bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beet taproot plasma membrane sugar transport revisited
Authors: Reyer Antonella , Bazihizina Nadia , Jaślan Justyna , Scherzer Sönke , Schäfer Nadine , Jaślan Dawid , Becker Dirk , Müller Thomas D. , Pommerrenig Benjamin , Neuhaus H. Ekkehard , Marten Irene , Hedrich Rainer 
Published: September 2021

SUMMARYSugar beet (Beta vulgaris) is the major sugar-producing crop in Europe and Northern America, as the taproot stores sucrose at a concentration of around 20%. Genome sequence analysis together with biochemical and electrophysiological approaches led to the identification and characterization of the TST sucrose transporter driving vacuolar sugar accumulation in the taproot. However, the sugar transporters mediating sucrose uptake across the plasma membrane of taproot parenchyma cells remained unknown. As with glucose, sucrose stimulation of taproot parenchyma cells caused inward proton fluxes and plasma membrane depolarization, indicating a sugar/proton symport mechanism. To decipher the nature of the corresponding proton-driven sugar transporters, we performed transcriptomic taproot profiling and identified the cold-induced PMT5a and STP13 transporters. When expressed inXenopus laevisoocytes, BvPMT5a was characterized as a voltage- and H+-driven low-affinity glucose transporter, which does not transport sucrose. In contrast, BvSTP13 operated as a high-affinity H+/sugar symporter, transporting glucose better than sucrose, and being more cold-tolerant than BvPMT5a. Modeling of the BvSTP13 structure with bound mono- and disaccharides suggests plasticity of the binding cleft to accommodate the different saccharides. The identification of BvPMT5a and BvSTP13 as taproot sugar transporters could improve breeding of sugar beet to provide a sustainable energy crop.Significance StatementIn vivoelectrophysiological studies with sugar beet taproots provide clear evidence for proton-coupled glucose and sucrose uptake into taproot parenchyma cells. In search for the molecular entities, the taproot-expressed BvPMT5a and BvSTP13 carriers were studied in detail, because they mediate proton-driven import of glucose and sucrose and thus provide proper candidates for sugar beet plasma membrane sugar-proton cotransporters.
Cryptococcus neoformans releases proteins during intracellular residence that affect the outcome of the fungal-macrophage interaction
Authors: Jung Eric H. , Park Yoon-Dong , Dragotakes Quigly , Ramirez Lia Sanchez , Smith Daniel Q. , Dziedzic Amanda , Williamson Peter R. , Jedlicka Anne , Casadevall Arturo , Coelho Carolina 
Published: September 2021

AbstractCryptococcus neoformans is a facultative intracellular pathogen that can replicate and disseminate in mammalian macrophages. In this study, we analyzed fungal proteins identified in murine macrophage-like cells after infection with C. neoformans. To accomplish this, we developed a protocol to identify proteins released from cryptococcal cells inside macrophage-like cells; we identified 127 proteins of fungal origin in infected macrophage-like cells. Among the proteins identified was urease, a known virulence factor, and others such as transaldolase and phospholipase D, which have catalytic activities that could contribute to virulence. This method provides a straightforward methodology to study host-pathogen interactions. We chose to study further Yor1, a relatively uncharacterized protein belonging to the large family of ATP binding cassette transporter (ABC transporters). These transporters belong to a large and ancient protein family found in all extant phyla. While ABC transporters have an enormous diversity of functions across varied species, in pathogenic fungi they are better studied as drug efflux pumps. Analysis of C. neoformans yor1Δ strains revealed defects in non-lytic exocytosis and capsule size, when compared to wild-type strains. We detected no difference in growth rates, cell body size and vesicle secretion. Our results indicate that C. neoformans releases a large suite of proteins during macrophage infection, some of which can modulate fungal virulence and are likely to affect the fungal-macrophage interaction.
High-resolution imaging and manipulation of endogenous AMPA receptor surface mobility during synaptic plasticity and learning
Authors: Getz Angela M. , Ducros Mathieu , Breillat Christelle , Lampin-Saint-Amaux Aurélie , Daburon Sophie , François Urielle , Nowacka Agata , Fernández-Monreal Mónica , Hosy Eric , Lanore Frédéric , Zieger Hanna , Sainlos Matthieu , Humeau Yann , Choquet Daniel 
Published: September 2021

SUMMARYRegulation of synaptic neurotransmitter receptor content is a fundamental mechanism for tuning synaptic efficacy during experience-dependent plasticity and behavioral adaptation. However, experimental approaches to track and modify receptor movements in integrated experimental systems are limited. Exploiting AMPA-type glutamate receptors (AMPAR) as a model, we generated a knock-in mouse expressing the biotin acceptor peptide (AP) tag on the GluA2 extracellular N-terminus. Cell-specific introduction of biotin ligase allows the use of monovalent or tetravalent avidin variants to respectively monitor or manipulate the surface mobility of endogenous AMPAR containing biotinylated AP-GluA2 in neuronal subsets. AMPAR immobilization precluded the expression of long-term potentiation and formation of contextual fear memory, allowing for target-specific control of the expression of synaptic plasticity and animal behavior. The AP tag knock-in model offers unprecedented access to resolve and control the spatiotemporal dynamics of endogenous receptors, and opens new avenues to study the molecular mechanisms of synaptic plasticity and learning.
Over-expression of the brassinosteroid gene TaDWF4 increases wheat productivity under low and sufficient nitrogen through enhanced carbon assimilation
Authors: Milner Matthew J. , Swarbreck Stéphanie M. , Craze Melanie , Bowden Sarah , Griffiths Howard , Bentley Alison R. , Wallington Emma J. 
Published: September 2021

AbstractThere is a strong pressure to reduce nitrogen (N) fertiliser inputs while maintaining or increasing current cereal crop yields. Brassinosteroids, (BR), are a group of phytohormones essential for plant growth and development, that have been demonstrated to regulate several agronomic traits. DWF4 encodes a cytochrome P450 that catalyses a rate-limiting step in BR synthesis. We show that overexpression of the dominant shoot expressed homoeologue TaDWF4-B in wheat can increase plant productivity by up to 105% under a range of N levels on marginal soils, resulting in increased N use efficiency (NUE). We show that a two to four-fold increase in TaDWF4 transcript levels enhances the responsiveness of genes regulated by N. The productivity increases seen were primarily due to the maintenance of photosystem II operating efficiency and carbon assimilation in plants when grown under limiting N conditions and not an overall increase in photosynthesis capacity. The increased biomass production and yield per plant in TaDWF4 OE lines could be linked to modified carbon partitioning and changes in expression pattern of the growth regulator Target Of Rapamycin, offering a route towards breeding for sustained yield and lower N inputs.
miR2105 regulates ABA biosynthesis via OsbZIP86-OsNCED3module to contribute to drought tolerance in rice
Authors: Gao Weiwei , Li Mingkang , Yang Songguang , Gao Chunzhi , Su Yan , Zeng Xuan , Jiao Zhengli , Xu Weijuan , Zhang Mingyong , Xia Kuaifei 
Published: September 2021

AbstractInduced abscisic acid (ABA) biosynthesis plays an important role in plant tolerance to abiotic stresses, including drought, cold and salinity. However, regulation pathway of the ABA biosynthesis in response to stresses is unclear. Here, we identified a rice miRNA, osa-miR2105 (miR2105), which plays a crucial role in ABA biosynthesis under drought stress. Analysis of expression, transgenic rice and cleavage site showed thatOsbZIP86is a target gene of miR2105. Subcellular localization and luciferase activity assays showed that OsbZIP86 is a nuclear transcription factor.In vivoandin vitroanalyses showed that OsbZIP86 directly binds to the promoter ofOsNCED3, and interacts with OsSAPK10, resulting in enhanced-expression ofOsNCED3. Transgenic rice plants with knock-down of miR2105 or overexpression ofOsbZIP86showed higher ABA content, more tolerance to drought, a lower rate of water loss, more stomatal closure than wild type rice ZH11 under drought stress. These rice plants showed no penalty with respect to agronomic traits under normal conditions. By contrast, transgenic rice plants with miR2105 overexpression,OsbZIP86downregulation, orOsbZIP86knockout displayed less tolerance to drought stress and other phenotypes. Collectively, our results show that a regulatory network of ‘miR2105-OsSAPK10/OsbZIP86-OsNCED3’ control ABA biosynthesis in response to drought stress.One-sentence summary‘miR2105-OsbZIP86-OsNCED3’ module plays crucial role in mediating ABA biosynthesis to contribute to drought tolerance with no penalty with respect to agronomic traits under normal conditions.
Investigation of the impact of stool collection methods on the metabolomics analysis/profiles of infant fecal samples
Authors: Homann Chiara-Maria , Dizzell Sara , Azab Sandi M. , Hutton Eileen K. , Morrison Katherine M. , Stearns Jennifer C. 
Published: September 2021

AbstractMetabolomic studies are important to understand microbial metabolism and interaction between the host and the gut microbiome. Although there have been efforts to standardize sample processing in metabolomic studies, infant samples are mostly disregarded. In birth cohort studies, the use of diaper liners is prevalent and its impact on fecal metabolic profile remains untested. In this study, we compared metabolite profiles of fecal samples collected as solid stool and those collected from stool saturated liner. One infant’s stool sample was collected in triplicate for solid stool and stool saturated liner. Comprehensive metabolomics analysis of the fecal samples was performed using NMR, UPLC and DI-MS. The total number, identities and concentrations of the metabolites were determined and compared between stool sample collection methods (stool vs. liner). The number and identity of metabolites did not differ between collection methods for NMR and DI-MS when excluding metabolites with a coefficient of variation (CV) > 40%. NMR analysis demonstrated lowest bias between collection methods, and lowest technical precision between triplicates of the same method followed by DI-MS then UPLC. Concentrations of many metabolites from stool and stool saturated liner differed significantly as revealed by Bland-Altman plots and t-tests. Overall, a mean bias of 10.2% in the Bland-Altman analysis was acceptable for some metabolites confirming mutual agreement but not for others with a wide range of bias (−97-117%). Consequently, stool and stool-saturated liner could be used interchangeably only for some select metabolite classes e.g. amino acids. Differences between the metabolomic profiles of solid stool samples and stool saturated liner samples for some important molecules e.g., ethanol, fumarate, short chain fatty acids and bile acids, indicate the need for standardization in stool collection method for metabolomic studies performed in infants.
Selective Microautophagy of Proteasomes is Initiated by ESCRT-0 and Is Promoted by Proteasome Ubiquitylation
Authors: Li Jianhui , Hochstrasser Mark 
Published: September 2021

AbstractThe proteasome is central to proteolysis by the ubiquitin-proteasome system under normal growth conditions but is itself degraded through macroautophagy under nutrient stress. A recently described AMPK (AMP-activated protein kinase)-regulated ESCRT (endosomal sorting complex required for transport)-dependent microautophagy pathway also regulates proteasome trafficking and degradation in low glucose conditions in yeast. Aberrant proteasomes are more prone to microautophagy, suggesting the ESCRT system fine-tunes proteasome quality control under low glucose stress. Here we uncover additional features of the selective microautophagy of proteasomes. Genetic or pharmacological induction of aberrant proteasomes is associated with increased mono- or oligo-ubiquitylation of proteasome components, which appear to be recognized by ESCRT-0. AMPK controls this pathway in part by regulating the trafficking of ESCRT-0 to the vacuole surface, which also leads to degradation of the Vps27 subunit of ESCRT-0. The Rsp5 ubiquitin ligase contributes to proteasome subunit ubiquitylation, and multiple ubiquitin-binding elements in Vps27 are involved in their recognition. We propose that ESCRT-0 at the vacuole surface recognizes ubiquitylated proteasomes and initiates their microautophagic elimination during glucose depletion.Saummary statementESCRT-0 selectively targets aberrant proteasomes for microautophagy by recognition of proteasome ubiquitylation status to fine-tune proteasome quality control under low glucose conditions.
The nuclear transport factor CSE1 drives macronuclear volume increase and macronuclear node coalescence inStentor coeruleus
Authors: McGillivary Rebecca M. , Sood Pranidhi , Hammar Katherine , Marshall Wallace F. 
Published: September 2021

SummaryThe giant ciliate,Stentor coeruleus, provides a unique opportunity to study nuclear shape because its macronucleus undergoes a rapid, dramatic, and developmentally regulated shape change. During a 2 hour time period within cell division and regeneration, the 400 um long moniliform macronucleus coalesces into a single mass, elongates into a vermiform shape, and then renodulates, returning to its original beads-on-a-string morphology.1Previous work from the 1960’s - 1980’s demonstrated that the macronuclear shape change is a highly regulated part of cell division and regeneration2,3, but the molecular pathways driving these changes are unknown. With the recent availability of a sequencedStentorgenome, a transcriptome during regeneration, and molecular tools like RNAi4–6, it is now possible to investigate the molecular mechanisms that drive macronuclear shape change. We found that the volume of the macronucleus increases during coalescence, suggesting an inflation-based mechanism. When the nuclear transport factor, CSE1, is knocked down by RNAi, the shape and volume changes of the macronucleus are attenuated, and nuclear morphology is altered. CSE1 protein undergoes a dynamic relocalization correlated with nuclear shape changes, being mainly cytoplasmic prior to nuclear coalescence, and accumulating inside the macronucleus during coalescence. At the end of regeneration, CSE1 is degraded during the period when the macronucleus returns to its pre-coalescence volume. We propose a model in which nuclear transport via CSE1 increases the volume of the macronucleus, thereby decreasing the surface to volume ratio and driving coalescence of the many nodes into a single mass.
Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants
Authors: Parn Simone , Jabbour Gabriel , Nguyenkhoa Vincent , Dakshanamurthy Sivanesan 
Published: September 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has challenged public health at an unprecedented scale which has led to a dramatic loss of human life worldwide. To design a protective vaccine against SARS-CoV-2, it is necessary to understand which SARS-CoV-2 specific epitopes can elicit a T cell response and provide protection across a broad population. In this study, PLpro and RdRp, two immunogenic non-structural proteins from an immunodominant gene region ORF1ab, as well as ORF3a and ORF9b are identified as potential vaccine targets against SARS-CoV-2. To select top epitopes for vaccine design, we used various clinical properties, such as antigenicity, allergenicity, toxicity and IFN-y secretion. The analysis of CD8 and CD4 T cell epitopes revealed multiple potential vaccine constructs that cover a high percentage of the world population. We identified 8 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 proteins for nsp3, 4 for nsp12, 11 for ORF3a and 3 for ORF9b that are common across four lineages of variants of concern – B.1.1.7, P.1, B.1.351 and B.1.617.2, which protect 98.12%, 87.08%, 96.07% and 63.8% of the world population, respectively. We also identified variant specific T cell epitopes that could be useful in targeting each variant strain separately. Including the prediction of mouse MHC affinity towards our top CD8 epitopes, our study revealed a total of 3 immunogenic, antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD8 epitopes overlapping with 6 antigenic, non-allergenic, non-toxic, stable and IFN-y inducing CD4 epitopes across all four variants of concern which can effectively be utilized in pre-clinical studies. The landscape of SARS-CoV-2 T cell epitopes that we identified can help lead SARS-CoV-2 vaccine development as well as epitope-based peptide vaccine research in the future.
Association of RACK1 protein with ribosomes in Plasmodium falciparum
Authors: Erath Jessey , Djuranovic Sergej 
Published: September 2021

AbstractThe receptor for activated C-kinase 1 (RACK1), a highly conserved eukaryotic protein, is known to have many, varying biological roles and functions. Previous work has established RACK1 as a ribosomal protein, with defined regions important for binding ribosomes in both human and yeast cells. In Plasmodium falciparum, RACK1 has been shown to be required for parasite growth, however conflicting evidence has been presented about the RACK1 ribosome binding and its role in mRNA translation. Given the importance of RACK1 as a regulatory component of mRNA translation and ribosome quality control, the case could be made in parasites for either of the binary options: bound or unbound to the ribosome. Here we used bioinformatics and transcription analyses to describe P. falciparum RACK1 protein. Based on homology modeling and structural analyses, we generated a model of P. falciparum RACK1 protein. We created and explored mutant and chimeric human and P. falciparum RACK1 proteins binding properties to the human and P. falciparum ribosome. Wild type, chimeric and mutant RACK1 proteins suggest different binding characteristics for P. falciparum and human RACK1 proteins and different regions being involved in their ribosome association. The ribosomal binding of RACK1 variants in human and parasite cells shown here demonstrates that although RACK1 proteins have highly conserved sequences and structures across species, ribosomal binding is affected by species specific alterations to the protein. In conclusion, we show that in the case of P. falciparum, contrary to the structural data, RACK1 is found to be bound to ribosomes and in actively translating polysomes of P. falciparum cells.
Visuospatial information foraging describes search behavior in learning latent environmental features
Authors: Barack David L , Bakkour Akram , Shohamy Daphna , Salzman C Daniel 
Published: September 2021

AbstractIn the real world, making sequences of decisions to achieve goals often depends upon the ability to learn aspects of the environment that are not directly perceptible. Learning these so-called latent features requires seeking information about them, a process distinct from learning about near-term reward contingencies. Prior efforts to study latent feature learning often use single decisions, use few features, and fail to distinguish between reward-seeking and informationseeking. To overcome this, we designed a task in which humans and monkeys made a series of choices to search for shapes hidden on a grid. Reward and information outcomes from uncovering parts of shapes were not perfectly correlated and their effects could be disentangled. Members of both species adeptly learned the shapes and preferred to select informative tiles earlier in trials than rewarding ones, searching a part of the grid until their outcomes dropped below the average information outcome–a pattern consistent with foraging behavior. In addition, how quickly humans learned the shapes was predicted by how well their choice sequences matched the foraging pattern. This adaptive search for information may underlie the ability in humans and monkeys to learn latent features to support goal-directed behavior in the long run.
Epithelial Plasticity and Innate Immune Activation Promote Lung Tissue Remodeling following Respiratory Viral Infection
Authors: Beppu Andrew K. , Zhao Juanjuan , Yao Changfu , Carraro Gianni , Israely Edo , Coelho Anna Lucia , Hogaboam Cory M , Parks William C. , Kolls Jay K. , Stripp Barry R. 
Published: September 2021

SummaryEpithelial plasticity has been suggested in lungs of mice following genetic depletion of stem cells but is of unknown physiological relevance. Viral infection and chronic lung disease share similar pathological features of stem cell loss in alveoli, basal cell (BC) hyperplasia in small airways, and innate immune activation, that contribute to epithelial remodeling and loss of lung function. We show that a novel subset of distal airway secretory cells, intralobar serous (IS) cells, are activated to assume BC fates following influenza virus infection. Injury-induced hyperplastic BC (hBC) differ from pre-existing BC by high expression of IL-22Ra1 and undergo IL-22-dependent expansion for colonization of injured alveoli. Resolution of virus-elicited inflammation resulted in BC>IS re-differentiation in repopulated alveoli, and increased local expression of antimicrobial factors, but failed to replace normal alveolar epithelium. Epithelial plasticity therefore protects against mortality from acute respiratory viral infection but results in distal lung remodeling and loss of lung function.
Applying systematic bibliometric methods to track a journal’s impact and review its knowledge contribution
Authors: Anand Amitabh , Tripathi Ritu , Karumathil Anjana , Kalra Tanvika 
Published: September 2021

PurposeAdvanced bibliometric methods have emerged as key tools in mapping the history and trends of a discipline. This paper aims to demonstrate on applying various bibliometric methods to track a journal’s impact and review its knowledge contribution. In doing so, the authors take the case ofIIMB Management Review (IMR)journal focused on management discipline, in consideration of its 10 years of publication presence.Design/methodology/approachUsing bibliometric and Scopus metric methods, the authors map and analyze the productivity of IMR Journal and map its knowledge contributions.FindingsThe authors identify the IMR journal’s impact, its growth, the most prolific authors/affiliations, key research hotspots, cross-country collaboration and emerging trends over the past decade.Originality/valueA 10-year longitudinal review helps the target group identify the main themes. It also provides key empirical insights to the journal editorial board and library managers for future planning and growth of the journal.