bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formamide-based production of amines by metabolically engineering Corynebacterium glutamicum
Authors: Schwardmann Lynn S. , Wu Tong , Dransfeld Aron K. , Lindner Steffen N. , Wendisch Volker F. 
Published: May 2023

Abstract
Formamide is rarely used as nitrogen source
by microorganisms. Therefore, formamide and formamidase have been used as protection system to allow for growth under non-sterile conditions and for non-sterile production of acetoin, a product lacking nitrogen. Here, we equipped Corynebacterium glutamicum, a renowned workhorse for industrial amino acid production for 60 years, with formamidase from Helicobacter pylori 26695, enabling growth with formamide as sole nitrogen source. Thereupon, the formamide/formamidase system was exploited for efficient formamide-based production of the nitrogenous compounds L-glutamate, L-lysine, N-methylphenylalanine, and dipicolinic acid by transfer of the formamide/formamidase system to established producer strains. Stable isotope labeling verified the incorporation of nitrogen from formamide into biomass and the representative product L-lysine. Moreover, we showed ammonium leakage during formamidase-based access of formamide to be exploitable to support growth of formamidase-deficient C. glutamicum in co-cultivation and demonstrated that efficient utilization of formamide as sole nitrogen source benefitted from overexpression of formate dehydrogenase.

Key points
• C. glutamicum was engineered to access formamide.
• Formamide-based production of nitrogenous compounds was established.
• Nitrogen cross-feeding supported growth of a formamidase-negative strain.
Effects of different fracture parameters on microseisms induced by hydraulic fracturing
Authors: Shan Kun , Zheng Yanhao , Zhang Yanjun , Shan Zhigang , Li Zhihai 
Published: May 2023

AbstractThe microseism induced by hydraulic fracturing is of great significance to the development of geothermal reservoirs and the site selection of geothermal systems. In this study, taking geothermal field data from Qiabuqia as a geological reference, several models are developed for hydraulic fracturing simulations based on the models included in the commercial FracMan™ software suit. A series of numerical simulations are carried out to explore the effects of different fracture parameters, including the existence of faults, in-situ stress state, fracture occurrence, and fracture distribution near faults, on the induced microseisms. The results show that during hydraulic fracturing, the existence of faults does affect the propagation direction of the newly generated fractures, causing the fractures to extend toward the fault. The faults also increase the magnitude of microseismic events and make the distribution of microseismic events farther. Under three different in-situ stress states, the magnitudes of induced microseisms and the distance between microseismic events and injection wells are different, mainly due to the different forms of energy release. The total energy of induced microseisms under the reverse faulting stress state (RF) is the largest. Under the normal faulting stress state (NF), the number of microseismic events is the least, with only 28, and these microseismic events are concentrated near the well, with the farthest distribution distance of only 150 m. The fracture occurrence has a significant effect on induced microseisms, mainly affecting the number and distribution range of induced microseisms. With the same number of fractures, as the fracture concentration to the fault increases, both the maximum magnitude and the farthest distribution distance of the induced microseisms increase.
137Cs and isotopic ratios of Pu and U in lichens and mosses from Russian Arctic areas
Authors: Dutheil Paul , Paatero Jussi , Rodushkin Ilia , Sundström Timo , Leppänen Ari-Pekka , Salminen-Paatero Susanna 
Published: May 2023

Abstract
Knowledge of past anthropogenic sources of radionuclide contamination in Russian Arctic areas is important to assess the radioecological situation of these less-studied regions. Therefore, we investigated the sources of radionuclide contamination in Russian Arctic in the 1990s. Lichen and moss samples were collected from 1993 to 1996 in Kola Peninsula, Franz Josef Land, and few other locations. The activity concentration of 137Cs was determined from the archived samples by gamma spectrometry in 2020. After radiochemical separation of Pu and U isotopes from the lichens and mosses, mass ratios 240Pu/239Pu, 234U/238U, 235U/238U, and 236U/238U were determined by mass spectrometry. 137Cs activity concentrations at the sampling date were found to vary from 3.1 ± 1.4 (Inari, Finnish-Russian border) to 303 ± 7 (Kola Peninsula) Bq/kg. The ranges of isotopic ratios were 0.0592 ± 0.0007 to 0.253 ± 0.082 for 240Pu/239Pu, (4.89 ± 3.91) × 10−5 to (6.86 ± 0.04) × 10−5 for 234U/238U, 0.0072104(21) to 0.007376(41) for 235U/238U, and from below 1 × 10−7 to (2.65 ± 0.19) × 10−6 for 236U/238U, respectively. Based on the measured isotopic ratios and characteristic isotopic ratios of known contamination sources, the main Pu and U sources in the sampled lichens and mosses are global fallout, the Chernobyl accident, and possibly local nuclear activities. These results contribute to further understanding of past nuclear events and resulting nuclear contamination in Russian Arctic terrestrial areas.
Identifying Novel Drug Targets for Epilepsy Through a Brain Transcriptome-Wide Association Study and Protein-Wide Association Study with Chemical-Gene-Interaction Analysis
Authors: Lu Mengnan , Feng Ruoyang , Zhang Chenglin , Xiao Yanfeng , Yin Chunyan 
Published: May 2023

AbstractEpilepsy is a severe neurological condition affecting 50–65 million individuals worldwide that can lead to brain damage. Nevertheless, the etiology of epilepsy remains poorly understood. Meta-analyses of genome-wide association studies involving 15,212 epilepsy cases and 29,677 controls of the ILAE Consortium cohort were used to conduct transcriptome-wide association studies (TWAS) and protein-wide association studies (PWAS). Furthermore, a protein-protein interaction (PPI) network was generated using the STRING database, and significant epilepsy-susceptible genes were verified using chip data. Chemical-related gene set enrichment analysis (CGSEA) was performed to determine novel drug targets for epilepsy. TWAS analysis identified 21,170 genes, of which 58 were significant (TWASfdr < 0.05) in ten brain regions, and 16 differentially expressed genes were verified based on mRNA expression profiles. The PWAS identified 2249 genes, of which 2 were significant (PWASfdr < 0.05). Through chemical-gene set enrichment analysis, 287 environmental chemicals associated with epilepsy were identified. We identified five significant genes (WIPF1, IQSEC1, JAM2, ICAM3, and ZNF143) that had causal relationships with epilepsy. CGSEA identified 159 chemicals that were significantly correlated with epilepsy (Pcgsea < 0.05), such as pentobarbital, ketone bodies, and polychlorinated biphenyl. In summary, we performed TWAS, PWAS (for genetic factors), and CGSEA (for environmental factors) analyses and identified several epilepsy-associated genes and chemicals. The results of this study will contribute to our understanding of genetic and environmental factors for epilepsy and may predict novel drug targets.
A biologically inspired decision-making system for the autonomous adaptive behavior of social robots
Authors: Maroto-Gómez Marcos , Castro-González Álvaro , Malfaz María , Salichs Miguel Ángel 
Published: May 2023

AbstractThe decisions made by social robots while they fulfill their tasks have a strong influence on their performance. In these contexts, autonomous social robots must exhibit adaptive and social-based behavior to make appropriate decisions and operate correctly in complex and dynamic scenarios. This paper presents a Decision-Making System for social robots working on long-term interactions like cognitive stimulation or entertainment. The Decision-making System employs the robot’s sensors, user information, and a biologically inspired module to replicate how human behavior emerges in the robot. Besides, the system personalizes the interaction to maintain the users’ engagement while adapting to their features and preferences, overcoming possible interaction limitations. The system evaluation was in terms of usability, performance metrics, and user perceptions. We used the Mini social robot as the device where we integrated the architecture and carried out the experimentation. The usability evaluation consisted of 30 participants interacting with the autonomous robot in 30 min sessions. Then, 19 participants evaluated their perceptions of robot attributes of the Godspeed questionnaire by playing with the robot in 30 min sessions. The participants rated the Decision-making System with excellent usability (81.08 out of 100 points), perceiving the robot as intelligent (4.28 out of 5), animated (4.07 out of 5), and likable (4.16 out of 5). However, they also rated Mini as unsafe (security perceived as 3.15 out of 5), probably because users could not influence the robot’s decisions.
All-Polymer Solar Cells and Photodetectors with Improved Stability Enabled by Terpolymers Containing Antioxidant Side Chains
Authors: Zhang Chunyang , Song Ao , Huang Qiri , Cao Yunhao , Zhong Zuiyi , Liang Youcai , Zhang Kai , Liu Chunchen , Huang Fei , Cao Yong 
Published: May 2023

AbstractIt is of vital importance to improve the long-term and photostability of organic photovoltaics, including organic solar cells (OSCs) and organic photodetectors (OPDs), for their ultimate industrialization. Herein, two series of terpolymers featuring with an antioxidant butylated hydroxytoluene (BHT)-terminated side chain, PTzBI-EHp-BTBHTx and N2200-BTBHTx (x = 0.05, 0.1, 0.2), are designed and synthesized. It was found that incorporating appropriate ratio of benzothiadiazole (BT) with BHT side chains on the conjugated backbone would induce negligible effect on the molecular weight, absorption spectra and energy levels of polymers, however, which would obviously enhance the photostability of these polymers. Consequently, all-polymer solar cells (all-PSCs) and photodetectors were fabricated, and the all-PSC based on PTzBI-EHp-BTBHT0.05: N2200 realized an optimal power conversion efficiency (PCE) approaching ~ 10%, outperforming the device based on pristine PTzBI-EHp: N2200. Impressively, the all-PSCs based on BHT-featuring terpolymers displayed alleviated PCEs degradation under continuous irradiation for 300 h due to the improved morphological and photostability of active layers. The OPDs based on BHT-featuring terpolymers achieved a lower dark current at − 0.1 bias, which could be stabilized even after irradiation over 400 h. This study provides a feasible approach to develop terpolymers with antioxidant efficacy for improving the lifetime of OSCs and OPDs.
Response of Salmonella enterica serovar Typhimurium to alginate oligosaccharides fermented with fecal inoculum: integrated transcriptomic and metabolomic analyses
Authors: Cheng Jiaying , Xiao Mengshi , Ren Xinmiao , Secundo Francesco , Yu Ying , Nan Shihao , Chen Weimiao , Zhu Changliang , Kong Qing , Huang Youtao , Fu Xiaodan , Mou Haijin 
Published: May 2023

Abstract
Alginate oligosaccharides (AOS), extracted from marine brown algae, are a common functional feed additive; however, it remains unclear whether they modulate the gut microbiota and microbial metabolites. The response of Salmonella enterica serovar Typhimurium, a common poultry pathogen, to AOS fermented with chicken fecal inocula was investigated using metabolomic and transcriptomic analyses. Single-strain cultivation tests showed that AOS did not directly inhibit the growth of S. Typhimurium. However, when AOS were fermented by chicken fecal microbiota, the supernatant of fermented AOS (F-AOS) exhibited remarkable antibacterial activity against S. Typhimurium, decreasing the abundance ratio of S. Typhimurium in the fecal microbiota from 18.94 to 2.94%. Transcriptomic analyses showed that the 855 differentially expressed genes induced by F-AOS were mainly enriched in porphyrin and chlorophyll metabolism, oxidative phosphorylation, and Salmonella infection-related pathways. RT-qPCR confirmed that F-AOS downregulated key genes involved in flagellar assembly and the type III secretory system of S. Typhimurium, indicating metabolites in F-AOS can influence the growth and metabolism of S. Typhimurium. Metabolomic analyses showed that 205 microbial metabolites were significantly altered in F-AOS. Among them, the increase in indolelactic acid and 3-indolepropionic acid levels were further confirmed using HPLC. This study provides a new perspective for the application of AOS as a feed additive against pathogenic intestinal bacteria.
Variation in eye lenses of two new Late Devonian phacopid trilobites from western Junggar, NW China
Authors: Zong Rui-Wen 
Published: May 2023

AbstractThe suborder Phacopina, characterized by schizochroal eyes, is among the most common groups of trilobites in Devonian strata. The marine sediments of the Famennian in western Junggar, Xinjiang, contain abundant low-disparity phacopids, which have previously been designated toOmegops accipitrinus mobilis,Phacops circumspectans tuberculosus, andOmegops corneliuson the basis of small numbers of poorly preserved specimens. In this study, these phacopids were identified as two new species ofOmegops,O. honggulelengensisn. sp. andO. xiangin. sp., on the basis of nearly 200 well-preserved specimens. The intraspecific variations of eye lenses of these specimens were quantitatively analyzed. On the basis of differences in the total number, number of dorsoventral files, and arrangement of the eye lenses, the absence of lenses in the middle part of the visual surface, and asymmetry of the number and/or arrangement of lenses in the two eyes, it was concluded that the reasons for intraspecific variation in eye lenses of Late DevonianOmegopsfrom western Junggar were different from previously described factors but were likely genetic or embryological malfunctions or abnormalities caused by pathological conditions. Diversity of lenses in the schizochroal eyes shows that the number and arrangement of eye lenses was not stable in Phacopina. Therefore, many specimens are needed for quantitative study to determine the true characteristics of the number or arrangement of eye lenses when these features are used in the systematic taxonomy of Phacopina.UUID:http://zoobank.org/6bd14390-05fe-45ad-8eeb-3bf397a46a68
Symbiotic Zooxanthellae Drive the δ13C Changes of Tridacna gigas Shell in the Southern South China Sea
Authors: Ma Xiaolin , Yan Hong , Ma Wentao , Jin Xiaobo , Zhang Hongrui , Dang Haowen , Zhang Yuehuan 
Published: May 2023

AbstractThe carbon isotope (δ13C) in marine biogenic carbonate is a valuable tool for comprehending the marine carbon cycle. However, the absence of monthly resolved δ13C records before the instrumental era (since 1850) hinders us to fully understand the global carbon cycle. In this study, we present a δ13C record from a modern Tridacna gigas shell (δ13Cshell) collected from the southern South China Sea (SCS) with an average resolution of ∼10 days. The δ13C record illustrates seasonal and interannual cycles which are superimposed by long‐term decreasing trend. We investigate the environmental controls influencing the δ13Cshell on different time scales. We suggest that more positive δ13Cshell values observed during the juvenile stage (first 8–10 years), which correspond to a high growth rate, can be attributed to 13C enrichment of the internal dissolved inorganic carbon pool. This resulted from the exponential increase of symbiotic zooxanthellae, and preferential 12C sequestration by the accelerated buildup of productive tissues. On the interannual time scale, changes in δ13Cshell were likely affected by both internal (vital effect) and external processes (sea water δ13C), as well as being disturbed by the super El Niño‐La Niña event. Seasonal changes of δ13Cshell were mainly dominated by the intensity of photosynthesis and respiration of symbiotic zooxanthellae, which depend on the seasonal solar irradiance variations in association with precipitation and the South Asian summer monsoon. Our study sheds light on the controlling factors of δ13Cshell variations on seasonal timescale and the long‐term trend, providing insight into the carbon cycle over geological history.
Impairment of rigidity sensing caused by mutant TP53 gain of function in osteosarcoma
Authors: Luo Ming , Huang Mingyang , Yang Ningning , Zhu Yufan , Huang Peng , Xu Zhujun , Wang Wengang , Cai Lin 
Published: May 2023

AbstractOsteosarcoma (OS) is the most common primary malignant pediatric bone tumor and is characterized by high heterogeneity. Studies have revealed a wide range of phenotypic differences among OS cell lines in terms of their in vivo tumorigenicity and in vitro colony-forming abilities. However, the underlying molecular mechanism of these discrepancies remains unclear. The potential role of mechanotransduction in tumorigenicity is of particular interest. To this end, we tested the tumorigenicity and anoikis resistance of OS cell lines both in vitro and in vivo. We utilized a sphere culture model, a soft agar assay, and soft and rigid hydrogel surface culture models to investigate the function of rigidity sensing in the tumorigenicity of OS cells. Additionally, we quantified the expression of sensor proteins, including four kinases and seven cytoskeletal proteins, in OS cell lines. The upstream core transcription factors of rigidity-sensing proteins were further investigated. We detected anoikis resistance in transformed OS cells. The mechanosensing function of transformed OS cells was also impaired, with general downregulation of rigidity-sensing components. We identified toggling between normal and transformed growth based on the expression pattern of rigidity-sensing proteins in OS cells. We further uncovered a novel TP53 mutation (R156P) in transformed OS cells, which acquired gain of function to inhibit rigidity sensing, thus sustaining transformed growth. Our findings suggest a fundamental role of rigidity-sensing components in OS tumorigenicity as mechanotransduction elements through which cells can sense their physical microenvironment. In addition, the gain of function of mutant TP53 appears to serve as an executor for such malignant programs.
Rapid evolution of A(H5N1) influenza viruses after intercontinental spread to North America
Authors: Kandeil Ahmed , Patton Christopher , Jones Jeremy C. , Jeevan Trushar , Harrington Walter N. , Trifkovic Sanja , Seiler Jon P. , Fabrizio Thomas , Woodard Karlie , Turner Jasmine C. , Crumpton Jeri-Carol , Miller Lance , Rubrum Adam , DeBeauchamp Jennifer , Russell Charles J. , Govorkova Elena A. , Vogel Peter , Kim-Torchetti Mia , Berhane Yohannes , Stallknecht David , Poulson Rebecca , Kercher Lisa , Webby Richard J. 
Published: May 2023

AbstractHighly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry across Asia, Europe, and Africa. By the end of 2021, 2.3.4.4b viruses were detected in North America, signifying further intercontinental spread. Here we show that the western movement of clade 2.3.4.4b was quickly followed by reassortment with viruses circulating in wild birds in North America, resulting in the acquisition of different combinations of ribonucleoprotein genes. These reassortant A(H5N1) viruses are genotypically and phenotypically diverse, with many causing severe disease with dramatic neurologic involvement in mammals. The proclivity of the current A(H5N1) 2.3.4.4b virus lineage to reassort and target the central nervous system warrants concerted planning to combat the spread and evolution of the virus within the continent and to mitigate the impact of a potential influenza pandemic that could originate from similar A(H5N1) reassortants.
Fibroblasts are a site of murine cytomegalovirus lytic replication and Stat1-dependent latent persistence in vivo
Authors: Sitnik Katarzyna M. , Krstanović Fran , Gödecke Natascha , Rand Ulfert , Kubsch Tobias , Maaß Henrike , Kim Yeonsu , Brizić Ilija , Čičin-Šain Luka 
Published: May 2023

AbstractTo date, no herpesvirus has been shown to latently persist in fibroblastic cells. Here, we show that murine cytomegalovirus, a β-herpesvirus, persists for the long term and across organs in PDGFRα-positive fibroblastic cells, with similar or higher genome loads than in the previously known sites of murine cytomegalovirus latency. Whereas murine cytomegalovirus gene transcription in PDGFRα-positive fibroblastic cells is almost completely silenced at 5 months post-infection, these cells give rise to reactivated virus ex vivo, arguing that they support latent murine cytomegalovirus infection. Notably, PDGFRα-positive fibroblastic cells also support productive virus replication during primary murine cytomegalovirus infection. Mechanistically, Stat1-deficiency promotes lytic infection but abolishes latent persistence of murine cytomegalovirus in PDGFRα-positive fibroblastic cells in vivo. In sum, fibroblastic cells have a dual role as a site of lytic murine cytomegalovirus replication and a reservoir of latent murine cytomegalovirus in vivo and STAT1 is required for murine cytomegalovirus latent persistence in vivo.
A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology
Authors: Petersen Julian , Englmaier Lukas , Artemov Artem V. , Poverennaya Irina , Mahmoud Ruba , Bouderlique Thibault , Tesarova Marketa , Deviatiiarov Ruslan , Szilvásy-Szabó Anett , Akkuratov Evgeny E. , Pajuelo Reguera David , Zeberg Hugo , Kaucka Marketa , Kastriti Maria Eleni , Krivanek Jan , Radaszkiewicz Tomasz , Gömöryová Kristína , Knauth Sarah , Potesil David , Zdrahal Zbynek , Ganji Ranjani Sri , Grabowski Anna , Buhl Miriam E. , Zikmund Tomas , Kavkova Michaela , Axelson Håkan , Lindgren David , Kramann Rafael , Kuppe Christoph , Erdélyi Ferenc , Máté Zoltán , Szabó Gábor , Koehne Till , Harkany Tibor , Fried Kaj , Kaiser Jozef , Boor Peter , Fekete Csaba , Rozman Jan , Kasparek Petr , Prochazka Jan , Sedlacek Radislav , Bryja Vitezslav , Gusev Oleg , Adameyko Igor 
Published: May 2023

AbstractIn this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby nameFAME(Factor Associated with Metabolism and Energy). We observe thatFAMEshows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow ofFAMEfrom Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure inFameknockout animals, corresponding to genome-wide association studies linkingFAMEwith higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.