bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glutaredoxin 1 controls monocyte reprogramming during nutrient stress and protects mice against obesity and atherosclerosis in a sex-specific manner
Authors: Ahn Yong Joo , Wang Luxi , Tavakoli Sina , Nguyen Huynh Nga , Short John D. , Asmis Reto 
Published: February 2022

AbstractHigh-calorie diet-induced nutrient stress promotes thiol oxidative stress and the reprogramming of blood monocytes, giving rise to dysregulated, obesogenic, proatherogenic monocyte-derived macrophages. We report that in chow-fed, reproductively senescent female mice but not in age-matched male mice, deficiency in the thiol transferase glutaredoxin 1 (Grx1) promotes dysregulated macrophage phenotypes as well as rapid weight gain and atherogenesis. Grx1 deficiency derepresses distinct expression patterns of reactive oxygen species and reactive nitrogen species generators in male versus female macrophages, poising female but not male macrophages for increased peroxynitrate production. Hematopoietic Grx1 deficiency recapitulates this sexual dimorphism in high-calorie diet-fed LDLR-/-mice, whereas macrophage-restricted overexpression of Grx1 eliminates the sex differences unmasked by high-calorie diet-feeding and protects both males and females against atherogenesis. We conclude that loss of monocytic Grx1 activity disrupts the immunometabolic balance in mice and derepresses sexually dimorphic oxidative stress responses in macrophages. This mechanism may contribute to the sex differences reported in cardiovascular disease and obesity in humans.
Unraveling the rate-limiting step of two-electron transfer electrochemical reduction of carbon dioxide
Authors: Deng Wanyu , Zhang Peng , Seger Brian , Gong Jinlong 
Published: February 2022

AbstractElectrochemical reduction of CO2 (CO2ER) has received significant attention due to its potential to sustainably produce valuable fuels and chemicals. However, the reaction mechanism is still not well understood. One vital debate is whether the rate-limiting step (RLS) is dominated by the availability of protons, the conversion of water molecules, or the adsorption of CO2. This paper describes insights into the RLS by investigating pH dependency and kinetic isotope effect with respect to the rate expression of CO2ER. Focusing on electrocatalysts geared towards two-electron transfer reactions, we find the generation rates of CO and formate to be invariant with either pH or deuteration of the electrolyte over Au, Ag, Sn, and In. We elucidate the RLS of two-electron transfer CO2ER to be the adsorption of CO2 onto the surface of electrocatalysts. We expect this finding to provide guidance for improving CO2ER activity through the enhancement of the CO2 adsorption processes by strategies such as surface modification of catalysts as well as careful control of pressure and interfacial electric field within reactors.
SM-Omics is an automated platform for high-throughput spatial multi-omics
Authors: Vickovic S. , Lötstedt B. , Klughammer J. , Mages S. , Segerstolpe Å , Rozenblatt-Rosen O. , Regev A. 
Published: February 2022

AbstractThe spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. Here, we advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate SM-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.
Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies
Authors: Elsemman Ibrahim E. , Rodriguez Prado Angelica , Grigaitis Pranas , Garcia Albornoz Manuel , Harman Victoria , Holman Stephen W. , van Heerden Johan , Bruggeman Frank J. , Bisschops Mark M. M. , Sonnenschein Nikolaus , Hubbard Simon , Beynon Rob , Daran-Lapujade Pascale , Nielsen Jens , Teusink Bas 
Published: February 2022

AbstractWhen conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation—known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells.
dCas9-based gene editing for cleavage-free genomic knock-in of long sequences
Authors: Wang Chengkun , Qu Yuanhao , Cheng Jason K. W. , Hughes Nicholas W. , Zhang Qianhe , Wang Mengdi , Cong Le 
Published: February 2022

AbstractGene editing is a powerful tool for genome and cell engineering. Exemplified by CRISPR–Cas, gene editing could cause DNA damage and trigger DNA repair processes that are often error-prone. Such unwanted mutations and safety concerns can be exacerbated when altering long sequences. Here we couple microbial single-strand annealing proteins (SSAPs) with catalytically inactive dCas9 for gene editing. This cleavage-free gene editor, dCas9–SSAP, promotes the knock-in of long sequences in mammalian cells. The dCas9–SSAP editor has low on-target errors and minimal off-target effects, showing higher accuracy than canonical Cas9 methods. It is effective for inserting kilobase-scale sequences, with an efficiency of up to approximately 20% and robust performance across donor designs and cell types, including human stem cells. We show that dCas9–SSAP is less sensitive to inhibition of DNA repair enzymes than Cas9 references. We further performed truncation and aptamer engineering to minimize its size to fit into a single adeno-associated-virus vector for future application. Together, this tool opens opportunities towards safer long-sequence genome engineering.
A gelation transition enables the self-organization of bipolar metaphase spindles
Authors: Dalton Benjamin A. , Oriola David , Decker Franziska , Jülicher Frank , Brugués Jan 
Published: February 2022

AbstractThe mitotic spindle is a highly dynamic bipolar structure that emerges from the self-organization of microtubules, molecular motors and other proteins. Sustained motor-driven poleward flows of dynamic microtubules play a key role in the bipolar organization of spindles. However, it is not understood how the local activity of motor proteins generates these large-scale coherent poleward flows. Here we show that a gelation transition enables long-range microtubule transport causing the spindles to self-organize into two oppositely polarized microtubule gels. Laser ablation experiments reveal that local active stresses generated at the spindle midplane propagate through the structure, thereby driving global coherent microtubule flows. Simulations show that microtubule gels undergoing rapid turnover can exhibit long stress relaxation times, in agreement with the long-range flows observed in experiments. Finally, our model predicts that in the presence of branching microtubule nucleation, either disrupting such flows or decreasing the network connectivity can lead to a microtubule polarity reversal in spindles. We experimentally confirm this inversion of polarity by abolishing the microtubule transport in spindles. Overall, we uncover a connection between spindle rheology and architecture in spindle self-organization.
A cross-sectional analysis of the association between physical activity, depression, and all-cause mortality in Americans over 50 years old
Authors: Perez-Lasierra Jose Luis , Moreno-Franco Belén , González-Agüero Alejandro , Lobo Elena , Casajus Jose A. 
Published: February 2022

AbstractDepression is estimated to be the second leading cause of disability in the United States and is associated with a 52% increased risk of death. Lifestyle components may have an important role in depression pathogenesis. The aims of this study were to analyze the association of meeting the physical activity (PA) recommendation guidelines and depression, and to analyze the all-cause mortality risk of the joint association of PA and depression. This cross-sectional study included 7201 participants from the 2007–2014 National Health and Nutrition Examination Survey aged ≥ 50 years and linked to National Death Index records through December 31, 2015. Depression was defined as a score ≥ 10 using the Patient Health Questionnaire (PHQ-9). PA was self-reported, and total PA was used to classify participants as more active (≥ 600 MET-min/week) or less active (< 600 MET-min/week). The odds ratios for depression were examined according to be more active or less active. The hazard ratios (HR) for the association of PA level and depression status with all-cause mortality were examined. Being more active was associated with reduced odds for depression. Compared with less active participants with depression, those who were more active and having depression had HR 0.45 (95% CI 0.22, 0.91, p = 0.026) for all-cause mortality. Being more active is associated with lower odds for depression and seems to be a protective factor against the increased all-cause mortality risk due to depression.
Examining potential confounding factors in gene expression analysis of human saliva and identifying potential housekeeping genes
Authors: Ostheim P. , Alemu S. W. , Tichý A. , Sirak I. , Davidkova M. , Stastna M. Markova , Kultova G. , Schuele S. , Paunesku T. , Woloschak G. , Ghandhi S. A. , Amundson S. A. , Haimerl M. , Stroszczynski C. , Port M. , Abend M. 
Published: February 2022

AbstractIsolation of RNA from whole saliva, a non-invasive and easily accessible biofluid that is an attractive alternative to blood for high-throughput biodosimetry of radiological/nuclear victims might be of clinical significance for prediction and diagnosis of disease. In a previous analysis of 12 human samples we identified two challenges to measuring gene expression from total RNA: (1) the fraction of human RNA in whole saliva was low and (2) the bacterial contamination was overwhelming. To overcome these challenges, we performed selective cDNA synthesis for human RNA species only by employing poly(A)+-tail primers followed by qRT-PCR. In the current study, this approach was independently validated on 91 samples from 61 healthy donors. Additionally, we used the ratio of human to bacterial RNA to adjust the input RNA to include equal amounts of human RNA across all samples before cDNA synthesis, which then ensured comparable analysis using the same base human input material. Furthermore, we examined relative levels of ten known housekeeping genes, and assessed inter- and intra-individual differences in 61 salivary RNA isolates, while considering effects of demographical factors (e.g. sex, age), epidemiological factors comprising social habits (e.g. alcohol, cigarette consumption), oral hygiene (e.g. flossing, mouthwash), previous radiological diagnostic procedures (e.g. number of CT-scans) and saliva collection time (circadian periodic). Total human RNA amounts appeared significantly associated with age only (P ≤ 0.02). None of the chosen housekeeping genes showed significant circadian periodicity and either did not associate or were weakly associated with the 24 confounders examined, with one exception, 60% of genes were altered by mouthwash. ATP6, ACTB and B2M represented genes with the highest mean baseline expression (Ct-values ≤ 30) and were detected in all samples. Combining these housekeeping genes for normalization purposes did not decrease inter-individual variance, but increased the robustness. In summary, our work addresses critical confounders and provides important information for the successful examination of gene expression in human whole saliva.
Blood and adipose tissue steroid metabolomics and mRNA expression of steroidogenic enzymes in periparturient dairy cows differing in body condition
Authors: Schuh K. , Häussler S. , Sadri H. , Prehn C. , Lintelmann J. , Adamski J. , Koch C. , Frieten D. , Ghaffari M. H. , Dusel G. , Sauerwein H. 
Published: February 2022

AbstractIn high-yielding dairy cows, the rapidly increasing milk production after parturition can result in a negative nutrient balance, since feed intake is insufficient to cover the needs for lactation. Mobilizing body reserves, mainly adipose tissue (AT), might affect steroid metabolism. We hypothesized, that cows differing in the extent of periparturient lipomobilization, will have divergent steroid profiles measured in serum and subcutaneous (sc)AT by a targeted metabolomics approach and steroidogenic enzyme profiles in scAT and liver. Fifteen weeks antepartum, 38 multiparous Holstein cows were allocated to a high (HBCS) or normal body condition (NBCS) group fed differently until week 7 antepartum to either increase (HBCS BCS: 3.8 ± 0.1 and BFT: 2.0 ± 0.1 cm; mean ± SEM) or maintain BCS (NBCS BCS: 3.0 ± 0.1 and BFT: 0.9 ± 0.1 cm). Blood samples, liver, and scAT biopsies were collected at week −7, 1, 3, and 12 relative to parturition. Greater serum concentrations of progesterone, androsterone, and aldosterone in HBCS compared to NBCS cows after parturition, might be attributed to the increased mobilization of AT. Greater glucocorticoid concentrations in scAT after parturition in NBCS cows might either influence local lipogenesis by differentiation of preadipocytes into mature adipocytes and/or inflammatory response.
Gadolinium-oxide nanoparticles for cryogenic magnetocaloric applications
Authors: Zeleňáková A. , Hrubovčák P. , Berkutova A. , Šofranko O. , Kučerka N. , Ivankov O. , Kuklin A. , Girman V. , Zeleňák V. 
Published: February 2022

AbstractThe series of advanced nanocomposites consisting of Gd2O3 nanoparticles (NPs) embedded into periodic porous SiO2 matrix have been investigated with respect to their structural and magnetocaloric properties. By means of small angle neutron scattering and transmission electron microscopy, regular nanopores organized in the cubic or hexagonal superlattice have been documented. The pores are occupied by the NPs of progressive concentration within the nanocomposite series. All of the examined systems have exhibited extraordinarily high values of magnetic entropy change (up to 70 J kg−1 K−1) at low temperatures with the absence of thermal hysteresis, indicating their perspective utilization in cryogenic refrigeration. Profound analysis of magnetic entropy change data via scaling laws has been applied to the nanocomposite materials for the very first time. With the aid of scaling analysis, conclusions on magnetic properties and phase transition type have been made, even for the conditions unavailable in the laboratory.
Climate change threatens native potential agroforestry plant species in Brazil
Authors: Lima Valdeir Pereira , de Lima Renato Augusto Ferreira , Joner Fernando , Siddique Ilyas , Raes Niels , ter Steege Hans 
Published: February 2022

AbstractClimate change is one of the main drivers of species extinction in the twentyfirst-century. Here, we (1) quantify potential changes in species' bioclimatic area of habitat (BAH) of 135 native potential agroforestry species from the Brazilian flora, using two different climate change scenarios (SSP2-4.5 and SSP5-8.5) and dispersal scenarios, where species have no ability to disperse and reach new areas (non-dispersal) and where species can migrate within the estimated BAH (full dispersal) for 2041–2060 and 2061–2080. We then (2) assess the preliminary conservation status of each species based on IUCN criteria. Current and future potential habitats for species were predicted using MaxEnt, a machine-learning algorithm used to estimate species' probability distribution. Future climate is predicted to trigger a mean decline in BAH between 38.5–56.3% under the non-dispersal scenario and between 22.3–41.9% under the full dispersal scenario for 135 native potential agroforestry species. Additionally, we found that only 4.3% of the studied species could be threatened under the IUCN Red List criteria B1 and B2. However, when considering the predicted quantitative habitat loss due to climate change (A3c criterion) the percentages increased between 68.8–84.4% under the non-dispersal scenario and between 40.7–64.4% under the full dispersal scenario. To lessen such threats, we argue that encouraging the use of these species in rural and peri-urban agroecosystems are promising, complementary strategies for their long-term conservation.
Electrochemical evaluation of proton beam radiation effect on the B16 cell culture
Authors: Onea Melania , Bacalum Mihaela , Radulescu Andreea Luminita , Raileanu Mina , Craciun Liviu , Esanu Tiberiu Relu , Enache Teodor Adrian 
Published: February 2022

AbstractThe interaction of radiation with matter takes place through energy transfer and is accomplished especially by ionized atoms or molecules. The effect of radiation on biological systems involves multiple physical, chemical and biological steps. Direct effects result in a large number of reactive oxygen species (ROS) within and outside and inside of the cells as well, which are responsible for oxidative stress. Indirect effects are defined as alteration of normal biological processes and cellular components (DNA, protein, lipids, etc.) caused by the reactive oxygen species directly induced by radiation. In this work, a classical design of an electrochemical (EC) three-electrodes system was employed for analyzing the effects of proton beam radiation on melanoma B16 cell line. In order to investigate the effect of proton radiation on the B16 cells, the cells were grown on the EC surface and irradiated. After optimization of the experimental set-up and dosimetry, the radiobiological experiments were performed at doses ranging between 0 and 2 Gy and the effect of proton beam irradiation on the cells was evaluated by the means of cyclic voltammetry and measuring the open circuit potential between working and reference electrodes.
A handy and accessible tool for identification of Sn(II) in toothpaste
Authors: Kundu Shampa , Truong Khai-Nghi , Saha Shrabani , Rissanen Kari , Sahoo Prithidipa 
Published: February 2022

AbstractAn easily accessible colorimetric probe, a carbazole–naphthaldehyde conjugate (CNP), was successfully prepared for the selective and sensitive recognition of Sn(II) in different commercially-available toothpaste and mouth wash samples. The binding mechanism of CNP for Sn2+ was confirmed by UV–Vis, 1H, and 13C NMR titrations. The proposed sensing mechanism was supported by quantum chemical calculations. Selective detection of Sn(II) in the nanomolar range (85 nM), among other interfering metal ions, makes it exclusive. Moreover, Sn2+ can be detected with a simple paper strip from toothpaste, which makes this method handy and easily accessible. The potential application of this system for monitoring Sn2+ can be used as an expedient tool for environmental and industrial purposes.
Physicochemical and antioxidant activity of fruit harvested from eight jujube (Ziziphus jujuba Mill.) cultivars at different development stages
Authors: Yan Min , Wang Yan , Watharkar Ritesh Balaso , Pu Yunfeng , Wu Cuiyun , Lin Minjuan , Lu Dengyang , Liu Mingzhe , Bao Jingkai , Xia Yilei 
Published: February 2022

AbstractJujube is a crop highly resistant to drought and salinity, making it one of the main fruit trees in Xinjiang. The present study evaluated the changes in the physicochemical and antioxidant activities of jujube fruit of eight different cultivars from Xinjiang, China. The developmental stages were selected according to the days after full bloom and fruit peel colour during ripening; these stages included young (S1), fruit core-hardening (S2), green ripening (S3), half-red maturity (S4) and complete red. In present study, different cultivars of jujube fruit showed similar chemical profiles, but their amounts showed great variation. HZ had the highest content of sugars, and JY had the highest content of cAMP and cGMP, while relatively higher levels of ascorbic acid, catechin, epicatechin, rutin, proanthocyanidin and antioxidant activity were found in ‘FS’ than in other cultivars, indicating that ‘FS’ could be used as a potential natural antioxidant. Regarding the development stages of jujube fruit, the moisture, ascorbic acid, total polyphenol, catechin, epicatechin, proanthocyanidin and rutin contents decreased during the development of all jujube cultivars, while the fructose, glucose, sucrose, cAMP, and cGMP contents greatly increased. The antioxidant activity determined by DPPH and ABTS radical scavenging decreased as the fruits matured. Therefore, the results suggest that green jujube (S1) could be used for natural antioxidants (catechin, epicatechin, proanthocyanidin) and that the advanced ripening stage(S5) is the proper picking period for fresh fruit and commercial processing.
Newly detected data from Haestasaurus and review of sauropod skin morphology suggests Early Jurassic origin of skin papillae
Authors: Pittman Michael , Enriquez Nathan J. , Bell Phil R. , Kaye Thomas G. , Upchurch Paul 
Published: February 2022

AbstractDiscovered in 1852, the scaly skin belonging to Haestasaurus becklesii was the first to be described in any non-avian dinosaur. Accordingly, it has played a crucial role in the reconstruction of sauropod integument and dinosaurs more broadly. Here, we reassess this historic specimen using Laser-Stimulated Fluorescence (LSF), revealing extensive, previously unknown regions of skin that augment prior interpretations of its integumentary morphology and taphonomy. Under white light, polygonal–subrounded, convex scales are visible on one side of the block (‘side A’), but LSF reveals extensive smaller and more flattened scales, which are diagenetically fragmented, on the reverse block surface (‘side B’). Contrary to the prior interpretation that the visible scales are the epidermal undersides, the presence of convex, intrascale papilliform textures on side A suggests that the external skin surface is exposed. We define intrascale papillae and provide a review of sauropod skin morphology, which clarifies that intrascale papillae are unique to and widespread across stem Neosauropoda, and likely have an evolutionary origin in the Early Jurassic. Intrascale papillae may ultimately have been integral to the evolution of gigantism in this charismatic clade.