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Tamas Jilling, Namasivayam Ambalavanan, C Michael Cotten, Colin A Martin, Akhil Maheshwari, Kurt Schibler, Joshua Levy, Grier P Page
BACKGROUND: Twin studies suggest that genetic factors may account for up to 50% increased risk for necrotizing enterocolitis (NEC), but genome-wide association studies (GWAS) for NEC are lacking. METHODS: Genotyping was done on Illumina BeadChip, followed by analysis using PLINK with logistic regression under an additive model. RESULTS: Among 751 extremely low birth weight (<1000 g, >401 g) neonates, 30 had surgical NEC. 261 single nucleotide polymorphisms (SNPs) showed association with NEC at P<0...
March 14, 2018: Pediatric Research
Yojiro Yutaka, Toshihiko Sato, Koichi Matsushita, Hiroyuki Aiba, Yusuke Muranishi, Yasuto Sakaguchi, Tadao Sugiura, Minoru Okada, Tatsuo Nakamura, Hiroshi Date
OBJECTIVE: We developed a novel localization technique for small intrapulmonary lesions using radiofrequency identification (RFID) technology. Micro-RFID markers with nickel-titanium coils were designed to be placed from subsegmental bronchi to the peripheral parenchyma. In this preclinical study, thoracoscopic subsegmentectomy of a canine pseudotumor model was performed to demonstrate the feasibility and three-dimensional positional accuracy of the system. METHODS: To recover subcentimeter pseudotumors, markers were bronchoscopically placed to determine the resection line: 1) next to the pseudotumor, 2) in the responsible subsegmental bronchi as the central margin, 3) on the intersubsegmental plane as the lateral margin...
March 9, 2018: Seminars in Thoracic and Cardiovascular Surgery
L Montrose, V Padmanabhan, J M Goodrich, S E Domino, M C Treadwell, J D Meeker, D J Watkins, D C Dolinoy
Endocrine disrupting chemicals (EDCs) pose a public health risk through disruption of normal biological processes. Identifying toxicoepigenetic mechanisms of developmental exposure-induced effects for EDCs, such as phthalates or bisphenol A (BPA), is essential. Here, we investigate whether maternal exposure to EDCs is predictive of infant DNA methylation at candidate gene regions. In the Michigan Mother-Infant Pairs (MMIP) cohort, DNA was extracted from cord blood leukocytes for methylation analysis by pyrosequencing (n = 116) and methylation changes related to first trimester levels of 9 phthalate metabolites and BPA...
March 7, 2018: Epigenetics: Official Journal of the DNA Methylation Society
Yvette N Lamb, Yahiya Y Syed
Page 91, abstract, lines 1-6: The following sentence, which previously read.
March 6, 2018: BioDrugs: Clinical Immunotherapeutics, Biopharmaceuticals and Gene Therapy
Richard N McLaughlin
Transposable elements comprise a huge portion of most animal genomes. Unlike many pathogens, these elements leave a mark of their impact via their insertion into host genomes. With proper teasing, these sequences can relay information about the evolutionary history of transposons and their hosts. In a new publication, Larson and colleagues describe a previously unappreciated density of long interspersed element-1 (LINE-1) sequences that have been spliced (LINE-1 and other reverse transcribing elements are necessarily intronless)...
March 5, 2018: PLoS Biology
Daniela Matei, Sharad Ghamande, Lynda D Roman, Angeles Alvarez Secord, John Nemunaitis, Merry Jennifer Markham, Kenneth P Nephew, Simone Jueliger, Aram Oganesian, Sue Naim, Xiang-Yao Su, Harold N Keer, Mohammad Azab, Gini Fleming
PURPOSE: Epigenetic changes are implicated in acquired resistance to platinum. Guadecitabine is a next-generation hypomethylating agent (HMA). Here we report the clinical results, along with pharmacokinetic (PK) and pharmacodynamic analyses of the phase 1 study of guadecitabine and carboplatin (G+C) in patients with recurrent, platinum resistant high-grade serous ovarian cancer (OC), primary peritoneal carcinoma (PPC), or fallopian tube cancer (FTC). EXPERIMENTAL DESIGN: Guadecitabine was administered once daily on Days 1-5 followed by carboplatin IV on Day 8 of a 28-day cycle...
March 2, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Ling Wei, Li Xie, Xingwu Wang, Hongxin Ma, Liyan Lv, Lisheng Liu, Xianrang Song
Genotype-directed targeted therapy has become one of the standard treatment options for non-small cell lung cancer (NSCLC). There have been numerous limitations associated with mutation analysis of tissue samples. Consequently, mutational profile analysis of circulating cell-free DNA (cfDNA) by highly sensitive droplet digital PCR (ddPCR) assay has been developed. Possibly due to differences in cfDNA concentrations, previous studies have shown numerous discrepancies in mutation detection consistency between tissue and cfDNA...
March 1, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Patcharawalai Whongsiri, Chaowat Pimratana, Udomsak Wijitsettakul, Depicha Jindatip, Anapat Sanpavat, Wolfgang A Schulz, Michèle J Hoffmann, Wolfgang Goering, Chanchai Boonla
BACKGROUND/AIM: Reactivation of long interspersed nuclear element-1 (LINE-1) and oxidative stress are suggested to have oncogenic potential to drive tumorigenesis and cancer progression. We previously demonstrated that reactive oxygen species (ROS) caused hypomethylation of LINE-1 elements in bladder cancer cells. In this study, we investigated the expression of LINE-1-encoded protein (ORF1p) and oxidative stress marker 4-hydroxynonenal (4-HNE) in human bladder cancer tissues, as well as induction of ORF1p expression by ROS in bladder cancer cell lines...
March 2018: Cancer Genomics & Proteomics
Melannie Alexander, Stella Koutros, Matthew R Bonner, Kathryn Hughes Barry, Michael C R Alavanja, Gabriella Andreotti, Hyang-Min Byun, Ligong Chen, Laura E Beane Freeman, Jonathan N Hofmann, Freya Kamel, Lee E Moore, Andrea Baccarelli, Jennifer Rusiecki
Cancer risk may be associated with DNA methylation (DNAm) levels in Long Interspersed Nucleotide Element 1 (LINE-1), a surrogate for global DNAm. Exposure to certain pesticides may increase risk of particular cancers, perhaps mediated in part through global DNAm alterations. To date, human data on pesticide exposure and global DNAm alterations are limited. The goal of this study was to evaluate alterations of LINE-1 DNAm by pesticides in a variety of classes. Data from 596 cancer-free male participants enrolled in the Agricultural Health Study (AHS) were used to examine associations between use of 57 pesticides and LINE-1 DNAm measured via Pyrosequencing in peripheral blood leucocytes...
May 2017: Environmental Epigenetics
Sandra L Martin
The mechanisms by which a retrotransposon called LINE-1 duplicates itself and spreads through the human genome are becoming clearer.
February 21, 2018: ELife
Maurizio Cardelli
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation...
February 16, 2018: Mechanisms of Ageing and Development
Hequan Sun, Jia Ding, Mathieu Piednoël, Korbinian Schneeberger, Inanc Birol
Motivation: Analyzing k-mer frequencies in whole-genome sequencing data is becoming a common method for estimating genome size (GS). However, it remains uninvestigated how accurate the method is, especially if it can capture intra-species GS variation. Results: We present findGSE, which fits skew normal distributions to k-mer frequencies to estimate GS. findGSE outperformed existing tools in an extensive simulation study. Estimating GSs of 89 Arabidopsis thaliana accessions, findGSE showed the highest capability in capturing GS variations...
February 15, 2018: Bioinformatics
Kaizhao Zhang, Xiaotong Tan, Ying Li, Guan Liang, Zhangyong Ning, Yongjiang Ma, Yugu Li
Zearalenone (ZEA) was a mycotoxin biosynthesized by a variety of Fusarium fungi via a polypeptide pathway. ZEA has significant toxic reaction on immune cells. Thymic epithelial cells (TECs) as a crucial constituent of thymic stroma can provide unique microenvironment for thymocyte maturation, but the mechanism of ZEA affecting the TECs is poorly understood. The basic data about gene expression differences for the ZEA on thymic epithelial cell line 1 (MTEC1) will help us to elucidate this mechanism. Here, cell viability and proliferation assay and transcriptome sequencing on MTEC1 treated with ZEA were performed...
February 6, 2018: Ecotoxicology and Environmental Safety
Antonio Caronni, Irma Sterpi, Paola Antoniotti, Evdoxia Aristidou, Fortunato Nicolaci, Michela Picardi, Giuseppe Pintavalle, Valentina Redaelli, Gianluca Achille, Luciana Sciumè, Massimo Corbo
The Timed Up and Go (TUG) test is a common mobility measure in rehabilitation. With the instrumental TUG test (ITUG; i.e. the TUG measured by inertial measurement units, IMUs), several movement measures are newly available. However, the clinical meaning of these new measures is not totally clear. Aim of the current work is to evaluate the validity of different ITUG parameters as a measure of balance. Neurological patients (n = 122; 52 females; 89 older than 65 years) completed the TUG test with IMUs secured to their back...
January 31, 2018: Gait & Posture
Jin Yang, Yanli Liu, Huitao Zhang, Hongjie Zhang, Wubin Wang, Yanfeng Fan
Coke oven emissions (COE) containing polycyclic aromatic hydrocarbons (PAHs) are predominant toxic constituents of particulate air pollution that have been linked to increased risk of lung cancer. Aberrant DNA methylation is one of the best known epigenetic changes in human cancers and healthy subjects exposed to carcinogens. The purpose of this study is to explore the factors influencing the methylation of long interspersed nuclear element-1 (LINE-1) and aryl-hydrocarbon receptor repressor (AhRR) in coke oven workers...
February 2018: Mutation Research
Elisa Orecchini, Loredana Frassinelli, Silvia Galardi, Silvia Anna Ciafrè, Alessandro Michienzi
Long interspersed element-1 (LINE-1 or L1) retrotransposons represent the only functional family of autonomous transposable elements in humans and formed 17% of our genome. Even though most of the human L1 sequences are inactive, a limited number of copies per individual retain the ability to mobilize by a process termed retrotransposition. The ongoing L1 retrotransposition may result in insertional mutagenesis that could lead to negative consequences such as genetic disease and cancer. For this reason, cells have evolved several mechanisms of defense to restrict L1 activity...
February 2, 2018: Chromosome Research
Yoshifumi Baba, Taisuke Yagi, Hiroshi Sawayama, Yukiharu Hiyoshi, Takatsugu Ishimoto, Masaaki Iwatsuki, Yuji Miyamoto, Naoya Yoshida, Hideo Baba
Epigenetic changes play a crucial role in human cancer development. DNA methylation is a central epigenetic process that regulates levels of gene expression. Changes in DNA methylation that occur in human tumors include global DNA hypomethylation and site-specific CpG island promoter hypermethylation. Long interspersed element-1 (LINE-1) is a repetitive DNA retrotransposon that duplicates via a copy-and-paste genetic mechanism. As LINE-1 constitutes approximately 17% of the human genome, the extent of LINE-1 methylation is regarded as a surrogate marker of global DNA methylation...
February 1, 2018: Digestion
Young-Hoo Kim, Jang-Won Park, Jun-Shik Kim
BACKGROUND: Proponents of computer-assisted TKA suggest that better alignment of the TKAs will lead to improved long-term patient functional outcome and survivorship of the implants. However, there is little evidence about whether the improved position and alignment of the knee components obtained using computer navigation improve patient function and the longevity of the TKA. QUESTIONS/PURPOSES: The purpose of this study was to determine whether (1) clinical results; (2) radiographic and CT scan results; and (3) the survival rate of TKA components would be better in patients having computer-assisted TKA than results of patients having TKA without computer-assisted TKA...
January 2018: Clinical Orthopaedics and related Research
Cebisile Ngcamphalala, John E Ataguba
BACKGROUND: As the drive towards universal coverage is gaining momentum globally, the need for assessing levels of financial health protection in countries, particularity the developing world, has increasingly become important. In Swaziland, the level of financial health protection is not clearly understood. OBJECTIVE: To assess financial catastrophe and impoverishment from out-of-pocket payments for health services in Swaziland. METHODS: The nationally representative Swaziland Household Income and Expenditure Survey (2009/2010) dataset is used for the analyses...
2018: Global Health Action
Alma Betsaida Benitez-Trinidad, Irma Martha Medina-Díaz, Yael Yvette Bernal-Hernández, Briscia Socorro Barrón-Vivanco, Cyndia Azucena González-Arias, José Francisco Herrera-Moreno, Isabel Alvarado-Cruz, Betzabet Quintanilla-Vega, Aurora Elizabeth Rojas-García
Recently a relationship has been reported between pesticide exposure and changes in global DNA methylation patterns. Urban sprayers are a particularly vulnerable population because of the high risk of pesticide exposure that their work implies. Therefore, the aim of this study was to estimate the changes in the Long Interspersed Nucleotide Element (LINE-1) in urban sprayers and its relationship with pesticide exposure. The study population consisted of 190 individuals stratified into three study groups: no occupational pesticide exposure; moderate exposure, and high exposure...
January 25, 2018: Food and Chemical Toxicology
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