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Nicole A Szydlowski, Jane S Go, Ying S Hu
Synergistic developments in advanced fluorescent imaging and labeling techniques enable direct visualization of the chromatin structure and dynamics at the nanoscale level and in live cells. Super-resolution imaging encompasses a class of constantly evolving techniques that break the diffraction limit of fluorescence microscopy. Structured illumination microscopy provides a twofold resolution improvement and can readily achieve live multicolor imaging using conventional fluorophores. Single-molecule localization microscopy increases the spatial resolution by approximately 10-fold at the expense of slower acquisition speed...
November 19, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
Abdol-Reza Shamari, Ali-Ashraf Mehrabi, Abbas Maleki, Ali Rostami
Oak decline is a complex syndrome in which several damaging agents interact and bring about a serious dieback in tree condition. Genetic diversity is a key factor for better adoption of natural populations to environmental stresses. The objective of this research was to identify the association of polymorphism patterns of different reproducible genomic Inter simple sequence repeats (ISSR markers) to level of dieback phenomena and also growth type in 18 different stands of Persian oak in central Zagros region...
October 30, 2018: Cellular and Molecular Biology
Jianwei Shan, Zhongquan Cai, Yu Zhang, Hannan Xu, Jianglei Rao, Yourong Fan, Jiangyi Yang
f5 locus in rice (Oryza sativa L.) confers significant effects on hybrid male sterility and segregation distortion. BC14 F2 plants with f5-i/i, f5-j/j and f5-i/j genotypes were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. A total of 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs f5-j/j, f5-j/j vs f5-i/i, and f5-i/j vs f5-i/i, respectively. 145 DEGs were identified simultaneously in f5-i/j vs f5-j/j and f5-i/j vs f5-i/i...
October 15, 2018: Genomics
Luz Yaqueline Ladino, Johanna Galvis, Diana Yasnó, Adriana Ramírez, Orietta Ivonne Beltrán
The Bardet-Biedl syndrome is an autosomal recessive hereditary disorder with vast locus heterogeneity that belongs to the so-called ciliopathies, whose proteins are localized in the primary cilia and present functional deficiency. The multisystemic features of the disease include ocular, renal, cognitive, skeletal, as well as gonadal involvement and obesity, among others, with high inter- and intrafamilial variability. We describe the clinical case of an adolescent male patient with Bardet-Biedl syndrome, including the approach, the results from a 22-gene sequencing panel, and the analysis of updated scientific literature...
September 1, 2018: Biomédica: Revista del Instituto Nacional de Salud
Lindsey A Waddell, Lucas Lefevre, Stephen J Bush, Anna Raper, Rachel Young, Zofia M Lisowski, Mary E B McCulloch, Charity Muriuki, Kristin A Sauter, Emily L Clark, Katharine M Irvine, Clare Pridans, Jayne C Hope, David A Hume
The F4/80 antigen, encoded by the Adgre1 locus, has been widely-used as a monocyte-macrophage marker in mice, but its value as a macrophage marker in other species is unclear, and has even been questioned. ADGRE1 is a seven transmembrane G protein-coupled receptor with an extracellular domain containing repeated Epidermal Growth Factor (EGF)-like calcium binding domains. Using a new monoclonal antibody, we demonstrated that ADGRE1 is a myeloid differentiation marker in pigs, absent from progenitors in bone marrow, highly-expressed in mature granulocytes, monocytes, and tissue macrophages and induced by macrophage colony-stimulating factor (CSF1) treatment in vivo ...
2018: Frontiers in Immunology
Estela Dámaso, Adela Castillejo, María Del Mar Arias, Julia Canet-Hermida, Matilde Navarro, Jesús Del Valle, Olga Campos, Anna Fernández, Fátima Marín, Daniela Turchetti, Juan de Dios García-Díaz, Conxi Lázaro, Maurizio Genuardi, Daniel Rueda, Ángel Alonso, Jose Luis Soto, Megan Hitchins, Marta Pineda, Gabriel Capellá
BACKGROUND: Constitutional MLH1 epimutations are characterised by monoallelic methylation of the MLH1 promoter throughout normal tissues, accompanied by allele-specific silencing. The mechanism underlying primary MLH1 epimutations is currently unknown. The aim of this study was to perform an in-depth characterisation of constitutional MLH1 epimutations targeting the aberrantly methylated region around MLH1 and other genomic loci. METHODS: Twelve MLH1 epimutation carriers, 61 Lynch syndrome patients, and 41 healthy controls, were analysed by Infinium 450 K array...
October 2018: British Journal of Cancer
Taro Tsujimura, Osamu Takase, Masahiro Yoshikawa, Etsuko Sano, Matsuhiko Hayashi, Tsuyoshi Takato, Atsushi Toyoda, Hideyuki Okano, Keiichi Hishikawa
BACKGROUND: Contact domains of chromatin serve as a fundamental unit to regulate action of enhancers for target genes. Looping between a pair of CCCTC-binding factor (CTCF)-binding sites in convergent orientations underlies the formation of contact domains, while those in divergent orientations establish domain boundaries. However, every CTCF site is not necessarily engaged in loop or boundary structures, leaving functions of CTCF in varied genomic contexts still elusive. The locus containing Tfap2c and Bmp7 encompasses two contact domains separated by a region between the two genes, termed transition zone (TZ), characterized by two arrays of CTCF sites in divergent configuration...
September 14, 2018: Epigenetics & Chromatin
Seunghoon Baek, Kyung Choi, Goon-Bo Kim, Hee-Ju Yu, Ara Cho, Hoyeol Jang, Changkyun Kim, Hyuk-Jin Kim, Kae Sun Chang, Joo-Hwan Kim, Jeong-Hwan Mun
BACKGROUND: Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. RESULTS: We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis...
September 4, 2018: Genome Biology
Zhiqiang Zhou, Chaoshu Zhang, Xiaohuan Lu, Liwei Wang, Zhuanfang Hao, Mingshun Li, Degui Zhang, Hongjun Yong, Hanyong Zhu, Jianfeng Weng, Xinhai Li
Maize plant height related traits including plant height, ear height, and internode number are tightly linked with biomass, planting density, and grain yield in the field. Previous studies have focused on understanding the genetic basis of plant architecture traits per se , but the genetic basis of combining ability remains poorly understood. In this study, 328 recombinant inbred lines were inter-group crossed with two testers to produce 656 hybrids using the North Carolina II mating design. Both of the parental lines and hybrids were evaluated in two summer maize-growing regions of China in 2015 and 2016...
2018: Frontiers in Plant Science
Raazesh Sainudiin, Amandine Véber
We develop a novel importance sampler to compute the full likelihood function of a demographic or structural scenario given the site frequency spectrum (SFS) at a locus free of intra-locus recombination. This sampler, instead of representing the hidden genealogy of a sample of individuals by a labelled binary tree, uses the minimal level of information about such a tree that is needed for the likelihood of the SFS and thus takes advantage of the huge reduction in the size of the state space that needs to be integrated...
July 23, 2018: Theoretical Population Biology
Steven L Anderson, Adam L Mahan, Seth C Murray, Patricia E Klein
Multiparent advanced generation inter-cross (MAGIC) populations can provide improved genetic mapping resolution by increasing allelic diversity and effective recombination. The Four Parent Maize (FPM; L.) population implemented five different mating designs used in MAGIC and bi-parental populations to compare empirical effects on genetic resolution and power of quantitative trait locus (QTL) detection; the combined population here comprised of 1149 individuals with 118,509 genetic markers. Measurements were recorded for plant height (PH), ear height (EH), days to anthesis (DTA) and silking (DTS) in seven environments, spanning three years...
July 2018: Plant Genome
Rowena C Downie, Laura Bouvet, Eiko Furuki, Nick Gosman, Keith A Gardner, Ian J Mackay, Camila Campos Mantello, Greg Mellers, Huyen T T Phan, Gemma A Rose, Kar-Chun Tan, Richard P Oliver, James Cockram
Parastagonospora nodorum is a necrotrophic fungal pathogen of wheat ( Triticum aestivum L.), one of the world's most important crops. P. nodorum mediates host cell death using proteinaceous necrotrophic effectors, presumably liberating nutrients that allow the infection process to continue. The identification of pathogen effectors has allowed host genetic resistance mechanisms to be separated into their constituent parts. In P. nodorum , three proteinaceous effectors have been cloned: SnToxA , SnTox1 , and SnTox3 ...
2018: Frontiers in Plant Science
Nikola Winter, Friedrich Kragler
High throughput studies identified approximately one fifth of Arabidopsis protein encoding transcripts to be graft transmissible and to move over long distances in phloem. In roots, one fifth of transcription factors were annotated as non-cell-autonomous moving between cells. Is this massive transport a way of inter-organ and cell-to-cell communication or does it serve different purposes? On the tissue level, many miRNAs and all siRNAs act non-cell autonomously. Why are these RNAs and proteins not just expressed in cells where they exert their function? Short and long distance transport of these macromolecules raises the question whether all mobile mRNAs and transcription factors could be defined as signalling molecules...
July 18, 2018: Plant & Cell Physiology
Thomas Blankers, Kevin P Oh, Kerry L Shaw
Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variations in the crickets Laupala eukolea and Laupala cerasina , which occur on different islands (Maui and Hawaii)...
July 10, 2018: Genes
David R Goulding, Viktoriya D Nikolova, Lopa Mishra, Lisheng Zhuo, Koji Kimata, Sandra J McBride, Sheryl S Moy, G J Harry, Stavros Garantziotis
In recent years, several genome-wide association studies have identified candidate regions for genetic susceptibility in major mood disorders. Most notable are regions in a locus in chromosome 3p21, encompassing the genes NEK4-ITIH1-ITIH3-ITIH4. Three of these genes represent heavy chains of the composite protein inter-α-inhibitor (IαI). In order to further establish associations of these genes with mood disorders, we evaluated behavioral phenotypes in mice deficient in either Ambp/bikunin, which is necessary for functional ITIH1 and ITIH3 complexes, or in Itih4, the gene encoding the heavy chain Itih4...
July 10, 2018: Genes, Brain, and Behavior
Lizan Kawa, Alaa Kamnaksh, Joseph B Long, Ulf P Arborelius, Tomas Hökfelt, Denes V Agoston, Mårten Risling
Repeated mild blast-induced traumatic brain injury (rmbTBI), caused by recurrent exposure to low levels of explosive blast, is a significant concern for military health systems. However, the pathobiology of rmbTBI is currently poorly understood. Animal models are important tools to identify the molecular changes of rmbTBI, but comparisons across different models can present their own challenges. In this study, we compared two well-established rodent models of mbTBI, the "KI model" and the "USU/WRAIR model...
2018: Frontiers in Neurology
Lavanya Rishishwar, Lu Wang, Jianrong Wang, Soojin V Yi, Joseph Lachance, I King Jordan
Insertional activity of transposable elements (TEs) has had a major impact on the human genome; approximately one-half to two-thirds of the genome sequence is likely to be derived from TE insertions. Several families of human TEs - primarily Alu, L1 and SVA - continue to actively transpose, thereby generating insertional polymorphisms among individual genomes. The impact that TE insertions have on their human hosts' fitness, and accordingly the role that natural selection plays in shaping patterns of TE polymorphisms among populations, have yet to be systematically evaluated using whole genome sequence data...
October 30, 2018: Gene
Steffi Köcher, Petra Müller, Burkhard Berger, Martin Bodner, Walther Parson, Lutz Roewer, Sascha Willuweit
The implementation of massively parallel sequencing (MPS) in forensic science revealed the advantages of the new method compared to the forensic benchmark in DNA-STR analysis, the capillary-electrophoresis (CE): Sequence information and the possibility to multiplex hundreds of markers in one multiplex PCR increase the discrimination power of a forensic (STR-) profile. The EU funded project DNASeqEx (DNA-STR Massive Sequencing & International Information Exchange) aims to evaluate MPS-based materials in their respective developmental stages using the two established platforms MiSeq FGx (Illumina) and Ion S5™ (Thermo Fisher Scientific)...
September 2018: Forensic Science International. Genetics
Xin Sun, Anne Bedos, Louis Deharveng
Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species...
2018: PeerJ
Gérald Umhang, Frédéric Grenouillet, Vanessa Bastid, Selim M'Rad, Benoît Valot, Myriam Oudni-M'Rad, Hamouda Babba, Franck Boué
Cystic echinococcosis is a zoonotic disease with worldwide distribution caused by the larval stage of the Cestode parasite Echinococcus granulosus sensu lato. Due to the predominance or even the exclusive presence of E. granulosus sensu stricto (s.s.) among E. granulosus species in many areas, the genetic diversity needs to be further investigated at the species level to better understand the inter- and intra-focus epidemiological features. Short sequences of mitochondrial or nuclear genes generally lack or have limited discriminatory power, hindering the detection of polymorphisms to reflect geographically based peculiarities and/or any history of infection...
September 2018: Parasitology Research
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