bluuebunny/crossref_metadata_2025_split huggingface dataset:
Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations
Authors: Wenk Christine B , Wing Boswell A , Halevy Itay 
Published: October 2017

Abstract
Dissimilatory sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth’s history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation—the electron carriers selected for survival under energy-limited conditions. Employing a quantitative biochemical-isotopic model, we find that the large S isotope fractionations (&gt;55‰) observed in a wide range of natural environments and culture experiments at low respiration rates are only possible when the standard-state Gibbs free energy (ΔG′°) of all steps during DSR is more positive than −10 kJ mol−1. This implies that at low respiration rates, only electron carriers with modestly negative reduction potentials are involved, such as menaquinone, rubredoxin, rubrerythrin or some flavodoxins. Furthermore, the constraints from S isotope fractionation imply that ferredoxins with a strongly negative reduction potential cannot be the direct electron donor to S intermediates at low respiration rates. Although most sulfate reducers have the genetic potential to express a variety of electron carriers, our results suggest that a key physiological adaptation of sulfate reducers to low-energy environments is to use electron carriers with modestly negative reduction potentials.
The impact of elevated CO2 on Prochlorococcus and microbial interactions with ‘helper’ bacterium Alteromonas
Authors: Hennon Gwenn M M , Morris J Jeffrey , Haley Sheean T , Zinser Erik R , Durrant Alexander R , Entwistle Elizabeth , Dokland Terje , Dyhrman Sonya T 
Published: October 2017

Abstract
Prochlorococcus is a globally important marine cyanobacterium that lacks the gene catalase and relies on ‘helper’ bacteria such as Alteromonas to remove reactive oxygen species. Increasing atmospheric CO2 decreases the need for carbon concentrating mechanisms and photorespiration in phytoplankton, potentially altering their metabolism and microbial interactions even when carbon is not limiting growth. Here, Prochlorococcus (VOL4, MIT9312) was co-cultured with Alteromonas (strain EZ55) under ambient (400 p.p.m.) and elevated CO2 (800 p.p.m.). Under elevated CO2, Prochlorococcus had a significantly longer lag phase and greater apparent die-offs after transfers suggesting an increase in oxidative stress. Whole-transcriptome analysis of Prochlorococcus revealed decreased expression of the carbon fixation operon, including carboxysome subunits, corresponding with significantly fewer carboxysome structures observed by electron microscopy. Prochlorococcus co-culture responsive gene 1 had significantly increased expression in elevated CO2, potentially indicating a shift in the microbial interaction. Transcriptome analysis of Alteromonas in co-culture with Prochlorococcus revealed decreased expression of the catalase gene, known to be critical in relieving oxidative stress in Prochlorococcus by removing hydrogen peroxide. The decrease in catalase gene expression was corroborated by a significant ~6-fold decrease in removal rates of hydrogen peroxide from co-cultures. These data suggest Prochlorococcus may be more vulnerable to oxidative stress under elevated CO2 in part from a decrease in ecosystem services provided by heterotrophs like Alteromonas. This work highlights the importance of considering microbial interactions in the context of a changing ocean.
In situ metabolomic- and transcriptomic-profiling of the host-associated cyanobacteria Prochloron and Acaryochloris marina
Authors: Behrendt Lars , Raina Jean-Baptiste , Lutz Adrian , Kot Witold , Albertsen Mads , Halkjær-Nielsen Per , Sørensen Søren J , Larkum Anthony W D , Kühl Michael 
Published: October 2017

Abstract
The tropical ascidian Lissoclinum patella hosts two enigmatic cyanobacteria: (1) the photoendosymbiont Prochloron spp., a producer of valuable bioactive compounds and (2) the chlorophyll-d containing Acaryochloris spp., residing in the near-infrared enriched underside of the animal. Despite numerous efforts, Prochloron remains uncultivable, restricting the investigation of its biochemical potential to cultivation-independent techniques. Likewise, in both cyanobacteria, universally important parameters on light-niche adaptation and in situ photosynthetic regulation are unknown. Here we used genome sequencing, transcriptomics and metabolomics to investigate the symbiotic linkage between host and photoendosymbiont and simultaneously probed the transcriptional response of Acaryochloris in situ. During high light, both cyanobacteria downregulate CO2 fixing pathways, likely a result of O2 photorespiration on the functioning of RuBisCO, and employ a variety of stress-quenching mechanisms, even under less stressful far-red light (Acaryochloris). Metabolomics reveals a distinct biochemical modulation between Prochloron and L. patella, including noon/midnight-dependent signatures of amino acids, nitrogenous waste products and primary photosynthates. Surprisingly, Prochloron constitutively expressed genes coding for patellamides, that is, cyclic peptides of great pharmaceutical value, with yet unknown ecological significance. Together these findings shed further light on far-red-driven photosynthesis in natural consortia, the interplay of Prochloron and its ascidian partner in a model chordate photosymbiosis and the uncultivability of Prochloron.
Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors
Authors: Adalsteinsson Viktor A. , Ha Gavin , Freeman Samuel S. , Choudhury Atish D. , Stover Daniel G. , Parsons Heather A. , Gydush Gregory , Reed Sarah C. , Rotem Denisse , Rhoades Justin , Loginov Denis , Livitz Dimitri , Rosebrock Daniel , Leshchiner Ignaty , Kim Jaegil , Stewart Chip , Rosenberg Mara , Francis Joshua M. , Zhang Cheng-Zhong , Cohen Ofir , Oh Coyin , Ding Huiming , Polak Paz , Lloyd Max , Mahmud Sairah , Helvie Karla , Merrill Margaret S. , Santiago Rebecca A. , O’Connor Edward P. , Jeong Seong H. , Leeson Rachel , Barry Rachel M. , Kramkowski Joseph F. , Zhang Zhenwei , Polacek Laura , Lohr Jens G. , Schleicher Molly , Lipscomb Emily , Saltzman Andrea , Oliver Nelly M. , Marini Lori , Waks Adrienne G. , Harshman Lauren C. , Tolaney Sara M. , Van Allen Eliezer M. , Winer Eric P. , Lin Nancy U. , Nakabayashi Mari , Taplin Mary-Ellen , Johannessen Cory M. , Garraway Levi A. , Golub Todd R. , Boehm Jesse S. , Wagle Nikhil , Getz Gad , Love J. Christopher , Meyerson Matthew 
Published: October 2017

AbstractWhole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.
Structural basis for receptor recognition of pollen tube attraction peptides
Authors: Zhang Xiaoxiao , Liu Weijia , Nagae Takuya T. , Takeuchi Hidenori , Zhang Heqiao , Han Zhifu , Higashiyama Tetsuya , Chai Jijie 
Published: October 2017

AbstractTransportation of the immobile sperms directed by pollen tubes to the ovule-enclosed female gametophytes is important for plant sexual reproduction. The defensin-like (DEFL) cysteine-rich peptides (CRPs) LUREs play an essential role in pollen tube attraction to the ovule, though their receptors still remain controversial. Here we provide several lines of biochemical evidence showing that the extracellular domain of the leucine-rich repeat receptor kinase (LRR-RK) PRK6 from Arabidopsis thaliana directly interacts with AtLURE1 peptides. Structural study reveals that a C-terminal loop of the LRR domain (AtPRK6LRR) is responsible for recognition of AtLURE1.2, mediated by a set of residues largely conserved among PRK6 homologs from Arabidopsis lyrata and Capsella rubella, supported by in vitro mutagenesis and semi-in-vivo pollen tube growth assays. Our study provides evidence showing that PRK6 functions as a receptor of the LURE peptides in A. thaliana and reveals a unique ligand recognition mechanism of LRR-RKs.
Depth dependent stress revealed by aftershocks
Authors: Shebalin Peter , Narteau Clément 
Published: October 2017

AbstractCharacterising the state of stress in the brittle upper-crust is essential in mechanics of faulting, industrial production processes, and operational earthquake forecasting. Nevertheless, unresolved questions concern the variation of pore-fluid with depth and the absolute strength on tectonically active faults. Here we show that, along the San Andreas fault system, the time-delay before the onset of the power-law aftershock decay rate (the c-value) varies by three orders of magnitude in the first 20 km below the surface. Despite the influence of the lithostatic stress, there is no continuous change in c-value with depth. Instead, two decay phases are separated by an abrupt increase at an intermediate depth range of 2–5 km. This transitional regime is the only one observed in fluid-injection-induced seismic areas. This provides strong evidence for the role of fluid and a porosity reduction mechanism at depth of few kilometres in active fault zones. Aftershock statistics can then be used to predict changes in differential shear stress with depth until the brittle-ductile transition is reached.
Colour selective control of terahertz radiation using two-dimensional hybrid organic inorganic lead-trihalide perovskites
Authors: Chanana Ashish , Zhai Yaxin , Baniya Sangita , Zhang Chuang , Vardeny Z. Valy , Nahata Ajay 
Published: October 2017

AbstractControlling and modulating terahertz signals is of fundamental importance to allow systems level applications. We demonstrate an innovative approach for controlling the propagation properties of terahertz (THz) radiation, through use of both the excitation optical wavelength (colour) and intensity. We accomplish this using two-dimensional (2D) layered hybrid trihalide perovskites that are deposited onto silicon substrates. The absorption properties of these materials in the visible range can be tuned by changing the number of inorganic atomic layers in between the organic cation layers. Optical absorption in 2D perovskites occurs over a broad spectral range above the bandgap, resulting in free carrier generation, as well as over a narrow spectral range near the bandedge due to exciton formation. We find that only the latter contribution gives rise to photo-induced THz absorption. By patterning multiple 2D perovskites with different optical absorption properties onto a single device, we demonstrate both colour selective modulation and focusing of THz radiation. These findings open new directions for creating active THz devices.
Small infrarenal aortic diameter associated with lower-extremity peripheral artery disease in Chinese hypertensive adults
Authors: Liu Jie , Jia Xin , Jia Senhao , Qin Xianhui , Zhang Tao , Liu Lishun , Li Haibo , Rong Dan , Zhou Ziyi , Song Yuxiang , Zuo Shangwei , Duan Chen , Wu Zhongyin , Wei Ren , Ge Yangyang , Wang Xian , Kong Wei , Xu Xiping , Khalil Raouf A. , Huo Yong , Guo Wei 
Published: October 2017

AbstractSeveral studies suggest that infrarenal aortic diameter is associated with lower-extremity peripheral artery disease (LE-PAD). However, data regarding the associations between infrarenal aortic diameter and LE-PAD are limited, especially in large sample populations and Asian or Chinese populations. Our analysis included 17279 Chinese hypertensive adults comprising 6590 men and 10689 women with a mean age of 64.74 ± 7.41 years. Participants were selected from 22693 candidates from two large population-based cohort-studies. The primary noninvasive test for diagnosis of LE-PAD is the ankle–brachial index (ABI) at rest and typically an ABI ≤ 0.90 is used to define LE-PAD. The prevalence of LE-PAD was found to significantly decrease as the aortic diameter increased according to the tertile of the aortic diameter. LE-PAD was significantly more prevalent in the lowest tertile (OR = 1.58, 95% CI = 1.29–1.94, p < 0.001) and similarly prevalent in the highest tertile (OR = 0.92, 95% CI = 0.73–1.16, p = 0.49) when compared with the median tertile. No significant interactions between the aortic diameter and any of the stratified variables were found (all p > 0.05). In conclusion, Small aortic diameter (as opposed to large aortic diameter) is significantly associated with LE-PAD in Chinese hypertensive adults.
Two novel diterpenoid heterodimers, Bisebracteolasins A and B, from Euphorbia ebracteolata Hayata, and the cancer chemotherapeutic potential of Bisebracteolasin A
Authors: Yuan Wen-Juan , Ding Xiao , Wang Zhe , Yang Bi-Juan , Li Xiao-Nian , Zhang Yu , Chen Duo-Zhi , Li Shun-Lin , Chen Quan , Di Ying-Tong , Aisa Haji Akber , Hao Xiao-Jiang 
Published: October 2017

AbstractRare ent-abietane-rosane diterpenoid heterodimers, Bisebracteolasins A and B (1 and 2, respectively), were isolated from the roots of Euphorbia ebracteolata Hayata. Their structures and absolute configurations were elucidated from spectroscopic data and X-ray diffraction analysis. Compounds 1 and 2 exhibited moderate cytotoxic effects against five cancer cell lines. Compound 1 showed more effective antiproliferative activities against human tumour cells, HL-60 and SMMC-7721, with IC50 values of 2.61 and 4.08 μM, respectively, than 2. Both compounds 1 and 2 inhibit the colorectal cancer stem cell line P6C with IC50 values of 16.48 and 34.76 μM, respectively. Moreover, preliminary biological tests showed compound 1 exhibited inhibitory activity towards tumoursphere formation and migration of the P6C cell line. Overall, we identified two novel diterpenoid heterodimers, and Bisebracteolasin A exhibits therapeutic potential in impeding tumour growth and metastatic ability of cancer stem cells.
Involvement of autophagy in the outcome of mitotic catastrophe
Authors: Sorokina Irina V. , Denisenko Tatiana V. , Imreh Gabriela , Tyurin-Kuzmin Pyotr A. , Kaminskyy Vitaliy O. , Gogvadze Vladimir , Zhivotovsky Boris 
Published: October 2017

AbstractEvading cell death is a major driving force for tumor progression that is one of the main problems in current cancer research. Mitotic catastrophe (MC) represents attractive platform compromising tumor resistance to current therapeutic modalities. MC appeared as onco-suppressive mechanism and is defined as a stage driving the cell to an irreversible destiny, i.e. cell death via apoptosis or necrosis. Our study highlights that MC induction in colorectal carcinoma cell lines ultimately leads to the autophagy followed by apoptosis. We show that autophagy suppression in Atg 13 knockout non-small cell lung carcinoma cells lead to the dramatic decrease of MC rate. Furthermore, mitochondria-linked anti-apoptotic proteins Mcl-1 and Bcl-xL play a crucial role in the duration of MC and a cross-talk between autophagy and apoptosis. Thus, the suppression of apoptosis by overexpression of Mcl-1 or Bcl-xL affected MC and lead to a significant induction of autophagy in HCT116 wt and HCT116 14-3-3σ−/− cells. Our data demonstrate that MC induction is a critical stage, in which a cell decides how to die, while mitochondria are responsible for the maintaining the balance between MC – autophagy – apoptosis.
Molecular-trapping in Emulsion’s Monolayer: A New Strategy for Production and Purification of Bioactive Saponins
Authors: Obasi Titus C. , Moldovan Radu , Toiu Anca , Braicu Cornelia , Bodoki Ede , Berindan-Neagoe Ioana , Oniga Ilioara , Sandulescu Robert , Oprean Radu 
Published: October 2017

AbstractSaponins from defatted root-extract of Securidaca longipedunculata were systematically entrapped in emulsion monolayer-barrier and finally recovered in pure form through demulsification. First, their molecules were dispersed in water to engineer a monomolecular film architecture, via self-assembly. Emulsifying with ethyl-ether resulted in swollen micelles and engendered phase-inversion and phase-separation, by disrupting the thermodynamic equilibrium. As positive outcome, a Winsor II system was obtained, having saponin-rich upper phase (ethyl-ether) and impurities bound lower phase (aqueous). Saponin particles underwent transition in insoluble ethyl-ether, precipitated and recovered as solids. The entire process was bioactivity-guided and validated using pooled fractions of securidaca saponins, purified by TLC (RP-C18, F254S). TEM and SEM revealed interesting morphologies and particle sizes between nanometer and micron. At the end, purity output of 90% and total recovery of 94% were achieved. Here we show that “molecular-trapping in emulsion’s monolayer” is an effective method for recovery, production and purification of saponins of plant origin.
N-Myc-Interacting Protein Negatively Regulates TNF-α-Induced NF-κB Transcriptional Activity by Sequestering NF-κB/p65 in the Cytoplasm
Authors: Hou Jingjing , Jiang Shihao , Zhao Jiabao , Zhu Dong , Zhao Xinmeng , Cai Jian-chun , Zhang Si Qing 
Published: October 2017

AbstractNF-κB is a major regulator of gene transcription involved in immune, inflammation, apoptosis and stress responses. However, the regulation of NF-κB is not completely understood. Here, we report that the N-Myc and STATs Interactor (NMI), an IFN-inducible protein, is an important negative regulator of NF-κB activity. We found that NMI negatively regulates TNF-α-induced IL-6 and IL-1β production in HeLa cells. Overexpression of NMI inhibits NF-κB transcriptional activity, in contrast, depletion of NMI by shRNA increases NF-κB transcriptional activity. Mechanistically, NMI associates with NF-κB/p65 and inhibits NF-κB/p65 nuclear translocation and thereby negatively regulates NF-κB/p65 transcriptional activity. Taken together, our results demonstrate that NMI modulates the NF-κB signaling pathway by sequestering NF-κB/p65 in the cytoplasm, resulting in reduced IL-6 and IL-1β production after TNF-α stimulation. Treatment with IFNα in the presence of NMI leads to increased apoptosis in tumor cells. These findings reveal a novel mechanism by which NMI regulates NF-κB activity.
First Evidence of Coherent Bands of Strong Turbulent Layers Associated with High-Wavenumber Internal-Wave Shear in the Upstream Kuroshio
Authors: Nagai Takeyoshi , Hasegawa Daisuke , Tanaka Takahiro , Nakamura Hirohiko , Tsutsumi Eisuke , Inoue Ryuichiro , Yamashiro Toru 
Published: October 2017

AbstractThe upstream Kuroshio flows through Okinawa Trough and the Tokara island chain, the region near the continental shelf of the East China Sea and shallow seamounts, where the Kuroshio can induce strong mixing over the shallow topography. Also, tidal currents over the rough topography may produce internal tides, and associated turbulence. The previous observations show energetic high vertical wavenumber near-inertial wave shear in the Kuroshio thermocline, which implies strong turbulent mixing. However, direct turbulence measurements in this region are very scarce. Using high lateral resolution (1–2 km) direct turbulence measurements, we show here, for the first time, that strong turbulent layers form spatially coherent banded structures with lateral scales of >O(10 km), associated with bands of near-inertial wave/diurnal internal tide shear of high vertical wavenumber in the upstream Kuroshio. The turbulent kinetic energy dissipation rates within these turbulent layers are >O(10−7 W kg−1), and estimated vertical eddy diffusivity shows >O(10−4 m2 s−1) on average. These results suggest that the high vertical wavenumber near-inertial waves propagating in the upstream Kuroshio could have large impacts on the watermass modifications, momentum mixing, nutrient supply, and associated biogeochemical responses in its downstream.
The RNA binding protein La/SS-B promotes RIG-I-mediated type I and type III IFN responses following Sendai viral infection
Authors: Mahony Rebecca , Broadbent Lindsay , Maier-Moore Jacen S. , Power Ultan F. , Jefferies Caroline A. 
Published: October 2017

AbstractLa/SS-B (or La) is a 48 kDa RNA-binding protein and an autoantigen in autoimmune disorders such as systemic lupus erythematosus (SLE) and Sjögren’s syndrome (SS). La involvement in regulating the type I interferon (IFN) response is controversial - acting through both positive and negative regulatory mechanisms; inhibiting the IFN response and enhancing viral growth, or directly inhibiting viral replication. We therefore sought to clarify how La regulates IFN production in response to viral infection. ShRNA knockdown of La in HEK 293 T cells increased Sendai virus infection efficiency, decreased IFN-β, IFN-λ1, and interferon-stimulated chemokine gene expression. In addition, knockdown attenuated CCL-5 and IFN-λ1 secretion. Thus, La has a positive role in enhancing type I and type III IFN production. Mechanistically, we show that La directly binds RIG-I and have mapped this interaction to the CARD domains of RIG-I and the N terminal domain of La. In addition, we showed that this interaction is induced following RIG-I activation and that overexpression of La enhances RIG-I-ligand binding. Together, our results demonstrate a novel role for La in mediating RIG-I-driven responses downstream of viral RNA detection, ultimately leading to enhanced type I and III IFN production and positive regulation of the anti-viral response.
The lunar core can be a major reservoir for volatile elements S, Se, Te and Sb
Authors: Steenstra Edgar S. , Lin Yanhao , Dankers Dian , Rai Nachiketa , Berndt Jasper , Matveev Sergei , van Westrenen Wim 
Published: October 2017

AbstractThe Moon bears a striking compositional and isotopic resemblance to the bulk silicate Earth (BSE) for many elements, but is considered highly depleted in many volatile elements compared to BSE due to high-temperature volatile loss from Moon-forming materials in the Moon-forming giant impact and/or due to evaporative loss during subsequent magmatism on the Moon. Here, we use high-pressure metal-silicate partitioning experiments to show that the observed low concentrations of volatile elements sulfur (S), selenium (Se), tellurium (Te), and antimony (Sb) in the silicate Moon can instead reflect core-mantle equilibration in a largely to fully molten Moon. When incorporating the core as a reservoir for these elements, their bulk Moon concentrations are similar to those in the present-day bulk silicate Earth. This suggests that Moon formation was not accompanied by major loss of S, Se, Te, Sb from Moon-forming materials, consistent with recent indications from lunar carbon and S isotopic compositions of primitive lunar materials. This is in marked contrast with the losses of other volatile elements (e.g., K, Zn) during the Moon-forming event. This discrepancy may be related to distinctly different cosmochemical behavior of S, Se, Te and Sb within the proto-lunar disk, which is as of yet virtually unconstrained.