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Yue Li, Yunyan Wei, Weiwei Yuan, Qiqing Huang, Yaya Zhao, Weihong Zhao, Wei Xu, Jianqing Wu
The ligand of CD40, known as CD154 or CD40L, is the key to immunostimulatory and anticancer activity, but how CD40L affects cellular senescence is unclear. Thus, we studied a membrane‑stable mutant form CD40L (CD40L‑M) to explore tumor growth and cellular senescence in CD40‑positive NSCLC cells. We found that CD40L‑M‑expressing cells had senescent characteristics, including reduced cell proliferation and enlargement, increased SA‑β‑gal staining activity, and overexpression of several cell cycle regulators p53 and p21...
May 2018: Oncology Reports
Neeladri Sekhar Roy, Subrata Debnath, Abhijit Chakraborty, Prasenjit Chakraborty, Indrani Bera, Raka Ghosh, Nanda Ghoshal, Saikat Chakrabarti, Siddhartha Roy
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication. Little is known about how these strand separations occur. The strand-separated E.coli RNA polymerase-promoter open-complex structure showed four bases of the non-template strand, the master base -11A, -7, -6 and +2, in a flipped state and inserted into protein pockets. To explore whether any property of these bases in the duplex state pre-disposes them to flipping, NMR studies were performed on a wild-type promoter in the duplex state...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Alain Wuethrich, Abu Ali Ibn Sina, Mostak Ahmed, Ting-Yun Lin, Laura G Carrascosa, Matt Trau
Interfacial biosensing performs the detection of biomolecules at the bare-metal interface for disease diagnosis by comparing how biological species derived from patients and healthy individuals interact with bare metal surfaces. This technique retrieves clinicopathological information without complex surface functionalisation which is a major limitation of conventional techniques. However, it is still challenging to detect subtle molecular changes by interfacial biosensing, and the detection often requires prolonged sensing times due to the slow diffusion process of the biomolecules towards the sensor surface...
March 22, 2018: Nanoscale
Hongmin Hou, Hui Jia, Qin Yan, Xiping Wang
Salinity and drought are two major abiotic stresses that limit grape productivity. Responses to stress in grape are known to be regulated by several families of transcription factors. However, little is known about the role of grape Squamosa promoter binding protein (SBP)-box transcription factor genes in response to abiotic stress. To better understand the functions of the grape SBP-box genes in abiotic stress tolerance, a full-length complementary DNA (cDNA) sequence of the putative SBP-box transcription factor gene, VpSBP16 was amplified from Chinese wild grapevine Vitis pseudoreticulata clone "Baihe-35-1"...
March 22, 2018: International Journal of Molecular Sciences
Juliana Naldoni, Antônio A M Maia, Lincoln L Correa, Marcia R M da Silva, Edson A Adriano
Myxozoans are a diverse group of parasitic cnidarians, with some species recognized as serious pathogens to their hosts. The present study describes 2 new myxobolid species (Myxobolus figueirae sp. nov. and Henneguya santarenensis sp. nov.) infecting skin and gill filaments of the Amazonian pimelodid fish Phractocephalus hemioliopterus, based on ultrastructural, histology and phylogenetic analysis. The fish were caught in the Amazon River, Pará, Brazil. The plasmodial development of M. figueirae sp. nov. was in the dermis and those of H...
March 22, 2018: Diseases of Aquatic Organisms
Pei-Tseng Lee, Jonathan Zirin, Oguz Kanca, Wen-Wen Lin, Karen L Schulze, David Li-Kroeger, Rong Tao, Colby Devereaux, Yanhui Hu, Verena Chung, Ying Fang, Yuchun He, Hongling Pan, Ming Ge, Zhongyuan Zuo, Benjamin E Housden, Stephanie E Mohr, Shinya Yamamoto, Robert W Levis, Allan C Spradling, Norbert Perrimon, Hugo J Bellen
We generated a library of ~1,000 Drosophila stocks in which we inserted a construct in the intron of genes allowing expression of GAL4 under control of endogenous promoters while arresting transcription with a polyadenylation signal 3' of the GAL4. This allows numerous applications. First, ~90% of insertions in essential genes cause a severe loss-of-function phenotype, an effective way to mutagenize genes. Interestingly, 12/14 chromosomes engineered through CRISPR do not carry second-site lethal mutations. Second, 26/36(70%) of lethal insertions tested are rescued with a single UAS- cDNA construct...
March 22, 2018: ELife
Dario de Biase, Michela Visani, Giorgia Acquaviva, Adele Fornelli, Michele Masetti, Carlo Fabbri, Annalisa Pession, Giovanni Tallini
CONTEXT: - Integration of the analysis of genetic markers with endoscopic ultrasound-guided fine-needle aspiration and cytologic evaluation has increased the accuracy of the preoperative diagnosis of pancreatic lesions. The application of high-throughput gene panel analysis using next-generation sequencing platforms is now offering a great opportunity for further improvements. OBJECTIVE: - To review the application of next-generation sequencing to the preoperative diagnosis of pancreatic lesions...
April 2018: Archives of Pathology & Laboratory Medicine
Subrata Kundu, Hong Liang
No abstract text is available yet for this article.
March 22, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Nigel W Beebe
Mosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification - a target whose utility for discriminating mosquitoes is now escalating...
March 22, 2018: Parasitology
Sidi M Ghaber, Nawel Trabelsi, Mohamed L Salem, Faten Haddad, Aminetou Abba, Imen Darragi, Salem Abbes
Unstable hemoglobins (Hbs) are a group of Hb disorders that could be the origin of chronic hemolytic anemia. Most of these disorders are caused by point mutations taking place in the globin genes and affecting the stability of the Hb molecule. They are inherited as autosomal dominant diseases and described worldwide. Herein we report a new observation of an unstable variant in the Mauritanian population. The patient was a young girl of Mauritanian origin. She presented with chronic hemolytic anemia with an unknown etiology after being referred to several medical centers...
March 22, 2018: Hemoglobin
Kfir Kuchuk, Uri Sivan
Hydration interaction shapes biomolecules and is a dominant inter-molecular force. Mapping the hydration patterns of biomolecules is therefore essential for understanding molecular processes in biology. Numerous studies have been devoted to this challenge but current methods cannot map the hydration of single biomolecules, let alone under physiological conditions. Here, we show that FM-AFM can fill this gap and generate 3D hydration maps of single DNA molecules under near-physiological conditions. Additionally, we present real space images of DNA in which the double helix is resolved with unprecedented resolution, clearly revealing individual phosphate groups along the DNA backbone...
March 22, 2018: Nano Letters
Jia-Li Liu, Zhi-Ling Tang, Jia-Qi Zhang, Yaqin Chai, Ying Zhuo, Ruo Yuan
The electrochemiluminescence (ECL) properties of polycyclic aromatic hydrocarbons (PAHs) are excellent on account of the high photoluminescence quantum yield. However, the poor solubility and radical instability of PAHs in the aqueous solution severely restricted the further biological application. Here, 9,10 - diphenylanthracene (DPA) nano blocks (NBs) with good dispersibility and stability in aqueous solution were prepared according to morphology-controlled technology employing water-soluble polymers as a protectant...
March 22, 2018: Analytical Chemistry
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
Cayetana Vázquez-Diez, Greg FitzHarris
Chromothripsis is a phenomenon observed in cancer cells, wherein a single or few chromosome(s) exhibit vast genomic rearrangements. Recent studies elucidated a striking series of events in which defective segregation of chromosomes causes their incorporation into micronuclei, where they are subject to extensive DNA damage prior to re-joining the main mass of chromosomes in a subsequent cell cycle, which provide an appealing mechanism for the etiology of chromothripsis. Micronuclei are well known to be common in human preimplantation embryos...
2018: Methods in Molecular Biology
Martin Poot
The highly complex structural genome variations chromothripsis, chromoanasynthesis, and chromoplexy are subsumed under the term chromoanagenesis, which means chromosome rebirth. Precipitated by numerous DNA double-strand breaks, they differ in number of and distances between breakpoints, associated copy number variations, order and orientation of segments, and flanking sequences at joining points. Results from patients with the autosomal dominant cancer susceptibility disorder Li-Fraumeni syndrome implicated somatic TP53 mutations in chromothripsis...
2018: Methods in Molecular Biology
Mariona Terradas, Marta Martín, Anna Genescà
The physical isolation of chromosomes within micronuclei offers an attractive mechanistic explanation for the local DNA fragmentation and clustered genome rearrangements that characterize chromothripsis. Localized shattering of the chromatin confined in micronuclei can be a consequence of defects in micronuclei basic general functions, such as DNA replication and repair. The detection of DNA repair and replication defects in micronuclei is described here, as well as the analysis of chromosome breakage and inaccurate reassembly of broken segments in the daughter cells, as indirect methods to detect chromothripsis...
2018: Methods in Molecular Biology
Monique N H Luijten, Jeannie X T Lee, Sixun Chen, Karen C Crasta
Lagging chromosomes that arise after chromosome mis-segregation during cell division can be encapsulated within small structures known as micronuclei. A link between whole-chromosome mis-segregation and chromothripsis has been demonstrated via micronuclear chromosome pulverization. Here, we describe methods to efficiently generate micronuclei and examine downstream cell fates, specifically with regard to DNA damage and chromosome pulverization.
2018: Methods in Molecular Biology
Dustin C Hancks
Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects...
2018: Methods in Molecular Biology
Lucy H Swift, Roy M Golsteyn
Cells that undergo checkpoint adaptation arrest at and then abrogate the G2/M cell cycle checkpoint to enter mitosis with damaged DNA. Cells surviving this process frequently contain micronuclei, which can lead to genomic change and chromothripsis. In this chapter we describe how to induce checkpoint adaptation and detect it by time-lapse video and immunofluorescence microscopy and how to isolate cells undergoing checkpoint adaptation from a total cell population.
2018: Methods in Molecular Biology
Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, Thérèse Commes
RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a complete procedure including a novel way of analyzing reads that combines genomic locations and local coverage to directly infer chimeric junctions with a high sensitivity and specificity, allowing identification of different classes of chimeric RNA events. We also recommend the best practices for the bioinformatics analysis and describe the experimental process for RNA validation using real-time PCR and sequencing...
2018: Methods in Molecular Biology
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