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https://www.readbyqxmd.com/read/29236185/genome-wide-identification-and-cadmium-induced-expression-profiling-of-sulfate-transporter-sultr-genes-in-sorghum-sorghum-bicolor-l
#1
M Aydın Akbudak, Ertugrul Filiz, Kubra Kontbay
Sulfur is an essential element for all living organisms. Plants can convert inorganic sulfur into organic sulfur compounds by complex enzymatic steps. In this study, we conducted a genome-wide analysis of sulfate transporter genes (SULTRs) in the sorghum (Sorghum bicolor) genome and examined expression profiles of SbSULTR genes under 200 µM cadmium (Cd) exposure. As a result of sorghum genome analysis, 11 SULTR genes were identified, including SbSULTR1;1, SbSULTR1;2, SbSULTR1;3, SbSULTR2;1, SbSULTR2;2, SbSULTR3;1, SbSULTR3;2, SbSULTR3;3, SbSULTR3;4, SbSULTR3;5, and SbSULTR4...
December 13, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/29235146/development-of-metal-active-site-and-zinccluster-tool-to-predictactive-site-pockets
#2
M Ajitha, K Sundar, S Arul Mugilan, S Arumugam
The advent of whole genome sequencing leads to increasing number of proteins with known amino acid sequences. Despite many efforts, the number of proteins with resolved three dimensional structures is still low. One of the challenging tasks the structural biologists face is the prediction of the interaction of metal ion with any protein for which the structure is unknown. Based on the information available in PDB, a site (METALACTIVE INTERACTION) has been generated which displays information for significant high preferential and low-preferential combination of endogenous ligands for 49 metal ions...
December 13, 2017: Proteins
https://www.readbyqxmd.com/read/29229825/network-analysis-identifies-chromosome-intermingling-regions-as-regulatory-hotspots-for-transcription
#3
Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G V Shivashankar, Caroline Uhler
The 3D structure of the genome plays a key role in regulatory control of the cell. Experimental methods such as high-throughput chromosome conformation capture (Hi-C) have been developed to probe the 3D structure of the genome. However, it remains a challenge to deduce from these data chromosome regions that are colocalized and coregulated. Here, we present an integrative approach that leverages 1D functional genomic features (e.g., epigenetic marks) with 3D interactions from Hi-C data to identify functional interchromosomal interactions...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29224139/antibody-based-detection-of-global-nuclear-dna-methylation-in-cells-tissue-sections-and-mammalian-embryos
#4
Nathalie Beaujean, Juliette Salvaing, Nur Annies Abd Hadi, Sari Pennings
Immunostaining is widely used in cell biology for the in situ detection of proteins in fixed cells. The method is based on the specificity of antibodies for recognizing and binding to a selected target, combined with immunolabeling techniques for microscopic imaging. Antibodies with high specificities for modified nucleotides have also been widely developed, and among those, antibodies that recognize modified cytosine: 5-methylcytosine (5mC), and more recently, its derivates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223331/the-nos-like-protein-from-the-microalgae-ostreococcus-tauri-is-a-genuine-and-ultrafast-no-producing-enzyme
#5
Marine Weisslocker-Schaetzel, François André, Nabila Touazi, Noelia Foresi, Mehdi Lembrouk, Pierre Dorlet, Annie Frelet-Barrand, Lorenzo Lamattina, Jérôme Santolini
The exponential increase of genomes' sequencing has revealed the presence of NO-Synthases (NOS) throughout the tree of life, uncovering an extraordinary diversity of genetic structure and biological functions. Although NO has been shown to be a crucial mediator in plant physiology, NOS sequences seem present solely in green algae genomes, with a first identification in the picoplankton species Ostreococcus tauri. There is no rationale so far to account for the presence of NOS in this early-diverging branch of the green lineage and its absence in land plants...
December 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29217127/epigenome-in-early-mammalian-development-inheritance-reprogramming-and-establishment
#6
REVIEW
Qianhua Xu, Wei Xie
Drastic epigenetic reprogramming takes place during preimplantation development, leading to the conversion of terminally differentiated gametes to a totipotent embryo. Deficiencies in remodeling of the epigenomes can cause severe developmental defects, including embryonic lethality. However, how chromatin modifications and chromatin organization are reprogrammed upon fertilization in mammals has long remained elusive. Here, we review recent progress in understanding how the epigenome is dynamically regulated during early mammalian development...
December 4, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/29215605/cone-snails-a-big-store-of-conotoxins-for-novel-drug-discovery
#7
REVIEW
Bingmiao Gao, Chao Peng, Jiaan Yang, Yunhai Yi, Junqing Zhang, Qiong Shi
Marine drugs have developed rapidly in recent decades. Cone snails, a group of more than 700 species, have always been one of the focuses for new drug discovery. These venomous snails capture prey using a diverse array of unique bioactive neurotoxins, usually named as conotoxins or conopeptides. These conotoxins have proven to be valuable pharmacological probes and potential drugs due to their high specificity and affinity to ion channels, receptors, and transporters in the nervous systems of target prey and humans...
December 7, 2017: Toxins
https://www.readbyqxmd.com/read/29210065/hdac-inhibitors-restore-braf-inhibitor-sensitivity-by-altering-pi3k-and-survival-signalling-in-a-subset-of-melanoma
#8
Stuart J Gallagher, Dilini Gunatilake, Kimberley A Beaumont, Danae M Sharp, Jessamy C Tiffen, Anja Heinemann, Wolfgang Weninger, Nikolas K Haass, James S Wilmott, Jason Madore, Peter M Ferguson, Helen Rizos, Peter Hersey
Mutations in BRAF activate oncogenic MAPK signalling in almost half of cutaneous melanomas. Inhibitors of BRAF (BRAFi) and its target MEK are widely used to treat melanoma patients with BRAF mutations but unfortunately acquired resistance occurs in the majority of patients. Resistance results from mutations or non-genomic changes that either reactivate MAPK signalling or activate other pathways that provide alternate survival and growth signalling. Here we show the histone deacetylase inhibitor (HDACi) panobinostat overcomes BRAFi resistance in melanoma, but this is dependent on the resistant cells showing a partial response to BRAFi treatment...
December 6, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29205813/high-throughput-block-optical-dna-sequence-identification
#9
Dodderi Manjunatha Sagar, Lee Erik Korshoj, Katrina Bethany Hanson, Partha Pratim Chowdhury, Peter Britton Otoupal, Anushree Chatterjee, Prashant Nagpal
Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm-1 ...
December 4, 2017: Small
https://www.readbyqxmd.com/read/29203764/3d-genome-of-multiple-myeloma-reveals-spatial-genome-disorganization-associated-with-copy-number-variations
#10
Pengze Wu, Tingting Li, Ruifeng Li, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu, Cheng Li
The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations...
December 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/29193055/facial-shape-manifestations-of-growth-faltering-in-tanzanian-children
#11
Joanne B Cole, Mange F Manyama, Dejana Nikitovic, Paula N Gonzalez, Denise K Liberton, Warren M Wilson, Campbell Rolian, Jacinda R Larson, Emmanuel Kimwaga, Joshua Mathayo, Charles C Roseman, Stephanie A Santorico, Ken Lukowiak, Richard A Spritz, Benedikt Hallgrimsson
Variation in the shape of the human face and in stature is determined by complex interactions between genetic and environmental influences. One such environmental influence is malnourishment, which can result in growth faltering, usually diagnosed by means of comparing an individual's stature with a set of age-appropriate standards. These standards for stature, however, are typically ascertained in groups where people are at low risk for growth faltering. Moreover, genetic differences among populations with respect to stature are well established, further complicating the generalizability of stature-based diagnostic tools...
November 28, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/29187597/emerging-roles-of-transcriptional-enhancers-in-chromatin-looping-and-promoter-proximal-pausing-of-rna-polymerase-ii
#12
Huan Meng, Blaine Bartholomew
Initiation and regulation of transcription by RNA polymerase II (RNAPII) in eukaryotes relies upon the control elements of promoters and enhancers. Promoters and enhancers share common architectures and functions in similar ways. The prevailing view is functional promoters and enhancers can initiate bidirectional transcription. With the acceleration of recent genome-wide studies of regulated transcription, it has become clear that transcriptional enhancers in mammalian genomes are major sources of pervasive non-coding RNA transcription...
November 29, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29186182/identification-of-a-novel-linear-b-cell-epitope-in-nonstructural-protein-11-of-porcine-reproductive-and-respiratory-syndrome-virus-that-are-conserved-in-both-genotypes
#13
Nan Jiang, Huan Jin, Yi Li, Xinna Ge, Jun Han, Xin Guo, Lei Zhou, Hanchun Yang
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important pathogens, that hinder the development of global pork industry. Its nonstructural protein 11 (nsp11), with the nidoviral uridylate-specific endoribonuclease (NendoU) domain, is essential for PRRSV genome replication and it also contributes to host innate immunity suppression. However, the immunogenicity and immune structure of PRRSV nsp11 have not been well investigated yet. In this study, a monoclonal antibody (mAb), designated 3F9, that against nsp11 was generated...
2017: PloS One
https://www.readbyqxmd.com/read/29183987/spotlearn-convolutional-neural-network-for-detection-of-fluorescence-in-situ-hybridization-fish-signals-in-high-throughput-imaging-approaches
#14
Prabhakar R Gudla, Koh Nakayama, Gianluca Pegoraro, Tom Misteli
DNA fluorescence in situ hybridization (FISH) is the technique of choice to map the position of genomic loci in three-dimensional (3D) space at the single allele level in the cell nucleus. High-throughput DNA FISH methods have recently been developed using complex libraries of fluorescently labeled synthetic oligonucleotides and automated fluorescence microscopy, enabling large-scale interrogation of genomic organization. Although the FISH signals generated by high-throughput methods can, in principle, be analyzed by traditional spot-detection algorithms, these approaches require user intervention to optimize each interrogated genomic locus, making analysis of tens or hundreds of genomic loci in a single experiment prohibitive...
November 28, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/29175436/3d-chromatin-architecture-of-large-plant-genomes-determined-by-local-a-b-compartments
#15
Pengfei Dong, Xiaoyu Tu, Po-Yu Chu, Peitao Lü, Ning Zhu, Donald Grierson, Baijuan Du, Pinghua Li, Silin Zhong
The spatial organization of the genome plays an important role in the regulation of gene expression. However, the core structural features of animal genomes, such as topologically associated domains (TADs) and chromatin loops, are not prominent in the extremely compact Arabidopsis genome. In this study, we have examined the chromatin architecture, as well as their DNA methylation, histone modifications, accessible chromatin and gene expression, of maize, tomato, sorghum, foxtail millet and rice with genome sizes ranging from 0...
November 21, 2017: Molecular Plant
https://www.readbyqxmd.com/read/29174549/identification-and-characterization-of-potential-druggable-targets-among-hypothetical-proteins-of-extensively-drug-resistant-mycobacterium-tuberculosis-xdr-kzn-605-through-subtractive-genomics-approach
#16
Reaz Uddin, Quratulain Nehal Siddiqui, Syed Sikander Azam, Bibi Saima, Abdul Wadood
Among the resistant isolates of tuberculosis (TB), the multidrug resistance tuberculosis (MDR-TB) and extensively drug resistant tuberculosis (XDR-TB) are the areas of growing concern for which the front-line antibiotics are no more effective. As a result, the search of new therapeutic targets against TB is an imperative need of time. On the other hand, the target identification is an a priori step in drug discovery based research. Furthermore, the availability of the complete proteomic data of extensively drug resistant Mycobacterium tuberculosis (XDR-MTB) made it possible to carry out in silico analysis for the discovery of new drug targets...
November 22, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29169344/genome-wide-association-mapping-of-black-point-reaction-in-common-wheat-triticum-aestivum-l
#17
Jindong Liu, Zhonghu He, Awais Rasheed, Weie Wen, Jun Yan, Pingzhi Zhang, Yingxiu Wan, Yong Zhang, Chaojie Xie, Xianchun Xia
BACKGROUND: Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. RESULTS: Black point reactions were evaluated in 166 elite wheat cultivars in five environments...
November 23, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29163559/genome-wide-association-study-of-calcium-accumulation-in-grains-of-european-wheat-cultivars
#18
Dalia Z Alomari, Kai Eggert, Nicolaus von Wirén, Klaus Pillen, Marion S Röder
Mineral concentrations in cereals are important for human health, especially for people who depend mainly on consuming cereal diet. In this study, we carried out a genome-wide association study (GWAS) of calcium concentrations in wheat (Triticum aestivum L.) grains using a European wheat diversity panel of 353 varieties [339 winter wheat (WW) plus 14 of spring wheat (SW)] and phenotypic data based on two field seasons. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA chip and a 35k Affymetrix chip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29160840/cloning-and-molecular-characterization-of-an-alpha-glucosidase-malh-from-the-halophilic-archaeon-haloquadratum-walsbyi
#19
Mara F Cuebas-Irizarry, Ricardo A Irizarry-Caro, Carol López-Morales, Keyla M Badillo-Rivera, Carlos M Rodríguez-Minguela, Rafael Montalvo-Rodríguez
We report the heterologous expression and molecular characterization of the first extremely halophilic alpha-glucosidase (EC 3.2.1.20) from the archaeon Haloquadratum walsbyi. A 2349 bp region (Hqrw_2071) from the Hqr. walsbyi C23 annotated genome was PCR-amplified and the resulting amplicon ligated into plasmid pET28b(+), expressed in E. coli Rosetta cells, and the resulting protein purified by Ni-NTA affinity chromatography. The recombinant protein showed an estimated molecular mass of 87 kDa, consistent with the expected value of the annotated protein, and an optimal activity for the hydrolysis of α-PNPG was detected at 40 °C, and at pH 6...
November 21, 2017: Life
https://www.readbyqxmd.com/read/29157061/the-dna-pol-%C3%AF%C2%B5-stimulatory-activity-of-mrc1-is-modulated-by-phosphorylation
#20
Zhong-Xin Zhang, Jingjing Zhang, Qinhong Cao, Judith L Campbell, Huiqiang Lou
DNA replication checkpoint (Mec1-Mrc1-Rad53 in budding yeast) is an evolutionarily conserved surveillance system to ensure proper DNA replication and genome stability in all eukaryotes. Compared to its well-known function as a mediator of replication checkpoint, the exact role of Mrc1 as a component of normal replication forks remains relatively unclear. In this study, we provide in vitro biochemical evidence to support that yeast Mrc1 is able to enhance the activity of DNA polymerase ϵ (Pol ϵ), the major leading strand replicase...
November 20, 2017: Cell Cycle
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