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human artificial chromosome

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https://www.readbyqxmd.com/read/28333343/centromere-destiny-in-dicentric-chromosomes-new-insights-from-the-evolution-of-human-chromosome-2-ancestral-centromeric-region
#1
Giorgia Chiatante, Giuliana Giannuzzi, Francesco Maria Calabrese, Evan E Eichler, Mario Ventura
Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells...
March 15, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28243228/plasmid-replicons-from-pseudomonas-are-natural-chimeras-of-functional-exchangeable-modules
#2
Leire Bardaji, Maite Añorga, José A Ruiz-Masó, Gloria Del Solar, Jesús Murillo
Plasmids are a main factor for the evolution of bacteria through horizontal gene exchange, including the dissemination of pathogenicity genes, resistance to antibiotics and degradation of pollutants. Their capacity to duplicate is dependent on their replication determinants (replicon), which also define their bacterial host range and the inability to coexist with related replicons. We characterize a second replicon from the virulence plasmid pPsv48C, from Pseudomonas syringae pv. savastanoi, which appears to be a natural chimera between the gene encoding a newly described replication protein and a putative replication control region present in the widespread family of PFP virulence plasmids...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28224202/germline-specific-dgcr8-knockout-in-zebrafish-using-a-back-approach
#3
Yun Liu, Zeyao Zhu, Idy H T Ho, Yujian Shi, Yuxin Xie, Jianzhen Li, Yong Zhang, Matthew T V Chan, Christopher H K Cheng
Zebrafish is an important model to study developmental biology and human diseases. However, an effective approach to achieve spatial and temporal gene knockout in zebrafish has not been well established. In this study, we have developed a new approach, namely bacterial artificial chromosome-rescue-based knockout (BACK), to achieve conditional gene knockout in zebrafish using the Cre/loxP system. We have successfully deleted the DiGeorge syndrome critical region gene 8 (dgcr8) in zebrafish germ line and demonstrated that the maternal-zygotic dgcr8 (MZdgcr8) embryos exhibit MZdicer-like phenotypes with morphological defects which could be rescued by miR-430, indicating that canonical microRNAs play critical role in early development...
February 21, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28139373/development-of-caco-2-cells-co-expressing-cyp3a4-and-nadph-cytochrome-p450-reductase-using-a-human-artificial-chromosome-for-the-prediction-of-intestinal-extraction-ratio-of-cyp3a4-substrates
#4
Toru Takenaka, Kanako Kazuki, Naomoto Harada, Jiro Kuze, Masato Chiba, Takahiro Iwao, Tamihide Matsunaga, Satoshi Abe, Mitsuo Oshimura, Yasuhiro Kazuki
The Caco-2 cells co-expressing cytochrome P450 (CYP) 3A4 and NADPH-cytochrome P450 reductase (CPR) were developed using a human artificial chromosome (HAC) vector. The CYP3A4 and CPR genes were cloned into the HAC vector in CHO cells using the Cre-loxP system, and the microcell-mediated chromosome transfer technique was used to transfer the CYP3A4-CPR-HAC vector to Caco-2 cells. After seeding onto semipermeable culture inserts, the CYP3A4-CPR-HAC/Caco-2 cells were found to form tight monolayers, similar to the parental cells, as demonstrated by the high transepithelial electrical resistance (TEER) value and comparable permeability of non-CYP3A4 substrates between parent and CYP3A4-CPR-HAC/Caco-2 cell monolayers...
August 26, 2016: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/28111305/correlation-between-luminescence-intensity-and-cytotoxicity-in-cell-based-cytotoxicity-assay-using-luciferase
#5
S Wakuri, K Yamakage, Y Kazuki, K Kazuki, M Oshimura, S Aburatani, M Yasunaga, Y Nakajima
The luciferase reporter assay has become one of the conventional methods for cytotoxicity evaluation. Typically, the decrease of luminescence expressed by a constitutive promoter is used as an index of cytotoxicity. However, to our knowledge, there have been no reports of the correlation between cytotoxicity and luminescence intensity. In this study, to accurately verify the correlation between them, beetle luciferase was stably expressed in human hepatoma HepG2 cells harboring the multi-integrase mouse artificial chromosome vector...
January 20, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28077560/mechanistic-insights-into-type-i-toxin-antitoxin-systems-in-helicobacter-pylori-the-importance-of-mrna-folding-in-controlling-toxin-expression
#6
Hélène Arnion, Dursun Nizam Korkut, Sara Masachis Gelo, Sandrine Chabas, Jérémy Reignier, Isabelle Iost, Fabien Darfeuille
Type I toxin-antitoxin (TA) systems have been identified in a wide range of bacterial genomes. Here, we report the characterization of a new type I TA system present on the chromosome of the major human gastric pathogen, Helicobacter pylori We show that the aapA1 gene encodes a 30 amino acid peptide whose artificial expression in H. pylori induces cell death. The synthesis of this toxin is prevented by the transcription of an antitoxin RNA, named IsoA1, expressed on the opposite strand of the toxin gene. We further reveal additional layers of post-transcriptional regulation that control toxin expression: (i) transcription of the aapA1 gene generates a full-length transcript whose folding impedes translation (ii) a 3' end processing of this message generates a shorter transcript that, after a structural rearrangement, becomes translatable (iii) but this rearrangement also leads to the formation of two stem-loop structures allowing formation of an extended duplex with IsoA1 via kissing-loop interactions...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27980064/efficient-size-independent-chromosome-delivery-from-yeast-to-cultured-cell-lines
#7
David M Brown, Yujia A Chan, Prashant J Desai, Peter Grzesik, Lauren M Oldfield, Sanjay Vashee, Jeffrey C Way, Pamela A Silver, John I Glass
The delivery of large DNA vectors (>100 000 bp) remains a limiting step in the engineering of mammalian cells and the development of human artificial chromosomes (HACs). Yeast is commonly used to assemble genetic constructs in the megabase size range, and has previously been used to transfer constructs directly into cultured cells. We improved this method to efficiently deliver large (1.1 Mb) synthetic yeast centromeric plasmids (YCps) to cultured cell lines at rates similar to that of 12 kb YCps. Synchronizing cells in mitosis improved the delivery efficiency by 10-fold and a statistical design of experiments approach was employed to boost the vector delivery rate by nearly 300-fold from 1/250 000 to 1/840 cells, and subsequently optimize the delivery process for multiple mammalian, avian, and insect cell lines...
December 15, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27956473/diabetes-induced-by-gain-of-function-mutations-in-the-kir6-1-subunit-of-the-katp-channel
#8
Maria S Remedi, Jonathan B Friedman, Colin G Nichols
Gain-of-function (GOF) mutations in the pore-forming (Kir6.2) and regulatory (SUR1) subunits of KATP channels have been identified as the most common cause of human neonatal diabetes mellitus. The critical effect of these mutations is confirmed in mice expressing Kir6.2-GOF mutations in pancreatic β cells. A second KATP channel pore-forming subunit, Kir6.1, was originally cloned from the pancreas. Although the prominence of this subunit in the vascular system is well documented, a potential role in pancreatic β cells has not been considered...
January 2017: Journal of General Physiology
https://www.readbyqxmd.com/read/27940549/repression-of-telomerase-gene-promoter-requires-human-specific-genomic-context-and-is-mediated-by-multiple-hdac1-containing-corepressor-complexes
#9
De Cheng, Yuanjun Zhao, Shuwen Wang, Fan Zhang, Mariano Russo, Steven B McMahon, Jiyue Zhu
The human telomerase reverse transcriptase (hTERT) gene is repressed in most somatic cells, whereas the expression of the mouse mTert gene is widely detected. To understand the mechanisms of this human-specific repression, we constructed bacterial artificial chromosome (BAC) reporters using human and mouse genomic DNAs encompassing the TERT genes and neighboring loci. Upon chromosomal integration, the hTERT, but not the mTert, reporter was stringently repressed in telomerase-negative human cells in a histone deacetylase (HDAC)-dependent manner, replicating the expression of their respective endogenous genes...
March 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27743290/the-combination-of-calcium-ionophore-a23187-and-gm-csf-can-safely-salvage-aged-human-unfertilized-oocytes-after-icsi
#10
Konstantinos A Economou, Dimitra Christopikou, Erika Tsorva, Stephen Davies, Minas Mastrominas, Haris Cazlaris, Michael Koutsilieris, Panagoula Angelogianni, Dimitris Loutradis
PURPOSE: Artificial oocyte activation using calcium ionophores and enhancement of embryonic developmental potential by the granulocyte-macrophage colony-stimulating factor (GM-CSF) have already been reported. In this study, we evaluated the synergistic effect of these two methods on aged human unfertilized oocytes after intracytoplasmic sperm injection (ICSI). Then, we cultured the resulting embryos to the blastocyst stage and screened them for chromosomal abnormalities, to assess the safety of this protocol...
January 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/27709566/mutagenesis-and-genome-engineering-of-epstein-barr-virus-in-cultured-human-cells-by-crispr-cas9
#11
Kit-San Yuen, Chi-Ping Chan, Kin-Hang Kok, Dong-Yan Jin
The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 nuclease (Cas9) system is a powerful genome-editing tool for both chromosomal and extrachromosomal DNA. DNA viruses such as Epstein-Barr virus (EBV), which undergoes episomal replication in human cells, can be effectively edited by CRISPR/Cas9. We have demonstrated targeted editing of the EBV genome by CRISPR/Cas9 in several lines of EBV-infected cells. CRISPR/Cas9-based mutagenesis and genome engineering of EBV provides a new method for genetic analysis, which has some advantages over bacterial artificial chromosome-based recombineering...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27706134/de-novo-assembly-and-phasing-of-a-korean-human-genome
#12
Jeong-Sun Seo, Arang Rhie, Junsoo Kim, Sangjin Lee, Min-Hwan Sohn, Chang-Uk Kim, Alex Hastie, Han Cao, Ji-Young Yun, Jihye Kim, Junho Kuk, Gun Hwa Park, Juhyeok Kim, Hanna Ryu, Jongbum Kim, Mira Roh, Jeonghun Baek, Michael W Hunkapiller, Jonas Korlach, Jong-Yeon Shin, Changhoon Kim
Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17...
October 13, 2016: Nature
https://www.readbyqxmd.com/read/27639575/the-kaposi-s-sarcoma-associated-herpesvirus-orf35-gene-product-is-required-for-efficient-lytic-virus-reactivation
#13
Shir Bergson, Inbal Itzhak, Talya Wasserman, Anastasia Gelgor, Inna Kalt, Ronit Sarid
Kaposi's sarcoma-associated herpesvirus (KSHV) is implicated in the etiology of several human malignancies. KSHV open reading frame (orf) 35 encodes a conserved gammaherpesvirus protein with an, as yet, unknown function. Employing the bacterial artificial chromosome (BAC) system, we generated a recombinant viral clone that fails to express ORF35 (BAC16-ORF35-stop) but preserves intact adjacent and overlapping reading frames. Using this construct, we studied the role of this previously uncharacterized gene product during lytic reactivation of KSHV...
September 15, 2016: Virology
https://www.readbyqxmd.com/read/27608724/transcription-of-telomeric-dna-leads-to-high-levels-of-homologous-recombination-and-t-loops
#14
Anirban Kar, Smaranda Willcox, Jack D Griffith
The formation of DNA loops at chromosome ends (t-loops) and the transcription of telomeres producing G-rich RNA (TERRA) represent two central features of telomeres. To explore a possible link between them we employed artificial human telomeres containing long arrays of TTAGGG repeats flanked by the T7 or T3 promoters. Transcription of these DNAs generates a high frequency of t-loops within individual molecules and homologous recombination events between different DNAs at their telomeric sequences. T-loop formation does not require a single strand overhang, arguing that both terminal strands insert into the preceding duplex...
November 2, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27602518/m-6-a-rna-methylation-promotes-xist-mediated-transcriptional-repression
#15
Deepak P Patil, Chun-Kan Chen, Brian F Pickering, Amy Chow, Constanza Jackson, Mitchell Guttman, Samie R Jaffrey
The long non-coding RNA X-inactive specific transcript (XIST) mediates the transcriptional silencing of genes on the X chromosome. Here we show that, in human cells, XIST is highly methylated with at least 78 N(6)-methyladenosine (m(6)A) residues-a reversible base modification of unknown function in long non-coding RNAs. We show that m(6)A formation in XIST, as well as in cellular mRNAs, is mediated by RNA-binding motif protein 15 (RBM15) and its paralogue RBM15B, which bind the m(6)A-methylation complex and recruit it to specific sites in RNA...
September 15, 2016: Nature
https://www.readbyqxmd.com/read/27591740/a-kidney-injury-molecule-1-kim-1-gene-reporter-in-a-mouse-artificial-chromosome-the-responsiveness-to-cisplatin-toxicity-in-immortalized-mouse-kidney-s3-cells
#16
Kenji Kokura, Yasushi Kuromi, Takeshi Endo, Naohiko Anzai, Yasuhiro Kazuki, Mitsuo Oshimura, Tetsuya Ohbayashi
BACKGROUND: Kidney injury molecule-1 (Kim-1) has been validated as a urinary biomarker for acute and chronic renal damage. The expression of Kim-1 mRNA is also activated by acute kidney injury induced by cisplatin in rodents and humans. To date, the measurement of Kim-1 expression has not fully allowed the detection of in vitro cisplatin nephrotoxicity in immortalized culture cells such as human kidney-2 cells and immortalized proximal tubular epithelial cells. METHODS: We measured the augmentation of Kim-1 mRNA expression after cisplatin addition using immortalized S3 cells established from the kidneys of transgenic mice harboring temperature-sensitive large T antigen from Simian virus 40...
September 3, 2016: Journal of Gene Medicine
https://www.readbyqxmd.com/read/27568550/effects-of-duration-of-electric-pulse-on-in-vitro-development-of-cloned-cat-embryos-with-human-artificial-chromosome-vector
#17
Ltk Do, M Wittayarat, T Terazono, Y Sato, M Taniguchi, F Tanihara, T Takemoto, Y Kazuki, K Kazuki, M Oshimura, T Otoi
The current applications for cat cloning include production of models for the study of human and animal diseases. This study was conducted to investigate the optimal fusion protocol on in vitro development of transgenic cloned cat embryos by comparing duration of electric pulse. Cat fibroblast cells containing a human artificial chromosome (HAC) vector were used as genetically modified nuclear donor cells. Couplets were fused and activated simultaneously with a single DC pulse of 3.0 kV/cm for either 30 or 60 μs...
December 2016: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/27503586/brain-enhancer-activities-at-the-gene-poor-5p14-1-autism-associated-locus
#18
Yukiko U Inoue, Takayoshi Inoue
Due to the vast clinical and genetic heterogeneity, identification of causal genetic determinants for autism spectrum disorder (ASD) has proven to be complex. Whereas several dozen 'rare' genetic variants for ASD susceptibility have been identified, studies are still underpowered to analyse 'common' variants for their subtle effects. A recent application of genome-wide association studies (GWAS) to ASD indicated significant associations with the single nucleotide polymorphisms (SNPs) on chromosome 5p14.1, located in a non-coding region between cadherin10 (CDH10) and cadherin9 (CDH9)...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27502218/spliced-synthetic-genes-as-internal-controls-in-rna-sequencing-experiments
#19
Simon A Hardwick, Wendy Y Chen, Ted Wong, Ira W Deveson, James Blackburn, Stacey B Andersen, Lars K Nielsen, John S Mattick, Tim R Mercer
RNA sequencing (RNA-seq) can be used to assemble spliced isoforms, quantify expressed genes and provide a global profile of the transcriptome. However, the size and diversity of the transcriptome, the wide dynamic range in gene expression and inherent technical biases confound RNA-seq analysis. We have developed a set of spike-in RNA standards, termed 'sequins' (sequencing spike-ins), that represent full-length spliced mRNA isoforms. Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome...
September 2016: Nature Methods
https://www.readbyqxmd.com/read/27502217/representing-genetic-variation-with-synthetic-dna-standards
#20
Ira W Deveson, Wendy Y Chen, Ted Wong, Simon A Hardwick, Stacey B Andersen, Lars K Nielsen, John S Mattick, Tim R Mercer
The identification of genetic variation with next-generation sequencing is confounded by the complexity of the human genome sequence and by biases that arise during library preparation, sequencing and analysis. We have developed a set of synthetic DNA standards, termed 'sequins', that emulate human genetic features and constitute qualitative and quantitative spike-in controls for genome sequencing. Sequencing reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, which allows them them to be partitioned for parallel analysis...
September 2016: Nature Methods
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