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Homologous recombination

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https://www.readbyqxmd.com/read/28822035/identification-and-functional-characterization-of-a-p-coumaroyl-coa-2-hydroxylase-involved-in-the-biosynthesis-of-coumarin-skeleton-from-peucedanum-praeruptorum-dunn
#1
Ruolan Yao, Yucheng Zhao, Tingting Liu, Chuanlong Huang, Sheng Xu, Ziwei Sui, Jun Luo, Lingyi Kong
A p-coumaroyl CoA 2'-hydroxylase responsible for the formation of coumarin lactone ring was identified from Peucedanum praeruptorum Dunn and functionally characterized in vitro. Coumarins are important plant secondary metabolites with a variety of biological activities. Ortho-hydroxylation of cinnamates leads to the formation of coumarin lactone ring and is generally thought to be a key step in coumarin biosynthesis. However, ortho-hydroxylases, especially p-coumaroyl CoA 2'-hydroxylase (C2'H) responsible for the biosynthesis of the most common coumarin skeleton, have received insufficient attention...
August 18, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28822007/brca1-like-profile-is-not-significantly-associated-with-survival-benefit-of-non-myeloablative-intensified-chemotherapy-in-the-gain-randomized-controlled-trial
#2
A G J van Rossum, P C Schouten, K E Weber, V Nekljudova, C Denkert, C Solbach, C H Köhne, C Thomssen, H Forstbauer, G Hoffmann, A Kohls, S Schmatloch, C Schem, G von Minckwitz, T Karn, V J Möbus, S C Linn, S Loibl, F Marmé
PURPOSE: The BRCA1-like profile identifies tumors with a defect in homologous recombination due to inactivation of BRCA1. This profile has been shown to predict which stage III breast cancer patients benefit from myeloablative, DNA double-strand-break-inducing chemotherapy. We tested the predictive potential of the BRCA1-like profile for adjuvant non-myeloablative, intensified dose-dense chemotherapy in the GAIN trial. METHODS: Lymph node positive breast cancer patients were randomized to 3 × 3 dose-dense cycles of intensified epirubicin, paclitaxel, and cyclophosphamide (ETC) or 4 cycles concurrent epirubicin and cyclophosphamide followed by 10 cycles of weekly paclitaxel combined with 4 cycles capecitabine (EC-TX)...
August 18, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28821733/three-recombinantly-expressed-apple-tyrosinases-suggest-the-amino-acids-responsible-for-mono-versus-diphenolase-activity-in-plant-polyphenol-oxidases
#3
Ioannis Kampatsikas, Aleksandar Bijelic, Matthias Pretzler, Annette Rompel
Tyrosinases and catechol oxidases belong to the polyphenol oxidase (PPO) enzyme family, which is mainly responsible for the browning of fruits. Three cDNAs encoding PPO pro-enzymes have been cloned from leaves of Malus domestica (apple, MdPPO). The three pro-enzymes MdPPO1-3 were heterologously expressed in E. coli yielding substantial amounts of protein and have been characterized with regard to their optimum of activity resulting from SDS, acidic and proteolytic activation. Significant differences were found in the kinetic characterization of MdPPO1-3 when applying different mono- and diphenolic substrates...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821267/small-size-recombinant-adenoviral-hexon-protein-fragments-for-the-production-of-virus-type-specific-antibodies
#4
Martin Pacesa, Rodinde Hendrickx, Manuela Bieri, Justin W Flatt, Urs F Greber, Silvio Hemmi
BACKGROUND: Adenoviruses are common pathogens infecting animals and humans. They are classified based on serology, or genome sequence information. These methods have limitations due to lengthy procedures or lack of infectivity data. Adenoviruses are easy to produce and amenable to genetic and biochemical modifications, which makes them a powerful tool for biological studies, and clinical gene-delivery and vaccine applications. Antibodies directed against adenoviral proteins are important diagnostic tools for virus identification in vivo and in vitro, and are used to elucidate infection mechanisms, often in combination with genomic sequencing and type specific information from hyper-variable regions of structural proteins...
August 18, 2017: Virology Journal
https://www.readbyqxmd.com/read/28818366/expression-of-recombinant-snrk1-in-e-coli-characterization-of-adenine-nucleotide-binding-to-the-snrk1-1-akin%C3%AE-%C3%AE-%C3%AE-3-complex
#5
José Luis Maya-Bernal, Alejandra Ávila, Ana Ruiz-Gayosso, Ricardo Trejo-Fregoso, Nancy Pulido, Alejandro Sosa-Peinado, Esther Zúñiga-Sánchez, Eleazar Martínez-Barajas, Rogelio Rodríguez-Sotres, Patricia Coello
The SnRK1 complexes in plants belong to the family of AMPK/SNF1 kinases, which have been associated with the control of energy balance, in addition to being involved in the regulation of other aspects of plant growth and development. Analysis of complex formation indicates that increased activity is achieved when the catalytic subunit is phosphorylated and bound to regulatory subunits. SnRK1.1 subunit activity is higher than that of SnRK1.2, which also exhibits reduced activation due to the regulatory subunits...
October 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28815851/basics-of-genome-editing-technology-and-its-application-in-livestock-species
#6
REVIEW
Bjoern Petersen
In the last decade, the research community has witnessed a blooming of targeted genome editing tools and applications. Novel programmable DNA nucleases such as zinc finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs) and the clustered regularly interspaced short palindromic repeats/Cas9 system (CRISPR/Cas9) possess long recognition sites and are capable of cutting DNA in a very specific manner. These DNA nucleases mediate targeted genetic alterations by enhancing the DNA mutation rate via induction of double-strand breaks at a predetermined genomic site...
August 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28815403/overexpression-of-topoisomerase-2-alpha-confers-a-poor-prognosis-in-pancreatic-adenocarcinoma-identified-by-co-expression-analysis
#7
Zhou Zhou, Shi Liu, Meng Zhang, Rui Zhou, Jing Liu, Ying Chang, Qiu Zhao
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is the fourth most common cause of human cancer-related death in the developed countries. Its progression and prognosis are influenced by a complex network of gene interactions. AIMS: The purpose of this study is to explore key genes associated with pancreatic ductal adenocarcinoma and to predict the possible mechanisms. METHODS: A weighted gene co-expression network was constructed to identify gene modules associated with the progression of PDAC...
August 16, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28815215/structural-characterization-of-acidic-m17-leucine-aminopeptidases-from-the-tritryps-and-evaluation-of-their-role-in-nutrient-starvation-in-trypanosoma-brucei
#8
Jennifer Timm, Maria Valente, Daniel García-Caballero, Keith S Wilson, Dolores González-Pacanowska
Leucine aminopeptidase (LAP) is found in all kingdoms of life and catalyzes the metal-dependent hydrolysis of the N-terminal amino acid residue of peptide or amino acyl substrates. LAPs have been shown to participate in the N-terminal processing of certain proteins in mammalian cells and in homologous recombination and transcription regulation in bacteria, while in parasites, they are involved in host cell invasion and provision of essential amino acids for growth. The enzyme is essential for survival in Plasmodium falciparum, where its drug target potential has been suggested...
July 2017: MSphere
https://www.readbyqxmd.com/read/28814514/ba71%C3%AE-cd2-a-new-recombinant-live-attenuated-african-swine-fever-virus-with-cross-protective-capabilities
#9
Paula L Monteagudo, Anna Lacasta, Elisabeth López, Laia Bosch, Javier Collado, Sonia Pina-Pedrero, Florencia Correa-Fiz, Francesc Accensi, María Jesús Navas, Enric Vidal, María J Bustos, Javier M Rodríguez, Andreas Gallei, Veljko Nikolin, María L Salas, Fernando Rodríguez
African swine fever is a highly contagious viral disease of mandatory declaration to the World Organization for Animal Health (OIE). Lack of available vaccines make its control difficult and thus ASFV represents a major threat to the swine industry. Inactivated vaccines do not confer solid protection against African swine fever virus (ASFV). Conversely, live attenuated viruses (LAV), either naturally isolated or obtained by genetic manipulation, have demonstrated reliable protection against homologous ASFV strains, albeit little or no protection has been demonstrated against heterologous viruses...
August 16, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28814116/the-dark-side-of-the-ring-role-of-the-dna-sliding-surface-of-pcna
#10
Matteo De March, Alfredo De Biasio
The proliferating cell nuclear antigen (PCNA) sliding clamp lies at the heart of the accurate duplication of eukaryotic genomes. While the outer surface of the PCNA ring interacts with polymerases and other factors, the role of the inner wall facing the DNA is elusive. Recent evidence shows that conserved basic residues in the PCNA central channel create a specific surface that recognizes the DNA backbone and enables the clamp to slide by rotationally tracking the DNA helix. The sliding surface can be modulated (i) through lysine acetylation, which triggers PCNA degradation during nucleotide excision repair (NER) and stimulates repair by homologous recombination (HR) or (ii) through binding of the protein factor p15(PAF), which turns off DNA lesion bypass...
August 17, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28811335/the-conserved-and-unique-genetic-architecture-of-kernel-size-and-weight-in-maize-and-rice
#11
Jie Liu, Juan Huang, Huan Guo, Liu Lan, Hongze Wang, Yuancheng Xu, Xiaohong Yang, Wenqiang Li, Hao Tong, Yingjie Xiao, Qingchun Pan, Feng Qiao, Mohammad Sharif Raihan, Haijun Liu, Xuehai Zhang, Ning Yang, Xiaqing Wang, Min Deng, Minliang Jin, Lijun Zhao, Xin Luo, Yang Zhou, Xiang Li, Wei Zhan, Nannan Liu, Hong Wang, Gengshen Chen, Qing Li, Jianbing Yan
Maize is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation...
August 15, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28807928/role-of-translesion-synthesis-dna-polymerases-in-dna-replication-in-the-presence-of-a-weak-dna-polymerase-%C3%AE-in-saccharomyces-cerevisiae
#12
Likui Zhang, Yanchao Huang, Xinyuan Zhu, Yuxiao Wang, Haoqiang Shi, Min Chen, Kunming Dong, Xiaojian Zhou
Translesion synthesis (TLS) DNA polymerases (pols) are often mutagenic for lesion bypass due to their low fidelity. Here, we isolated a weak yeast DNA pol δ mutant that possessed amino acid substitution V592G by genetic selection. The pol3-V592G cells were sensitive to hydroxyurea (HU), which increases the requirement for dNTPs, and their HU sensitivity was suppressed by L612M substitution. We also demonstrated that V592G substitution suppressed the phosphonoacetic acid (PAA) sensitivity of pol3-L612M cells, suggesting a cycle of mutual suppression in the HU- and PAA-sensitive yeast DNA pol δ mutants as similarly observed in the optA1- and PAA-sensitive T4 DNA pol mutants...
August 14, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28804739/selection-of-genetically-modified-bacteriophages-using-the-crispr-cas-system
#13
Miriam Manor, Udi Qimron
We present a CRISPR-Cas based technique for deleting genes from the T7 bacteriophage genome. A DNA fragment encoding homologous arms to the target gene to be deleted is first cloned into a plasmid. The T7 phage is then propagated in Escherichia coli harboring this plasmid. During this propagation, some phage genomes undergo homologous recombination with the plasmid, thus deleting the targeted gene. To select for these genomes, the CRISPR-Cas system is used to cleave non-edited genomes, enabling isolation of the desired recombinant phages...
August 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28803862/recombinant-lcmv-vectors-induce-protective-immunity-following-homologous-and-heterologous-vaccinations
#14
Jessica Wingerath, Dmitrij Ostroumov, Norman Woller, Michael P Manns, Daniel D Pinschewer, Klaus Orlinger, Ursula Berka, Florian Kühnel, Thomas C Wirth
Successful vaccination against cancer and infectious diseases relies on the induction of adaptive immune responses that induce high-titer antibodies or potent cytoxic T cell responses. In contrast to humoral vaccines, the amplification of cellular immune responses is often hampered by anti-vector immunity that either pre-exists or develops after repeated homologous vaccination. Replication-defective lymphocytic choriomeningitis virus (LCMV) vectors represent a novel generation of vaccination vectors that induce potent immune responses while escaping recognition by neutralizing antibodies...
July 20, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28803330/bime2-a-novel-gene-required-for-interhomolog-meiotic-recombination-in-the-protist-model-organism-tetrahymena
#15
Anura Shodhan, Maria Novatchkova, Josef Loidl
Meiotic recombination is initiated by DNA double-strand breaks (DSBs). Most DSBs are converted into nonreciprocal exchanges (gene conversions) or crossovers (COs) between sister chromatids. Only a minority of DSBs are processed toward interhomolog COs, the precursors of the chiasmata that connect homologous chromosomes. Dmc1, the meiosis-specific paralog of the universal recombination protein Rad51, is required for interhomolog COs; in its absence, univalents are primarily formed. Here, we report a ciliate-specific novel meiotic gene, BIME2, which also promotes interhomolog crossing over...
August 12, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28801912/computational-sequence-design-with-r2odna-designer
#16
James T MacDonald, Velia Siciliano
Recently developed DNA assembly methods have enabled the rapid and simultaneous assembly of multiple parts to create complex synthetic gene circuits. A number of groups have proposed the use of computationally designed orthogonal spacer sequences to guide the ordered assembly of parts using overlap-directed or homologous recombination-based methods. This approach is particularly useful for assembling multiple parts with repetitive elements. Orthogonal spacer sequences (sometimes called UNSs-unique nucleotide sequences) also have a number of other potential uses including in the design of synthetic promoters regulated by novel regulatory elements...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801308/egfr-mutations-compromise-hypoxia-associated-radiation-resistance-through-impaired-replication-fork-associated-dna-damage-repair
#17
Mohammad Saki, Haruhiko Makino, Prashanthi Javvadi, Nozomi Tomimatsu, Lianghao Ding, Jennifer E Clark, Elaine Gavin, Kenichi Takeda, Joel Andrews, Debabrata Saha, Michael D Story, Sandeep Burma, Chaitanya Nirodi
Epidermal growth factor receptor (EGFR) signaling has been implicated in hypoxia-associated resistance to radiation or chemotherapy. Non-small cell lung carcinomas (NSCLC) with activating L858R or ΔE746-E750 EGFR mutations exhibit elevated EGFR activity and downstream signaling. Here, relative to wild type (WT) EGFR, mutant (MT) EGFR expression significantly increases radiosensitivity in hypoxic cells. Gene expression profiling in human bronchial epithelial cells (HBEC) revealed that MT-EGFR expression elevated transcripts related to cell cycle and replication in aerobic and hypoxic conditions and down-regulated RAD50, a critical component of non-homologous end-joining (NHEJ) and homologous recombination (HR) DNA repair pathways...
August 11, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28800848/cold-generation-of-smoke-flavour-by-the-first-phenolic-acid-decarboxylase-from-a-filamentous-ascomycete-isaria-farinosa
#18
Diana Linke, Stephanie J L Riemer, Silke Schimanski, Annabel Nieter, Ulrich Krings, Ralf G Berger
A decarboxylase (IfPAD) from the ascomycete Isaria farinosa converted ferulic acid to 4-vinylguaiacol (4-VG), a volatile which imparts the distinct "smoke flavor" of pyrolized wood. The activity was enhanced by adding (E)-ferulic acid to the culture medium and peaked with 3.6 U g(-1) mycelium (1 μmol 4-VG min(-1)). The coding sequence of 543 bp was translated into a 25 kDa protein with a homology of 91 % to putative phenolic acid decarboxylases of its teleomorph, Cordyceps militaris, and Beauveria bassiana, the anamorph of Cordyceps bassiana...
September 2017: Fungal Biology
https://www.readbyqxmd.com/read/28797117/analysis-of-the-impact-of-the-absence-of-rad51-strand-exchange-activity-in-arabidopsis-meiosis
#19
Gunjita Singh, Olivier Da Ines, Maria Eugenia Gallego, Charles I White
The ploidy of eukaryote gametes must be halved to avoid doubling of numbers of chromosomes with each generation and this is carried out by meiosis, a specialized cell division in which a single chromosomal replication phase is followed by two successive nuclear divisions. With some exceptions, programmed recombination ensures the proper pairing and distribution of homologous pairs of chromosomes in meiosis and recombination defects thus lead to sterility. Two highly related recombinases are required to catalyse the key strand-invasion step of meiotic recombination and it is the meiosis-specific DMC1 which is generally believed to catalyse the essential non-sister chromatid crossing-over, with RAD51 catalysing sister-chromatid and non-cross-over events...
2017: PloS One
https://www.readbyqxmd.com/read/28796463/defensin-neurotoxin-dyad-in-a-basally-branching-metazoan-sea-anemone
#20
Chan-Hee Kim, Ye Jin Lee, Hye-Jin Go, Hye Young Oh, Tae Kwan Lee, Ji Been Park, Nam Gyu Park
Recent studies suggest that vertebrate and invertebrate defensins have evolved from two independent ancestors, and that both defensins could share origins with animal toxins. Here, we purified novel sea anemone neurotoxin (BDS)-like antimicrobial peptides (AMPs)-Crassicorin-I and its putative homolog (Crassicorin-II)-from the pharynx extract of an anthozoan sea anemone (Urticina crassicornis). Based on structural analyses and cDNA cloning, mature Crassicorin-I represents a cationic AMP likely generated from a precursor and comprising 40 amino acid residues, including six cysteines forming three intramolecular disulphide bonds...
August 10, 2017: FEBS Journal
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