keyword
MENU ▼
Read by QxMD icon Read
search

Combinatorial genomics

keyword
https://www.readbyqxmd.com/read/28221768/formation-of-nitrogenase-nifdk-tetramers-in-the-mitochondria-of-saccharomyces-cerevisiae
#1
Stefan Burén, Eric M Young, Elizabeth A Sweeny, Gema López-Torrejón, Marcel Veldhuizen, Christopher A Voigt, Luis M Rubio
Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N2 fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle's high O2 consumption and the presence of bacterial-type iron-sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae where transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome...
February 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28219948/genomic-integration-of-wnt-%C3%AE-catenin-and-bmp-smad1-signaling-coordinates-foregut-and-hindgut-transcriptional-program
#2
Mariana L Stevens, Praneet Chaturvedi, Scott A Rankin, Melissa Macdonald, Sajjeev Jagannathan, Masashi Yukawa, Artem Barski, Aaron M Zorn
Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how these signals are integrated in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts as a genome-wide toggle between foregut and hindgut programs...
February 20, 2017: Development
https://www.readbyqxmd.com/read/28217858/golden-gate-assembly-system-dedicated-to-complex-pathway-manipulation-in-yarrowia-lipolytica
#3
Ewelina Celińska, Rodrigo Ledesma-Amaro, Macarena Larroude, Tristan Rossignol, Cyrille Pauthenier, Jean-Marc Nicaud
In this study, we have adopted Golden Gate modular cloning strategy to develop a robust and versatile DNA assembly platform for the nonconventional yeast Yarrowia lipolytica. To this end, a broad set of destination vectors and interchangeable building blocks have been constructed. The DNA modules were assembled on a scaffold of predesigned 4 nt overhangs covering three transcription units (each bearing promoter, gene and terminator), selection marker gene and genomic integration targeting sequences, constituting altogether thirteen elements...
February 19, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28216108/crispr-enabled-trackable-genome-engineering-for-isopropanol-production-in-escherichia-coli
#4
Liya Liang, Rongming Liu, Andrew D Garst, Thomas Lee, Violeta Sànchez I Nogué, Gregg T Beckham, Ryan T Gill
Isopropanol is an important target molecule for sustainable production of fuels and chemicals. Increases in DNA synthesis and synthetic biology capabilities have resulted in the development of a range of new strategies for the more rapid design, construction, and testing of production strains. Here, we report on the use of such capabilities to construct and test 903 different variants of the isopropanol production pathway in Escherichia coli. We first constructed variants to explore the effect of codon optimization, copy number, and translation initiation rates on isopropanol production...
February 16, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28201946/sorting-permutations-by-prefix-and-suffix-rearrangements
#5
Carla Negri Lintzmayer, Guillaume Fertin, Zanoni Dias
Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations...
February 9, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28187425/computational-lipidomics-and-lipid-bioinformatics-filling-in-the-blanks
#6
Josch Pauling, Edda Klipp
Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand for specialized computational support to analyze these spectral libraries...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28186491/combinatorial-bzip-dimers-define-complex-dna-binding-specificity-landscapes
#7
Jose A Rodriguez-Martinez, Aaron W Reinke, Devesh Bhimsaria, Amy E Keating, Aseem Z Ansari
How transcription factor dimerization impacts DNA binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or 'emergent' sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers...
February 10, 2017: ELife
https://www.readbyqxmd.com/read/28186197/new-natural-products-identified-by-combined-genomics-metabolomics-profiling-of-marine-streptomyces-sp-mp131-18
#8
Constanze Paulus, Yuriy Rebets, Bogdan Tokovenko, Suvd Nadmid, Larisa P Terekhova, Maksym Myronovskyi, Sergey B Zotchev, Christian Rückert, Simone Braig, Stefan Zahler, Jörn Kalinowski, Andriy Luzhetskyy
Marine actinobacteria are drawing more and more attention as a promising source of new natural products. Here we report isolation, genome sequencing and metabolic profiling of new strain Streptomyces sp. MP131-18 isolated from marine sediment sample collected in the Trondheim Fjord, Norway. The 16S rRNA and multilocus phylogenetic analysis showed that MP131-18 belongs to the genus Streptomyces. The genome of MP131-18 isolate was sequenced, and 36 gene clusters involved in the biosynthesis of 18 different types of secondary metabolites were predicted using antiSMASH analysis...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185564/comparative-genomics-meets-topology-a-novel-view-on-genome-median-and-halving-problems
#9
Nikita Alexeev, Pavel Avdeyev, Max A Alekseyev
BACKGROUND: Genome median and genome halving are combinatorial optimization problems that aim at reconstruction of ancestral genomes by minimizing the number of evolutionary events between them and genomes of the extant species. While these problems have been widely studied in past decades, their solutions are often either not efficient or not biologically adequate. These shortcomings have been recently addressed by restricting the problems solution space. RESULTS: We show that the restricted variants of genome median and halving problems are, in fact, closely related...
November 11, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28176813/a-combinational-crispr-cas9-gene-editing-approach-can-halt-hiv-replication-and-prevent-viral-escape
#10
Robert Jan Lebbink, Dorien C M de Jong, Femke Wolters, Elisabeth M Kruse, Petra M van Ham, Emmanuel J H J Wiertz, Monique Nijhuis
HIV presents one of the highest evolutionary rates ever detected and combination antiretroviral therapy is needed to overcome the plasticity of the virus population and control viral replication. Conventional treatments lack the ability to clear the latent reservoir, which remains the major obstacle towards a cure. Novel strategies, such as CRISPR/Cas9 gRNA-based genome-editing, can permanently disrupt the HIV genome. However, HIV genome-editing may accelerate viral escape, questioning the feasibility of the approach...
February 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166730/transcriptome-analysis-reveals-the-complexity-of-alternative-splicing-regulation-in-the-fungus-verticillium-dahliae
#11
Lirong Jin, Guanglin Li, Dazhao Yu, Wei Huang, Chao Cheng, Shengjie Liao, Qijia Wu, Yi Zhang
BACKGROUND: Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS: This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, using two different strains and multiple methods for cDNA library preparations. We identified alternatively spliced mRNA isoforms in over a half of the multi-exonic fungal genes...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28155643/identification-of-recurrent-combinatorial-patterns-of-chromatin-modifications-at-promoters-across-various-tissue-types
#12
Nan Meng, Raghu Machiraju, Kun Huang
BACKGROUND: Identification and analysis of recurrent combinatorial patterns of multiple chromatin modifications provide invaluable information for understanding epigenetic regulations. Furthermore, as more data becomes available, it is computationally expensive and unnecessary to study combinatorial patterns of all modifications. METHODS: A novel framework is proposed to investigate recurrent combinatorial patterns of a subset of quantitatively selected chromatin modifications...
December 23, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28137571/recent-achievements-in-characterizing-the-histone-code-and-approaches-to-integrating-epigenomics-and-systems-biology
#13
K A Janssen, S Sidoli, B A Garcia
Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28135258/sequencing-thousands-of-single-cell-genomes-with-combinatorial-indexing
#14
Sarah A Vitak, Kristof A Torkenczy, Jimi L Rosenkrantz, Andrew J Fields, Lena Christiansen, Melissa H Wong, Lucia Carbone, Frank J Steemers, Andrew Adey
Single-cell genome sequencing has proven valuable for the detection of somatic variation, particularly in the context of tumor evolution. Current technologies suffer from high library construction costs, which restrict the number of cells that can be assessed and thus impose limitations on the ability to measure heterogeneity within a tissue. Here, we present single-cell combinatorial indexed sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single-cell libraries for detection of somatic copy-number variants...
January 30, 2017: Nature Methods
https://www.readbyqxmd.com/read/28135255/massively-multiplex-single-cell-hi-c
#15
Vijay Ramani, Xinxian Deng, Ruolan Qiu, Kevin L Gunderson, Frank J Steemers, Christine M Disteche, William S Noble, Zhijun Duan, Jay Shendure
We present single-cell combinatorial indexed Hi-C (sciHi-C), a method that applies combinatorial cellular indexing to chromosome conformation capture. In this proof of concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells. We use sciHi-C data to separate cells by karyotypic and cell-cycle state differences and identify cell-to-cell heterogeneity in mammalian chromosomal conformation. Our results demonstrate that combinatorial indexing is a generalizable strategy for single-cell genomics...
January 30, 2017: Nature Methods
https://www.readbyqxmd.com/read/28133586/possible-health-impacts-of-bt-toxins-and-residues-from-spraying-with-complementary-herbicides-in-genetically-engineered-soybeans-and-risk-assessment-as-performed-by-the-european-food-safety-authority-efsa
#16
REVIEW
Christoph Then, Andreas Bauer-Panskus
BACKGROUND: MON89788 was the first genetically engineered soybean worldwide to express a Bt toxin. Under the brand name Intacta, Monsanto subsequently engineered a stacked trait soybean using MON89788 and MON87701-this stacked soybean expresses an insecticidal toxin and is, in addition, tolerant to glyphosate. After undergoing risk assessment by the European Food Safety Authority (EFSA), the stacked event was authorised for import into the EU in June 2012, including for use in food and feed...
2017: Environmental Sciences Europe
https://www.readbyqxmd.com/read/28131767/the-florida-manatee-trichechus-manatus-latirostris-immunoglobulin-heavy-chain-suggests-the-importance-of-clan-iii-variable-segments-in-repertoire-diversity
#17
Breanna Breaux, Thaddeus C Deiss, Patricia L Chen, Maria Paula Cruz-Schneider, Leonardo Sena, Margaret E Hunter, Robert K Bonde, Michael F Criscitiello
Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis...
January 25, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28129330/meneco-a-topology-based-gap-filling-tool-applicable-to-degraded-genome-wide-metabolic-networks
#18
Sylvain Prigent, Clémence Frioux, Simon M Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel
Increasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors...
January 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28105934/charm-discovery-of-combinatorial-chromatin-modification-patterns-in-hepatitis-b-virus-x-transformed-mouse-liver-cancer-using-association-rule-mining
#19
Sung Hee Park, Sun-Min Lee, Young-Joon Kim, Sangsoo Kim
BACKGROUND: Various chromatin modifications, identified in large-scale epigenomic analyses, are associated with distinct phenotypes of different cells and disease phases. To improve our understanding of these variations, many computational methods have been developed to discover novel sites and cell-specific chromatin modifications. Despite the availability of existing methods, there is still room for further improvement when they are applied to resolve the histone code hypothesis. Hence, we aim to investigate the development of a computational method to provide new insights into de novo combinatorial pattern discovery of chromatin modifications to characterize epigenetic variations in distinct phenotypes of different cells...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#20
Ramsey I Zeitoun, Gur Pines, Willliam C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory time scales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 24, 2017: ACS Synthetic Biology
keyword
keyword
66402
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"