bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea
Authors: Yu Hang , Skennerton Connor T , Chadwick Grayson L , Leu Andy O , Aoki Masataka , Tyson Gene W , Orphan Victoria J 
Published: July 2021

Abstract
Sulfate-coupled anaerobic oxidation of methane (AOM) is a major methane sink in marine sediments. Multiple lineages of anaerobic methanotrophic archaea (ANME) often coexist in sediments and catalyze this process syntrophically with sulfate-reducing bacteria (SRB), but the potential differences in ANME ecophysiology and mechanisms of syntrophy remain unresolved. A humic acid analog, anthraquinone 2,6-disulfonate (AQDS), could decouple archaeal methanotrophy from bacterial sulfate reduction and serve as the terminal electron acceptor for AOM (AQDS-coupled AOM). Here in sediment microcosm experiments, we examined variations in physiological response between two co-occurring ANME-2 families (ANME-2a and ANME-2c) and tested the hypothesis of sulfate respiration by ANME-2. Sulfate concentrations as low as 100 µM increased AQDS-coupled AOM nearly 2-fold matching the rates of sulfate-coupled AOM. However, the SRB partners remained inactive in microcosms with sulfate and AQDS and neither ANME-2 families respired sulfate, as shown by their cellular sulfur contents and anabolic activities measured using nanoscale secondary ion mass spectrometry. ANME-2a anabolic activity was significantly higher than ANME-2c, suggesting that ANME-2a was primarily responsible for the observed sulfate stimulation of AQDS-coupled AOM. Comparative transcriptomics showed significant upregulation of ANME-2a transcripts linked to multiple ABC transporters and downregulation of central carbon metabolism during AQDS-coupled AOM compared to sulfate-coupled AOM. Surprisingly, genes involved in sulfur anabolism were not differentially expressed during AQDS-coupled AOM with and without sulfate amendment. Collectively, this data indicates that ANME-2 archaea are incapable of respiring sulfate, but sulfate availability differentially stimulates the growth and AOM activity of different ANME lineages.
Seasonal niche differentiation among closely related marine bacteria
Authors: Auladell Adrià , Barberán Albert , Logares Ramiro , Garcés Esther , Gasol Josep M , Ferrera Isabel 
Published: July 2021

Abstract
Bacteria display dynamic abundance fluctuations over time in marine environments, where they play key biogeochemical roles. Here, we characterized the seasonal dynamics of marine bacteria in a coastal oligotrophic time series station, tested how similar the temporal niche of closely related taxa is, and what are the environmental parameters modulating their seasonal abundance patterns. We further explored how conserved the niche is at higher taxonomic levels. The community presented recurrent patterns of seasonality for 297 out of 6825 amplicon sequence variants (ASVs), which constituted almost half of the total relative abundance (47%). For certain genera, niche similarity decreased as nucleotide divergence in the 16S rRNA gene increased, a pattern compatible with the selection of similar taxa through environmental filtering. Additionally, we observed evidence of seasonal differentiation within various genera as seen by the distinct seasonal patterns of closely related taxa. At broader taxonomic levels, coherent seasonal trends did not exist at the class level, while the order and family ranks depended on the patterns that existed at the genus level. This study identifies the coexistence of closely related taxa for some bacterial groups and seasonal differentiation for others in a coastal marine environment subjected to a strong seasonality.
Response to substrate limitation by a marine sulfate-reducing bacterium
Authors: Marietou Angeliki , Kjeldsen Kasper U , Glombitza Clemens , Jørgensen Bo Barker 
Published: July 2021

Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood–Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (−28 to −33 kJ mol−1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
Single-cell transcriptome and TCR profiling reveal activated and expanded T cell populations in Parkinson’s disease
Authors: Wang Pingping , Yao Lifen , Luo Meng , Zhou Wenyang , Jin Xiyun , Xu Zhaochun , Yan Shi , Li Yiqun , Xu Chang , Cheng Rui , Huang Yan , Lin Xiaoyu , Ma Kexin , Cao Huimin , Liu Hongxin , Xue Guangfu , Han Fang , Nie Huan , Jiang Qinghua 
Published: July 2021

AbstractGiven the chronic inflammatory nature of Parkinson’s disease (PD), T cell immunity may be important for disease onset. Here, we performed single-cell transcriptome and TCR sequencing, and conducted integrative analyses to decode composition, function and lineage relationship of T cells in the blood and cerebrospinal fluid of PD. Combined expression and TCR-based lineage tracking, we discovered a large population of CD8+ T cells showing continuous progression from central memory to terminal effector T cells in PD patients. Additionally, we identified a group of cytotoxic CD4+ T cells (CD4 CTLs) remarkably expanded in PD patients, which derived from Th1 cells by TCR-based fate decision. Finally, we screened putative TCR–antigen pairs that existed in both blood and cerebrospinal fluid of PD patients to provide potential evidence for peripheral T cells to participate in neuronal degeneration. Our study provides valuable insights and rich resources for understanding the adaptive immune response in PD.
Three epitope-distinct human antibodies from RenMab mice neutralize SARS-CoV-2 and cooperatively minimize the escape of mutants
Authors: Nie Jianhui , Xie Jingshu , Liu Shuo , Wu Jiajing , Liu Chuan , Li Jianhui , Liu Yacui , Wang Meiyu , Zhao Huizhen , Zhang Yabo , Yao Jiawei , Chen Lei , Shen Yuelei , Yang Yi , Wang Hong-Wei , Wang Youchun , Huang Weijin 
Published: July 2021

AbstractCoronavirus disease 2019 (COVID-19), a pandemic disease caused by the newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused more than 3.8 million deaths to date. Neutralizing antibodies are effective therapeutic measures. However, many naturally occurring mutations at the receptor-binding domain (RBD) have emerged, and some of them can evade existing neutralizing antibodies. Here, we utilized RenMab, a novel mouse carrying the entire human antibody variable region, for neutralizing antibody discovery. We obtained several potent RBD-blocking antibodies and categorized them into four distinct groups by epitope mapping. We determined the involved residues of the epitope of three representative antibodies by cryo-electron microscopy (Cryo-EM) studies. Moreover, we performed neutralizing experiments with 50 variant strains with single or combined mutations and found that the mixing of three epitope-distinct antibodies almost eliminated the mutant escape. Our study provides a sound basis for the rational design of fully human antibody cocktails against SARS-CoV-2 and pre-emergent coronaviral threats.
Hyperprolinemia type I caused by homozygous p.T466M mutation in PRODH
Authors: Hama Rina , Kido Jun , Sugawara Keishin , Nakamura Toshiro , Nakamura Kimitoshi 
Published: July 2021

AbstractHyperprolinemia type I (HPI) is an autosomal recessive metabolic disorder caused by defects in proline oxidase. We herein describe a case of a patient with HPI and harboring the NM_016335.4 (PRODH_v001):c.1397 C > T (p.T466M) mutation and polymorphisms in thePRODHgene, as detected by plasma amino acid analysis and Sanger sequencing. The patient presented with short stature, carbohydrate-rich dietary preferences, and mild intellectual disability that was suggestive of a neurodevelopmental or learning disorder.
Reversible electroadhesion of hydrogels to animal tissues for suture-less repair of cuts or tears
Authors: Borden Leah K. , Gargava Ankit , Raghavan Srinivasa R. 
Published: July 2021

AbstractElectroadhesion, i.e., adhesion induced by an electric field, occurs between non-sticky cationic and anionic hydrogels. Here, we demonstrate electroadhesion between cationic gels and animal (bovine) tissues. When gel and tissue are placed under an electric field (DC, 10 V) for 20 s, the pair strongly adhere, and the adhesion persists indefinitely thereafter. Applying the DC field with reversed polarity eliminates the adhesion. Electroadhesion works with the aorta, cornea, lung, and cartilage. We demonstrate the use of electroadhesion to seal cuts or tears in tissues or model anionic gels. Electroadhered gel-patches provide a robust seal over openings in bovine aorta, and a gel sleeve is able to rejoin pieces of a severed gel tube. These studies raise the possibility of using electroadhesion in surgery while obviating the need for sutures. Advantages include the ability to achieve adhesion on-command, and moreover the ability to reverse this adhesion in case of error.
Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm
Authors: Stager Maria , Senner Nathan R. , Swanson David L. , Carling Matthew D. , Eddy Douglas K. , Greives Timothy J. , Cheviron Zachary A. 
Published: July 2021

AbstractPhenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individual’s relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We test this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combine field measures of thermogenic capacity for 335 individuals, 22,006 single nucleotide polymorphisms genotyped in 181 individuals, and laboratory acclimations replicated on five populations. We show thatJuncopopulations: (1) differ in their thermogenic responses to temperature variation in the field; (2) harbor allelic variation that also correlates with temperature heterogeneity; and (3) exhibit intra-specific variation in thermogenic flexibility in the laboratory that correlates with the heterogeneity of their native thermal environment. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.
Refractoriness of STING therapy is relieved by AKT inhibitor through effective vascular disruption in tumour
Authors: Jeong Seung-hwan , Yang Myung Jin , Choi Seunghyeok , Kim JungMo , Koh Gou Young 
Published: July 2021

AbstractStimulator of interferon genes (STING) promotes anti-tumour immunity by linking innate and adaptive immunity, but it remains unclear how intratumoural treatment with STING agonists yields anti-tumour effects. Here we demonstrate that intratumoural injection of the STING agonist cGAMP induces strong, rapid, and selective apoptosis of tumour endothelial cells (ECs) in implanted LLC tumour, melanoma and breast tumour, but not in spontaneous breast cancer and melanoma. In both implanted and spontaneous tumours, cGAMP greatly increases TNFα from tumour-associated myeloid cells. However, compared to spontaneous tumour ECs, implanted tumour ECs are more vulnerable to TNFα-TNFR1 signalling-mediated apoptosis, which promotes effective anti-tumour activity. The spontaneous tumour’s refractoriness to cGAMP is abolished by co-treatment with AKT 1/2 inhibitor (AKTi). Combined treatment with cGAMP and AKTi induces extensive tumour EC apoptosis, leading to extensive tumour apoptosis and marked growth suppression of the spontaneous tumour. These findings propose an advanced avenue for treating primary tumours that are refractory to single STING agonist therapy.
A generalizable and accessible approach to machine learning with global satellite imagery
Authors: Rolf Esther , Proctor Jonathan , Carleton Tamma , Bolliger Ian , Shankar Vaishaal , Ishihara Miyabi , Recht Benjamin , Hsiang Solomon 
Published: July 2021

AbstractCombining satellite imagery with machine learning (SIML) has the potential to address global challenges by remotely estimating socioeconomic and environmental conditions in data-poor regions, yet the resource requirements of SIML limit its accessibility and use. We show that a single encoding of satellite imagery can generalize across diverse prediction tasks (e.g., forest cover, house price, road length). Our method achieves accuracy competitive with deep neural networks at orders of magnitude lower computational cost, scales globally, delivers label super-resolution predictions, and facilitates characterizations of uncertainty. Since image encodings are shared across tasks, they can be centrally computed and distributed to unlimited researchers, who need only fit a linear regression to their own ground truth data in order to achieve state-of-the-art SIML performance.
Central American mountains inhibit eastern North Pacific seasonal tropical cyclone activity
Authors: Fu Dan , Chang Ping , Patricola Christina M. , Saravanan R. , Liu Xue , Beck Hylke E. 
Published: July 2021

AbstractThe eastern North Pacific (ENP) has the highest density of tropical cyclones (TCs) on earth, and yet the controls on TCs, from individual events to seasonal totals, remain poorly understood. One effect that has not been fully considered is the unique geography of the Central American mountains. Although observational studies suggest these mountains can readily fuel individual TCs through dynamical processes, here we show that these mountains indeed play the opposite role on the seasonal timescale, hindering seasonal ENP TC activity by up to 35%. We found that these mountains significantly interrupt the abundant moisture transport from the Caribbean Sea to the ENP, limiting deep convection over the open ocean area where TCs preferentially occur. This study advances our fundamental understanding of ENP TC genesis mechanisms across the weather-to-climate timescales, and also highlights the importance of topography representation in improving the ENP regional climate simulations, as well as TC seasonal predictions and future projections.
Molecular insights into the endoperoxide formation by Fe(II)/α-KG-dependent oxygenase NvfI
Authors: Mori Takahiro , Zhai Rui , Ushimaru Richiro , Matsuda Yudai , Abe Ikuro 
Published: July 2021

AbstractEndoperoxide-containing natural products are a group of compounds with structurally unique cyclized peroxide moieties. Although numerous endoperoxide-containing compounds have been isolated, the biosynthesis of the endoperoxides remains unclear. NvfI from Aspergillus novofumigatus IBT 16806 is an endoperoxidase that catalyzes the formation of fumigatonoid A in the biosynthesis of novofumigatonin. Here, we describe our structural and functional analyses of NvfI. The structural elucidation and mutagenesis studies indicate that NvfI does not utilize a tyrosyl radical in the reaction, in contrast to other characterized endoperoxidases. Further, the crystallographic analysis reveals significant conformational changes of two loops upon substrate binding, which suggests a dynamic movement of active site during the catalytic cycle. As a result, NvfI installs three oxygen atoms onto a substrate in a single enzyme turnover. Based on these results, we propose a mechanism for the NvfI-catalyzed, unique endoperoxide formation reaction to produce fumigatonoid A.
Engineering self-organized criticality in living cells
Authors: Vidiella Blai , Guillamon Antoni , Sardanyés Josep , Maull Victor , Pla Jordi , Conde Nuria , Solé Ricard 
Published: July 2021

AbstractComplex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic display bursting dynamics consistent with a critical state between order and disorder. Living close to the critical point has adaptive advantages and it has been conjectured that evolution could select these critical states. Is this the case of living cells? A system can poise itself close to the critical point by means of the so-called self-organized criticality (SOC). In this paper we present an engineered gene network displaying SOC behaviour. This is achieved by exploiting the saturation of the proteolytic degradation machinery in E. coli cells by means of a negative feedback loop that reduces congestion. Our critical motif is built from a two-gene circuit, where SOC can be successfully implemented. The potential implications for both cellular dynamics and behaviour are discussed.
The tectonigral pathway regulates appetitive locomotion in predatory hunting in mice
Authors: Huang Meizhu , Li Dapeng , Cheng Xinyu , Pei Qing , Xie Zhiyong , Gu Huating , Zhang Xuerong , Chen Zijun , Liu Aixue , Wang Yi , Sun Fangmiao , Li Yulong , Zhang Jiayi , He Miao , Xie Yuan , Zhang Fan , Qi Xiangbing , Shang Congping , Cao Peng 
Published: July 2021

AbstractAppetitive locomotion is essential for animals to approach rewards, such as food and prey. The neuronal circuitry controlling appetitive locomotion is unclear. In a goal-directed behavior—predatory hunting, we show an excitatory brain circuit from the superior colliculus (SC) to the substantia nigra pars compacta (SNc) to enhance appetitive locomotion in mice. This tectonigral pathway transmits locomotion-speed signals to dopamine neurons and triggers dopamine release in the dorsal striatum. Synaptic inactivation of this pathway impairs appetitive locomotion but not defensive locomotion. Conversely, activation of this pathway increases the speed and frequency of approach during predatory hunting, an effect that depends on the activities of SNc dopamine neurons. Together, these data reveal that the SC regulates locomotion-speed signals to SNc dopamine neurons to enhance appetitive locomotion in mice.
A cost-effective and humidity-tolerant chloride solid electrolyte for lithium batteries
Authors: Wang Kai , Ren Qingyong , Gu Zhenqi , Duan Chaomin , Wang Jinzhu , Zhu Feng , Fu Yuanyuan , Hao Jipeng , Zhu Jinfeng , He Lunhua , Wang Chin-Wei , Lu Yingying , Ma Jie , Ma Cheng 
Published: July 2021

AbstractLi-ion-conducting chloride solid electrolytes receive considerable attention due to their physicochemical characteristics such as high ionic conductivity, deformability and oxidative stability. However, the raw materials are expensive, and large-scale use of this class of inorganic superionic conductors seems unlikely. Here, a cost-effective chloride solid electrolyte, Li2ZrCl6, is reported. Its raw materials are several orders of magnitude cheaper than those for the state-of-the-art chloride solid electrolytes, but high ionic conductivity (0.81 mS cm–1 at room temperature), deformability, and compatibility with 4V-class cathodes are still simultaneously achieved in Li2ZrCl6. Moreover, Li2ZrCl6 demonstrates a humidity tolerance with no sign of moisture uptake or conductivity degradation after exposure to an atmosphere with 5% relative humidity. By combining Li2ZrCl6 with the Li-In anode and the single-crystal LiNi0.8Mn0.1Co0.1O2 cathode, we report a room-temperature all-solid-state cell with a stable specific capacity of about 150 mAh g–1 for 200 cycles at 200 mA g–1.
Single-atom Pt-I3 sites on all-inorganic Cs2SnI6 perovskite for efficient photocatalytic hydrogen production
Authors: Zhou Peng , Chen Hui , Chao Yuguang , Zhang Qinghua , Zhang Weiyu , Lv Fan , Gu Lin , Zhao Qiang , Wang Ning , Wang Jinshu , Guo Shaojun 
Published: July 2021

AbstractOrganic-inorganic lead halide perovskites are a new class of semiconductor materials with great potential in photocatalytic hydrogen production, however, their development is greatly plagued by their low photocatalytic activity, instability of organic component and lead toxicity in particular. Herein, we report an anti-dissolution environmentally friendly Cs2SnI6 perovskite anchored with a new class of atomically dispersed Pt-I3 species (PtSA/Cs2SnI6) for achieving the highly efficient photocatalytic hydrogen production in HI aqueous solution at room temperature. Particularly, we discover that Cs2SnI6 in PtSA/Cs2SnI6 has a greatly enhanced tolerance towards HI aqueous solution, which is very important for achieving excellent photocatalytic stability in perovskite-based HI splitting system. Remarkably, the PtSA/Cs2SnI6 catalyst shows a superb photocatalytic activity for hydrogen production with a record turnover frequency of 70.6 h−1per Pt, about 176.5 times greater than that of Pt nanoparticles supported Cs2SnI6 perovskite, along with superior cycling durability. Charge-carrier dynamics studies in combination with theory calculations reveal that the dramatically boosted photocatalytic performance on PtSA/Cs2SnI6 originates from both unique coordination structure and electronic property of Pt-I3 sites, and strong metal-support interaction effect that can not only greatly promote the charge separation and transfer, but also substantially reduce the energy barrier for hydrogen production. This work opens a new way for stimulating more research on perovskite composite materials for efficient hydrogen production.
Experimental observation of topological Z2 exciton-polaritons in transition metal dichalcogenide monolayers
Authors: Li Mengyao , Sinev Ivan , Benimetskiy Fedor , Ivanova Tatyana , Khestanova Ekaterina , Kiriushechkina Svetlana , Vakulenko Anton , Guddala Sriram , Skolnick Maurice , Menon Vinod M. , Krizhanovskii Dmitry , Alù Andrea , Samusev Anton , Khanikaev Alexander B. 
Published: July 2021

AbstractThe rise of quantum science and technologies motivates photonics research to seek new platforms with strong light-matter interactions to facilitate quantum behaviors at moderate light intensities. Topological polaritons (TPs) offer an ideal platform in this context, with unique properties stemming from resilient topological states of light strongly coupled with matter. Here we explore polaritonic metasurfaces based on 2D transition metal dichalcogenides (TMDs) as a promising platform for topological polaritonics. We show that the strong coupling between topological photonic modes of the metasurface and excitons in TMDs yields a topological polaritonic Z2 phase. We experimentally confirm the emergence of one-way spin-polarized edge TPs in metasurfaces integrating MoSe2 and WSe2. Combined with the valley polarization in TMD monolayers, the proposed system enables an approach to engage the photonic angular momentum and valley and spin of excitons, offering a promising platform for photonic/solid-state interfaces for valleytronics and spintronics.