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Current Genomics

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https://www.readbyqxmd.com/read/28367077/protein-and-genetic-composition-of-four-chromatin-types-in-drosophila-melanogaster-cell-lines
#1
Lidiya V Boldyreva, Fyodor P Goncharov, Olga V Demakova, Tatyana Yu Zykova, Victor G Levitsky, Nikolay N Kolesnikov, Alexey V Pindyurin, Valeriy F Semeshin, Igor F Zhimulev
BACKGROUND: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby. RESULTS: Here, we describe the properties of these chromatin types across different cell lines...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367076/genetic-imbalance-in-patients-with-cervical-artery-dissection
#2
Caspar Grond-Ginsbach, Bowang Chen, Michael Krawczak, Rastislav Pjontek, Philip Ginsbach, Yanxiang Jiang, Shérine Abboud, Marie-Luise Arnold, Anna Bersano, Tobias Brandt, Valeria Caso, Stéphanie Debette, Martin Dichgans, Andreas Geschwendtner, Giacomo Giacalone, Juan-José Martin, Antti J Metso, Tiina M Metso, Armin J Grau, Manja Kloss, Christoph Lichy, Alessandro Pezzini, Christopher Traenka, Stefan Schreiber, Vincent Thijs, Emmanuel Touzé, Elisabetta Del Zotto, Turgut Tatlisumak, Didier Leys, Philippe A Lyrer, Stefan T Engelter
BACKGROUND: Genetic and environmental risk factors are assumed to contribute to the susceptibility to cervical artery dissection (CeAD). To explore the role of genetic imbalance in the etiology of CeAD, copy number variants (CNVs) were identified in high-density microarrays samples from the multicenter CADISP (Cervical Artery Dissection and Ischemic Stroke Patients) study and from control subjects from the CADISP study and the German PopGen biobank. Microarray data from 833 CeAD patients and 2040 control subjects (565 subjects with ischemic stroke due to causes different from CeAD and 1475 disease-free individuals) were analyzed...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367075/anticancer-natural-compounds-as-epigenetic-modulators-of-gene-expression
#3
REVIEW
Edward A Ratovitski
Accumulating evidence shows that hallmarks of cancer include: "genetic and epigenetic alterations leading to inactivation of cancer suppressors, overexpression of oncogenes, deregulation of intracellular signaling cascades, alterations of cancer cell metabolism, failure to undergo cancer cell death, induction of epithelial to mesenchymal transition, invasiveness, metastasis, deregulation of immune response and changes in cancer microenvironment, which underpin cancer development". Natural compounds as bioactive ingredients isolated from natural sources (plants, fungi, marine life forms) have revolutionized the field of anticancer therapeutics and rapid developments in preclinical studies are encouraging...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367074/anti-cancer-phytometabolites-targeting-cancer-stem-cells
#4
REVIEW
Heron F V Torquato, Márcia I Goettert, Giselle Z Justo, Edgar J Paredes-Gamero
Medicinal plants are a plentiful source of bioactive molecules with much structural diversity. In cancer treatment, molecules obtained from plants represent an attractive alternative to other treatments because several plant-derived compounds have exhibited lower toxicity and higher selectivity against cancer cells. In this review, we focus on the possible application of bioactive molecules obtained from plants against more primitive cell populations in cancers, cancer stem cells. Cancer stem cells are present in several kinds of tumors and are responsible for recurrences and metastases...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367073/natural-compounds-as-modulators-of-non-apoptotic-cell-death-in-cancer-cells
#5
Luis Miguel Guamán-Ortiz, Maria Isabel Ramirez Orellana, Edward A Ratovitski
Cell death is an innate capability of cells to be removed from microenvironment, if and when they are damaged by multiple stresses. Cell death is often regulated by multiple molecular pathways and mechanism, including apoptosis, autophagy, and necroptosis. The molecular network underlying these processes is often intertwined and one pathway can dynamically shift to another one acquiring certain protein components, in particular upon treatment with various drugs. The strategy to treat human cancer ultimately relies on the ability of anticancer therapeutics to induce tumor-specific cell death, while leaving normal adjacent cells undamaged...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367072/natural-compounds-as-modulators-of-cell-cycle-arrest-application-for-anticancer-chemotherapies
#6
REVIEW
Natalia Bailon-Moscoso, Gabriela Cevallos-Solorzano, Juan Carlos Romero-Benavides, Maria Isabel Ramirez Orellana
Natural compounds from various plants, microorganisms and marine species play an important role in the discovery novel components that can be successfully used in numerous biomedical applications, including anticancer therapeutics. Since uncontrolled and rapid cell division is a hallmark of cancer, unraveling the molecular mechanisms underlying mitosis is key to understanding how various natural compounds might function as inhibitors of cell cycle progression. A number of natural compounds that inhibit the cell cycle arrest have proven effective for killing cancer cells in vitro, in vivo and in clinical settings...
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28367071/anticancer-natural-compounds-molecular-mechanisms-and-functions-%C3%A2-part-ii
#7
Edward A Ratovitski
No abstract text is available yet for this article.
April 2017: Current Genomics
https://www.readbyqxmd.com/read/28217009/meta-analysis-reveals-no-association-of-dnmt3b-149-c-t-gene-polymorphism-with-overall-cancer-risk
#8
Raju Kumar Mandal, Shafiul Haque, Mohd Wahid, Arshad Jawed, Naseem Akhter, Md Ekhlaque Ahmed Khan, Aditya Kumar Panda, Mohammed Yahya Areeshi, Sajad Ahmad Dar
BACKGROUND: DNA methyltransferase-3B (DNMT3B) plays a key role in establishment and maintenance of genomic methylation patterns. Polymorphism in promoter region -149 C>T (C46359T) of DNMT3B gene may alter DNMT3B activity which leads to increased susceptibility to cancer. Inconsistent results regarding this have been reported in a number of studies. OBJECTIVE: To carry out a meta-analysis of the studies reported to assess the precise relationship between the DNMT3B -149 C>T polymorphism and the overall cancer risk...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217008/toxicogenomics-to-evaluate-endocrine-disrupting-effects-of-environmental-chemicals-using-the-zebrafish-model
#9
Karina Caballero-Gallardo, Jesus Olivero-Verbel, Jennifer L Freeman
The extent of our knowledge on the number of chemical compounds related to anthropogenic activities that can cause damage to the environment and to organisms is increasing. Endocrine disrupting chemicals (EDCs) are one group of potentially hazardous substances that include natural and synthetic chemicals and have the ability to mimic endogenous hormones, interfering with their biosynthesis, metabolism, and normal functions. Adverse effects associated with EDC exposure have been documented in aquatic biota and there is widespread interest in the characterization and understanding of their modes of action...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217007/computational-tools-for-genomic-studies-in-plants
#10
Manuel Martinez
In recent years, the genomic sequence of numerous plant species including the main crop species has been determined. Computational tools have been developed to deal with the issue of which plant has been sequenced and where is the sequence hosted. In this mini-review, the databases for genome projects, the databases created to host species/clade projects and the databases developed to perform plant comparative genomics are revised. Because of their importance in modern research, an in-depth analysis of the plant comparative genomics databases has been performed...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217006/mutagenesis-and-tilling-to-dissect-gene-function-in-plants
#11
Zerihun Tadele
Mutagenesis can be random or targeted and occur by nature or artificially by humans. However, the bulk of mutagenesis employed in plants are random and caused by physical agents such as x-ray and gamma-ray or chemicals such as ethyl-methane sulfonate (EMS). Researchers are interested in first identifying these mutations and/or polymorphisms in the genome followed by investigating their effects in the plant function as well as their application in crop improvement. The high-throughput technique called TILLING (Targeting Induced Local Lesion IN Genomes) has been already established and become popular for identifying candidate mutant individuals harboring mutations in the gene of interest...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217005/chromatin-based-epigenetic-regulation-of-plant-abiotic-stress-response
#12
Garima Pandey, Namisha Sharma, Pranav Pankaj Sahu, Manoj Prasad
Plants are continuously exposed to various abiotic and biotic factors limiting their growth and reproduction. In response, they need various sophisticated ways to adapt to adverse environmental conditions without compromising their proper development, reproductive success and eventually survival. This requires an intricate network to regulate gene expression at transcriptional and post-transcriptional levels, including epigenetic switches. Changes in chromatin modifications such as DNA and histone methylation have been observed in plants upon exposure to several abiotic stresses...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217004/rna-silencing-in-plants-mechanisms-technologies-and-applications-in-horticultural-crops
#13
Qigao Guo, Qing Liu, Neil A Smith, Guolu Liang, Ming-Bo Wang
Understanding the fundamental nature of a molecular process or a biological pathway is often a catalyst for the development of new technologies in biology. Indeed, studies from late 1990s to early 2000s have uncovered multiple overlapping but functionally distinct RNA silencing pathways in plants, including the posttranscriptional microRNA and small interfering RNA pathways and the transcriptional RNA-directed DNA methylation pathway. These findings have in turn been exploited for developing artificial RNA silencing technologies such as hairpin RNA, artificial microRNA, intrinsic direct repeat, 3' UTR inverted repeat, artificial trans-acting siRNA, and virus-induced gene silencing technologies...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28217003/reverse-genetics-and-high-throughput-sequencing-methodologies-for-plant-functional-genomics
#14
Anis Ben-Amar, Samia Daldoul, Götz M Reustle, Gabriele Krczal, Ahmed Mliki
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/27499686/applications-of-dna-technologies-in-agriculture
#15
Jinggui Fang, Xudong Zhu, Chen Wang, Lingfei Shangguan
With the development of molecular biology, some DNA-based technologies have showed great potentiality in promoting the efficiency of crop breeding program, protecting germplasm resources, improving the quality and outputs of agricultural products, and protecting the eco-environment etc., making their roles in modern agriculture more and more important. To better understand the application of DNA technologies in agriculture, and achieve the goals to promote their utilities in modern agriculture, this paper describes, in some different way, the applications of molecular markers, transgenic engineering and gene's information in agriculture...
August 2016: Current Genomics
https://www.readbyqxmd.com/read/27499685/bioinformatics-approach-in-plant-genomic-research
#16
Quang Ong, Phuc Nguyen, Nguyen Phuong Thao, Ly Le
The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study...
August 2016: Current Genomics
https://www.readbyqxmd.com/read/27499684/exploring-genetic-diversity-in-plants-using-high-throughput-sequencing-techniques
#17
Yoshihiko Onda, Keiichi Mochida
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed...
August 2016: Current Genomics
https://www.readbyqxmd.com/read/27499683/genomics-approaches-for-improving-salinity-stress-tolerance-in-crop-plants
#18
Ramsong Chantre Nongpiur, Sneh Lata Singla-Pareek, Ashwani Pareek
Salinity is one of the major factors which reduces crop production worldwide. Plant responses to salinity are highly complex and involve a plethora of genes. Due to its multigenicity, it has been difficult to attain a complete understanding of how plants respond to salinity. Genomics has progressed tremendously over the past decade and has played a crucial role towards providing necessary knowledge for crop improvement. Through genomics, we have been able to identify and characterize the genes involved in salinity stress response, map out signaling pathways and ultimately utilize this information for improving the salinity tolerance of existing crops...
August 2016: Current Genomics
https://www.readbyqxmd.com/read/27499682/genome-assisted-breeding-for-drought-resistance
#19
Awais Khan, Valpuri Sovero, Dorcus Gemenet
Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant...
August 2016: Current Genomics
https://www.readbyqxmd.com/read/27499681/role-of-cyclic-nucleotide-gated-channels-in-stress-management-in-plants
#20
Saroj K Jha, Manisha Sharma, Girdhar K Pandey
Tolerance of plants to a number of biotic and abiotic stresses such as pathogen and herbivore attack, drought, salinity, cold and nutritional limitations is ensued by complex multimodule signaling pathways. The outcome of this complex signaling pathways results in adaptive responses by restoring the cellular homeostasis and thus promoting survival. Functions of many plant cation transporter and channel protein families such as glutamate receptor homologs (GLRs), cyclic nucleotide-gated ion channel (CNGC) have been implicated in providing biotic and abiotic stress tolerance...
August 2016: Current Genomics
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