bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variations in soil nutrient dynamics and bacterial communities in long-term tea monoculture production systems
Authors: Gui Heng , Fan Lichao , Wang Donghui , Yan Peng , Li Xin , Pang Yinghua , Zhang Liping , Zamanian Kazem , Xu Jianchu , Han Wenyan 
Published: April 2021

AbstractLong-term monoculture agriculture systems could lead to soil degradation and yield decline. The ways in which soil microbiotas interact with one another, particularly in response to long-term tea monoculture systems are currently unclear. In this study, through the comparison of three independent tea plantations across eastern China composed of varying stand ages (from 3 years to 90 years after conversion from forest), we found that long-term tea monoculture led to significant increases in soil total organic carbon (TOC) and microbial nitrogen (MBN). Additionally, the structure, function and co-occurrence network of soil microbial communities were investigated by pyrosequencing 16S rRNA genes. The pyrosequencing analysis revealed that structures and functions of soil bacterial communities were significantly affected by different stand ages of tea plantations, but sampling sites and land-use conversion (from forest to tea plantation) still outcompeted stand age to control the diversity and structure of soil bacterial communities. Further RDA analysis revealed that the C and N availability improvement in tea plantation soils led to variation of structure and function in soil microbial communities. Moreover, co-occurrence network analysis of soil bacterial communities also demonstrated that interactions among soil bacteria taxa were strengthened with the increasing stand age of respective tea stands. Overall, this study provides a comprehensive understanding of the impact of long-term monoculture stand age on soil nutrient dynamics and bacterial communities in tea production.
Soil depth gradients in microbial growth kinetics under deeply- vs. shallow-rooted plants
Authors: Min Kyungjin , Slessarev Eric , Kan Megan , McFarlane Karis , Oerter Erik , Pett-Ridge Jennifer , Nuccio Erin , Berhe Asmeret Asefaw 
Published: April 2021

AbstractClimate-smart land management practices that replace shallow-rooted annual crop systems with deeply-rooted perennial plants can contribute to soil carbon sequestration. However, deep soil carbon accrual may be influenced by active microbial biomass and their capacity to assimilate fresh carbon at depth. Incorporating active microbial biomass, dormancy and growth in microbially-explicit models can improve our ability to predict soil’s capacity to store carbon. But, so far, the microbial parameters that are needed for such modeling are poorly constrained, especially in deep soil layers. Here, we investigated whether a change in crop rooting depth affects microbial growth kinetics in deep soils compared to surface soils. We used a lab incubation experiment and growth kinetics model to estimate how microbial parameters vary along 240 cm of soil depth in profiles under shallow- (soy) and deeply-rooted plants (switchgrass) 11 years after plant cover conversion. We also assessed resource origin and availability (total organic carbon,14C, dissolved organic carbon, specific UV absorbance, total nitrogen, total dissolved nitrogen) along the soil profiles to examine associations between soil chemical and biological parameters. Even though root biomass was higher and rooting depth was deeper under switchgrass than soy, resource availability and microbial growth parameters were generally similar between vegetation types. Instead, depth significantly influenced soil chemical and biological parameters. For example, resource availability, and total and relative active microbial biomass decreased with soil depth. Decreases in the relative active microbial biomass coincided with increased lag time (response time to external carbon inputs) along the soil profiles. Even at a depth of 210-240 cm, microbial communities were activated to grow by added resources within a day. Maximum specific growth rate decreased to a depth of 90 cm and then remained consistent in deeper layers. Our findings show that > 10 years of vegetation and rooting depth changes may not be long enough to alter microbial growth parameters, and suggest that at least a portion of the microbial community in deep soils can grow rapidly in response to added resources. Our study determined microbial growth parameters that can be used in microbially-explicit models to simulate carbon dynamics in deep soil layers.
HGDiscovery: an online tool providing functional and phenotypic information on novel variants of homogentisate 1,2- dioxigenase
Authors: Karmakar Malancha , Cicaloni Vittoria , Rodrigues Carlos H.M. , Spiga Ottavia , Santucci Annalisa , Ascher David B. 
Published: April 2021

AbstractAlkaptonuria (AKU), a rare genetic disorder, is characterized by the accumulation of homogentisic acid (HGA) in the body. Affected individuals lack enough functional levels of an enzyme required to breakdown HGA. Mutations in theHGDgene cause AKU and they are responsible for deficient levels of functional homogentisate 1,2-dioxygenase (HGD), which, in turn, leads to excess levels of HGA. Although HGA is rapidly cleared from the body by the kidneys, in the long term it starts accumulating in various tissues, especially cartilage. Over time (rarely before adulthood), it eventually changes the color of affected tissue to slate blue or black. Here we report a comprehensive mutation analysis of 111 pathogenic and 190 non-pathogenic HGD missense mutations using protein structural information. Using our comprehensive suite of graph-based signature methods, mCSM complemented with sequence-based tools, we studied the functional and molecular consequences of each mutation on protein stability, interaction and evolutionary conservation. The scores generated from the structure and sequence-based tools were used to train a supervised machine learning algorithm with 84% accuracy. The empirical classifier was used to generate the variant phenotype for novel HGD missense mutations. All this information is deployed as a user friendly freely available web server called HGDiscovery (http://biosig.unimelb.edu.au/hgdiscovery/).
Guidance by followers ensures long-range coordination of cell migration through α-Catenin mechanoperception
Authors: Boutillon Arthur , Escot Sophie , Elouin Amélie , Jahn Diego , González-Tirado Sebastián , Starruß Jörn , Brusch Lutz , David Nicolas B. 
Published: April 2021

SummaryMorphogenesis, wound healing and some cancer metastases depend upon migration of cell collectives that need to be guided to their destination as well as coordinated with other cell movements. During zebrafish gastrulation, extension of the embryonic axis is led by the mesendodermal polster that migrates towards the animal pole, followed by axial mesoderm that undergoes convergence and extension. We here investigate how polster cells are guided towards the animal pole. Using a combination of precise laser ablations, advanced transplants and functional as well as in silico approaches, we establish that each polster cell is oriented by its immediate follower cells. Each cell perceives the migration of followers, through E-Cadherin/α-Catenin mechanotransduction, and aligns with them. Directional information therefore propagates from cell to cell over the whole tissue. Such guidance of migrating cells by followers ensures long-range coordination of movements and developmental robustness.
Niclosamide shows strong antiviral activity in a human airway model of SARS-CoV-2 infection and a conserved potency against the UK B.1.1.7 and SA B.1.351 variant
Authors: Weiss Anne , Touret Franck , Baronti Cecile , Gilles Magali , Hoen Bruno , Nougairède Antoine , de Lamballerie Xavier , Sommer Morten Otto Alexander 
Published: April 2021

AbstractSARS-CoV-2 variants are emerging with potential increased transmissibility highlighting the great unmet medical need for new therapies. Niclosamide is a potent anti-SARS-CoV-2 agent that has advanced in clinical development. We validate the potent antiviral efficacy of niclosamide in a SARS-CoV-2 human airway model. Furthermore, niclosamide is effective against the D614G, B.1.1.7 and B.1.351 variants. Our data further support the potent anti-SARS-CoV-2 properties of niclosamide and highlights its great potential as a therapeutic agent for COVID-19.
The AP-1 factorsFOSL1andFOSL2co-regulate human Th17 responses
Authors: Shetty Ankitha , Tripathi Subhash Kumar , Junttila Sini , Buchacher Tanja , Biradar Rahul , Bhosale Santosh D. , Envall Tapio , Laiho Asta , Moulder Robert , Rasool Omid , Galande Sanjeev , Elo Laura L. , Lahesmaa Riitta 
Published: April 2021

ABSTRACTTh17 cells protect mucosal barriers, but their aberrant activity can cause autoimmunity. Molecular networks dictating human Th17 function are largely unexplored, and this hinders disease-studies. Here, we investigated the roles of the AP-1 factors,FOSL1andFOSL2,in inducing human Th17 responses. Transient knockdown and over-expression strategies found the two proteins to inhibit Th17-cell identity, while revealing a distinct cooperativity between their functions. Strikingly,FOSL1plays different roles in human and mouse and FOSL-mediated Th17 regulation is opposed by the AP-1 factor, BATF. Genome-wide occupancy analysis demonstrated the co-localization of FOSL1, FOSL2 and BATF in the vicinity of key Th17 genes. The functional interplay among these factors is possibly governed by sharing interactions with a common set of lineage-associated proteins. We further discovered that the genomic binding sites of these factors harbour a large number of disease-linked SNPs, many of which alter the ability of a given factor to bind DNA. Our findings thus provide crucial insights into the transcriptional regulation of human Th17 function and associated pathologies.ONE SENTENCE SUMMARYFOSL1- and FOSL2-mediated transcription during early human Th17 differentiation
Non-breeding waterbirds benefit from protected areas when adjusting their distribution to climate warming
Authors: Gaget Elie , Pavón-Jordán Diego , Johnston Alison , Lehikoinen Aleksi , Hochachka Wesley M. , Sandercock Brett K. , Soultan Alaaeldin , Azafzaf Hichem , Bendjedda Nadjiba , Bino Taulant , Božič Luca , Clausen Preben , Dakki Mohamed , Devos Koen , Domsa Cristi , Encarnação Vitor , Erciyas-Yavuz Kiraz , Faragó Sándor , Frost Teresa , Gaudard Clemence , Gosztonyi Lívia , Haas Fredrik , Hornman Menno , Langendoen Tom , Ieronymidou Christina , Kostyushin Vasiliy A. , Lewis Lesley J. , Lorentsen Svein-Håkon , Luiujoe Leho , Meissner Włodzimierz , Mikuska Tibor , Molina Blas , Musilová Zuzana , Natykanets Viktor , Paquet Jean-Yves , Petkov Nicky , Portolou Danae , Ridzoň Jozef , Sayoud Samir , Šćiban Marko , Sniauksta Laimonas , Stīpniece Antra , Strebel Nicolas , Teufelbauer Norbert , Topić Goran , Uzunova Danka , Vizi Andrej , Wahl Johannes , Zenatello Marco , Brommer Jon E. 
Published: April 2021

AbstractClimate warming is driving changes in species distributions, although many species show a so-called climatic debt, where their range shifts lag behind the fast shift in temperature isoclines. Protected areas (PAs) may impact the rate of distribution changes both positively and negatively. At the cold edges of species distributions, PAs can facilitate species distribution changes by increasing the colonization required for distribution change. At the warm edges, PAs can mitigate the loss of species, by reducing the local extinction of vulnerable species. To assess the importance of PAs to affect species distribution change, we evaluated the changes in a non-breeding waterbird community as a response to temperature increase and PA status, using changes of species occurrence in the Western-Palearctic over 25 years (97 species, 7,071 sites, 39 countries, 1993– 2017). We used a community temperature index (CTI) framework based on species thermal affinities to investigate the species turn-over induced by temperature increase. In addition, we measured whether the thermal community adjustment was led by cold-dwelling species extinction and/or warm-dwelling species colonization, by modelling the change in standard deviation of the CTI (CTIsd). Using linear mixed-effects models, we investigated whether communities within PAs had lower climatic debt and different patterns of community change regarding the local PA surface. Thanks to the combined use of the CTI and CTIsd, we found that communities inside PAs had more species, higher colonization, lower extinction and the climatic debt was 16% lower than outside PAs. The results suggest the importance of PAs to facilitate warm-dwelling species colonization and attenuate cold-dwelling species extinction. The community adjustment was however not sufficiently fast to keep pace with the strong temperature increase in central and northeastern Western-Palearctic regions. Our study underlines the potential of the combined CTI and CTIsdmetrics to understand the colonization-extinction patterns driven by climate warming.
The dorsal blastopore lip is a source of signals inducing PCP in theXenopusneural plate
Authors: Mancini Pamela , Ossipova Olga , Sokol Sergei Y. 
Published: April 2021

AbstractCoordinated polarization of cells in the tissue plane, known as planar cell polarity (PCP), is associated with a signaling pathway critical for the control of morphogenetic processes. Although the segregation of PCP components to opposite cell borders is believed to play a critical role in this pathway, whether PCP derives from egg polarity or preexistent long-range gradient, or forms in response to a localized cue remains a challenging question. Here we investigate theXenopusneural plate, a tissue that has been previously shown to exhibit PCP. By imaging Vangl2 and Prickle3, we show that PCP is progressively acquired in the neural plate and requires a signal from the posterior region of the embryo. Tissue transplantations indicated that PCP is triggered in the neural plate by a planar cue from the dorsal blastopore lip. The PCP cue did not depend on the orientation of the graft and was distinct from neural inducers. These observations suggest that neuroectodermal PCP is not instructed by a preexisting molecular gradient, but induced by a signal from the dorsal blastopore lip.HighlightsTheXenopusneural plate progressively acquires PCP in a posterior-to-anterior direction.The dorsal blastopore lip is likely the source of the PCP-instructing signal for theXenopusneural plate.The PCP cue is distinct from neural inducers and has a planar mode of transmission.
The effects of epigallocatechin gallate and caffeine on risky decision-making
Authors: Liley A. E. , Joyner H. , Gabriel D. B. K. , Simon N. W. 
Published: April 2021

AbstractEpigallocatechin-3-gallate (EGCG) and caffeine are the two primary compounds found in green tea. While EGCG has anxiolytic and anti-inflammatory effects, its acute effects on cognition are not well understood. Furthermore, despite widespread green tea consumption, little is known about how EGCG and caffeine co-administration impact behavior. Here, we investigated the effects of multiple doses of either EGCG or caffeine on a rat model of risk-taking. This was assessed using the risky decision-making task (RDT), in which rats choose between a small, safe reward and a large reward with escalating risk of mild footshock. Rats were tested in RDT after acute systemic administration of EGCG, caffeine, or joint EGCG and caffeine. EGCG caused a dose dependent reduction in risk-taking without affecting reward discrimination or task engagement. Caffeine did not impact risk taking, but elevated locomotor activity and reduced task engagement at high doses. Finally, exposure to both EGCG and caffeine had no effect on risk-taking, suggesting that low-dose caffeine is sufficient to mask the risk-aversion caused by EGCG. These data suggest EGCG as a potential therapeutic treatment for psychological disorders that induce compulsive risky decision-making.
Dedifferentiation alters chondrocyte nuclear mechanics during in vitro culture and expansion
Authors: Ghosh Soham , Scott Adrienne K. , Seelbinder Benjamin , Barthold Jeanne E. , St. Martin Brittany M , Kaonis Samantha , Schneider Stephanie E. , Henderson Jonathan T. , Neu Corey P. 
Published: April 2021

ABSTRACTDedifferentiation of chondrocytes duringin vitropassaging before implantation, and post implantationin vivo, is a critical limitation in cartilage tissue engineering. Several biophysical features define the dedifferentiated state including a flattened cell morphology and increased stress fiber formation. However, how dedifferentiation influences nuclear mechanics, and the possible long-term implications of this state, are unknown. In this study, we investigated how chondrocyte dedifferentiation affects the mechanics of the chromatin architecture inside the cell nucleus and the gene expression of the structural proteins located at the nuclear envelope. Through an experimental model of cell stretching and a detailed spatial intranuclear strain quantification, we identified that strain is amplified and distribution of strain within the chromatin is altered under tensile loading in the dedifferentiated state. Further, using a confocal microscopy image-based finite element model and simulation of cell stretching, we found that the cell shape is the primary determinant of the strain amplification inside the chondrocyte nucleus in the dedifferentiated state. Additionally, we found that nuclear envelope proteins have lower gene expression in the dedifferentiated state suggesting a weaker nuclear envelope which can further intensify the intranuclear strain amplification. Our results indicate that dedifferentiation and altered nuclear strain could promote gene expression changes at the nuclear envelope, thus promoting further deviation from chondrocyte phenotype. This study highlights the role of cell shape on nuclear mechanics and lays the groundwork to design biophysical strategies for the maintenance and enhancement of the chondrocyte phenotype during expansion with a goal of successful cartilage tissue engineering.SIGNIFICANCEChondrocytes dedifferentiate into a fibroblast-like phenotype in a non-native biophysical environment. Using high resolution microscopy, intranuclear strain analysis, finite element method based computational modeling, and molecular biology techniques, we investigated how mechanical force causes abnormal intranuclear strain distribution in chondrocytes during the dedifferentiation process. Overall, our results suggest that the altered cell geometry aided by an altered or weakened nuclear envelope structure are responsible for abnormal intranuclear strain during chondrocyte dedifferentiation that can further deviate chondrocytes to a more dedifferentiated state.
Modeling breast cancer by grafting patient tumor samples in the avian embryo: anin vivoplatform for therapy evaluation coupled to large scale molecular analyses
Authors: Jarrosson Loraine , Costechareyre Clélia , Gallix Fanny , Ciré Séverine , Gay Fabien , Imbaud Olivier , Marangoni Elisabetta , Aguéra Karine , Delloye-Bourgeois Céline , Castellani Valérie 
Published: April 2021

AbstractLack of preclinical patient-derived xenograft (PDX) cancer models in which to conduct large scale molecular studies seriously impairs the development of effective personalized therapies. We report here on anin vivoconcept consisting of implanting human tumor cells in targeted tissues of an avian embryo, delivering therapeutics, evaluating their efficacy by measuring tumors using light sheet confocal microscopy, and conducting large scale RNAseq analysis to characterize therapeutic-induced changes in gene expression. The model was established to recapitulate triple negative breast cancer (TNBC) and validated using TNBC standards of care (SOCs) and an investigational therapeutic agent.
Chemo-Mechanical Cues Modulate Nano-Scale Chromatin Organization in Healthy and Diseased Connective Tissue Cells
Authors: Heo Su-Jin , Thakur Shreyasi , Chen Xingyu , Loebel Claudia , Xia Boao , McBeath Rowena , Burdick Jason A. , Shenoy Vivek B. , Mauck Robert L. , Lakadamyali Melike 
Published: April 2021

AbstractMicroscale changes in tissue environment are translated to changes in cell behavior and phenotype, yet the mechanisms behind how these phenotypic changes occur are poorly understood. Here, we describe and model chromatin, which stores genetic information within the cell nucleus, as a dynamic nanomaterial whose configuration is modulated by chemo-mechanical cues in the microenvironment. Our findings indicate that physiologic chemo-mechanical cues can directly regulate chromatin architecture in progenitor cell populations. Via direct experimental observation and modeling that incorporates phase transitions and histone methylation kinetics, we demonstrate that soft environmental cues drive chromatin relocalization to the nuclear boundary and compaction. Conversely, dynamic stiffening attenuates these changes. Interestingly, in diseased human fibrous tissue cells, this link between mechanical inputs and chromatin nano-scale remodeling is abrogated. These data indicate that chromatin dynamics and plasticity may be hallmarks of disease progression and targets for therapeutic intervention.
Chemical and deep-frying oxidative stability of sunflower–red palm olein blends
Authors: Zulu Nombulelo , Kayitesi Eugenie , Ogundele Opeolu M. 
Published: April 2021

PurposeThe effect of the addition of red palm olein (RPO) as a natural antioxidant to sunflower (SF) on chemical properties and deep-frying oxidative stability of resultant oil during storage.Design/methodology/approachRPO was added to SF at different levels 0, 5, 10, 15, 20, 25, 50, 75 and 100 (w/w), and potato chips were fried in oil blends repeatedly at 180 °C for 2.5 min for five days to evaluate the effect on chemical properties and oxidative stability.FindingsThe results revealed that linoleic acid and total polar compound (TPC) contents decreased in all RPO and SF resultant oil after five days of storage. Colour significantly (p = 0.05) decreased, while peroxide and iodine values were significantly lowered during storage. The oxidative stability increased significantly in the resultant oil. However, an increase in free fatty acid (FFA) before frying significantly reduced with repeated frying of resultant oil during storage. RPO (5–75%) therefore retards oxidative rancidity in the resultant oil after repeated deep frying and storage.Originality/valueSF oil is high in polyunsaturated fatty acids but prone to oxidation upon heating and storage. RPO is an important ingredient used in industrial frying rich in phytonutrients and a better replacement to synthetic antioxidants. This study indicated that supplementing SF oil with RPO may be recommended to improve the oxidative stability of oils during frying.