bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Microbial Community Patterns During Incipient Soil Formation From Basalt
Authors: Sengupta Aditi , Stegen James C. , Meira Neto Antonio A. , Wang Yadi , Neilson Julia W. , Tatarin Triffon , Hunt Edward , Dontsova Katerina , Chorover Jon , Troch Peter A. , Maier Raina M. 
Published: March 2019

AbstractMicrobial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt‐soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth‐dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.
Breakdown of Earthquake Self‐Similar Scaling and Source Rupture Directivity in the 2016–2017 Central Italy Seismic Sequence
Authors: Wang Hongwei , Ren Yefei , Wen Ruizhi , Xu Peibin 
Published: March 2019

AbstractTo analyze the source characteristics of the 2016–2017 central Italy seismic sequence, source spectra of 78 earthquakes of ML = 3.5–6.1 were separated from the S wave Fourier spectra using the two‐step nonparametric generalized inversion technique. Source parameters (e.g., stress drop) were estimated from the source spectra following the ω‐square model. Stress drops were found mainly in the range 0.113–12.190 MPa. The significant dependence of stress drop on magnitude indicates the breakdown of earthquake self‐similar scaling in this sequence. The low stress drops for small events following the release of high stress by the mainshock might have led to stress accumulation on the unruptured fault, which could explain the subsequent occurrence of multiple major events. We investigated the source rupture directivity for 36 events through the azimuthal variation of apparent source spectra. Significant variation was observed at specific frequency bands (generally, over corner frequencies) in 10 events caused by rupture directivity, which was verified by the stable estimation of rupture plane. The rupture parameters confirmed unilateral ruptures predominantly on the NNW–SSE striking fault with fast rupture velocity (2.52–2.84 km/s) for the 10 events. Rupture parameters for an additional four events with stable estimated rupture plane were also analyzed. These were characterized by slow rupture velocity causing weak directivity effects. According to the rupture parameters for the 14 events, prevailing SSE or SEE (NNW or NNE) rupture directivity was a common feature for events to the north (south) of the mainshock in this earthquake sequence.
Distributed Hydrological Modeling Framework for Quantitative and Spatial Bias Correction for Rainfall, Snowfall, and Mixed‐Phase Precipitation Using Vertical Profile of Temperature
Authors: Naseer Asif , Koike Toshio , Rasmy Mohamad , Ushiyama Tomoki , Shrestha Maheswor 
Published: March 2019

AbstractMountain snowpack and its distribution both have intimate connections to regional hydrology by preserving winter precipitation to sustain streamflows during the summer months. One of the key knowledge gaps in mountainous region is the interplay of precipitation and temperature with changing altitudes. Three‐dimensional temperature distribution is pivotal for the realistic temporal and spatial distribution of precipitation with pattern (rain/snow). The environmental/linear lapse rates are inadequate to address snow processes, resulting in significant uncertainties. An effort is made in this study to develop a vertical profile of temperature (VPT) and apply it as a dynamic temperature lapse rate to curtail uncertainties. The VPT was used for the spatiotemporal bias correction of precipitation by targeting accessible data sources based on the quantitative and spatial analysis in a distributed hydrologic modeling framework with a logical calibration and validation. The water and energy budget‐based distributed hydrological model with snow was utilized to simulate the streamflows and spatial distribution of snow cover based on VPT and corrected precipitation. During calibration and validation phase, the simulated discharge resulted with Nash‐Sutcliffe Efficiency over 0.76 and 0.71, respectively. Moreover, the output for the spatial distribution of snow cover evaluated against Moderate Resolution Imaging Spectroradiometer‐derived 8‐day maximum snow cover extents by employing pixel‐by‐pixel analysis with average model accuracy over 88.28% and 85.89%. To the authors' knowledge, it is the first study to integrate VPT in hydrologic modeling with robust potential for optimal water resource management in the data scarce region.
Efficient 3‐D Large‐Scale Forward Modeling and Inversion of Gravitational Fields in Spherical Coordinates With Application to Lunar Mascons
Authors: Zhao Guangdong , Chen Bo , Uieda Leonardo , Liu Jianxin , Kaban Mikhail K. , Chen Longwei , Guo Rongwen 
Published: March 2019

AbstractAn efficient forward modeling algorithm for calculation of gravitational fields in spherical coordinates is developed for 3‐D large‐scale gravity inversion problems. The 3‐D Gauss‐Legendre quadrature (GLQ) is used to calculate the gravitational fields of mass distributions discretized into tesseroids. Equivalence relations in the kernel matrix of the forward modeling are exploited to decrease storage and computation time. The numerical tests demonstrate that the computation time of the proposed algorithm is reduced by approximately 2 orders of magnitude, and the memory requirement is reduced by N′λ times compared with the traditional GLQ method, where N′λ is the number of the model elements in the longitudinal direction. These significant improvements in computational efficiency and storage make it possible to calculate and store the dense Jacobian matrix in 3‐D large‐scale gravity inversions. The equivalence relations can be applied to the Taylor series method or combined with the adaptive discretization to ensure high accuracy. To further illustrate the capability of the algorithm, we present a regional synthetic example. The inverted results show density distributions consistent with the actual model. The computation took about 6.3 hr and 0.88 GB of memory compared with about a dozen days and 245.86 GB for the traditional 3‐D GLQ method. Finally, the proposed algorithm is applied to the gravity field derived from the latest lunar gravity model GL1500E. Three‐dimensional density distributions of the Imbrium and Serenitatis basins are obtained, and high‐density bodies are found at the depths 10–60 km, likely indicating a significant uplift of the high‐density mantle beneath the two mascon basins.
Mice with Calr mutations homologous to human CALR mutations only exhibit mild thrombocytosis
Authors: Shide Kotaro , Kameda Takuro , Kamiunten Ayako , Oji Asami , Ozono Yoshinori , Sekine Masaaki , Honda Arata , Kitanaka Akira , Akizuki Keiichi , Tahira Yuki , Nakamura Kenichi , Hidaka Tomonori , Kubuki Yoko , Abe Hiroo , Miike Tadashi , Iwakiri Hisayoshi , Tahara Yoshihiro , Sueta Mitsue , Hasuike Satoru , Yamamoto Shojiro , Nagata Kenji , Ikawa Masahito , Shimoda Kazuya 
Published: March 2019

AbstractCalreticulin (CALR) exon 9 frameshift mutations, commonly detected in essential thrombocythemia (ET) and primary myelofibrosis patients, activate signal transducer and activator of transcription (STAT) proteins in the presence of Myeloproliferative Leukemia Virus (MPL) and induce ET in vivo. Loss of the KDEL motif, an endoplasmic reticulum retention signal, and generation of many positively charged amino acids (AAs) in the mutated C-terminus are thought to be important for disease induction. To test this hypothesis, we generated mice harboring a Calr frameshift mutation using the CRISPR/Cas9 system. Deletion of 19-base pairs in exon 9 (c.1099-1117del), designated the del19 mutation, induced loss of the KDEL motif and generated many positively charged AAs, similar to human mutants. Calr del19 mice exhibited mild thrombocytosis, slightly increased megakaryocytes, and mild splenomegaly. In vitro experiments revealed that the murine CALR del19 mutant had a weaker ability to combine with murine MPL than the human CALR del52 mutant. Consequently, STAT5 activation was also very weak downstream of the murine mutant and murine MPL, and may be the reason for the mild disease severity. In summary, loss of the KDEL motif and positively charged AAs in the C-terminus of CALR is insufficient for MPL binding and ET development.
Lysine methylation of transcription factors in cancer
Authors: Han Dong , Huang Mengxi , Wang Ting , Li Zhiping , Chen Yanyan , Liu Chao , Lei Zengjie , Chu Xiaoyuan 
Published: March 2019

AbstractProtein lysine methylation is a critical and dynamic post-translational modification that can regulate protein stability and function. This post-translational modification is regulated by lysine methyltransferases and lysine demethylases. Recent studies using mass-spectrometric techniques have revealed that in addition to histones, a great number of transcription factors are also methylated, often at multiple sites and to different degrees (mono-, di-, trimethyl lysine). The biomedical significance of transcription factor methylation in human diseases, including cancer, has been explored recently. Some studies have demonstrated that interfering with transcription factor lysine methylation both in vitro and in vivo can inhibit cancer cell proliferation, thereby reversing tumor progression. The inhibitors targeting lysine methyltransferases and lysine demethylases have been under development for the past two decades, and may be used as potential anticancer agents in the clinic. In this review, we focus on the current findings of transcription factor lysine methylation, and the effects on both transcriptional activity and target gene expression. We outlined the biological significance of transcription factor lysine methylation on tumor progression and highlighted its clinical value in cancer therapy.
PiggyBac transposon tools for recessive screening identify B-cell lymphoma drivers in mice
Authors: Weber Julia , de la Rosa Jorge , Grove Carolyn S. , Schick Markus , Rad Lena , Baranov Olga , Strong Alexander , Pfaus Anja , Friedrich Mathias J. , Engleitner Thomas , Lersch Robert , Öllinger Rupert , Grau Michael , Menendez Irene Gonzalez , Martella Manuela , Kohlhofer Ursula , Banerjee Ruby , Turchaninova Maria A. , Scherger Anna , Hoffman Gary J. , Hess Julia , Kuhn Laura B. , Ammon Tim , Kim Johnny , Schneider Günter , Unger Kristian , Zimber-Strobl Ursula , Heikenwälder Mathias , Schmidt-Supprian Marc , Yang Fengtang , Saur Dieter , Liu Pentao , Steiger Katja , Chudakov Dmitriy M. , Lenz Georg , Quintanilla-Martinez Leticia , Keller Ulrich , Vassiliou George S. , Cadiñanos Juan , Bradley Allan , Rad Roland 
Published: March 2019

AbstractB-cell lymphoma (BCL) is the most common hematologic malignancy. While sequencing studies gave insights into BCL genetics, identification of non-mutated cancer genes remains challenging. Here, we describe PiggyBac transposon tools and mouse models for recessive screening and show their application to study clonal B-cell lymphomagenesis. In a genome-wide screen, we discover BCL genes related to diverse molecular processes, including signaling, transcriptional regulation, chromatin regulation, or RNA metabolism. Cross-species analyses show the efficiency of the screen to pinpoint human cancer drivers altered by non-genetic mechanisms, including clinically relevant genes dysregulated epigenetically, transcriptionally, or post-transcriptionally in human BCL. We also describe a CRISPR/Cas9-based in vivo platform for BCL functional genomics, and validate discovered genes, such as Rfx7, a transcription factor, and Phip, a chromatin regulator, which suppress lymphomagenesis in mice. Our study gives comprehensive insights into the molecular landscapes of BCL and underlines the power of genome-scale screening to inform biology.
Structure mapping of dengue and Zika viruses reveals functional long-range interactions
Authors: Huber Roland G. , Lim Xin Ni , Ng Wy Ching , Sim Adelene Y. L. , Poh Hui Xian , Shen Yang , Lim Su Ying , Sundstrom Karin B. , Sun Xuyang , Aw Jong Ghut , Too Horng Khit , Boey Peng Hee , Wilm Andreas , Chawla Tanu , Choy Milly M. , Jiang Lu , de Sessions Paola Florez , Loh Xian Jun , Alonso Sylvie , Hibberd Martin , Nagarajan Niranjan , Ooi Eng Eong , Bond Peter J. , Sessions October M. , Wan Yue 
Published: March 2019

AbstractDengue (DENV) and Zika (ZIKV) viruses are clinically important members of the Flaviviridae family with an 11 kb positive strand RNA genome that folds to enable virus function. Here, we perform structure and interaction mapping on four DENV and ZIKV strains inside virions and in infected cells. Comparative analysis of SHAPE reactivities across serotypes nominates potentially functional regions that are highly structured, conserved, and contain low synonymous mutation rates. Interaction mapping by SPLASH identifies many pair-wise interactions, 40% of which form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared interactions between serotypes reveals a conserved macro-organization whereby interactions can be preserved at physical locations beyond sequence identities. We further observe that longer-range interactions are preferentially disrupted inside cells, and show the importance of new interactions in virus fitness. These findings deepen our understanding of Flavivirus genome organization and serve as a resource for designing therapeutics in targeting RNA viruses.
Phosphatidylethanolamine made in the inner mitochondrial membrane is essential for yeast cytochrome bc1 complex function
Authors: Calzada Elizabeth , Avery Erica , Sam Pingdewinde N. , Modak Arnab , Wang Chunyan , McCaffery J. Michael , Han Xianlin , Alder Nathan N. , Claypool Steven M. 
Published: March 2019

AbstractOf the four separate PE biosynthetic pathways in eukaryotes, one occurs in the mitochondrial inner membrane (IM) and is executed by phosphatidylserine decarboxylase (Psd1). Deletion of Psd1 is lethal in mice and compromises mitochondrial function. We hypothesize that this reflects inefficient import of non-mitochondrial PE into the IM. Here, we test this by re-wiring PE metabolism in yeast by re-directing Psd1 to the outer mitochondrial membrane or the endomembrane system and show that PE can cross the IMS in both directions. Nonetheless, PE synthesis in the IM is critical for cytochrome bc1 complex (III) function and mutations predicted to disrupt a conserved PE-binding site in the complex III subunit, Qcr7, impair complex III activity similar to PSD1 deletion. Collectively, these data challenge the current dogma of PE trafficking and demonstrate that PE made in the IM by Psd1 support the intrinsic functionality of complex III.
Water-mediated deracemization of a bisporphyrin helicate assisted by diastereoselective encapsulation of chiral guests
Authors: Ousaka Naoki , Yamamoto Shinya , Iida Hiroki , Iwata Takuya , Ito Shingo , Hijikata Yuh , Irle Stephan , Yashima Eiji 
Published: March 2019

AbstractDeracemization is a powerful method by which a racemic mixture can be transformed into an excess of one enantiomer with the aid of chiral auxiliaries, but has been applied only to small chiral molecular systems. Here we report a deracemization of a racemic double-stranded spiroborate helicate containing a bisporphyrin unit upon encapsulation of chiral aromatic guests between the bisporphyrin. The chiral guest-included helicate is kinetically stable, existing as a mixture of right- and left-handed double helices, which eventually undergo an inversion of the helicity triggered by water resulting from the water-mediated reversible diastereoselective B-O bond cleavage/reformation of the spiroborate groups, thus producing an optically-active helicate with a high enantioselectivity. Quantum chemical calculations suggest that the stereospecific CH-π interactions between the porphyrin hydrogen atoms of the helicate and an aromatic pendant group of the chiral guest play a key role in the enhancement of the helical handedness of the helicate.
Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine
Authors: Mazal Hisham , Iljina Marija , Barak Yoav , Elad Nadav , Rosenzweig Rina , Goloubinoff Pierre , Riven Inbal , Haran Gilad 
Published: March 2019

AbstractLarge protein machines are tightly regulated through allosteric communication channels. Here we demonstrate the involvement of ultrafast conformational dynamics in allosteric regulation of ClpB, a hexameric AAA+ machine that rescues aggregated proteins. Each subunit of ClpB contains a unique coiled-coil structure, the middle domain (M domain), proposed as a control element that binds the co-chaperone DnaK. Using single-molecule FRET spectroscopy, we probe the M domain during the chaperone cycle and find it to jump on the microsecond time scale between two states, whose structures are determined. The M-domain jumps are much faster than the overall activity of ClpB, making it an effectively continuous, tunable switch. Indeed, a series of allosteric interactions are found to modulate the dynamics, including binding of nucleotides, DnaK and protein substrates. This mode of dynamic control enables fast cellular adaptation and may be a general mechanism for the regulation of cellular machineries.
Intrinsic functional architecture of the non-human primate spinal cord derived from fMRI and electrophysiology
Authors: Wu Tung-Lin , Yang Pai-Feng , Wang Feng , Shi Zhaoyue , Mishra Arabinda , Wu Ruiqi , Chen Li Min , Gore John C. 
Published: March 2019

AbstractResting-state functional MRI (rsfMRI) has recently revealed correlated signals in the spinal cord horns of monkeys and humans. However, the interpretation of these rsfMRI correlations as indicators of functional connectivity in the spinal cord remains unclear. Here, we recorded stimulus-evoked and spontaneous spiking activity and local field potentials (LFPs) from monkey spinal cord in order to validate fMRI measures. We found that both BOLD and electrophysiological signals elicited by tactile stimulation co-localized to the ipsilateral dorsal horn. Temporal profiles of stimulus-evoked BOLD signals covaried with LFP and multiunit spiking in a similar way to those observed in the brain. Functional connectivity of dorsal horns exhibited a U-shaped profile along the dorsal-intermediate-ventral axis. Overall, these results suggest that there is an intrinsic functional architecture within the gray matter of a single spinal segment, and that rsfMRI signals at high field directly reflect this underlying spontaneous neuronal activity.
Temperature-controlled repeatable scrambling and induced-sorting of building blocks between cubic assemblies
Authors: Zhan Yi-Yang , Kojima Tatsuo , Ishii Kentaro , Takahashi Satoshi , Haketa Yohei , Maeda Hiromitsu , Uchiyama Susumu , Hiraoka Shuichi 
Published: March 2019

AbstractSeparation of a homogeneous mixture of different components to reach an ordered out-of-equilibrium state in solution has attracted continuous attention. While this can be achieved using external chemical fuels or photo energy, an alternative energy source is heat. Here we realize a temperature-controlled cycle of transitions between ordered and disordered states based on a mixture of two kinds of building blocks that self-assemble into cubic structures (nanocubes). An almost statistical mixture of nanocubes (disordered state) is thermodynamically most stable at lower temperature (25 °C), while homoleptic assemblies composed of single components are preferentially produced at higher temperature (100 °C) followed by rapid cooling. The scrambling of the building blocks between the nanocubes takes place through the exchange of free building blocks dissociated from the nanocubes. Based on this mechanism, it is possible to accelerate, retard, and perfectly block the scrambling by the guest molecules encapsulated in the nanocubes.
Reduced expression of pyruvate kinase in kidney proximal tubule cells is a potential mechanism of pravastatin altered glucose metabolism
Authors: Lee Yong Pyo , Cho Yuri , Kim Eun Jee , Lee Hyojung , Choi Hoon Young , Wang Hye Jin , Kang Eun Seok , Kim Yu Seun , Kim Myoung Soo , Kim Beom Seok 
Published: March 2019

AbstractRecent studies have reported that statins are associated with increased incidence of diabetes. Although several mechanisms have been proposed, the role of the kidney’s glucose metabolism upon statin treatment is still unclear. Thus, we investigated the role of pravastatin in gluconeogenesis and glycolysis. HK-2 and HepG2 cells were treated with pravastatin and cultured under either high- or normal-cholesterol conditions. In HK-2 cells treated with pravastatin under both high- and normal-cholesterol conditions, the protein expression of only pyruvate kinase isozymes L/R (PKLR) decreased in a dose-dependent manner, while the protein expression of other glucose metabolism related enzymes remained unchanged. Within the in vivo experiment, male C57BL/6 mice were fed either pravastatin-treated normal-fat diets for 2 or 4 weeks or pravastatin-treated high-fat diets for 16 weeks. Protein expression of PKLR in the kidneys from mice that consumed pravastatin-treated high-fat diets decreased significantly compared to the controls. Upon the treatments of pravastatin, only the PKLR expression decreased in lean mice. Furthermore, PKLR activity decreased significantly in the kidney after pravastatin treatments. However, there was no change in enzyme activity in the liver, suggesting that pravastatin decreased PKLR activity only in the kidney. This change may be associated with the hyperglycemic effect of statins.