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https://www.readbyqxmd.com/read/29168755/regulation-of-g2-m-transition-by-inhibition-of-wee1-and-pkmyt1-kinases
#1
REVIEW
Matthias Schmidt, Alexander Rohe, Charlott Platzer, Abdulkarim Najjar, Frank Erdmann, Wolfgang Sippl
In the cell cycle, there are two checkpoint arrests that allow cells to repair damaged DNA in order to maintain genomic integrity. Many cancer cells have defective G1 checkpoint mechanisms, thus depending on the G2 checkpoint far more than normal cells. G2 checkpoint abrogation is therefore a promising concept to preferably damage cancerous cells over normal cells. The main factor influencing the decision to enter mitosis is a complex composed of Cdk1 and cyclin B. Cdk1/CycB is regulated by various feedback mechanisms, in particular inhibitory phosphorylations at Thr14 and Tyr15 of Cdk1...
November 23, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29168654/integrating-clinicopathologic-and-genomic-tools-in-chemotherapy-decision-making-for-early-stage-breast-cancer
#2
Robert Havard, N Lynn Henry
No abstract text is available yet for this article.
November 23, 2017: Future Oncology
https://www.readbyqxmd.com/read/29168653/utilizing-biomarkers-in-colorectal-cancer-an-interview-with-ajay-goel
#3
Ajay Goel
Ajay Goel, PhD, is a Professor and Director, Center for Gastrointestinal Research, and Director, Center for Translational Genomics and Oncology, at the Baylor Scott & White Research Institute, Baylor University Medical Center in Dallas, Texas. Dr Goel has spent more than 20 years researching cancer and has been the lead author or contributor to over 240 scientific articles published in peer-reviewed international journals and several book chapters. He is also a primary inventor on more than 15 international patents aimed at developing various biomarkers for the diagnosis, prognosis and prediction of gastrointestinal cancers...
November 23, 2017: Future Oncology
https://www.readbyqxmd.com/read/29168417/a-dna-segment-encoding-the-anticodon-stem-loop-of-trna-determines-the-specific-recombination-of-integrative-conjugative-elements-in-acidithiobacillus-species
#4
Andrés Castillo, Mario Tello, Kenneth Ringwald, Lillian G Acuña, Raquel Quatrini, Omar Orellana
Horizontal gene transfer is crucial for the adaptation of microorganisms to environmental cues. The acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans encodes an integrative-conjugative genetic element (ICEAfe1) inserted in the gene encoding a tRNA(Ala). This genetic element is actively excised from the chromosome upon induction of DNA damage. A similar genetic element (ICEAcaTY.2) is also found in an equivalent position in the genome of Acidithiobacillus caldus. The local genomic context of both mobile genetic elements is highly syntenous and the cognate integrases are well conserved...
November 23, 2017: RNA Biology
https://www.readbyqxmd.com/read/29168053/the-sociobiology-of-genes-the-gene-s-eye-view-as-a-unifying-behavioural-ecological-framework-for-biological-evolution
#5
Alexis De Tiège, Yves Van de Peer, Johan Braeckman, Koen B Tanghe
Although classical evolutionary theory, i.e., population genetics and the Modern Synthesis, was already implicitly 'gene-centred', the organism was, in practice, still generally regarded as the individual unit of which a population is composed. The gene-centred approach to evolution only reached a logical conclusion with the advent of the gene-selectionist or gene's eye view in the 1960s and 1970s. Whereas classical evolutionary theory can only work with (genotypically represented) fitness differences between individual organisms, gene-selectionism is capable of working with fitness differences among genes within the same organism and genome...
November 22, 2017: History and Philosophy of the Life Sciences
https://www.readbyqxmd.com/read/29167391/integrated-genomic-and-interfacility-patient-transfer-data-reveal-the-transmission-pathways-of-multidrug-resistant-klebsiella-pneumoniae-in-a-regional-outbreak
#6
Evan S Snitkin, Sarah Won, Ali Pirani, Zena Lapp, Robert A Weinstein, Karen Lolans, Mary K Hayden
Development of effective strategies to limit the proliferation of multidrug-resistant organisms requires a thorough understanding of how such organisms spread among health care facilities. We sought to uncover the chains of transmission underlying a 2008 U.S. regional outbreak of carbapenem-resistant Klebsiella pneumoniae by performing an integrated analysis of genomic and interfacility patient-transfer data. Genomic analysis yielded a high-resolution transmission network that assigned directionality to regional transmission events and discriminated between intra- and interfacility transmission when epidemiologic data were ambiguous or misleading...
November 22, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/29167280/knotty-problems-during-mitosis-mechanistic-insight-into-the-processing-of-ultrafine-dna-bridges-in-anaphase
#7
Kata Sarlós, Andreas Biebricher, Erwin J G Petermann, Gijs J L Wuite, Ian D Hickson
To survive and proliferate, cells have to faithfully segregate their newly replicated genomic DNA to the two daughter cells. However, the sister chromatids of mitotic chromosomes are frequently interlinked by so-called ultrafine DNA bridges (UFBs) that are visible in the anaphase of mitosis. UFBs can only be detected by the proteins bound to them and not by staining with conventional DNA dyes. These DNA bridges are presumed to represent entangled sister chromatids and hence pose a threat to faithful segregation...
November 22, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29167269/ring-finger-protein-126-rnf126-suppresses-ionizing-radiation-induced-p53-binding-protein-1-53bp1-foci-formation
#8
Nam Soo Lee, Hae Ryung Chang, Soomi Kim, Jae-Hoon Ji, Joorak Lee, Hyun Ji Lee, Yoojeong Seo, Misun Kang, Joo Seok Han, Kyungjae Myung, Yonghwan Kim, Hongtae Kim
Cells have evolved sophisticated mechanisms to maintain genomic integrity in response to DNA damage. Ionizing radiation (IR) induced DNA damage results in the formation of IR induced foci (iRIF) in the nucleus. The iRIF formation is part of the DNA damage response (DDR), which is an essential signaling cascade that must be strictly regulated because either the loss of or an augmented DDR leads to loss of genome integrity. Accordingly, negative regulation of the DDR is as critical as its activation. In this study, we have identified ring finger protein 126 (RNF126) as a negative regulator of the DDR from a screen of iRIF containing 53BP1...
November 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29167199/the-germline-specific-factor-oef-1-facilitates-coordinated-progression-through-germ-cell-cevelopment-in-caenorhabditis-elegans
#9
Catherine McManus, Valerie Reinke
The purpose of germ cells is to ensure the faithful transmission of genetic material to the next generation. In order to develop into mature gametes, germ cells must pass through cell cycle checkpoints while maintaining totipotency and genomic integrity. How germ cells coordinate developmental events while simultaneously protecting their unique fate is not well understood. Here we characterize a novel nuclear protein OEF-1 with highly specific germline expression in C. elegans OEF-1 is initially detected early in embryogenesis and is expressed in the nuclei of all germ cells during larval stages...
November 22, 2017: Genetics
https://www.readbyqxmd.com/read/29166606/sumoylation-promotes-nuclear-import-and-stabilization-of-polo-like-kinase-1-to-support-its-mitotic-function
#10
Donghua Wen, Jianguo Wu, Lei Wang, Zheng Fu
As a pivotal mitotic regulator, polo-like kinase 1 (PLK1) is under highly coordinated and multi-layered regulation. However, the pathways that control PLK1's activity and function have just begun to be elucidated. PLK1 has recently been shown to be functionally modulated by post-translational modifications (PTMs), including phosphorylation and ubiquitination. Herein, we report that SUMOylation plays an essential role in regulating PLK1's mitotic function. We found that Ubc9 was recruited to PLK1 upon initial phosphorylation and activation by CDK1/cyclin B...
November 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/29165708/separase-prevents-genomic-instability-by-controlling-replication-fork-speed
#11
Francesco Cucco, Elisa Palumbo, Serena Camerini, Barbara D'Alessio, Valentina Quarantotti, Maria Luisa Casella, Ilaria Maria Rizzo, Dubravka Cukrov, Domenico Delia, Antonella Russo, Marco Crescenzi, Antonio Musio
Proper chromosome segregation is crucial for preserving genomic integrity, and errors in this process cause chromosome mis-segregation, which may contribute to cancer development. Sister chromatid separation is triggered by Separase, an evolutionary conserved protease that cleaves the cohesin complex, allowing the dissolution of sister chromatid cohesion. Here we provide evidence that Separase participates in genomic stability maintenance by controlling replication fork speed. We found that Separase interacted with the replication licensing factors MCM2-7, and genome-wide data showed that Separase co-localized with MCM complex and cohesin...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165643/expanding-the-repertoire-of-dna-shape-features-for-genome-scale-studies-of-transcription-factor-binding
#12
Jinsen Li, Jared M Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165610/gramene-2018-unifying-comparative-genomics-and-pathway-resources-for-plant-research
#13
Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M Bolser, Guy Naamati, Electra Tapanari, Nuno Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Munoz-Pomer Fuentes, Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D Stein, Robert Petryszak, Irene Papatheodorou, Paul J Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classification, whole-genome alignments, and synteny. Additional gene annotations include ontology-based protein structure and function; genetic, epigenetic, and phenotypic diversity; and pathway associations...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165593/funcoup-4-new-species-data-and-visualization
#14
Christoph Ogris, Dimitri Guala, Mateusz Kaduk, Erik L L Sonnhammer
This release of the FunCoup database (http://funcoup.sbc.su.se) is the fourth generation of one of the most comprehensive databases for genome-wide functional association networks. These functional associations are inferred via integrating various data types using a naive Bayesian algorithm and orthology based information transfer across different species. This approach provides high coverage of the included genomes as well as high quality of inferred interactions. In this update of FunCoup we introduce four new eukaryotic species: Schizosaccharomyces pombe, Plasmodium falciparum, Bos taurus, Oryza sativa and open the database to the prokaryotic domain by including networks for Escherichia coli and Bacillus subtilis...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165426/the-mitochondrial-upr-mechanisms-physiological-functions-and-implications-in-ageing
#15
REVIEW
Tomer Shpilka, Cole M Haynes
Mitochondrial function declines during ageing owing to the accumulation of deleterious mitochondrial genomes and damage resulting from the localized generation of reactive oxygen species, both of which are often exacerbated in diseases such as Parkinson disease. Cells have several mechanisms to assess mitochondrial function and activate a transcriptional response known as the mitochondrial unfolded protein response (UPR(mt)) when mitochondrial integrity and function are impaired. The UPR(mt) promotes cell survival and the recovery of the mitochondrial network to ensure optimal cellular function...
November 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29165335/integral-phylogenomic-approach-over-ilex-l-species-from-southern-south-america
#16
Jimena Cascales, Mariana Bracco, Mariana J Garberoglio, Lidia Poggio, Alexandra M Gottlieb
The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I.paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses...
November 22, 2017: Life
https://www.readbyqxmd.com/read/29164518/reducing-production-of-fumonisin-mycotoxins-in-fusarium-verticillioides-by-rna-interference
#17
Eric T Johnson, Robert H Proctor, Christopher A Dunlap, Mark Busman
The fungus Fusarium verticillioides is a maize pathogen that can produce fumonisin mycotoxins in ears under certain environmental conditions. Because fumonisins pose health risks to humans and livestock, control strategies with minimal risk to the environment are needed to reduce fumonisin contamination. Host-induced gene silencing is a promising technique in which double-stranded RNA expressed in the plant host is absorbed by an invading fungus and down-regulates genes critical for pathogenicity or mycotoxin production in the fungus...
November 22, 2017: Mycotoxin Research
https://www.readbyqxmd.com/read/29164058/delineation-of-the-hpv11e6-and-hpv18e6-pathways-in-initiating-cellular-transformation
#18
Lamech M Mwapagha, Nicki Tiffin, M Iqbal Parker
Although high-risk human papillomaviruses (HPVs) are the major risk factors for cervical cancer they have been associated with several other cancers, such as head and neck and oral cancers. Since integration of low-risk HPV11 DNA has been demonstrated in esophageal tumor genomes, this study compared the effects of low-risk HPV11E6 and high-risk HPV18E6 on cellular gene expression. The HPV11E6 and HPV18E6 genes were cloned into an adenoviral vector and expressed in human keratinocytes (HaCaT) in order to investigate early events and to eliminate possible artifacts introduced by selective survival of fast growing cells in stable transfection experiments...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29163825/maternal-histone-acetyltransferase-kat8-is-required-for-porcine-preimplantation-embryo-development
#19
Zubing Cao, Ronghua Wu, Di Gao, Tengteng Xu, Lei Luo, Yunsheng Li, Jianyong Han, Yunhai Zhang
K (lysine) acetyltransferase 8 (KAT8), an acetyltransferase that specifically catalyzes histone H4 lysine 16 acetylation, is critical for key biological processes including cell proliferation and maintenance of genome stability. However, the role of KAT8 during preimplantation development in pigs remains unclear. Results herein showed that KAT8 mRNA is maternally derived and it is required for successful development of early embryos. An abundance of KAT8 transcripts are expressed in oocytes and its abundance continuously decreases throughout meiotic maturation and preimplantation development...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29163774/integrative-analysis-of-novel-hypomethylation-and-gene-expression-signatures-in-glioblastomas
#20
Anan Yin, Amandine Etcheverry, Yalong He, Marc Aubry, Jill Barnholtz-Sloan, Luhua Zhang, Xinggang Mao, Weijun Chen, Bolin Liu, Wei Zhang, Jean Mosser, Xiang Zhang
Molecular and clinical heterogeneity critically hinders better treatment outcome for glioblastomas (GBMs); integrative analysis of genomic and epigenomic data may provide useful information for improving personalized medicine. By applying training-validation approach, we identified a novel hypomethylation signature comprising of three CpGs at non-CpG island (CGI) open sea regions for GBMs. The hypomethylation signature consistently predicted poor prognosis of GBMs in a series of discovery and validation datasets...
October 27, 2017: Oncotarget
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