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https://www.readbyqxmd.com/read/28212875/genotyping-by-sequencing-provides-the-first-well-resolved-phylogeny-for-coffee-coffea-and-insights-into-the-evolution-of-caffeine-content-in-its-species-gbs-coffee-phylogeny-and-the-evolution-of-caffeine-content
#1
Perla Hamon, Corrinne E Grover, Aaron P Davis, Jean-Jacques Rakotomalala, Nathalie E Raharimalala, Victor A Albert, Hosahalli L Sreenath, Piet Stoffelen, Sharon E Mitchell, Emmanuel Couturon, Serge Hamon, Alexandre de Kochko, Dominique Crouzillat, Michel Rigoreau, Ucu Sumirat, Sélastique Akaffou, Romain Guyot
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples...
February 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28212371/circulating-tumor-cells-in-prostate-cancer-beyond-enumeration
#2
Jie-Fu Chen, Yi-Tsung Lu, Shirley Cheng, Hsian-Rong Tseng, Robert A Figlin, Edwin M Posadas
Circulating tumor cells (CTCs) are a population of rare cancer cells that have detached from the primary tumor and/or metastatic lesions and entered the peripheral circulation. Enumeration of CTCs has demonstrated value as a prognostic biomarker, and newer studies have pointed to information beyond enumeration that is of critical importance in prostate cancer. Technologic advances that permit examination of the morphology, function, and molecular content of CTCs have made it possible to measure these factors as part of liquid biopsy...
January 2017: Clinical Advances in Hematology & Oncology: H&O
https://www.readbyqxmd.com/read/28212262/molecular-cytogenetic-approach-to-characterize-novel-and-cryptic-chromosome-abnormalities-in-childhood-myeloid-malignances-of-fanconi-anemia
#3
Maria L R Borges, Roberto R Capela de Matos, Bethânia D A Silva Amaral, Eliane M Soares-Ventura, Edinalva P Leite, Mariluze O D Silva, Maria T M Nogueira Cornélio, Maria L M Silva, Thomas Liehr, Terezinha D J Marques-Salles
Myeloid malignancies can be either primary or secondary, whether or not a specific cause can be determined. Fanconi anemia (FA), a rare constitutional bone marrow failure, usually presents an increased possibility of clonal evolution, due to the increase in chromosomal instability, TP53 activation, and cell death. The evolution of FA may include aplastic anemia by the progressive failure of the bone marrow and myelod neoplasias, such as acute myeloid leukemia and myelodysplastic syndrome. Chromosome abnormalities, particularly of chromosomes, 1, 3, and 7, during the aplastic phase of the disease are predictive of evolution to acute myeloid leukemia/myelodysplastic syndrome...
March 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28212112/cancer-as-robust-intrinsic-state-shaped-by-evolution-a-key-issues-review
#4
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
https://www.readbyqxmd.com/read/28211601/biogeography-of-nodulated-legumes-and-their-nitrogen-fixing-symbionts
#5
REVIEW
Janet I Sprent, Julie Ardley, Euan K James
Contents I. II. III. IV. V. VI. VII. VIII. References SUMMARY: In the last decade, analyses of both molecular and morphological characters, including nodulation, have led to major changes in our understanding of legume taxonomy. In parallel there has been an explosion in the number of genera and species of rhizobia known to nodulate legumes. No attempt has been made to link these two sets of data or to consider them in a biogeographical context. This review aims to do this by relating the data to the evolution of the two partners: it highlights both longitudinal and latitudinal trends and considers these in relation to the location of major land masses over geological time...
February 17, 2017: New Phytologist
https://www.readbyqxmd.com/read/28211464/molecular-basis-of-abhd5-lipolysis-activation
#6
Matthew A Sanders, Huamei Zhang, Ljiljana Mladenovic, Yan Yuan Tseng, James G Granneman
Alpha-beta hydrolase domain-containing 5 (ABHD5), the defective gene in human Chanarin-Dorfman syndrome, is a highly conserved regulator of adipose triglyceride lipase (ATGL)-mediated lipolysis that plays important roles in metabolism, tumor progression, viral replication, and skin barrier formation. The structural determinants of ABHD5 lipolysis activation, however, are unknown. We performed comparative evolutionary analysis and structural modeling of ABHD5 and ABHD4, a functionally distinct paralog that diverged from ABHD5 ~500 million years ago, to identify determinants of ABHD5 lipolysis activation...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210491/film-morphology-evolution-during-solvent-vapor-annealing-of-highly-efficient-small-molecule-donor-acceptor-blends
#7
Sebastian Engmann, Hyun Wook Ro, Andrew Herzing, Chad R Snyder, Lee J Richter, Paul B Geraghty, David J Jones
Solution-processable small molecule photovoltaics based on the novel molecular donor, benzodithiophene terthiophene rhodanine (BTR), recently have shown maximum power conversion efficiencies above 8 % for active layer thicknesses up to 400 nm, using post process solvent vapor annealing (SVA) with tetrahydrofuran (THF). Here we report an in-situ study on the morphology evolution during SVA using the moderate solvent THF and the good solvent chloroform (CF). The combination of real-time grazing incidence X-ray diffraction (GIXD) and grazing incidence small angle X-ray scattering (GISAXS) allows us to draw a complete picture of the evolution of crystallinity and phase purity during post process annealing...
October 28, 2016: Journal of Materials Chemistry. A, Materials for Energy and Sustainability
https://www.readbyqxmd.com/read/28209339/vitamin-e-stabilized-highly-crosslinked-polyethylenes-the-role-and-effectiveness-in-total-hip-arthroplasty
#8
Kengo Yamamoto, Toshiyuki Tateiwa, Yasuhito Takahashi
Morphology and design of ultra-high molecular weight polyethylene (UHMWPE or simply PE) acetabular components used in total hip arthroplasty (THA) have been evolving for more than half a century. Since the late-1990s, there were two major technological innovations in PE emerged from necessity to overcome the wear-induced periprosthetic osteolysis, i.e., the development of highly crosslinked PEs (HXLPEs). There are many literature reporting that radiation crosslinked and remelted/annealed (first-generation) HXLPEs markedly reduced the incidence of osteolysis and aseptic loosening...
February 10, 2017: Journal of Orthopaedic Science: Official Journal of the Japanese Orthopaedic Association
https://www.readbyqxmd.com/read/28209121/evolution-of-toll-like-receptors-in-the-context-of-terrestrial-ungulates-and-cetaceans-diversification
#9
Edson Ishengoma, Morris Agaba
BACKGROUND: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined...
February 16, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28209119/plastome-phylogeny-and-early-diversification-of-brassicaceae
#10
Xinyi Guo, Jianquan Liu, Guoqian Hao, Lei Zhang, Kangshan Mao, Xiaojuan Wang, Dan Zhang, Tao Ma, Quanjun Hu, Ihsan A Al-Shehbaz, Marcus A Koch
BACKGROUND: The family Brassicaceae encompasses diverse species, many of which have high scientific and economic importance. Early diversifications and phylogenetic relationships between major lineages or clades remain unclear. Here we re-investigate Brassicaceae phylogeny with complete plastomes from 51 species representing all four lineages or 5 of 6 major clades (A, B, C, E and F) as identified in earlier studies. RESULTS: Bayesian and maximum likelihood phylogenetic analyses using a partitioned supermatrix of 77 protein coding genes resulted in nearly identical tree topologies exemplified by highly supported relationships between clades...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28208451/mori-zwanzig-theory-for-dissipative-forces-in-coarse-grained-dynamics-in-the-markov-limit
#11
Sergei Izvekov
We derive alternative Markov approximations for the projected (stochastic) force and memory function in the coarse-grained (CG) generalized Langevin equation, which describes the time evolution of the center-of-mass coordinates of clusters of particles in the microscopic ensemble. This is done with the aid of the Mori-Zwanzig projection operator method based on the recently introduced projection operator [S. Izvekov, J. Chem. Phys. 138, 134106 (2013)10.1063/1.4795091]. The derivation exploits the "generalized additive fluctuating force" representation to which the projected force reduces in the adopted projection operator formalism...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28205437/surface-and-interface-engineering-of-noble-metal-free-electrocatalysts-for-efficient-energy-conversion-processes
#12
Yun Pei Zhu, Chunxian Guo, Yao Zheng, Shi-Zhang Qiao
Developing cost-effective and high-performance electrocatalysts for renewable energy conversion and storage is motivated by increasing concerns regarding global energy security and creating sustainable technologies dependent on inexpensive and abundant resources. Recent achievements in the design and synthesis of efficient non-precious-metal and even non-metal electrocatalysts make the replacement of noble metal counterparts for the hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and oxygen reduction reaction (ORR) with earth-abundant elements, for example, C, N, Fe, Mn, and Co, a realistic possibility...
February 16, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28203307/epigenetic-strategies-to-reverse-drug-resistance-in-heterogeneous-multiple-myeloma
#13
REVIEW
Mark E Issa, Farnaz Sedigheh Takhsha, Chandra Sekhar Chirumamilla, Claudina Perez-Novo, Wim Vanden Berghe, Muriel Cuendet
Multiple myeloma (MM) is a hematological malignancy, which remains incurable because most patients eventually relapse or become refractory to current treatments. Due to heterogeneity within the cancer cell microenvironment, cancer cell populations employ a dynamic survival strategy to chemotherapeutic treatments, which frequently results in a rapid acquisition of therapy resistance. Besides resistance-conferring genetic alterations within a tumor cell population selected during drug treatment, recent findings also reveal non-mutational mechanisms of drug resistance, involving a small population of "cancer stem cells" (CSCs) which are intrinsically more refractory to the effects of a variety of anticancer drugs...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28202180/chemical-structure-influence-on-napl-mixture-nonideality-evolution-rate-limited-dissolution-and-contaminant-mass-flux
#14
Mark C Padgett, Geoffrey R Tick, Kenneth C Carroll, William R Burke
The influence of chemical structure on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux was examined. The variability of measured and UNIFAC modeled NAPL activity coefficients as a function of mole fraction was compared for two NAPL mixtures containing structurally-different contaminants of concern including toluene (TOL) or trichloroethene (TCE) within a hexadecane (HEXDEC) matrix. The results showed that dissolution from the NAPL mixtures transitioned from ideality for mole fractions >0...
February 3, 2017: Journal of Contaminant Hydrology
https://www.readbyqxmd.com/read/28201779/comprehensive-molecular-characterization-of-multifocal-glioblastoma-proves-its-monoclonal-origin-and-reveals-novel-insights-into-clonal-evolution-and-heterogeneity-of-glioblastomas
#15
Khalil Abou-El-Ardat, Michael Seifert, Kerstin Becker, Sophie Eisenreich, Matthias Lehmann, Karl Hackmann, Andreas Rump, Gerrit Meijer, Beatriz Carvalho, Achim Temme, Gabriele Schackert, Evelin Schröck, Dietmar Krex, Barbara Klink
No abstract text is available yet for this article.
February 13, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28199083/shape-memory-hydrogels-evolution-of-structural-principles-to-enable-shape-switching-of-hydrophilic-polymer-networks
#16
Candy Löwenberg, Maria Balk, Christian Wischke, Marc Behl, Andreas Lendlein
The ability of hydrophilic chain segments in polymer networks to strongly interact with water allows the volumetric expansion of the material and formation of a hydrogel. When polymer chain segments undergo reversible hydration depending on environmental conditions, smart hydrogels can be realized, which are able to shrink/swell and thus alter their volume on demand. In contrast, implementing the capacity of hydrogels to switch their shape rather than volume demands more sophisticated chemical approaches and structural concepts...
February 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28198504/complete-mitochondrial-genome-of-the-amur-hedgehog-erinaceus-amurensis-erinaceidae-and-higher-phylogeny-of-the-family-erinaceidae
#17
N H Kim, S J Lim, H M Chae, Y C Park
We sequenced and characterized the complete mitogenome (KX964606) of the Amur hedgehog Erinaceus amurensis to provide more data for comparative mitogenomics of the genus Erinaceus (Erinaceidae). The mitogenome of E. amurensis is a circular molecule 16,941 bp long, consisting of a control region and a conserved set of 37 genes containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes (12S rRNA and 16S rRNA). The mitogenome of E. amurensis is AT-biased, with a nucleotide composition of 33.9% A, 21...
February 8, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28198110/emergence-of-a-novel-highly-pathogenic-porcine-reproductive-and-respiratory-syndrome-virus-in-china
#18
J-K Liu, X Zhou, J-Q Zhai, B Li, C-H Wei, A-L Dai, X-Y Yang, M-L Luo
From 2014 to 2015, four novel highly pathogenic PRRS virus (HP-PRRSV) strains named 14LY01-FJ, 14LY02-FJ 15LY01-FJ, and 15LY02-FJ were isolated from high morbidity (100%) and mortality (40%-80%) in piglets and sows in Fujian Province. To further our knowledge about these novel virus strains, we characterized their complete genomes and determined their pathogenicity in piglets. Full-length genome sequencing analysis showed that these four isolates were closely related to type 2 (North American type, NA-type) isolates, with 88...
February 14, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28197941/properties-and-evolution-of-dissolved-organic-matter-during-co-composting-of-dairy-manure-and-chinese-herbal-residues
#19
Qunliang Li, Yanyu Lu, Xiaobo Guo, Guangchun Shan, Junhao Huang
Composting is an effective method in treating solid organic wastes, in which dissolved organic matter (DOM) plays an important role in transformation of organic matter and microbial activity. Therefore, an understanding of the properties and evolution of DOM during composting is crucial. In this study, DOM was studied using elemental analysis, spectroscopic analysis (UV-vis, FTIR, and pyrolysis-GC/MS), and colloidal analysis during a 120-day composting. Results showed that the content of N and O in DOM increased while C and H content declined progressively over the composting time...
February 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28197415/pharmacoinformatics-adaptive-evolution-and-elucidation-of-six-novel-compounds-for-schizophrenia-treatment-by-targeting-daoa-g72-isoforms
#20
Sheikh Arslan Sehgal
Studies on Schizophrenia so far reveal a complex picture of neurological malfunctioning reported to be strongly associated with DAOA. Detailed sequence analyses proved DAOA as a primate specific gene having conserved gene desert region on both upstream and downstream region. The analyses of 10 MB chromosomal region of primates, birds, rodents, and reptiles having DAOA evidenced the conserved part in primates and in the rest of species, while DAOA is only present in primates. DAOA has four isoforms having one interaction partner DAO...
2017: BioMed Research International
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