bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solution structures and dynamics of ADF/cofilins UNC-60A and UNC-60B fromCaenorhabditis elegans
Authors: Shukla Vaibhav Kumar , Kabra Ashish , Maheshwari Diva , Yadav Rahul , Jain Anupam , Tripathi Sarita , Ono Shoichiro , Kumar Dinesh , Arora Ashish 
Published: October 2014

The nematode Caenorhabditis elegans has two ADF (actin-depolymerizing factor)/cofilin isoforms, UNC-60A and UNC-60B, which are expressed by the unc60 gene by alternative splicing. UNC-60A has higher activity to cause net depolymerization, and to inhibit polymerization, than UNC-60B. UNC-60B, on the other hand, shows much stronger severing activity than UNC-60A. To understand the structural basis of their functional differences, we have determined the solution structures of UNC-60A and UNC-60B proteins and characterized their backbone dynamics. Both UNC-60A and UNC-60B show a conserved ADF/cofilin fold. The G-actin (globular actin)-binding regions of the two proteins are structurally and dynamically conserved. Accordingly, UNC-60A and UNC-60B individually bind to rabbit muscle ADP–G-actin with high affinities, with Kd values of 32.25 nM and 8.62 nM respectively. The primary differences between these strong and weak severing proteins were observed in the orientation and dynamics of the F-actin (filamentous actin)-binding loop (F-loop). In the strong severing activity isoform UNC-60B, the orientation of the F-loop was towards the recently identified F-loop-binding region on F-actin, and the F-loop was relatively more flexible with 14 residues showing motions on a nanosecond–picosecond timescale. In contrast, in the weak severing protein isoform UNC-60A, the orientation of the F-loop was away from the F-loop-binding region and inclined towards its own C-terminal and strand β6. It was also relatively less flexible with only five residues showing motions on a nanosecond–picosecond timescale. These differences in structure and dynamics seem to directly correlate with the differential F-actin site-binding and severing properties of UNC-60A and UNC-60B, and other related ADF/cofilin proteins.
NMR structure of the water soluble Aβ17–34 peptide
Authors: Fonar Genadiy , Samson Abraham O. 
Published: October 2014

Alzheimer's disease is the most common neurodegenerative disorder in the world. Its most significant symptoms are memory loss and decrease in cognition. Alzheimer's disease is characterized by aggregation of two proteins in the brain namely Aβ (amyloid β) and tau. Recent evidence suggests that the interaction of soluble Aβ with nAChR (nicotinic acetylcholine receptors) contributes to disease progression. In this study, we determine the NMR structure of an Aβ17–34 peptide solubilized by the addition of two glutamic acids at each terminus. Our results indicate that the Aβ peptide adopts an α-helical structure for residues 19–26 and 28–33. The α-helical structure is broken around residues S26, N27 and K28, which form a kink in the helical conformation. This α-helix was not described earlier in an aqueous solution without organic solvents, and at physiological conditions (pH 7). These data are in agreement with Aβ adopting an α-helical conformation in the membrane before polymerizing into amyloid β-sheets and provide insight into the intermediate state of Aβ in Alzheimer's disease.
Non‐enzymatic electrochemical sensors for the detection of H2O2 based on Mn3O4 octahedron submicrostructures
Authors: Wang Liang , Wu Kong‐Lin , Jiang Bin‐Bin , Zhang Zai‐Xian , Li Xiang‐Zi , Zhang Bei , Lv Ju , Suan Jian , Dong Chao 
Published: October 2014

In this reported work, Mn3O4 octahedron submicrostructures (Mn3O4OSMs) were obtained through a facile solvothermal method in mixed solvent. The authors have modified a glassy carbon electrode (GCE) with Mn3O4OSMs and Nafion to obtain a sensing platform (Mn3O4OSMs/Nafion/GCE) for the non‐enzymatic detection of H2O2. The resulting Mn3O4OSMs/Nafion/GCE exhibited good electrochemical catalytic activity towards the reduction of H2O2 in a phosphate buffered solution (0.1 M, pH = 7.0). The linear detection range was estimated to be in the range from 5 µM to 17 mM (R = 0.9998), and the detection limit was estimated to be 1.5 µM at S/N = 3. Real sample analyses show that the sensor developed in this work could be efficiently used for the determination of H2O2.
Selective patterning of indium tin oxide films using 1064 nm laser for microparts processing
Authors: Chung Chen‐Kuei , Tu Kun‐Tse 
Published: October 2014

Conventional metal microparts were fabricated by a series of complex photolithography, sputtering, sacrificial layer and release processes. This reported work demonstrates the integrated process of metal microparts using 1064 nm Nd:YVO4 laser direct‐write patterning of indium tin oxide (ITO) thin films on glass, followed by the electrochemical deposition of copper (Cu) on the pattern. The ITO thin film could be removed without any damage to the glass structure through the diffractive multiple Nd:YVO4 beam. A high overlapping area of the laser spot was used to pattern the electrode layer on the film surface for obtaining a 50 µm ablated edge profile with a linear boundary after laser patterning. A high quality of surface could be achieved at a proper parameter control without numerous processing steps. Compared with conventional photolithography and etching technologies, direct‐write micropatterns of ITO using the Nd:YVO4 laser is a maskless, dry and low‐cost process. Accordingly, the micrometal parts can be obtained using the electrochemical deposition and release process of laser‐patterned ITO films because of the adhesion property of Cu on ITO.
Impact of heterogeneity and socioeconomic factors on individual behavior in decentralized sharing ecosystems
Authors: Gavaldà-Miralles Arnau , Choffnes David R. , Otto John S. , Sánchez Mario A. , Bustamante Fabián E. , Amaral Luís A. N. , Duch Jordi , Guimerà Roger 
Published: October 2014

Significance
The emergence of the Internet as the primary medium for information exchange has led to the development of many decentralized sharing systems. The most popular among them, BitTorrent, is used by tens of millions of people monthly and is responsible for more than one-third of the total Internet traffic. Despite its growing social, economic, and technological importance, there is little understanding of how users behave in this ecosystem. Because of the decentralized structure of peer-to-peer services, it is very difficult to gather data on users behaviors, and it is in this sense that peer-to-peer file-sharing has been called the “dark matter” of the Internet. Here, we investigate users activity patterns and uncover socioeconomic factors that could explain their behavior.
Reputation and impact in academic careers
Authors: Petersen Alexander Michael , Fortunato Santo , Pan Raj K. , Kaski Kimmo , Penner Orion , Rungi Armando , Riccaboni Massimo , Stanley H. Eugene , Pammolli Fabio 
Published: October 2014

Significance
Over a scientist’s career, a reputation is developed, a standing within a research community, based largely upon the quantity and quality of his/her publications. Here, we develop a framework for quantifying the influence author reputation has on a publication’s future impact. We find author reputation plays a key role in driving a paper’s citation count early in its citation life cycle, before a tipping point, after which reputation has much less influence relative to the paper’s citation count. In science, perceived quality, and decisions made based on those perceptions, is increasingly linked to citation counts. Shedding light on the complex mechanisms driving these quantitative measures facilitates not only better evaluation of scientific outputs but also a more transparent evaluation of the scientists producing them.
Estrogen-related receptor α decreases RHOA stability to induce orientated cell migration
Authors: Sailland Juliette , Tribollet Violaine , Forcet Christelle , Billon Cyrielle , Barenton Bruno , Carnesecchi Julie , Bachmann Alice , Gauthier Karine Cécile , Yu Shan , Giguère Vincent , Chan Franky L. , Vanacker Jean-Marc 
Published: October 2014

SignificanceSeveral developmental and physiological processes require that cells display a controlled ability to migrate in an orientated manner. This capacity is also reacquired by certain cancer cells during their progression toward aggressiveness that allows them to establish distant metastases. The Rho GTPases are instrumental in the control of orientated migration. Here, we demonstrate that the estrogen-related receptor α (ERRα), whose high expression correlates with tumor aggressiveness and poor prognosis, decreases the stability and activity of the RHOA protein and induces orientated cell migration. Together with other published data, our results show that inactivation of ERRα may reduce tumor aggressiveness.
Netrin-4 regulates thalamocortical axon branching in an activity-dependent fashion
Authors: Hayano Yasufumi , Sasaki Kensuke , Ohmura Nami , Takemoto Makoto , Maeda Yurie , Yamashita Toshihide , Hata Yoshio , Kitada Kazuhiro , Yamamoto Nobuhiko 
Published: October 2014

Significance
The environmental control of neuronal wiring is one of the most intriguing issues in neuroscience. However, the molecular mechanisms are largely unknown. Here, we demonstrate that the expression of the netrin family member netrin-4 (NTN4) is activity-dependent in the developing cortex and promotes terminal branching of thalamocortical axons. Evidence further shows that unc-5 homolog B (Unc5B), a putative receptor of NTN4, is expressed in the developing thalamus and mediates NTN4 signaling. These results suggest that NTN4 is the key molecule that underlies activity-dependent axon branch formation in neocortical circuits.
Host cell entry of Middle East respiratory syndrome coronavirus after two-step, furin-mediated activation of the spike protein
Authors: Millet Jean Kaoru , Whittaker Gary R. 
Published: October 2014

Significance
The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV), a deadly human coronavirus, has triggered considerable interest in the biomedical community. Similar to other enveloped viruses, coronaviruses access host cells by membrane fusion, a process mediated by specific fusion or “spike” proteins on the virion, often activated by cellular proteases. We have identified unique features of the MERS-CoV spike (S) protein cleavage activation. Our findings suggest that S can be activated by furin, a broadly expressed protease, by a two-step cleavage mechanism, occurring at distinct sites, with cleavage events temporally separated. Such furin-mediated activation is unusual in that it occurs in part during virus entry. Our findings may explain the polytropic nature, pathogenicity, and life cycle of this zoonotic coronavirus.
Structural basis of the regulatory mechanism of the plant CIPK family of protein kinases controlling ion homeostasis and abiotic stress
Authors: Chaves-Sanjuan Antonio , Sanchez-Barrena Maria Jose , Gonzalez-Rubio Juana Maria , Moreno Maria , Ragel Paula , Jimenez Marta , Pardo Jose M. , Martinez-Ripoll Martin , Quintero Francisco J. , Albert Armando 
Published: October 2014

Significance
The transport of ions through the plant cell membrane establishes the key physicochemical parameters for cell function. Stress situations such as those created by soil salinity or low potassium conditions alter the ion transport across the membrane producing dramatic changes in the cell turgor, the membrane potential, and the intracellular pH and concentrations of toxic cations such as sodium and lithium. As a consequence, fundamental metabolic routes are inhibited. The CIPK family of 26 protein kinases regulates the function of several ion transporters at the cell membrane to restore ion homeostasis under stress situations. Our analyses provide an explanation on how the CIPKs are differentially activated to coordinate the adequate cell response to a particular stress.
The negligible chondritic contribution in the lunar soils water
Authors: Stephant Alice , Robert François 
Published: October 2014

Significance
The hydrogen isotopic ratio of water is commonly used to identify water sources. However, because the Moon is an airless body, the external fluxes of particles and solids that reach its surface should represent an important contribution to its hydrogen budget and thus alter its pristine D/H ratio. To estimate the relative proportions of the solar wind and of the cosmogenic deuterium in the hydrogen budget, the lithium and the hydrogen isotope ratios were measured simultaneously with the Cameca NanoSIMS 50. Analyses demonstrate that all D comes from spallation reactions. On the surface of the soil grains, their D/H ratios indicate that this source of “water” can be ascribed to solar wind implantation and that the chondritic contribution is negligible.
Fluid-induced organic synthesis in the solar nebula recorded in extraterrestrial dust from meteorites
Authors: Vollmer Christian , Kepaptsoglou Demie , Leitner Jan , Busemann Henner , Spring Nicole H. , Ramasse Quentin M. , Hoppe Peter , Nittler Larry R. 
Published: October 2014

Significance
Organic matter from the parent molecular cloud of our solar system can be located in primitive extraterrestrial samples like meteorites and cometary grains. This pristine matter contains among the most primitive organic molecules that were delivered to the early Earth 4.5 billion years ago. We have analyzed these organics by a high-resolution electron microscope that is exceptionally suited to study these beam-sensitive materials. Different carbon and nitrogen functional groups were identified on a submicron scale and can be attributed to early cometary and meteoritic organic reservoirs. Our results demonstrate for the first time to our knowledge that certain highly aromatic and nitrogen-containing ubiquitous organics were transformed from an oxygen-rich organic reservoir by parent body fluid synthesis in the early solar system.
Structure of the ArgRS–GlnRS–AIMP1 complex and its implications for mammalian translation
Authors: Fu Yaoyao , Kim Youngran , Jin Kyeong Sik , Kim Hyun Sook , Kim Jong Hyun , Wang DongMing , Park Minyoung , Jo Chang Hwa , Kwon Nam Hoon , Kim Doyeun , Kim Myung Hee , Jeon Young Ho , Hwang Kwang Yeon , Kim Sunghoon , Cho Yunje 
Published: October 2014

Significance
In higher eukaryotes, aminoacyl-tRNA synthetases (ARSs) are assembled to form a multisynthetase complex (MSC), which plays critical roles in translation and nontranslation functions essential for cell growth and survival of organisms. The MSC complex is comprised of nine different ARSs and three accessary proteins. The crystal structure of the arginyl-tRNA synthetase (ArgRS)–glutaminyl-tRNA synthase–aminoacyl tRNA synthetase complex-interacting multifunctional protein 1 (AIMP1) subcomplex reveals that the N-terminal domains of ArgRS and AIMP1 form an extended coiled-coil structure, which provides a central depot for the assembly of a ternary complex. The stability of the N-terminal helix of ArgRS is critical for its ARS activity and noncanonical function of the subcomplex, explaining the significance of the MSC structure in translation and cellular functions.
Cross-modal effects of value on perceptual acuity and stimulus encoding
Authors: Pooresmaeili Arezoo , FitzGerald Thomas H. B. , Bach Dominik R. , Toelch Ulf , Ostendorf Florian , Dolan Raymond J. 
Published: October 2014

Significance
Reward-predicting signals could be acquired through any of our different sensory modalities, but should be used by other senses to achieve fast and accurate behavior. How reward information is communicated across different sensory modalities is unknown. We demonstrate that sounds associated with high rewards increase the sensitivity of vision, even when sounds and their reward associations are task-irrelevant. Multivariate analysis of the simultaneously acquired functional MRI data revealed that high-reward sounds increased the accuracy of stimulus representation in the visual cortex. Multisensory regions of the temporal cortex were modulated by sound values, and the strength of this modulation was correlated with the change in visual acuity. Our results demonstrate a value-driven cross-modal interaction that affects early stages of sensory processing and involves multisensory areas.
Activation of the pseudokinase MLKL unleashes the four-helix bundle domain to induce membrane localization and necroptotic cell death
Authors: Hildebrand Joanne M. , Tanzer Maria C. , Lucet Isabelle S. , Young Samuel N. , Spall Sukhdeep K. , Sharma Pooja , Pierotti Catia , Garnier Jean-Marc , Dobson Renwick C. J. , Webb Andrew I. , Tripaydonis Anne , Babon Jeffrey J. , Mulcair Mark D. , Scanlon Martin J. , Alexander Warren S. , Wilks Andrew F. , Czabotar Peter E. , Lessene Guillaume , Murphy James M. , Silke John 
Published: October 2014

Significance
The four-helix bundle (4HB) domain of Mixed Lineage Kinase Domain-Like (MLKL) bears two clusters of residues that are required for cell death by necroptosis. Mutations within a cluster centered on the α4 helix of the 4HB domain of MLKL prevented its membrane translocation, oligomerization, and ability to induce necroptosis. This cluster is composed principally of acidic residues and therefore challenges the idea that the 4HB domain engages negatively charged phospholipid membranes via a conventional positively charged interaction surface. The importance of membrane translocation to MLKL-mediated death is supported by our identification of a small molecule that binds the MLKL pseudokinase domain and retards membrane translocation to inhibit necroptotic signaling.
Human TLR10 is an anti-inflammatory pattern-recognition receptor
Authors: Oosting Marije , Cheng Shih-Chin , Bolscher Judith M. , Vestering-Stenger Rachel , Plantinga Theo S. , Verschueren Ineke C. , Arts Peer , Garritsen Anja , van Eenennaam Hans , Sturm Patrick , Kullberg Bart-Jan , Hoischen Alexander , Adema Gosse J. , van der Meer Jos W. M. , Netea Mihai G. , Joosten Leo A. B. 
Published: October 2014

SignificanceWe demonstrate the biological role of TLR10, the only member of the Toll-like receptor (TLR)-family so far without a known function. We show that TLR10 acts as an inhibitory receptor, with suppressive effects. Blocking TLR10 by specific antibodies significantly upregulated TLR2-mediated cytokine production. Additionally, we show that individuals carrying loss-of-function SNPs in TLR10 display upregulation of TLR2-mediated cytokine production. After challenging human TLR10 transgenic mice with TLR2 ligand pam3CSK4 (Pam3Cys), less inflammation could be observed when compared with wild-type mice. Taking these data together, we show that TLR10 is the only pattern-recognition receptor within the TLR family that is able to dampen TLR2 responses, thereby suppressing immune responses through production of IL-1Ra.
Quantitation of interactions between two DNA loops demonstrates loop domain insulation in
E. coli
cells
Authors: Priest David G. , Kumar Sandip , Yan Yan , Dunlap David D. , Dodd Ian B. , Shearwin Keith E. 
Published: October 2014

Significance
Genes are frequently regulated by interactions between proteins that bind to the DNA near the gene and proteins that bind to DNA sites located far away, with the intervening DNA looped out. In eukaryotic genomes, genes and their distant sites are intermingled in complex ways and it is not understood how the correct connections are formed. Using two pairs of DNA-looping sites in bacterial cells, we tested the idea that one DNA loop can either assist or interfere with the formation of another DNA loop. By measuring the strength of these interactions between loops, we showed that this mechanism is capable of directing a distant site to the correct gene and preventing it contacting the wrong gene.
Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors
Authors: Simon Anna J. , Vallée-Bélisle Alexis , Ricci Francesco , Plaxco Kevin W. 
Published: October 2014

Significance
Control over the sensitivity with which biomolecular receptors respond to small changes in the concentration of their target ligand is crucial to many cellular processes and likely could be of value in many biotechnologies. In nature, this control is often achieved using “Hill-type” allosteric cooperativity, an elegant mechanism that has, unfortunately, hitherto proven difficult to achieve via generalizable design strategies. In response, we demonstrate here a quantitative and apparently versatile means of rationally introducing this useful mechanism into a range of normally noncooperative receptors. We achieve in the best of our examples cooperativity, and thus sensitivity, experimentally indistinguishable from the theoretically expected maximum.
Computational design of a self-assembling symmetrical β-propeller protein
Authors: Voet Arnout R. D. , Noguchi Hiroki , Addy Christine , Simoncini David , Terada Daiki , Unzai Satoru , Park Sam-Yong , Zhang Kam Y. J. , Tame Jeremy R. H. 
Published: October 2014

Significance
In this study, we have designed and experimentally validated, to our knowledge, the first perfectly symmetrical β-propeller protein. Our results provide insight not only into protein evolution through duplication events, but also into methods for creating designer proteins that self-assemble according to simple arithmetical rules. Such proteins may have very wide uses in bionanotechnology. Furthermore our design approach is both rapid and applicable to many different protein templates. Our novel propeller protein consists of six identical domains known as “blades.” Using a variety of biophysical techniques, we show it to be highly stable and report several high-resolution crystal structures of different forms of the protein. Domain swapping allows us to generate related oligomeric forms with fixed numbers of blades per complex.
Structural studies on the authentic mumps virus nucleocapsid showing uncoiling by the phosphoprotein
Authors: Cox Robert , Pickar Adrian , Qiu Shihong , Tsao Jun , Rodenburg Cynthia , Dokland Terje , Elson Andrew , He Biao , Luo Ming 
Published: October 2014

Significance
In this paper, we reveal several insights into how mumps virus (MuV) replicates its RNA genome. The MuV genomic RNA is packaged by the nucleocapsid protein (N), forming a helical structure called the nucleocapsid. The nucleocapsid is the template for RNA synthesis. MuV genomes cannot be copied unless the viral polymerase (vRdRp) can read the sequestered RNA. The MuV phosphoprotein (P) appears to play a central role in this process. In this paper, we provide the first evidence, to our knowledge, of P inducing the nucleocapsid to uncoil. MuV P uses two separate domains to promote viral RNA synthesis. One domain attaches to the nucleocapsid while the other domain relaxes the helical structure to allow vRdRp to easily read the viral genome.
PGC-1β promotes enterocyte lifespan and tumorigenesis in the intestine
Authors: Bellafante Elena , Morgano Annalisa , Salvatore Lorena , Murzilli Stefania , Di Tullio Giuseppe , D’Orazio Andria , Latorre Dominga , Villani Gaetano , Moschetta Antonio 
Published: October 2014

Significance
The mucosa of the small intestine is renewed completely every 3–5 d during the entire lifetime through the continuous steps of proliferation, migration, and differentiation of the cells of the mucosa from the crypt site on the bottom to the villus site on the top of the mucosa. The factors that regulate enterocyte lifespan and aging are of special interest as related to colon cancer susceptibility. Here, using genetically modified gain- and loss-of-function models, we present the importance of the mitochondrial respiration chain and reactive oxygen species homeostasis in the gut and identify the protein peroxisome proliferator-activated receptor-γ coactivator-1β as a gene-expression modulator of enterocyte lifespan in both normal and tumoral conditions.