keyword
MENU ▼
Read by QxMD icon Read
search

Genome analysis

keyword
https://www.readbyqxmd.com/read/29236385/lipoxygenases-and-their-metabolites-in-formation-of-plant-stress-tolerance
#1
L M Babenko, M M Shcherbatiuk, T D Skaterna, I V Kosakivska
The review focuses on the analysis of new information concerning molecular enzymology of lipoxygenases – proteins involved in lipid peroxidation and found in animals and plants. Modern concept of structural features, catalytic characteristics and functions of lipoxygenase family enzymes as well as products of their catalytic activity in plants have been discussed and summarized. Issues of enzyme localization in plant cells and tissues, evolution and distribution of lipoxygenases, involvement in production of signaling substances involved in formation of adaptation response to abiotic and biotic stress factors and in regulation of lipoxygenase signal system activity are highlighted...
January 2017: Ukrainian Biochemical Journal
https://www.readbyqxmd.com/read/29236255/identifying-mirna-targets-using-ago-ripseq
#2
Rebecca Petri, Johan Jakobsson
microRNAs (miRNA) are small, noncoding RNAs that bind to messenger RNAs (mRNAs) and regulate their activity. They are, therefore, important posttranscriptional regulators. In recent years it has become clear that miRNAs regulate large genetic networks, rather than single genes, and that one gene can be targeted by several miRNAs. To understand the role of miRNAs in cells or tissues, it is therefore important to analyze the targetome of miRNAs. Here, we present a technique called Argonaute-RNA Immunoprecipitation (AGO-RIP) which takes advantages of the fact that miRNAs and their targets are directly bound by the Argonaute protein family...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236249/metabolic-labeling-of-newly-synthesized-rna-with-4su-to-in-parallel-assess-rna-transcription-and-decay
#3
Wei Sun, Wei Chen
The development of genome-wide RNA profiling technologies greatly facilitates the global analysis of gene expression. However, such technologies alone could not distinguish the contribution to cellular RNA abundance by transcription versus decay. To overcome such limitation, metabolic labeling of newly synthesized RNA with 4-thiouridine (4sU) combined with genome-wide RNA profiling was used to in parallel measure RNA transcription and decay. Here, we describe the detailed protocol for using metabolic labeling with 4sU to separate newly synthesized RNA from the preexisting RNA in mammalian cells...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236247/5-bromouridine-ip-chase-bric-seq-to-determine-rna-half-lives
#4
Toshimichi Yamada, Naoto Imamachi, Rena Onoguchi-Mizutani, Katsutoshi Imamura, Yutaka Suzuki, Nobuyoshi Akimitsu
Analysis of RNA stability at genome-wide level is an advanced method in RNA biology that examines the half-life of each transcript. In particular, a pulse-labeling method using uridine analogs enables the determination of half-life of each transcript under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromouridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236233/thauera-sinica-sp-nov-a-phenol-derivative-degrading-bacterium-isolated-from-activated-sludge
#5
Nenghu Qiao, Lijun Xi, Jingjing Zhang, Dejian Liu, Baosheng Ge, Jianguo Liu
A bacterial strain, K11T, capable of degrading phenol derivatives was isolated from activated sludge of a sewage treatment plant in China. This strain, which can degrade more than ten phenol derivatives, was identified as a Gram-stain negative, rod-shaped, asporogenous, facultative anaerobic bacterium with a polar flagellum. The strain was found to grow in tryptic soy broth in the presence of 0-2.5% (w/v) NaCl (optimum 0-1%), at 4-43 °C (optimum 30-35 °C) and pH 4.5-10.5 (optimum 7.5-8). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that this strain belongs to the genus Thauera...
December 13, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#6
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29236091/noncoding-copy-number-variations-are-associated-with-congenital-limb-malformation
#7
Ricarda Flöttmann, Bjørt K Kragesteen, Sinje Geuer, Magdalena Socha, Lila Allou, Anna Sowińska-Seidler, Laure Bosquillon de Jarcy, Johannes Wagner, Aleksander Jamsheer, Barbara Oehl-Jaschkowitz, Lars Wittler, Deepthi de Silva, Ingo Kurth, Idit Maya, Fernando Santos-Simarro, Wiebke Hülsemann, Eva Klopocki, Roger Mountford, Alan Fryer, Guntram Borck, Denise Horn, Pablo Lapunzina, Meredith Wilson, Bénédicte Mascrez, Denis Duboule, Stefan Mundlos, Malte Spielmann
PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing...
October 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29235981/paenibacillus-limicola-sp-nov-isolated-from-tidal-flat-sediment
#8
Shamsun Nahar, Chang-Jun Cha
An aerobic, Gram-staining-variable, rod-shaped, endospore-forming and motile bacterial strain, designated CJ6T, was isolated from a tidal flat on Ganghwa Island, South Korea. The isolate was characterized based on a polyphasic taxonomy approach. Strain CJ6T grew optimally on R2A agar media at 30 °C and pH 7. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ6T belonged to the genus Paenibacillus, displaying the highest sequence similarity to Paenibacillus vulneris CCUG 53270T (97...
December 13, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29235576/the-unfolded-protein-response-impacts-melanoma-progression-by-enhancing-fgf-expression-and-can-be-antagonized-by-a-chemical-chaperone
#9
Karin Eigner, Yüksel Filik, Florian Mark, Birgit Schütz, Günter Klambauer, Richard Moriggl, Markus Hengstschläger, Herbert Stangl, Mario Mikula, Clemens Röhrl
The mechanisms hallmarking melanoma progression are insufficiently understood. Here we studied the impact of the unfolded protein response (UPR) - a signalling cascade playing ambiguous roles in carcinogenesis - in melanoma malignancy. We identified isogenic patient-derived melanoma cell lines harboring BRAFV600E-mutations as a model system to study the role of intrinsic UPR in melanoma progression. We show that the activity of the three effector pathways of the UPR (ATF6, PERK and IRE1) was increased in metastatic compared to non-metastatic cells...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235508/genetic-adaptation-of-microbial-populations-present-in-high-intensity-catfish-production-systems-with-therapeutic-oxytetracycline-treatment
#10
Qifan Zeng, Xiangli Tian, Luxin Wang
Microbial communities that are present in aquaculture production systems play significant roles in degrading organic matter, controlling diseases, and formation of antibiotic resistance. It is important to understand the diversity and abundance of microbial communities and their genetic adaptations associated with environmental physical and chemical changes. Here we collected water and sediment samples from a high-intensity catfish production system and its original water reservoir. The metagenomic analysis showed that Proteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes were the top five phyla identified from all samples...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#11
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29235454/a-large-multi-ethnic-genome-wide-association-study-identifies-novel-genetic-loci-for-intraocular-pressure
#12
Hélène Choquet, Khanh K Thai, Jie Yin, Thomas J Hoffmann, Mark N Kvale, Yambazi Banda, Catherine Schaefer, Neil Risch, K Saidas Nair, Ronald Melles, Eric Jorgenson
Elevated intraocular pressure (IOP) is a major risk factor for glaucoma, a leading cause of blindness. IOP heritability has been estimated to up to 67%, and to date only 11 IOP loci have been reported, accounting for 1.5% of IOP variability. Here, we conduct a genome-wide association study of IOP in 69,756 untreated individuals of European, Latino, Asian, and African ancestry. Multiple longitudinal IOP measurements were collected through electronic health records and, in total, 356,987 measurements were included...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29234908/characterization-of-type-iv-antifreeze-gene-in-nile-tilapia-oreochromis-niloticus-and-influence-of-cold-and-hot-weather-on-its-expression-and-some-immune-related-genes
#13
Asmma Y Ammar, Abeer F El Nahas, Shawky Mahmoud, Mohamed E Barakat, Asmaa M Hassan
The aim of this work is to study the effect of the thermal stress of ambient temperature during winter and summer on the expression of type IV antifreeze gene (ANF IV) in different tissues of Nile tilapia (Oreochromis niloticus) as well as some immune-related genes. At first, genomic ANF IV gene was characterized from one fish; 124 amino acids were identified with 92.7% similarity with that on the gene bank. Expression of ANF IV and immune-related genes were done twice, once at the end of December (winter sample, temperature 14 °C) and the other at August (summer sample, temperature 36 °C)...
December 12, 2017: Fish Physiology and Biochemistry
https://www.readbyqxmd.com/read/29234904/post-genomics-era-for-orchid-research
#14
REVIEW
Wen-Chieh Tsai, Anne Dievart, Chia-Chi Hsu, Yu-Yun Hsiao, Shang-Yi Chiou, Hsin Huang, Hong-Hwa Chen
Among 300,000 species in angiosperms, Orchidaceae containing 30,000 species is one of the largest families. Almost every habitats on earth have orchid plants successfully colonized, and it indicates that orchids are among the plants with significant ecological and evolutionary importance. So far, four orchid genomes have been sequenced, including Phalaenopsis equestris, Dendrobium catenatum, Dendrobium officinale, and Apostaceae shengen. Here, we review the current progress and the direction of orchid research in the post genomics era...
December 12, 2017: Botanical Studies (Taipei, Taiwan)
https://www.readbyqxmd.com/read/29234880/reorganization-of-wheat-and-rye-genomes-in-octoploid-triticale-%C3%A3-%C3%A2-triticosecale
#15
Anna Kalinka, Magdalena Achrem
The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes...
December 12, 2017: Planta
https://www.readbyqxmd.com/read/29234412/genome-wide-profiling-reveals-that-herbal-medicine-jinfukang-induced-polyadenylation-alteration-is-involved-in-anti-lung-cancer-activity
#16
Yao Kou, Guoqing Li, Jinhui Shao, Cong Liu, Jun Wu, Jun Lu, Xiaodong Zhao, Jing Tian
Alternative polyadenylation (APA) plays an important role in regulation of genes expression and is involved in many biological processes. As eukaryotic cells receive a variety of external signals, genes produce diverse transcriptional isoforms and exhibit different translation efficiency. The traditional Chinese medicine (TCM) Jinfukang (JFK) has been effectively used for lung cancer treatment. In this study, we investigated whether JFK exerts its antitumor effect by modulating APA patterns in lung cancer cells...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/29234350/genetic-diversity-and-connectivity-in-maurolicus-muelleri-in-the-bay-of-biscay-inferred-from-thousands-of-snp-markers
#17
Naiara Rodriguez-Ezpeleta, Paula Álvarez, Xabier Irigoien
Mesopelagic fish are largely abundant poorly studied fish that are still intact, but which, due to their potentially great added value, will be imminently exploited by humans. Therefore, studies that provide information to anticipate the anthropogenic impact on this important resource are urgently needed. In particular, knowledge about their connectivity, potential adaptation and resilience are needed. This information can be obtained through the analysis of genome-wide markers which are now relatively easily and cost-efficiently discovered thanks to high-throughput sequencing technologies...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29234336/evolution-and-expansion-of-the-prokaryote-like-lipoxygenase-family-in-the-brown-alga-saccharina-japonica
#18
Linhong Teng, Wentao Han, Xiao Fan, Dong Xu, Xiaowen Zhang, Simon M Dittami, Naihao Ye
Lipoxygenase (LOX) plays important roles in fatty acid oxidation and lipid mediator biosynthesis. In this study, we give first insights into brown algal LOX evolution. Whole genome searches revealed four, three, and eleven LOXs in Ectocarpus siliculosus, Cladosiphon okamuranus, and Saccharina japonica, respectively. In phylogenetic analyses, LOXs from brown algae form a robust clade with those from prokaryotes, suggesting an ancestral origin and slow evolution. Brown algal LOXs were divided into two clades, C1 and C2 in a phylogenetic tree...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234333/putative-microsatellite-dna-marker-based-wheat-genomic-resource-for-varietal-improvement-and-management
#19
Sarika Jaiswal, Sonia Sheoran, Vasu Arora, Ulavappa B Angadi, Mir A Iquebal, Nishu Raghav, Bharti Aneja, Deepender Kumar, Rajender Singh, Pradeep Sharma, G P Singh, Anil Rai, Ratan Tiwari, Dinesh Kumar
Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29234331/rna-seq-profiling-shows-divergent-gene-expression-patterns-in-arabidopsis-grown-under-different-densities
#20
Di Guo, Xiaoming Song, Min Yuan, Zhenyi Wang, Weina Ge, Li Wang, Jinpeng Wang, Xiyin Wang
Plants growing under high-density (HD) conditions experience increased competition for water, nutrients, and light, possibly leading to changes in size, biomass, morphology, and productivity. However, no research has focused on the relationship between whole-genome expression patterns and growth density. Here, we performed whole-genome RNA sequencing to examine the gene expression patterns in Arabidopsis grown under low and high densities. Of the 20,660 detected genes, the expression levels of 98 were enhanced and 107 were repressed under HD growth...
2017: Frontiers in Plant Science
keyword
keyword
16873
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"