bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially integrative metrics reveal hidden vulnerability of microtidal salt marshes
Authors: Ganju Neil K. , Defne Zafer , Kirwan Matthew L. , Fagherazzi Sergio , D’Alpaos Andrea , Carniello Luca 
Published: January 2017

AbstractSalt marshes are valued for their ecosystem services, and their vulnerability is typically assessed through biotic and abiotic measurements at individual points on the landscape. However, lateral erosion can lead to rapid marsh loss as marshes build vertically. Marsh sediment budgets represent a spatially integrated measure of competing constructive and destructive forces: a sediment surplus may result in vertical growth and/or lateral expansion, while a sediment deficit may result in drowning and/or lateral contraction. Here we show that sediment budgets of eight microtidal marsh complexes consistently scale with areal unvegetated/vegetated marsh ratios (UVVR) suggesting these metrics are broadly applicable indicators of microtidal marsh vulnerability. All sites are exhibiting a sediment deficit, with half the sites having projected lifespans of less than 350 years at current rates of sea-level rise and sediment availability. These results demonstrate that open-water conversion and sediment deficits are holistic and sensitive indicators of salt marsh vulnerability.
Prehistorical and historical declines in Caribbean coral reef accretion rates driven by loss of parrotfish
Authors: Cramer Katie L. , O’Dea Aaron , Clark Tara R. , Zhao Jian-xin , Norris Richard D. 
Published: January 2017

AbstractCaribbean coral reefs have transformed into algal-dominated habitats over recent decades, but the mechanisms of change are unresolved due to a lack of quantitative ecological data before large-scale human impacts. To understand the role of reduced herbivory in recent coral declines, we produce a high-resolution 3,000 year record of reef accretion rate and herbivore (parrotfish and urchin) abundance from the analysis of sediments and fish, coral and urchin subfossils within cores from Caribbean Panama. At each site, declines in accretion rates and parrotfish abundance were initiated in the prehistorical or historical period. Statistical tests of direct cause and effect relationships using convergent cross mapping reveal that accretion rates are driven by parrotfish abundance (but not vice versa) but are not affected by total urchin abundance. These results confirm the critical role of parrotfish in maintaining coral-dominated reef habitat and the urgent need for restoration of parrotfish populations to enable reef persistence.
Synchronous deglacial thermocline and deep-water ventilation in the eastern equatorial Pacific
Authors: Umling Natalie E. , Thunell Robert C. 
Published: January 2017

AbstractThe deep ocean is most likely the primary source of the radiocarbon-depleted CO2 released to the atmosphere during the last deglaciation. While there are well-documented millennial scale Δ14C changes during the most recent deglaciation, most marine records lack the resolution needed to identify more rapid ventilation events. Furthermore, potential age model problems with marine Δ14C records may obscure our understanding of the phase relationship between inter-ocean ventilation changes. Here we reconstruct changes in deep water and thermocline radiocarbon content over the last deglaciation in the eastern equatorial Pacific (EEP) using benthic and planktonic foraminiferal 14C. Our records demonstrate that ventilation of EEP thermocline and deep waters occurred synchronously during the last deglaciation. In addition, both gradual and rapid deglacial radiocarbon changes in these Pacific records are coeval with changes in the Atlantic records. This in-phase behaviour suggests that the Southern Ocean overturning was the dominant driver of changes in the Atlantic and Pacific ventilation during deglaciation.
A human immunodeficiency syndrome caused by mutations in CARMIL2
Authors: Schober T. , Magg T. , Laschinger M. , Rohlfs M. , Linhares N. D. , Puchalka J. , Weisser T. , Fehlner K. , Mautner J. , Walz C. , Hussein K. , Jaeger G. , Kammer B. , Schmid I. , Bahia M. , Pena S. D. , Behrends U. , Belohradsky B. H. , Klein C. , Hauck F. 
Published: January 2017

AbstractHuman T-cell function is dependent on T-cell antigen receptor (TCR) and co-signalling as evidenced by immunodeficiencies affecting TCR-dependent signalling pathways. Here, we show four human patients with EBV+ disseminated smooth muscle tumours that carry two homozygous loss-of-function mutations in the CARMIL2 (RLTPR) gene encoding the capping protein regulator and myosin 1 linker 2. These patients lack regulatory T cells without evidence of organ-specific autoimmunity, and have defective CD28 co-signalling associated with impaired T-cell activation, differentiation and function, as well as perturbed cytoskeletal organization associated with T-cell polarity and migration disorders. Human CARMIL2-deficiency is therefore an autosomal recessive primary immunodeficiency disorder associated with defective CD28-mediated TCR co-signalling and impaired cytoskeletal dynamics.
MetaSort untangles metagenome assembly by reducing microbial community complexity
Authors: Ji Peifeng , Zhang Yanming , Wang Jinfeng , Zhao Fangqing 
Published: January 2017

AbstractMost current approaches to analyse metagenomic data rely on reference genomes. Novel microbial communities extend far beyond the coverage of reference databases and de novo metagenome assembly from complex microbial communities remains a great challenge. Here we present a novel experimental and bioinformatic framework, metaSort, for effective construction of bacterial genomes from metagenomic samples. MetaSort provides a sorted mini-metagenome approach based on flow cytometry and single-cell sequencing methodologies, and employs new computational algorithms to efficiently recover high-quality genomes from the sorted mini-metagenome by the complementary of the original metagenome. Through extensive evaluations, we demonstrated that metaSort has an excellent and unbiased performance on genome recovery and assembly. Furthermore, we applied metaSort to an unexplored microflora colonized on the surface of marine kelp and successfully recovered 75 high-quality genomes at one time. This approach will greatly improve access to microbial genomes from complex or novel communities.
CaTe: a new topological node-line and Dirac semimetal
Authors: Du Yongping , Tang Feng , Wang Di , Sheng Li , Kan Er-jun , Duan Chun-Gang , Savrasov Sergey Y. , Wan Xiangang 
Published: January 2017

AbstractCombining first-principles calculations and effective model analysis, we predict that CaTe is a topological node-line semimetal in the absence of the spin-orbit coupling. Using a slab model, we obtain the nearly flat drumhead surface state near the Fermi level. When the spin-orbit coupling is included, three node lines will evolve into a pair of Dirac points along the M−R line. These Dirac points are robust and protected by the C4 rotation symmetry. Once this crystal symmetry is broken, the Dirac points will be eliminated, and the system becomes a strong topological insulator.
Structure-based modelling of hemocyanin allergenicity in squid and its response to high hydrostatic pressure
Authors: Zhang Yifeng , Deng Yun , Zhao Yanyun 
Published: January 2017

AbstractThe secondary, tertiary, and quaternary structures of squid hemocyanin (Hc) were characterised, and the relationship between Hc structure and allergenicity responses to high hydrostatic pressure (HHP) was modelled. The Hc allergenicity varied with its protein structure. Electrophoresis analysis revealed that HHP treatment significantly decreased the band intensity of Hc when increasing pressure from 200 and 400 MPa to 600 MPa. The protein structure analysis of squid Hc showed that while HHP treatment decreased the α-helix content, free sulfhydryl content, and Rg, it increased the random coil content, surface hydrophobicity index (Ho), Guinier aggregation number (〈Nagg〉G) and average aggregation number (〈Nagg〉Q). The α-helix and random coil contents of the 600 MPa treated samples were 23.67% and 37.54%, respectively, compared to 32.37% and 32.02% in the control, respectively. HHP treatment decreased the IgE and IgG-binding capacities, indicating a significant decrease in the allergenicity (P< 0.05) of squid Hc. This study provided meaningful information of applying HHP to reduce allergenicity, and explained the responses of Hc protein structure to HHP for lowering the allergenicity of squid.
Loss of Merlin induces metabolomic adaptation that engages dependence on Hedgehog signaling
Authors: Das Shamik , Jackson William P. , Prasain Jeevan K. , Hanna Ann , Bailey Sarah K. , Tucker J. Allan , Bae Sejong , Wilson Landon S. , Samant Rajeev S. , Barnes Stephen , Shevde Lalita A. 
Published: January 2017

AbstractThe tumor suppressor protein Merlin is proteasomally degraded in breast cancer. We undertook an untargeted metabolomics approach to discern the global metabolomics profile impacted by Merlin in breast cancer cells. We discerned specific changes in glutathione metabolites that uncovered novel facets of Merlin in impacting the cancer cell metabolome. Concordantly, Merlin loss increased oxidative stress causing aberrant activation of Hedgehog signaling. Abrogation of GLI-mediated transcription activity compromised the aggressive phenotype of Merlin-deficient cells indicating a clear dependence of cells on Hedgehog signaling. In breast tumor tissues, GLI1 expression enhanced tissue identification and discriminatory power of Merlin, cumulatively presenting a powerful substantiation of the relationship between these two proteins. We have uncovered, for the first time, details of the tumor cell metabolomic portrait modulated by Merlin, leading to activation of Hedgehog signaling. Importantly, inhibition of Hedgehog signaling offers an avenue to target the vulnerability of tumor cells with loss of Merlin.
Chlorpyrifos inhibits neural induction via Mfn1-mediated mitochondrial dysfunction in human induced pluripotent stem cells
Authors: Yamada Shigeru , Kubo Yusuke , Yamazaki Daiju , Sekino Yuko , Kanda Yasunari 
Published: January 2017

AbstractOrganophosphates, such as chlorpyrifos (CPF), are widely used as insecticides in agriculture. CPF is known to induce cytotoxicity, including neurodevelopmental toxicity. However, the molecular mechanisms of CPF toxicity at early fetal stage have not been fully elucidated. In this study, we examined the mechanisms of CPF-induced cytotoxicity using human induced pluripotent stem cells (iPSCs). We found that exposure to CPF at micromolar levels decreased intracellular ATP levels. As CPF suppressed energy production that is a critical function of the mitochondria, we focused on the effects of CPF on mitochondrial dynamics. CPF induced mitochondrial fragmentation via reduction of mitochondrial fusion protein mitofusin 1 (Mfn1) in iPSCs. In addition, CPF reduced the expression of several neural differentiation marker genes in iPSCs. Moreover, knockdown of Mfn1 gene in iPSCs downregulated the expression of PAX6, a key transcription factor that regulates neurogenesis, suggesting that Mfn1 mediates neural induction in iPSCs. Taken together, these results suggest that CPF induces neurotoxicity via Mfn1-mediated mitochondrial fragmentation in iPSCs. Thus, mitochondrial dysfunction in iPSCs could be used as a possible marker for cytotoxic effects by chemicals.
The potential role of spectrin network in the mechanotransduction of MLO-Y4 osteocytes
Authors: Wu Xin-Tong , Sun Lian-Wen , Yang Xiao , Ding Dong , Han Dong , Fan Yu-Bo 
Published: January 2017

AbstractThe spectrin is first identified as the main component of erythrocyte membrane skeleton. It is getting growing attention since being found in multiple nonerythroid cells, providing complex mechanical properties and signal interface under the cell membrane. Recent genomics studies have revealed that the spectrin is highly relevant to bone disorders. However, in osteocytes, the important mechanosensors in bone, the role of spectrin is poorly understood. In this research, the role of spectrin in the mechanotransduction of MLO-Y4 osteocytes was studied. Immunofluorescence staining showed that, the spectrins were elaborately organized as a porous network throughout the cytoplasm, and linked with F-actin into a dense layer underlying the cell membrane. AFM results indicate that, the spectrin is pivotal for maintaining the overall elasticity of osteocytes, especially for the cell cortex stiffiness. Disruption of the spectrin network caused obvious softening of osteocytes, and resulted in a significant increase of Ca2+ influx, NO secretion, cell-cell connections and also induced a translocation of eNOS from membrane to cytoplasm. These results indicate that the spectrin network is a global structural support for osteocytes involving in the mechanotransduction process, making it a potential therapeutic target for bone disorders.
Design of an expression system to enhance MBP-mediated crystallization
Authors: Jin Tengchuan , Chuenchor Watchalee , Jiang Jiansheng , Cheng Jinbo , Li Yajuan , Fang Kang , Huang Mo , Smith Patrick , Xiao Tsan Sam 
Published: January 2017

AbstractCrystallization chaperones have been used to facilitate the crystallization of challenging proteins. Even though the maltose-binding protein (MBP) is one of the most commonly used crystallization chaperones, the design of optimal expression constructs for crystallization of MBP fusion proteins remains a challenge. To increase the success rate of MBP-facilitated crystallization, a series of expression vectors have been designed with either a short flexible linker or a set of rigid helical linkers. Seven death domain superfamily members were tested for crystallization with this set of vectors, six of which had never been crystallized before. All of the seven targets were crystallized, and their structures were determined using at least one of the vectors. Our successful crystallization of all of the targets demonstrates the validity of our approach and expands the arsenal of the crystallization chaperone toolkit, which may be applicable to crystallization of other difficult protein targets, as well as to other crystallization chaperones.
STAC3 stably interacts through its C1 domain with CaV1.1 in skeletal muscle triads
Authors: Campiglio Marta , Flucher Bernhard E. 
Published: January 2017

AbstractThe adaptor protein STAC3 is essential for skeletal muscle excitation-contraction (EC) coupling and a mutation in the STAC3 gene has been linked to a severe muscle disease, Native American myopathy (NAM). However the function of STAC3, its interaction partner, and the mode of interaction within the EC-coupling complex remained elusive. Here we demonstrate that STAC3 forms a stable interaction with the voltage-sensor of EC-coupling, CaV1.1, and that this interaction depends on a hitherto unidentified protein-protein binding pocket in the C1 domain of STAC3. While the NAM mutation does not affect the stability of the STAC3-CaV1.1 interaction, mutation of two crucial residues in the C1 binding pocket increases the turnover of STAC3 in skeletal muscle triads. Thus, the C1 domain of STAC3 is responsible for its stable incorporation into the CaV1.1 complex, whereas the SH3 domain containing the NAM mutation site may be involved in low-affinity functional interactions in EC-coupling.
SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems
Authors: An Yi , Wang Jiawei , Li Chen , Revote Jerico , Zhang Yang , Naderer Thomas , Hayashida Morihiro , Akutsu Tatsuya , Webb Geoffrey I. , Lithgow Trevor , Song Jiangning 
Published: January 2017

AbstractBacteria translocate effector molecules to host cells through highly evolved secretion systems. By definition, the function of these effector proteins is to manipulate host cell biology and the sequence, structural and functional annotations of these effector proteins will provide a better understanding of how bacterial secretion systems promote bacterial survival and virulence. Here we developed a knowledgebase, termed SecretEPDB (Bacterial Secreted Effector Protein DataBase), for effector proteins of type III secretion system (T3SS), type IV secretion system (T4SS) and type VI secretion system (T6SS). SecretEPDB provides enriched annotations of the aforementioned three classes of effector proteins by manually extracting and integrating structural and functional information from currently available databases and the literature. The database is conservative and strictly curated to ensure that every effector protein entry is supported by experimental evidence that demonstrates it is secreted by a T3SS, T4SS or T6SS. The annotations of effector proteins documented in SecretEPDB are provided in terms of protein characteristics, protein function, protein secondary structure, Pfam domains, metabolic pathway and evolutionary details. It is our hope that this integrated knowledgebase will serve as a useful resource for biological investigation and the generation of new hypotheses for research efforts aimed at bacterial secretion systems.
Reduction of hepatic fibrosis by overexpression of von Hippel–Lindau protein in experimental models of chronic liver disease
Authors: Wang Jizhou , Lu Zhaoyang , Xu Zhilin , Tian Pei , Miao Hui , Pan Shangha , Song Ruipeng , Sun Xueying , Zhao Baolei , Wang Dawei , Ma Yong , Song Xuan , Zhang Shugeng , Liu Lianxin , Jiang Hongchi 
Published: January 2017

AbstractHypoxia-inducible factor (HIF)-1α and HIF-2α play an important role in liver fibrosis. von Hippel–Lindau protein (VHL), a key mediator of HIF-α, regulates fibrosis in an organ- and cell-specific way. In this study, human liver samples were collected from hepatitis C-, alcoholic-, and cholestatic-associated fibrotic and healthy individuals. Two mouse models of liver fibrosis were established: bile duct ligation and carbon tetrachloride injection. We constructed adenovirus vectors to overexpress VHL, normoxia-active HIF-α, and lentiviral vectors to silence HIF-α. The results showed that liver sections from fibrosis patients had a lower level of VHL and higher levels of HIF-1α and HIF-2α compared with healthy sections, a finding which was confirmed in mice. Overexpression of VHL attenuated liver fibrosis, downregulated fibrogenic genes, and inhibited liver inflammation, apoptosis, and angiogenesis. Overexpression of VHL was more successful at inhibiting fibrosis compared with silencing HIF-1α plus HIF-2α. Normoxia-active HIF-1α or HIF-2α prevented the inhibitory effect of VHL on liver fibrosis, indicating that attenuating fibrosis via VHL is HIF-1α- and HIF-2α-dependent to some extent. In addition, overexpression of VHL inhibited mouse hepatic stellate cells activation and proliferation and promoted apoptosis. Taken together, VHL may be considered a new target to inhibit liver fibrosis.
Tunable spin and valley dependent magneto-optical absorption in molybdenum disulfide quantum dots
Authors: Qu Fanyao , Dias A. C. , Fu Jiyong , Villegas-Lelovsky L. , Azevedo David L. 
Published: January 2017

AbstractPhotonic quantum computer, quantum communication, quantum metrology and quantum optical technologies rely on the single-photon source (SPS). However, the SPS with valley-polarization remains elusive and the tunability of magneto-optical transition frequency and emission/absorption intensity is restricted, in spite of being highly in demand for valleytronic applications. Here we report a new class of SPSs based on carriers spatially localized in two-dimensional monolayer transition metal dichalcogenide quantum dots (QDs). We demonstrate that the photons are absorbed (or emitted) in the QDs with distinct energy but definite valley-polarization. The spin-coupled valley-polarization is invariant under either spatial or magnetic quantum quantization. However, the magneto-optical absorption peaks undergo a blue shift as the quantization is enhanced. Moreover, the absorption spectrum pattern changes considerably with a variation of Fermi energy. This together with the controllability of absorption spectrum by spatial and magnetic quantizations, offers the possibility of tuning the magneto-optical properties at will, subject to the robust spin-coupled valley polarization.
Crude venom from nematocysts of Pelagia noctiluca (Cnidaria: Scyphozoa) elicits a sodium conductance in the plasma membrane of mammalian cells
Authors: Morabito Rossana , Costa Roberta , Rizzo Valentina , Remigante Alessia , Nofziger Charity , La Spada Giuseppa , Marino Angela , Paulmichl Markus , Dossena Silvia 
Published: January 2017

AbstractCnidarians may negatively impact human activities and public health but concomitantly their venom represents a rich source of bioactive substances. Pelagia noctiluca is the most venomous and abundant jellyfish of the Mediterranean Sea and possesses a venom with hemolytic and cytolytic activity for which the mechanism is largely unknown. Here we show that exposure of mammalian cells to crude venom from the nematocysts of P. noctiluca profoundly alters the ion conductance of the plasma membrane, therefore affecting homeostatic functions such as the regulation and maintenance of cellular volume. Venom-treated cells exhibited a large, inwardly rectifying current mainly due to permeation of Na+ and Cl−, sensitive to amiloride and completely abrogated following harsh thermal treatment of crude venom extract. Curiously, the plasma membrane conductance of Ca2+ and K+ was not affected. Current-inducing activity was also observed following delivery of venom to the cytosolic side of the plasma membrane, consistent with a pore-forming mechanism. Venom-induced NaCl influx followed by water and consequent cell swelling most likely underlie the hemolytic and cytolytic activity of P. noctiluca venom. The present study underscores unique properties of P. noctiluca venom and provides essential information for a possible use of its active compounds and treatment of envenomation.