keyword
MENU ▼
Read by QxMD icon Read
search

Landscape architecture

keyword
https://www.readbyqxmd.com/read/29349531/an-all-in-one-pharmacophoric-architecture-for-the-discovery-of-potential-broad-spectrum-anti-flavivirus-drugs
#1
Nomagugu B Ncube, Pritika Ramharack, Mahmoud E S Soliman
A precipitous increase in the number of flaviviral infections has been noted over the last 5 years. Despite these outbreaks, treatment protocols for infected individuals remain ambiguous. Numerous studies have identified NITD008 as a potent flavivirus inhibitor; however, clinical testing was dismissed due to undesirable toxic effects. The binding landscape of NITD008 in complex with five detrimental flaviviruses at the RNA-dependent RNA polymerase active sites was explored. An "all-in-one" pharmacophore model was created for the design of small molecules that may inhibit a broad spectrum of flaviviruses...
January 18, 2018: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/29348569/genomelandscaper-landscape-analysis-of-genome-fingerprints-maps-assessing-chromosome-architecture
#2
Hannan Ai, Yuncan Ai, Fanmei Meng
Assessing correctness of an assembled chromosome architecture is a central challenge. We create a geometric analysis method (called GenomeLandscaper) to conduct landscape analysis of genome-fingerprints maps (GFM), trace large-scale repetitive regions, and assess their impacts on the global architectures of assembled chromosomes. We develop an alignment-free method for phylogenetics analysis. The human Y chromosomes (GRCh.chrY, HuRef.chrY and YH.chrY) are analysed as a proof-of-concept study. We construct a galaxy of genome-fingerprints maps (GGFM) for them, and a landscape compatibility among relatives is observed...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29347841/evolutionary-effect-on-the-embodied-beauty-of-landscape-architectures
#3
Wei Zhang, Xiaoxiang Tang, Xianyou He, Guangyao Chen
According to the framework of evolutionary aesthetics, a sense of beauty is related to environmental adaptation and plasticity of human beings, which has adaptive value and biological foundations. Prior studies have demonstrated that organisms derive benefits from the landscape. In this study, we investigated whether the benefits of landscape might elicit a stronger sense of beauty and what the nature of this sense of beauty is. In two experiments, when viewing classical landscape and nonlandscape architectures photographs, participants rated the aesthetic scores (Experiment 1) and had a two-alternative forced choice aesthetic judgment by pressing the reaction button located near to (15 cm) or far from (45 cm) the presenting stimuli (Experiment 2)...
January 2018: Evolutionary Psychology: An International Journal of Evolutionary Approaches to Psychology and Behavior
https://www.readbyqxmd.com/read/29339410/maintenance-of-genome-integrity%C3%A2-by-mi2-homologs-chd-3-and-let-418-in%C3%A2-caenorhabditis-elegans
#4
Carolyn A Turcotte, Solomon A Sloat, Julia A Rigothi, Erika Rosenkranse, Alexandra L Northrup, Nicolas P Andrews, Paula M Checchi
Meiotic recombination depends upon the tightly coordinated regulation of chromosome dynamics and is essential for the production of haploid gametes. Central to this process is the formation and repair of meiotic double-stranded breaks (DSBs), which must take place within the constraints of a specialized chromatin architecture. Here, we demonstrate a role for the nucleosome remodeling and deacetylase (NuRD) complex in orchestrating meiotic chromosome dynamics in Caenorhabditis elegans. Our data reveal that the conserved Mi2 homologs Chromodomain helicase DNA binding protein (CHD-3) and its paralog LET-418 facilitate meiotic progression by ensuring faithful repair of DSBs through homologous recombination...
January 16, 2018: Genetics
https://www.readbyqxmd.com/read/29335443/elucidating-the-genomic-architecture-of-asian-egfr-mutant-lung-adenocarcinoma-through-multi-region-exome-sequencing
#5
Rahul Nahar, Weiwei Zhai, Tong Zhang, Angela Takano, Alexis J Khng, Yin Yeng Lee, Xingliang Liu, Chong Hee Lim, Tina P T Koh, Zaw Win Aung, Tony Kiat Hon Lim, Lavanya Veeravalli, Ju Yuan, Audrey S M Teo, Cheryl X Chan, Huay Mei Poh, Ivan M L Chua, Audrey Ann Liew, Dawn Ping Xi Lau, Xue Lin Kwang, Chee Keong Toh, Wan-Teck Lim, Bing Lim, Wai Leong Tam, Eng-Huat Tan, Axel M Hillmer, Daniel S W Tan
EGFR-mutant lung adenocarcinomas (LUAD) display diverse clinical trajectories and are characterized by rapid but short-lived responses to EGFR tyrosine kinase inhibitors (TKIs). Through sequencing of 79 spatially distinct regions from 16 early stage tumors, we show that despite low mutation burdens, EGFR-mutant Asian LUADs unexpectedly exhibit a complex genomic landscape with frequent and early whole-genome doubling, aneuploidy, and high clonal diversity. Multiple truncal alterations, including TP53 mutations and loss of CDKN2A and RB1, converge on cell cycle dysregulation, with late sector-specific high-amplitude amplifications and deletions that potentially beget drug resistant clones...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29334896/global-analysis-of-prokaryotic-trna-derived-cyclodipeptide-biosynthesis
#6
Michael A Skinnider, Chad W Johnston, Nishanth J Merwin, Chris A Dejong, Nathan A Magarvey
BACKGROUND: Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery. RESULTS: We developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29244145/biological-and-therapeutic-implications-of-multisector-sequencing-in-newly-diagnosed-glioblastomas
#7
Tatenda Mahlokozera, Ananth K Vellimana, Tiandao Li, Diane D Mao, Zohny S Zohny, David H Kim, David D Tran, Daniel S Marcus, Sarah J Fouke, Jian L Campian, Gavin P Dunn, Christopher A Miller, Albert H Kim
Background: Diagnostic workflows for glioblastoma (GBM) patients increasingly include DNA sequencing-based analysis of a single tumor site following biopsy or resection. We hypothesized that sequencing of multiple sectors within a given tumor would provide a more comprehensive representation of the molecular landscape and potentially inform therapeutic strategies. Methods: 10 newly diagnosed, IDH1 wildtype GBM tumor samples were obtained from two (n = 9) or four (n = 1) spatially distinct tumor regions...
December 13, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29241326/the-awsem-amylometer-predicting-amyloid-propensity-and-fibril-topology-using-an-optimized-folding-landscape-model
#8
Mingchen Chen, Nicholas P Schafer, Weihua Zheng, Peter G Wolynes
Amyloids are fibrillar protein aggregates with simple repeated structural motifs in their cores, usually β-strands but sometimes α-helices. Identifying the amyloid-prone regions within protein sequences is important both for understanding the mechanisms of amyloid-associated diseases and for understanding functional amyloids. Based on the crystal structures of seven cross-β amyloidogenic peptides with different topologies and one recently solved cross-α fiber structure, we have developed a computational approach for identifying amyloidogenic segments in protein sequences using the Associative memory, Water mediated, Structure and Energy Model...
December 14, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29237136/biomimetic-structural-materials-inspiration-from-design-and-assembly
#9
Nicholas A Yaraghi, David Kisailus
Nature assembles weak organic and inorganic constituents into sophisticated hierarchical structures, forming structural composites that demonstrate impressive combinations of strength and toughness. Two such composites are the nacre structure forming the inner layer of many mollusk shells, whose brick-and-mortar architecture has been the gold standard for biomimetic composites, and the cuticle forming the arthropod exoskeleton, whose helicoidal fiber-reinforced architecture has only recently attracted interest for structural biomimetics...
December 13, 2017: Annual Review of Physical Chemistry
https://www.readbyqxmd.com/read/29220667/transient-and-permanent-reconfiguration-of-chromatin-and-transcription-factor-occupancy-drive-reprogramming
#10
Anja S Knaupp, Sam Buckberry, Jahnvi Pflueger, Sue Mei Lim, Ethan Ford, Michael R Larcombe, Fernando J Rossello, Alex de Mendoza, Sara Alaei, Jaber Firas, Melissa L Holmes, Shalima S Nair, Susan J Clark, Christian M Nefzger, Ryan Lister, Jose M Polo
Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) induces changes in genome architecture reflective of the embryonic stem cell (ESC) state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of the process. Here, we characterize the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of intermediates poised to become iPSCs. Widespread reconfiguration of chromatin states and transcription factor (TF) occupancy occurs early during reprogramming, and cells that fail to reprogram partially retain their original chromatin states...
December 7, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/29219068/predicting-enhancers-with-deep-convolutional-neural-networks
#11
Xu Min, Wanwen Zeng, Shengquan Chen, Ning Chen, Ting Chen, Rui Jiang
BACKGROUND: With the rapid development of deep sequencing techniques in the recent years, enhancers have been systematically identified in such projects as FANTOM and ENCODE, forming genome-wide landscapes in a series of human cell lines. Nevertheless, experimental approaches are still costly and time consuming for large scale identification of enhancers across a variety of tissues under different disease status, making computational identification of enhancers indispensable. RESULTS: To facilitate the identification of enhancers, we propose a computational framework, named DeepEnhancer, to distinguish enhancers from background genomic sequences...
December 1, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29211852/migration-selection-balance-drives-genetic-differentiation-in-genes-associated-with-high-altitude-function-in-the-speckled-teal-anas-flavirostris-in-the-andes
#12
Allie M Graham, Philip Lavretsky, Violeta Muñoz-Fuentes, Andy J Green, Robert E Wilson, Kevin G McCracken
Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29203909/dynamic-epigenomic-landscapes-during-early-lineage-specification-in-mouse-embryos
#13
Yu Zhang, Yunlong Xiang, Qiangzong Yin, Zhenhai Du, Xu Peng, Qiujun Wang, Miguel Fidalgo, Weikun Xia, Yuanyuan Li, Zhen-Ao Zhao, Wenhao Zhang, Jing Ma, Feng Xu, Jianlong Wang, Lei Li, Wei Xie
In mammals, all somatic development originates from lineage segregation in early embryos. However, the dynamics of transcriptomes and epigenomes acting in concert with initial cell fate commitment remains poorly characterized. Here we report a comprehensive investigation of transcriptomes and base-resolution methylomes for early lineages in peri- and postimplantation mouse embryos. We found allele-specific and lineage-specific de novo methylation at CG and CH sites that led to differential methylation between embryonic and extraembryonic lineages at promoters of lineage regulators, gene bodies, and DNA-methylation valleys...
December 4, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29186518/diversity-generating-retroelements-natural-variation-classification-and-evolution-inferred-from-a-large-scale-genomic-survey
#14
Li Wu, Mari Gingery, Michael Abebe, Diego Arambula, Elizabeth Czornyj, Sumit Handa, Hamza Khan, Minghsun Liu, Mechthild Pohlschroder, Kharissa L Shaw, Amy Du, Huatao Guo, Partho Ghosh, Jeff F Miller, Steven Zimmerly
Diversity-generating retroelements (DGRs) are novel genetic elements that use reverse transcription to generate vast numbers of sequence variants in specific target genes. Here, we present a detailed comparative bioinformatic analysis that depicts the landscape of DGR sequences in nature as represented by data in GenBank. Over 350 unique DGRs are identified, which together form a curated reference set of putatively functional DGRs. We classify target genes, variable repeats and DGR cassette architectures, and identify two new accessory genes...
November 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29183131/resolving-the-nf%C3%AE%C2%BAb-hetero-dimer-binding-paradox-strain-and-frustration-guide-the-binding-of-dimeric-transcription-factors
#15
Davit A Potoyan, Carlos Bueno, Weihua Zheng, Elizabeth A Komives, Peter G Wolynes
Many eukaryotic transcription factors function after forming oligomers. The choice of protein partners is a non random event that has distinct functional consequences for gene regulation. In the present work we examine three dimers of transcription factors in the NFκB family; p50p50, p50p65 and p65p65. The NFκB dimers bind to a myriad of genomic sites and switch the targeted genes on or off with precision. The p65p50 hetero-dimer of NFκB is the strongest DNA binder and its unbinding is controlled kinetically by molecular stripping from the DNA induced by IκB...
November 28, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29181193/in-what-ways-do-synthetic-nucleotides-and-natural-base-lesions-alter-the-structural-stability-of-g-quadruplex-nucleic-acids
#16
REVIEW
Janos Sagi
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation...
2017: Journal of Nucleic Acids
https://www.readbyqxmd.com/read/29170589/the-past-ubiquity-and-environment-of-the-lost-earth-buildings-of-scotland
#17
Simon J Parkin, W Paul Adderley
This paper investigates the once ubiquitous vernacular earth-built structures of Scotland and how perceptions of such buildings were shaped and developed through periods of intense cultural and environmental change. We focus upon the past exploitation of traditional resources to construct vernacular architectures and on changes in the perception of the resultant buildings. Historic earth-built structures are today deeply hidden within the landscapes of Scotland, although they were once a common feature of both urban and rural settlements...
2017: Human Ecology: An Interdisciplinary Journal
https://www.readbyqxmd.com/read/29134741/contemporary-evolution-of-a-lepidopteran-species-heliothis-virescens-in-response-to-modern-agricultural-practices
#18
Megan L Fritz, Alexandra M DeYonke, Alexie Papanicolaou, Stephen Micinski, John Westbrook, Fred Gould
Adaptation to human-induced environmental change has the potential to profoundly influence the genomic architecture of affected species. This is particularly true in agricultural ecosystems, where anthropogenic selection pressure is strong. Heliothis virescens primarily feeds on cotton in its larval stages and US populations have been declining since the widespread planting of transgenic cotton, which endogenously expresses proteins derived from Bacillus thuringiensis (Bt). No physiological adaptation to Bt toxin has been found in the field, so adaptation in this altered environment could involve: 1) shifts in host plant selection mechanisms to avoid cotton, 2) changes in detoxification mechanisms required for cotton-feeding versus feeding on other hosts, or 3) loss of resistance to previously used management practices including insecticides...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29133448/origin-of-life-in-a-digital-microcosm
#19
Nitash C G, Thomas LaBar, Arend Hintze, Christoph Adami
While all organisms on Earth share a common descent, there is no consensus on whether the origin of the ancestral self-replicator was a one-off event or whether it only represented the final survivor of multiple origins. Here, we use the digital evolution system Avida to study the origin of self-replicating computer programs. By using a computational system, we avoid many of the uncertainties inherent in any biochemical system of self-replicators (while running the risk of ignoring a fundamental aspect of biochemistry)...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131160/human-primary-liver-cancer-derived-organoid-cultures-for-disease-modeling-and-drug-screening
#20
Laura Broutier, Gianmarco Mastrogiovanni, Monique Ma Verstegen, Hayley E Francies, Lena Morrill Gavarró, Charles R Bradshaw, George E Allen, Robert Arnes-Benito, Olga Sidorova, Marcia P Gaspersz, Nikitas Georgakopoulos, Bon-Kyoung Koo, Sabine Dietmann, Susan E Davies, Raaj K Praseedom, Ruby Lieshout, Jan N M IJzermans, Stephen J Wigmore, Kourosh Saeb-Parsy, Mathew J Garnett, Luc Jw van der Laan, Meritxell Huch
Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors...
December 2017: Nature Medicine
keyword
keyword
56509
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"