bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complementary Phenotyping of Maize Root Architecture by Root Pulling Force and X-Ray Computed Tomography
Authors: Shao Mon-Ray , Jiang Ni , Li Mao , Howard Anne , Lehner Kevin , Mullen Jack L. , Gunn Shayla L. , McKay John K. , Topp Christopher N 
Published: March 2021

ABSTRACTThe root system is critical for the survival of nearly all land plants and a key target for improving abiotic stress tolerance, nutrient accumulation, and yield in crop species. Although many methods of root phenotyping exist, within field studies one of the most popular methods is the extraction and measurement of the upper portion of the root system, known as the root crown, followed by trait quantification based on manual measurements or 2D imaging. However, 2D techniques are inherently limited by the information available from single points of view. Here, we used X-ray computed tomography to generate highly accurate 3D models of maize root crowns and created computational pipelines capable of measuring 71 features from each sample. This approach improves estimates of the genetic contribution to root system architecture, and is refined enough to detect various changes in global root system architecture over developmental time as well as more subtle changes in root distributions as a result of environmental differences. We demonstrate that root pulling force, a high-throughput method of root extraction that provides an estimate of root biomass, is associated with multiple 3D traits from our pipeline. Our combined methodology can therefore be used to calibrate and interpret root pulling force measurements across a range of experimental contexts, or scaled up as a stand-alone approach in large genetic studies of root system architecture.
Nemertean, brachiopod and phoronid neuropeptidomics reveals ancestral spiralian signalling systems
Authors: Thiel Daniel , Yañez Guerra Luis A. , Franz-Wachtel Mirita , Hejnol Andreas , Jékely Gáspár 
Published: March 2021

AbstractNeuropeptides are diverse signalling molecules in animals commonly acting through G-protein coupled receptors (GPCRs). Neuropeptides and their receptors underwent extensive diversification in bilaterians and the relationships of many peptide-receptor systems have been clarified. However, we lack a detailed picture of neuropeptide evolution in lophotrochozoans as in-depth studies only exist for molluscs and annelids. Here we analyse peptidergic systems in Nemertea, Brachiopoda and Phoronida. We screened transcriptomes from thirteen nemertean, six brachiopod and four phoronid species for proneuropeptides and neuropeptide GPCRs. With mass spectrometry from the nemerteanLineus longissimus, we validated several predicted peptides and identified novel ones. Molecular phylogeny combined with peptide-sequence and gene-structure comparisons allowed us to comprehensively map spiralian neuropeptide evolution. We found most mollusc and annelid peptidergic systems also in nemerteans, brachiopods and phoronids. We uncovered previously hidden relationships including the orthologies of spiralian CCWamides to arthropod agatoxin-like peptides and of mollusc APGWamides to RGWamides from annelids, with orthologues systems in nemerteans, brachiopods and phoronids. We found that pleurin neuropeptides previously only found in molluscs are also present in nemerteans and brachiopods. We also identified cases of gene family duplications and losses. These include a protostome-specific expansion of RFamide/Wamide signalling, a spiralian expansion of GnRH-related peptides, and duplications of vasopressin/oxytocin before the divergence of brachiopods, phoronids and nemerteans. This analysis expands our knowledge of peptidergic signalling in spiralians and protostomes. Our annotated dataset of nearly 1,300 proneuropeptide sequences and 600 GPCRs presents a useful resource for further studies of neuropeptide signalling in protostomes.
Mass Dynamics 1.0: A streamlined, web-based environment for analyzing, sharing and integrating Label-Free Data
Authors: Bloom Joseph , Triantafyllidis Aaron , Burton (Ngov) Paula , Infusini Giuseppe , Webb Andrew 
Published: March 2021

AbstractLabel Free Quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web based analysis environment that can analyze and visualize LFQ data produced by software such as Maxquant. Unlike other tools, MD 1.0 utilizes cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardisation in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range.The MD 1.0 platform is available globally via:https://app.massdynamics.com/.Contactwebb@wehi.edu.au
A novel, anatomy-similar in vitro model of 3D airway epithelial for anti-coronavirus drug discovery
Authors: Zhang Yaling , Ma Dingailu , Zhang David Jitao , Liu Xin’an , Zhu Qihui , Wang Li , Gao Lu 
Published: March 2021

AbstractSARS-CoV-2 and its induced COVID-19 remains as a global health calamity. Severe symptoms and high mortality, caused by cytokine storm and acute respiratory distress syndrome in the lower respiratory airway, are always associated with elderly individuals and those with comorbidities; whereas mild or moderate COVID-19 patients have limited upper respiratory flu-like symptoms. There is an urgent need to investigate SARS-CoV-2 and other coronaviruses replication and immune responses in human respiratory systems. The human reconstituted airway epithelial air-liquid interface (ALI) models are the most physiologically relevant model for the investigation of coronavirus infection and virus-triggered innate immune signatures. We established ALI models representing both the upper and the lower respiratory airway to characterize the coronavirus infection kinetics, tissue pathophysiology, and innate immune signatures from upper and lower respiratory tract perspective. Our data suggested these in vitro ALI models maintain high physiological relevance with human airway tissues. The coronavirus induced immune response observed in these upper and lower respiratory airway models are similar to what has been reported in COVID-19 patients. The antiviral efficacy results of a few promising anti-coronavirus drugs in these models were consistent with previous reports and could be valuable for the human dose prediction. Taken together, our study demonstrates the importance of 3D airway epithelial ALI model for the understanding of coronavirus pathogenesis and the discovery and development of anti-coronavirus drugs.
Identification of a fully dechlorinated product of chlordecone in soil microcosms and enrichment cultures
Authors: Lomheim Line , Flick Robert , Rambinaising Suly , Gaspard Sarra , Edwards Elizabeth A. 
Published: March 2021

ABSTRACTAnaerobic microcosms constructed with soil from Guadeloupe, amended with electron donor (ethanol and acetone) and incubated for more than a decade, transformed chlordecone (CLD) into a suite of progressively more dechlorinated products, including a fully dechlorinated carboxylated indene product. This fully dechlorinated transformation product has never before been observed and indicates that complete dechlorination of CLD is possible. The carboxylated indene was detected by LC-MS and structure was confirmed by LC-MS/MS using a Q-Exactive Orbitrap mass spectrometer.
Laboratory Yeast Strains Rely On Oxidative Phosphorylation For Efficient ATP Production
Authors: Moharir Akshay , Gay Lincoln , Babst Markus 
Published: March 2021

AbstractEven though it is a well-accepted fact that the energy metabolism of yeast is likely to impact all cellular activities, surprising little is known about the ATP homeostasis of particular yeast strains that are commonly used in cell biological studies. Therefore, we determined key parameters such as oxygen consumption and fermentation rates of the lab strain SEY6210. Our data indicated that even at high glucose concentrations, SEY6210 produces 30-50% of cellular ATP from oxidative phosphorylation. Loss of respiration, either by disrupting ATP synthase function or by growth in anaerobic conditions, was not fully compensated by fermentation and as a result affected energy intensive processes such as the maintenance of the plasma membrane proton gradient and the associated import of nutrients.
Intra-species transcriptional profiling reveals key regulators ofCandida albicanspathogenic traits
Authors: Wang Joshua M. , Woodruff Andrew L. , Dunn Matthew J , Fillinger Robert J. , Bennett Richard J. , Anderson Matthew Z. 
Published: March 2021

ABSTRACTThe human commensal and opportunistic fungal pathogenCandida albicansdisplays extensive genetic and phenotypic variation across clinical isolates. Here, we performed RNA sequencing on 21 well-characterized isolates to examine how genetic variation contributes to gene expression differences, and to link these differences to phenotypic traits.C. albicansadapts primarily through clonal evolution and yet hierarchical clustering of gene expression profiles in this set of isolates did not reproduce their phylogenetic relationship. Strikingly, strain-specific gene expression was prevalent in some strain backgrounds. Association of gene expression with phenotypic data by differential analysis, linear correlation, and assembly of gene networks connected both previously characterized and novel genes with 23C. albicanstraits. Construction ofde novogene modules produced a gene atlas incorporating 67% ofC. albicansgenes and revealed correlations between expression modules and important phenotypes such as systemic virulence. Furthermore, targeted investigation of two modules that have novel roles in growth and filamentation supported our bioinformatic predictions. Together, these studies reveal widespread transcriptional variation acrossC. albicansisolates and identify genetic and epigenetic links to phenotypic variation based on co-expression network analysis.ImportanceInfectious fungal species are often treated uniformly despite clear evidence of genotypic and phenotypic heterogeneity being widespread across strains. Identifying the genetic basis for this phenotypic diversity is extremely challenging because of the tens or hundreds of thousands of variants that may distinguish two strains. Here we use transcriptional profiling to determine differences in gene expression that can be linked to phenotypic variation among a set of 21Candida albicansisolates. Analysis of this transcriptional dataset uncovered clear tends in gene expression characteristics for this species and new genes and pathways that associated with variation in pathogenic processes. Direct investigation confirmed functional predictions for a number of new regulators associated with growth and filamentation, demonstrating the utility of these approaches in linking genes to important phenotypes.
NPEPPS is a novel and druggable driver of platinum resistance
Authors: Jones Robert T. , Scholtes Mathijs , Goodspeed Andrew , Akbarzadeh Maryam , Mohapatra Saswat , Feldman Lily Elizabeth , Vekony Hedvig , Jean Annie , Tilton Charlene B. , Orman Michael V. , Romal Shahla , Deiter Cailin , Kan Tsung Wai , Xander Nathaniel , Araki Stephanie , Joshi Molishree , Javaid Mahmood , Layer Ryan , Laajala Teemu D. , Parker Sarah , Mahmoudi Tokameh , Zuiverloon Tahlita , Theodorescu Dan , Costello James C. 
Published: March 2021

ABSTRACTThere is an unmet need to improve efficacy of platinum-based cancer chemotherapy. Using multi-omic assessment of cisplatin-responsive and -resistant human bladder cancer cell lines and whole-genome CRISPR screens, we identified Puromycin-Sensitive Aminopeptidase, NPEPPS, as a novel driver of cisplatin resistance. NPEPPS depletion sensitizes resistant bladder cancer cells to cisplatinin vitroandin vivo. Conversely, overexpression of NPEPPS in sensitive cells increased cisplatin resistance. We show that NPEPPS affects treatment response by regulating intracellular cisplatin concentrations. Patient-derived organoids (PDOs) generated from bladder cancer samples before and after cisplatin-based treatment, and from patients who did not receive cisplatin, were evaluated for sensitivity to cisplatin and they were found to be concordant with clinical response. In PDOs, shRNA depletion or pharmacologic inhibition of NPEPPS led to increased cisplatin sensitivity, while NPEPPS overexpression had the opposite effect. Our data present NPEPPS as a novel and druggable driver of cisplatin resistance by regulating intracellular cisplatin concentrations, along with providing the preclinical data to support clinical trials combining NPEPPS inhibition with cisplatin.
Intraspecific variation in elemental accumulation and its association with salt tolerance inPaspalum vaginatum
Authors: Goad David M. , Kellogg Elizabeth A. , Baxter Ivan , Olsen Kenneth M. 
Published: March 2021

ABSTRACTMost plant species, including most crops, perform poorly in salt-affected soils because high sodium levels are cytotoxic and can disrupt uptake of water and important nutrients. Halophytes are species that have evolved adaptations to overcome these challenges and may be a useful source of knowledge for salt tolerance mechanisms and genes that may be transferable to crop species. The salt content of saline habitats can vary dramatically by location, providing ample opportunity for different populations of halophytic species to adapt to their local salt concentrations; however, the extent of this variation, and the physiology and polymorphisms that drive it, remain poorly understood. Differential accumulation of inorganic elements between genotypes or populations may play an important role in local salinity adaptation. To test this, we investigated the relationships between population structure, tissue ion concentrations (i.e., ionomic profiles) and salt tolerance in 17 “fine-textured” genotypes of the halophytic turfgrass seashore paspalum (Paspalum vaginatumSwartz). A high-throughput ionomics pipeline was used to quantify the shoot concentration of 18 inorganic elements across three salinity treatments. We found a significant relationship between population structure and ion accumulation, with strong correlations between principal components derived from genetic and ionomic data. Additionally, genotypes with higher salt tolerance accumulated more K and Fe and less Ca than less tolerant genotypes. Together these results indicate that differences in ion accumulation betweenP. vaginatumpopulations may reflect locally adapted salt stress responses.
Evaluation of protein kinase D auto-phosphorylation as biomarker for NLRP3 inflammasome activation
Authors: Heiser Diane , Rubert Joëlle , Unterreiner Adeline , Maurer Claudine , Kamke Marion , Bodendorf Ursula , Farady Christopher J. , Roediger Ben , Bornancin Frédéric 
Published: March 2021

AbstractBackgroundThe NLRP3 inflammasome is a critical component of sterile inflammation, which is involved in many diseases. However, there is currently no known proximal biomarker for measuring NLRP3 activation in pathological conditions. Protein kinase D (PKD) has emerged as an important NLRP3 kinase that catalyzes the release of a phosphorylated NLRP3 species that is competent for inflammasome complex assembly.MethodsTo explore the potential for PKD activation to serve as a selective biomarker of the NLRP3 pathway, we tested various stimulatory conditions in THP-1 and U937 cell lines, probing the inflammasome space beyond NLRP3. We analyzed the correlation between PKD activation (monitored by its auto-phosphorylation) and functional inflammasome readouts.ResultsPKD activation/auto-phosphorylation always preceded cleavage of caspase-1 and gasdermin D, and treatment with the PKD inhibitor CRT0066101 could block NLRP3 inflammasome assembly and interleukin-1β production. Conversely, blocking NLRP3 either genetically or using the MCC950 inhibitor prevented PKD auto-phosphorylation, indicating a bidirectional functional crosstalk between NLRP3 and PKD. Further assessments of the pyrin and NLRC4 pathways, however, revealed that PKD auto-phosphorylation can be triggered by a broad range of stimuli unrelated to NLRP3 inflammasome assembly.ConclusionAlthough PKD and NLRP3 become functionally interconnected during NLRP3 activation, the promiscuous reactivity of PKD challenges its potential use for tracing the NLRP3 inflammasome pathway.
Homothorax Controls a Binary Rhodopsin Switch inDrosophilaOcelli
Authors: Mishra Abhishek Kumar , Fritsch Cornelia , Voutev Roumen , Mann Richard S. , Sprecher Simon G. 
Published: March 2021

AbstractVisual perception of the environment is mediated by specialized photoreceptor (PR) neurons of the eye. Each PR expresses photosensitive opsins, which are activated by a particular wavelength of light. In most insects, the visual system comprises a pair of compound eyes that are mainly associated with motion detection, color or polarized light perception and a triplet of ocelli that are thought to be critical during flight to detect horizon and movements. It is widely believed that evolutionary diversification of compound eye and ocelli in insects occurred from an ancestral visual organ around 500 million years ago. Concurrently, opsin genes were also duplicated to provide distinct spectral sensitivities to different PRs of compound eye and ocelli. In the fruit flyDrosophila melanogaster, Rhodopsin1 (Rh1) and Rh2 are closely related opsins that are originated from the duplication of a single ancestral gene. However, in the visual organs, Rh2 is uniquely expressed in ocelli whereas Rh1 is uniquely expressed in outer PRs of the compound eye. It is currently unknown how this differential expression of Rh1 and Rh2 in the two visual organs is controlled to provide unique spectral sensitivities to ocelli and compound eyes. Here, we show that Homothorax (Hth) is expressed in ocelli and confers properrhodopsinexpression. We find that Hth controls a binary Rhodopsin switch in ocelli to promote Rh2 expression and repress Rh1 expression. Genetic and molecular analysis ofrh1andrh2supports that Hth acts through their promoters to regulate Rhodopsin expression in the ocelli. Finally, we also show that when ectopically expressed in the retina,hthis sufficient to induce Rh2 expression only at the outer PRs in a cell autonomous manner. We therefore propose that the diversification ofrhodpsinsin the ocelli and retinal outer PRs occurred by duplication of an ancestral gene, which is under the control of Homothorax.
Basement membrane proteins as a substrate for efficientTrypanosoma bruceidifferentiation in vitro
Authors: Rojas Federico , Cayla Mathieu , Matthews Keith R. 
Published: March 2021

AbstractThe ability to reproduce the developmental events of trypanosomes that occur in their mammalian hostin vitrooffers significant potential to assist in understanding of the underlying biology of the process. For example, the transition from bloodstream slender to bloodstream stumpy forms is a quorum-sensing response to the parasite-derived peptidase digestion products of environmental proteins. As an abundant physiological substratein vivo, we studied the ability of a basement membrane matrix enriched gel (BME) in the culture medium to support differentiation of pleomorphicTrypanosoma bruceito stumpy forms. BME comprises extracellular matrix proteins, which are among the most abundant proteins found in connective tissues in mammals and known substrates of parasite-released peptidases. We previously showed that two of these released peptidases are involved in generating a signal that promotes slender-to-stumpy differentiation. Here, we tested the ability of basement membrane extract to enhance parasite differentiation through its provision of suitable substrates to generate the quorum sensing signal, namely oligopeptides. Our results show that when grown in the presence of BME,T. bruceipleomorphic cells arrest at the G0/1 phase of the cell cycle and express the differentiation marker PAD1, the response being restricted to differentiation-competent parasites. Further, the stumpy forms generated in BME medium are able to efficiently proceed onto the next life cycle stagein vitro, procyclic forms, when incubated with cis-aconitate, further validating thein vitroBME differentiation system. Hence, BME provides a suitablein vitrosubstrate able to accurately recapitulate physiological parasite differentiation without the use of experimental animals.Author summaryAfrican trypanosome parasites responsible for human and animal trypanosomiasis, live extracellularly in their mammalian host and exploit environmental information to regulate their virulence and transmissibility. Morphological slender forms that proliferate in the mammalian host transform into the non-proliferative stumpy forms by receiving an extracellular signal generated by the accumulating parasites. Parasites secrete peptidases into the host that degrade extracellular matrix (ECM) proteins. In this study, we evaluated the capacity to generate stumpy formsin vitroby including a basement membrane extract into the culture medium. We show that cells exposed to ECM proteins are able to differentiate efficiently into cell-cycle arrested stumpy forms and that the generated differentiation signal depends on the stumpy induction signalling pathway. This method can be used to generate stumpy formsin vitro, these being suitable for experimental analysis, thereby reducing the use of mice.
Intestine-enrichedapolipoprotein borthologs are required for stem cell differentiation and regeneration in planarians
Authors: Wong Lily L. , Bruxvoort Christina G. , Cejda Nicholas I. , Otero Jannette Rodriguez , Forsthoefel David J. 
Published: March 2021

AbstractLipid metabolism plays an instructive role in regulating stem cell state and differentiation. However, the roles of lipid mobilization and utilization in stem cell-driven regeneration are unclear. Planarian flatworms readily restore missing tissue due to injury-induced activation of pluripotent somatic stem cells called neoblasts. Here, we identify two intestine-enriched orthologs ofapolipoprotein b, apob-1andapob-2,which mediate transport of neutral lipid stores from the intestine to target tissues including neoblasts, and are required for tissue homeostasis and regeneration. Inhibition ofapobfunction by RNAi causes head regression and lysis in uninjured animals, and delays body axis re-establishment and regeneration of multiple organs in amputated fragments. Furthermore,apobRNAi causes expansion of the population of differentiating neoblast progeny and dysregulates expression of genes enriched in differentiating and mature cells in eight major cell type lineages. We conclude that intestine-derived lipids serve as a source of metabolites required for neoblast differentiation.