Read by QxMD icon Read


Yanwei Xing, Zhiwei Zhao, Yuekun Zhu, Liangliang Zhao, Anlong Zhu, Daxun Piao
The objective of this study was to identify potentially significant genes and long non-coding RNAs (lncRNAs) in colon cancer for a panel of lncRNA signatures that could be used as prognostic markers for colon adenocarcinoma (COAD) based on the data from The Cancer Genome Atlas (TCGA). RNA-seq V2 exon data of COAD were downloaded from the TCGA data portal for 285 tumor samples and 41 normal tissue samples adjacent to tumors. Differentially expressed mRNAs and lncRNAs were identified. A functional enrichment analysis of differentially expressed mRNAs was performed, followed by protein-protein interaction (PPI) network construction and significant module selection...
May 2018: Oncology Reports
Wenhui Jiang, Tianxiang Liu, Wenzhi Nan, Diddugodage Chamila Jeewani, Yanlu Niu, Chunlian Li, Yong Wang, Xue Shi, Cong Wang, Jiahuan Wang, Yang Li, Xin Gao, Zhonghua Wang
The purple pericarp of bread wheat (Triticum aestivum L.) is a useful source of dietary anthocyanins. Previous mapping results indicated that the purple pericarp is controlled by two complementary genes located on chromosomes 7D and 2A. However, the related genes and their effects on regulating the purple pericarp are unknown. In this study, two transcription factors were characterised as anthocyanin activators in purple pericarp: TaPpm1 (purple pericarp-MYB 1) and TaPpb1 (purple pericarp-bHLH 1). Three nonfunctional variants were detected in the coding sequence of TaPpm1 from non-purple seed lines, in which the function of TaPpm1 was destroyed by insertion-caused frame shift or truncated peptides...
March 17, 2018: Journal of Experimental Botany
Yuan Sun, Hong-Hong Guo, Dan-Dan Guo, Xia-Yun Jiang, Shu-Ming Zou
The proteins CITED belong to a family of non-DNA-binding transcriptional co-regulators involved in the regulation of various transcriptional responses. Previous studies suggest that members of CITED family may function in response to hypoxia in mammals. however, the molecular and functional information on CITED genes in aquaculture fish is unclear. Here, we characterized and examined the transcriptional patterns of CITED1 and CITED2 genes in the hypoxia-sensitive blunt snout bream ( Megalobrama amblycephala )...
2018: Frontiers in Physiology
Alyssa K Carlson, Rachel A Rawle, Erik Adams, Mark C Greenwood, Brian Bothner, Ronald K June
Osteoarthritis affects over 250 million individuals worldwide. Currently, there are no options for early diagnosis of osteoarthritis, demonstrating the need for biomarker discovery. To find biomarkers of osteoarthritis in human synovial fluid, we used high performance liquid-chromatography mass spectrometry for global metabolomic profiling. Metabolites were extracted from human osteoarthritic (n = 5), rheumatoid arthritic (n = 3), and healthy (n = 5) synovial fluid, and a total of 1233 metabolites were detected...
March 15, 2018: Biochemical and Biophysical Research Communications
Davar Abedini, Sajad Rashidi Monfared
A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments...
March 17, 2018: Molecular Biology Reports
Kumar Parijat Tripathi, Marina Piccirillo, Mario Rosario Guarracino
BACKGROUND: The endomembrane system, known as secretory pathway, is responsible for the synthesis and transport of protein molecules in cells. Therefore, genes involved in the secretory pathway are essential for the cellular development and function. Recent scientific investigations show that ER and Golgi apparatus may provide a convenient drug target for cancer therapy. On the other hand, it is known that abundantly expressed genes in different cellular organelles share interconnected pathways and co-regulate each other activities...
March 8, 2018: BMC Bioinformatics
Anna Maikova, Johann Peltier, Pierre Boudry, Eliane Hajnsdorf, Nicolas Kint, Marc Monot, Isabelle Poquet, Isabelle Martin-Verstraete, Bruno Dupuy, Olga Soutourina
Clostridium difficile, a major human enteropathogen, must cope with foreign DNA invaders and multiple stress factors inside the host. We have recently provided an experimental evidence of defensive function of the C. difficile CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system important for its survival within phage-rich gut communities. Here, we describe the identification of type I toxin-antitoxin (TA) systems with the first functional antisense RNAs in this pathogen...
February 26, 2018: Nucleic Acids Research
Marcelo Bueno Batista, Govind Chandra, Rose Adele Monteiro, Emanuel Maltempi de Souza, Ray Dixon
Bacteria adjust the composition of their electron transport chain (ETC) to efficiently adapt to oxygen gradients. This involves differential expression of various ETC components to optimize energy generation. In Herbaspirillum seropedicae, reprogramming of gene expression in response to oxygen availability is controlled at the transcriptional level by three Fnr orthologs. Here, we characterised Fnr regulons using a combination of RNA-Seq and ChIP-Seq analysis. We found that Fnr1 and Fnr3 directly regulate discrete groups of promoters (Groups I and II, respectively), and that a third group (Group III) is co-regulated by both transcription factors...
February 26, 2018: Nucleic Acids Research
Gunng-Shinng Chen, Shiao-Pieng Lee, Shu-Fu Huang, Shih-Chi Chao, Chung-Yi Chang, Gwo-Jang Wu, Chung-Hsing Li, Shih-Hurng Loh
OBJECTIVE: Homeostasis of intracellular pH (pHi ) plays vital roles in many cell functions, such as proliferation, apoptosis, differentiation and metastasis. Thus far, Na+ -H+ exchanger (NHE), Na+ -HCO3 - co-transporter (NBC), Cl- /HCO3 - exchanger (AE) and Cl- /OH- exchanger (CHE) have been identified to co-regulate pHi homeostasis. However, functional and biological pHi -regulators in human dental pulp stem cells (hDPSCs) have yet to be identified. DESIGN: Microspectrofluorimetry technique with pH-sensitive fluorescent dye, BCECF, was used to detect pHi changes...
March 6, 2018: Archives of Oral Biology
Jiaojiao Hou, Yuan Li, Xüxia Ren, Fei Gao, Yuqin Chen, Yaoxing Yi, Lili Kang, Yürui Luo, Mei Yang
Aquaporin-9 (AQP9) is an aquaglyceroporin that biophysically conducts water, glycerol, and other small solutes. AQP9 is expressed in hepatocytes on the sinusoidal surfaces of hepatocyte plates in the liver, where it is considered responsible for the glycerol uptake in gluconeogenesis. However, limited information is available on the expression and regulating mechanism of AQP9 in different hyperglycemia models. Thus, this study examined the expression patterns of AQP9 and mitogen-activated protein kinase (MAPK) in Types 1 and 2 diabetes mellitus (DM) to clarify the roles and regulating mechanism of AQP9 in gluconeogenesis...
March 9, 2018: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
Laura E Pascal, Yao Wang, Mingming Zhong, Dan Wang, Anish Bhaswanth Chakka, Zhenyu Yang, Feng Li, Qiong Song, Lora H Rigatti, Srilakshmi Chaparala, Uma Chandran, Anil V Parwani, Zhou Wang
The tumor suppressor genes EAF2 and p53 are frequently dysregulated in prostate cancers. Recently, we reported that concurrent p53 nuclear staining and EAF2 downregulation were associated with high Gleason score. Combined loss of EAF2 and p53 in a murine model induced prostate tumors, and concurrent knockdown of EAF2 and p53 in prostate cancer cells enhanced proliferation and migration, further suggesting that EAF2 and p53 could functionally interact in the suppression of prostate tumorigenesis. Here, RNA-seq analyses identified differentially regulated genes in response to concurrent knockdown of p53 and EAF2...
March 5, 2018: Neoplasia: An International Journal for Oncology Research
Jingshu Xu, Stephanie J Church, Stefano Patassini, Paul Begley, Katherine A B Kellett, Emma R L C Vardy, Richard D Unwin, Nigel M Hooper, Garth J S Cooper
Sporadic Alzheimer's disease (AD) is a neurodegenerative disorder that causes the most prevalent form of age-related dementia but its pathogenesis remains obscure. Altered regulation of metals, particularly pan-cerebral copper deficiency, and more regionally-localized perturbation of other metals, are prominent in AD brain although data on how these CNS perturbations are reflected in the peripheral bloodstream are inconsistent to date. To assess the potential use of metal dysregulation to generate biomarkers in AD, we performed a case-control study of seven essential metals and selenium, measured by inductively coupled plasma mass-spectrometry, in samples from AD and matched control cases...
March 7, 2018: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
Paja Sijacic, Marko Bajic, Elizabeth C McKinney, Richard B Meagher, Roger B Deal
Cell differentiation is driven by changes in transcription factor (TF) activity and subsequent alterations in transcription. To study this process, differences in TF binding between cell types can be deduced by probing chromatin accessibility. We used cell type-specific nuclei purification followed by the Assay for Transposase Accessible Chromatin (ATAC-seq) to delineate differences in chromatin accessibility and TF regulatory networks between stem cells of the shoot apical meristem (SAM) and differentiated leaf mesophyll cells in Arabidopsis thaliana...
March 7, 2018: Plant Journal: for Cell and Molecular Biology
Qin Yang, Qi Wan, Letian Zhang, Yibo Li, Pei Zhang, Dong Li, Chao Feng, Fan Yi, Liangren Zhang, Xianfeng Ding, Hua Li, Quan Du
Lineage-specific cell differentiation is a precise and coordinated biological process. To explore the roles of long noncoding RNA (lncRNA) in this process, the expression of polyA-minus RNAs was comparatively studied during the course of myocyte and adipocyte differentiation. In addition to identifying thousands of novel lncRNAs, distinct lncRNA profiles were revealed during lineage-specific differentiation, showing their active involvement in this process. This study further found that lncRNAs were organized in clusters and are co-regulated, constituting transcription open domains (TODs)...
March 6, 2018: RNA Biology
Marc Santolini, Milagros C Romay, Clara L Yukhtman, Christoph D Rau, Shuxun Ren, Jeffrey J Saucerman, Jessica J Wang, James N Weiss, Yibin Wang, Aldons J Lusis, Alain Karma
A traditional approach to investigate the genetic basis of complex diseases is to identify genes with a global change in expression between diseased and healthy individuals. However, population heterogeneity may undermine the effort to uncover genes with significant but individual contribution to the spectrum of disease phenotypes within a population. Here we investigate individual changes of gene expression when inducing hypertrophy and heart failure in 100 + strains of genetically distinct mice from the Hybrid Mouse Diversity Panel (HMDP)...
2018: NPJ Systems Biology and Applications
Julieta M Acevedo, Bernhard Hoermann, Tilo Schlimbach, Aurelio A Teleman
The sequence context surrounding the AUG start codon of an open reading frame - the 'Kozak sequence' - affects the probability with which a scanning ribosome will recognize the start codon and start translating there. A significant number of transcripts in animals such as Drosophila contain weak Kozak sequences. This is predicted to cause constitutively low translation of these transcripts. We study here the additional possibility that these mRNAs have weak Kozak sequences to allow for the regulation of their translation in response to stress or altered cellular signaling...
March 5, 2018: Scientific Reports
Emilia Kuuluvainen, Eva Domènech-Moreno, Elina H Niemelä, Tomi P Mäkelä
In cancer, oncogene activation is partly mediated by acquired super-enhancers therefore representing potential targets for inhibition. Super-enhancers are enriched for BRD4 and Mediator and both BRD4 and the Mediator MED12 subunit are disproportionally required for expression of super-enhancer associated genes in stem cells. Here, we find that depletion of Mediator kinase module subunits MED12, and MED13 with MED13L, can be used to reduce expression of cancer acquired super-enhancer genes such as MYC in colon cancer cells with a concomitant decrease in proliferation...
March 5, 2018: Molecular and Cellular Biology
Jalal K Siddiqui, Elizabeth Baskin, Mingrui Liu, Carmen Z Cantemir-Stone, Bofei Zhang, Russell Bonneville, Joseph P McElroy, Kevin R Coombes, Ewy A Mathé
BACKGROUND: Integration of transcriptomic and metabolomic data improves functional interpretation of disease-related metabolomic phenotypes, and facilitates discovery of putative metabolite biomarkers and gene targets. For this reason, these data are increasingly collected in large (> 100 participants) cohorts, thereby driving a need for the development of user-friendly and open-source methods/tools for their integration. Of note, clinical/translational studies typically provide snapshot (e...
March 5, 2018: BMC Bioinformatics
Silvia Belluti, Valentina Semeghini, Valentina Basile, Giovanna Rigillo, Valentina Salsi, Filippo Genovese, Diletta Dolfini, Carol Imbriano
The heterotrimeric NF-Y complex is a pioneer factor that binds to CCAAT-genes and regulates their transcription. NF-Y cooperates with multiple transcription factors and co-regulators in order to positively or negatively influence gene transcription. The recruitment of NF-Y to CCAAT box is significantly enriched in cancer-associated gene promoters loci and positively correlates with malignancy. NF-Y subunits, in particular the DNA-binding subunit NF-YA and the histone-fold subunit NF-YC, appear overexpressed in specific types of cancer...
March 2, 2018: Biochimica et Biophysica Acta
Noelia Luna-Peláez, Mario García-Domínguez
During development, cellular differentiation programs need of tight regulation for proper display of the activity of multiple factors in time and space. Chromatin adaptors of the BET family (Brd2, Brd3, Brd4 and Brdt in vertebrates) are transcription co-regulators tightly associated with the progression of the cell cycle. A key question regarding their function is whether they work as part of the general transcription machinery or, on the contrary, they are precisely recruited to the chromatin through specific transcription factors...
March 2, 2018: Journal of Molecular Biology
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"