bluuebunny/crossref_metadata_2025_split huggingface dataset:
Attracted to membranes: lipid-binding domains in plants
Authors: de Jong Femke , Munnik Teun 
Published: January 2021

AbstractMembranes are essential for cells and organelles to function. As membranes are impermeable to most polar and charged molecules, they provide electrochemical energy to transport molecules across and create compartmentalized microenvironments for specific enzymatic and cellular processes. Membranes are also responsible for guided transport of cargoes between organelles and during endo- and exocytosis. In addition, membranes play key roles in cell signaling by hosting receptors and signal transducers and as substrates and products of lipid second messengers. Anionic lipids and their specific interaction with target proteins play an essential role in these processes, which are facilitated by specific lipid-binding domains. Protein crystallography, lipid-binding studies, subcellular localization analyses, and computer modeling have greatly advanced our knowledge over the years of how these domains achieve precision binding and what their function is in signaling and membrane trafficking, as well as in plant development and stress acclimation.
ThePhyscomitrella patenschromatin adaptor PpMRG1 interacts with H3K36me3 and regulates light-responsive alternative splicing
Authors: Wang Chien-Chang , Hsieh Hsin-Yu , Hsieh Hsu-Liang , Tu Shih-Long 
Published: January 2021

AbstractPlants perceive dynamic light conditions and optimize their growth and development accordingly by regulating gene expression at multiple levels. Alternative splicing (AS), a widespread mechanism in eukaryotes that post-transcriptionally generates two or more messenger RNAs (mRNAs) from the same pre-mRNA, is rapidly controlled by light. However, a detailed mechanism of light-regulated AS is still not clear. In this study, we demonstrate that histone 3 lysine 36 trimethylation (H3K36me3) rapidly and differentially responds to light at specific gene loci with light-regulated intron retention (IR) of their transcripts in the moss Physcomitrella patens. However, the level of H3K36me3 following exposure to light is inversely related to that of IR events. Physcomitrella patens MORF-related gene 1 (PpMRG1), a chromatin adaptor, bound with higher affinity to H3K36me3 in light conditions than in darkness and was differentially targeted to gene loci showing light-responsive IR. Transcriptome analysis indicated that PpMRG1 functions in the regulation of light-mediated AS. Furthermore, PpMRG1 was also involved in red light-mediated phototropic responses. Our results suggest that light regulates histone methylation, which leads to alterations of AS patterns. The chromatin adaptor PpMRG1 potentially participates in light-mediated AS, revealing that chromatin-coupled regulation of pre-mRNA splicing is an important aspect of the plant’s response to environmental changes.
WARPP—web application for the research of parasitic plants
Authors: Kösters Lara M , Wiechers Sarah , Lyko Peter , Müller Kai F , Wicke Susann 
Published: January 2021

Abstract
The lifestyle of parasitic plants is associated with peculiar morphological, genetic, and physiological adaptations that existing online plant-specific resources fail to adequately represent. Here, we introduce the Web Application for the Research of Parasitic Plants (WARPP) as an online resource dedicated to advancing research and development of parasitic plant biology. WARPP is a framework to facilitate international efforts by providing a central hub of curated evolutionary, ecological, and genetic data. The first version of WARPP provides a community hub for researchers to test this web application, for which curated data revolving around the economically important Broomrape family (Orobanchaceae) is readily accessible. The initial set of WARPP online tools includes a genome browser that centralizes genomic information for sequenced parasitic plant genomes, an orthogroup summary detailing the presence and absence of orthologous genes in parasites compared with nonparasitic plants, and an ancestral trait explorer showing the evolution of life-history preferences along phylogenies. WARPP represents a project under active development and relies on the scientific community to populate the web app’s database and further the development of new analysis tools. The first version of WARPP can be securely accessed at https://parasiticplants.app. The source code is licensed under GNU GPLv2 and is available at https://github.com/wickeLab/WARPP.
Biotin attachment domain-containing proteins mediate hydroxy fatty acid-dependent inhibition of acetyl CoA carboxylase
Authors: Yu Xiao-Hong , Cai Yuanheng , Keereetaweep Jantana , Wei Kenneth , Chai Jin , Deng Elen , Liu Hui , Shanklin John 
Published: January 2021

Abstract
Hundreds of naturally occurring specialized fatty acids (FAs) have potential as desirable chemical feedstocks if they could be produced at large scale by crop plants; however, transgenic expression of their biosynthetic genes has generally been accompanied by dramatic reductions in oil yield. For example, expression of castor (Ricinus communis) FA hydroxylase (FAH) in the Arabidopsis thaliana FA elongation mutant fae1 resulted in a 50% reduction of FA synthesis rate that was attributed to inhibition of acetyl-CoA carboxylase (ACCase) by an undefined mechanism. Here, we tested the hypothesis that the ricinoleic acid-dependent decrease in ACCase activity is mediated by biotin attachment domain-containing (BADC) proteins. BADCs are inactive homologs of biotin carboxy carrier protein that lack a biotin cofactor and can inhibit ACCase. Arabidopsis contains three BADC genes. To reduce expression levels of BADC1 and BADC3 in fae1/FAH plants, a homozygous badc1,3/fae1/FAH line was created. The rate of FA synthesis in badc1,3/fae1/FAH seeds doubled relative to fae1/FAH, restoring it to fae1 levels, increasing both native FA and HFA accumulation. Total FA per seed, seed oil content, and seed yield per plant all increased in badc1,3/fae1/FAH, to 5.8 µg, 37%, and 162 mg, respectively, relative to 4.9 µg, 33%, and 126 mg, respectively, for fae1/FAH. Transcript levels of FA synthesis-related genes, including those encoding ACCase subunits, did not significantly differ between badc1,3/fae1/FAH and fae1/FAH. These results demonstrate that BADC1 and BADC3 mediate ricinoleic acid-dependent inhibition of FA synthesis. We propose that BADC-mediated FAS inhibition as a general mechanism that limits FA accumulation in specialized FA-accumulating seeds.
Characterization of the Bubblegum acyl-CoA synthetase of Microchloropsis gaditana
Authors: Billey Elodie , Magneschi Leonardo , Leterme Sébastien , Bedhomme Mariette , Andres-Robin Amélie , Poulet Laurent , Michaud Morgane , Finazzi Giovanni , Dumas Renaud , Crouzy Serge , Laueffer Frédéric , Fourage Laurent , Rébeillé Fabrice , Amato Alberto , Collin Séverine , Jouhet Juliette , Maréchal Eric 
Published: January 2021

Abstract
The metabolic pathways of glycerolipids are well described in cells containing chloroplasts limited by a two-membrane envelope but not in cells containing plastids limited by four membranes, including heterokonts. Fatty acids (FAs) produced in the plastid, palmitic and palmitoleic acids (16:0 and 16:1), are used in the cytosol for the synthesis of glycerolipids via various routes, requiring multiple acyl-Coenzyme A (CoA) synthetases (ACS). Here, we characterized an ACS of the Bubblegum subfamily in the photosynthetic eukaryote Microchloropsis gaditana, an oleaginous heterokont used for the production of lipids for multiple applications. Genome engineering with TALE-N allowed the generation of MgACSBG point mutations, but no knockout was obtained. Point mutations triggered an overall decrease of 16:1 in lipids, a specific increase of unsaturated 18-carbon acyls in phosphatidylcholine and decrease of 20-carbon acyls in the betaine lipid diacylglyceryl–trimethyl–homoserine. The profile of acyl-CoAs highlighted a decrease in 16:1-CoA and 18:3-CoA. Structural modeling supported that mutations affect accessibility of FA to the MgACSBG reaction site. Expression in yeast defective in acyl-CoA biosynthesis further confirmed that point mutations affect ACSBG activity. Altogether, this study supports a critical role of heterokont MgACSBG in the production of 16:1-CoA and 18:3-CoA. In M. gaditana mutants, the excess saturated and monounsaturated FAs were diverted to triacylglycerol, thus suggesting strategies to improve the oil content in this microalga.
Identification and characterization of sorgomol synthase in sorghum strigolactone biosynthesis
Authors: Wakabayashi Takatoshi , Ishiwa Shunsuke , Shida Kasumi , Motonami Noriko , Suzuki Hideyuki , Takikawa Hirosato , Mizutani Masaharu , Sugimoto Yukihiro 
Published: January 2021

Abstract
Strigolactones (SLs), first identified as germination stimulants for root parasitic weeds, act as endogenous phytohormones regulating shoot branching and as root-derived signal molecules mediating symbiotic communications in the rhizosphere. Canonical SLs typically have an ABCD ring system and can be classified into orobanchol- and strigol-type based on the C-ring stereochemistry. Their simplest structures are 4-deoxyorobanchol (4DO) and 5-deoxystrigol (5DS), respectively. Diverse canonical SLs are chemically modified with one or more hydroxy or acetoxy groups introduced into the A- and/or B-ring of these simplest structures, but the biochemical mechanisms behind this structural diversity remain largely unexplored. Sorgomol in sorghum (Sorghum bicolor [L.] Moench) is a strigol-type SL with a hydroxy group at C-9 of 5DS. In this study, we characterized sorgomol synthase. Microsomal fractions prepared from a high-sorgomol-producing cultivar of sorghum, Sudax, were shown to convert 5DS to sorgomol. A comparative transcriptome analysis identified SbCYP728B subfamily as candidate genes encoding sorgomol synthase. Recombinant SbCYP728B35 catalyzed the conversion of 5DS to sorgomol in vitro. Substrate specificity revealed that the C-8bS configuration in the C-ring of 5DS stereoisomers was essential for this reaction. The overexpression of SbCYP728B35 in Lotus japonicus hairy roots, which produce 5DS as an endogenous SL, also resulted in the conversion of 5DS to sorgomol. Furthermore, SbCYP728B35 expression was not detected in nonsorgomol-producing cultivar, Abu70, suggesting that this gene is responsible for sorgomol production in sorghum. Identification of the mechanism modifying parental 5DS of strigol-type SLs provides insights on how plants biosynthesize diverse SLs.
The gibberellin signaling negative regulator RGA-LIKE3 promotes seed storage protein accumulation
Authors: Hu Yilong , Zhou Limeng , Yang Yuhua , Zhang Wenbin , Chen Zhonghui , Li Xiaoming , Qian Qian , Kong Fanjiang , Li Yuge , Liu Xu , Hou Xingliang 
Published: January 2021

Abstract
Seed storage protein (SSP) acts as one of the main components of seed storage reserves, of which accumulation is tightly mediated by a sophisticated regulatory network. However, whether and how gibberellin (GA) signaling is involved in this important biological event is not fully understood. Here, we show that SSP content in Arabidopsis (Arabidopsis thaliana) is significantly reduced by GA and increased in the GA biosynthesis triple mutant ga3ox1/3/4. Further investigation shows that the DELLA protein RGA-LIKE3 (RGL3), a negative regulator of GA signaling, is important for SSP accumulation. In rgl3 and 35S:RGL3-HA, the expression of SSP genes is down- and upregulated, respectively, compared with that in the wild-type. RGL3 interacts with ABSCISIC ACID INSENSITIVE3 (ABI3), a critical transcription factor for seed developmental processes governing SSP accumulation, both in vivo and in vitro, thus greatly promoting the transcriptional activating ability of ABI3 on SSP genes. In addition, genetic evidence shows that RGL3 and ABI3 regulate SSP accumulation in an interdependent manner. Therefore, we reveal a function of RGL3, a little studied DELLA member, as a coactivator of ABI3 to promote SSP biosynthesis during seed maturation stage. This finding advances the understanding of mechanisms in GA-mediated seed storage reserve accumulation.
Phosphorus deprivation affects composition and spatial distribution of membrane lipids in legume nodules
Authors: Dokwal Dhiraj , Romsdahl Trevor B , Kunz Daniel A , Alonso Ana Paula , Dickstein Rebecca 
Published: January 2021

Abstract
In legumes, symbiotic nitrogen (N) fixation (SNF) occurs in specialized organs called nodules after successful interactions between legume hosts and rhizobia. In a nodule, N-fixing rhizobia are surrounded by symbiosome membranes, through which the exchange of nutrients and ammonium occurs between bacteria and the host legume. Phosphorus (P) is an essential macronutrient, and N2-fixing legumes have a higher requirement for P than legumes grown on mineral N. As in the previous studies, in P deficiency, barrel medic (Medicago truncatula) plants had impaired SNF activity, reduced growth, and accumulated less phosphate in leaves, roots, and nodules compared with the plants grown in P sufficient conditions. Membrane lipids in M. truncatula tissues were assessed using electrospray ionization–mass spectrometry. Galactolipids were found to increase in P deficiency, with declines in phospholipids (PL), especially in leaves. Lower PL losses were found in roots and nodules. Subsequently, matrix-assisted laser desorption/ionization–mass spectrometry imaging was used to spatially map the distribution of the positively charged phosphatidylcholine (PC) species in nodules in both P-replete and P-deficient conditions. Our results reveal heterogeneous distribution of several PC species in nodules, with homogeneous distribution of other PC classes. In P poor conditions, some PC species distributions were observed to change. The results suggest that specific PC species may be differentially important in diverse nodule zones and cell types, and that membrane lipid remodeling during P stress is not uniform across the nodule.
Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Authors: Höhner Ricarda , Day Philip M , Zimmermann Sandra E , Lopez Laura S , Krämer Moritz , Giavalisco Patrick , Correa Galvis Viviana , Armbruster Ute , Schöttler Mark Aurel , Jahns Peter , Krueger Stephan , Kunz Hans-Henning 
Published: January 2021

AbstractDuring photosynthesis, electrons travel from light-excited chlorophyll molecules along the electron transport chain to the final electron acceptor nicotinamide adenine dinucleotide phosphate (NADP) to form NADPH, which fuels the Calvin–Benson–Bassham cycle (CBBC). To allow photosynthetic reactions to occur flawlessly, a constant resupply of the acceptor NADP is mandatory. Several known stromal mechanisms aid in balancing the redox poise, but none of them utilizes the structurally highly similar coenzyme NAD(H). Using Arabidopsis (Arabidopsis thaliana) as a C3-model, we describe a pathway that employs the stromal enzyme PHOSPHOGLYCERATE DEHYDROGENASE 3 (PGDH3). We showed that PGDH3 exerts high NAD(H)-specificity and is active in photosynthesizing chloroplasts. PGDH3 withdrew its substrate 3-PGA directly from the CBBC. As a result, electrons become diverted from NADPH via the CBBC into the separate NADH redox pool. pgdh3 loss-of-function mutants revealed an overreduced NADP(H) redox pool but a more oxidized plastid NAD(H) pool compared to wild-type plants. As a result, photosystem I acceptor side limitation increased in pgdh3. Furthermore, pgdh3 plants displayed delayed CBBC activation, changes in nonphotochemical quenching, and altered proton motive force partitioning. Our fluctuating light-stress phenotyping data showed progressing photosystem II damage in pgdh3 mutants, emphasizing the significance of PGDH3 for plant performance under natural light environments. In summary, this study reveals an NAD(H)-specific mechanism in the stroma that aids in balancing the chloroplast redox poise. Consequently, the stromal NAD(H) pool may provide a promising target to manipulate plant photosynthesis.
Autophagy is required for lipid homeostasis during dark-induced senescence
Authors: Barros Jessica A S , Magen Sahar , Lapidot-Cohen Taly , Rosental Leah , Brotman Yariv , Araújo Wagner L , Avin-Wittenberg Tamar 
Published: January 2021

AbstractAutophagy is an evolutionarily conserved mechanism that mediates the degradation of cytoplasmic components in eukaryotic cells. In plants, autophagy has been extensively associated with the recycling of proteins during carbon-starvation conditions. Even though lipids constitute a significant energy reserve, our understanding of the function of autophagy in the management of cell lipid reserves and components remains fragmented. To further investigate the significance of autophagy in lipid metabolism, we performed an extensive lipidomic characterization of Arabidopsis (Arabidopsis thaliana) autophagy mutants (atg) subjected to dark-induced senescence conditions. Our results revealed an altered lipid profile in atg mutants, suggesting that autophagy affects the homeostasis of multiple lipid components under dark-induced senescence. The acute degradation of chloroplast lipids coupled with the differential accumulation of triacylglycerols (TAGs) and plastoglobuli indicates an alternative metabolic reprogramming toward lipid storage in atg mutants. The imbalance of lipid metabolism compromises the production of cytosolic lipid droplets and the regulation of peroxisomal lipid oxidation pathways in atg mutants.
Designing Ghosts, Queer Readership, and the Phantom Public in E. M. Forster’s ‘Dr Woolacott’
Authors: Christie Stuart 
Published: January 2021

Abstract
In an undated manuscript from the 1920s, E. M. Forster sketched out notes towards a theory he called ‘writing to the body with the body’, a ‘melting’ of sentiment into disinterested aesthetics, he identified as pornographic. The ‘On Pornography and Sentiment’ fragment not only reframes our understanding of Forster’s emerging stance during this period as a champion of free speech but also highlights his less well-known status as the nodal figure for a younger generation of gay writers with whom he shared drafts of his erotic short stories. My close readings of selections from Forster’s unfinished notes, his roughly contemporary work of criticism, Aspects of the Novel (1927), as well as his posthumously published short story, ‘Dr Woolacott’, suggest that Forster’s theory of sentimentalized aesthetics made the beginnings of a capable critique. By circulating his short stories, Forster sought to check mainstream censoriousness concerning ‘obscene’ texts; moreover, his ‘refunctioning’ of illicit desires to an ethical purpose enlivened the ‘phantom’ potential of the modernist public sphere (Robbins) and actively facilitated the formation of an inter-generational intimate public (Berlant).
Abnormal Brain Bioenergetics in First-Episode Psychosis
Authors: Yuksel Cagri , Chen Xi , Chouinard Virginie-Anne , Nickerson Lisa D , Gardner Margaret , Cohen Talia , Öngür Dost , Du Fei 
Published: January 2021

Abstract

Background
Converging evidence indicates impaired brain energy metabolism in schizophrenia and other psychotic disorders. Creatine kinase (CK) is pivotal in providing adenosine triphosphate in the cell and maintaining its levels when energy demand is increased. However, the activity of CK has not been investigated in patients with first-episode schizophrenia spectrum disorders.

Methods
Using in vivo phosphorus magnetization transfer spectroscopy, we measured CK first-order forward rate constant (kf) in the frontal lobe, in patients with first-episode psychosis (FEP; n = 16) and healthy controls (n = 34), at rest.

Results
CK kf was significantly reduced in FEP compared to healthy controls. There were no differences in other energy metabolism-related measures, including phosphocreatine (PCr) or ATP, between groups. We also found increase in glycerol-3-phosphorylcholine, a putative membrane breakdown product, in patients.

Conclusions
The results of this study indicate that brain bioenergetic abnormalities are already present early in the course of schizophrenia spectrum disorders. Future research is needed to identify the relationship of reduced CK kf with psychotic symptoms and to test treatment alternatives targeting this pathway. Increased glycerol-3-phosphorylcholine is consistent with earlier studies in medication-naïve patients and later studies in first-episode schizophrenia, and suggest enhanced synaptic pruning.
Using ecological variables to predict Ross River virus disease incidence in South Australia
Authors: Liu Jingwen , Hansen Alana , Cameron Scott , Williams Craig , Fricker Stephen , Bi Peng 
Published: January 2021

Abstract

Background
Ross River virus (RRV) disease is Australia's most widespread vector-borne disease causing significant public health concern. The aim of this study was to identify the ecological covariates of RRV risk and to develop epidemic forecasting models in a disease hotspot region of South Australia.

Methods
Seasonal autoregressive integrated moving average models were used to predict the incidence of RRV disease in the Riverland region of South Australia, an area known to have a high incidence of the disease. The model was developed using data from January 2000 to December 2012 then validated using disease notification data on reported cases for the following year.

Results
Monthly numbers of the mosquito Culex annulirostris (β=0.033, p&lt;0.001) and total rainfall (β=0.263, p=0.002) were significant predictors of RRV transmission in the study region. The forecasted RRV incidence in the predictive model was generally consistent with the actual number of cases in the study area.

Conclusions
A predictive model has been shown to be useful in forecasting the occurrence of RRV disease, with increased vector populations and rainfall being important factors associated with transmission. This approach may be useful in a public health context by providing early warning of vector-borne diseases in other settings.
What's in an “ASAM-based Assessment?” Variations in Assessment and Level of Care Determination in Systems Required to Use ASAM Patient Placement Criteria
Authors: Padwa Howard , Mark Tami L. , Wondimu Betselot 
Published: January 2021

Objectives:
When clients begin substance use disorder (SUD) treatment, it is critical to ensure that they receive treatment that matches their needs and preferences. A growing number of payors are requiring the use of multidimensional assessments such as assessments based on the American Society of Addiction Medicine (ASAM) criteria, which describe 6 dimensions that should be used to inform decisions about patient placement. However, ASAM guidance does not list specific questions to ask or instruments to use to elicit this information. This paper evaluates differences among the assessment tools being used by SUD service systems that are required to use ASAM-based assessments to make patient placement decisions.

Methods:
We analyzed 29 different ASAM-based assessments being used by California counties to make patient placement decisions using conventional and summative content analysis techniques.

Results:
All assessments were organized by the 6 ASAM dimensions. However, some of them only ask 1 or 2 questions per dimension, while others ask over 20, and some ask over 100 depending on patient responses. There is significant heterogeneity in the information the assessments collect and how it is used to generate patient placement decisions. Among the 29 assessments examined, there are 8 different algorithms or instructions on how to translate information from assessments into level of care recommendations.

Conclusions:
The differences among the ASAM-based assessments examined in this paper suggest a need to implement fidelity standards, enhance training, and create resources to help systems create and utilize assessment and patient placement tools that are consistent across the SUD treatment field.