neonatal-piglets
#16
Qiaoli Yang, Xiaoyu Huang, Shengguo Zhao, Wenyang Sun, Zunqiang Yan, Pengfei Wang, Shenggui Li, Wangzhou Huang, Shengwei Zhang, Lixia Liu, Shuangbao Gun
Diarrhea is a leading cause of increased mortality in neonatal and young piglets. Aberration of the gut microbiota is one important factor in the etiology of piglet diarrhea. However, information regarding the structure and function of the gut microbiome in diarrheic neonatal piglets is limited. To investigate the composition and functional potential of the fecal microbiota in neonatal piglets, we performed 16S rRNA gene sequencing on 20 fecal samples from diarrheic piglets and healthy controls, and metagenomics sequencing on a subset of six samples...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28392174/eif5a-functions-globally-in-translation-elongation-and-termination
#17
Anthony P Schuller, Colin Chih-Chien Wu, Thomas E Dever, Allen R Buskirk, Rachel Green
The eukaryotic translation factor eIF5A, originally identified as an initiation factor, was later shown to promote translation elongation of iterated proline sequences. Using a combination of ribosome profiling and in vitro biochemistry, we report a much broader role for eIF5A in elongation and uncover a critical function for eIF5A in termination. Ribosome profiling of an eIF5A-depleted strain reveals a global elongation defect, with abundant ribosomes stalling at many sequences, not limited to proline stretches...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28390868/small-nucleolar-noncoding-rna-snora23-upregulated-in-human-pancreatic-ductal-adenocarcinoma-regulates-expression-of-syne2-to-promote-growth-and-metastasis-of-xenograft-tumors-in-mice
#18
Lin Cui, Kenji Nakano, Sumalee Obchoei, Kiyoko Setoguchi, Masaki Matsumoto, Tsuyoshi Yamamoto, Satoshi Obika, Kazuaki Shimada, Nobuyoshi Hiraoka
BACKGROUND & AIMS: Small nucleolar noncoding RNAs (snoRNAs) regulate function of ribosomes, and specific snoRNAs are dysregulated in some cancer cells. We investigated dysregulation of snoRNAs in pancreatic ductal adenocarcinoma (PDAC) cells. METHODS: We investigated snoRNA expression in PDAC cell lines by cDNA microarray and quantitative reverse transcription (qRT)-PCR. In PDAC (n=133), intraductal papillary mucinous neoplasm (IPMN, n=16), mucinous cystic neoplasm-associated PDAC (n=1), and non-tumor pancreas (n=8) and liver (n=3) tissues from subjects who underwent surgical resection, levels of snoRNA were measured by qRT-PCR and compared with clinicopathological parameters and survival times determined by Kaplan Meier analysis...
April 5, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28386228/dynamic-expression-changes-in-the-transcriptome-of-the-prefrontal-cortex-after-repeated-exposure-to-cocaine-in-mice
#19
Mingzhen Li, Peng Xu, Yanhua Xu, Huajing Teng, Weiping Tian, Quansheng Du, Mei Zhao
Prefrontal cortex (PFC)-dependent functions, such as executive function, explicit learning, and memory, are negatively affected in cocaine abusers and experimental animal models of cocaine treatment. However, its molecular mechanisms are less understood. In the present study, we performed transcriptome profiling of the dynamic changes in the PFC after repeated cocaine administration in mice. We found 463, 14, and 535 differentially expressed genes (DEGs) at 2 h, 24 h, and 7 days, respectively, after the withdrawal of chronic cocaine treatment...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28383283/global-analysis-of-gene-expression-reveals-mrna-superinduction-is-required-for-the-inducible-immune-response-to-a-bacterial-pathogen
#20
Kevin C Barry, Nicholas T Ingolia, Russell E Vance
The inducible innate immune response to infection requires a concerted process of gene expression that is regulated at multiple levels. Most global analyses of the innate immune response have focused on transcription induced by defined immunostimulatory ligands, such as lipopolysaccharide. However, the response to pathogens involves additional complexity, as pathogens interfere with virtually every step of gene expression. How cells respond to pathogen-mediated disruption of gene expression to nevertheless initiate protective responses remains unclear...
April 6, 2017: ELife
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