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https://www.readbyqxmd.com/read/28434188/drivers-of-community-assembly-in-tropical-forest-restoration-sites-role-of-local-environment-landscape-and-space
#1
Lívia D Audino, Stephen J Murphy, Ludimila Zambaldi, Julio Louzada, Liza S Comita
There is increasing recognition that community assembly theory can offer valuable insights for ecological restoration. We studied community assembly processes following tropical forest restoration efforts, using dung beetles (Scarabaeidae) as a focal taxon to investigate taxonomic and functional patterns of biodiversity recovery. We evaluated the relative importance of the local environment (i.e., canopy cover, understory cover, tree basal area, and soil texture), landscape context (i.e., habitat patch proximity and availability and percentage of surrounding area classified as natural forest or Eucalyptus spp...
April 23, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28433895/evaluating-network-level-predictors-of-behavior-change-among-injection-networks-enrolled-in-the-hptn-037-randomized-controlled-trial
#2
Laramie R Smith, Steffanie A Strathdee, David Metzger, Carl Latkin
BACKGROUND: Little is known about ways network-level factors that may influence the adoption of combination prevention behaviors among injection networks, or how network-oriented interventions might moderate this behavior change process. METHODS: A total of 232 unique injection risk networks in Philadelphia, PA, were randomized to a peer educator network-oriented intervention or standard of care control arm. Network-level aggregates reflecting the injection networks' baseline substance use dynamics, social interactions, and the networks exposure to gender- and structural-related vulnerabilities were calculated and used to predict changes in the proportion of network members adopting safer injection practices at 6-month follow-up...
April 5, 2017: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/28433884/synthetic-control-of-the-size-shape-and-polydispersity-of-anisotropic-silica-colloids
#3
Ryan P Murphy, Kunlun Hong, Norman J Wagner
The microstructure and rheological properties of colloidal suspensions depend on particle size and shape. This work aims to further control the size, shape, and polydispersity of anisotropic silica colloids, to reduce particle size, and to provide additional mechanistic insights on a prevalent, water-in-oil emulsion synthesis method. Key findings show that the dimensions of anisotropic silica particles can be systematically varied by approximately fivefold, with a limiting minimum particle size (D≈60nm, L≈300nm) obtained from emulsions with excess polyvinylpyrrolidone (PVP) and sodium citrate...
April 11, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28433748/the-repertoire-of-epithelial-morphogenesis-on-display-progressive-elaboration-of-drosophila-egg-structure
#4
REVIEW
Juan Carlos Duhart, Travis T Parsons, Laurel A Raftery
Epithelial structures are foundational for tissue organization in all metazoans. Sheets of epithelial cells form lateral adhesive junctions and acquire apico-basal polarity perpendicular to the surface of the sheet. Genetic analyses in the insect model, Drosophila melanogaster, have greatly advanced our understanding of how epithelial organization is established, and how it is modulated during tissue morphogenesis. Major insights into collective cell migrations have come from analyses of morphogenetic movements within the adult follicular epithelium that cooperates with female germ cells to build a mature egg...
April 19, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28433636/malassezia-globosa-mgmdl2-lipase-crystal-structure-and-rational-modification-of-substrate-specificity
#5
Dongming Lan, Huan Xu, JinXin Xu, Grzegorz Dubin, Jinsong Liu, Yonghua Wang
Lipases play an important role in physiological metabolism and diseases, and also have multiple industrial applications. Rational modification of lipase specificity may increase the commercial utility of this group of enzymes, but is hindered by insufficient mechanistic understanding. Here, we report the 2.0 Å resolution crystal structure of a mono- and di-acylglycerols lipase from Malassezia globosa (MgMDL2). Interestingly, residues Phe278 and Glu282 were found to involve in substrate recognition because mutation on each residue led to convert MgMDL2 to a triacylglycerol (TAG) lipase...
April 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28433539/rationally-designed-pi3k%C3%AE-mutants-to-mimic-atr-and-their-use-to-understand-binding-specificity-of-atr-inhibitors
#6
Yipin Lu, Mark Knapp, Kenneth Crawford, Robert Warne, Robert Elling, Kelly Yan, Michael Doyle, Gwynn Pardee, Li Zhang, Sylvia Ma, Mulugeta Mamo, Elizabeth Ornelas, Yue Pan, Dirksen Bussiere, Johanna Jansen, Isabel Zaror, Albert Lai, Paul Barsanti, Janet Sim
ATR, a protein kinase in the PIKK family, plays a critical role in the cell DNA-damage response and is an attractive anticancer drug target. Several potent and selective inhibitors of ATR have been reported showing significant antitumor efficacy, with most advanced ones entering clinical trials. However, due to the absence of an experimental ATR structure, the determinants contributing to ATR inhibitors' potency and specificity are not well understood. Here we present the mutations in the ATP-binding site of PI3Kα to progressively transform the pocket to mimic that of ATR...
April 19, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28433468/environmental-structure-and-energetic-consequences-in-groups-of-young-mice
#7
Delia S Shelton, Paul M Meyer, Karen M Ocasio
Microenvironments can have considerable physiological consequences for the inhabitants by influencing the movements of individual members. The microenvironment can permit more diverse aggregation patterns or restrict movements to certain dimensions. Here, we tested whether aspects of the microenvironment that influenced aggregation patterns also influenced the energetics of groups of young animals. We tested the effects of enclosure configuration on the group temperature and respiration of infant mice (Mus musculus)...
April 19, 2017: Physiology & Behavior
https://www.readbyqxmd.com/read/28433022/electrolyte-solutions-at-curved-electrodes-ii-microscopic-approach
#8
Andreas Reindl, Markus Bier, S Dietrich
Density functional theory is used to describe electrolyte solutions in contact with electrodes of planar or spherical shape. For the electrolyte solutions, we consider the so-called civilized model, in which all species present are treated on equal footing. This allows us to discuss the features of the electric double layer in terms of the differential capacitance. The model provides insight into the microscopic structure of the electric double layer, which goes beyond the mesoscopic approach studied in Paper I...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433018/atomistic-insight-into-the-non-classical-nucleation-mechanism-during-solidification-in-ni
#9
Grisell Díaz Leines, Ralf Drautz, Jutta Rogal
Nucleation is a key step during crystallization, but a complete understanding of the fundamental atomistic processes remains elusive. We investigate the mechanism of nucleation during solidification in nickel for various undercoolings using transition path sampling simulations. The temperature dependence of the free energy barriers and rate constants that we obtain is consistent with the predictions of classical nucleation theory and experiments. However, our analysis of the transition path ensemble reveals a mechanism that deviates from the classical picture of nucleation: the growing solid clusters have predominantly non-spherical shapes and consist of face-centered-cubic and random hexagonal-close-packed coordinated atoms surrounded by a cloud of prestructured liquid...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28432789/probing-protein-flexibility-reveals-a-mechanism-for-selective-promiscuity
#10
Nicolas A Pabon, Carlos J Camacho
Many eukaryotic regulatory proteins adopt distinct bound and unbound conformations, and use this structural flexibility to bind specifically to multiple partners. However, we lack an understanding of how an interface can select some ligands, but not others. Here, we present a molecular dynamics approach to identify and quantitatively evaluate the interactions responsible for this selective promiscuity. We apply this approach to the anti-cancer target PD-1 and its ligands PD-L1 and PD-L2. We discover that while unbound PD-1 exhibits a hard-to-drug hydrophilic interface, conserved specific triggers encoded in the cognate ligands activate a promiscuous binding pathway that reveals a flexible hydrophobic binding cavity...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28432788/structure-of-fam20a-reveals-a-pseudokinase-featuring-unique-disulfide-pattern-and-inverted-atp-binding
#11
Jixin Cui, Qinyu Zhu, Hui Zhang, Michael A Cianfrocco, Andres E Leschziner, Jack E Dixon, Junyu Xiao
Mutations in FAM20A cause tooth enamel defects known as Amelogenesis Imperfecta (AI) and renal calcification. We previously showed that Fam20A is a secretory pathway pseudokinase and allosterically activates the physiological casein kinase Fam20C to phosphorylate secreted proteins important for biomineralization (Cui et al., 2015). Here we report the nucleotide-free and ATP-bound structures of Fam20A. Fam20A exhibits a distinct disulfide bond pattern mediated by a unique insertion region. Loss of this insertion due to abnormal mRNA splicing interferes with the structure and function of Fam20A, resulting in AI...
April 22, 2017: ELife
https://www.readbyqxmd.com/read/28432593/talking-about-breast-cancer-which-symptoms-and-treatment-side-effects-are-important-to-patients-with-advanced-disease
#12
Anna Niklasson, Jean Paty, Anna Rydén
BACKGROUND: Patients' experience of symptoms and associated treatment is an increasingly important consideration in both regulatory and health technology assessments, and can inform treatment decisions. OBJECTIVE: This study aimed to gain insight directly from patients with advanced breast cancer about which symptoms and treatment side effects are important to them. METHODS: Women with locally advanced or metastatic breast cancer were interviewed individually by trained interviewers, using a semi-structured interview guide...
April 21, 2017: Patient
https://www.readbyqxmd.com/read/28432336/structure-function-analysis-of-the-dna-binding-domain-of-a-transmembrane-transcriptional-activator
#13
Andreas Schlundt, Sophie Buchner, Robert Janowski, Thomas Heydenreich, Ralf Heermann, Jürgen Lassak, Arie Geerlof, Ralf Stehle, Dierk Niessing, Kirsten Jung, Michael Sattler
The transmembrane DNA-binding protein CadC of E. coli, a representative of the ToxR-like receptor family, combines input and effector domains for signal sensing and transcriptional activation, respectively, in a single protein, thus representing one of the simplest signalling systems. At acidic pH in a lysine-rich environment, CadC activates the transcription of the cadBA operon through recruitment of the RNA polymerase (RNAP) to the two cadBA promoter sites, Cad1 and Cad2, which are directly bound by CadC...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432308/network-aided-bi-clustering-for-discovering-cancer-subtypes
#14
Guoxian Yu, Xianxue Yu, Jun Wang
Bi-clustering is a widely used data mining technique for analyzing gene expression data. It simultaneously groups genes and samples of an input gene expression data matrix to discover bi-clusters that relevant samples exhibit similar gene expression profiles over a subset of genes. The discovered bi-clusters bring insights for categorization of cancer subtypes, gene treatments and others. Most existing bi-clustering approaches can only enumerate bi-clusters with constant values. Gene interaction networks can help to understand the pattern of cancer subtypes, but they are rarely integrated with gene expression data for exploring cancer subtypes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432306/simple-rectangular-gratings-as-a-near-field-anti-reflection-pattern-for-gasb-tpv-cells
#15
Haitong Yu, Dong Liu, Zhen Yang, Yuanyuan Duan
We show theoretically that 2D rectangular gratings on the surface of GaSb can serve as an "anti-reflection" pattern for nano-gap thermophotovoltaic (TPV) devices, which significantly enhances near-field radiative flux from the emitter to a GaSb cell, thus improving output power and conversion efficiency. The system in this study is a 200-nm gap TPV power generation system with a planar infrared plasmonic emitter and GaSb cell. Rigorous coupled-wave analysis is used to calculate the spectral near-field radiative flux involving periodic structures...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432300/entropic-uncertainty-relations-for-markovian-and-non-markovian-processes-under-a-structured-bosonic-reservoir
#16
Dong Wang, Ai-Jun Huang, Ross D Hoehn, Fei Ming, Wen-Yang Sun, Jia-Dong Shi, Liu Ye, Sabre Kais
The uncertainty relation is a fundamental limit in quantum mechanics and is of great importance to quantum information processing as it relates to quantum precision measurement. Due to interactions with the surrounding environment, a quantum system will unavoidably suffer from decoherence. Here, we investigate the dynamic behaviors of the entropic uncertainty relation of an atom-cavity interacting system under a bosonic reservoir during the crossover between Markovian and non-Markovian regimes. Specifically, we explore the dynamic behavior of the entropic uncertainty relation for a pair of incompatible observables under the reservoir-induced atomic decay effect both with and without quantum memory...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431962/structural-basis-chemical-driving-forces-and-biological-implications-of-flavones-as-cu-ii-ionophores
#17
Fang Dai, Wen-Jing Yan, Yu-Ting Du, Xia-Zhen Bao, Xiu-Zhuang Li, Bo Zhou
A main biochemical property of cancer cells, compared with normal cells, is altered redox status including increased levels of copper to maintain their malignant phenotypes. Thus, increasing copper accumulation, by using ionophores, to disrupt abnormal redox homeostasis of cancer cells may be an important anticancer strategy. Naturally occurring molecules with extraordinarily diverse chemical scaffolds are an important source of inspiration for developing copper ionophores. Dietary flavonoids are well-characterized copper chelators and show cancer chemopreventive potential, but their ionophoric role for redox-active copper and the related biological implications have remained unknown...
April 18, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28431535/ion-and-water-binding-sites-inside-an-occluded-hourglass-pore-of-a-trimeric-intracellular-cation-tric-channel
#18
Xiaomin Ou, Jianli Guo, Longfei Wang, Hanting Yang, Xiuying Liu, Jianyuan Sun, Zhenfeng Liu
BACKGROUND: Trimeric intracellular cation (TRIC) channels are crucial for Ca(2+) handling in eukaryotes and are involved in K(+) uptake in prokaryotes. Recent studies on the representative members of eukaryotic and prokaryotic TRIC channels demonstrated that they form homotrimeric units with the ion-conducting pores contained within each individual monomer. RESULTS: Here we report detailed insights into the ion- and water-binding sites inside the pore of a TRIC channel from Sulfolobus solfataricus (SsTRIC)...
April 22, 2017: BMC Biology
https://www.readbyqxmd.com/read/28431230/structural-basis-for-guide-rna-processing-and-seed-dependent-dna-targeting-by-crispr-cas12a
#19
Daan C Swarts, John van der Oost, Martin Jinek
The CRISPR-associated protein Cas12a (Cpf1), which has been repurposed for genome editing, possesses two distinct nuclease activities: endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. To elucidate the molecular basis of both activities, we determined crystal structures of Francisella novicida Cas12a bound to guide RNA and in complex with an R-loop formed by a non-cleavable guide RNA precursor and a full-length target DNA. Corroborated by biochemical experiments, these structures reveal the mechanisms of guide RNA processing and pre-ordering of the seed sequence in the guide RNA that primes Cas12a for target DNA binding...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431135/reconstitution-of-a-functional-7sk-snrnp
#20
John E Brogie, David H Price
The 7SK small nuclear ribonucleoprotein (snRNP) plays a central role in RNA polymerase II elongation control by regulating the availability of active P-TEFb. We optimized conditions for analyzing 7SK RNA by SHAPE and demonstrated a hysteretic effect of magnesium on 7SK folding dynamics including a 7SK GAUC motif switch. We also found evidence that the 5΄ end pairs alternatively with two different regions of 7SK giving rise to open and closed forms that dictate the state of the 7SK motif. We then used recombinant P-TEFb, HEXIM1, LARP7 and MEPCE to reconstruct a functional 7SK snRNP in vitro...
April 20, 2017: Nucleic Acids Research
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