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https://www.readbyqxmd.com/read/28548104/genomic-analysis-of-oesophageal-squamous-cell-carcinoma-identifies-alcohol-drinking-related-mutation-signature-and-genomic-alterations
#1
Jiang Chang, Wenle Tan, Zhiqiang Ling, Ruibin Xi, Mingming Shao, Mengjie Chen, Yingying Luo, Yanjie Zhao, Yun Liu, Xiancong Huang, Yuchao Xia, Jinlin Hu, Joel S Parker, David Marron, Qionghua Cui, Linna Peng, Jiahui Chu, Hongmin Li, Zhongli Du, Yaling Han, Wen Tan, Zhihua Liu, Qimin Zhan, Yun Li, Weimin Mao, Chen Wu, Dongxin Lin
Approximately half of the world's 500,000 new oesophageal squamous-cell carcinoma (ESCC) cases each year occur in China. Here, we show whole-genome sequencing of DNA and RNA in 94 Chinese individuals with ESCC. We identify six mutational signatures (E1-E6), and Signature E4 is unique in ESCC linked to alcohol intake and genetic variants in alcohol-metabolizing enzymes. We discover significantly recurrent mutations in 20 protein-coding genes, 4 long non-coding RNAs and 10 untranslational regions. Functional analyses show six genes that have recurrent copy-number variants in three squamous-cell carcinomas (oesophageal, head and neck and lung) significantly promote cancer cell proliferation, migration and invasion...
May 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28547888/mapping-the-free-energy-of-lithium-solvation-in-the-protic-ionic-liquid-ethylammonuim-nitrate-a-metadynamics-study
#2
Ali Kachmar, Marcelo Carignano, Teodoro Laino, Marcella Iannuzzi, Jürg Hutter
The understanding of lithium solvation and transport in ionic liquids is important due to the possible applications in electrochemical devices. Using first principles simulations aided with the metadynamics approach we study the free energy landscape for lithium at infinite dilution conditions in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and find a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium solvated either by 3 or 4 nitrates ions with a transition barrier between them of 0...
May 26, 2017: ChemSusChem
https://www.readbyqxmd.com/read/28546842/opportunities-and-challenges-for-the-sustainable-production-of-structurally-complex-diterpenoids-in-recombinant-microbial-systems
#3
REVIEW
Katarina Kemper, Max Hirte, Markus Reinbold, Monika Fuchs, Thomas Brück
With over 50.000 identified compounds terpenes are the largest and most structurally diverse group of natural products. They are ubiquitous in bacteria, plants, animals and fungi, conducting several biological functions such as cell wall components or defense mechanisms. Industrial applications entail among others pharmaceuticals, food additives, vitamins, fragrances, fuels and fuel additives. Central building blocks of all terpenes are the isoprenoid compounds isopentenyl diphosphate and dimethylallyl diphosphate...
2017: Beilstein Journal of Organic Chemistry
https://www.readbyqxmd.com/read/28545576/a-computational-assessment-of-ph-dependent-differential-interaction-of-t7-lysozyme-with-t7-rna-polymerase
#4
Subhomoi Borkotoky, Ayaluru Murali
BACKGROUND: T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions...
May 25, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28545397/jed-a-java-essential-dynamics-program-for-comparative-analysis-of-protein-trajectories
#5
Charles C David, Ettayapuram Ramaprasad Azhagiya Singam, Donald J Jacobs
BACKGROUND: Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two common approaches to determine PCA modes (eigenvectors) and their eigenvalues. Protein dynamics can be characterized in terms of Cartesian coordinates or internal distance pairs. In understanding protein dynamics, a comparison of trajectories taken from a set of proteins for similarity assessment provides insight into conserved mechanisms...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28545209/the-footprint-of-marginal-agriculture-in-the-mediterranean-mountain-landscape-an-analysis-of-the-central-spanish-pyrenees
#6
T Lasanta, E Nadal-Romero, M P Errea
Agriculture forms an essential part of the mountains of the Mediterranean. For centuries, large areas were cultivated to feed the local population, with highly marginal slopes being tilled at times of heavy demographic pressure, using the shifting agriculture system. A great deal of agricultural land was abandoned during the 20th century, giving rise to secondary succession processes that tend to eliminate the agricultural footprint. However, revegetation is a highly complex process leading to areas with dense, well-structured plant cover, and other open areas of scrubland...
May 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28542919/context-dependent-colonization-dynamics-regional-reward-contagion-drives-local-compression-in-aquatic-beetles
#7
Matthew R Pintar, William J Resetarits
1.Habitat selection by colonizing organisms is an important factor in determining species abundance and community dynamics at multiple spatial scales. Many organisms select habitat patches based on intrinsic patch quality, but patches exist in complex landscapes linked by dispersal and colonization, forming metapopulations and metacommunities. Perceived patch quality can be influenced by neighboring patches through spatial contagion, wherein perceived quality of one patch can extend beyond its borders and either increase or decrease the colonization of neighboring patches and localities...
May 19, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28541439/the-evolutionary-landscape-of-dbl-like-rhogef-families-adapting-eukaryotic-cells-to-environmental-signals
#8
Philippe Fort, Anne Blangy
The dynamics of cell morphology in eukaryotes is largely controlled by small GTPases of the Rho family. Rho GTPases are activated by Guanine nucleotide Exchange Factors (RhoGEFs), of which Diffuse B-cell Lymphoma (Dbl)-like members form the largest family. Here we surveyed Dbl-like sequences from 175 eukaryotic genomes and illuminate how the Dbl family evolved in all eukaryotic supergroups. By combining probabilistic phylogenetic approaches and functional domain analysis, we show that the human Dbl-like family is made of 71 members, structured into 20 subfamilies...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541292/long-range-allosteric-regulation-of-the-human-26s-proteasome-by-20s-proteasome-targeting-cancer-drugs
#9
David Haselbach, Jil Schrader, Felix Lambrecht, Fabian Henneberg, Ashwin Chari, Holger Stark
The proteasome holoenzyme is the major non-lysosomal protease; its proteolytic activity is essential for cellular homeostasis. Thus, it is an attractive target for the development of chemotherapeutics. While the structural basis of core particle (CP) inhibitors is largely understood, their structural impact on the proteasome holoenzyme remains entirely elusive. Here, we determined the structure of the 26S proteasome with and without the inhibitor Oprozomib. Drug binding modifies the energy landscape of conformational motion in the proteasome regulatory particle (RP)...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28539360/a-dock-and-coalesce-mechanism-driven-by-hydrophobic-interactions-governs-cdc42-binding-with-its-effector-protein-ack
#10
George J N Tetley, Helen R Mott, R Neil Cooley, Darerca Owen
Cdc42 is a Rho-family small G protein that has been widely studied for its role in controlling the actin cytoskeleton and plays a part in several potentially oncogenic signalling networks. Similar to most other small G proteins, Cdc42 binds to many downstream effector proteins to elicit its cellular effects. These effector proteins all engage the same face of Cdc42, the conformation of which is governed by the activation state of the G protein. Previously, the importance of individual residues in conferring binding affinity has been explored for residues within Cdc42 for three of its CRIB effectors, activated Cdc42 kinase (ACK), p21-activated kinase (PAK), and Wiskott-Aldrich syndrome protein (WASP)...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28535588/pedogenic-knowledge-aided-modelling-of-soil-inorganic-carbon-stocks-in-an-alpine-environment
#11
Ren-Min Yang, Fan Yang, Fei Yang, Lai-Ming Huang, Feng Liu, Jin-Ling Yang, Yu-Guo Zhao, De-Cheng Li, Gan-Lin Zhang
Accurate estimation of soil carbon is essential for accounting carbon cycling on the background of global environment change. However, previous studies made little contribution to the patterns and stocks of soil inorganic carbon (SIC) in large scales. In this study, we defined the structure of the soil depth function to fit vertical distribution of SIC based on pedogenic knowledge across various landscapes. Soil depth functions were constructed from a dataset of 99 soil profiles in the alpine area of the northeastern Tibetan Plateau...
May 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28533982/lid-opening-and-conformational-stability-of-t1-lipase-is-mediated-by-increasing-chain-length-polar-solvents
#12
Jonathan Maiangwa, Mohd Shukuri Mohamad Ali, Abu Bakar Salleh, Raja Noor Zaliha Raja Abd Rahman, Yahaya M Normi, Fairolniza Mohd Shariff, Thean Chor Leow
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%...
2017: PeerJ
https://www.readbyqxmd.com/read/28531354/monomeric-polyglutamine-structures-that-evolve-into-fibrils
#13
David Punihaole, Ryan S Jakubek, Riley James Workman, Lauren E Marbella, Patricia Campbell, Jeffry D Madura, Sanford A Asher
We investigate the solution and fibril conformations and structural transitions of the polyglutamine (polyQ) peptide, D2Q10K2 (Q10), by synergistically using UV Resonance Raman (UVRR) spectroscopy and Molecular Dynamics (MD) simulations. We show that Q10 adopts two distinct, monomeric solution conformational states, a collapsed β-strand and a PPII-like structure that do not readily interconvert. This clearly indicates a high activation barrier in solution that prevents equilibration between these structures...
May 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28530242/interface-driven-formation-of-a-two-dimensional-dodecagonal-fullerene-quasicrystal
#14
M Paßens, V Caciuc, N Atodiresei, M Feuerbacher, M Moors, R E Dunin-Borkowski, S Blügel, R Waser, S Karthäuser
Since their discovery, quasicrystals have attracted continuous research interest due to their unique structural and physical properties. Recently, it was demonstrated that dodecagonal quasicrystals could be used as bandgap materials in next-generation photonic devices. However, a full understanding of the formation mechanism of quasicrystals is necessary to control their physical properties. Here we report the formation of a two-dimensional dodecagonal fullerene quasicrystal on a Pt3Ti(111) surface, which can be described in terms of a square-triangle tiling...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529358/how-do-psychiatrists-in-india-construct-their-professional-identity-a-critical-literature-review
#15
Clement Bayetti, Sushrut Jadhav, Smita N Deshpande
Psychiatric practice in India is marked by an increasing gulf between largely urban-based mental health professionals and a majority rural population. Based on the premise that any engagement is a mutually constructed humane process, an understanding of the culture of psychiatry including social process of local knowledge acquisition by trainee psychiatrists is critical. This paper reviews existing literature on training of psychiatrists in India, the cultural construction of their professional identities and autobiographical reflections...
January 2017: Indian Journal of Psychiatry
https://www.readbyqxmd.com/read/28529152/coevolution-of-patch-type-dependent-emigration-and-patch-type-dependent-immigration
#16
Helene C Weigang
The three phases of dispersal - emigration, transfer and immigration - are affecting each other and the former and latter decisions may depend on patch types. Despite the inevitable fact of the complexity of the dispersal process, patch-type dependencies of dispersal decisions modelled as emigration and immigration are usually missing in theoretical dispersal models. Here, I investigate the coevolution of patch-type dependent emigration and patch-type dependent immigration in an extended Hamilton-May model...
May 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28528024/structure-diverse-phylomer-libraries-as-a-rich-source-of-bioactive-hits-from-phenotypic-and-target-directed-screens-against-intracellular-proteins
#17
REVIEW
Paul M Watt, Nadia Milech, Shane R Stone
Phylomers are peptides derived from biodiverse protein fragments. Genetically encoded Phylomer libraries have been constructed, containing hundreds of billions of peptides derived from virtually all of the few thousand fold families found in the protein universe. They offer a rich source of high quality hits against diverse target sequences and have been used for three main purposes: firstly, to identify and validate targets in phenotypic screens; secondly, to block protein interactions with nanomolar potency binding affinities; thirdly as a source of more efficient cell penetrating peptides for the delivery of a wide range of biologics...
May 18, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28524879/energy-landscape-driven-non-equilibrium-evolution-of-inherent-structure-in-disordered-material
#18
Yue Fan, Takuya Iwashita, Takeshi Egami
Complex states in glasses can be neatly expressed by the potential energy landscape (PEL). However, because PEL is highly multi-dimensional it is difficult to describe how the system moves around in PEL. Here we demonstrate that it is possible to predict the evolution of macroscopic state in a metallic glass, such as ageing and rejuvenation, through a set of simple equations describing excitations in the PEL. The key to this simplification is the realization that the step of activation from the initial state to the saddle point in PEL and the following step of relaxation to the final state are essentially decoupled...
May 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28524624/pulmonary-arterial-hypertension-progress-in-understanding-the-disease-and-prioritizing-strategies-for-drug-development
#19
REVIEW
P Ghataorhe, C J Rhodes, L Harbaum, M Attard, J Wharton, M R Wilkins
Pulmonary arterial hypertension (PAH), at one time a largely overlooked disease, is now the subject of intense study in many academic and biotech groups. The availability of new treatments has increased awareness of the condition. This in turn has driven a change in the demographics of PAH, with an increase in the mean age at diagnosis. The diagnosis of PAH in more elderly patients has highlighted the need for careful phenotyping of patients and for further studies to understand how best to manage pulmonary hypertension associated with, for example, left heart disease...
May 19, 2017: Journal of Internal Medicine
https://www.readbyqxmd.com/read/28523552/epigenetics-of-huntington-s-disease
#20
Silvia Bassi, Takshashila Tripathi, Alan Monziani, Francesca Di Leva, Marta Biagioli
Huntington's disease (HD) is a genetic, fatal autosomal dominant neurodegenerative disorder typically occurring in midlife with symptoms ranging from chorea, to dementia, to personality disturbances (Philos Trans R Soc Lond Ser B Biol Sci 354:957-961, 1999). HD is inherited in a dominant fashion, and the underlying mutation in all cases is a CAG trinucleotide repeat expansion within exon 1 of the HD gene (Cell 72:971-983, 1993). The expanded CAG repeat, translated into a lengthened glutamine tract at the amino terminus of the huntingtin protein, affects its structural properties and functional activities...
2017: Advances in Experimental Medicine and Biology
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