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Proceedings of the National Academy of Sciences of the United States of America

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https://www.readbyqxmd.com/read/28733276/whether-the-hearing-brain-hears-it-or-the-deaf-brain-sees-it-it-s-just-the-same
#1
Marcin Szwed, Łukasz Bola, Maria Zimmermann
No abstract text is available yet for this article.
July 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28733275/which-way-to-low-density-liquid-water
#2
Francesco Sciortino
No abstract text is available yet for this article.
July 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28733274/designing-toughness-and-strength-for-soft-materials
#3
Xuanhe Zhao
No abstract text is available yet for this article.
July 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28729375/rainforest-initiated-wet-season-onset-over-the-southern-amazon
#4
Jonathon S Wright, Rong Fu, John R Worden, Sudip Chakraborty, Nicholas E Clinton, Camille Risi, Ying Sun, Lei Yin
Although it is well established that transpiration contributes much of the water for rainfall over Amazonia, it remains unclear whether transpiration helps to drive or merely responds to the seasonal cycle of rainfall. Here, we use multiple independent satellite datasets to show that rainforest transpiration enables an increase of shallow convection that moistens and destabilizes the atmosphere during the initial stages of the dry-to-wet season transition. This shallow convection moisture pump (SCMP) preconditions the atmosphere at the regional scale for a rapid increase in rain-bearing deep convection, which in turn drives moisture convergence and wet season onset 2-3 mo before the arrival of the Intertropical Convergence Zone (ITCZ)...
July 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28724725/protein-diversity-in-discrete-structures-at-the-distal-tip-of-the-trypanosome-flagellum
#5
Vladimir Varga, Flavia Moreira-Leite, Neil Portman, Keith Gull
The distal end of the eukaryotic flagellum/cilium is important for axonemal growth and signaling and has distinct biomechanical properties. Specific flagellum tip structures exist, yet their composition, dynamics, and functions are largely unknown. We used biochemical approaches to identify seven constituents of the flagella connector at the tip of an assembling trypanosome flagellum and three constituents of the axonemal capping structure at the tips of both assembling and mature flagella. Both tip structures contain evolutionarily conserved as well as kinetoplastid-specific proteins, and component assembly into the structures occurs very early during flagellum extension...
July 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28724724/brct-domain-protein-brit1-influences-class-switch-recombination
#6
Wei-Feng Yen, Ashutosh Chaudhry, Bharat Vaidyanathan, William T Yewdell, Joseph N Pucella, Rahul Sharma, Yulong Liang, Kaiyi Li, Alexander Y Rudensky, Jayanta Chaudhuri
DNA double-strand breaks (DSBs) serve as obligatory intermediates for Ig heavy chain (Igh) class switch recombination (CSR). The mechanisms by which DSBs are resolved to promote long-range DNA end-joining while suppressing genomic instability inherently associated with DSBs are yet to be fully elucidated. Here, we use a targeted short-hairpin RNA screen in a B-cell lymphoma line to identify the BRCT-domain protein BRIT1 as an effector of CSR. We show that conditional genetic deletion of BRIT1 in mice leads to a marked increase in unrepaired Igh breaks and a significant reduction in CSR in ex vivo activated splenic B cells...
July 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28724723/nucleoredoxin-guards-against-oxidative-stress-by-protecting-antioxidant-enzymes
#7
Sophie Kneeshaw, Rumana Keyani, Valérie Delorme-Hinoux, Lisa Imrie, Gary J Loake, Thierry Le Bihan, Jean-Philippe Reichheld, Steven H Spoel
Cellular accumulation of reactive oxygen species (ROS) is associated with a wide range of developmental and stress responses. Although cells have evolved to use ROS as signaling molecules, their chemically reactive nature also poses a threat. Antioxidant systems are required to detoxify ROS and prevent cellular damage, but little is known about how these systems manage to function in hostile, ROS-rich environments. Here we show that during oxidative stress in plant cells, the pathogen-inducible oxidoreductase Nucleoredoxin 1 (NRX1) targets enzymes of major hydrogen peroxide (H2O2)-scavenging pathways, including catalases...
July 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28724722/effect-of-directional-pulling-on-mechanical-protein-degradation-by-atp-dependent-proteolytic-machines
#8
Adrian O Olivares, Hema Chandra Kotamarthi, Benjamin J Stein, Robert T Sauer, Tania A Baker
AAA+ proteases and remodeling machines couple hydrolysis of ATP to mechanical unfolding and translocation of proteins following recognition of sequence tags called degrons. Here, we use single-molecule optical trapping to determine the mechanochemistry of two AAA+ proteases, Escherichia coli ClpXP and ClpAP, as they unfold and translocate substrates containing multiple copies of the titin(I27) domain during degradation initiated from the N terminus. Previous studies characterized degradation of related substrates with C-terminal degrons...
July 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720709/overfishing-causes-frequent-fish-population-collapses-but-rare-extinctions
#9
LETTER
Olivier Le Pape, Sylvain Bonhommeau, Anne-Elise Nieblas, Jean-Marc Fromentin
No abstract text is available yet for this article.
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720708/reply-to-le-pape-et-al-management-is-key-to-preventing-marine-extinctions
#10
Matthew G Burgess, Alexa Fredston-Hermann, Malin L Pinsky, Steven D Gaines, David Tilman
No abstract text is available yet for this article.
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720707/intrinsically-disordered-chromatin-protein-nupr1-binds-to-the-c-terminal-region-of-polycomb-ring1b
#11
Patricia Santofimia-Castaño, Bruno Rizzuti, Ángel L Pey, Philippe Soubeyran, Miguel Vidal, Raúl Urrutia, Juan L Iovanna, José L Neira
Intrinsically disordered proteins (IDPs) are ubiquitous in eukaryotes, and they are often associated with diseases in humans. The protein NUPR1 is a multifunctional IDP involved in chromatin remodeling and in the development and progression of pancreatic cancer; however, the details of such functions are unknown. Polycomb proteins are involved in specific transcriptional cascades and gene silencing. One of the proteins of the Polycomb complex is the Ring finger protein 1 (RING1). RING1 is related to aggressive tumor features in multiple cancer types...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720706/broadly-expressed-repressors-integrate-patterning-across-orthogonal-axes-in-embryos
#12
Theodora Koromila, Angelike Stathopoulos
The role of spatially localized repressors in supporting embryonic patterning is well appreciated, but, alternatively, the role ubiquitously expressed repressors play in this process is not well understood. We investigated the function of two broadly expressed repressors, Runt (Run) and Suppressor of Hairless [Su(H)], in patterning the Drosophila embryo. Previous studies have shown that Run and Su(H) regulate gene expression along anterior-posterior (AP) or dorsal-ventral (DV) axes, respectively, by spatially limiting activator action, but here we characterize a different role...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720705/conceptual-framework-of-the-eco-physiological-phases-of-insect-diapause-development-justified-by-transcriptomic-profiling
#13
Vladimír Koštál, Tomáš Štětina, Rodolphe Poupardin, Jaroslava Korbelová, Alexander William Bruce
Insects often overcome unfavorable seasons in a hormonally regulated state of diapause during which their activity ceases, development is arrested, metabolic rate is suppressed, and tolerance of environmental stress is bolstered. Diapausing insects pass through a stereotypic succession of eco-physiological phases termed "diapause development." The phasing is varied in the literature, and the whole concept is sometimes criticized as being too artificial. Here we present the results of transcriptional profiling using custom microarrays representing 1,042 genes in the drosophilid fly, Chymomyza costata Fully grown, third-instar larvae programmed for diapause by a photoperiodic (short-day) signal were assayed as they traversed the diapause developmental program...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720704/cytosolic-interaction-of-type-iii-human-cd38-with-cib1-modulates-cellular-cyclic-adp-ribose-levels
#14
Jun Liu, Yong Juan Zhao, Wan Hua Li, Yun Nan Hou, Ting Li, Zhi Ying Zhao, Cheng Fang, Song Lu Li, Hon Cheung Lee
CD38 catalyzes the synthesis of the Ca(2+) messenger, cyclic ADP-ribose (cADPR). It is generally considered to be a type II protein with the catalytic domain facing outside. How it can catalyze the synthesis of intracellular cADPR that targets the endoplasmic Ca(2+) stores has not been resolved. We have proposed that CD38 can also exist in an opposite type III orientation with its catalytic domain facing the cytosol. Here, we developed a method using specific nanobodies to immunotarget two different epitopes simultaneously on the catalytic domain of the type III CD38 and firmly established that it is naturally occurring in human multiple myeloma cells...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720703/canopy-structure-drives-orangutan-habitat-selection-in-disturbed-bornean-forests
#15
Andrew B Davies, Marc Ancrenaz, Felicity Oram, Gregory P Asner
The conservation of charismatic and functionally important large species is becoming increasingly difficult. Anthropogenic pressures continue to squeeze available habitat and force animals into degraded and disturbed areas. Ensuring the long-term survival of these species requires a well-developed understanding of how animals use these new landscapes to inform conservation and habitat restoration efforts. We combined 3 y of highly detailed visual observations of Bornean orangutans with high-resolution airborne remote sensing (Light Detection and Ranging) to understand orangutan movement in disturbed and fragmented forests of Malaysian Borneo...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720702/identification-of-a-vesicular-atp-release-inhibitor-for-the-treatment-of-neuropathic-and-inflammatory-pain
#16
Yuri Kato, Miki Hiasa, Reiko Ichikawa, Nao Hasuzawa, Atsushi Kadowaki, Ken Iwatsuki, Kazuhiro Shima, Yasuo Endo, Yoshiro Kitahara, Tsuyoshi Inoue, Masatoshi Nomura, Hiroshi Omote, Yoshinori Moriyama, Takaaki Miyaji
Despite the high incidence of neuropathic and inflammatory pain worldwide, effective drugs with few side effects are currently unavailable for the treatment of chronic pain. Recently, researchers have proposed that inhibitors of purinergic chemical transmission, which plays a key role in the pathological pain response, may allow for targeted treatment of pathological neuropathic and inflammatory pain. However, such therapeutic analgesic agents have yet to be developed. In the present study, we demonstrated that clodronate, a first-generation bisphosphonate with comparatively fewer side effects than traditional treatments, significantly attenuates neuropathic and inflammatory pain unrelated to bone abnormalities via inhibition of vesicular nucleotide transporter (VNUT), a key molecule for the initiation of purinergic chemical transmission...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#17
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720700/hitchhiking-and-epistasis-give-rise-to-cohort-dynamics-in-adapting-populations
#18
Sean W Buskirk, Ryan Emily Peace, Gregory I Lang
Beneficial mutations are the driving force of adaptive evolution. In asexual populations, the identification of beneficial alleles is confounded by the presence of genetically linked hitchhiker mutations. Parallel evolution experiments enable the recognition of common targets of selection; yet these targets are inherently enriched for genes of large target size and mutations of large effect. A comprehensive study of individual mutations is necessary to create a realistic picture of the evolutionarily significant spectrum of beneficial mutations...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720699/cellular-trade-offs-and-optimal-resource-allocation-during-cyanobacterial-diurnal-growth
#19
Alexandra-M Reimers, Henning Knoop, Alexander Bockmayr, Ralf Steuer
Cyanobacteria are an integral part of Earth's biogeochemical cycles and a promising resource for the synthesis of renewable bioproducts from atmospheric CO2 Growth and metabolism of cyanobacteria are inherently tied to the diurnal rhythm of light availability. As yet, however, insight into the stoichiometric and energetic constraints of cyanobacterial diurnal growth is limited. Here, we develop a computational framework to investigate the optimal allocation of cellular resources during diurnal phototrophic growth using a genome-scale metabolic reconstruction of the cyanobacterium Synechococcus elongatus PCC 7942...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28720698/catalysis-and-chemical-mechanisms-of-calcite-dissolution-in-seawater
#20
Adam V Subhas, Jess F Adkins, Nick E Rollins, John Naviaux, Jonathan Erez, William M Berelson
Near-equilibrium calcite dissolution in seawater contributes significantly to the regulation of atmospheric [Formula: see text] on 1,000-y timescales. Despite many studies on far-from-equilibrium dissolution, little is known about the detailed mechanisms responsible for calcite dissolution in seawater. In this paper, we dissolve (13)C-labeled calcites in natural seawater. We show that the time-evolving enrichment of [Formula: see text] in solution is a direct measure of both dissolution and precipitation reactions across a large range of saturation states...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
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