bluuebunny/crossref_metadata_2025_split huggingface dataset:
The environmental factors limiting the distribution of shallow-water terebratulid brachiopods
Authors: García-Ramos Diego A. , Ćorić Stjepan , Joachimski Michael M. , Zuschin Martin 
Published: May 2020

AbstractThe Cenozoic genusTerebratulaseems to be an exception to the post-Permian trend in brachiopod retreat to offshore habitats, because it was species rich and numerically abundant in warm-temperate shallow-water environments in the Mediterranean and the Paratethys realms. This was so despite the general dominance of bivalves and the pervasive bioturbation and predation pressure during the Neogene.Terebratula, however, went extinct in the Calabrian (Pleistocene). The optimal environmental conditions forTerebratuladuring its prime are poorly known. The Águilas Basin (SE Spain) is an ideal study area to investigate the habitat ofTerebratula, because shell beds of this brachiopod occur there cyclically in early Pliocene deposits. We evaluate the paleoecological boundary conditions controlling the distribution ofTerebratulaby estimating its environmental tolerances using benthic and planktic foraminiferal and nannoplanktic assemblages and oxygen isotopes of the secondary layer brachiopod calcite. Our results suggest thatTerebratulain the Águilas Basin favored oligotrophic to mesotrophic, well-oxygenated environments at water depths of 60–90 m. Planktic foraminiferal assemblages and oxygen isotopes point to sea-surface temperatures between ~16°C and 22°C, and bottom-water temperatures between 17°C and 24°C. The analyzed proxies indicate thatTerebratulatolerated local variations in water depth, bottom temperature, oxygenation, productivity, and organic enrichment.Terebratulawas probably excluded by grazing pressure from well-lit environments and preferentially occupied sediment-starved, current-swept upper offshore habitats where coralline red algae were absent. Narrow temperature ranges ofTerebratulaspecies might have been a disadvantage during the high-amplitude seawater temperature fluctuations that started about 1 Ma, when the genus went extinct.
Germline variant inREXO2is a novel candidate gene in familial pheochromocytoma
Authors: Laitman Yael , Tzur Shay , Attali Ruben , Tirosh Amit , Friedman Eitan 
Published: May 2020

AbstractPheochromocytoma (PCC) is a rare, mostly benign tumour of the adrenal medulla. Hereditary PCC accounts for ~35% of cases and has been associated with germline mutations in several cancer susceptibility genes (e.g.,KIF1B,SDHB,VHL,SDHD,RET). We performed whole-exome sequencing in a family with four PCC-affected patients in two consecutive generations and identified a potential novel candidate pathogenic variant in theREXO2gene that affects splicing (c.531-1G>T (NM 015523.3)), which co-segregated with the phenotype in the family.REXO2encodes for RNA exonuclease 2 protein and localizes to 11q23, a chromosomal region displaying allelic imbalance in PCC. REXO2 protein has been associated with DNA repair, replication and recombination processes and thus its inactivation may contribute to tumorigenesis. While the study suggests that this novelREXO2gene variant underlies PCC in this family, additional functional studies are required in order to establish the putative role of theREXO2gene in PCC predisposition.
DECODING THE ARCHAEOLOGICAL SIGNIFICANCE OF PROBLEMATIC DEPOSITS IN THE MAYA LOWLANDS
Authors: Aimers James J. , Hoggarth Julie A. , Awe Jaime J. 
Published: May 2020

AbstractThe term “problematical deposits” was coined decades ago at Tikal to refer to special deposits that were neither burials nor caches. Since that time, the term has been expanded to refer to a range of deposits that have puzzled archaeologists. In this paper we review the various interpretations that have been offered for these deposits includingde factorefuse, squatter deposits, and the remains of dedication or termination ritual, feasting, or pilgrimage. We argue that the superficial similarity of these deposits can make it difficult to identify the range of activities that they represent and that detailed contextual analysis is required to distinguish them. We offer some of the archaeological correlates that have been associated with different types of problematic deposits.
THE LAST HURRAH: EXAMINING THE NATURE OF PERI-ABANDONMENT DEPOSITS AND ACTIVITIES AT CAHAL PECH, BELIZE
Authors: Awe Jaime J. , Ebert Claire E. , Hoggarth Julie A. , Aimers James J. , Helmke Christophe , Douglas John , Stemp W. James 
Published: May 2020

AbstractArchaeological investigations by the Belize Valley Archaeological Reconnaissance Project at Cahal Pech uncovered several Terminal Classic (a.d.750–900) peri-abandonment deposits and activity areas at this Belize River Valley center. The deposits contained a diverse assemblage of cultural remains located above and between collapsed architecture, associated with evidence for burning activities. In the past, archaeologists have generally interpreted similar assemblages as “problematic deposits”—“de facto” refuse (garbage)—as associated with building termination and desecration, or as evidence for rapid abandonment during the violent destruction of these ancient cities. It is argued here that the microstratigraphic excavation and contextual analysis of these features provide limited support for these explanations. Alternatively, we suggest that the deposits are more likely associated with peri-abandonment rituals that were conducted by a reduced remnant population at Cahal Pech, or by small groups who continued to reside in the site's periphery during the last stages of the Terminal Classic period.
LINC01116 promotes tumor proliferation and neutrophil recruitment via DDX5-mediated regulation of IL-1β in glioma cell
Authors: Wang Teng , Cao Lihua , Dong Xin , Wu Fei , De Wei , Huang Lin , Wan Qi 
Published: May 2020

AbstractTumor-associated neutrophils (TANs) are important inflammatory infiltrating cells in the tumor microenvironment and are closely related to the development of human tumor. However, the underlying mechanism of TANs recruiting to glioma remains unknown. Herein, we identified that LINC01116 was significantly upregulated in glioma, and positively correlated with clinical malignancy and survival prognosis. LINC01116 regulated the progression of glioma in vitro and in vivo. RNA-seq analysis demonstrated that LINC01116 knockdown affected the expression of IL-1β, which promoted glioma proliferation and neutrophil recruitment. Furthermore, the co-culture of glioma cells and neutrophils showed that the accumulation of TANs promoted tumor proliferation via producing a host of cytokines. Mechanistically, LINC01116 activated IL-1β expression by recruiting the transcriptional regulator DDX5 to the IL-1β promoter. Our findings reveal that LINC01116 can promote glioma proliferation and neutrophil recruitment by regulating IL-1β, and may be served as a novel target for glioma therapy and prognosis.
Dysfunction of ATG7-dependent autophagy dysregulates the antioxidant response and contributes to oxidative stress-induced biological impairments in human epidermal melanocytes
Authors: Qiao Zhuhui , Xu Zhongyi , Xiao Qing , Yang Yiwen , Ying Jiayi , Xiang Leihong , Zhang Chengfeng 
Published: May 2020

AbstractAutophagy is a process involving the self-digestion of components that participates in anti-oxidative stress responses and protects cells against oxidative damage. However, the role of autophagy in the anti-oxidative stress responses of melanocytes remains unclear. To investigate the role of autophagy in human epidermal melanocytes, we knocked down and overexpressed ATG7, the critical gene of autophagy, in normal human epidermal melanocytes. We demonstrated that ATG7-dependent autophagy could affect melanin content of melanocytes by regulating melanogenesis. Moreover, suppression of ATG7-dependent autophagy inhibits proliferation and promotes oxidative stress-induced apoptosis of melanocytes, whereas enhancement of ATG7-dependent autophagy protects melanocytes from oxidative stress-induced apoptosis. Meanwhile, deficiency of ATG7-dependent autophagy results in premature senescence of melanocytes under oxidative stress. Notably, we verified that ATG7-dependent autophagy could alter oxidative stress homeostasis by regulating reactive oxygen species (ROS) production, nuclear factor erythroid 2-related factor 2 (Nrf2) antioxidant pathway, and the activity of several antioxidant enzymes in melanocytes. In conclusion, our study suggested that ATG7-dependent autophagy is indispensable for redox homeostasis and the biological functions of melanocytes, such as melanogenesis, proliferation, apoptosis, and senescence, especially under oxidative stress.
Recent hybrids recapitulate ancient hybrid outcomes
Authors: Chaturvedi Samridhi , Lucas Lauren K. , Buerkle C. Alex , Fordyce James A. , Forister Matthew L. , Nice Chris C. , Gompert Zachariah 
Published: May 2020

AbstractGenomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone inLycaeidesbutterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa,Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reducedL. melissaancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown.
Mutualism increases diversity, stability, and function of multiplex networks that integrate pollinators into food webs
Authors: Hale Kayla R. S. , Valdovinos Fernanda S. , Martinez Neo D. 
Published: May 2020

AbstractEcosystems are composed of complex networks of many species interacting in different ways. While ecologists have long studied food webs of feeding interactions, recent studies increasingly focus on mutualistic networks including plants that exchange food for reproductive services provided by animals such as pollinators. Here, we synthesize both types of consumer-resource interactions to better understand the controversial effects of mutualism on ecosystems at the species, guild, and whole-community levels. We find that consumer-resource mechanisms underlying plant-pollinator mutualisms can increase persistence, productivity, abundance, and temporal stability of both mutualists and non-mutualists in food webs. These effects strongly increase with floral reward productivity and are qualitatively robust to variation in the prevalence of mutualism and pollinators feeding upon resources in addition to rewards. This work advances the ability of mechanistic network theory to synthesize different types of interactions and illustrates how mutualism can enhance the diversity, stability, and function of complex ecosystems.
Midkine activation of CD8+ T cells establishes a neuron–immune–cancer axis responsible for low-grade glioma growth
Authors: Guo Xiaofan , Pan Yuan , Xiong Min , Sanapala Shilpa , Anastasaki Corina , Cobb Olivia , Dahiya Sonika , Gutmann David H. 
Published: May 2020

AbstractBrain tumors (gliomas) are heterogeneous cellular ecosystems, where non-neoplastic monocytic cells have emerged as key regulators of tumor maintenance and progression. However, relative to macrophages/microglia, comparatively less is known about the roles of neurons and T cells in glioma pathobiology. Herein, we leverage genetically engineered mouse models and human biospecimens to define the axis in which neurons, T cells, and microglia interact to govern Neurofibromatosis-1 (NF1) low-grade glioma (LGG) growth. NF1-mutant human and mouse brain neurons elaborate midkine to activate naïve CD8+ T cells to produce Ccl4, which induces microglia to produce a key LGG growth factor (Ccl5) critical for LGG stem cell survival. Importantly, increased CCL5 expression is associated with reduced survival in patients with LGG. The elucidation of the critical intercellular dependencies that constitute the LGG neuroimmune axis provides insights into the role of neurons and immune cells in controlling glioma growth, relevant to future therapeutic targeting.
Real-time monitoring of PARP1-dependent PARylation by ATR-FTIR spectroscopy
Authors: Krüger Annika , Bürkle Alexander , Hauser Karin , Mangerich Aswin 
Published: May 2020

AbstractPoly-ADP-ribosylation (PARylation) is a fully reversible post-translational modification with key roles in cellular physiology. Due to the multi-domain structure of poly(ADP-ribose) polymerase-1 (PARP1) and the highly dynamic nature of the PARylation reaction, studies on the biochemical mechanism and structural dynamics remain challenging. Here, we report label-free, time-resolved monitoring of PARP1-dependent PARylation using ATR-FTIR spectroscopy. This includes PARP1 activation by binding to DNA strand break models, NAD+ substrate binding, PAR formation, and dissociation of automodified PARP1 from DNA. Analyses of PARP1 activation at different DNA models demonstrate a strong positive correlation of PARylation and PARP1 dissociation, with the strongest effects observed for DNA nicks and 3’ phosphorylated ends. Moreover, by examining dynamic structural changes of PARP1, we reveal changes in the secondary structure of PARP1 induced by NAD+ and PARP inhibitor binding. In summary, this approach enables holistic and dynamic insights into PARP1-dependent PARylation with molecular and temporal resolution.
Repressive chromatin modification underpins the long-term expression trend of a perennial flowering gene in nature
Authors: Nishio Haruki , Buzas Diana M. , Nagano Atsushi J. , Iwayama Koji , Ushio Masayuki , Kudoh Hiroshi 
Published: May 2020

AbstractNatural environments require organisms to possess robust mechanisms allowing responses to seasonal trends. InArabidopsis halleri, the flowering regulatorAhgFLCshows upregulation and downregulation phases along with long-term past temperature, but the underlying machinery remains elusive. Here, we investigate the seasonal dynamics of histone modifications, H3K27me3 and H3K4me3, atAhgFLCin a natural population. Our advanced modelling and transplant experiments reveal that H3K27me3-mediated chromatin regulation atAhgFLCprovides two essential properties. One is the ability to respond to the long-term temperature trends via bidirectional interactions between H3K27me3 and H3K4me3; the other is the ratchet-like character of theAhgFLCsystem, i.e. reversible in the entire perennial life cycle but irreversible during the upregulation phase. Furthermore, we show that the long-term temperature trends are locally indexed atAhgFLCin the form of histone modifications. Our study provides a more comprehensive understanding of H3K27me3 function atAhgFLCin a complex natural environment.
Evidence for a serpentinized plate interface favouring continental subduction
Authors: Zhao Liang , Malusà Marco G. , Yuan Huaiyu , Paul Anne , Guillot Stéphane , Lu Yang , Stehly Laurent , Solarino Stefano , Eva Elena , Lu Gang , Bodin Thomas ,   CIFALPS Group, Zhao Liang , Malusà Marco G. , Paul Anne , Guillot Stéphane , Solarino Stefano , Eva Elena , Lu Gang ,   AlpArray Working Group, Paul Anne , Solarino Stefano 
Published: May 2020

AbstractThe dynamics of continental subduction is largely controlled by the rheological properties of rocks involved along the subduction channel. Serpentinites have low viscosity at geological strain rates. However, compelling geophysical evidence of a serpentinite channel during continental subduction is still lacking. Here we show that anomalously low shear-wave seismic velocities are found beneath the Western Alps, along the plate interface between the European slab and the overlying Adriatic mantle. We propose that these seismic velocities indicate the stacked remnants of a weak fossilised serpentinite channel, which includes both slivers of abyssal serpentinite formed at the ocean floor and mantle-wedge serpentinite formed by fluid release from the subducting slab. Our results suggest that this serpentinized plate interface may have favoured the subduction of continental crust into the upper mantle and the formation/exhumation of ultra-high pressure metamorphic rocks, providing new constraints to develop the conceptual and quantitative understanding of continental-subduction dynamics.
Exploiting racemism enhanced organic room-temperature phosphorescence to demonstrate Wallach’s rule in the lighting chiral chromophores
Authors: Wu Xiugang , Huang Chun-Ying , Chen Deng-Gao , Liu Denghui , Wu Chichi , Chou Keh-Jiunh , Zhang Bin , Wang Yafei , Liu Yu , Li Elise Y. , Zhu Weiguo , Chou Pi-Tai 
Published: May 2020

AbstractThe correlation between molecular packing structure and its room-temperature phosphorescence (RTP), hence rational promotion of the intensity, remains unclear. We herein present racemism enhanced RTP chiral chromophores by 2,2-bis-(diphenylphosphino)-1,1-napthalene (rac-BINAP) in comparison to its chiral counterparts. The result shows that rac-BINAP in crystal with denser density, consistent with a long standing Wallach’s rule, exhibits deeper red RTP at 680 nm than that of the chiral counterparts. The cross packing between alternative R- and S- forms in rac-BINAP crystal significantly retards the bimolecular quenching pathway, triplet-triplet annihilation (TTA), and hence suppresses the non-radiative pathway, boosting the RTP intensity. The result extends the Wallach’s rule to the fundamental difference in chiral-photophysics. In electroluminescence, rac-BINAP exhibits more balanced fluorescence versus phosphorescence intensity by comparison with that of photoluminescence, rendering a white-light emission. The result paves an avenue en route for white-light organic light emitting diodes via full exploitation of intrinsic fluorescence and phosphorescence.
Lattice distortion induced internal electric field in TiO2 photoelectrode for efficient charge separation and transfer
Authors: Hu Yuxiang , Pan Yuanyuan , Wang Zhiliang , Lin Tongen , Gao Yuying , Luo Bin , Hu Han , Fan Fengtao , Liu Gang , Wang Lianzhou 
Published: May 2020

AbstractProviding sufficient driving force for charge separation and transfer (CST) is a critical issue in photoelectrochemical (PEC) energy conversion. Normally, the driving force is derived mainly from band bending at the photoelectrode/electrolyte interface but negligible in the bulk. To boost the bulky driving force, we report a rational strategy to create effective electric field via controllable lattice distortion in the bulk of a semiconductor film. This concept is verified by the lithiation of a classic TiO2 (Li-TiO2) photoelectrode, which leads to significant distortion of the TiO6 unit cells in the bulk with well-aligned dipole moment. A remarkable internal built-in electric field of ~2.1 × 102 V m−1 throughout the Li-TiO2 film is created to provide strong driving force for bulky CST. The photoelectrode demonstrates an over 750% improvement of photocurrent density and 100 mV negative shift of onset potential upon the lithiation compared to that of pristine TiO2 film.
Alternative splicing controls teneurin-latrophilin interaction and synapse specificity by a shape-shifting mechanism
Authors: Li Jingxian , Xie Yuan , Cornelius Shaleeka , Jiang Xian , Sando Richard , Kordon Szymon P. , Pan Man , Leon Katherine , Südhof Thomas C. , Zhao Minglei , Araç Demet 
Published: May 2020

AbstractThe trans-synaptic interaction of the cell-adhesion molecules teneurins (TENs) with latrophilins (LPHNs/ADGRLs) promotes excitatory synapse formation when LPHNs simultaneously interact with FLRTs. Insertion of a short alternatively-spliced region within TENs abolishes the TEN-LPHN interaction and switches TEN function to specify inhibitory synapses. How alternative-splicing regulates TEN-LPHN interaction remains unclear. Here, we report the 2.9 Å resolution cryo-EM structure of the TEN2-LPHN3 complex, and describe the trimeric TEN2-LPHN3-FLRT3 complex. The structure reveals that the N-terminal lectin domain of LPHN3 binds to the TEN2 barrel at a site far away from the alternatively spliced region. Alternative-splicing regulates the TEN2-LPHN3 interaction by hindering access to the LPHN-binding surface rather than altering it. Strikingly, mutagenesis of the LPHN-binding surface of TEN2 abolishes the LPHN3 interaction and impairs excitatory but not inhibitory synapse formation. These results suggest that a multi-level coincident binding mechanism mediated by a cryptic adhesion complex between TENs and LPHNs regulates synapse specificity.
Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas
Authors: Inoue Kimiko , Ogonuki Narumi , Kamimura Satoshi , Inoue Hiroki , Matoba Shogo , Hirose Michiko , Honda Arata , Miura Kento , Hada Masashi , Hasegawa Ayumi , Watanabe Naomi , Dodo Yukiko , Mochida Keiji , Ogura Atsuo 
Published: May 2020

AbstractSomatic cell nuclear transfer (SCNT) in mammals is an inefficient process that is frequently associated with abnormal phenotypes, especially in placentas. Recent studies demonstrated that mouse SCNT placentas completely lack histone methylation (H3K27me3)-dependent imprinting, but how it affects placental development remains unclear. Here, we provide evidence that the loss of H3K27me3 imprinting is responsible for abnormal placental enlargement and low birth rates following SCNT, through upregulation of imprinted miRNAs. When we restore the normal paternal expression of H3K27me3-dependent imprinted genes (Sfmbt2, Gab1, and Slc38a4) in SCNT placentas by maternal knockout, the placentas remain enlarged. Intriguingly, correcting the expression of clustered miRNAs within the Sfmbt2 gene ameliorates the placental phenotype. Importantly, their target genes, which are confirmed to cause SCNT-like placental histology, recover their expression level. The birth rates increase about twofold. Thus, we identify loss of H3K27me3 imprinting as an epigenetic error that compromises embryo development following SCNT.
Precise control of the interlayer twist angle in large scale MoS2 homostructures
Authors: Liao Mengzhou , Wei Zheng , Du Luojun , Wang Qinqin , Tang Jian , Yu Hua , Wu Fanfan , Zhao Jiaojiao , Xu Xiaozhi , Han Bo , Liu Kaihui , Gao Peng , Polcar Tomas , Sun Zhipei , Shi Dongxia , Yang Rong , Zhang Guangyu 
Published: May 2020

AbstractTwist angle between adjacent layers of two-dimensional (2D) layered materials provides an exotic degree of freedom to enable various fascinating phenomena, which opens a research direction—twistronics. To realize the practical applications of twistronics, it is of the utmost importance to control the interlayer twist angle on large scales. In this work, we report the precise control of interlayer twist angle in centimeter-scale stacked multilayer MoS2 homostructures via the combination of wafer-scale highly-oriented monolayer MoS2 growth techniques and a water-assisted transfer method. We confirm that the twist angle can continuously change the indirect bandgap of centimeter-scale stacked multilayer MoS2 homostructures, which is indicated by the photoluminescence peak shift. Furthermore, we demonstrate that the stack structure can affect the electrical properties of MoS2 homostructures, where 30° twist angle yields higher electron mobility. Our work provides a firm basis for the development of twistronics.