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Yipeng Wang, Liping Guo, Lin Feng, Wen Zhang, Ting Xiao, Xuebing Di, Guoji Chen, Kaitai Zhang
Circulating tumour cell (CTC) behaviours are distinct from those of bulk tissues. Thus, treatments to eliminate CTCs differ from the regimens followed to reduce the primary tumour and its metastases. Accordingly, comprehensively deciphering the single nucleotide variant (SNV) profiles in CTCs, which partially determine CTC behaviours, is a priority. Using viable CTCs isolated with the oHSV1‑hTERT‑GFP virus coupled with fluorescence‑activated cell sorting (FACS), the whole genome was amplified using the multiple annealing and looping‑based amplification cycle (MALBAC) method...
May 2018: Oncology Reports
Nicole Hoppman, Kandelaria Rumilla, Emily Lauer, Hutton Kearney, Erik Thorland
PurposeSingle-nucleotide polymorphism (SNP) microarrays can easily identify whole-chromosome isodisomy but are unable to detect whole-chromosome heterodisomy. However, most cases of uniparental disomy (UPD) involve combinations of heterodisomy and isodisomy, visualized on SNP microarrays as long continuous stretches of homozygosity (LCSH). LCSH raise suspicion for, but are not diagnostic of, UPD, and reporting necessitates confirmatory testing. The goal of this study was to define optimal LCSH reporting standards...
March 22, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Hyuck Jun Jung, Myoung Jin Ho, Sungwan Ahn, Young Taek Han, Myung Joo Kang
The oral bioavailability of entecavir (EV), an anti-viral agent commonly prescribed to treat hepatitis B infections, is drastically reduced under a post-prandial state. This is primarily due to its low permeability in the gastrointestinal tract. To reduce the food effect on the intestinal absorption of the nucleotide analogue, four lipidic prodrugs were synthesized via the esterification of the primary alcohol of EV with fatty acids (hexanoic acid, octanoic acid, decanoic acid, and dodecanoic acid). EV-3-dodecanoate (or EV-C12) exhibited high solubility in a fed state simulated intestinal fluid (78...
March 22, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Claire M Ouimet, Mohamed Dawod, James Grinias, Victoria A Assimon, Jean Lodge, Anna K Mapp, Jason E Gestwicki, Robert T Kennedy
Tools for measuring affinities and stoichiometries of protein-protein complexes are valuable for elucidating the role of protein-protein interactions (PPIs) in governing cell functions and screening for PPI modulators. Such measurements can be challenging because PPIs can span a wide range of affinities and include stoichiometries from dimers to high order oligomers. Also, most techniques require large amounts of protein which can hamper research for difficult to obtain proteins. Protein cross-linking capillary electrophoresis (PXCE) has the potential to directly measure PPIs and even resolve multiple PPIs while consuming attomole quantities...
March 22, 2018: Analyst
J Woo, J E Kim, J J Im, J Lee, H S Jeong, S Park, S-Y Jung, H An, S Yoon, S M Lim, S Lee, J Ma, E Y Shin, Y-E Han, B Kim, E H Lee, L Feng, H Chun, B-E Yoon, I Kang, S R Dager, I K Lyoo, C J Lee
The role of astrocytes in brain plasticity has not been extensively studied compared with that of neurons. Here we adopted integrative translational and reverse-translational approaches to explore the role of an astrocyte-specific major water channel in the brain, aquaporin-4 (AQP4), in brain plasticity and learning. We initially identified the most prevalent genetic variant of AQP4 (single nucleotide polymorphism of rs162008 with C or T variation, which has a minor allele frequency of 0.21) from a human database (n=60 706) and examined its functionality in modulating the expression level of AQP4 in an in vitro luciferase reporter assay...
April 2018: Molecular Psychiatry
Veronica Ortega, Christina Mendiola, Gopalrao V N Velagaleti
One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes...
2018: Methods in Molecular Biology
Rikke B Holmstrøm, Ditte V Mogensen, Jørn Brynskov, Mark A Ainsworth, Jacob Nersting, Kjeld Schmiegelow, Casper Steenholdt
BACKGROUND: Interactions between thiopurines and infliximab presumably contribute to superior effect of infliximab-thiopurine combination therapy in patients with inflammatory bowel disease (IBD). We examined whether principal cytotoxic thiopurine metabolites influence adalimumab (ADL) and anti-ADL antibodies (Abs). METHODS: Ninety-eight IBD patients previously treated with infliximab (96%) in whom trough ADL and anti-ADL Abs had been assessed as part of their clinical care were included...
March 21, 2018: Digestive Diseases and Sciences
Norman Goodacre, Aisha Aljanahi, Subhiksha Nandakumar, Mike Mikailov, Arifa S Khan
Detection of distantly related viruses by high-throughput sequencing (HTS) is bioinformatically challenging because of the lack of a public database containing all viral sequences, without abundant nonviral sequences, which can extend runtime and obscure viral hits. Our reference viral database (RVDB) includes all viral, virus-related, and virus-like nucleotide sequences (excluding bacterial viruses), regardless of length, and with overall reduced cellular sequences. Semantic selection criteria (SEM-I) were used to select viral sequences from GenBank, resulting in a first-generation viral database (VDB)...
March 2018: MSphere
Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R Waters
Plants have evolved a variety of mechanisms to respond and adapt to abiotic stress. High temperature stress induces the heat shock response. During the heat shock response a large number of genes are up-regulated, many of which code for chaperone proteins that prevent irreversible protein aggregation and cell death. However, it is clear that heat shock is not the only mechanism involved in the plant heat stress response. Alternative splicing (AS) is also important during heat stress since this post-transcriptional regulatory mechanism can produce significant transcriptome and proteome variation...
March 2018: AoB Plants
Miganoosh Simonian, Meysam Mosallayi, Maryam Miraghajani, Awat Feizi, Sharifeh Khosravi, Ahmad Reza Salehi, Deniz Mortazavi, Farideh Saberi, Rasoul Salehi
Aim: In present study we have elucidated the role of 2758 A>G (rs696), in the recognition site of miR449a in the 3' UTR of NFKB inhibitor alpha (NFKBIA) gene, in development of sporadic colorectal cancer. Background: Colorectal cancer (CRC) is rated as second cause of cancer death. Genetic determinants are considered as driving forces in development of sporadic CRC. Single nucleotide polymorphisms (SNPs), are attributed as the main genetic factor in cancers susceptibility...
2018: Gastroenterology and Hepatology From Bed to Bench
Maryam Karkhane, Seyed Reza Mohebbi, Pedram Azimzadeh, Hasti Avarandeh, Shabnam Kazemian, Afsaneh Sharifian, Behzad Hatami, Hamid Asadzadeh Aghdaei
Aim: Our goal was to identify the putative association of rs4072111 variant in IL-16 gene and HCV susceptibility in an Iranian population. Background: Interleukin 16 (IL-16), a multifunctional cytokine, plays a vital role in modulation of immune system. Methods: In present case control and cross sectional study, IL-16 gene variant in 300 patients with hepatitis C (HCV) infection and 300 healthy individuals were analyzed. To evaluate this possible association, genomic DNA from venous blood was extracted and genotypes of IL-16 rs4072111 variant were determined by polymerase chain reaction- Fragments Length Polymorphism Technique (PCR-RFLP)...
2018: Gastroenterology and Hepatology From Bed to Bench
Giulia F Del Gobbo, E Magda Price, Courtney W Hanna, Wendy P Robinson
Background: 5,10-Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in one-carbon metabolism that ensures the availability of methyl groups for methylation reactions. Two single-nucleotide polymorphisms (SNPs) in the MTHFR gene, 677C>T and 1298A>C, result in a thermolabile enzyme with reduced function. These variants, in both the maternal and/or fetal genes, have been associated with pregnancy complications including miscarriage, neural tube defects (NTDs), and preeclampsia (PE), perhaps due to altered capacity for DNA methylation (DNAm)...
2018: Clinical Epigenetics
Michael S Parker, Ambikaipakan Balasubramaniam, Floyd R Sallee, Steven L Parker
Eukaryote ribosomal RNAs (rRNAs) have expanded in the course of phylogeny by addition of nucleotides in specific insertion areas, the expansion segments. These number about 40 in the larger (25-28S) rRNA (up to 2,400 nucleotides), and about 12 in the smaller (18S) rRNA (<700 nucleotides). Expansion of the larger rRNA shows a clear phylogenetic increase, with a dramatic rise in mammals and especially in hominids. Substantial portions of expansion segments in this RNA are not bound to ribosomal proteins, and may engage extraneous interactants, including messenger RNAs (mRNAs)...
2018: Frontiers in Genetics
Mariana Alves, Edward Beamer, Tobias Engel
Epilepsy encompasses a heterogeneous group of neurological syndromes which are characterized by recurrent seizures affecting over 60 million people worldwide. Current anti-epileptic drugs (AEDs) are mainly designed to target ion channels and/or GABA or glutamate receptors. Despite recent advances in drug development, however, pharmacoresistance in epilepsy remains as high as 30%, suggesting the need for the development of new AEDs with a non-classical mechanism of action. Neuroinflammation is increasingly recognized as one of the key players in seizure generation and in the maintenance of the epileptic phenotype...
2018: Frontiers in Pharmacology
Duan Zeng, Shen He, Shunying Yu, Guanjun Li, Changlin Ma, Yi Wen, Yifeng Shen, Yimin Yu, Huafang Li
Background: Increasing evidence has indicated that dysfunction of miR-124 and target gene regulator of G protein signaling 4 ( RGS4 ) may be involved in the etiology and treatment of major depressive disorder (MDD). However, the molecular mechanisms are not fully understood. This study aimed to investigate whether common genetic variations in these two genes are associated with MDD and therapeutic response to antidepressants in the Chinese population. Methods: Three polymorphisms including rs531564 (a functional single-nucleotide polymorphism [SNP] in MIR124-1 ), rs10759 (a microRNA-binding site SNP in RGS4 ), and rs951436 (a promoter SNP in RGS4 ) were genotyped in 225 Chinese MDD patients and 436 controls...
2018: Neuropsychiatric Disease and Treatment
Harita Gogri, Sabita Ray, Snehal Agrawal, S Aruna, Kanjaksha Ghosh, Ajit Gorakshakar
BACKGROUND: Molecular genotyping of ABO blood group system has identified more than 60 "O" group alleles based on the single-nucleotide polymorphisms present in the ABO gene. Heterogeneity of O group alleles has been observed in various countries from South America, Europe, Middle East, and Asia. India is a vast country with more than 1300 million population which is divided into various ethnic and tribal groups. However, very little is known about the heterogeneity of O alleles in Indians...
January 2018: Asian Journal of Transfusion Science
Jin-Yu Yang, Xiang-Yu Deng, Yi-Sheng Li, Xian-Cai Ma, Jian-Xiong Feng, Bing Yu, Yang Chen, Yi-Ling Luo, Xi Wang, Mei-Ling Chen, Zhi-Xin Fang, Fu-Xiang Zheng, Yi-Ping Li, Qian Zhong, Tie-Bang Kang, Li-Bing Song, Rui-Hua Xu, Mu-Sheng Zeng, Wei Chen, Hui Zhang, Wei Xie, Song Gao
Cleavage of transfer (t)RNA and ribosomal (r)RNA are critical and conserved steps of translational control for cells to overcome varied environmental stresses. However, enzymes that are responsible for this event have not been fully identified in high eukaryotes. Here, we report a mammalian tRNA/rRNA-targeting endoribonuclease: SLFN13, a member of the Schlafen family. Structural study reveals a unique pseudo-dimeric U-pillow-shaped architecture of the SLFN13 N'-domain that may clamp base-paired RNAs. SLFN13 is able to digest tRNAs and rRNAs in vitro, and the endonucleolytic cleavage dissevers 11 nucleotides from the 3'-terminus of tRNA at the acceptor stem...
March 21, 2018: Nature Communications
Brian S White, Irena Lanc, Julie O'Neal, Harshath Gupta, Robert S Fulton, Heather Schmidt, Catrina Fronick, Edward A Belter, Mark Fiala, Justin King, Greg J Ahmann, Mary DeRome, Elaine R Mardis, Ravi Vij, John F DiPersio, Joan Levy, Daniel Auclair, Michael H Tomasson
Multiple myeloma (MM) is a disease of copy number variants (CNVs), chromosomal translocations, and single-nucleotide variants (SNVs). To enable integrative studies across these diverse mutation types, we developed a capture-based sequencing platform to detect their occurrence in 465 genes altered in MM and used it to sequence 95 primary tumor-normal pairs to a mean depth of 104×. We detected cases of hyperdiploidy (23%), deletions of 1p (8%), 6q (21%), 8p (17%), 14q (16%), 16q (22%), and 17p (4%), and amplification of 1q (19%)...
March 21, 2018: Blood Cancer Journal
Jun Muratsu, Masahiro Koseki, Daisaku Masuda, Yuji Yasuga, Satoki Tomoyama, Keiji Ataka, Yoshiki Yagi, Atsushi Nakagawa, Hidehumi Hamada, Shigeki Fujita, Hiroaki Hattori, Tohru Ohama, Makoto Nishida, Hisatoyo Hiraoka, Yuji Matsuzawa, Shizuya Yamashita
We report a case of Tangier disease with Leriche syndrome and bleeding tendency. In this male patient, nasal hemorrhage had been observed frequently throughout childhood. At 46 years old, he experienced effort angina, and coronary angiography demonstrated 75% stenosis in the right coronary artery. Orange-colored tonsils, mild hepatosplenomegaly and very low levels of serum high-density lipoprotein cholesterol (HDL-C) were observed, and the patient was diagnosed with Tangier disease. At 52 years old, effort angina recurred...
March 20, 2018: Journal of Atherosclerosis and Thrombosis
Dan Chen, Chao Yang, Sha Liu, Weijian Hang, Xianghong Wang, Juan Chen, Anbing Shi
Arf6/ARF-6 is a crucial regulator of the endosomal phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) pool in endocytic recycling. To further characterize ARF-6 regulation, we performed an ARF-6 interactor screen in Caenorhabditis elegans and identified SAC-1, the homologue of the phosphoinositide phosphatase Sac1p in yeast, as a novel ARF-6 partner. In the absence of ARF-6, basolateral endosomes show a loss of SAC-1 staining in epithelial cells. Steady-state cargo distribution assays revealed that loss of SAC-1 specifically affected apical secretory delivery and basolateral recycling...
March 21, 2018: Journal of Cell Biology
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