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Jie Sun, Guojun Chen, Yuanwen Jing, Xiang He, Jianting Dong, Junmeng Zheng, Meisheng Zou, Hairui Li, Shifei Wang, Yili Sun, Wangjun Liao, Yulin Liao, Li Feng, Jianping Bin
BACKGROUND/AIMS: In this study, the long non-coding RNA (lncRNA) expression profile in human thoracic aortic dissection (TAD), a highly lethal cardiovascular disease, was investigated. METHODS: Human TAD (n=3) and normal aortic tissues (NA) (n=3) were examined by high-throughput sequencing. Bioinformatics analyses were performed to predict the roles of aberrantly expressed lncRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results...
April 13, 2018: Cellular Physiology and Biochemistry
Qianli Dong, Ning Li, Xiaochong Li, Zan Yuan, Dejian Xie, Xiaofei Wang, Jianing Li, Yanan Yu, Jinbin Wang, Baoxu Ding, Zhibin Zhang, Changping Li, Yao Bian, Ai Zhang, Ying Wu, Bao Liu, Lei Gong
The non-random spatial packing of chromosomes in the nucleus plays critical roles in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome...
April 16, 2018: Plant Journal: for Cell and Molecular Biology
Kevin J Campbell, Philip K Louie, Derek A Khorsand, Nicholas B Frisch, Tad L Gerlinger, Brett R Levine
Orthopedic surgeons are tasked with treating complex patients while employing critical surgical skills, clinical knowledge, and new technologies. The constant inundation of information, coupled with hours in the hospital setting, provides unique perspectives on various aspects of how health care is delivered, thereby creating a milieu ripe for innovation. The rigors of an orthopedic career make it challenging for physicians to translate an idea into a great product. Through the authors' experiences at a tertiary orthopedic practice, they review the process of taking an idea from concept to fruition...
April 16, 2018: Orthopedics
Tianfeng Yang, Xianpeng Shi, Yuan Kang, Man Zhu, Mengying Fan, Dongdong Zhang, Yanmin Zhang
Cervical carcinoma remains the second most common malignancy with a high mortality rate among women worldwide. TAD-1822-7-F2 (F2) and TAD-1822-7-F5 (F5) are novel compounds synthesized on the chemical structure of taspine derivatives, and show an effective suppression for HeLa cells. Our study aims to confirm the potential targets of F2 and F5, and investigate the underlying mechanism of the inhibitory effect on HeLa cells. In this study, Real Time Cell Analysis and crystal violet staining assay were conducted to investigate the effect of F2 and F5 on HeLa cells proliferation...
April 9, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Shereen Mowaka, Bassam M Ayoub, Mostafa A Hassan, Wafaa A Zaghary
New spectrophotometric and chemometric methods were carried out for the simultaneous assay of trelagliptin (TRG) and its acid degradation product (TAD) and applied successfully as a stability indicating assay to recently approved Zafatek® tablets. TAD was monitored using TLC to ensure complete degradation. Furthermore, HPLC was used to confirm dealing with one major acid degradation product. The proposed methods were developed by manipulating zero-order, first-derivative, and ratio spectra of TRG and TAD using simultaneous equation, first-derivative, and mean-centering methods, respectively...
2018: Journal of Analytical Methods in Chemistry
Nan Hua, Harianto Tjong, Hanjun Shin, Ke Gong, Xianghong Jasmine Zhou, Frank Alber
Chromosome conformation capture technologies such as Hi-C are widely used to investigate the spatial organization of genomes. Because genome structures can vary considerably between individual cells of a population, interpreting ensemble-averaged Hi-C data can be challenging, in particular for long-range and interchromosomal interactions. We pioneered a probabilistic approach for the generation of a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments...
May 2018: Nature Protocols
Trevor E Angell, Le Min, Tad J Wieczorek, F Stephen Hodi
Blockade of immune checkpoint molecules to reverse cancer-induced immune suppression can improve anti-tumor immune responses in cancer patients. Monoclonal antibodies targeting two such molecules, Programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte associated protein 4 (CTLA-4) have shown clinical benefit in the treatment of advanced malignancies, including metastatic melanoma. Adverse effects of these immune checkpoint inhibitors include immune-related adverse events (irAE) and the inducing of new autoimmunity, of which one of the most common is autoimmune thyroiditis...
March 2018: Genes & Diseases
Nicholas J Lodato, Andy Rampersaud, David J Waxman
Activation of the nuclear receptor and transcription factor CAR (Nr1i3) by its specific agonist ligand TCPOBOP (1,4-bis[2-(3,5-dichloropyridyloxy)]benzene) dysregulates hundreds of genes in mouse liver and is linked to male-biased hepatocarcinogenesis. To elucidate the genomic organization of CAR-induced gene responses, we investigated the distribution of TCPOBOP-responsive RefSeq coding and long non-coding RNA (lncRNA) genes across the megabase-scale topologically associating domains (TADs) that segment the genome, and which provide a structural framework that functionally constrains enhancer-promoter interactions...
April 2, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
Ida Lindström, Jakob Dogan
Intrinsically disordered proteins (IDPs) are abundant in the eukaryotic proteome. However, little is known about the role of sub-nanosecond dynamics and the conformational entropy that it represents in protein-protein interactions involving IDPs. Using NMR side chain and backbone relaxation, stopped-flow kinetics, ITC, and computational studies, we have here characterized the interaction between the globular TAZ1 domain of CREB binding protein, and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2)...
April 3, 2018: ACS Chemical Biology
B H van Duren, K Sugand, R Wescott, R Carrington, A Hart
BACKGROUND: Hip fractures contribute to a significant clinical burden globally with over 1.6 million cases per annum and up to 30% mortality rate within the first year. Insertion of a dynamic hip screw (DHS) is a frequently performed procedure to treat extracapsular neck of femur fractures. Poorly performed DHS fixation of extracapsular neck of femur fractures can result in poor mobilisation, chronic pain, and increased cut-out rate requiring revision surgery. A realistic, affordable, and portable fluoroscopic simulation system can improve performance metrics in trainees, including the tip-apex distance (the only clinically validated outcome), and improve outcomes...
March 29, 2018: Medical Engineering & Physics
Hirokazu Takai, Masatoshi Murayama, Sakumo Kii, Daisuke Mito, Chihiro Hayai, Satoru Motohashi, Tomoki Takahashi
PURPOSE: ADAPT is a fluoroscopic computer-assisted surgery system which intraoperatively shows the distance from the tip of the screw to the surface of the femoral head, tip-to-head-surface distance (TSD), and the tip-apex distance (TAD) advocated by Baumgaertner et al. The study evaluated the accuracy of ADAPT. PATIENTS AND METHODS: A total of 55 patients operated with ADAPT between August 2016 and March 2017 were included as subjects. TSD and TAD were measured postoperatively using computed tomography (CT) and X-rays...
March 19, 2018: Injury
Douglas P Terry, Magdalena Wojtowicz, Nathan E Cook, Bruce A Maxwell, Ross Zafonte, Tad Seifert, Noah D Silverberg, Paul D Berkner, Grant L Iverson
OBJECTIVE: Identifying personal characteristics associated with sustaining a concussion is of great interest, yet only a few have examined this in children. The purpose of this study was to examine the association between sex, neurodevelopmental disorders, health history, and lifetime history of self-reported concussion in 12- and 13-year-old athletes. DESIGN: Cross-sectional study. SETTING: Middle schools. PARTICIPANTS: Participants were 1744 twelve- and thirteen-year-old student athletes who completed preseason Immediate Post-Concussion Assessment and Cognitive Testing (ImPACT) testing, including a self-report questionnaire about previous concussions, developmental diagnoses, and previous medical treatment...
March 27, 2018: Clinical Journal of Sport Medicine: Official Journal of the Canadian Academy of Sport Medicine
Ziad Al Bkhetan, Dariusz Plewczynski
This study aims to understand through statistical learning the basic biophysical mechanisms behind three-dimensional folding of epigenomes. The 3DEpiLoop algorithm predicts three-dimensional chromatin looping interactions within topologically associating domains (TADs) from one-dimensional epigenomics and transcription factor profiles using the statistical learning. The predictions obtained by 3DEpiLoop are highly consistent with the reported experimental interactions. The complex signatures of epigenomic and transcription factors within the physically interacting chromatin regions (anchors) are similar across all genomic scales: genomic domains, chromosomal territories, cell types, and different individuals...
March 26, 2018: Scientific Reports
Francesca B Aiello, Tad Guszczynski, Wenqing Li, Qiong Jiang, Deborah L Hodg, Tania Massignan, Chiara Di Lisio, Anand Merchand, Antonio D Procopio, Valentina Bonetto, Scott K Durum
IL-7 is required for T cell differentiation and mature T cell homeostasis and promotes pro-B cell proliferation and survival. Tyrosine phosphorylation plays a central role in IL-7 signaling. We identified by two-dimensional electrophoresis followed by anti-phosphotyrosine immunoblotting and mass spectrometry sixteen tyrosine phosphorylated proteins from the IL-7-dependent cell line D1. IL-7 stimulation induced the phosphorylation of the proteins STI1, ATIC and hnRNPH, involved in pathways related to survival, proliferation and gene expression, respectively, and increased the phosphorylation of CrkL, a member of a family of adaptors including the highly homologous Crk isoforms CrkII and CrkI, important in multiple signaling pathways...
March 23, 2018: Cellular Signalling
Anthony N Cutrupi, Megan H Brewer, Garth A Nicholson, Marina L Kennerson
Inherited peripheral neuropathies (IPNs) are a clinically and genetically heterogeneous group of diseases affecting the motor and sensory peripheral nerves. IPNs have benefited from gene discovery and genetic diagnosis using next-generation sequencing with over 80 causative genes available for testing. Despite this success, up to 50% of cases remain genetically unsolved. In the absence of protein coding mutations, noncoding DNA or structural variation (SV) mutations are a possible explanation. The most common IPN, Charcot-Marie-Tooth neuropathy type 1A (CMT1A), is caused by a 1...
March 23, 2018: Molecular Genetics & Genomic Medicine
Tad Kroczak, Luke F Reynolds, Michael Ordon
PURPOSE OF REVIEW: We set out to review the current published experience with robotic autotransplantation. Although the experience to date is limited, this surgery appears to be safe and technically feasible. We also examined the use of the robotic surgical platform for the management of post-transplant uretero-vesical anastomotic strictures. RECENT FINDINGS: To date, only four reported cases of robotic autotransplantation have been described with two being performed completely intra-corporeally...
March 23, 2018: Current Urology Reports
Wanqing Xiang, M Julia Roberti, Jean-Karim Hériché, Sébastien Huet, Stephanie Alexander, Jan Ellenberg
Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs...
March 23, 2018: Journal of Cell Biology
Kevin Yauy, Vincent Gatinois, Thomas Guignard, Satish Sati, Jacques Puechberty, Jean Baptiste Gaillard, Anouck Schneider, Franck Pellestor
Apparition of next-generation sequencing (NGS) was a breakthrough on knowledge of genome structure. Bioinformatic tools are a key point to analyze this huge amount of data from NGS and characterize the three-dimensional organization of chromosomes. This chapter describes usage of different browsers to explore publicly available online data and to search for possible 3D chromatin changes involved during complex chromosomal rearrangements as chromothripsis. Their pathogenic impact on clinical phenotype and gene misexpression can also be evaluated with annotated databases...
2018: Methods in Molecular Biology
Yao Xu, Jing Ye, Menglong Wang, Yuan Wang, Qingwei Ji, Ying Huang, Tao Zeng, Zhen Wang, Di Ye, Huimin Jiang, Jianfang Liu, Yingzhong Lin, Jun Wan
BACKGROUND: Interleukin (IL) 11 is closely related to tumor and hematological system diseases. Recent studies have demonstrated that IL-11 also participates in cardiovascular diseases, including ischemia-reperfusion mediated heart injury and acute myocardial infarction. This study aimed to investigate whether IL-11 is involved in acute thoracic aortic dissection (TAD). METHODS: Aortic tissue samples from normal donors and acute TAD patients were collected, and the expression of IL-11 in all aortic tissue was analyzed...
March 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Saurabh Sudha Dhiman, Namita Shrestha, Aditi David, Neha Basotra, Glenn R Johnson, Bhupinder S Chadha, Venkataramana Gadhamshetty, Rajesh K Sani
Residual solid and liquid streams from the one-pot CRUDE (Conversion of Raw and Untreated Disposal into Ethanol) process were treated with two separate biochemical routes for renewable energy transformation. The solid residual stream was subjected to thermophilic anaerobic digestion (TAD), which produced 95 ± 7 L methane kg-1 volatile solid with an overall energy efficiency of 12.9 ± 1.7%. A methanotroph, Methyloferula sp., was deployed for oxidation of mixed TAD biogas into methanol. The residual liquid stream from CRUDE process was used in a Microbial Fuel Cell (MFC) to produce electricity...
March 12, 2018: Bioresource Technology
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