bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient electrogenic survival metabolism of β -proteobacterial ammonia oxidizers for oxygen deficiency
Authors: Gülay Arda , Fournier Greg , Smets Barth F. , Girguis Peter R. 
Published: June 2022

SUMMARYOxygen availability is critical for microbes as some are obligatorily dependent on oxygen for energy conservation. However, aerobic microbes that live in environments with varying oxygen concentrations experience pressures over evolutionary time, selecting alternative energy metabolisms that relax the dependence on oxygen. One such capacity is extracellular electron transfer (or EET), which is the ability to transfer electrons from central metabolism to extracellular oxidants such as iron and manganese oxides. We posit that the β-proteobacterial ammonia-oxidizing bacteria, highly specialized lineages heretofore recognized as strict aerobes, can be capable of EET as they have been constantly observed in oxygen-limiting and depleted environments. Here, we show that a strictly aerobic ammonia-oxidizer, Nitrosomonas communis, utilized a poised electrode to maintain metabolic activity in anoxic conditions. The presence and activity of multi-heme cytochromes suggested that direct electron transfer is the mechanism underlying EET. Molecular clock models suggest that the ancestors of β-proteobacterial ammonia oxidizers appeared after the oxygenation of Earth when the oxygen levels were >10-4pO2 (PAL), suggesting their aerobic origins. Phylogenetic reconciliations of gene and species trees show that the multi-heme c-type EET proteins in Nitrosomonas and Nitrosospira were acquired by gene transfer from β-proteobacteria during oxygen scarcity. The preservation of EET metabolism over billions of years under fluctuating oxygen levels and aspects of EET physiology in β-proteobacterial ammonia oxidizers might explain how they have been coped with oxygen stress and survived under oxygen deprivation.SIGNIFICANCEMetabolic versatility can permit typically aerobic microbes to survive in anaerobic conditions when oxygen is deficient as a terminal electron acceptor. This article demonstrates a previously unidentified anaerobic extracellular electron transfer metabolism that operates in aerobic β–proteobacterial ammonia oxidizers and reconstructs the evolutionary history of this metabolism, linking it to the early history of Earth’s oxygenation. Our approach contributes to the understanding of metabolisms in the N-cycle and their evolution on Earth, as well as how aerobic microbes manage to retain energy generation under oxygen-limiting or depleted conditions.AUTHOR CONTRIBUTIONSAG designed the physiological research with PRG and the phylogenetic research with GF; AG performed the research, AG analyzed the data with PRG and GF. AG wrote the paper, and all authors edited and approved the manuscript.
Trajectories for the evolution of bacterial CO2-concentrating mechanisms
Authors: Flamholz Avi I. , Dugan Eli , Panich Justin , Desmarais John J. , Oltrogge Luke M. , Fischer Woodward W. , Singer Steven W. , Savage David F. 
Published: June 2022

AbstractCyanobacteria rely on CO2 concentrating mechanisms (CCMs) that depend on ≈15 genes to produce two protein complexes: an inorganic carbon (Ci) transporter and a 100+ nm carboxysome compartment that encapsulates rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting CCM components prohibit growth in today’s atmosphere (0.04% CO2), indicating that CCMs evolved to cope with declining environmental CO2. Indeed, geochemical data and models indicate that atmospheric CO2 has been generally decreasing from high concentrations over the last ≈3.5 billion years. We used a synthetic reconstitution of a bacterial CCM in E. coli to study the co-evolution of CCMs with atmospheric CO2. We constructed strains expressing putative ancestors of modern CCMs — strains lacking one or more CCM components — and evaluated their growth in a variety of CO2 concentrations. Partial forms expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%); we observed similar phenotypes in genetic studies of two autotrophic bacteria, H. neapolitanus and C. necator. To explain how partial CCMs improve growth, we advance a model of co-limitation of autotrophic growth by CO2 and HCO3-, as both are required to produce biomass. Our model and results delineated a viable trajectory for bacterial CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CAs or Ci uptake genes, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.SignificanceThe greenhouse gas content of the ancient atmosphere is estimated using models and measurements of geochemical proxies. Some inferred high ancient CO2 levels using models of biological CO2 fixation to interpret the C isotopes found in preserved organic matter. Others argued that elevated CO2 could reconcile a faint young Sun with evidence for liquid water on Earth. We took a complementary “synthetic biological” approach to understanding the composition of the ancient atmosphere by studying present-day bacteria engineered to resemble ancient autotrophs. By showing that it is simpler to rationalize the emergence of modern bacterial autotrophs if CO2 was once high, these investigations provided independent evidence for the view that CO2 concentrations were significantly elevated in the atmosphere of early Earth.
Response of sugarcane rhizosphere soil fungal communities on a temporal gradient to changes in critical growth periods
Authors: Yuan Zhaonian , Liu Qiang , Pang Ziqin , Liu Yueming , Nyumah Fallah , Hu Chaohua , Lin Wenxiong 
Published: June 2022

ABSTRACTUnderstanding the normal variation of the sugarcane rhizosphere fungal microbiota throughout its life cycle is essential for the development of agricultural practices for fungal diseases (e.g., sugarcane tip rot, sugarcane red rot, and sugarcane smut) and ecological health associated with the microbiota. Therefore, we performed high-throughput sequencing of 18S rDNA of soil samples using the Illumina sequencing platform for correlation analysis of sugarcane rhizosphere microbiota time series, covering information from 84 samples in four growth periods. The results revealed that the sugarcane rhizosphere fungi possessed the maximum fungal richness in July (Tillering). Rhizosphere fungi are closely associated with sugarcane growth, including Ascomycota, Basidiomycota, and Ochrophyta showed high abundance in a stage-specific manner. Through the Manhattan plots, 11 fungal genera were found to show a decreasing trend throughout the sugarcane growth period, and two fungal genera were significantly enriched at three stages of sugarcane growth (p < 0.05) including Pseudallescheria and Nectriaceae. In addition, soil pH, soil temperature (Tem), total nitrogen (TN) and total potassium (TP) were important drivers of fungal community structure at different stages of sugarcane growth. Using structural equation modeling (SEM) found that sugarcane disease status showed a significant and strong negative effect with selected soil properties, suggesting that poor soil may increase the likelihood of sugarcane disease. In addition changes in sugarcane rhizosphere community structure over time were mainly influenced by stochastic factors, but the contribution decreased to the lowest value after the sugarcane root adaptation system was stabilized (Maturity).IMPORTANCERhizosphere microbes are closely related to plant growth, and more studies have shown that the rhizosphere fungal microbial community has an important influence on plant health and growth status. However, little is known about the response of the rhizosphere fungal community to plant growth during the critical plant reproductive period. In this study, we analyzed the important response of the rhizosphere fungal community of sugarcane through the pattern of abundance changes in its critical growth nodes by various methods to investigate the subtle changes in the assembly of the rhizosphere fungal community with the growth of sugarcane. Our work provides innovative ideas for the prevention of soil-borne diseases in plants and also provides a solid basis for the development of microbial models of crops rhizosphere soil.
Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome
Authors: Hassan Asem , Byju Sandra , Freitas Frederico Campos , Roc Claude , Pender Nisaa , Nguyen Kien , Kimbrough Evelyn M. , Mattingly Jacob , Gonzalez Ruben L. , de Oliveira Ronaldo Junio , Dunham Christine M. , Whitford Paul C. 
Published: June 2022

AbstractProtein synthesis by the ribosome involves large-scale rearrangements of the “small” subunit (SSU; ∼1 MDa), which include inter- and intra-subunit rotational motions. With more than 1000 structures of ribosomes and ribosomal subunits now publicly available, it is becoming increasingly difficult to design precise experiments that are based on a comprehensive analysis of all known rotation states. To overcome this limitation, we present the Ribosome Angle Decomposition (RAD) method, where the orientation of each small subunit head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. To demonstrate the utility of the accompanying software (RADtool) we applied it to all published ribosome and mitoribosome structures. This identified and analyzed 1077 fully-assembled ribosome complexes, as well as 280 isolated small subunits from 48 organisms. The RAD approach quantitatively distinguishes between previously described qualitative rotational features, determines when rotation-only descriptions are insufficient, and shows that tilt-like rearrangements of the SSU head and body are pervasive in both prokaryotic and eukaryotic ribosomes. Together, the presented database and technique provide a robust platform for systematically analyzing, visualizing, and comparing subunit orientations of ribosomes from all kingdoms of life. Accordingly, the RAD resource establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can precisely interrogate the dynamics of this prototypical molecular machine.
Navigation task and action space drive the emergence of egocentric and allocentric spatial representations
Authors: Vijayabaskaran Sandhiya , Cheng Sen 
Published: June 2022

AbstractIn general, strategies for spatial navigation could employ one of two spatial reference frames: egocentric or allocentric. Notwithstanding intuitive explanations, it remains unclear however under what circumstances one strategy is chosen over another, and how neural representations should be related to the chosen strategy. Here, we first use a deep reinforcement learning model to investigate whether a particular type of navigation strategy arises spontaneously during spatial learning without imposing a bias onto the model. We then examine the spatial representations that emerge in the network to support navigation. To this end, we study two tasks that are ethologically valid for mammals – guidance, where the agent has to navigate to a goal location fixed in allocentric space, and aiming, where the agent navigates to a visible cue. We find that when both navigation strategies are available to the agent, the solutions it develops for guidance and aiming are heavily biased towards the allocentric or the egocentric strategy, respectively, as one might expect. Nevertheless, the agent can learn both tasks using either type of strategy. Furthermore, we find that place-cell-like allocentric representations emerge preferentially in guidance when using an allocentric strategy, whereas egocentric vector representations emerge when using an egocentric strategy in aiming. We thus find that alongside the type of navigational strategy, the nature of the task plays a pivotal role in the type of spatial representations that emerge.
Rotations improve the diversity of rhizosphere soil bacterial communities, enzyme activities and tomato yield
Authors: Feng Cui , Yi Zhengwei , Qian Wei , Liu Huiying , Jiang Xiaosan 
Published: June 2022

AbstractThe use of rotations is an effective strategy to control crop diseases and improve plant health. The soil bacterial communities in the rhizosphere are highly important for maintaining soil productivity. However, the composition and structure of soil bacterial communities in the rotations of vegetable crops remain unclear. In this study, we explored the bacterial diversity and community structure of the tomato rhizosphere, including enzyme activities, yield, and fruit quality, under three different cropping systems: tomato-tomato continuous cropping (TY1), eggplant-tomato (S. melongena) rotation (TY2) and arrowhead-tomato (Sagittaria trifolia-Solanum lycopersicum) rotation (TY3). The composition and diversity of the rhizosphere bacterial communities differed significantly. The diversity was more in the TY2 and TY3 treatments than those in the TY1 treatment. Chujaibacter and Rhodanobacter were two predominant and unique strains detected only in TY1, while the relative abundances of Curvibacter and Luteimonas were the highest in TY2 and TY3, respectively. Moreover, Lysobacterium was a relatively abundant type of biocontrol bacterium found only in the TY3 treatment, which could contribute to alleviating the obstacle of tomato continuous cropping. Compared with the TY1 treatment, the activities of catalase were significantly higher in the TY2 and TY3 treatments. In addition, compared with TY1, the TY2 and TY3 plots increased the following parameters: tomato yields by 24–46%, total soluble solids by 37-93%, total organic acid by 10-15.7% and soluble protein by 10-21%, while the content of nitrate was significantly reduced by 23%. Altogether, compared with the tomato monoculture, the rotations of tomato with eggplant and arrowhead shifted the rhizosphere bacterial communities and improved the yield and quality of the vegetables. Moreover, a tomato rotation, particularly with arrowhead, was an effective way to alleviate the obstacles of continuous cropping.
Identification of Circular Dorsal Ruffles as Signal Platforms for the AKT pathways in Glomerular Podocytes
Authors: Hua Rui , Torres Mauricio , Wei Jinzi , Sun Xiaowei , Wang Li , Inoki Ken , Yoshida Sei 
Published: June 2022

ABSTRACTCircular dorsal ruffles (CDRs) are rounded membrane ruffles induced by growth factors to function as precursors of the large-scale endocytosis called macropinocytosis. In cell line systems, CDR/macropinocytosis regulate the AKT-mTORC1 pathway, a canonical growth factor signaling. However, it is not known if this mechanism occurs in tissues. Here, utilizing ultra-high-resolution scanning electron microscopy, we report that CDRs are expressed in glomerular podocytes ex vivo and in vivo. Biochemical and imaging analysis revealed that AKT phosphorylation is localized to CDRs upstream of mTORC1 activation in podocyte cell line and isolated glomeruli, indicating that CDRs function as signal platforms for AKT-mTORC1 pathway in podocytes to maintain the kidney function. Because mTORC1 has critical roles in the podocyte metabolism and the aberrant activation of mTORC1 triggers podocytopathies, these results suggest that targeting CDR formation would be a potential therapeutic approach for the diseases.
ARHGAP17 regulates the spatiotemporal activity of Cdc42 at invadopodia
Authors: Kreider-Letterman Gabriel , Castillo Abel , Mahlandt Eike K. , Goedhart Joachim , Rabino Agustin , Goicoechea Silvia , Garcia-Mata Rafael 
Published: June 2022

AbstractInvadopodia formation is regulated by Rho GTPases. However, the molecular mechanisms that control Rho GTPase signaling at invadopodia remain poorly understood. Here, we have identified ARHGAP17, a Cdc42-specific RhoGAP, as a key regulator of invadopodia in breast cancer cells and by RhoGAPs characterized a novel ARHGAP17-mediated signaling pathway that controls the spatiotemporal activity of Cdc42 during invadopodia turnover. Our results show that during invadopodia assembly, ARHGAP17 localizes to the invadopodia ring and restricts the activity of Cdc42 to the invadopodia core, where it promotes invadopodia growth. Invadopodia disassembly starts when ARHGAP17 translocates from the invadopodia ring to the core, in a process that is mediated by its interaction with the Cdc42 effector CIP4. Once at the core, ARHGAP17 inactivates Cdc42 to promote invadopodia disassembly. Our results in invadopodia provide new insights on the coordinated transition between the activation and inactivation of Rho GTPases.
Development and magnetic field measurement of a 0.5-m-long superconducting undulator at IHEP
Authors: Wei Junhao , Li Yuhui , Yang Xiangchen , Chen Zilin , Zhang Xiangzhen , Bian Xiaojuan 
Published: June 2022

Undulators are important devices for accelerator-based light sources whose magnetic field quality determines the photon beam performance. Superconducting-type undulators have been developing rapidly in recent years around the world. The insertion device group at the Institute of High Energy Physics (IHEP) in China started an R&D project to develop prototypes of superconducting undulators (SCUs). A half-meter-long planar SCU has been produced recently. The SCU was designed based on the simulation program OPERA-3D giving a period length of 15 mm and a gap of 7 mm. This prototype was manufactured and fabricated precisely, and was then tested by vertically submerging in liquid helium in a Dewar. After quench training several times, the maximum current in the main coils reached 480 A. The magnetic field was measured by Hall probes mounted on a sledge in the middle of the undulator gap. The peak magnetic field reached 1 T. The measurement results indicate that correction coils with suitable current can not only optimize the magnetic first and second integrals but also reduce the phase error, which is expected by design.
Digital technology in agriculture: a review of issues, applications and methodologies
Authors: Du Xiaoxue , Wang Xuejian , Hatzenbuehler Patrick 
Published: June 2022

PurposeThe purpose of this paper is to show the impact of digital agriculture on food supply chain, research trend, emphasis and implications for future research.Design/methodology/approachThe paper analyzes how the digital technology reshapes the production, assembly, transaction, retail and logistics. Impact from each main technological progress is discussed.FindingsFirst, digital agriculture develops quickly and changes all parts of the food supply chain. Second, while many technological progresses show their impacts in agriculture and food sector, e-commerce and progress of artificial intelligence show its comprehensive impact on the argi-food sector.Originality/valueThe paper shows the technological trend and progress in food and agriculture sector. Researchers focusing on agricultural economics and agribusiness should pay attention to recent developments in the real world, know the recent developments from other disciplines, get more data for empirical research and show the impact of digital agriculture on consumer's preference and social welfare.
Negative spillover of moral irresponsibility into anti-brand behaviors: the role of moral emotion and disengagement in ethical and social transgressions
Authors: Youn Song-yi 
Published: June 2022

Purpose
As one of the largest industries in the global economy, the fashion industry has emphasized the symbolic and aspirational features of its products while maximizing the efficiency of its manufacturing processes. However, the labor-intensive and competitive nature of the industry has meant that brand moral transgressions often occur. This study aims to understand the role of moral emotions and concerns (i.e. perceived spillover) caused by different moral transgressions and explain consumer anti-brand behaviors (i.e. negative word of mouth [WOM] and patronage cessation).

Design/methodology/approach
Structural equation modeling was conducted to examine group differences (ethical vs social transgressions) in Study 1 (n = 584). Also, the moderation effect of moral disengagement was examined in Study 2 (n = 324).

Findings
The results indicate that, for ethical transgressions, both moral emotions and perceived spillovers explain negative behaviors while moral emotions alone explain negative WOM on social media for social transgressions. Additionally, for social transgressions, the results of Study 2 indicate a negative interaction effect of moral emotions and moral disengagement on anti-brand behavior of patronage cessation.

Originality/value
Based on the literature’s theoretical approach to moral crises, this paper examines the emotional and cognitive reactions of consumers to the fashion industry’s moral transgressions.
The effect of methyl donor supplementation on body composition, homocysteine, lipid profile and appetite regulatory hormones in overweight and obese adults: a randomized placebo-controlled trial
Authors: Ranjbar Zahedani Maryam , Eftekhari Mohammad Hassan , Nouri Mehran , Alipour Shohreh , Hassanzadeh Jafar , Fardaei Majid 
Published: June 2022

Purpose
The purpose of this study was to evaluate the effects of methyl donor supplementation on anthropometric indices, body composition, glycemic control, lipid profile, homocysteine and appetite regulatory hormones in overweight and obese subjects.

Design/methodology/approach
This randomized double-blind placebo-controlled trial was conducted on overweight and obese subjects in Shiraz, Iran, in 2018. The 25 participants in each intervention and control group were required to take methyl donor supplement and placebo, respectively, for eight weeks. A variety of measurements was collected at baseline and the end of the study. The data were analyzed using SPSS 21 software.

Findings
The results indicated a significant reduction in weight, body mass index, body fat and waist and hip circumference (p < 0.001 for all parameters) within both groups and a significant improvement in skeletal muscle (p = 0.005), fat-free mass (p = 0.006), visceral fat area (p < 0.001) and body cell mass (p = 0.004) in the intervention group. Also, the results showed a significant difference between the two groups regarding serum homocysteine concentration at the end of the intervention (p < 0.001).

Originality/value
The results demonstrated that methyl donor supplementation might have effects on the improvement of anthropometric indices, body composition, glycemic and lipid profile status and appetite regulatory hormones among obese and overweight individuals. These effects might be attributed to their roles in energy metabolism, protein synthesis and epigenetics regulation.